Systematic Analysis of Gene Expression Differences between Left and Right Atria in Different Mouse Strains and in Human Atrial Tissue

Background: Normal development of the atria requires left-right differentiation during embryonic development. Reduced expression of Pitx2c (paired-like homeodomain transcription factor 2, isoform c), a key regulator of left-right asymmetry, has recently been linked to atrial fibrillation. We therefore systematically studied the molecular composition of left and right atrial tissue in adult murine and human atria. Methods: We compared left and right atrial gene expression in healthy, adult mice of different strains and ages by employing whole genome array analyses on freshly frozen atrial tissue. Selected genes with enriched expression in either atrium were validated by RT-qPCR and Western blot in further animals and in shock-frozen left and right atrial appendages of patients undergoing open heart surgery. Results: We identified 77 genes with preferential expression in one atrium that were common in all strains and age groups analysed. Independent of strain and age, Pitx2c was the gene with the highest enrichment in left atrium, while Bmp10, a member of the TGFb family, showed highest enrichment in right atrium. These differences were validated by RT-qPCR in murine and human tissue. Western blot showed a 2-fold left-right concentration gradient in PITX2 protein in adult human atria. Several of the genes and gene groups enriched in left atria have a known biological role for maintenance of healthy physiology, specifically the prevention of atrial pathologies involved in atrial fibrillation, including membrane electrophysiology, metabolic cellular function, and regulation of inflammatory processes. Comparison of the array datasets with published array analyses in heterozygous Pitx2c+/2 atria suggested that approximately half of the genes with left-sided enrichment are regulated by Pitx2c. Conclusions: Our study reveals systematic differences between left and right atrial gene expression and supports the hypothesis that Pitx2c has a functional role in maintaining ‘‘leftness’’ in the atrium in adult murine and human hearts

Octamer binding proteins confer transcriptional activity in early mouse embryogenesis.

Oct4 and Oct5 are two mouse maternally expressed proteins binding to the octamer motif. Both are found in unfertilized oocytes and embryonic stem cells, whereas Oct4 is also found in primordial germ cells. In this study, the activity of the octamer motif was analysed in two embryonic stem cell lines containing Oct4 and Oct5, the teratocarcinoma-derived cell line F9 and the blastocyst-derived cell line D3. It is known that oligomerization of the octamer motif creates a powerful B-cell specific enhancer. As shown here, this oligomerized transcriptional element is also a very strong enhancer in F9 and D3 embryonic stem cells. After differentiation of the stem cells, both enhancer activity and the amount of the octamer binding proteins decrease. An intact octamer stimulates heterologous promoters in embryonic stem cells, whereas mutations in the octamer motif abolish transcriptional stimulation and binding of the octamer factors. The use of transgenic embryos demonstrates transcriptional activation in the inner cell mass but not in the trophoblast of blastocysts. The results indicate that Oct4 and Oct5 are active early in mouse development

A family of octamer-specific proteins present during mouse embryogenesis: Evidence for germline-specific expression of an Oct factor.

We have analysed various adult organs and different developmental stages of mouse embryos for the presence of octamer-binding proteins. A variety of new octamer-binding proteins were identified in addition to the previously described Oct1 and Oct2. Oct1 is ubiquitously present in murine tissues, in agreement with cell culture data. Although Oct2 has been described as a B-cell-specific protein, similar complexes were also found with extracts from brain, kidney, embryo and sperm. In embryo and brain at least two other proteins, Oct3 and Oct7, are present. A new microextraction procedure allowed the detection of two maternally expressed octamer-binding proteins, Oct4 and Oct5. Both proteins are present in unfertilized oocytes and embryonic stem cells, the latter containing an additional protein, Oct6. Whereas Oct4 was not found in sperm or testis, it is expressed in male and female primordial germ cells. Therefore Oct4 expression is specific for the female germline at later stages of germ cell development. Our results indicate that a family of octamer-binding proteins is present during mouse development and is differentially expressed during early embryogenesis. Protease clipping experiments of Oct4 and Oct1 suggest that both proteins contain similar DNA-binding domains

Effects of erythropoietin in murine-induced pluripotent cell-derived panneural progenitor cells

Induced cell fate changes by reprogramming of somatic cells offers an efficient strategy to generate autologous pluripotent stem (iPS) cells from any adult cell type. The potential of iPS cells to differentiate into various cell types is well established, however the efficiency to produce functional neurons from iPS cells remains modest. Here, we generated panneural progenitor cells (pNPCs) from mouse iPS cells and investigated the effect of the neurotrophic growth factor erythropoietin (EPO) on their survival, proliferation and neurodifferentiation. Under neural differentiation conditions, iPS-derived pNPCs gave rise to microtubule-associated protein-2 positive neuronlike cells (34% to 43%) and platelet-derived growth factor receptor positive oligodendrocytelike cells (21% to 25%) while less than 1% of the cells expressed the astrocytic marker glial fibrillary acidic protein. Neuronlike cells generated action potentials and developed active presynaptic terminals. The pNPCs expressed EPO receptor (EPOR) mRNA and displayed functional EPOR signaling. In proliferating cultures, EPO (0.1–3 U/mL) slightly improved pNPC survival but reduced cell proliferation and neurosphere formation in a concentration-dependent manner. In differentiating cultures EPO facilitated neurodifferentiation as assessed by the increased number of β-III-tubulin positive neurons. Our results show that EPO inhibits iPS pNPC self-renewal and promotes neurogenesis

A comparison of local phosphorescence detection and fluid dynamic gauging methods for studying the removal of cohesive fouling layers: Effect of layer roughness

The performance of industrial cleaning in place (CIP) procedures is critically important for food manufacture. CIP has yet to be optimised for many processes, in part since the mechanisms involved in cleaning are not fully understood. Laboratory tests have an important role in guiding industrial trials, and this paper introduces and compares two experimental techniques developed for studying CIP mechanisms: local phosphorescence detection (LPD), and scanning fluid dynamic gauging (sFDG). To illustrate the comparison, each technique is used to investigate the influence of soil topology on the cleaning of pre-gelatinised starch-based layers from 316 stainless steel substrates by aqueous NaOH solutions at ambient temperature. The roughness of the soil surface is varied by incorporating zinc sulphide particles with different particle size distributions (range 1 - 80 μm) into the starch suspensions. The soil roughness increased with the use of larger particles, increasing the 3D arithmetic mean roughness (Sa) of the dry layers (range 0.37 - 3.33 μm). Rough layers were cleaned more readily than those containing small inclusions, with a good correlation between the cleaning rates observed during LPD and FDG measurements. The LPD technique, which is an instrumented CIP test, gives a better indication of the cleaning time, while sFDG measurements provide further insight into the removal mechanisms.NOTICE: this is the author's version of a work that was accepted for publication in Food Bioproducts Processing. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Food Bioproducts Proc., 92, 46-53 DOI http://dx.doi.org/10.1016/j.fbp.2013.07.01

Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells

The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells (ESCs) and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2

Natural formation of chloro- and bromoacetone in salt lakes of Western Australia

Western Australia is a semi-/arid region known for saline lakes with a wide range of geochemical parameters (pH 2.5-7.1, Cl- 10-200 g L-1. This study reports on the haloacetones chloro- and bromoacetone in air over 6 salt lake shorelines. Significant emissions of chloroacetone (up to 0.2 µmol m-2 h-1) and bromoacetone (up to 1. 5 µmol m-2 h-1) were detected, and a photochemical box model was employed to evaluate the contribution of their atmospheric formation from the olefinic hydrocarbons propene and methacrolein in the gas phase. The measured concentrations could not explain the photochemical halogenation reaction, indicating a strong hitherto unknown source of haloacetones. Aqueous-phase reactions of haloacetones, investigated in the laboratory using humic acid in concentrated salt solutions, were identified as alternative formation pathway by liquid-phase reactions, acid catalyzed enolization of ketones, and subsequent halogenation. In order to verify this mechanism, we made measurements of the Henry's law constants, rate constants for hydrolysis and nucleophilic exchange with chloride, UV-spectra and quantum yields for the photolysis of bromoacetone and 1,1-dibromoacetone in the aqueous phase. We suggest that heterogeneous processes induced by humic substances in the quasi-liquid layer of the salt crust, particle surfaces and the lake water are the predominating pathways for the formation of the observed haloacetones

GAA Deficiency in Pompe Disease Is Alleviated by Exon Inclusion in iPSC-Derived Skeletal Muscle Cells

Pompe disease is a metabolic myopathy caused by deficiency of the acid α-glucosidase (GAA) enzyme and results in progressive wasting of skeletal muscle cells. The c.-32-13T>G (IVS1) GAA variant promotes exon 2 skipping during pre-mRNA splicing and is the most common variant for the childhood/adult disease form. We previously identified antisense oligonucleotides (AONs) that promoted GAA exon 2 inclusion in patient-derived fibroblasts. It was unknown how these AONs would affect GAA splicing in skeletal muscle cells. To test this, we expanded induced pluripotent stem cell (iPSC)-derived myogenic progenitors and differentiated these to multinucleated myotubes. AONs restored splicing in myotubes to a similar extent as in fibroblasts, suggesting that they act by modulating the action of shared splicing regulators. AONs targeted the putative polypyrimidine tract of a cryptic splice acceptor site that was part of a pseudo exon in GAA intron 1. Blocking of the cryptic splice donor of the pseudo exon with AONs likewise promoted GAA exon 2 inclusion. The simultaneous blocking of the cryptic acceptor and cryptic donor sites restored the majority of canonical splicing and alleviated GAA enzyme deficiency. These results highlight the relevance of cryptic splicing in human disease and its potential as therapeutic target for splicing modulation using AONs

Associations between preschool attendance and developmental impairments in pre-school children in a six-year retrospective survey

BACKGROUND: Many school-aged children suffer physical and mental impairments which can adversely affect their development and result in significant morbidity. A high proportion of children in western countries attend pre-school, and it is likely that the preschool environment influences the prevalence and severity of these impairments. Currently there is insufficient data available on the prevalence of these impairments and their causal associations. The influence that location of a pre-school and the duration of preschool attendance have on the prevalence of these impairments is not known. METHODS: In a retrospective survey spanning six years (1997–2002) we reviewed the records of 6,230 preschool children who had undergone routine school entry assessments. These children had been assessed utilising a modified manual of the "Bavarian Model" for school entry examinations. This model outlines specific criteria for impairments of motor, cognitive, behavioural and psychosocial functioning. Prevalence rates for physical and behavioural impairments were based on the results of these assessments. The relationship between the prevalence of impairments and the duration of preschool attendance and the location of the preschool attended was estimated utilizing logistic regression models. RESULTS: We found that 20.7% of children met the criteria for at least one type of impairment. Highest prevalence rates (11.5%) were seen for speech impairments and lowest (3.5%) for arithmetic impairments. Boys were disproportionately over represented, with 25.5% meeting the criteria for impairment, compared to 13.0% for girls. Children who had attended preschool for less than one year demonstrated higher rates of impairment (up to 19.1% for difficulties with memory, concentration or perseverance) compared to those who had attended for a longer duration (up to 11.6% for difficulties with pronouncation). Children attending preschool in an urban location had slightly elevated rates of impairment (up to 12.7%), compared to their rural counterparts (up to 11.1%). CONCLUSION: Our results demonstrate that there are high prevalence rates for physical and mental impairments among preschool children. Furthermore, children without preschool experience are a risk group for struggling with educational successes. The associations between the duration of preschool attendance and location of preschool attended and rates of impairment need replication and further exploration. Larger prospective studies are needed to examine if these relationships are causal and may therefore lend themselves to specific intervention strategies