Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis

Abstract Human CD23 is a 45-kD type II membrane glycoprotein, which functions as a low-affinity receptor for IgE and as a ligand for the CD21 and CD11b/CD11c differentiation antigens. CD23 is released from the surface of cells as soluble fragments, and a 25-kD species of soluble CD23 (sCD23) appears to act as a multifunctional cytokine. In this report, sCD23 is shown to sustain the growth of low cell density cultures of a human pre-B–acute lymphocytic leukemia cell line, SMS-SB: no other cytokine tested was able to induce this effect. Flow cytometric analysis indicates that sCD23 acts to prevent apoptosis of SMS-SB cells. SMS-SB cells cultured at low cell density possess low levels of bcl-2 protein. Addition of sCD23 to cells at low cell density maintained bcl-2 expression at levels equivalent to those observed in SMS-SB cells cultured at higher cell densities. No CD23 mRNA was found in SMS-SB cells, ruling out an autocrine function for CD23 in this cell line model. Although SMS-SB cells do not express the known receptors for CD23, namely CD21, CD11b-CD18, or CD11c-CD18, the cells specifically bind CD23-containing liposomes, but not glycophorin-containing liposomes. Binding of CD23-containing liposomes is inhibited by anti-CD23 but not by anti-CD21 or anti-CD11b/c monoclonal antibodies. The data show that sCD23 prevents apoptosis of the SMS-SB cell line by acting through a novel receptor.

Download Full-text

Quorum Sensing Controls Biofilm Formation in Vibrio cholerae through Modulation of Cyclic Di-GMP Levels and Repression of vpsT

Journal of Bacteriology ◽

10.1128/jb.01756-07 ◽

2008 ◽

Vol 190 (7) ◽

pp. 2527-2536 ◽

Cited By ~ 266

Author(s):

Christopher M. Waters ◽

Wenyun Lu ◽

Joshua D. Rabinowitz ◽

Bonnie L. Bassler

Keyword(s):

Quorum Sensing ◽

Vibrio Cholerae ◽

Cell Density ◽

Biofilm Formation ◽

High Cell Density ◽

High Cell ◽

Chemical Signaling ◽

Signaling Systems ◽

Genes Encoding ◽

Low Cell Density

ABSTRACT Two chemical signaling systems, quorum sensing (QS) and 3′,5′-cyclic diguanylic acid (c-di-GMP), reciprocally control biofilm formation in Vibrio cholerae. QS is the process by which bacteria communicate via the secretion and detection of autoinducers, and in V. cholerae, QS represses biofilm formation. c-di-GMP is an intracellular second messenger that contains information regarding local environmental conditions, and in V. cholerae, c-di-GMP activates biofilm formation. Here we show that HapR, a major regulator of QS, represses biofilm formation in V. cholerae through two distinct mechanisms. HapR controls the transcription of 14 genes encoding a group of proteins that synthesize and degrade c-di-GMP. The net effect of this transcriptional program is a reduction in cellular c-di-GMP levels at high cell density and, consequently, a decrease in biofilm formation. Increasing the c-di-GMP concentration at high cell density to the level present in the low-cell-density QS state restores biofilm formation, showing that c-di-GMP is epistatic to QS in the control of biofilm formation in V. cholerae. In addition, HapR binds to and directly represses the expression of the biofilm transcriptional activator, vpsT. Together, our results suggest that V. cholerae integrates information about the vicinal bacterial community contained in extracellular QS autoinducers with the intracellular environmental information encoded in c-di-GMP to control biofilm formation.

Download Full-text

Targeted transcript quantification in single disseminated cancer cells after whole transcriptome amplification

PLoS ONE ◽

10.1371/journal.pone.0216442 ◽

2019 ◽

Vol 14 (8) ◽

pp. e0216442 ◽

Cited By ~ 2

Author(s):

Franziska C. Durst ◽

Ana Grujovic ◽

Iris Ganser ◽

Martin Hoffmann ◽

Peter Ugocsai ◽

...

Keyword(s):

Cancer Cells ◽

Transcript Quantification ◽

Whole Transcriptome Amplification ◽

Whole Transcriptome

Download Full-text

Evidence for cooperation between cells during sporulation of the yeast Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.8.12.5166 ◽

1988 ◽

Vol 8 (12) ◽

pp. 5166-5178 ◽

Cited By ~ 13

Author(s):

H Jakubowski ◽

E Goldman

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Density ◽

De Novo ◽

High Cell Density ◽

Degradation Products ◽

Yeast Cells ◽

High Cell ◽

Yeast Saccharomyces Cerevisiae ◽

Type Locus ◽

Low Cell Density

Diploid Saccharomyces cerevisiae cells heterozygous for the mating type locus (MATa/MAT alpha) undergo meiosis and sporulation when starved for nitrogen in the presence of a poor carbon source such as potassium acetate. Diploid yeast adenine auxotrophs sporulated well at high cell density (10(7) cells per ml) under these conditions but failed to differentiate at low cell density (10(5) cells per ml). The conditional sporulation-deficient phenotype of adenine auxotrophs could be complemented by wild-type yeast cells, by medium from cultures that sporulate at high cell density, or by exogenously added adenine (or hypoxanthine with some mutants). Adenine and hypoxanthine in addition to guanine, adenosine, and numerous nucleotides were secreted into the medium, each in its unique temporal pattern, by sporulating auxotrophic and prototrophic yeast strains. The major source of these compounds was degradation of RNA. The data indicated that differentiating yeast cells cooperate during sporulation in maintaining sufficiently high concentrations of extracellular purines which are absolutely required for sporulation of adenine auxotrophs. Yeast prototrophs, which also sporulated less efficiently at low cell density (10(3) cells per ml), reutilized secreted purines in preference to de novo-made purine nucleotides whose synthesis was in fact inhibited during sporulation at high cell density. Adenine enhanced sporulation of yeast prototrophs at low cell density. The behavior of adenine auxotrophs bearing additional mutations in purine salvage pathway genes (ade apt1, ade aah1 apt1, ade hpt1) supports a model in which secretion of degradation products, uptake, and reutilization of these products is a signal between cells synchronizing the sporulation process.

Download Full-text

Sox9 expression of alginate-encapsulated chondrocytes is stimulated by low cell density

Journal of Biomedical Materials Research Part A ◽

10.1002/jbm.a.32308 ◽

2009 ◽

Vol 91A (3) ◽

pp. 910-918 ◽

Cited By ~ 15

Author(s):

Peter Bernstein ◽

Meng Dong ◽

Sylvi Graupher ◽

Denis Corbeil ◽

Michael Gelinsky ◽

...

Keyword(s):

Cell Density ◽

Sox9 Expression ◽

Low Cell Density

Download Full-text

The impacts of replacing air bubbles with microspheres for the clarification of algae from low cell-density culture

Water Research ◽

10.1016/j.watres.2014.01.012 ◽

2014 ◽

Vol 53 ◽

pp. 168-179 ◽

Cited By ~ 22

Author(s):

Francesco Ometto ◽

Carlo Pozza ◽

Rachel Whitton ◽

Beatrice Smyth ◽

Andrea Gonzalez Torres ◽

...

Keyword(s):

Cell Density ◽

Air Bubbles ◽

Low Cell Density

Download Full-text

Application of feeder layer method for improved colony formation of grape cells and protoplasts at low cell density.

Agricultural and Biological Chemistry ◽

10.1271/bbb1961.49.3583 ◽

1985 ◽

Vol 49 (12) ◽

pp. 3583-3585 ◽

Cited By ~ 3

Author(s):

Takashi YAMAKAWA ◽

Kazuya ONOMICHI ◽

Tohru KODAMA ◽

Yasuji MINODA

Keyword(s):

Cell Density ◽

Colony Formation ◽

Feeder Layer ◽

Layer Method ◽

Low Cell Density

Download Full-text

Sociality in Escherichia coli: Enterochelin Is a Private Good at Low Cell Density and Can Be Shared at High Cell Density

Journal of Bacteriology ◽

10.1128/jb.02596-14 ◽

2015 ◽

Vol 197 (13) ◽

pp. 2122-2128 ◽

Cited By ~ 35

Author(s):

Rebecca L. Scholz ◽

E. Peter Greenberg

Keyword(s):

Escherichia Coli ◽

Cell Density ◽

Iron Acquisition ◽

Partial Privatization ◽

High Cell ◽

Wild Type ◽

Content Type ◽

Cell Densities ◽

The Cost ◽

Low Cell Density

ABSTRACTMany bacteria produce secreted iron chelators called siderophores, which can be shared among cells with specific siderophore uptake systems regardless of whether the cell produces siderophores. Sharing secreted products allows freeloading, where individuals use resources without bearing the cost of production. Here we show that theEscherichia colisiderophore enterochelin is not evenly shared between producers and nonproducers. Wild-typeEscherichia coligrows well in low-iron minimal medium, and an isogenic enterochelin synthesis mutant (ΔentF) grows very poorly. The enterochelin mutant grows well in low-iron medium supplemented with enterochelin. At high cell densities the ΔentFmutant can compete equally with the wild type in low-iron medium. At low cell densities the ΔentFmutant cannot compete. Furthermore, the growth rate of the wild type is unaffected by cell density. The wild type grows well in low-iron medium even at very low starting densities. Our experiments support a model where at least some enterochelin remains associated with the cells that produce it, and the cell-associated enterochelin enables iron acquisition even at very low cell density. Enterochelin that is not retained by producing cells at low density is lost to dilution. At high cell densities, cell-free enterochelin can accumulate and be shared by all cells in the group. Partial privatization is a solution to the problem of iron acquisition in low-iron, low-cell-density habitats. Cell-free enterochelin allows for iron scavenging at a distance at higher population densities. Our findings shed light on the conditions under which freeloaders might benefit from enterochelin uptake systems.IMPORTANCESociality in microbes has become a topic of great interest. One facet of sociality is the sharing of secreted products, such as the iron-scavenging siderophores. We present evidence that theEscherichia colisiderophore enterochelin is relatively inexpensive to produce and is partially privatized such that it can be efficiently shared only at high producer cell densities. At low cell densities, cell-free enterochelin is scarce and only enterochelin producers are able to grow in low-iron medium. Because freely shared products can be exploited by freeloaders, this partial privatization may help explain how enterochelin production is stabilized inE. coliand may provide insight into when enterochelin is available for freeloaders.

Download Full-text