A protocol to study three-dimensional genome structure in individual mutant preimplantation mouse embryos

Hi-C studies the three-dimensional structure of the genome by detecting genome-wide chromatin regions that are in spatial proximity within the nucleus. We developed single-blastocyst Hi-C in mutant mouse embryos to genotype them on sequence. We describe steps for embryo fixation and nuclei permeabilization, after which chromatin is digested and re-ligated having incorporated a biotin-labeled nucleotide at the ligation junction. After cross-link reversal, we then detail purification of immobilized chimeric DNA ligations, library generation, sequencing, and genome-wide analysis of interactions. For complete details on the use and execution of this protocol, please refer to Andreu et al. (2022).¹.

Chromatin dynamics through mouse preimplantation development revealed by single molecule localisation microscopy

Most studies addressing chromatin behaviour during preimplantation development are based on biochemical assays that lack spatial and cell-specific information, crucial during early development. Here, we describe the changes in chromatin taking place at the transition from totipotency to lineage specification, by using direct stochastical optical reconstruction microscopy (dSTORM) in whole-mount embryos during the first stages of mouse development. Through the study of two post-translational modifications of Histone 3 related to active and repressed chromatin, H3K4me3 and H3K9me3 respectively, we obtained a time-course of chromatin states, showing spatial differences between cell types, related to their differentiation state. This analysis adds a new layer of information to previous biochemical studies and provides novel insight to current models of chromatin organisation during the first stages of development.

SUMMARY: We have applied super-resolution microscopy to analyse changes in the state of chromatin during the first stages of mouse development, from the two-cell stage to the blastocyst.

Transitions in cell potency during early mouse development are driven by Notch

The Notch signalling pathway plays fundamental roles in diverse developmental processes in metazoans, where it is important in driving cell fate and directing differentiation of various cell types. However, we still have limited knowledge about the role of Notch in early preimplantation stages of mammalian development, or how it interacts with other signalling pathways active at these stages such as Hippo. By using genetic and pharmacological tools in vivo, together with image analysis of single embryos and pluripotent cell culture, we have found that Notch is active from the 4-cell stage. Transcriptomic analysis in single morula identified novel Notch targets, such as early naïve pluripotency markers or transcriptional repressors such as TLE4. Our results reveal a previously undescribed role for Notch in driving transitions during the gradual loss of potency that takes place in the early mouse embryo prior to the first lineage decisions.

We start life as a single cell, which immediately begins to divide to form an embryo that will eventually contain all the different kinds of cells found in the adult body. During the first few rounds of cell division, embryonic cells can become any type of adult cells, but also form the placenta, the organ that sustains the embryo while in the womb. As cells keep on dividing, they lose this ability, called potency, and they take on more specific and inflexible roles.

The first choice embryonic cells must make is whether to become part of the placenta or part of the future body. These types of decisions are controlled by molecular cascades known as signalling pathways, which relay information from the cells surface to its control centre. There, specific genes get turned on or off in response to an outside signal.

Previous research showed that two signalling pathways, Hippo and Notch, help separate placenta cells from those that will form the rest of the body. However, it was not known whether the two pathways worked independently, or if they were overlapping. Menchero et al. therefore wanted to find out when exactly the Notch pathway started to be active, and examine how it helped cells to either become the placenta or part of the future body.

Experiments with developing mouse embryos showed that the Notch pathway was activated after the very first two cell divisions, when the embryo consists of only four cells. Genetic manipulations combined with drug treatments that changed the activity of the Notch pathway confirmed that Notch and Hippo acted independently at this stage. Further, larger-scale analysis of gene activity in these embryos also revealed that Notch signalling was working in a previously unknown way: it turned off the genes that maintain potency, pushing the cells to become more specialised.

Ultimately, identifying this new mode of action for the Notch pathway in the early embryo may help to understand how the signalling cascade acts in other types of processes. This knowledge could be useful, for example, to push embryonic cells grown in the laboratory towards a desired fate.

Cholecystokinin innervation of the cerebral cortex in a reptile, the lizard, Psammodromus algirus

We used light and electron microscopic and immunohistochemical methods to map the distribution of cholecystokinin (CCK) in the cerebral cortex of a lizard, Psammodromus algirus. At light microscopy, the CCK immunoreactivity was limited to fibers and terminals densely innervating all cortical regions except for the lateral (pyriform) cortex which was very slightly immunostained. The CCK-positive terminals were almost restricted to the cell layers in every cortical region where they surrounded immunonegative cell bodies and proximal dendrites of neurons within the layer. No CCK-containing neurons were observed within the cerebral cortex. At the electron microscopic level, most positive structures were presynaptic boutons contacting cell bodies and proximal dendrites. All contacts appeared to form symmetric junctions, both the distribution and type of synaptic contacts of CCK fibers in the cerebral cortex of Psammodromus are very similar to the corresponding features in the hippocampus of mammals, although in this lizard the CCK cortical innervation, unlike that in mammals, is probably of extrinsic origin. Double HRP-retrograde labeling and CCK immunohistochemistry show that part of the CCK in the cerebral cortex of Psammodromus arises from the hypothalamic supramammillary nuclei.

Calcium-binding proteins in the dorsal ventricular ridge of the lizard Psammodromus algirus

The aim of the present work was to study further the intrinsic organization of the dorsal ventricular ridge of lizards. For that purpose, the morphology and distribution of cells and fibers containing the calcium-binding proteins calbindin-D28k, parvalbumin, and calretinin were investigated by using immunohistochemical methods. Colocalization of calcium-binding proteins with the neurotransmitter gamma-aminobutyric acid (GABA) was also studied because they are shown to coexist in many areas of the telencephalon where they define distinct subpopulations of GABAergic local circuit neurons. Neurons containing calcium-binding proteins are limited to the anterior part of the dorsal ventricular ridge (ADVR), whereas the posterior or caudal portion of the ridge is devoid of immunoreactive cells. This result gives further evidence for defining both regions of the dorsal ventricular ridge. Calcium-binding proteins mark three distinct populations of neurons within the ADVR. Two of them, parvalbumin- and calretinin-expressing cells, are GABAergic. On the other hand, calbindin-containing neurons do not express GABA, and the possibility is discussed that these cells are projection neurons. The distribution and overall density of fibers immunoreactive to calcium-binding proteins suggests that most fibers are of extrinsic origin, the thalamic nuclei projecting to the ADVR and the lateral amygdala being good candidates for their origin. The comparison of data on the populations of calcium-binding protein-containing neurons in the reptilian ADVR with those of mammals illustrate the difficulty in finding a mammalian homologue for this controversial region of the reptilian telencephalon.

Calbindin-D28k in cortical regions of the lizard Psammodromus algirus

The morphology, distribution, and ultrastructural features of calbindin-D28k-immunoreactive neurons and fibers in the cortical regions of the lizard Psammodromus algirus, considered homologues to the mammalian hippocampal formation, were analyzed by using the peroxidase anti-peroxidase technique at the light and electron microscopic level. On the basis of staining properties and localization, two distinct populations of calbindin-D28k-immunoreactive neurons were observed in both the medial and dorsal cortices. Those located in the cell layer, namely principal neurons, were weakly immunostained, whereas a number of Golgi-like stained neurons were observed in plexiform layers. Double immunocytochemistry showed that all calbindin immunoreactive neurons in the deep plexiform layers were also gamma-aminobutyric acid immunoreactive. We consider them as a population of nonprincipal neurons different from those containing the calcium-binding proteins parvalbumin and calretinin. Two types of immunoreactive Boutons were revealed by electron microscopy on the basis of the synaptic specialization: Boutons making asymmetrical synapses were generally smaller in size and contacted on small dendritic profiles or cell bodies, whereas larger boutons established symmetrical synapses mainly on dendritic shafts. We propose that the first type of boutons arises from principal neurons and that the second type arises from nonprincipal ones. Finally, the staining pattern, localization, and the circuit in which nonprincipal calbindin-immunoreactive neurons and other neurochemically defined neurons could be involved in cortical regions of Psammodromus are compared with those of mammalian hippocampus.

Pathogenicity of Vibrio alginolyticus for cultured gilt-head sea bream (Sparus aurata L.)

The in vivo and in vitro pathogenic activities of whole cells and extracellular products of Vibrio alginolyticus for cultured gilt-head sea bream were evaluated. The 50% lethal doses ranged from 5.4 x 10(4) to 1.0 x 10(6) CFU/g of body weight. The strains examined had the ability to adhere to skin, gill, and intestinal mucus of sea bream and to cultured cells of a chinook salmon embryo cell line. In addition, the in vitro ability of V. alginolyticus to adhere to mucus and skin cells of sea bream was demonstrated by scanning electron microscopy. The biological activities of extracellular products of V. alginolyticus were hydrolytic activities; the products were able to degrade sea bream mucus. V. alginolyticus was cytotoxic for fish cell lines and lethal for sea bream. Moreover, the extracellular products could degrade sea bream tissues. However, experiments performed with the bath immersion inoculation technique demonstrated that V. alginolyticus should be considered a pathogen for sea bream only when the mucus layer is removed and the skin is damaged.

[Bronchial mucoepidermoid carcinoma]

We submit the case of a child afflicted with a mucoepidermoid bronchial tumor. The patient is a boy, aged seven, who after undergoing antibiotic treatment for six weeks because of a fever and atelectasia-condensation in the right lower lobe showed no signs of clinical improvement and was sent to our department to undergo further study and treatment. A bronchoscopy performed shows a polypoid mass that partially blocks the main bronchial tube a few milimiters under the access to the right upper lobe. A biopsy is carried out and the anatomopathological test shows there is a low degree epidermoid carcinoma. We decide to perform a lobectomy which for the tumor location and the lung condition has to be medium and lower right. We proceed to remove the adenopaty of hilium not affected by the tumor. The postoperative period develops without incidents. A check-up bronchoscopy performed three months later shows two polypoid masses in the right bronchial tube which, once a biopsy is performed, proved to be granulation tissue. Twelve months after undergoing surgery, the patient's condition is good, there is no evidence of tumor relapse and the breathing capacity is adequate, though there is an obstructive restrictive pattern in the espirometry. Even taking into consideration that lung tumors are extremely unusual, the epidermoid carcinoma is the one which most frequently occurs. The tumor's low malignancy is a sign that points to a good prognosis. Performing conservative surgery by means of bronchoplasty should be taken into account so as to keep the sequelae on the lung condition to a minimum, even though in this case the tumor location made it impossible.

Calretinin immunoreactivity in the cerebral cortex of the lizard Psammodromus algirus: a light and electron microscopic study

The present study describes the distribution and structural features of calretinin-immunoreactive neurons and fiber plexuses in the cerebral cortex of a lacertid lizard, at the light and electron microscopic levels, and also examines the colocalization of calretinin with parvalbumin and gamma-aminobutyric acid (GABA) in certain cortical regions. Calretinin-immunoreactive neurons are present throughout the cerebral cortex of Psammodromus and can be classified according to morphological and neurochemical criteria. Neurons in the medial cortex are small, spine-free and lack parvalbumin, whereas in the lateral cortex, calretinin-immunoreactive neurons display sparsely spiny dendrites and also lack parvalbumin. The dorsomedial and dorsal cortices contain most of the calretinin cortical neurons, which were located almost exclusively in the deep plexiform layer. These neurons are large, with an extensive spine-free dendritic tree. Most of the calretinin-immunoreactive neurons of dorsomedial and dorsal cortices are GABAergic and contain parvalbumin. Calretinin-immunoreactive fibers form two main afferent systems in the cortical areas. One probably intrinsic inhibitory system, arising from the calretinin and parvalbumin GABAergic neurons in the dorsomedial and dorsal cortices, makes symmetrical synapses on the soma and proximal dendrites of neurons located in the cell layers of the same cortical areas. The other system is formed by extremely thin axons running within the superficial plexiform layers of the medial, dorsomedial and dorsal cortices. These axons make asymmetrical synapses on dendrites or dendritic spines. We suggest that this system, probably extrinsic excitatory, arises from neurons located in the basal forebrain.

Intrinsic connections in the anterior dorsal ventricular ridge of the lizard Psammodromus algirus

We have studied the intrinsic connections of the anterior dorsal ventricular ridge (ADVR) in the lacertid lizard Psammodromus algirus by means of retrograde transport of horseradish peroxidase (HRP) and fluorescent labeling with the lipophilic carbocyanine dye DiI. We injected HRP into different regions in the ADVR arrayed in a medial-to-lateral sequence, with each consisting of three distinct superficial-to-deep zones. When HRP was injected into a given region, many labeled neurons (always located ipsilateral to the injection site) were found at all mediolateral regions of ADVR in locations rostrally distant from the injection site. DiI crystals were applied on different superficial-to-deep zones within each region. Two patterns could be recognized: DiI crystals applied on the periventricular (most superficial) zone resulted in a labeling of cells widely distributed throughout the ADVR independently of the mediolateral region of the application site, whereas DiI crystals applied on deeper zones resulted in a staining of cells mostly restricted to a narrow radial area. Results from both types of labeling confirm that the ADVR has a prominent radial component in its intrinsic organization, but they also demonstrate that some areas of the ADVR receive projections from distant, rostrally located neurons in every ipsilateral region of the ridge itself, which establishes a clear non-radial component. This organization may have important functional properties with regard to a putative integration of different sensory modalities conveyed by thalamic afferent fibers to the ADVR. Last, we analyzed some evolutionary implications of our results.

Multivariate statistical analysis of Golgi stained neurons

The multivariate statistical analysis provides a useful method to study neuronal populations. It allows both the objective classification of neuronal types and the study of the morphological variation within a neuronal population. We report a particular example of the use of these techniques on a Golgi study of a complex telencephalic structure, the reptilian anterior dorsal ventricular ridge (aDVR). We present a R-mode factor analysis and a cluster analysis on the results of the factor analysis. Sixteen original variables were chosen for the study in order to obtain the greatest information about the cell body, the dendritic field and the location of 96 Golgi-stained cells. Six factors were obtained after the R-mode factor analysis, the interpretation of which was clear in five of them. This contributed to explain the morphological variation of the neuronal types within the aDVR. The cluster analysis classified the 96 cells into eight groups. Some groups could be ascribed to specific regions of the aDVR.

NADPH diaphorase-positive neurons in the lizard hippocampus: a distinct subpopulation of GABAergic interneurons

We analyzed the distribution and light-microscopic features of the NADPH diaphorase-containing structures in the lizard hippocampus, likely to correspond to nitric oxide synthase-containing cells and fibers, and thus likely to release nitric oxide. We also studied co-localization of NADPH diaphorase with the neurotransmitter GABA, the calcium-binding protein parvalbumin, and the neuropeptide somatostatin, in order to examine whether putative nitric oxide-synthesizing neurons represent a different subpopulation of GABA cells, on which the authors recently reported in lizards. We also studied co-localization of NADPH diaphorase with parvalbumin or somatostatin in mice to ascertain whether the characteristics of this population in reptiles parallel the situation in mammals. Most of the positive NADPH diaphorase neurons were stained in a Golgi-like manner and were in the plexiform layers of the lizard hippocampus with morphologies ranging from bipolar to multipolar. Co-localization with GABA was 100%, and NADPH diaphorase-positive neurons in the lizard hippocampus did not contain parvalbumin or somatostatin. The results indicate that putative nitric oxide-synthesizing neurons represent a distinct subpopulation of GABA interneurons in the lizard hippocampus. Two different types of fibers were described in the plexiform layers: one type bearing thick varicosities, and the other thinner ones. We discuss the possibility that at least part of the positive fibers arise from a hypothalamic aminergic nucleus contacting the third ventricle, the periventricular hypothalamic organ. Most radial glia were stained almost completely and formed typical end-feet both at the pia and around capillaries. The results of this study confirm that the capacity for synthesizing nitric oxide is linked to a determined set of neuronal markers depending on the specific brain region, and they provide new resemblances between hippocampal regions in different classes of vertebrates.

Monoaminergic innervation patterns in the anterior dorsal ventricular ridge of a lacertid lizard, Psammodromus algirus

In contrast to the view of a diffuse monoaminergic innervation of the telencephalon, studies on the monoaminergic innervation in certain mammalian isocortical regions have shown a high degree of regional and laminar specificity. The present study was designed to examine the distribution patterns of dopamine, noradrenaline and serotonin in a telencephalic structure, the anterior dorsal ventricular ridge, of the sand lizard Psammodromus algirus (Lacertidae) using specific antibodies against each monoamine. The anterior dorsal ventricular ridge receives an abundant monoaminergic innervation compared to that of cortical telencephalic regions. The distribution of the different monoamines presented zonal and regional patterns throughout the ridge. The cell cluster zone was profusely innervated by catecholamines, whereas no serotoninergic fibers innervated the cell bodies in the cluster zone. On the other hand, the periventricular zone was heavily innervated by serotonin, but catecholaminergic fibers were almost lacking. With regard to regional patterns, dopamine exhibited major differences in the mediolateral axis of the anterior dorsal ventricular ridge: dopaminergic innervation was densest in the lateral region, which in other reptiles is described as a target of visual thalamic projections. Whereas the zonal pattern of the monoaminergic innervation of the anterior dorsal ventricular ridge seems to be a constant feature in the reptiles studied to date, the regional pattern varies among reptilian groups, especially taking into account the density of monoaminergic innervation.

Distribution of neuropeptide Y (NPY) in the cerebral cortex of the lizards Psammodromus algirus and podarcis hispanica: co-localization of NPY, somatostatin, and GABA

The aim of the present study was to analyze the distribution and characteristics of NPY immunoreactive structures in the cerebral cortex of lizards and to investigate the degree of co-existence of this neuropeptide with somatostatin and GABA. The immunoperoxidase method was applied to vibratome sections as well as to semithin sections. NPY neurons are multipolar or fusiform and were unevenly distributed throughout the brain cortex. Within the medial, dorsomedial and dorsal cortices, most NPY perikarya were located in the plexiform layers, especially in the deep one. This suggests that these cells could be regarded as interneurons. In the lateral cortex, NPY neurons were found throughout all layers. The dorsomedial cortex displayed the highest NPY cell density. Here, neuronal perikarya projected many immunoreactive processes toward two distinct zones: the deep plexiform layer of the medial cortex and the superpositio medialis. The NPY neurons of the dorsomedial cortex differed from the other NPY cortical immunoreactive cells in that the latter displayed very few immunoreactive processes. A high degree of co-existence among NPY, somatostatin, and GABA (approx. 80%) was found. This co-existence rate is very similar to that reported in mammals and suggests that co-localization is a phylogenetically ancient phenomenon.