Cell adhesion in embryo morphogenesis

Microfluidic characterization of single-cell biophysical properties and the applications in cancer diagnosis

Single-cell biophysical properties play a crucial role in regulating cellular physiological states and functions, demonstrating significant potential in the fields of life sciences and clinical diagnostics. Therefore, over the last few decades, researchers have developed various detection tools to explore the relationship between the biophysical changes of biological cells and human diseases. With the rapid advancement of modern microfabrication technology, microfluidic devices have quickly emerged as a promising platform for single-cell analysis offering advantages including high-throughput, exceptional precision, and ease of manipulation. Consequently, this paper provides an overview of the recent advances in microfluidic analysis and detection systems for single-cell biophysical properties and their applications in the field of cancer. The working principles and latest research progress of single-cell biophysical property detection are first analyzed, highlighting the significance of electrical and mechanical properties. The development of data acquisition and processing methods for real-time, high-throughput, and practical applications are then discussed. Furthermore, the differences in biophysical properties between tumor and normal cells are outlined, illustrating the potential for utilizing single-cell biophysical properties for tumor cell identification, classification, and drug response assessment. Lastly, we summarize the limitations of existing microfluidic analysis and detection systems in single-cell biophysical properties, while also pointing out the prospects and future directions of their applications in cancer diagnosis and treatment.

Morphological control enables nanometer-scale dissection of cell-cell signaling complexes

Protein micropatterning enables robust control of cell positioning on electron-microscopy substrates for cryogenic electron tomography (cryo-ET). However, the combination of regulated cell boundaries and the underlying electron-microscopy substrate (EM-grids) provides a poorly understood microenvironment for cell biology. Because substrate stiffness and morphology affect cellular behavior, we devised protocols to characterize the nanometer-scale details of the protein micropatterns on EM-grids by combining cryo-ET, atomic force microscopy, and scanning electron microscopy. Measuring force displacement characteristics of holey carbon EM-grids, we found that their effective spring constant is similar to physiological values expected from skin tissues. Despite their apparent smoothness at light-microscopy resolution, spatial boundaries of the protein micropatterns are irregular at nanometer scale. Our protein micropatterning workflow provides the means to steer both positioning and morphology of cell doublets to determine nanometer details of punctate adherens junctions. Our workflow serves as the foundation for studying the fundamental structural changes governing cell-cell signaling.

Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis

Developmental processes are intrinsically robust so as to preserve a normal-like state in response to genetic and environmental fluctuations. However, the robustness and potential phenotypic plasticity of individual developing cells under genetic perturbations remain to be systematically evaluated. Using large-scale gene perturbation, live imaging, lineage tracing, and single-cell phenomics, we quantified the phenotypic landscape of C. elegans embryogenesis in >2,000 embryos following individual knockdown of over 750 conserved genes. We observed that cellular genetic systems are not sufficiently robust to single-gene perturbations across all cells; rather, gene knockdowns frequently induced cellular defects. Dynamic phenotypic analyses revealed many cellular defects to be transient, with cells exhibiting phenotypic plasticity that serves to alleviate, correct, and accommodate the defects. Moreover, potential developmentally related cell modules may buffer the phenotypic effects of individual cell position changes. Our findings reveal non-negligible contributions of cellular plasticity and multicellularity as compensatory strategies to increase developmental robustness.

Expression profiles of circular RNA in human placental villus and decidua and prediction of drugs for recurrent spontaneous abortion

PROBLEM

We aimed to evaluate potential biomarkers and candidate drugs for recurrent spontaneous abortion (RSA) and explore functional circular RNA pathways involved in regulating RSA.

METHOD OF STUDY

Expression profiles of placental villus and decidua samples derived from females with RSA and those with healthy pregnancies who underwent induced abortion were analyzed using high-throughput RNA whole transcriptome sequencing. Abnormally expressed circular RNAs in a larger cohort of samples were validated using real-time quantitative polymerase chain reaction. Drug discovery and molecular docking were performed using online databases and the Autodock tool, respectively.

RESULTS

In total, 2103 and 2160 circular RNAs were detected in three pairs of villi and three pairs of decidual tissues, respectively. A total of 22 circular RNAs, 58 miRNAs, and 393 mRNAs with significantly different expression patterns were identified. Five circular RNAs were verified, and the expression of hsa_circ_0088485 was significantly upregulated in the RSA group (P = .041) with a high area under the curve value (.727), sensitivity (76.5%), and specificity (64.7%). GO and KEGG enrichment analyses indicated that differentially expressed genes were associated with angiogenesis and cell adhesion. Drug discovery and molecular docking were analyzed based on 93 differentially expressed mRNAs of the ceRNA network. A total of 36 chemicals were identified as putative bioactive molecules for RSA, and one representative chemical was identified for docking with six proteins.

CONCLUSIONS

These findings provide novel insights into the mechanism of regulation of RSA by circular RNA and its clinical diagnosis and treatment.

Adhesion as a trigger of droplet polarization in flowing emulsions

Tissues are subjected to large external forces and undergo global deformations during morphogenesis. We use synthetic analogues of tissues to study the impact of cell-cell adhesion on the response of cohesive cellular assemblies under such stresses. In particular, we use biomimetic emulsions in which the droplets are functionalized in order to exhibit specific droplet-droplet adhesion. We flow these emulsions in microfluidic constrictions and study their response to this forced deformation via confocal microscopy. We find that the distributions of avalanche sizes are conserved between repulsive and adhesive droplets. However, adhesion locally impairs the rupture of droplet-droplet contacts, which in turn pulls on the rearranging droplets. As a result, adhesive droplets are a lot more deformed along the axis of elongation in the constriction. This finding could shed light on the origin of polarization processes during morphogenesis.

Molecular signatures of in vitro produced embryos derived from ovum pick up or slaughterhouse oocytes in buffalo

This study was performed to investigate the difference in developmental competence of oocytes derived from ovum pick-up (OPU) and slaughterhouse ovaries (SLH), and its underlying mechanisms. The OPU and SLH oocytes were in-vitro maturated and fertilized to produce blastocysts, and these blastoycsts were collected to explore the expression of key genes for developmental potential and telomere (Oct-4, Sox2, Nanog, Cdx2, Gata3, E-cadherin, β-catenin, TERT, TERF1 and TERF2). The results showed that both the cleavage and blastocyst rates were significantly higher for the OPU group (68.31%, 39.48%, respectively) than SLH group (57.59%, 26.50%, respectively) (P < 0.01). The relative mRNA abundances of Sox2, Oct-4, Nanog and E-cadherin were significantly higher in the OPU blastocysts than the SLH ones (P < 0.01). Protein expression analysis by Western blot and immunofluorescence also revealed that the expression of E-cadherin and Sox2 was significantly higher in OPU blastocysts than SLH ones. However, there was no significant differences between the two groups in the expression of Cdx2, β-catenin, Gata3, TERT, TERF1, TERF2. These results imply oocyte sources modify the expression of development and adhesion related genes in blastocysts, which may elucidate a possible reasoning for the low development competence of buffalo SLH embryos.

Physical constraints on early blastomere packings

At very early embryonic stages, when embryos are composed of just a few cells, establishing the correct packing arrangements (contacts) between cells is essential for the proper development of the organism. As early as the 4-cell stage, the observed cellular packings in different species are distinct and, in many cases, differ from the equilibrium packings expected for simple adherent and deformable particles. It is unclear what are the specific roles that different physical parameters, such as the forces between blastomeres, their division times, orientation of cell division and embryonic confinement, play in the control of these packing configurations. Here we simulate the non-equilibrium dynamics of cells in early embryos and systematically study how these different parameters affect embryonic packings at the 4-cell stage. In the absence of embryo confinement, we find that cellular packings are not robust, with multiple packing configurations simultaneously possible and very sensitive to parameter changes. Our results indicate that the geometry of the embryo confinement determines the packing configurations at the 4-cell stage, removing degeneracy in the possible packing configurations and overriding division rules in most cases. Overall, these results indicate that physical confinement of the embryo is essential to robustly specify proper cellular arrangements at very early developmental stages.

At the initial stages of embryogenesis, the precise arrangement of cells in the embryo is critical to ensure that each cell gets the right chemical and physical signals to guide the formation of the organism. Even when the embryo is made of only four cells, different species feature varying cellular arrangements: cells in mouse embryos arrange as a tetrahedron, in the nematode worm C. elegans cells make a diamond and in sea urchins cells arrange in a square configuration. How do cells in embryos of different species control their arrangements? Using computer simulations, we studied how cell divisions, physical contacts between cells and the confinement of the embryo by an eggshell affect the arrangements of cells when the embryos have only 4 cells. We find that the shape of the confining eggshell plays a key role in controlling the cell arrangements, removing unwanted arrangements and robustly specifying the proper contacts between cells. Our results highlight the important roles of embryonic confinement in establishing the proper cell-cell contacts as the embryo starts to develop.

Adhesion molecules in gamete transport, fertilization, early embryonic development, and implantation-role in establishing a pregnancy in cattle: A review

Cell-cell adhesion molecules have critically important roles in the early events of reproduction including gamete transport, sperm-oocyte interaction, embryonic development, and implantation. Major adhesion molecules involved in reproduction include cadherins, integrins, and disintegrin and metalloprotease domain-containing (ADAM) proteins. ADAMs on the surface of sperm adhere to integrins on the oocyte in the initial stages of sperm-oocyte interaction and fusion. Cadherins act in early embryos to organize the inner cell mass and trophectoderm. The trophoblast and uterine endometrial epithelium variously express cadherins, integrins, trophinin, and selectin, which achieve apposition and attachment between the elongating conceptus and uterine epithelium before implantation. An overview of the major cell-cell adhesion molecules is presented and this is followed by examples of how adhesion molecules help shape early reproductive events. The argument is made that a deeper understanding of adhesion molecules and reproduction will inform new strategies that improve embryo survival and increase the efficiency of natural mating and assisted breeding in cattle.

Contraction dynamics of dental pulp cell rod microtissues

OBJECTIVES

The factors that contribute to the morphological changes of dental pulp cell-derived microtissues are unknown. Here, we investigated the contraction dynamics of rod-shaped microtissues derived from dental pulp cells and examined the underlying cell signaling pathways.

METHODS

Human dental pulp cells were seeded into agarose molds to assemble into rod-shaped microtissues. Resazurin- and tetrazolium-based cytotoxicity assays, Live/Dead staining, and hematoxylin and eosin staining for histological evaluation of rods were performed. Rod contraction was evaluated and measured for a period of 10 days. The role of TGF-β, phosphoinositide 3-kinase (PI3K)/AKT, and mitogen-activated protein kinase (MAPK) signaling pathway was analyzed.

RESULTS

Dental pulp cells readily assembled into rods, maintaining the geometric shape for 48 h. Following this period, they condensed to form stable spheroidal structures that remained vital for 10 days from seeding. Inhibition of phosphoinositide 3-kinase signaling pathway by LY294002 significantly prolonged the diminution in the length of rods formed by dental pulp cells. TGF-β and pharmacological inhibition of TGF-β signaling did not show pronounced effects.

CONCLUSION

Overall, dental pulp cells readily formed rod-shaped patterns of microtissues which, over a period of time, condensed into more stable spheroidal structures. Hence, technologies like bioprinting, using direct fabrication of microtissues need to consider the contraction dynamics.

CLINICAL RELEVANCE

The field of regenerative endodontology will benefit from our findings as it can be applied as a novel platform to test the impact of pharmacological agents, biomaterials, and regenerative approaches including bioprinting.

Density fields for branching, stiff networks in rigid confining regions

We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin filaments with branching due to the Arp2/3 complex. We develop a grand ensemble formalism that enables the computation of segment density and polarisation profiles within the confines of the cell. This is expressed in terms of the solution to nonlinear integral equations for auxiliary functions. We find three specific classes of behaviour depending on filament length, degree of branching and the ratio of persistence length to the dimensions of the geometry. Our method allows a numerical approach for semi-flexible filaments that are networked.

Contraction Dynamics of Rod Microtissues of Gingiva-Derived and Periodontal Ligament-Derived Cells

Tissue engineering strategies using microtissues as "building blocks" have high potential in regenerative medicine. Cognition of contraction dynamics involved in the in vitro self-assembly of these microtissues can be conceived as the bedrock of an effective periodontal tissue regenerative therapy. Our study was directed at evaluating the shrinkage in the rod-shaped structure of a directed self-assembly of human gingiva-derived cells (GC) and periodontal ligament-derived cells (PDLC) and developing insights into the potential mechanisms responsible for the shrinkage. GC and PDLC were seeded in non-adherent agarose molds to form rod microtissues. Cells used for the experiments were characterized using fluorescence-activated cell sorting (FACS). To assess the viability, resazurin-based cytotoxicity assays, trypan blue dye exclusion assay, MTT and live/dead staining, and histological evaluation of rods based on hematoxylin and eosin staining were performed. Rod contraction was evaluated and measured at 0, 2, 6, and 24 h and compared to L-929 cells. The role of transforming growth factor (TGF)-β signaling, phosphoinositide 3-kinase (PI3K)/AKT, and mitogen activated protein kinase (MAPK) signaling was analyzed. Our results show that the rod microtissues were vital after 24 h. A reduction in the length of rods was seen in the 24 h period. While the recombinant TGF-β slightly reduced contraction, inhibition of TGF-β signaling did not interfere with the contraction of the rods. Interestingly, inhibition of phosphoinositide 3-kinase by LY294002 significantly delayed contraction in GC and PDLC rods. Overall, GC and PDLC have the ability to form rod microtissues which contract over time. Thus, approaches for application of these structures as "building blocks" for periodontal tissue regeneration should consider that rods have the capacity to contract substantially. Further investigation will be needed to unravel the mechanisms behind the dynamics of contraction.

Quantitative Dynamics of Proteome, Acetylome, and Succinylome during Stem-Cell Differentiation into Hepatocyte-like Cells

Stem-cell differentiation is a complex biological process controlled by a series of functional protein clusters and signaling transductions, especially metabolism-related pathways. Although previous studies have quantified the proteome and phosphoproteome for stem-cell differentiation, the investigation of acylation-mediated regulation is still absent. In this study, we quantitatively profiled the proteome, acetylome, and succinylome in pluripotent human embryonic stem cells (hESCs) and differentiated hepatocyte-like cells (HLCs). In total, 3843 proteins, 185 acetylation sites in 103 proteins, and 602 succinylation sites in 391 proteins were quantified. The quantitative proteome showed that in differentiated HLCs the TGF-β, JAK-STAT, and RAS signaling pathways were activated, whereas ECM-related processes such as sulfates and leucine degradation were depressed. Interestingly, it was observed that the acetylation and succinylation were more intensive in hESCs, whereas protein processing in endoplasmic reticulum and the carbon metabolic pathways were especially highly succinylated. Because the metabolism patterns in pluripotent hESCs and the differentiated HLCs were different, we proposed that the dynamic acylations, especially succinylation, might regulate the Warburg-like effect and TCA cycle during differentiation. Taken together, we systematically profiled the protein and acylation levels of regulation in pluripotent hESCs and differentiated HLCs, and the results indicated the important roles of acylation in pluripotency maintenance and differentiation.

An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate

Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo.

The mechanical properties of individual cell spheroids

The overall physical properties of tissues emerge in a complex manner from the properties of the component cells and other constituent materials from which the tissue is formed, across multiple length scales ranging from nanometres to millimetres. Recent studies have suggested that interfacial tension between cells contributes significantly to the mechanical properties of tissues and that the overall surface tension is determined by the ratio of adhesion tension to cortical tension. Using cavitation rheology (CR), we have measured the interfacial properties and the elastic modulus of spheroids formed from HEK cells. By comparing the work of bubble formation with deformation of the cell spheroid at different length scales, we have estimated the cortical tension for HEK cells. This innovative approach to understanding the fundamental physical properties associated with tissue mechanics may guide new approaches for the generation of materials to replace or regenerate damaged or diseased tissues.

Optogenetic inhibition of apical constriction during Drosophila embryonic development

Morphogenesis of multicellular organisms is driven by changes in cell behavior, which happen at precise locations and defined developmental stages. Therefore, the studying of morphogenetic events would greatly benefit from tools that allow the perturbation of cell activity with spatial and temporal precision. We recently developed an optogenetic approach to modulate cell contractility with cellular precision and on fast (seconds) timescales during Drosophila embryogenesis. We present here a protocol to handle genetically engineered photosensitive Drosophila embryos and achieve light-mediated inhibition of apical constriction during tissue invagination. The possibility to modulate the levels of optogenetic activation at different laser powers makes this method suited also for studying how mechanical stresses are sensed and interpreted in vivo. Given the conserved function of cell contractility during animal development, the application of this method to other morphogenetic processes will facilitate our understanding of tissue mechanics and cell-cell interaction during morphogenesis.

Optogenetic Control of Protein Function: From Intracellular Processes to Tissue Morphogenesis

Optogenetics is an emerging and powerful technique that allows the control of protein activity with light. The possibility of inhibiting or stimulating protein activity with the spatial and temporal precision of a pulse of laser light is opening new frontiers for the investigation of developmental pathways and cell biological bases underlying organismal development. With this powerful technique in hand, it will be possible to address old and novel questions about how cells, tissues, and organisms form. In this review, we focus on the applications of existing optogenetic tools for addressing issues in animal morphogenesis.

Optogenetics allows the manipulation of gene expression and cell behaviors in individual cells or group of cells in the context of intact organisms.

Precise spatiotemporal and quantitative perturbation of signaling systems using optogenetics provides a powerful new approach to study morphogenesis of multicellular systems.

The possibility to combine optogenetics with genetically encoded biosensors (e.g., tension sensors) or chemical probes enables the perturbation and monitoring of biochemical reactions of interest in vivo.

By allowing the control of key behaviors, such as cell motility, polarity, and proliferation, optogenetics will be instrumental for characterizing the mechanisms underlying organ regeneration and cancer growth/invasion in living organisms.

Increasing throughput of AFM-based single cell adhesion measurements through multisubstrate surfaces

Mammalian cells regulate adhesion by expressing and regulating a diverse array of cell adhesion molecules on their cell surfaces. Since different cell types express distinct sets of cell adhesion molecules, substrate-specific adhesion is cell type- and condition-dependent. Single-cell force spectroscopy is used to quantify the contribution of cell adhesion molecules to adhesion of cells to specific substrates at both the cell and single molecule level. However, the low throughput of single-cell adhesion experiments greatly limits the number of substrates that can be examined. In order to overcome this limitation, segmented polydimethylsiloxane (PDMS) masks were developed, allowing the measurement of cell adhesion to multiple substrates. To verify the utility of the masks, the adhesion of four different cell lines, HeLa (Kyoto), prostate cancer (PC), mouse kidney fibroblast and MDCK, to three extracellular matrix proteins, fibronectin, collagen I and laminin 332, was examined. The adhesion of each cell line to different matrix proteins was found to be distinct; no two cell lines adhered equally to each of the proteins. The PDMS masks improved the throughput limitation of single-cell force spectroscopy and allowed for experiments that previously were not feasible. Since the masks are economical and versatile, they can aid in the improvement of various assays.

Essential role of the zinc finger transcription factor Casz1 for mammalian cardiac morphogenesis and development

Chromosome 1p36 deletion syndrome is one of the most common terminal deletions observed in humans and is related to congenital heart disease (CHD). However, the 1p36 genes that contribute to heart disease have not been clearly delineated. Human CASZ1 gene localizes to 1p36 and encodes a zinc finger transcription factor. Casz1 is required for Xenopus heart ventral midline progenitor cell differentiation. Whether Casz1 plays a role during mammalian heart development is unknown. Our aim is to determine 1p36 gene CASZ1 function at regulating heart development in mammals. We generated a Casz1 knock-out mouse using Casz1-trapped embryonic stem cells. Casz1 deletion in mice resulted in abnormal heart development including hypoplasia of myocardium, ventricular septal defect, and disorganized morphology. Hypoplasia of myocardium was caused by decreased cardiomyocyte proliferation. Comparative genome-wide RNA transcriptome analysis of Casz1 depleted embryonic hearts identifies abnormal expression of genes that are critical for muscular system development and function, such as muscle contraction genes TNNI2, TNNT1, and CKM; contractile fiber gene ACTA1; and cardiac arrhythmia associated ion channel coding genes ABCC9 and CACNA1D. The transcriptional regulation of some of these genes by Casz1 was also found in cellular models. Our results showed that loss of Casz1 during mouse development led to heart defect including cardiac noncompaction and ventricular septal defect, which phenocopies 1p36 deletion syndrome related CHD. This suggests that CASZ1 is a novel 1p36 CHD gene and that the abnormal expression of cardiac morphogenesis and contraction genes induced by loss of Casz1 contributes to the heart defect.

Assay for characterizing the recovery of vertebrate cells for adhesion measurements by single-cell force spectroscopy

Single-cell force spectroscopy (SCFS) is becoming a widely used method to quantify the adhesion of a living cell to a substrate, another cell or tissue. The high sensitivity of SCFS permits determining the contributions of individual cell adhesion molecules (CAMs) to the adhesion force of an entire cell. However, to prepare adherent cells for SCFS, they must first be detached from tissue-culture flasks or plates. EDTA and trypsin are often applied for this purpose. Because cellular properties can be affected by this treatment, cells need to recover before being further characterized by SCFS. Here we introduce atomic force microscopy (AFM)-based SCFS to measure the mechanical and adhesive properties of HeLa cells and mouse embryonic kidney fibroblasts while they are recovering after detachment from tissue-culture. We find that mechanical and adhesive properties of both cell lines recover quickly (<10 min) after detachment using EDTA, while trypsin-detached fibroblasts require >60 min to fully recover. Our assay introduced to characterize the recovery of mammalian cells after detachment can in future be used to estimate the recovery behavior of other adherent cell types.

Excess PLAC8 promotes an unconventional ERK2-dependent EMT in colon cancer

The epithelial-to-mesenchymal transition (EMT) transcriptional program is characterized by repression of E-cadherin (CDH1) and induction of N-cadherin (CDH2), and mesenchymal genes like vimentin (VIM). Placenta-specific 8 (PLAC8) has been implicated in colon cancer; however, how PLAC8 contributes to disease is unknown, and endogenous PLAC8 protein has not been studied. We analyzed zebrafish and human tissues and found that endogenous PLAC8 localizes to the apical domain of differentiated intestinal epithelium. Colon cancer cells with elevated PLAC8 levels exhibited EMT features, including increased expression of VIM and zinc finger E-box binding homeobox 1 (ZEB1), aberrant cell motility, and increased invasiveness. In contrast to classical EMT, PLAC8 overexpression reduced cell surface CDH1 and upregulated P-cadherin (CDH3) without affecting CDH2 expression. PLAC8-induced EMT was linked to increased phosphorylated ERK2 (p-ERK2), and ERK2 knockdown restored cell surface CDH1 and suppressed CDH3, VIM, and ZEB1 upregulation. In vitro, PLAC8 directly bound and inactivated the ERK2 phosphatase DUSP6, thereby increasing p-ERK2. In a murine xenograft model, knockdown of endogenous PLAC8 in colon cancer cells resulted in smaller tumors, reduced local invasion, and decreased p-ERK2. Using MultiOmyx, a multiplex immunofluorescence-based methodology, we observed coexpression of cytosolic PLAC8, CDH3, and VIM at the leading edge of a human colorectal tumor, supporting a role for PLAC8 in cancer invasion in vivo.

Global transcriptome profiles of Italian Mediterranean buffalo embryos with normal and retarded growth

The transcriptome profiles were compared for buffalo embryos with normal growth and embryos with retarded growth on Day 25 after mating. Embryos with retarded growth on Day 25 after mating have a reduced likelihood of undergoing attachment to the uterine endometrium and establishing a pregnancy. Italian Mediterranean buffaloes were mated by AI and on Day 25 underwent trans-rectal ultrasonography to ascertain embryo development. Embryos with an embryonic width (EW)>2.7 mm were classed as normal embryos and embryos with an EW<2.7 mm were classed as retarded embryos. Three buffaloes with embryos of the largest EW (3.7, 3.7 and 3.9 mm) and three buffaloes with embryos of the smallest EW (1.5, 1.6 and 1.9 mm) were slaughtered on Day 27 to recover embryos for transcriptome analysis using a bovine custom designed oligo array. A total of 1,047 transcripts were differentially expressed between embryos with normal growth and embryos with retarded growth. Retarded embryos showed 773/1,047 (74%) transcripts that were down-regulated and 274/1,047 (26%) transcripts that were up-regulated relative to normal embryos; in silico analyses focused on 680/1,047 (65%) of the differentially expressed transcripts. The most altered transcripts observed in retarded embryos were associated with membrane structure and function and with metabolic and homeostasis maintenance functions. Other notable functions altered in retarded embryos were developmental processes and in particular nervous system differentiation and function. Specific biochemical pathways such as the complement cascade and coagulation were also altered in retarded embryos. It was concluded from the findings that buffalo embryos with retarded growth on Day 25 after mating show altered gene expression compared with normal embryos, and some de-regulated functions are associated with attachment to the uterine endometrium.

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish

Background

Zebrafish embryos are transcriptionally silent until activation of the zygotic genome during the 10^th cell cycle. Onset of transcription is followed by cellular and morphological changes involving cell speciation and gastrulation. Previous genome-wide surveys of transcriptional changes only assessed gene expression levels; however, recent studies have shown the necessity to map isoform-specific transcriptional changes. Here, we perform isoform discovery and quantification on transcriptome sequences from before and after zebrafish zygotic genome activation (ZGA).

Results

We identify novel isoforms and isoform switches during ZGA for genes related to cell adhesion, pluripotency and DNA methylation. Isoform switching events include alternative splicing and changes in transcriptional start sites and in 3’ untranslated regions. New isoforms are identified even for well-characterized genes such as pou5f1, sall4 and dnmt1. Genes involved in cell-cell interactions such as f11r and magi1 display isoform switches with alterations of coding sequences. We also detect over 1000 transcripts that acquire a longer 3’ terminal exon when transcribed by the zygote compared to their maternal transcript counterparts. ChIP-sequencing data mapped onto skipped exon events reveal a correlation between histone H3K36 trimethylation peaks and skipped exons, suggesting epigenetic marks being part of alternative splicing regulation.

Conclusions

The novel isoforms and isoform switches reported here include regulators of transcriptional, cellular and morphological changes taking place around ZGA. Our data display an array of isoform-related functional changes and represent a valuable resource complementary to existing early embryo transcriptomes.

Boundary formation in the development of the vertebrate hindbrain

The formation of a sharp interface of adjacent subdivisions is important for establishing the precision of tissue organization, and at specific borders it serves to organize key signaling centers. We discuss studies of vertebrate hindbrain development that have given important insights into mechanisms that underlie the formation and maintenance of sharp borders. The hindbrain is subdivided into a series of segments with distinct anteroposterior identity that underlies the specification of distinct neuronal cell types. During early stages of segmentation, cell identity switching contributes to the refinement of borders and enables homogenous territories to be maintained despite intermingling of cells between segments. At later stages, there is a specific restriction to cell intermingling between segments that is mediated by Eph receptor and ephrin signaling. Eph-ephrin signaling can restrict cell intermingling and sharpen borders through multiple mechanisms, including the regulation of cell adhesion and contact inhibition of cell migration.

Computational multiscale modeling of embryo development

Recent advances in live imaging and genetics of mammalian development which integrate observations of biochemical activity, cell-cell signaling and mechanical interactions between cells pave the way for predictive mathematical multi-scale modeling. In early mammalian embryo development, two of the most critical events which lead to tissue patterning involve changes in gene expression as well as mechanical interactions between cells. We discuss the relevance of mathematical modeling of multi-cellular systems and in particular in simulating these patterns and describe some of the technical challenges one encounters. Many of these issues are not unique for the embryonic system but are shared by other multi-cellular modeling areas.