In vitro impact of platinum nanoparticles on inner ear related cell culture models.

So far, it was supposed that the increase of electrical impedance following cochlear implant (CI) insertion was due to technical defects of the electrode, inflammatory and/or formation of scar tissue along the electrode. However, it was recently reported that corrosion of the platinum electrode contacts may be the reason for high impedances. It could be shown that platinum particles were stripped from the electrode surfaces. Its potential cytotoxic effects within the inner ear remains to be examined. In this study in vitro cell culture models of the mouse organ of Corti cell line (HEI-OC1) and the spiral ganglion (SG) cells derived from the cochleae neonatal rats were used to investigate the effects of the polyvinylpyrrolidone coated platinum nanoparticles (Pt-NPPVP, 3 nm) on cell metabolism, neuronal survival and neurite outgrowth. Our data revealed no decrease of the metabolic activity of the HEI-OC1 cells at Pt-NPPVP concentrations between 50-150 µg/ml. Also, staining with Calcein AM/EthD demonstrated prevalent presence of vital cells. As shown by transmission electron microscopy no Pt-NPPVP could be found at the cell surface or in the cytosol of the HEI-OC1 cells. Similarly, the SG cells exposed to 20-100 µg/ml Pt-NPPVP did not show any reduced survival rate and neurite outgrowth following staining of the neurofilament antigen even at the highest Pt-NPPVP concentration. Although the SG cells were exposed to Pt-NPPVP for further 72 h and 96 h immunocytochemical staining of the glial cells and fibroblasts presented normal cell morphology and growth independently of the cultivation period. Our data indicates that the used Pt-NPPVP do not trigger the cellular uptake and, thus, presumable do not initiate apoptotic pathways in cells of the organ of Corti cell line or the auditory nerve. The protection mechanisms to the Pt-NPPVP interactions remain to be clarified.

BDNF mRNA expression is significantly upregulated in vestibular schwannomas and correlates with proliferative activity.

The expression of neurotrophic factors, such as artemin, glial cell line-derived neurotrophic factor (GDNF), neurturin, transforming growth factors (TGF)-beta1/beta2 and brain-derived neurotrophic factor (BDNF), is enhanced in vestibular schwannomas compared to peripheral nerves. Furthermore, this upregulation may correlate with mitotic activity. Vestibular schwannoma arising from Schwann cells of the vestibular nerve are mostly benign and slow-growing. Most of the pathogenic mechanisms regulating the vestibular schwannoma growth process are unknown. An impaired growth regulation and imbalance between mitosis and apoptosis can be assumed. However, molecular mechanisms interfering with regulation of the vestibular schwannoma growth also modulated by mitogenic factors have to be identified. Neurotrophic factors are involved in regulation of developmental processes in neuronal tissues and regeneration after peripheral nerve trauma and also reveal mitogenic effects on glial cell populations. Gene expression profiles of artemin, BDNF, GDNF, TGF-beta1/beta2 and Ret were determined in the vestibular schwannoma in comparison to the peripheral nerve tissues by using semiquantitative RT-PCR. The expression data were correlated to the proliferation-associated Ki-67 labelling index. A significant higher BDNF expression was observed in the vestibular schwannoma, whereas gene expression of artemin and GDNF was upregulated in peripheral nerves. The correlation between LI and BDNF, TGF-beta1 and Ret was found to be significant in the vestibular schwannoma. Our results demonstrate a coherence between BDNF expression and proliferative activity in the vestibular schwannoma. Based on these results, we propose a pivotal role for BDNF in modulating the vestibular schwannoma growth.

Global expression profiling in leaves of free-growing aspen.

BACKGROUND: Genomic studies are routinely performed on young plants in controlled environments which is very different from natural conditions. In reality plants in temperate countries are exposed to large fluctuations in environmental conditions, in the case of perennials over several years. We have studied gene expression in leaves of a free-growing aspen (Populus tremula) throughout multiple growing seasons RESULTS: We show that gene expression during the first month of leaf development was largely determined by a developmental program although leaf expansion, chlorophyll accumulation and the speed of progression through this program was regulated by the temperature. We were also able to define "transcriptional signatures" for four different substages of leaf development. In mature leaves, weather factors were important for gene regulation. CONCLUSION: This study shows that multivariate methods together with high throughput transcriptional methods in the field can provide additional, novel information as to plant status under changing environmental conditions that is impossible to mimic in laboratory conditions. We have generated a dataset that could be used to e.g. identify marker genes for certain developmental stages or treatments, as well as to assess natural variation in gene expression.

Technical report: laser microdissection and pressure catapulting is superior to conventional manual dissection for isolating pure spiral ganglion fractions from the cochlea.

Isolating cells from the cochlea to perform molecular biology assessment presents a challenge, because it is not possible to dissect pure cell pools by conventional methods. Thus, we set out to demonstrate that laser microdissection and pressure catapulting (LMPC) is superior to conventional manual cochlea dissection for this purpose. Spiral ganglions (SG) were isolated from neonatal rat cochleae by manual dissection and LMPC. Also, modioli were manually dissected. Total RNA was isolated from all three cell pools. In order to demonstrate contamination of the dissected cell pool, we determined the expression of type II iodothyronine deiodinase (D2), claudin 11 (Cld-11), neurofilament light chain (NF-L) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) transcripts by RT-PCR. The results showed that LMPC is not only a suitable method for selectively dissecting cochlear tissues, but in addition the molecular markers confirmed pure spiral ganglion cell pools without indication for any contamination by other cells. This indicates that LMPC is capable of providing a pure SG cell pool in contrast to conventional manual dissection. Therefore, LMPC presents a new technique for cochlear tissue separation improving the validity of molecular biological studies of the inner ear.

Fibroblast-mediated delivery of GDNF induces neuronal-like outgrowth in PC12 cells.

HYPOTHESIS: Recombinantly modified cells deliver neurotrophic factors with the capacity to induce differentiation and the outgrowth of neurites of rat pheochromocytoma cells 12 (PC12) serving as a neuronal model. BACKGROUND: The benefit of cochlea implant (CI) is depending, among other factors, on the number of surviving spiral ganglion neurons (SGN). Studies have shown that the external application of neurotrophic factors in combination with electrical stimulation increases the survival rate of SGN after ototrauma. Therefore, functionalization of electrodes with recombinantly modified cells providing neurotrophic factors to the SGN for inducing survival mechanisms may be an approach to realize drug delivery to the cochlea. METHODS: Murine NIH3T3 cells were recombinantly modified with an infectious lentiviral monocistronic and bicistronic system to synthesize glial cell line-derived neurotrophic factor and the green fluorescent protein. Free glial cell line-derived neurotrophic factor from the supernatant of the modified NIH3T3 cells was added to rat PC12, and the neuronal-like outgrowth was determined for 10 days. RESULTS: A significant neuronal-like outgrowth appeared as early as Day 3 after the application of the supernatant. CONCLUSION: The results indicate that the established in vitro model represents a powerful basic model for determining signal pathways between neuronal-like processing PC12 cells and cellular drug delivery systems.

Platinum corrosion products from electrode contacts of human cochlear implants induce cell death in cell culture models.

Despite the technological progress made with cochlear implants (CI), impedances and their diagnosis remain a focus of interest. Increases in impedance have been related to technical defects of the electrode as well as inflammatory and/or fibrosis along the electrode. Recent studies have demonstrated highly increased impedances as the result of corroded platinum (Pt) electrode contacts. This in vitro study examined the effects of Pt ions and compounds generated by corrosion of the electrode contacts of a human CI on cell metabolism. Since traces of solid Pt in surrounding cochlear tissues have been reported, the impact of commercially available Pt nanoparticles (Pt-NP, size 3 nm) on the cell culture model was also determined. For this purpose, the electrode contacts were electrically stimulated in a 0.5% aqueous NaCl solution for four weeks and the mass fraction of the platinum dissolute (Pt-Diss) was determined by mass spectrometry (ICP-MS). Metabolic activity of the murine fibroblasts (NIH 3T3) and the human neuroblastoma (SH-SY5Y) cells was determined using the WST-1 assay following exposure to Pt-Diss and Pt-NP. It was found that 5-50 µg/ml of the Pt-NP did not affect the viability of both cell types. In contrast, 100 µg/ml of the nanoparticles caused significant loss in metabolic activity. Furthermore, transmission electron microscopy (TEM) revealed mitochondrial swelling in both cell types indicating cytotoxicity. Additionally, TEM demonstrated internalized Pt-NP in NIH 3T3 cells in a concentration dependent manner, whereas endocytosis in SH-SY5Y cells was virtually absent. In comparison with the Pt-NP, the corrosion products (Pt-Diss) with concentrations between 1.64 µg/ml and 8.2 µg/ml induced cell death in both cell lines in a concentration dependent manner. TEM imaging revealed both mitochondrial disintegration and swelling of the endoplasmic reticulum, suggesting that Pt ions trigger cytotoxicity in both NIH 3T3 and SH-SY5Y cell lines by interacting with the respiratory chain.

Burst-Like Transcription of Mutant and Wildtype MYH7-Alleles as Possible Origin of Cell-to-Cell Contractile Imbalance in Hypertrophic Cardiomyopathy.

Hypertrophic Cardiomyopathy (HCM) has been related to many different mutations in more than 20 different, mostly sarcomeric proteins. While development of the HCM-phenotype is thought to be triggered by the different mutations, a common mechanism remains elusive. Studying missense-mutations in the ventricular beta-myosin heavy chain (ß-MyHC, MYH7) we hypothesized that significant contractile heterogeneity exists among individual cardiomyocytes of HCM-patients that results from cell-to-cell variation in relative expression of mutated vs. wildtype ß-MyHC. To test this hypothesis, we measured force-calcium-relationships of cardiomyocytes isolated from myocardium of heterozygous HCM-patients with either ß-MyHC-mutation Arg723Gly or Arg200Val, and from healthy controls. From the myocardial samples of the HCM-patients we also obtained cryo-sections, and laser-microdissected single cardiomyocytes for quantification of mutated vs. wildtype MYH7-mRNA using a single cell RT-qPCR and restriction digest approach. We characterized gene transcription by visualizing active transcription sites by fluorescence in situ hybridization of intronic and exonic sequences of MYH7-pre-mRNA. For both mutations, cardiomyocytes showed large cell-to-cell variation in Ca++-sensitivity. Interestingly, some cardiomyocytes were essentially indistinguishable from controls what might indicate that they had no mutant ß-MyHC while others had highly reduced Ca++-sensitivity suggesting substantial fractions of mutant ß-MyHC. Single-cell MYH7-mRNA-quantification in cardiomyocytes of the same patients revealed high cell-to-cell variability of mutated vs. wildtype mRNA, ranging from essentially pure mutant to essentially pure wildtype MYH7-mRNA. We found 27% of nuclei without active transcription sites which is inconsistent with continuous gene transcription but suggests burst-like transcription of MYH7. Model simulations indicated that burst-like, stochastic on/off-switching of MYH7 transcription, which is independent for mutant and wildtype alleles, could generate the observed cell-to-cell variation in the fraction of mutant vs. wildtype MYH7-mRNA, a similar variation in ß-MyHC-protein, and highly heterogeneous Ca++-sensitivity of individual cardiomyocytes. In the long run, such contractile imbalance in the myocardium may well induce progressive structural distortions like cellular and myofibrillar disarray and interstitial fibrosis, as they are typically observed in HCM.

The biological effects of cell-delivered brain-derived neurotrophic factor on cultured spiral ganglion cells.

The benefit achieved by the use of cochlear implants depends among other factors on the number of surviving spiral ganglion cells (SGCs). Neurotrophic factors, especially brain-derived neurotrophic factor (BDNF), have a protective effect on spiral ganglions. Coating of the cochlear implant electrode with BDNF-producing cells may provide long-term delivery of the factor. Therefore, the hypothesis that BDNF-producing fibroblasts can enhance cell survival of cultured SGCs was tested. Lentiviral infection of fibroblasts resulted in BDNF production. Conditioned medium obtained from infected fibroblasts was used for the cultivation of SGCs. As a result, improved survival and neurite outgrowth was observed on SGCs. Our results demonstrate that lentivirally infected fibroblasts produce BDNF that has neurotrophic effects on spiral ganglions.

Photochemical coating of Kapton® with hydrophilic polymers for the improvement of neural implants.

The polyimide Kapton® was coated photochemically with hydrophilic polymers to prevent undesirable cell growth on the polyimide surface. The polymer coatings were generated using photochemically reactive polymers synthesized by a simple and modular strategy. Suitable polymers or previously synthesized copolymer precursors were functionalized with photoactive arylazide groups by a polymer analogous amide coupling reaction with 4-azidobenzoic acid. A photoactive chitosan derivative (chitosan-Az) and photochemically reactive copolymers containing DMAA, DEAA or MTA as primary monomers were synthesized using this method. The amount of arylazide groups in the polymers was adjusted to approximately 5%, 10% and 20%. As coating on Kapton® all polymers effect a significantly reduced water contact angle (WCA) and consequently a rise of the surface hydrophilicity compared to the untreated Kapton®. The presence of the polymer coatings was also proven by ATR-IR spectroscopy. Coatings with chitosan-Az and the DEAA copolymer cause a distinct inhibition of the growth of fibroblasts. In the case of the DMAA copolymer even a strong anti-adhesive behavior towards fibroblasts was verified. Biocompatibility of the polymer coatings was proven which enables their utilization in biomedical applications.

Differential brain-derived neurotrophic factor and transforming growth factor-beta expression in the rat cochlea following deafness.

Brain derived neurotrophic factor (BDNF) and transforming growth factor-beta (TGFbeta) subtypes have demonstrated their importance in cochlear functions. The aim of this study was to determine gene and protein expression patterns of BDNF, TGFbeta1/2 and their main receptors trkB and TGFbetaR1/R2 in the auditory nerve and inferior colliculus of normal hearing and deafened rats by reverse-transcriptase polymerase chain reaction and immunohistochemistry. Deafening was performed by cochlear injection of neomycin (10%). Significant gene expression changes were not found in the inferior colliculus after deafness; however, in the auditory nerve, BDNF, TGFbeta1 and TGFbetaR1 mRNA in particular were upregulated. Additionally, BDNF protein and the cytokines were found to be expressed in the auditory nerve after hair cell loss. These data indicate the importance of BDNF and TGFbeta1 as endogenous survival factors.

Upregulation of glial cell line-derived neurotrophic factor and artemin mRNA in the auditory nerve of deafened rats.

Nerve growth factors play key roles in spiral ganglion cells survival and excitability. Our aim was to determine gene expression patterns of glial cell line-derived neurotrophic factor family (GDNF) members and their receptors in the auditory nerve and inferior colliculus of deafened rats. The gene expression of GDNF, persephin, artemin and neurturin, and their receptors GFRalpha1, GFRalpha2, GFRalpha3 and Ret, was determined by semiquantitative reverse transcriptase-polymerase chain reaction using GAPDH expression as an internal standard. Following deafness, no significant changes in expression of GDNF family genes were found in inferior colliculus. In contrast, artemin, GDNF, GFRalpha1-3 and Ret RNA expression were strongly upregulated in the auditory nerve following deafness, indicating their importance in protecting the auditory nerve against cell damage.

Dissociated neurons and glial cells derived from rat inferior colliculi after digestion with papain.

The formation of gliosis around implant electrodes for deep brain stimulation impairs electrode-tissue interaction. Unspecific growth of glial tissue around the electrodes can be hindered by altering physicochemical material properties. However, in vitro screening of neural tissue-material interaction requires an adequate cell culture system. No adequate model for cells dissociated from the inferior colliculus (IC) has been described and was thus the aim of this study. Therefore, IC were isolated from neonatal rats (P3_5) and a dissociated cell culture was established. In screening experiments using four dissociation methods (Neural Tissue Dissociation Kit [NTDK] T, NTDK P; NTDK PN, and a validated protocol for the dissociation of spiral ganglion neurons [SGN]), the optimal media, and seeding densities were identified. Thereafter, a dissociation protocol containing only the proteolytic enzymes of interest (trypsin or papain) was tested. For analysis, cells were fixed and immunolabeled using glial- and neuron-specific antibodies. Adhesion and survival of dissociated neurons and glial cells isolated from the IC were demonstrated in all experimental settings. Hence, preservation of type-specific cytoarchitecture with sufficient neuronal networks only occurred in cultures dissociated with NTDK P, NTDK PN, and fresh prepared papain solution. However, cultures obtained after dissociation with papain, seeded at a density of 2×10(4) cells/well and cultivated with Neuro Medium for 6 days reliably revealed the highest neuronal yield with excellent cytoarchitecture of neurons and glial cells. The herein described dissociated culture can be utilized as in vitro model to screen interactions between cells of the IC and surface modifications of the electrode.

In vitro modifications of the scala tympani environment and the cochlear implant array surface.

OBJECTIVES/HYPOTHESIS: To investigate the influence of alterations of the scala tympani environment and modifications of the surface of cochlear implant electrode arrays on insertion forces in vitro. STUDY DESIGN: Research experimental study. METHODS: Fibroblasts producing neurotrophic factors were cultivated on the surface of Nucleus 24 Contour Advance electrodes. Forces were recorded by an Instron 5542 Force Measurement System as three modified arrays were inserted into an artificial scala tympani model filled with phosphate-buffered saline (PBS). The recorded forces were compared to control groups including three unmodified electrodes inserted into a model filled with PBS (unmodified environment) or Healon (current practice). Fluorescence microscopy was used before and after the insertions to identify any remaining fibroblasts. Additionally, three Contour Advance electrodes were inserted into an artificial model, filled with alginate/barium chloride solution at different concentrations, while insertion forces were recorded. RESULTS: Modification of the scala tympani environment with 50% to 75% alginate gel resulted in a significant decrease in the insertion forces. The fibroblast-coated arrays also led to decreased forces comparable to those recorded with Healon. Fluorescence microscopy revealed fully cell-covered arrays before and partially covered arrays after the insertion; the fibroblasts on the arrays' modiolar surface remained intact. CONCLUSIONS: Modifications of the scala tympani's environment with 50% to 75% alginate/barium chloride and of the cochlear implant electrode surface with neurotrophic factor-producing fibroblasts drastically reduce the insertion forces. As both modifications may serve future intracochlear therapies, it is expected that these might additionally reduce possible insertion trauma.

Stable release of BDNF from the fibroblast cell line NIH3T3 grown on silicone elastomers enhances survival of spiral ganglion cells in vitro and in vivo.

The treatment of choice for profound sensorineural hearing loss (SNHL) is direct electrical stimulation of spiral ganglion cells (SGC) via a cochlear implant (CI). The number and excitability of SGC seem to be critical for the success that can be achieved via CI treatment. However, SNHL is associated with degeneration of SGC. Long-term drug delivery to the inner ear for improving SGC survival may be achieved by functionalisation of CI electrodes with cells providing growth factors. Therefore, the capacity of brain-derived neurotrophic factor (BDNF)-secreting NIH3T3 cells grown on cylindrically shaped silicone elastomers (SE) to exert local and sustained neuroprotective effects was assessed in vitro and in vivo. An in vitro model to investigate adhesion and cell growth of lentivirally modified NIH3T3 cells synthesising BDNF on SE was established. The bioactivity of BDNF was characterised by co-cultivation of SGC with cell-coated SE. In addition, cell-coated SE were implanted into deafened guinea pigs. The recombinant NIH3T3 cells proliferated on silicone surfaces during 14 days of cultivation and expressed significantly increasing BDNF levels. Enhanced survival rates and neurite outgrowth of SGC demonstrated the bioactivity of BDNF in vitro. Implantation of SE with adhering BDNF-secreting NIH3T3 cells into the cochleae of systemically deafened guinea pigs induced a significant increase in SGC survival in comparison to SE without cell coating. Our data demonstrate a novel approach of cell-based long-term drug delivery to support SGC survival in vitro and in vivo. This therapeutic strategy--once transferred to cells suitable for clinical application--may improve CI performance.

Matrix metalloproteinases and their tissue inhibitors in cuprizone-induced demyelination and remyelination of brain white and gray matter.

Apart from their involvement in the pathogenesis of demyelinating diseases such as multiple sclerosis, there is emerging evidence that matrix metalloproteinases (MMPs) also promote remyelination. We investigated region-specific expression patterns of 11 MMPs and 4 tissueinhibitors of metalloproteinases (TIMPs) in the cuprizone murine demyelination model. Messenger RNA (mRNA) was extracted at different time points of exposure to cuprizone from microdissected samples of corpus callosum, cortex, and ex vivo isolated microglia and analyzedusing quantitative reverse transcription-polymerase chain reaction.Matrix metalloproteinase 12 and TIMP-1 mRNA were significantly upregulated versus age-matched controls in both areas during demyelination and remyelination. Matrix metalloproteinases 3, 11, and 14 mRNA were upregulated only in white matter during remyelination. Matrix metalloproteinase 24 mRNA was downregulated during both demyelination and remyelination. To identify potential cellular sources of the MMPs and TIMPs, we isolated microglia and detected high MMP-12and TIMP-2 mRNA upregulation at the peak of demyelination.By immunohistochemistry, MMP-3 protein was localized in astrocytes and MMP-12 was identified in microglia, astrocytes, and cells of oligodendrocyte lineage. These findings suggest that MMPs and TIMPs have roles in the regulation of demyelination and remyelination in thismodel. Moreover, differences in the expression levels of these genesbetween white and gray matter reveal region-specific molecularmechanisms.

Spatial and temporal profiles of growth factor expression during CNS demyelination reveal the dynamics of repair priming.

Demyelination is the cause of disability in various neurological disorders. It is therefore crucial to understand the molecular regulation of oligodendrocytes, the myelin forming cells in the CNS. Growth factors are known to be essential for the development and maintenance of oligodendrocytes and are involved in the regulation of glial responses in various pathological conditions. We employed the well established murine cuprizone model of toxic demyelination to analyze the expression of 13 growth factors in the CNS during de- and remyelination. The temporal mRNA expression profile during demyelination and the subsequent remyelination were analyzed separately in the corpus callosum and cerebral cortex using laser microdissection and real-time PCR techniques. During demyelination a similar pattern of growth factor mRNA expression was observed in both areas with a strong up-regulation of NRG1 and GDNF and a slight increase of CNTF in the first week of cuprizone treatment. HGF, FGF-2, LIF, IGF-I, and TGF-ß1 were up-regulated mainly during peak demyelination. In contrast, during remyelination there were regional differences in growth factor mRNA expression levels. GDNF, CNTF, HGF, FGF-2, and BDNF were elevated in the corpus callosum but not in the cortex, suggesting tissue differences in the molecular regulation of remyelination in the white and grey matter. To clarify the cellular source we isolated microglia from the cuprizone lesions. GDNF, IGF-1, and FGF mRNA were detected in the microglial fraction with a temporal pattern corresponding to that from whole tissue PCR. In addition, immunohistochemical analysis revealed IGF-1 protein expression also in the reactive astrocytes. CNTF was located in astrocytes. This study identified seven different temporal expression patterns for growth factors in white and grey matter and demonstrated the importance of early tissue priming and exact orchestration of different steps during callosal and cortical de- and remyelination.

Artemin improves survival of spiral ganglion neurons in vivo and in vitro.

Artemin and its receptors are upregulated in the auditory nerve of deafened rats as a possible intrinsic protective mechanism against ototoxicity-related apoptosis. Consequently, we examined the effect of artemin on spiral ganglion neurons in vitro and in vivo. Spiral ganglion neurons were isolated from neonatal rats and cultured in serum-free medium supplemented with artemin and/or brain-derived neurotrophic factor (BDNF). In vitro, the survival rate of spiral ganglion neurons cultivated with artemin or BDNF was significantly improved compared with negative controls. In addition, artemin was delivered to the inner ear of deafened guinea pigs for 28 days. In-vivo artemin was as effective as BDNF in spiral ganglion neuron protection. Therefore, artemin promotes the survival of spiral ganglion neurons in vitro and in vivo.

What affects mRNA levels in leaves of field-grown aspen? A study of developmental and environmental influences.

We have analyzed the abundance of mRNAs expressed from 11 nuclear genes in leaves of a free-growing aspen (Populus tremula) tree throughout the growing season. We used multivariate statistics to determine the influence of environmental factors (i.e. the weather before sampling) and developmental responses to seasonal changes at the mRNA level for each of these genes. The gene encoding a germin-like protein was only expressed early in the season, whereas the other tested genes were expressed throughout the season and showed mRNA variations on a day-to-day basis. For six of the genes, reliable models were found that described the mRNA level as a function of weather, but the leaf age was also important for all genes except one encoding an early light-inducible protein (which appeared to be regulated purely by environmental factors under these conditions). The results confirmed the importance of several environmental factors previously shown to regulate the genes, but we also detected a number of less obvious factors (such as the variation in weather parameters and the weather of the previous day) that correlated with the mRNA levels of individual genes. The study shows the power of multivariate statistical methods in analyzing gene regulation under field conditions.

A transcriptional timetable of autumn senescence.

BACKGROUND: We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. RESULTS: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. CONCLUSIONS: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.