148 research outputs found
Transcriptome analyses of the Giardia lamblia life cycle
Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Molecular and Biochemical Parasitology 174 (2010): 62-65, doi:10.1016/j.molbiopara.2010.05.010.We quantified mRNA abundance from 10 stages in the Giardia lamblia life cycle in vitro using
Serial Analysis of Gene Expression (SAGE). 163 abundant transcripts were expressed
constitutively. 71 transcripts were upregulated specifically during excystation and 42 during
encystation. Nonetheless, the transcriptomes of cysts and trophozoites showed major
differences. SAGE detected co-expressed clusters of 284 transcripts differentially expressed in
cysts and excyzoites and 287 transcripts in vegetative trophozoites and encysting cells. All
clusters included known genes and pathways as well as proteins unique to Giardia or
diplomonads. SAGE analysis of the Giardia life cycle identified a number of kinases,
phosphatases, and DNA replication proteins involved in excystation and encystation, which
could be important for examining the roles of cell signaling in giardial differentiation. Overall,
these data pave the way for directed gene discovery and a better understanding of the biology
of Giardia lamblia.BJD, DSR, and FDG were supported by NIH grants AI42488, GM61896, DK35108, and
AI051687. DP and SGS were supported by grants from the Swedish Natural Science Research
Council, the Swedish Medical Research Council, and the Karolinska Institutet. AGM, SRB,
SPP, and MJC were supported by NIH grant AI51089 and by the Marine Biological Laboratory’s
Program in Global Infectious Diseases, funded by the Ellison Medical Foundation
An Improved High Order Finite Difference Method for Non-conforming Grid Interfaces for the Wave Equation
This paper presents an extension of a recently developed high order finite difference method for the wave equation on a grid with non-conforming interfaces. The stability proof of the existing methods relies on the interpolation operators being norm-contracting, which is satisfied by the second and fourth order operators, but not by the sixth order operator. We construct new penalty terms to impose interface conditions such that the stability proof does not require the norm-contracting condition. As a consequence, the sixth order accurate scheme is also provably stable. Numerical experiments demonstrate the improved stability and accuracy property
Protein phosphatase 2A plays a crucial role in Giardia lamblia differentiation
Author Posting. © The Authors, 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Molecular and Biochemical Parasitology 152 (2007): 80-89, doi:10.1016/j.molbiopara.2006.12.001.The ability of Giardia lamblia to undergo two distinct differentiations in
response to physiologic stimuli is central to its pathogenesis. The giardial
cytoskeleton changes drastically during encystation and excystation. However, the
signal transduction pathways mediating these transformations are poorly
understood. We tested the hypothesis that PP2A, a highly conserved
serine/threonine protein phosphatase, might be important in giardial differentiation.
We found that in vegetatively growing trophozoites, gPP2A-C protein localizes to
basal bodies/centrosomes, and to cytoskeletal structures unique to Giardia: the
ventral disk, and the dense rods of the anterior, posterior-lateral, and caudal
flagella. During encystation, gPP2A-C protein disappears from only the anterior
flagellar dense rods. During excystation, gPP2A-C localizes to the cyst wall in
excysting cysts but is not found in the wall of cysts with emerging excyzoites.
Transcriptome and immunoblot analyses indicated that gPP2A-C mRNA and
protein are upregulated in mature cysts and during the early stage of excystation
that models passage through the host stomach. Stable expression of gPP2A-C
antisense RNA did not affect vegetative growth, but strongly inhibited the
formation of encystation secretory vesicles (ESV) and water-resistant cysts.
Moreover, the few cysts that formed were highly defective in excystation.
Thus, gPP2A-C localizes to universal cytoskeletal structures and to
structures unique to Giardia. It is also important for encystation and excystation,
crucial giardial transformations that entail entry into and exit from dormancy.This work was funded
by NIH grants GM61896, AI51687, AI42488, and DK35108. Dr. A.G. McArthur was
supported by NIH grant AI51089 and the Marine Biological Laboratory’s Program
in Global Infectious Diseases, funded by the Ellison Medical Foundation
Circulating secretory IgA antibodies against cyclic citrullinated peptides in early rheumatoid arthritis associate with inflammatory activity and smoking
Mice Lacking Alkbh1 Display Sex-Ratio Distortion and Unilateral Eye Defects
Escherichia coli AlkB is a 2-oxoglutarate- and iron-dependent dioxygenase that reverses alkylated DNA damage by oxidative demethylation. Mouse AlkB homolog 1 (Alkbh1) is one of eight members of the newly discovered family of mammalian dioxygenases.In the present study we show non-Mendelian inheritance of the Alkbh1 targeted allele in mice. Both Alkbh1(-/-) and heterozygous Alkbh1(+/-) offspring are born at a greatly reduced frequency. Additionally, the sex-ratio is considerably skewed against female offspring, with one female born for every three to four males. Most mechanisms that cause segregation distortion, act in the male gametes and affect male fertility. The skewing of the sexes appears to be of paternal origin, and might be set in the pachythene stage of meiosis during spermatogenesis, in which Alkbh1 is upregulated more than 10-fold. In testes, apoptotic spermatids were revealed in 5-10% of the tubules in Alkbh1(-/-) adults. The deficiency of Alkbh1 also causes misexpression of Bmp2, 4 and 7 at E11.5 during embryonic development. This is consistent with the incompletely penetrant phenotypes observed, particularly recurrent unilateral eye defects and craniofacial malformations.Genetic and phenotypic assessment suggests that Alkbh1 mediates gene regulation in spermatogenesis, and that Alkbh1 is essential for normal sex-ratio distribution and embryonic development in mice
Female responses to experimental removal of sexual selection components in Drosophila melanogaster
Despite the common assumption that multiple mating should in general be favored in males, but not in females, to date there is no consensus on the general impact of multiple mating on female fitness. Notably, very little is known about the genetic and physiological features underlying the female response to sexual selection pressures. By combining an experimental evolution approach with genomic techniques, we investigated the effects of single and multiple matings on female fecundity and gene expression. We experimentally manipulated the opportunity for mating in replicate populations of Drosophila melanogaster by removing components of sexual selection, with the aim of testing differences in short term post-mating effects of females evolved under different mating strategies
The Crystal Structure of the Human Co-Chaperone P58IPK
P58IPK is one of the endoplasmic reticulum- (ER-) localised DnaJ (ERdj) proteins which interact with the chaperone BiP, the mammalian ER ortholog of Hsp70, and are thought to contribute to the specificity and regulation of its diverse functions. P58IPK, expression of which is upregulated in response to ER stress, has been suggested to act as a co-chaperone, binding un- or misfolded proteins and delivering them to BiP. In order to give further insights into the functions of P58IPK, and the regulation of BiP by ERdj proteins, we have determined the crystal structure of human P58IPK to 3.0 Ã… resolution using a combination of molecular replacement and single wavelength anomalous diffraction. The structure shows the human P58IPK monomer to have a very elongated overall shape. In addition to the conserved J domain, P58IPK contains nine N-terminal tetratricopeptide repeat motifs, divided into three subdomains of three motifs each. The J domain is attached to the C-terminal end via a flexible linker, and the structure shows the conserved Hsp70-binding histidine-proline-aspartate (HPD) motif to be situated on the very edge of the elongated protein, 100 Ã… from the putative binding site for unfolded protein substrates. The residues that comprise the surface surrounding the HPD motif are highly conserved in P58IPK from other organisms but more varied between the human ERdj proteins, supporting the view that their regulation of different BiP functions is facilitated by differences in BiP-binding
Construction of Modern Robust Nodal Discontinuous Galerkin Spectral Element Methods for the Compressible Navier-Stokes Equations
Discontinuous Galerkin (DG) methods have a long history in computational
physics and engineering to approximate solutions of partial differential
equations due to their high-order accuracy and geometric flexibility. However,
DG is not perfect and there remain some issues. Concerning robustness, DG has
undergone an extensive transformation over the past seven years into its modern
form that provides statements on solution boundedness for linear and nonlinear
problems.
This chapter takes a constructive approach to introduce a modern incarnation
of the DG spectral element method for the compressible Navier-Stokes equations
in a three-dimensional curvilinear context. The groundwork of the numerical
scheme comes from classic principles of spectral methods including polynomial
approximations and Gauss-type quadratures. We identify aliasing as one
underlying cause of the robustness issues for classical DG spectral methods.
Removing said aliasing errors requires a particular differentiation matrix and
careful discretization of the advective flux terms in the governing equations.Comment: 85 pages, 2 figures, book chapte
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