Developmental biology. The Turing model comes of molecular age.
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Biomedical subjects
Cheng-Ming Chuong
Publications and source records attributed to Cheng-Ming Chuong.
Molecular signaling in feather morphogenesis.
The development and regeneration of feathers have gained much attention recently because of progress in the following areas. First, pattern formation. The exquisite spatial arrangement provides a simple model for decoding the rules of morphogenesis. Second, stem cell biology. In every molting, a few stem cells have to rebuild the entire epithelial organ, providing much to learn on how to regenerate an organ physiologically. Third, evolution and development ('Evo-Devo'). The discovery of feathered dinosaur fossils in China prompted enthusiastic inquiries about the origin and evolution of feathers. Progress has been made in elucidating feather morphogenesis in five successive phases: macro-patterning, micro-patterning, intra-bud morphogenesis, follicle morphogenesis and regenerative cycling.
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PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm.
BACKGROUND: Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. RESULTS: PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. CONCLUSION: We have developed citations' prioritisation algorithm based on journal impact factor, forward referencing volume, referencing dynamics, and author's contribution level. It can be applied either to the primary set of PubMed search results or to the subsets of these results identified through key terms from controlled biomedical vocabularies and ontologies. NCI (National Cancer Institute) thesaurus and MGD (Mouse Genome Database) mammalian gene orthology have been implemented for key terms analytics. PubFocus provides a scalable platform for the integration of multiple available ontology databases. PubFocus analytics can be adapted for input sources of biomedical citations other than PubMed.
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Wnt3a gradient converts radial to bilateral feather symmetry via topological arrangement of epithelia.
The evolution of bilaterally symmetric feathers is a fundamental process leading toward flight. One major unsolved mystery is how the feathers of a single bird can form radially symmetric downy feathers and bilaterally symmetric flight feathers. In developing downy feather follicles, barb ridges are organized parallel to the long axis of the feather follicle. In developing flight-feather follicles, the barb ridges are organized helically toward the anterior region, leading to the fusion and creation of a rachis. Here we discover an anterior-posterior molecular gradient of wingless int (Wnt3)a in flight but not downy feathers. Global inhibition of the Wnt gradient transforms bilaterally symmetric feathers into radially symmetric feathers. Production of an ectopic local Wnt3a gradient reoriented barb ridges toward the source and created an ectopic rachis. We further show that the orientation of the Wnt3a gradient is dictated by the dermal papilla (DP). Swapping DPs between wing covert and breast downy feathers demonstrates that both feather symmetry and molecular gradients are in accord with the origin of the DP. Thus the fates of feather epidermal cells are not predetermined through some molecular codes but can be modulated. Together, our data suggest feathers are shaped by a DP--> Wnt gradient-->helical barb ridge organization-->creation of rachis-->bilateral symmetry sequence. We speculate diverse feather forms can be achieved by adjusting the orientation and slope of molecular gradients, which then shape the topological arrangements of feather epithelia, thus linking molecular activities to organ forms and novel functions.
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Morphoregulation of avian beaks: comparative mapping of growth zone activities and morphological evolution.
Avian beak diversity is a classic example of morphological evolution. Recently, we showed that localized cell proliferation mediated by bone morphogenetic protein 4 (BMP4) can explain the different shapes of chicken and duck beaks (Wu et al. [2004] Science 305:1465). Here, we compare further growth activities among chicken (conical and slightly curved), duck (straight and long), and cockatiel (highly curved) developing beak primordia. We found differential growth activities among different facial prominences and within one prominence. The duck has a wider frontal nasal mass (FNM), and more sustained fibroblast growth factor 8 activity. The cockatiel has a thicker FNM that grows more vertically and a relatively reduced mandibular prominence. In each prominence the number, size, and position of localized growth zones can vary: it is positioned more rostrally in the duck and more posteriorly in the cockatiel FNM, correlating with beak curvature. BMP4 is enriched in these localized growth zones. When BMP activity is experimentally altered in all prominences, beak size was enlarged or reduced proportionally. When only specific prominences were altered, the prototypic conical shaped chicken beaks were converted into an array of beak shapes mimicking those in nature. These results suggest that the size of beaks can be modulated by the overall activity of the BMP pathway, which mediates the growth. The shape of the beaks can be fine-tuned by localized BMP activity, which mediates the range, level, and duration of locally enhanced growth. Implications of topobiology vs. molecular blueprint concepts in the Evo-Devo of avian beak forms are discussed.
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Engineering stem cells into organs: topobiological transformations demonstrated by beak, feather, and other ectodermal organ morphogenesis.
To accomplish regenerative medicine, several critical issues in stem cell biology have to be solved, including the identification of sources, the expanding population, building them into organs, and assimilating them to the host. Although many stem cells can now differentiate along certain lineages, knowledge on how to use them to build organs lags behind. Here we focus on topobiological events that bridge this gap, for example, the regulation of number, size, axes, shape, arrangement, and architecture during organogenesis. Rather than reviewing detail molecular pathways known to disrupt organogenesis when perturbed, we highlight conceptual questions at the topobiological level and ask how cellular and molecular mechanisms can work to explain these phenomena. The avian integument is used as the Rosetta stone because the molecular activities are linked to organ forms that are visually apparent and have functional consequences during evolution with fossil records and extant diversity. For example, we show that feather pattern formation is the equilibrium of stochastic interactions among multiple activators and inhibitors. Although morphogens and receptors are coded by the genome, the result is based on the summed physical-chemical properties on the whole cell's surface and is self-organizing. For another example, we show that developing chicken and duck beaks contain differently configured localized growth zones (LoGZs) and can modulate chicken beaks to phenocopy diverse avian beaks in nature by altering the position, number, size, and duration of LoGZs. Different organs have their unique topology and we also discuss shaping mechanisms of liver and different ways of branching morphogenesis. Multi-primordium organs (e.g., feathers, hairs, and teeth) have additional topographic specificities across the body surface, an appendage field, or within an appendage. Promises and problems in reconstitute feather/hair follicles and other organs are discussed. Finally, simple modification at the topobiological level may lead to novel morphology for natural selection at the evolution level.
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Mapping stem cell activities in the feather follicle.
It is important to know how different organs 'manage' their stem cells. Both hair and feather follicles show robust regenerative powers that episodically renew the epithelial organ. However, the evolution of feathers (from reptiles to birds) and hairs (from reptiles to mammals) are independent events and their follicular structures result from convergent evolution. Because feathers do not have the anatomical equivalent of a hair follicle bulge, we are interested in determining where their stem cells are localized. By applying long-term label retention, transplantation and DiI tracing to map stem cell activities, here we show that feather follicles contain slow-cycling long-term label-retaining cells (LRCs), transient amplifying cells and differentiating keratinocytes. Each population, located in anatomically distinct regions, undergoes dynamic homeostasis during the feather cycle. In the growing follicle, LRCs are enriched in a 'collar bulge' niche. In the moulting follicle, LRCs shift to populate a papillar ectoderm niche near the dermal papilla. On transplantation, LRCs show multipotentiality. In a three-dimensional view, LRCs are configured as a ring that is horizontally placed in radially symmetric feathers but tilted in bilaterally symmetric feathers. The changing topology of stem cell activities may contribute to the construction of complex feather forms.
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Molecular shaping of the beak.
Beak shape is a classic example of evolutionary diversification. Beak development in chicken and duck was used to examine morphological variations among avian species. There is only one proliferative zone in the frontonasal mass of chickens, but two in ducks. These growth zones are associated with bone morphogenetic protein 4 (BMP4) activity. By "tinkering" with BMP4 in beak prominences, the shapes of the chicken beak can be modulated.
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Morphogenesis of chicken liver: identification of localized growth zones and the role of beta-catenin/Wnt in size regulation.
During development and regeneration, new cells are added and incorporated to the liver parenchyma. Regulation of this process contributes to the final size and shape of the particular organs, including the liver. We identified the distribution of liver growth zones using an embryonic chicken model because of its accessibility to experimentation. Hepatocyte precursors were first generated all over the primordia surrounding the vitelline blood vessel at embryonic day 2 (E2), then became limited to the peripheral growth zones around E6. Differentiating daughter cells of the peripheral hepatocyte precursors were shown by DiI microinjection to be laid inward and were subsequently organized to form the hepatic architecture. At E8, hepatocyte precursor cells were further restricted to limited segments of the periphery, called localized growth zones (LoGZ). Adhesion and signaling molecules in the growth zone were studied. Among them, beta-catenin and Wnt 3a were highly enriched. We overexpressed constitutively active beta-catenin using replication competent avian sarcoma (RCAS) virus. Liver size increased about 3-fold with an expanded hepatocyte precursor cell population. In addition, blocking beta-catenin activity by either overexpression of dominant-negative LEF1 or overexpression of a secreted Wnt inhibitor Dickkopf (DKK) resulted in decreased liver size with altered liver shape. Our data suggest that (1) the duration of active growth zone activity modulates the size of the liver; (2) a shift in the position of the localized growth zone helps to shape the liver; and (3) beta-catenin/Wnt are involved in regulating growth zone activities during liver development.
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Distinct Wnt members regulate the hierarchical morphogenesis of skin regions (spinal tract) and individual feathers.
Skin morphogenesis occurs in successive stages. First, the skin forms distinct regions (macropatterning). Then skin appendages with particular shapes and sizes form within each region (micropatterning). Ectopic DKK expression inhibited dermis formation in feather tracts and individual buds, implying the importance of Wnts, and prompted the assessment of individual Wnt functions at different morphogenetic levels using the feather model. Wnt 1, 3a, 5a and 11 initially were expressed moderately throughout the feather tract then were up-regulated in restricted regions following two modes: Wnt 1 and 3a became restricted to the placodal epithelium, then to the elongated distal bud epidermis; Wnt 5a and 11 intensified in the inter-tract region and interprimordia epidermis or dermis, respectively, then appeared in the elongated distal bud dermis. Their role in feather tract formation was determined using RCAS mediated misexpression in ovo at E2/E3. Their function in periodic feather patterning was examined by misexpression in vitro using reconstituted E7 skin explant cultures. Wnt 1 reduced spinal tract size, but enhanced feather primordia size. Wnt 3a increased dermal thickness, expanded the spinal tract size, reduced interbud domain spacing, and produced non-tapering "giant buds". Wnt 11 and dominant negative Wnt 1 enhanced interbud spacing, and generated thinner buds. In cultured dermal fibroblasts, Wnt 1 and 3a stimulated cell proliferation and activated the canonical beta-catenin pathway. Wnt 11 inhibited proliferation but stimulated migration. Wnt 5a and 11 triggered the JNK pathway. Thus distinctive Wnts have positive and negative roles in forming the dermis, tracts, interbud spacing and the growth and shaping of individual buds.
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Morpho-regulation of ectodermal organs: integument pathology and phenotypic variations in K14-Noggin engineered mice through modulation of bone morphogenic protein pathway.
Ectodermal organs are composed of keratinocytes organized in different ways during induction, morphogenesis, differentiation, and regenerative stages. We hypothesize that an imbalance of fundamental signaling pathways should affect multiple ectodermal organs in a spatio-temporal-dependent manner. We produced a K14-Noggin transgenic mouse to modulate bone morphogenic protein (BMP) activity and test the extent of this hypothesis. We observed thickened skin epidermis, increased hair density, altered hair types, faster anagen re-entry, and formation of compound vibrissa follicles. The eyelid opening was smaller and ectopic cilia formed at the expense of Meibomian glands. In the distal limb, there were agenesis and hyperpigmentation of claws, interdigital webbing, reduced footpads, and trans-differentiation of sweat glands into hairs. The size of external genitalia increased in both sexes, but they remained fertile. We conclude that modulation of BMP activity can affect the number of ectodermal organs by acting during induction stages, influence the size and shape by acting during morphogenesis stages, change phenotypes by acting during differentiation stages, and facilitate new growth by acting during regeneration stages. Therefore during organogenesis, BMP antagonists can produce a spectrum of phenotypes in a stage-dependent manner by adjusting the level of BMP activity. The distinction between phenotypic variations and pathological changes is discussed.
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Sculpting skin appendages out of epidermal layers via temporally and spatially regulated apoptotic events.
Complex skin appendages are built from the epidermal cells through various cell events. Here we used TUNEL and caspase-3 immuno-localization to examine apoptosis in feather morphogenesis. We deduced three modes. In Mode 1A, apoptosis occurs within the localized growth zone (LoGZ) to regulate growth (feather buds). In Mode 1B, morphogen secreting cells are present adjacent to LoGZ and apoptosis may work to remove such signaling centers (barb ridges). In Mode 2, keratinocytes apoptosed before terminal differentiation and left spaces between branches (marginal plate). In Mode 3A, keratinocytes cornified and flaked off to free skin appendages (feather sheath, pulp epithelium). In Mode 3B, keratinized apoptosed epithelial cells became permanent structures (rachis, ramus, barbules). Thus, different apoptotic modes can have different impacts on morphogenesis. We further tested effects of imbalanced Shh on apoptosis. Shh suppression reduced marginal plate apoptosis and caused abnormal differentiation of barbule plates. Shh over-expression enhanced proliferation in barb ridges. Expression of Patched in the barbule plate epithelia implies a paracrine mechanism. The current work complements our recent work on LoGZ to show how adding and removing cell masses in temporally and spatially specific ways are coordinated to sculpt skin appendages from epidermal layers.
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Rooster feathering, androgenic alopecia, and hormone-dependent tumor growth: what is in common?
Different epithelial organs form as a result of epithelial-mesenchymal interactions and share a common theme modulated by variations (Chuong ed. In Molecular Basis of Epithelial Appendage Morphogenesis, 1998). One of the major modulators is the sex hormone pathway that acts on the prototype signaling pathway to alter organ phenotypes. Here, we focus on how the sex hormone pathway may interface with epithelia morphogenesis-related signaling pathways. We first survey these sex hormone-regulated morphogenetic processes in various epithelial organs. Sexual dimorphism of hairs and feathers has implications in sexual selection. Diseases of these pathways result in androgenic alopecia, hirsutism, henny feathering, etc. The growth and development of mammary glands, prostate glands, and external genitalia essential for reproductive function are also dependent on sex hormones. Diseases affecting these organs include congenital anomalies and hormone-dependent breast and prostate cancers. To study the role of sex hormones in new growth in the context of system biology/pathology, an in vivo model in which organ formation starts from stem cells is essential. With recent developments (Yu et al. (2002) The morphogenesis of feathers. Nature 420:308-312), the growth of tail feathers in roosters and hens has become a testable model in which experimental manipulations are possible. We show exemplary data of differences in their growth rate, proliferative cell population, and signaling molecule expression. Working hypotheses are proposed on how the sex hormone pathways may interact with growth pathways. It is now possible to test these hypotheses using the chicken model to learn fundamental mechanisms on how sex hormones affect organogenesis, epithelial organ cycling, and growth-related tumorigenesis.
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Evo-Devo of amniote integuments and appendages.
Integuments form the boundary between an organism and the environment. The evolution of novel developmental mechanisms in integuments and appendages allows animals to live in diverse ecological environments. Here we focus on amniotes. The major achievement for reptile skin is an adaptation to the land with the formation of a successful barrier. The stratum corneum enables this barrier to prevent water loss from the skin and allowed amphibian / reptile ancestors to go onto the land. Overlapping scales and production of beta-keratins provide strong protection. Epidermal invagination led to the formation of avian feather and mammalian hair follicles in the dermis. Both adopted a proximal - distal growth mode which maintains endothermy. Feathers form hierarchical branches which produce the vane that makes flight possible. Recent discoveries of feathered dinosaurs in China inspire new thinking on the origin of feathers. In the laboratory, epithelial - mesenchymal recombinations and molecular mis-expressions were carried out to test the plasticity of epithelial organ formation. We review the work on the transformation of scales into feathers, conversion between barbs and rachis and the production of "chicken teeth". In mammals, tilting the balance of the BMP pathway in K14 noggin transgenic mice alters the number, size and phenotypes of different ectodermal organs, making investigators rethink the distinction between morpho-regulation and pathological changes. Models on the evolution of feathers and hairs from reptile integuments are discussed. A hypothetical Evo-Devo space where diverse integument appendages can be placed according to complex phenotypes and novel developmental mechanisms is presented.
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Integument pattern formation involves genetic and epigenetic controls: feather arrays simulated by digital hormone models.
Pattern formation is a fundamental morphogenetic process. Models based on genetic and epigenetic control have been proposed but remain controversial. Here we use feather morphogenesis for further evaluation. Adhesion molecules and/or signaling molecules were first expressed homogenously in feather tracts (restrictive mode, appear earlier) or directly in bud or inter-bud regions ( de novo mode, appear later). They either activate or inhibit bud formation, but paradoxically colocalize in the bud. Using feather bud reconstitution, we showed that completely dissociated cells can reform periodic patterns without reference to previous positional codes. The patterning process has the characteristics of being self-organizing, dynamic and plastic. The final pattern is an equilibrium state reached by competition, and the number and size of buds can be altered based on cell number and activator/inhibitor ratio, respectively. We developed a Digital Hormone Model which consists of (1) competent cells without identity that move randomly in a space, (2) extracellular signaling hormones which diffuse by a reaction-diffusion mechanism and activate or inhibit cell adhesion, and (3) cells which respond with topological stochastic actions manifested as changes in cell adhesion. Based on probability, the results are cell clusters arranged in dots or stripes. Thus genetic control provides combinational molecular information which defines the properties of the cells but not the final pattern. Epigenetic control governs interactions among cells and their environment based on physical-chemical rules (such as those described in the Digital Hormone Model). Complex integument patterning is the sum of these two components of control and that is why integument patterns are usually similar but non-identical. These principles may be shared by other pattern formation processes such as barb ridge formation, fingerprints, pigmentation patterning, etc. The Digital Hormone Model can also be applied to swarming robot navigation, reaching intelligent automata and representing a self-re-configurable type of control rather than a follow-the-instruction type of control.
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The biology of feather follicles.
The feather is a complex epidermal organ with hierarchical branches and represents a multi-layered topological transformation of keratinocyte sheets. Feathers are made in feather follicles. The basics of feather morphogenesis were previously described (Lucas and Stettenheim, 1972). Here we review new molecular and cellular data. After feather buds form (Jiang et al., this issue), they invaginate into the dermis to form feather follicles. Above the dermal papilla is the proliferating epidermal collar. Distal to it is the ramogenic zone where the epidermal cylinder starts to differentiate into barb ridges or rachidial ridge. These neoptile feathers tend to be downy and radially symmetrical. They are replaced by teleoptile feathers which tend to be bilateral symmetrical and more diverse in shapes. We have recently developed a "transgenic feather" protocol that allows molecular analyses: BMPs enhance the size of the rachis, Noggin increases branching, while anti- SHH causes webbed branches. Different feather types formed during evolution (Wu et al., this issue). Pigment patterns along the body axis or intra-feather add more colorful distinctions. These patterns help facilitate the analysis of melanocyte behavior. Feather follicles have to be connected with muscles and nerve fibers, so they can be integrated into the physiology of the whole organism. Feathers, similarly to hairs, have the extraordinary ability to go through molting cycles and regenerate. Some work has been done and feather follicles might serve as a model for stem cell research. Feather phenotypes can be modulated by sex hormones and can help elucidate mechanisms of sex hormone-dependent growth control. Thus, the developmental biology of feather follicles provides a multi-dimension research paradigm that links molecular activities and cellular behaviors to functional morphology at the organismal level.
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New Early Cretaceous fossil from China documents a novel trophic specialization for Mesozoic birds.
We report on a new Mesozoic bird, Longirostravis hani, from the Early Cretaceous Jehol Biota of northeastern China. The new taxon has a long, slender rostrum and mandible, and a small number of rostralmost teeth. Postcranial characters such as a furcular ramus wider ventrally than dorsally, a centrally concave proximal margin of the humeral head, and a minor metacarpal that projects distally more than the major metacarpal, support the placement of Longirostravis within euenantiornithine Enantiornithes, the most diverse clade of Mesozoic birds. The morphology of the skull, however, suggests that Longirostravis had a probing feeding behavior, a specialization previously unknown for Enantiornithes. Indeed, this discovery provides the first evidence in support of the existence of such a foraging behavior among basal lineages of Mesozoic birds.
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