Search

The Tabula Gallus is a proposed project that aims to create a map of every cell type in the chicken body and chick embryos. Chickens (Gallus gallus) are one of the most recognized model animals that recapitulate the development and physiology of mammals. The Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide tools for the study of the biology of this species, similar to other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and humans, respectively). The Tabula Gallus will potentially become an international collaboration between many researchers. This project will be useful for the basic scientific study of Gallus gallus and other birds (e.g., cell biology, molecular biology, developmental biology, neuroscience, physiology, oncology, virology, behavior, ecology, and evolution). It will eventually be beneficial for a better understanding of human health and diseases.

SUMMARYRetinal structure and function have been studied in many vertebrate orders, but molecular characterization has been largely confined to mammals. We used single-cell RNA sequencing (scRNA-seq) to generate a cell atlas of the chick retina. From ∼40,000 single cell transcriptomes, we identified 136 cell types distributed among the six classes conserved across vertebrates – photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and glial cells. To match molecular profiles to morphology, we adapted a method for CRISPR-based integration of reporters into selectively expressed genes. For Müller glia, we found that transcriptionally distinct cells were regionally localized along the anterior-posterior, dorsal-ventral and central-peripheral retinal axes. We also identified immature photoreceptor, horizontal cell and oligodendrocyte types that persist into late embryonic stages. Finally, we analyzed relationships among chick, mouse and primate retinal cell classes and types. Taken together, our results provide a foundation for anatomical, physiological, evolutionary, and developmental studies of the avian visual system.

Sensitive and specific antibodies are essential for detecting molecules in cells and tissues. However, currently used polyclonal and monoclonal antibodies are often less specific than desired, difficult to produce, and available in limited quantities. A promising recent approach to circumvent these limitations is to employ chemically defined antigen-combining domains called "nanobodies," derived from single-chain camelid antibodies. Here, we used nanobodies to prepare sensitive unimolecular detection reagents by genetically fusing cDNAs encoding nanobodies to enzymatic or antigenic reporters. We call these fusions between a reporter and a nanobody "RANbodies." They can be used to localize epitopes and to amplify signals from fluorescent proteins. They can be generated and purified simply and in unlimited amounts and can be preserved safely and inexpensively in the form of DNA or digital sequence.

Summary Distinct neuronal types connect in complex ways to generate functional neural circuits. The molecular diversity required to specify this connectivity could be supplied by multigene families of synaptic recognition molecules, but most studies to date have assessed just one or a few members at a time. Here, we analyze roles of cadherins (Cdhs) in formation of retinal circuits comprising eight neuronal types that inform the brain about motion in four directions. We show that at least 15 classical Cdhs are expressed by neurons in these circuits and at least 6 (Cdh6–10 and 18) act individually or in combinations to promote specific connectivity among the cells. They act in part by directing the processes of output neurons and excitatory interneurons to a cellular scaffold formed by inhibitory interneurons. Because Cdhs are expressed combinatorially by many central neurons, similar interactions could be involved in patterning circuits throughout the brain.

Each P-RANbody consists of a HRP reporter and a nanobody that binds to antigen(s). This is a protocol to stain cells and tissues with P-RANbodies. The method is similar to common immunostaining protocols. However, this protocol focuses on some important tips.

This is a protocol for cell adhesion assays using 293T cells or N-cadherin-deficient 293NC cells (Yamagata et al., 2018). HEK293T(ATCC CRL-3216) cells are easily transfectable with plasmids. The 293NC cells lack N-cadherin (Cadherin-2), but maintain the property of its parental 293T cells. Thus, this 293T variant is useful to test cell adhesion (Goodman et al., 2016; Yamagata et al., 2018). Here, I describe a protocol and some technical tips.

In the mammalian retina, processes of approximately 70 types of interneurons form specific synapses on roughly 30 types of retinal ganglion cells (RGCs) in a neuropil called the inner plexiform layer. Each RGC type extracts salient features from visual input, which are sent deeper into the brain for further processing. The specificity and stereotypy of synapses formed in the inner plexiform layer account for the feature-detecting ability of RGCs. Here we analyse the development and function of synapses on one mouse RGC type, called the W3B-RGC. These cells have the remarkable property of responding when the timing of the movement of a small object differs from that of the background, but not when they coincide. Such cells, known as local edge detectors or object motion sensors, can distinguish moving objects from a visual scene that is also moving. We show that W3B-RGCs receive strong and selective input from an unusual excitatory amacrine cell type known as VG3-AC (vesicular glutamate transporter 3). Both W3B-RGCs and VG3-ACs express the immunoglobulin superfamily recognition molecule sidekick 2 (Sdk2), and both loss- and gain-of-function studies indicate that Sdk2-dependent homophilic interactions are necessary for the selectivity of the connection. The Sdk2-specified synapse is essential for visual responses of W3B-RGCs: whereas bipolar cells relay visual input directly to most RGCs, the W3B-RGCs receive much of their input indirectly, via the VG3-ACs. This non-canonical circuit introduces a delay into the pathway from photoreceptors in the centre of the receptive field to W3B-RGCs, which could improve their ability to judge the synchrony of local and global motion.

Chondroitin sulfate proteoglycans (CSPGs) of the extracellular matrix help stabilize synaptic connections in the postnatal brain and impede regeneration after injury. Here, we show that a CSPG of the lectican family, versican, also promotes presynaptic maturation in the developing brain. In the embryonic chick optic tectum, versican is expressed selectively by subsets of interneurons confined to the retinorecipient laminae, in which retinal axons arborize and form synapses. It is a major receptor for theVicia villosaB4lectin (VVA), shown previously to inhibit invasion of the retinorecipient lamina by retinal axons (Inoue and Sanes, 1997).In vitro, versican promotes enlargement of presynaptic varicosities in retinal axons. Depletion of versicanin ovo, by RNA interference, results in retinal arbors with smaller than normal varicosities. We propose that versican provides a lamina-specific cue for presynaptic maturation and discuss the related but distinct effects of versican depletion and VVA blockade.

Solid tumours develop an acidic extracellular environment with high concentration of lactic acid, and lactic acid produced by glycolysis has been assumed to be the major cause of tumour acidity. Experiments using lactate dehydrogenase (LDH)-deficient ras-transfected Chinese hamster ovarian cells have been undertaken to address directly the hypothesis that lactic acid production is responsible for tumour acidification. The variant cells produce negligible quantities of lactic acid and consume minimal amounts of glucose compared with parental cells. Lactate-producing parental cells acidified lightly-buffered medium but variant cells did not. Tumours derived from parental and variant cells implanted into nude mice were found to have mean values of extracellular pH (pHe) of 7.03 +/- 0.03 and 7.03 +/- 0.05, respectively, both of which were significantly lower than that of normal muscle (pHe = 7.43 +/- 0.03; P < 0.001). Lactic acid concentration in variant tumours (450 +/- 90 microg g(-1) wet weight) was much lower than that in parental tumours (1880 +/- 140 microg/g(-1)) and similar to that in serum (400 +/- 35 microg/g(-1)). These data show discordance between mean levels of pHe and lactate content in tumours; the results support those of Newell et al (1993) and suggest that the production of lactic acid via glycolysis causes acidification of culture medium, but is not the only mechanism, and is probably not the major mechanism responsible for the development of an acidic environment within solid tumours.

Mean values of extracellular pH (pHe) in tumours tend to be about 0.5 pH units lower than in normal tissues, whereas values of intracellular pH (pHi) in tumours and normal tissues are similar. Previous studies have shown that drugs that acidify cells at lower pHe such as nigericin, used alone or with agents that inhibit the regulation of pHi, have toxicity to cultured cells at pHe < 6.5 in short-term exposure; these agents also lead to modest anti-tumour effects in mice when given acutely. To evaluate the long-term effects of these drugs at levels of pHe that might occur commonly in tumours, we exposed cells for up to 72h at pHe 6.8 or 7.2 in vitro. Nigericin (0.033 microM) caused time-dependent cell killing of murine KHT and EMT-6 cells at pHe 6.8 (but not at pHe 7.2) with a surviving fraction approximately 5 x 10(-3) after 72 h exposure. Cell killing was increased in the presence of 4,4-diisothiocyanstilbene 2,2-disulphonic acid (DIDS), an inhibitor of Na+-dependent HCO3-/CI- exchange, and to a lesser extent in the presence of 5-(N-ethyl-N-isopropyl) amiloride (EIPA), an inhibitor of Na+/H+ exchange. Cell killing was exquisitely sensitive to the level of pHe. Osmotic pumps were used to obtain a 72 h continuous infusion of nigericin in mice; this led to dose-dependent killing of cells in KHT tumours with surviving fraction of approximately 0.1 at maximum tolerated doses. Hydralazine, which may cause tumour hypoxia and lower pHi as well as pHe, caused cytotoxity when given alone by chronic infusion, and enhanced the cytotoxicity due to nigericin. The addition of DIDS and/or EIPA (using two pumps) further enhanced anti-tumour toxicity, with a surviving fraction of approximately 0.002 at tolerated doses of the four drugs used to treat KHT tumours. The experiments demonstrate the activity of drugs that inhibit the regulation of pHi against murine tumours when delivered by chronic infusion.

In diverse vertebrate species, defined subsets of retinal ganglion cells (RGCs, the neurons that project from retina to brain) are distinguishable on the basis of their dendritic morphology, physiological properties, neurotransmitter content and synaptic targets. Little is known about when this diversity arises, whether diversification requires targetderived signals, and how subtype-specific projection patterns are established. Here, we have used markers for two chemically defined RGC subsets in chick retina to address these issues. Antibodies to substance P (SP) and the nicotinic acetylcholine receptor (AChR) β2 subunit label two small ( In the mature optic tectum, SPand AChR-positive RGC axonal arbors are confined to distinct retinorecipient (synaptic) laminae. In the developing tectum, Spand AChR-positive axons are initially intermingled in a superficial fiber layer, but then enter and arborize in appropriate laminae soon after those laminae form. Importantly, SPpositive axons, which synapse in a superficial lamina, never extend into the deeper, AChR-positive lamina. Tectal interneurons rich in SP receptors are concentrated in the lamina to which SP-positive RGC axons project, and a set of cholinergic (choline acetyltransferase-positive) tectal projection neurons elaborate dendrites in the lamina to which AChR-positive RGC axons project. These populations of tectal neurons, which are likely targets of the RGC subsets, form in tecta that develop following enucleation. Thus, RGCs and their targets can diversify in each others absence. Accordingly, we propose that the lamina-selective connectivity we observe reflects the presence of complementary cues on RGC subsets and their laminar targets.

The optic tectum is the major synaptic target of retinal axons in birds. In the chick, retinal ganglion cell axons enter the optic tectum through a superficial lamina (the stratum opticum), extended branches into deeper laminae, and arborize in specific “retinorecipient” laminae, where they form synapses. Studies using an organotypic culture system have provided evidence that the tectum bears a series of distinct, lamina-specific, cell surface-associated cues that direct these axonal behaviors (Yamagata and Sanes, 1995). Here, we have used a panel of antibodies to 30 membrane and matrix components to ask whether known adhesive molecules are distributed in lamina-specific patterns. Among many spatiotemporal pattern of expression documented, three were particularly noteworthy: (1) The cell adhesion molecules NgCAM/L1 and TAG-1/axonin-1 were concentrated in the stratum opticum. (2) SC1/JC7/DM- GRASP/BEN, N-cadherin, neuropilin, polysialylated N-CAM, and glycoconjugates recognized by the lectin VVA-B4 were concentrated in retinorecipient laminae. (3) Neurofascin, tenascin-C/cytotactin, and a matrix molecule defined by the “Sigma” antibody were present at highest levels in areas that border the retinorecipient laminae. Some members of each group (NgCAM/L1, TAG-1/axonin, SC1/JC7, polysialic acid, VVA-B4- receptors, and neurofascin) appeared on schedule and in lamina- restricted patterns in tecta from embryos that had been enucleated before retinal axons left the eye. Thus, molecules in these three categories could provide signals to retinal axons that promote extension through the stratum opticum, induce arborization or synaptogenesis in retinorecipient laminae, and prevent sprouting into adjoining laminae. Interestingly, N-cadherin accumulated in retinorecipient laminae only following the onset of synapse formation, and failed to accumulate in enucleated tecta. Immunoelectron microscopy of normal tecta demonstrated the presence of N-cadherin in the synaptic cleft, suggesting a role for this molecule in synaptic maintenance.

TOPOGRAPHICAL maps of neuronal connectivity occur in various brain regions1. In the visual system of birds, retinal ganglion-cell axons from the anterior retina connect to a posterior part of the optic tectum, and posterior retinal axons connect to the anterior part, thereby establishing a point-to-point projection map2,3. The chemoaffinity theory4 predicts that the orderly retinotectal projection is generated by a topographical arrangement of molecules. We report here that we have found several genes topographically expressed along the nasotemporal (anterior–posterior) axis in the embryonic chicken retina. Among these, two transcriptional regulators, belonging to the winged-helix family5 are expressed in a mutually exclusive manner in either the nasal or temporal part of the retina. Misexpression of each factor causes misprojection on the tectum along the rostrocaudal axis, showing that topographical expression of these transcription factors controls formation of the retinotectal map.

Publisher Summary This chapter discusses gene transfer using replication-defective retroviral and adenoviral vectors. Viruses are obligate intracellular parasites that live by invading a host cell and then using that cell's machinery to replicate their genetic material. As the understanding of viral genomes and their lifestyle has increased, it has been natural to envision harnessing their skills for the transfer of exogenous genes to vertebrate cells in vivo, both for experimental purposes and for gene therapy. Numerous viral vectors have been studied in these contexts, including retrovirus, adenovirus, herpes virus, sindbis virus, vaccinia virus, and adeno-associated virus. Retroviruses consist of an RNA genome encased in a protein core, which in turn is coated by a proteolipid envelope. The RNA encodes three classes of proteins called “pol” (for polymerase), “gag” (for group-associated antigens), and “env” (for envelope). The pol proteins are tightly associated with the RNA, gag proteins form the core, and env proteins are embedded in the lipid membrane.

In the chick, retinal axons enter the optic tectum through a superficial lamina, then branch into distinct deeper retinorecipient laminae, where they arborize and form synapses. To study factors that guide this laminar selectivity, we devised an organotypic culture system in which a transverse tectal section is overlaid with a retinal explant large enough to allow unimpeded access to all tectal laminae. Outgrowth, branching, and arborization patterns of retinal axons on tectal slices were lamina-selective, indicating the existence of localized cues that guide retinal axons. Further studies suggested that some of these cues are: (1) associated with cell membranes or extracellular matrix (because axons grew selectively on chemically fixed tectal sections); (2) intrinsic to the tectum (because axons grew selectively on tectal sections prepared from enucleated embryos); (3) distinct from topographic cues (because axons from nasal and temporal retina behaved similarly on anterior tectal slices); and (4) selective for retinal axons (because axons growing from other explants exhibited different laminar preferences).

PG-M and PG-H, chick large chondroitin sulfate proteoglycans corresponding to versican (fibroblast-type proteoglycan) and aggrecan (cartilage-characteristic proteoglycan), respectively, which are found in mammals, have been characterized in various tissues of chick embryos. Their distribution and the compositions of the core molecules were analyzed by immunofluorescence staining and immunoblotting, respectively, using various monospecific antibodies. Molecules reactive to a monoclonal antibody to the PG-M core protein (designated MY-174) were distributed in various tissues, including aorta, lung, cornea, brain, skeletal muscle and dermis. Immunoblotting with MY-174 of the chondroitinase ABC-digested tissue extracts showed a tissue variation of MY-174-reactive core molecules (550-kD, 500-kD, 450-kD, and 350-300-kD). In contrast, PG-H, besides massive occurrence in cartilage, was only found in a few tissues such as aorta and brain. In addition, PG-H in aorta, cornea, and skin was atypical in structure, because it lacked keratan sulfate. The expression of PG-M in developing chick embryos was then examined. PG-M was found in some developmentally active areas, such as the perinotochordal mesenchyme between notochord and neural tube, the basement membranes facing neuroepithelial cells, and condensing mesenchymal cells in limb buds, suggesting some functions distinctive of the developing tissues.

This study utilizes immunofluorescence to describe the distribution of several extracellular matrix molecules in the chick embryo during the process of limb outgrowth and the formation of precartilage condensations. A large chondroitin sulfate proteoglycan (PG-M) is detected at the wing level at Hamburger and Hamilton stage 14 in and under the dorsal ectoderm, and is associated with the basement membranes around the neural tube, notochord and pronephros, but not with other basement membranes. The galactose-specific lectin, peanut agglutinin (PNA), has a similar distribution except that it also binds to the dorsal side of the neural tube. PG-M is not detected in the limb mesenchyme until after stage 17, when it is present in the distal region, as is PNA-binding material. With further development of the wing bud, PG-M is present in the subectodermal mesenchyme, the mesenchyme at the distal tip and in the prechondrogenic core. After stage 22 PNA-binding material becomes localized in the prechondrogenic core, the basement membranes under the apical ectodermal ridge, and the ventral sulcus. The distribution of these components (PG-M and PNA binding material) overlaps, but differs from that of type I collagen and fibronectin and basement membrane components, such as laminin, basement membrane heparan sulfate proteoglycan, and type IV collagen. Tenascin, on the other hand, is not detected in the limb bud until stage 25, after the appearance of cartilage matrix components such as type II collagen and cartilage proteoglycan (PG-H). These results are considered in relation to the formation of precartilage aggregates, and indicate that PNA binds to components in precartilage aggregates other than PG-M or tenascin.

Fluorescein isothiocyanate (FITC)-labelled hyaluronic acid, when incubated with subconfluent cultures of mouse dermal fibroblasts, was incorporated into the extracellular matrix. Deposition of the fluorescent label reached the maximum about 48 h after its addition. Hyaluronic acid decasaccharide, but not octasaccharide, inhibited the incorporation of the fluorescent label, suggesting that at least 10 sugar units in length are necessary for the incorporation of hyaluronic acid. A 2 M-urea extract of the cell layer had the ability to bind [3H]hyaluronic acid. Again, the binding was inhibited by hyaluronic acid decasaccharide but not by octasaccharide, suggesting the presence in the urea extract of a hyaluronic acid-binding molecule that may participate in the incorporation of hyaluronic acid. A supramolecular aggregate prepared by rate-zonal sedimentation from the 2 M-urea extract contained chondroitin sulphate proteoglycans capable of interacting with hyaluronic acid. Their core molecules were identical in size with those from a hyaluronic acid-binding chondroitin sulphate proteoglycan (PG-M) previously described in chick embryo fibroblasts. Immunofluorescence analyses with anti-proteoheparan sulphate antibodies indicated that both exogenous addition of hyaluronic acid and enhanced synthesis of hyaluronic acid caused a preferential decline in the proteoheparan sulphate level in the extracellular matrix. Subsequent to this change, the cells began transient DNA synthesis. We suggest that hyaluronic acid-dependent modulation of the level of proteoheparan sulphate in the extracellular matrix could be a causal event of cell proliferation.

We have demonstrated previously that chick embryo fibroblasts synthesize and secrete a large chondroitin sulfate proteoglycan (designated PG-M) that binds to fibronectin. We now report the possibility that PG-M interactions with cell surfaces can modulate cell-substrate adhesion. When PG-M was added to the medium, various types of trypsinized cells failed to adhere not only to fibronectin-coated substrates but also to collagen- or vitronectin-coated substrates. Adhesion of the cells to laminin or glycyl-arginyl-glycyl-aspartyl-serine derivatized serum albumin (arginyl-glycyl-aspartic acid-containing molecules with no capacity to bind PG-M) was also inhibited by PG-M. Treatment of the proteoglycan with either proteolytic enzymes or chondroitinase abolished its inhibitory effects on the cell adhesion. These results suggest that direct binding between PG-M and fibronectin, if any, is not a cause of the inhibition by PG-M and that only the proteoglycan form is responsible for the activity. When the immobilization of added PG-M to available plastic surfaces of coated dishes was blocked by pretreating the dishes with serum albumin, the inhibitory effect of PG-M was abolished, suggesting that the immobilized fraction of PG-M can act as a cell adhesion inhibitor. In immobilized form, both cartilage chondroitin sulfate proteoglycan (designated PG-H) and chondroitin sulfate-derivatized serum albumin also inhibited cell adhesion. In contrast, heparan sulfate proteoglycan form LD and heparan sulfate-derivatized serum albumin had far lower inhibitory activities, indicating that the active site for the interaction between cells and PG-M is on the chondroitin sulfate chains.

When the concentration of hyaluronic acid was monitored in primary cultures of mouse skin dermal fibroblasts, there was an increase in hyaluronic acid proportional to the increase in cell number during the logarithmic growth phase. The concentration reached the maximum value 2 days before the cells became confluent, and then decreased gradually. Hyaluronic acid added at 1 mg ml-1 during the logarithmic phase either promoted or inhibited cell growth, depending on the density of cells at the time when hyaluronic acid was added. Hyaluronic acid (1 mg ml-1) added to subconfluent or postconfluent cultures induced a transient DNA synthesis with a consequent increase (greater than 20%) in cell number. The effects appeared to be specific, since neither hyaluronic acid oligosaccharides nor some other types of glycosaminoglycan (chondroitin, chondroitin sulphates, heparan sulphates and heparin) had any similar effects. Dibutyryl adenosine 3′,5′-cyclic monophosphate (dbcAMP), at 1 mM, added to subconfluent or postconfluent cultures had promoting effects successively on hyaluronic acid synthesis and on cell growth. An increase in hyaluronic acid synthesis also occurred when dbcAMP was added to day 1 cultures in the logarithmic growth phase, but the effect on cell growth was reversed; there was an inhibition rather than a promotion. The pattern of cell density-dependent variation of the dbcAMP effect is quite similar to that observed with exogenously added hyaluronic acid. Therefore, we propose that hyaluronic acid added exogenously or supplied endogenously by increased synthesis may act as a modulator of mouse dermal fibroblast proliferation.

We showed previously that a large chondroitin sulfate proteoglycan, PG-M (also known as versican), inhibits cell-substratum adhesion, while basement membrane heparan sulfate proteoglycan (recently named perlecan) does not (Yamagata et al. (1989) J. Biol. Chem. 264, 8012–8018). To extend our understanding of the adhesive function of these proteoglycans, we examined the pericellular localization of the proteoglycans and their ligands and also that of some matrix receptors and cytoskeletal molecules in various fibroblast culture systems. PG-M was abundant in the subcellular space of fibroblasts, but was excluded selectively from focal contacts where vinculin, integrins and fibronectin were localized. Hyaluronan, CD44 and tenascin were distributed similarly as PG-M. In contrast, perlecan was associated with fibronectin and was included in focal contacts. Syndecan-1, a membrane heparan sulfate/chondroitin sulfate proteoglycan, was associated with fibronectin at the cell surface, partly at focal contacts and in association with stress fibers. Thus, complexes of PG-M with hyaluronan, tenascin and CD44, are not involved in focal contacts. On the other hand, perlecan and syndecan-1 together with fibronectin may participate in focal contacts. The difference in localization between these proteoglycans may be related to their glycosaminoglycan content and to their distinctive roles in cell-substratum adhesion.

Preparations of cellular fibronectin from chick embryonic fibroblasts have previously been shown to have hyaluronate-binding activity. However, gel filtration and CsCl isopycnic centrifugation of fibronectin preparations showed that the binding activity was associated with molecules with a density and a molecular weight higher than those of fibronectin. An immunoprecipitation assay using antibodies to the chondroitin sulfate proteoglycan (PG-M) from the mesenchyme of chick embryo limb bud showed that the hyaluronate-binding activity of fibronectin preparations was precipitable with this antibody. The immunoprecipitation analyses also showed that fibronectin preparations as well as conditioned culture medium and extracts of chick embryonic fibroblasts contained a chondroitin sulfate proteoglycan, the protein-enriched core molecules from which were identical to those from PG-M with respect to electrophoretic mobility and immunological reactivity. This proteoglycan was purified from conditioned culture medium and extracts of fibroblasts by dissociative CsCl isopycnic centrifugation. The proteoglycans from medium or extracts gave core derivatives with electrophoretic mobility identical to those from PG-M, and they had equal hyaluronate-binding activities. These results, taken together, suggest that most, if not all, of the hyaluronate-binding activity in preparations of chick cellular fibronectin is due to a proteoglycan identical to PG-M. This proteoglycan was also found to bind directly to fibronectin and to type I collagen, but not to laminin or type IV collagen. It is possible that the fibroblast proteoglycan mediates interactions between hyaluronate, fibronectin, and type I collagen, thereby participating in formation of the pericellular matrix of fibroblasts.