Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo

Mammalian embryogenesis is a dynamic process involving gene expression and mechanical forces between proliferating cells. The exact nature of these interactions, which determine the lineage patterning of the trophectoderm and endoderm tissues occurring in a highly regulated manner at precise periods during the embryonic development, is an area of debate. We have developed a computational modeling framework for studying this process, by which the combined effects of mechanical and genetic interactions are analyzed within the context of proliferating cells. At a purely mechanical level, we demonstrate that the perpendicular alignment of the animal-vegetal (a-v) and embryonic-abembryonic (eb-ab) axes is a result of minimizing the total elastic conformational energy of the entire collection of cells, which are constrained by the zona pellucida. The coupling of gene expression with the mechanics of cell movement is important for formation of both the trophectoderm and the endoderm. In studying the formation of the trophectoderm, we contrast and compare quantitatively two hypotheses: (1) The position determines gene expression, and (2) the gene expression determines the position. Our model, which couples gene expression with mechanics, suggests that differential adhesion between different cell types is a critical determinant in the robust endoderm formation. In addition to differential adhesion, two different testable hypotheses emerge when considering endoderm formation: (1) A directional force acts on certain cells and moves them into forming the endoderm layer, which separates the blastocoel and the cells of the inner cell mass (ICM). In this case the blastocoel simply acts as a static boundary. (2) The blastocoel dynamically applies pressure upon the cells in contact with it, such that cell segregation in the presence of differential adhesion leads to the endoderm formation. To our knowledge, this is the first attempt to combine cell-based spatial mechanical simulations with genetic networks to explain mammalian embryogenesis. Such a framework provides the means to test hypotheses in a controlled in silico environment

Pancreatic Ductal Adenocarcinoma Associated with Autoimmune Pancreatitis

Autoimmune pancreatitis (AIP), in contrast to other benign chronic pancreatic diseases, can be cured with immunosuppressant drugs, thus the differentiation of AIP from pancreatic cancer is of particular interest in clinical practice. There is the possibility that some patients with AIP may develop pancreatic cancer, and this possibility contributes to increasing our difficulties in differentiating AIP from pancreatic cancer. We herein report the case of a 70-year-old man in whom pancreatic adenocarcinoma and AIP were detected simultaneously. We must carefully monitor AIP patients for the simultaneous presence of pancreatic cancer, even when a diagnosis of AIP is confirmed

Biochemical and structural studies of a L-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii

addresses: Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.types: Journal Article; Research Support, Non-U.S. Gov'tThis a post-print, author-produced version of an article accepted for publication in Extremophiles. Copyright © 2009 Springer Verlag. The definitive version is available at http://link.springer.com/article/10.1007%2Fs00792-008-0208-0Haloacid dehalogenases have potential applications in the pharmaceutical and fine chemical industry as well as in the remediation of contaminated land. The L: -2-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii has been cloned and over-expressed in Escherichia coli and successfully purified to homogeneity. Here we report the structure of the recombinant dehalogenase solved by molecular replacement in two different crystal forms. The enzyme is a homodimer with each monomer being composed of a core-domain of a beta-sheet bundle surrounded by alpha-helices and an alpha-helical sub-domain. This fold is similar to previously solved mesophilic L: -haloacid dehalogenase structures. The monoclinic crystal form contains a putative inhibitor L: -lactate in the active site. The enzyme displays haloacid dehalogenase activity towards carboxylic acids with the halide attached at the C2 position with the highest activity towards chloropropionic acid. The enzyme is thermostable with maximum activity at 60 degrees C and a half-life of over 1 h at 70 degrees C. The enzyme is relatively stable to solvents with 25% activity lost when incubated for 1 h in 20% v/v DMSO

IgG4-Related Diseases and the Liver

IgG4-related disease (IgG4-RD) is a systemic illness including autoimmune pancreatitis and IgG4-related sclerosing cholangitis (IgG4-SC). Although hepatic presentation of IgG4-RD has been reported, whether intrahepatic small bile ducts and hepatocytes are direct targets of IgG4-RD is uncertain. IgG4-RD is pathologically characterized by the numerous IgG4+ cells found in affected organs, but this IgG4 positivity is also frequently found in extrahepatic cholangiocarcinoma and is prominent, albeit rarely, in other hepatobiliary diseases including primary sclerosing cholangitis and autoimmune hepatitis. Moreover, cholangiocarcinoma arising from precedent IgG4-SC and IgG4-SC accompanying precursor lesions of cholangiocarcinoma (biliary intraepithelial neoplasia) are also reported. Diagnostic criteria for IgG-RD and IgG4-SC were recently proposed, but each individual case should be diagnosed clinicopathologically on the basis of its individual features. © Springer Japan 2016.[Book Chapter

IgG4-related kidney diseases and conditions: Renal pelvic and ureteral diseases

In the literature on IgG4-related urinary tract diseases, reports of cases with involvement of the renal pelvis and ureters are increasing. IgG4-related renal pelvic and ureteral lesions accompany extra-renal organ involvement, including IgG4-related type 1 autoimmune pancreatitis, sialadenitis, and orbital disease, and are characterized by the common pathological features of IgG4-related disease (IgG4-RD), including substantial numbers of IgG4-positive plasma cells, storiform fibrosis, and stenosis in the affected organs. Similar to other mucosal organs affected in IgG4-RD, these inflammatory findings are observed within the fibroadipose tissue in the renal hilum and around the ureters. The urothelial epithelium covering the renal pelvis and ureter is preserved. Nodular lesions such as pseudotumors can also form and it is important to differentiate these from malignant tumors. At present, comprehensive diagnostic criteria that include pathological parameters have been proposed for IgG4-RD; however, obtaining diagnostic findings in small biopsy specimens is often challenging. Therefore, the diagnosis can only be rendered following careful consideration of the patient’s clinical, serologic, radiologic, and pathologic features, including the possibility of involvement in other organs. © Springer Japan 2016.[Book Chapter