Browsing by Author "Jarvis, ED"
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Item Open Access A framework for integrating the songbird brain.(J Comp Physiol A Neuroethol Sens Neural Behav Physiol, 2002-12) Jarvis, ED; Smith, VA; Wada, K; Rivas, MV; McElroy, M; Smulders, TV; Carninci, P; Hayashizaki, Y; Dietrich, F; Wu, X; McConnell, P; Yu, J; Wang, PP; Hartemink, AJ; Lin, SBiological systems by default involve complex components with complex relationships. To decipher how biological systems work, we assume that one needs to integrate information over multiple levels of complexity. The songbird vocal communication system is ideal for such integration due to many years of ethological investigation and a discreet dedicated brain network. Here we announce the beginnings of a songbird brain integrative project that involves high-throughput, molecular, anatomical, electrophysiological and behavioral levels of analysis. We first formed a rationale for inclusion of specific biological levels of analysis, then developed high-throughput molecular technologies on songbird brains, developed technologies for combined analysis of electrophysiological activity and gene regulation in awake behaving animals, and developed bioinformatic tools that predict causal interactions within and between biological levels of organization. This integrative brain project is fitting for the interdisciplinary approaches taken in the current songbird issue of the Journal of Comparative Physiology A and is expected to be conducive to deciphering how brains generate and perceive complex behaviors.Item Open Access A membrane-associated progesterone-binding protein, 25-Dx, is regulated by progesterone in brain regions involved in female reproductive behaviors.(Proc Natl Acad Sci U S A, 2000-11-07) Krebs, CJ; Jarvis, ED; Chan, J; Lydon, JP; Ogawa, S; Pfaff, DWThe ventromedial hypothalamus (VMH) plays a central role in the regulation of the female reproductive behavior lordosis, a behavior dependent upon the sequential activation of receptors for the ovarian steroid hormones estradiol (E) and progesterone (P). These receptors function as transcription factors to alter the expression of target genes. To discover behaviorally relevant genes targeted by E and P in the VMH, we used the differential display PCR to identify messenger RNAs that are differentially expressed in the hypothalamus of ovariectomized (ovx) rats treated with E alone compared with ovariectomized rats treated with E and P. We show here that one interesting mRNA within the hypothalamus that is repressed by P after E priming encodes the protein 25-Dx, the rat homolog of the human membrane-associated P-binding protein Hpr6.6. Neurons in the brain containing the highest levels of 25-Dx are located in several nuclei of the basal forebrain, including the VMH. 25-Dx expression is also higher in the hypothalamus of female P receptor "knockout" mice than in their wild-type littermates. These findings suggest a mechanism in which the activation of nuclear P receptor represses expression of a membrane P receptor, 25-Dx, during lordosis facilitation.Item Open Access A relationship between behavior, neurotrophin expression, and new neuron survival.(Proc Natl Acad Sci U S A, 2000-07-18) Li, XC; Jarvis, ED; Alvarez Borda, B; Lim, DA; Nottebohm, FThe high vocal center (HVC) controls song production in songbirds and sends a projection to the robust nucleus of the archistriatum (RA) of the descending vocal pathway. HVC receives new neurons in adulthood. Most of the new neurons project to RA and replace other neurons of the same kind. We show here that singing enhances mRNA and protein expression of brain-derived neurotrophic factor (BDNF) in the HVC of adult male canaries, Serinus canaria. The increased BDNF expression is proportional to the number of songs produced per unit time. Singing-induced BDNF expression in HVC occurs mainly in the RA-projecting neurons. Neuronal survival was compared among birds that did or did not sing during days 31-38 after BrdUrd injection. Survival of new HVC neurons is greater in the singing birds than in the nonsinging birds. A positive causal link between pathway use, neurotrophin expression, and new neuron survival may be common among systems that recruit new neurons in adulthood.Item Open Access Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.(Nature, 2002-12-05) Okazaki, Y; Furuno, M; Kasukawa, T; Adachi, J; Bono, H; Kondo, S; Nikaido, I; Osato, N; Osato, N; Saito, R; Suzuki, H; Yamanaka, I; Kiyosawa, H; Yagi, K; Tomaru, Y; Hasegawa, Y; Nogami, A; Schönbach, C; Gojobori, T; Baldarelli, R; Hill, DP; Bult, C; Hume, DA; Hume, DA; Quackenbush, J; Schriml, LM; Kanapin, A; Matsuda, H; Batalov, S; Beisel, KW; Blake, JA; Bradt, D; Brusic, V; Chothia, C; Corbani, LE; Cousins, S; Dalla, E; Dragani, TA; Fletcher, CF; Forrest, A; Frazer, KS; Gaasterland, T; Gariboldi, M; Gissi, C; Godzik, A; Gough, J; Grimmond, S; Gustincich, S; Hirokawa, N; Jackson, IJ; Jarvis, ED; Kanai, A; Kawaji, H; Kawasawa, Y; Kedzierski, RM; King, BL; Konagaya, A; Kurochkin, IV; Lee, Y; Lenhard, B; Lyons, PA; Maglott, DR; Maltais, L; Marchionni, L; McKenzie, L; Miki, H; Nagashima, T; Numata, K; Okido, T; Pavan, WJ; Pertea, G; Pesole, G; Petrovsky, N; Pillai, R; Pontius, JU; Qi, D; Ramachandran, S; Ravasi, T; Reed, JC; Reed, DJ; Reid, J; Ring, BZ; Ringwald, M; Sandelin, A; Schneider, C; Semple, CAM; Setou, M; Shimada, K; Sultana, R; Takenaka, Y; Taylor, MS; Teasdale, RD; Tomita, M; Verardo, R; Wagner, L; Wahlestedt, C; Wang, Y; Watanabe, Y; Wells, C; Wilming, LG; Wynshaw-Boris, A; Yanagisawa, M; Yang, I; Yang, L; Yuan, Z; Zavolan, M; Zhu, Y; Zimmer, A; Carninci, P; Hayatsu, N; Hirozane-Kishikawa, T; Konno, H; Nakamura, M; Sakazume, N; Sato, K; Shiraki, T; Waki, K; Kawai, J; Aizawa, K; Arakawa, T; Fukuda, S; Hara, A; Hashizume, W; Imotani, K; Ishii, Y; Itoh, M; Kagawa, I; Miyazaki, A; Sakai, K; Sasaki, D; Shibata, K; Shinagawa, A; Yasunishi, A; Yoshino, M; Waterston, R; Lander, ES; Rogers, J; Birney, E; Hayashizaki, Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II TeamOnly a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.Item Open Access Behaviourally driven gene expression reveals song nuclei in hummingbird brain.(Nature, 2000-08-10) Jarvis, ED; Ribeiro, S; da Silva, ML; Ventura, D; Vielliard, J; Mello, CVHummingbirds have developed a wealth of intriguing features, such as backwards flight, ultraviolet vision, extremely high metabolic rates, nocturnal hibernation, high brain-to-body size ratio and a remarkable species-specific diversity of vocalizations. Like humans, they have also developed the rare trait of vocal learning, this being the ability to acquire vocalizations through imitation rather than instinct. Here we show, using behaviourally driven gene expression in freely ranging tropical animals, that the forebrain of hummingbirds contains seven discrete structures that are active during singing, providing the first anatomical and functional demonstration of vocal nuclei in hummingbirds. These structures are strikingly similar to seven forebrain regions that are involved in vocal learning and production in songbirds and parrots--the only other avian orders known to be vocal learners. This similarity is surprising, as songbirds, parrots and hummingbirds are thought to have evolved vocal learning and associated brain structures independently, and it indicates that strong constraints may influence the evolution of forebrain vocal nuclei.Item Open Access Bird Brain: Evolution(2010-12-01) Jarvis, EDThis article presents the classic and modern views of avian brain evolution in the context of vertebrate brain evolution. The classical view held that the avian cerebrum along with those of other vertebrates evolved in progressive dorsal-to-ventral stages from so-called primitive to advanced species. The modern view holds that the avian cerebrum and those of other vertebrates were inherited as a package consisting of pallial, striatal, and pallidal domains that together function in perceiving and producing complex behaviors. This modern view is associated with a new brain terminology for birds developed by a consortium of neuroscientists. © 2009 Elsevier Ltd All rights reserved.Item Open Access Bird song systems: Evolution(2010-12-01) Jarvis, EDThis article presents the vocal and auditory pathways of vocal-learning birds and a hypothesis about their evolution. These pathways control the ability to produce learned song in the few groups of birds that have vocal learning abilities, songbirds, parrots, and hummingbirds. These species have served as model systems to study neural mechanisms of spoken language, for which vocal learning is a critical behavioral substrate. Their vocal pathways are proposed to have evolved out of a preexisting motor pathway. © 2009 Elsevier Ltd All rights reserved.Item Open Access Birds, primates, and spoken language origins: Behavioral phenotypes and neurobiological substrates(Frontiers in Evolutionary Neuroscience, 2012-12-01) Petkov, CI; Jarvis, EDVocal learners such as humans and songbirds can learn to produce elaborate patterns of structurally organized vocalizations, whereas many other vertebrates such as non-human primates and most other bird groups either cannot or do so to a very limited degree. To explain the similarities among humans and vocal-learning birds and the differences with other species, various theories have been proposed. One set of theories are motor theories, which underscore the role of the motor system as an evolutionary substrate for vocal production learning. For instance, the motor theory of speech and song perception proposes enhanced auditory perceptual learning of speech in humans and song in birds, which suggests a considerable level of neurobiological specialization. Another, a motor theory of vocal learning origin, proposes that the brain pathways that control the learning and production of song and speech were derived from adjacent motor brain pathways. Another set of theories are cognitive theories, which address the interface between cognition and the auditory-vocal domains to support language learning in humans. Here we critically review the behavioral and neurobiological evidence for parallels and differences between the so-called vocal learners and vocal non-learners in the context of motor and cognitive theories. In doing so, we note that behaviorally vocal-production learning abilities are more distributed than categorical, as are the auditory-learning abilities of animals. We propose testable hypotheses on the extent of the specializations and cross-species correspondences suggested by motor and cognitive theories. We believe that determining how spoken language evolved is likely to become clearer with concerted efforts in testing comparative data from many non-human animal species. © 2012 Petkov and Jarvis.Item Open Access Brain gene regulation by territorial singing behavior in freely ranging songbirds.(Neuroreport, 1997-05-27) Jarvis, ED; Schwabl, H; Ribeiro, S; Mello, CVTo investigate the ecological relevance of brain gene regulation associated with singing behavior in songbirds, we challenged freely ranging song sparrows with conspecific song playbacks within their breeding territories. Males responded by approaching the speaker, searching for an intruder and actively singing. In situ hybridization of brain sections revealed significantly higher expression of the transcriptional regulator ZENK in challenged birds than in unstimulated controls in several auditory structures and song control nuclei. We conclude that singing behavior in the context of territorial defense is associated with gene regulation in brain centers that control song perception and production, and that behaviorally regulated gene expression can be used to investigate brain areas involved in the natural behaviors of freely ranging animals.Item Open Access Brains and birdsong(2004-10-01) Jarvis, EDScientists have a come a long way in their studies of brains and birdsong. The discovery of new neurons in the adult brain has revolutionary implications for medical science. The molecular biology of vocal learning is helpful in understanding genetic mechanisms of behavior, and in resolving the great mystery of how vocal learning evolved. Some areas as yet unexplored include the study of vocal brain areas in the other mammalian vocal learners, cetaceans, and bats. The extensive knowledge we now have about vocal learning in birds may provide a useful guide on how best to approach the study of these mammalian vocal learners, though cetaceans will always be a challenge. New techniques may emerge for exploring brain connectivity and behaviorally-driven gene expression in human brains in an ethically responsible manner, though it is not yet clear how best to proceed. © 2004 Elsevier Inc. All rights reserved.Item Open Access Classification and genetic characterization of pattern-forming Bacilli.(Mol Microbiol, 1998-02) Rudner, R; Martsinkevich, O; Leung, W; Jarvis, EDOne of the more natural but less commonly studied forms of colonial bacterial growth is pattern formation. This type of growth is characterized by bacterial populations behaving in an organized manner to generate readily identifiable geometric and predictable morphologies on solid and semi-solid surfaces. In our first attempt to study the molecular basis of pattern formation in Bacillus subtilis, we stumbled upon an enigma: some strains used to describe pattern formation in B. subtilis did not have the phenotypic or genotypic characteristics of B. subtilis. In this report, we show that these strains are actually not B. subtilis, but belong to a different class of Bacilli, group I. We show further that commonly used laboratory strains of B. subtilis can co-exist as mixed cultures with group I Bacilli, and that the latter go unnoticed when grown on frequently used laboratory substrates. However, when B. subtilis is grown under more stringent semiarid conditions, members of group I emerge in the form of complex patterns. When B. subtilis is grown under less stringent and more motile conditions, B. subtilis forms its own pattern, and members of group I remain unnoticed. These findings have led us to revise some of the mechanistic and evolutionary hypotheses that have been proposed to explain pattern growth in Bacilli.Item Open Access Core and Shell Song Systems Unique to the Parrot Brain.(PLoS One, 2015) Chakraborty, M; Walløe, S; Nedergaard, S; Fridel, EE; Dabelsteen, T; Pakkenberg, B; Bertelsen, MF; Dorrestein, GM; Brauth, SE; Durand, SE; Jarvis, EDThe ability to imitate complex sounds is rare, and among birds has been found only in parrots, songbirds, and hummingbirds. Parrots exhibit the most advanced vocal mimicry among non-human animals. A few studies have noted differences in connectivity, brain position and shape in the vocal learning systems of parrots relative to songbirds and hummingbirds. However, only one parrot species, the budgerigar, has been examined and no differences in the presence of song system structures were found with other avian vocal learners. Motivated by questions of whether there are important differences in the vocal systems of parrots relative to other vocal learners, we used specialized constitutive gene expression, singing-driven gene expression, and neural connectivity tracing experiments to further characterize the song system of budgerigars and/or other parrots. We found that the parrot brain uniquely contains a song system within a song system. The parrot "core" song system is similar to the song systems of songbirds and hummingbirds, whereas the "shell" song system is unique to parrots. The core with only rudimentary shell regions were found in the New Zealand kea, representing one of the only living species at a basal divergence with all other parrots, implying that parrots evolved vocal learning systems at least 29 million years ago. Relative size differences in the core and shell regions occur among species, which we suggest could be related to species differences in vocal and cognitive abilities.Item Open Access Empowering 21st century biology(BioScience, 2010-12-01) Robinson, GE; Banks, JA; Padilla, DK; Burggren, WW; Cohen, CS; Delwiche, CF; Funk, V; Hoekstra, HE; Jarvis, ED; Johnson, L; Martindale, MQ; Rio, CMD; Medina, M; Salt, DE; Sinha, S; Specht, C; Strange, K; Strassmann, JE; Swalla, BJ; Tomanek, LSeveral lists of grand challenges in biology have been published recently, highlighting the strong need to answer fundamental questions about how life evolves and is governed, and how to apply this knowledge to solve the pressing problems of our times. To succeed in addressing the challenges of 21st century biology, scientists need to generate, have access to, interpret, and archive more information than ever before. But for many important questions in biology, progress is stymied by a lack of essential tools. Discovering and developing necessary tools requires new technologies, applications of existing technologies, software, model organisms, and social structures. Such new social structures will promote tool building, tool sharing, research collaboration, and interdisciplinary training. Here we identify examples of the some of the most important needs for addressing critical questions in biology and making important advances in the near future. © 2010 by American Institute of Biological Sciences. All rights reserved.Item Open Access For whom the bird sings: context-dependent gene expression.(Neuron, 1998-10) Jarvis, ED; Scharff, C; Grossman, MR; Ramos, JA; Nottebohm, FMale zebra finches display two song behaviors: directed and undirected singing. The two differ little in the vocalizations produced but greatly in how song is delivered. "Directed" song is usually accompanied by a courtship dance and is addressed almost exclusively to females. "Undirected" song is not accompanied by the dance and is produced when the male is in the presence of other males, alone, or outside a nest occupied by its mate. Here, we show that the anterior forebrain vocal pathway contains medial and lateral "cortical-basal ganglia" subdivisions that have differential ZENK gene activation depending on whether the bird sings female-directed or undirected song. Differences also occur in the vocal output nucleus, RA. Thus, although these two vocal behaviors are very similar, their brain activation patterns are dramatically different.Item Open Access Molecular mapping of brain areas involved in parrot vocal communication.(J Comp Neurol, 2000-03-27) Jarvis, ED; Mello, CVAuditory and vocal regulation of gene expression occurs in separate discrete regions of the songbird brain. Here we demonstrate that regulated gene expression also occurs during vocal communication in a parrot, belonging to an order whose ability to learn vocalizations is thought to have evolved independently of songbirds. Adult male budgerigars (Melopsittacus undulatus) were stimulated to vocalize with playbacks of conspecific vocalizations (warbles), and their brains were analyzed for expression of the transcriptional regulator ZENK. The results showed that there was distinct separation of brain areas that had hearing- or vocalizing-induced ZENK expression. Hearing warbles resulted in ZENK induction in large parts of the caudal medial forebrain and in 1 midbrain region, with a pattern highly reminiscent of that observed in songbirds. Vocalizing resulted in ZENK induction in nine brain structures, seven restricted to the lateral and anterior telencephalon, one in the thalamus, and one in the midbrain, with a pattern partially reminiscent of that observed in songbirds. Five of the telencephalic structures had been previously described as part of the budgerigar vocal control pathway. However, functional boundaries defined by the gene expression patterns for some of these structures were much larger and different in shape than previously reported anatomical boundaries. Our results provide the first functional demonstration of brain areas involved in vocalizing and auditory processing of conspecific sounds in budgerigars. They also indicate that, whether or not vocal learning evolved independently, some of the gene regulatory mechanisms that accompany learned vocal communication are similar in songbirds and parrots.Item Open Access Motor-driven gene expression.(Proc Natl Acad Sci U S A, 1997-04-15) Jarvis, ED; Nottebohm, FThere is increased neuronal firing in the high vocal center (a motor nucleus) and other song nuclei of canaries, Serinus canaria, and zebra finches, Taeniopygia guttata, whenever these songbirds sing or hear song. These observations suggested that song perception involved sensory and motor pathways. We now show that the act of singing, but not hearing song, induces a rapid and striking increase (up to 60-fold) in expression of the transcriptional regulator ZENK in the high vocal center and other song nuclei. This motor-driven gene expression is independent of auditory feedback, since it occurs in deafened birds when they sing and in muted birds when they produce silent song. Conversely, hearing song, but not the act of singing, induces ZENK expression in parts of the auditory forebrain. Our observations show that even though the same auditory stimulus activates sensory and motor pathways, perception and production of song are accompanied by anatomically distinct patterns of gene expression.Item Open Access Phylogenomic analyses data of the avian phylogenomics project(2014) Jarvis, ED; Mirarah, S; Aberer, A; Houde, P; Li, C; Ho, S; Faircloth, BC; Nabholz, B; Howard, JT; Suh, A; Weber, CC; Fonseca, RR; Alfaro-Nunez, A; Narula, N; Liu, L; Burt, D; Ellegren, H; Edwards, SV; Stamatakis, A; Mindell, DP; Caracraft, J; Braun, EL; Warnow, T; Jun, W; Gilbert, MTP; Zhang, GItem Open Access Rapid behavioral and genomic responses to social opportunity.(PLoS Biol, 2005-11) Burmeister, SS; Jarvis, ED; Fernald, RDFrom primates to bees, social status regulates reproduction. In the cichlid fish Astatotilapia (Haplochromis) burtoni, subordinate males have reduced fertility and must become dominant to reproduce. This increase in sexual capacity is orchestrated by neurons in the preoptic area, which enlarge in response to dominance and increase expression of gonadotropin-releasing hormone 1 (GnRH1), a peptide critical for reproduction. Using a novel behavioral paradigm, we show for the first time that subordinate males can become dominant within minutes of an opportunity to do so, displaying dramatic changes in body coloration and behavior. We also found that social opportunity induced expression of the immediate-early gene egr-1 in the anterior preoptic area, peaking in regions with high densities of GnRH1 neurons, and not in brain regions that express the related peptides GnRH2 and GnRH3. This genomic response did not occur in stable subordinate or stable dominant males even though stable dominants, like ascending males, displayed dominance behaviors. Moreover, egr-1 in the optic tectum and the cerebellum was similarly induced in all experimental groups, showing that egr-1 induction in the anterior preoptic area of ascending males was specific to this brain region. Because egr-1 codes for a transcription factor important in neural plasticity, induction of egr-1 in the anterior preoptic area by social opportunity could be an early trigger in the molecular cascade that culminates in enhanced fertility and other long-term physiological changes associated with dominance.Item Open Access Selective expression of insulin-like growth factor II in the songbird brain.(J Neurosci, 1997-09-15) Holzenberger, M; Jarvis, ED; Chong, C; Grossman, M; Nottebohm, F; Scharff, CNeuronal replacement occurs in the forebrain of juvenile and adult songbirds. To address the molecular processes that govern this replacement, we cloned the zebra finch insulin-like growth factor II (IGF-II) cDNA, a factor known to regulate neuronal development and survival in other systems, and examined its expression pattern by in situ hybridization and immunocytochemistry in juvenile and adult songbird brains. The highest levels of IGF-II mRNA expression occurred in three nuclei of the song system: in the high vocal center (HVC), in the medial magnocellular nucleus of the neostriatum (mMAN), which projects to HVC, and to a lesser extent in the robust nucleus of the archistriatum (RA), which receives projections from HVC. IGF-II mRNA expression was developmentally regulated in zebra finches. In canary HVC, monthly changes in IGF-II mRNA expression covaried with previously reported monthly differences in neuron incorporation. Combining retrograde tracers with in situ hybridization and immunocytochemistry, we determined that the HVC neurons that project to area X synthesize the IGF-II mRNA, whereas the adjacent RA-projecting neurons accumulate the IGF-II peptide. Our findings raise the possibility that within HVC IGF-II acts as a paracrine signal between nonreplaceable area X-projecting neurons and replaceable RA-projecting neurons, a mode of action that is compatible with the involvement of IGF-II with the replacement of neurons. Additional roles for IGF-II expression in songbird brain are likely, because expression also occurs in some brain areas outside the song system, among them the cerebellar Purkinje cells in which neurogenesis is not known to occur.Item Open Access The 70-kDa heat shock cognate protein (Hsc73) gene is enhanced by ovarian hormones in the ventromedial hypothalamus.(Proc Natl Acad Sci U S A, 1999-02-16) Krebs, CJ; Jarvis, ED; Pfaff, DWEstrogen (E) and progesterone (P) orchestrate many cellular responses involved in female reproductive physiology, including reproductive behaviors. E- and P-binding neurons important for lordosis behavior have been located within the ventromedial hypothalamus (VMH), and several hormone-responsive genes have been observed there as well. In attempts to identify additional E- and P-responsive genes in the VMH that may contribute to sexual behaviors, we used the differential display mRNA screening technique. One of the genes identified encodes the 73-kDa heat shock cognate protein (Hsc73). Quantitative in situ hybridization analysis of brains from naturally cycling female rats revealed a significant increase in Hsc73 mRNA in the VMH and arcuate nucleus of animals during proestrus compared with those at diestrus-1. To confirm that these increases were steroid hormone dependent, we compared vehicle-treated ovariectomized females with ovariectomized females treated with estradiol benzoate and P. Northern analysis and in situ hybridizations showed that the Hsc73 gene is enhanced by E and P in the pituitary and subregions of the VMH. Incidentally, by examining the primary amino acid sequence of rat, human, and chicken progesterone receptors, we noticed that putative Hsc73 binding sites are conserved across species with similar sites existing in the androgen and glucocorticoid receptors. Together these findings suggest a possible mechanism through which E could influence the activities of progesterone, androgen, and glucocorticoid receptors, by enhancing the expression of Hsc73 in cells where these proteins colocalize.