Xenopus cDNA microarray identification of genes with endodermal organ expression

Mechanical Tensions Regulate Gene Expression in the Xenopus laevis Axial Tissues

During gastrulation and neurulation, the chordamesoderm and overlying neuroectoderm of vertebrate embryos converge under the control of a specific genetic programme to the dorsal midline, simultaneously extending along it. However, whether mechanical tensions resulting from these morphogenetic movements play a role in long-range feedback signaling that in turn regulates gene expression in the chordamesoderm and neuroectoderm is unclear. In the present work, by using a model of artificially stretched explants of Xenopus midgastrula embryos and full-transcriptome sequencing, we identified genes with altered expression in response to external mechanical stretching. Importantly, mechanically activated genes appeared to be expressed during normal development in the trunk, i.e., in the stretched region only. By contrast, genes inhibited by mechanical stretching were normally expressed in the anterior neuroectoderm, where mechanical stress is low. These results indicate that mechanical tensions may play the role of a long-range signaling factor that regulates patterning of the embryo, serving as a link coupling morphogenesis and cell differentiation.

Serum Fetuin A Levels: Are They a Reliable Marker for Hepatic Steatosis and Regional Adiposity in Renal Transplant Recipients?

BACKGROUND

Fetuin A is a protein expressed in the liver and it is an important inhibitor of ectopic calcification. High levels of fetuin A correlate with insulin resistance, hepatic steatosis, and regional adiposity in the general population. The association between hepatic steatosis and fetuin A level in renal transplant recipients (RTRs) remains unclear.

AIM

The aim of this study was to explore the relationships between fetuin A, hepatic steatosis, and regional adiposity in RTRs.

METHODS

Data from 44 patients with normal renal functions were included, all subjected to history taking for clinical data, assessment of central obesity and regional adiposity, assessment of hepatic steatosis using abdominal ultrasound (US), and measurements of serum fetuin A concentration using enzyme-linked immunosorbent assay (ELISA) kits.

RESULTS

Our study included 20 females (45.4%) and 24 males (54.6%) with mean age of 41.26 ± 11.2 years. Twenty-four subjects had hepatic steatosis. Fetuin A level in RTRs with hepatic steatosis with a mean of 1642.92 ± 358.91 is significantly higher (P < .001) than those without hepatic steatosis with a mean of 711.74 ± 57.85. Serum fetuin A level was positively correlated with regional adiposity (P = .021) and hepatic steatosis grade (P = .017). Fetuin A level increased with increased duration after renal transplantation (P < .001). The best cutoff value for detecting entrance into phase 3 or 4 steatosis is fetuin of 1862 with sensitivity of 88.9% and specificity of 87.7%.

CONCLUSIONS

Fetuin A is positively correlated with hepatic steatosis and regional adiposity in RTRs. Fetuin increases with increased duration after renal transplantation. Accordingly it may be used as a marker for hepatic steatosis and regional adiposity in these patients.

Differential requirement of bone morphogenetic protein receptors Ia (ALK3) and Ib (ALK6) in early embryonic patterning and neural crest development

Background

Bone morphogenetic proteins regulate multiple processes in embryonic development, including early dorso-ventral patterning and neural crest development. BMPs activate heteromeric receptor complexes consisting of type I and type II receptor-serine/threonine kinases. BMP receptors Ia and Ib, also known as ALK3 and ALK6 respectively, are the most common type I receptors that likely mediate most BMP signaling events. Since early expression patterns and functions in Xenopus laevis development have not been described, we have addressed these questions in the present study.

Results

Here we have analyzed the temporal and spatial expression patterns of ALK3 and ALK6; we have also carried out loss-of-function studies to define the function of these receptors in early Xenopus development. We detected both redundant and non-redundant roles of ALK3 and ALK6 in dorso-ventral patterning. From late gastrula stages onwards, their expression patterns diverged, which correlated with a specific, non-redundant requirement of ALK6 in post-gastrula neural crest cells. ALK6 was essential for induction of neural crest cell fate and further development of the neural crest and its derivatives.

Conclusions

ALK3 and ALK6 both contribute to the gene regulatory network that regulates dorso-ventral patterning; they play partially overlapping and partially non-redundant roles in this process. ALK3 and ALK6 are independently required for the spatially restricted activation of BMP signaling and msx2 upregulation at the neural plate border, whereas in post-gastrula development ALK6 exerts a highly specific, conserved function in neural crest development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12861-016-0101-5) contains supplementary material, which is available to authorized users.

Xenopus as a Model for GI/Pancreas Disease

Diseases affecting endodermal organs like the pancreas, lung and gastrointestinal (GI) tract have a substantial impact on human welfare. Since many of these are congenital defects that arise as a result of defects during development broad efforts are focused on understanding the development of these organs so as to better identify risk factors, disease mechanisms and therapeutic targets. Studies implementing model systems, like the amphibian Xenopus, have contributed immensely to our understanding of signaling (e.g. Wnt, FGF, BMP, RA) pathways and gene regulation (e.g. hhex, ptf1a, ngn3) that underlie normal development as well as disease progression. Recent advances in genome engineering further enhance the capabilities of the Xenopus model system for pursuing biomedical research, and will undoubtedly result in a boom of new information underlying disease mechanisms ultimately leading to advancements in diagnosis and therapy.

Understanding early organogenesis using a simplified in situ hybridization protocol in Xenopus

Organogenesis is the study of how organs are specified and then acquire their specific shape and functions during development. The Xenopuslaevis embryo is very useful for studying organogenesis because their large size makes them very suitable for identifying organs at the earliest steps in organogenesis. At this time, the primary method used for identifying a specific organ or primordium is whole mount in situ hybridization with labeled antisense RNA probes specific to a gene that is expressed in the organ of interest. In addition, it is relatively easy to manipulate genes or signaling pathways in Xenopus and in situ hybridization allows one to then assay for changes in the presence or morphology of a target organ. Whole mount in situ hybridization is a multi-day protocol with many steps involved. Here we provide a simplified protocol with reduced numbers of steps and reagents used that works well for routine assays. In situ hybridization robots have greatly facilitated the process and we detail how and when we utilize that technology in the process. Once an in situ hybridization is complete, capturing the best image of the result can be frustrating. We provide advice on how to optimize imaging of in situ hybridization results. Although the protocol describes assessing organogenesis in Xenopus laevis, the same basic protocol can almost certainly be adapted to Xenopus tropicalis and other model systems.

Role of fetuin-A in atherosclerosis associated with diabetic patients

Objectives

Fetuin-A is a circulating glycoprotein, formed in the liver. It regulates bone remodelling and calcium metabolism. Fetuin-A has adipogenic properties, so fat accumulation in the liver may be associated with higher levels of fetuin-A. Fetuin-A is an inhibitor of the phosphorylation of the insulin receptor tyrosine kinase.

Key findings

High concentrations of fetuin-A in humans causes insulin resistance. Insulin sensitivity is also found to be increased in fetuin-A knockout mice. Fetuin-A has been shown to cause insulin resistivity in type-2 diabetes mellitus and worsens the pro-atherogenic milieu.

Summary

Fetuin-A should be considered as a hepatic bio-marker. Vascular diseases like atherosclerosis are major causes of disability in patients with diabetes mellitus.

Expression of DNA transposable elements during nervous system development

Transposable elements (retrotransposons and DNA transposons) comprise a large proportion of animal genomes, for example 20% in D. melanogaster, 36% in X. tropicalis and 45% in humans. After invading a new genome, the transposable element increases its copy number and subsequently accumulates mutations. These may eventually result in inactive copies. Until recent days transposons have been considered “junk” DNA and no clear function have been assigned for this important amount of information on genomes.

Expression of transposable elements in neural tissues during Xenopus development

Transposable elements comprise a large proportion of animal genomes. Transposons can have detrimental effects on genome stability but also offer positive roles for genome evolution and gene expression regulation. Proper balance of the positive and deleterious effects of transposons is crucial for cell homeostasis and requires a mechanism that tightly regulates their expression. Herein we describe the expression of DNA transposons of the Tc1/mariner superfamily during Xenopus development. Sense and antisense transcripts containing complete Tc1-2_Xt were detected in Xenopus embryos. Both transcripts were found in zygotic stages and were mainly localized in Spemann's organizer and neural tissues. In addition, the Tc1-like elements Eagle, Froggy, Jumpy, Maya, Xeminos and TXr were also expressed in zygotic stages but not oocytes in X. tropicalis. Interestingly, although Tc1-2_Xt transcripts were not detected in Xenopus laevis embryos, transcripts from other two Tc1-like elements (TXr and TXz) presented a similar temporal and spatial pattern during X. laevis development. Deep sequencing analysis of Xenopus tropicalis gastrulae showed that PIWI-interacting RNAs (piRNAs) are specifically derived from several Tc1-like elements. The localized expression of Tc1-like elements in neural tissues suggests that they could play a role during the development of the Xenopus nervous system.

Identification of embryonic pancreatic genes using Xenopus DNA microarrays

The pancreas is both an exocrine and endocrine endodermal organ involved in digestion and glucose homeostasis. During embryogenesis, the anlagen of the pancreas arise from dorsal and ventral evaginations of the foregut that later fuse to form a single organ. To better understand the molecular genetics of early pancreas development, we sought to isolate markers that are uniquely expressed in this tissue. Microarray analysis was performed comparing dissected pancreatic buds, liver buds, and the stomach region of tadpole stage Xenopus embryos. A total of 912 genes were found to be differentially expressed between these organs during early stages of organogenesis. K-means clustering analysis predicted 120 of these genes to be specifically enriched in the pancreas. Of these, we report on the novel expression patterns of 24 genes. Our analyses implicate the involvement of previously unsuspected signaling pathways during early pancreas development. Developmental Dynamics 238:1455-1466, 2009. (c) 2009 Wiley-Liss, Inc.