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Open Access Highly Accessed Research article

Physiological responses of Daphnia pulex to acid stress

Anna K Weber and Ralph Pirow*

Author Affiliations

Institute of Zoophysiology, University of Münster, Münster, Germany

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BMC Physiology 2009, 9:9  doi:10.1186/1472-6793-9-9

Published: 21 April 2009

Additional files

Additional file 1:

Multiple sequence alignment of α-carbonic anhydrases. The α-CA sequences are divided into four groups according to similarity. Residues strictly conserved have a red background, residues well conserved within a group according to a Risler matrix [122] are indicated by red letters. Residues conserved between groups are boxed. Secondary structure elements of three human α-CAs are shown in blue on the top: helices with squiggles, beta strands with arrows, alpha and beta turns with TTT and TT letters. The numbering refers to HsCA2. Amino acid residues involved in zinc-binding and in the hydrogen-bonding network are indicated by red triangles. Yellow and orange backgrounds indicate mitochondrial targeting peptide or predicted signal peptides for secretory export. Pink and green backgrounds signify a transmembrane domain or potential glycosylphosphatidylinositol (GPI) anchor sites. Daphnia pulex sequences are indicated by red labels. Additionally included were related sequences from the blue crab Callinectes sapidus (Cs), Drosophila melanogaster (Dm), Anopheles gambiae (Ag), Caenorhabditis elegans (Ce), the sea urchin Strongylocentrotus purpuratus (Sp), and Homo sapiens (Hs). Sequences were aligned using the T-Coffee algorithm [158] and displayed with ESPript [120,161]. Sequence references, protein data bank (PDB) codes and NCBI accession numbers: Callinectes [124], Drosophila [119], Anopheles [125], HsCA2 (1CA2), HsCA4 (1ZNC), HsCA5A (NP_001730), HsCA6 (P23280), HsCA10 (AAH29865), HsCA12 (1JCZ), CeCAH2 (Q18932), SpCA8 (XP_795365), SpCAc (XP_782997), SpCA-RP (XP_784796), SpCA-GPI (XP_796525).

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Additional file 2:

Multiple sequence alignment of β-carbonic anhydrases. Numbering and the secondary structure elements on the top refer to the β-CA from Pisum sativum (PsCAb) [121]. The other sequences are from Daphnia pulex (CAB), Drosophila melanogaster (DmCG11967), Anopheles gambiae (AgCAb), Caenorhabditis elegans (CeCAb1), sea urchin Strongylocentrotus purpuratus (SpCAb), and the sea anemone Nematostella vectensis (NvCAb). A column is framed in blue if more than 70% of its residues are similar according to physico-chemical properties. Similar residues are indicated by red letters; strictly conserved residues have a red background. Secondary structure elements are presented as follows: helices with squiggles, beta strands with arrows, alpha and beta turns with TTT and TT letters. Amino acid residues involved in zinc and substrate binding are indicated by red and blue triangles. Sequences were aligned using the T-Coffee algorithm [158] and displayed with ESPript [120,161]. Protein data bank (PDB) code and NCBI accession numbers: PsCAb (2EKJ), DmCG11967 (NP_649849), AgCAb (XP_563117), CeCAb1 (NP_741809), SpCAb (XP_786120), NvCAb (XP_001632619).

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Additional file 3:

Determination of operational pK' values and correction for incomplete equilibration. This supplement describes experimental determination of pK'1 and pK'2 from standard bicarbonate solutions (4, 8, and 16 mM NaHCO3 plus 50 mM NaCl). It also outlines the analytical procedure for the correction of incomplete equilibration of bicarbonate and hemolymph samples at low CO2 partial pressures.

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Additional file 4:

Reiterative least-squares spectral resolution & multicomponent analysis. This supplement describes the reiterative least-squares spectral resolution, which was employed for the determination of the pK'a value and the acid/base spectra of cSNARF-1. It also outlines the multicomponent analysis, which was used to retrieve the in vivo pH from in vivo spectra of cSNARF.

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