Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores-0

of a residue with its descendant is that of identity, diagonal term of a substitution matrix) or modified due to random DNA mutations. Similarity decreases therefore with time, since no similarity is higher than that of identity. When the similarity falls below a threshold that is necessary for the residue to operate according to a standard (functional conservation), the component is damaged. In this case, the score distribution is exponential, suggesting that valine (V) is a non-aging component. Based on BLOSUM62, residues of this type are V, F, P, W, Y, E, G, H, I, L, K, R, N, D and C The score distribution shows a peak, indicating a probable accelerated process of aging (functional damage) when the residue is substituted by random mutation in some other amino acids. Based on BLOSUM62, residues of this type are T, S, M, A and Q. The complete distribution in the BLOSUM62 matrix is exponential (0.287.exp(-0.287.(+4))), supporting a general model of amino acids as nonaging components. The exponential law for positive scores is characterized by the same parameter (= 0.287). The original residue is termed ; its descent is termed .<p><b>Copyright information:</b></p><p>Taken from "Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores"</p><p>http://www.biomedcentral.com/1471-2105/9/332</p><p>BMC Bioinformatics 2008;9():332-332.</p><p>Published online 7 Aug 2008</p><p>PMCID:PMC2529321.</p><p></p

Diagram representing our strategies to quantify glycerolipids by LC-MS/MS.

<p>A) In MS/MS-Internal Stds method, one internal standard is used per lipid class. B) In MS/MS-QC method, one internal standard is used for each chromatographic segment: DAG 18:0–22:6 is used to adjust DAG, TAG, MGDG and DGDG amounts, PE 18:0–18:0 for PE amount and SQDG 16:0–18:0 for SQDG, DGTA, DGTS, PA, PC, PG, PS, DPG and PI amounts.</p

Fatty acid distribution of the main phospholipids produced by <i>Pichia pastoris</i> cells grown in a hydrogenated medium at 30°C (red) and at 18°C (green) and in a deuterated environment at 30°C (blue) and 18°C (cyan).

<p>In all individual phospholipids, the deuterated environment triggers the enrichment in C18:1 fatty acids PC, phosphatidylcholine; PE, phosphatidylethanolamine; PI, phosphatidylinositol; PS, phosphatidylserine. Errors bars represent the standard deviation from three different phospholipids extractions and separations. Data represent mean values ± s.d (n = 3). In histograms, *<i>P</i><0.05 from Student's <i>t</i>-test, assuming equal variance. PC: for C16:0, the difference is significant between H30°C and H18°C, between H30°C and D30°C and between H30°C and D18°C. For C16:1, there is a significant difference between H30°C and D30°C and between H18°C and D18°C. For C18:0, there is a significant difference between H18°C and D18°C, between H18°C and H30°C and between H18°C and D30°C. For C18:1, the difference is significant between all the different temperatures and isotopic contents. For C18:2, there is a significant difference between D30°C and D18°C, between D30°C and H30°C and between D30°C and H18°C. For C18:3, the difference is significant between all the different temperatures and isotopic contents. PE: for C16:0, the difference is significant between H30°C and D30°C, between H30°C and H18°C and between H30°C and D18°C. For C18:1 and C18:3, the difference is significant between all the different temperatures and isotopic contents. PS and PI: for C16:0, there is a significant difference between H30° and D30°C and between H30° and D18°C. For C16:2 and C18:1, there is a significant difference between H30°C and D30°C, between H18°C and D18°C and between D18°C and D30°C. For C18:2 and C18:3, there is a significant difference between H30°C and D30°C and between H18°C and D18°C.</p

Lipid distribution in P.t., N.g. and A.t..

<p>Lipids were extracted and each class of lipids was quantified either by TLC plus GC-FID (TLC+GC bars), or by LC-MS/MS with an internal standard for each class (MS/MS-Stds bars), or by LC-MS/MS using a QC extract run in tandem with the sample (MS/MS-QC bars) (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182423#sec002" target="_blank">Material and methods</a>). Values are the average ± SD of three biological repeats for each type of cells. Values are the average ± SD of three biological repeats. Significant differences (P < 0.05) are shown by an asterisk and were calculated by an unpaired multiple t test using GraphPad Prism software.</p

Conditions for the regiochemical assignment of fatty acids at <i>sn</i>-1, <i>sn</i>-2 and <i>sn</i>-3 positions in glycerolipids.

<p>Conditions for the regiochemical assignment of fatty acids at <i>sn</i>-1, <i>sn</i>-2 and <i>sn</i>-3 positions in glycerolipids.</p

Effect of nitrogen starvation on the glycerolipid and FA composition of P.t., N.g. and A.t..

<p>A) glycerolipid quantification using the LC-MS/MS-QC method. B) FA quantification by GC-FID. The data are the average ± SD of three biological repeats. Significant differences (p ≤ 0.05) are indicated by an asterisk. Significant differences (p < 0.05) are shown by an asterisk and were calculated by an unpaired multiple t test using GraphPad Prism software.</p

GC-MS analysis of ergosterol isotopomers from <i>Pichia pastoris</i> unsaponifiable extracts.

<p>A, TIC of an acetylated extract from cells grown in hydrogenated medium. The peak at RT = 36.10 min is ergosterol. B, TIC of an acetylated extract from cells grown in deuterated medium. The peak at RT = 35.26 min is deuterioergosterol. C, mass spectrum of ergosteryl acetate. Prominent ions and interpretation of the fragmentation pattern: M⁺(438), M⁺-acetate-H (378), M⁺-acetate-H-CH₃ (363), M+-acetate-H-side chain (253). D, mass spectrum of deuterioergosteryl acetate. Prominent ions and interpretation of the fragmentation pattern: M⁺(481), M⁺-acetate-D (420), M⁺-acetate-D-CD₃ (402), M⁺-acetate-D-side chain (278).</p

FA distribution in <i>Phaeodactylum tricornutum</i> (P.t.), <i>Nannochloropsis gaditana</i> (N.g.) and <i>Arabidopsis thaliana</i> (A.t.) cell cultures.

<p>Lipids were extracted and FA were converted to FAME before GC-FID analyses, as described in Material and Methods. Values are the average ± SD of three biological repeats for each type of cells.</p

Impact of nitrogen starvation on the amount of the various molecular species constituting MGDG, PC, DAG and TAG in P.t..

<p>Quantification were made by the LC-MS/MS method. Values are the average ± SD of three biological repeats. Significant differences (p ≤ 0.05) are indicated by an asterisk. Significant differences (P < 0.05) are shown by an asterisk and were calculated by an unpaired multiple t test using GraphPad Prism software.</p

Total fatty acid distribution in <i>Pichia pastoris</i> cells grown in a hydrogenated environment at 30°C (red) and 18°C (green) and in a deuterated environment at 30°C (blue) and 18°C (cyan).

<p>Data represent mean values ± s.d (n = 3). In histograms, *<i>P</i><0.05 from Student's <i>t</i>-test, assuming equal variance. For C16:0, there is a significant difference between H 30°C and H 18°C, between H 30°C and D30°C, H 30°C and D18°C, between H 18°C and D 30°C but not between H18°C and D18°C. For C16:1, there is a significant difference for all 4 different temperatures and isotopic contents. For C16:2, there is a significant difference between D30°C and D18°C. For C18:1, there is a significant difference for all 4 different temperatures and isotopic contents. For C18:2, there is a significant difference between D30°C and H30°C, between D30°C and D18°C, between D30°C and H18°C. For C18:3, there is a significant difference for all 4 different temperatures and isotopic contents.</p