Phospholipidome of Candida: each species of Candida has distinctive phospholipid molecular species

By employing electrospray ionization tandem mass spectrometry (ESI-MS/MS), the phospholipidomes of eight hemiascomycetous human pathogenic Candida species have been characterized. Over 200 phospholipid molecular species were identified and quantified. There were no large differences among Candida species in phosphoglyceride class composition; however, differences in phosphoglycerides components (i.e., fatty acyl chains) were identified. In contrast, differences in sphingolipid class composition as well as in molecular species were quite evident. The phospholipid compositions of C. albicans, C. glabrata, C. parapsilosis, C. kefyr, C. tropicalis, C. dubliniensis, C. krusei, and C. utilis could be further discriminated by principal component analysis. Notwithstanding that a single strain of each species was analyzed, our data do point to a typical molecular species imprint of Candida strains

CD47 Expression in Natural Killer Cells Regulates Homeostasis and Modulates Immune Response to Lymphocytic Choriomeningitis Virus

CD47 is a ubiquitous cell surface receptor that directly regulates T cell immunity by interacting with its inhibitory ligand thrombospondin-1 and limits clearance of cells by phagocytes that express its counter-receptor signal-regulatory protein-α. Murine natural killer (NK) cells express higher levels of CD47 than other lymphocytes, but the role of CD47 in regulating NK cell homeostasis and immune function remains unclear. Cd47−/− mice exhibited depletion of NK precursors in bone marrow, consistent with the antiphagocytic function of CD47. In contrast, antisense CD47 knockdown or gene disruption resulted in a dose dependent accumulation of immature and mature NK cells in spleen. Mature Cd47−/− NK cells exhibited increased expression of NK effector and interferon gene signatures and an increased proliferative response to interleukin-15 in vitro. Cd47−/− mice showed no defect in their early response to acute Armstrong lymphocytic choriomeningitis virus (LCMV) infection but were moderately impaired in controlling chronic Clone-13 LCMV infection, which was associated with depletion of splenic NK cells and loss of effector cytokine and interferon response gene expression in Cd47−/− NK cells. Broad CD47-dependent differences in NK activation, survival, and exhaustion pathways were observed in NK cell transcriptional signatures in LCMV infected mice. These data identify CD47 as a cell-intrinsic and systemic regulator of NK cell homeostasis and NK cell function in responding to a viral infection

sce_dlpfc_sgacc_final_DietSuerat_2023

Seurat object is being tested after subsetting 50,000 cells</p

Genome-Wide Analyses and Functional Classification of Proline Repeat-Rich Proteins: Potential Role of eIF5A in Eukaryotic Evolution

<div><p>The eukaryotic translation factor, eIF5A has been recently reported as a sequence-specific elongation factor that facilitates peptide bond formation at consecutive prolines in <i>Saccharomyces cerevisiae</i>, as its ortholog elongation factor P (EF-P) does in bacteria. We have searched the genome databases of 35 representative organisms from six kingdoms of life for PPP (Pro-Pro-Pro) and/or PPG (Pro-Pro-Gly)-encoding genes whose expression is expected to depend on eIF5A. We have made detailed analyses of proteome data of 5 selected species, <i>Escherichia coli</i>, <i>Saccharomyces cerevisiae</i>, <i>Drosophila melanogaster</i>, <i>Mus musculus</i> and <i>Homo sapiens</i>. The PPP and PPG motifs are low in the prokaryotic proteomes. However, their frequencies markedly increase with the biological complexity of eukaryotic organisms, and are higher in newly derived proteins than in those orthologous proteins commonly shared in all species. Ontology classifications of <i>S. cerevisiae</i> and human genes encoding the highest level of polyprolines reveal their strong association with several specific biological processes, including actin/cytoskeletal associated functions, RNA splicing/turnover, DNA binding/transcription and cell signaling. Previously reported phenotypic defects in actin polarity and mRNA decay of eIF5A mutant strains are consistent with the proposed role for eIF5A in the translation of the polyproline-containing proteins. Of all the amino acid tandem repeats (≥3 amino acids), only the proline repeat frequency correlates with functional complexity of the five organisms examined. Taken together, these findings suggest the importance of proline repeat-rich proteins and a potential role for eIF5A and its hypusine modification pathway in the course of eukaryotic evolution.</p></div

Number of consecutive proline repeats in the eight proteomes.

<p>Total proteome of each species was searched with XPnX (n = 3 to >10) where X is other than proline.</p><p>Number of consecutive proline repeats in the eight proteomes.</p

Number and frequency of tandem repeats of 20 individual amino acids in five proteomes and orthologous protein pools.

<p>(A) Amino acid repeats (≥3 amino acids) were estimated as triplet units. For repeats longer than 3 amino acids, the number of triplet units was assigned as the whole number from division of the consecutive amino acids with 3, as was done for PPP. (B) The frequency of each amino acid triplet unit was determined by division of the total number of triplet units with the total number of amino acids in each proteome listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111800#pone-0111800-t002" target="_blank">Table 2</a>. (C) The frequencies of tandem repeats of Glu, Pro and Leu in four orthologous protein pools used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111800#pone-0111800-g004" target="_blank">Fig. 4</a>.</p

Comparison of (A) average protein length, the frequency of (B) PPP and of (C) PPG in the total proteome and in orthologous protein pools.

<p>The orthologous protein pools were generated from each species: pool 1, those shared by all five species; pool 2, those shared by four eukaryotes; pool 3, those shared by the fly, mouse and human; pool 4, those shared by mouse and human and the values of ortholog pools were compared with those of the total proteins pool in each species. For each species, pool numbers are indicated, and T denotes total pool. The distribution of protein lengths is shown by box and whisker plots and the frequencies of PPP and PPG were determined as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111800#pone-0111800-g003" target="_blank">Fig. 3</a>.</p

Number and frequencies of PPP, PPG or proline in the five proteomes.

<p>Total number of PPP or PPG units in each proteome was calculated as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111800#s2" target="_blank">Materials and Methods</a>.</p><p>Number and frequencies of PPP, PPG or proline in the five proteomes.</p

Functional ontology diagrams of <i>S. cerevisiae</i> genes encoding ≥2 PPP units, or yeast orthologous genes and of human genes encoding PPP or PPG motifs at highest frequency (>0.01).

<p>(<b>A</b>) 76 <i>S. cerevisiae</i> genes encoding highest level of polyproline (listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111800#pone.0111800.s019" target="_blank">Table S18</a>) were classified based on the GO annotations available on SGD. (<b>B</b>) 257 <i>S. cerevisiae</i> orthologous genes (pool 1, genes common from <i>E. coli</i> to human, listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111800#pone.0111800.s020" target="_blank">Table S19</a>) were classified as in (A). (C) 148 human genes encoding PPP at high frequency (>0.01) listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111800#pone.0111800.s021" target="_blank">Table S20</a> and (<b>D</b>) 79 human genes encoding PPG at the frequency (>0.01) listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111800#pone.0111800.s022" target="_blank">Table S21</a> were functionally classified.</p

MHD mixed convection on an inclined stretching plate in Darcy porous medium with Soret effect and variable surface conditions

This work is concerned with a steady 2D laminar MHD mixed convective flow of an electrically conducting Newtonian fluid with low electrical conductivity along with heat and mass transfer on an isothermal stretching semi-infinite inclined plate embedded in a Darcy porous medium. Along with a strong uniform transverse external magnetic field, the Soret effect is considered. The temperature and concentration at the wall are varying with distance from the edge along the plate, but it is uniform at far away from the plate. The governing equations with necessary flow conditions are formulated under boundary layer approximations. Then a continuous group of symmetry transformations are employed to the governing equations and boundary conditions which determine a set of self-similar equations with necessary scaling laws. These equations are solved numerically and similar velocity, concentration, and temperature for various values of involved parameters are obtained and presented through graphs. The momentum boundary layer thickness becomes larger with increasing thermal and concentration buoyancy forces. The flow boundary layer thickness decreases with the angle of inclination of the stretching plate. The concentration increases considerably for larger values of the Soret number and it decreases with Lewis number. The skin friction coefficient increases for increasing angle of inclination of the plate, magnetic and porosity parameters, however it decreases for rise of thermal and solutal buoyancy parameters. In this double diffusive boundary layer flow, Nusselt and Sherweed numbers increase for rise of thermal and solutal buoyancy parameters, Prandtl number, but they behave opposite nature in case of angle of inclination of the plate, magnetic and porosity parameters. The Sherwood number increases for increasing Lewis number but it decreases for increasing Soret number