Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Correction to: Cluster identification, selection, and description in Cluster randomized crossover trials: the PREP-IT trials

An amendment to this paper has been published and can be accessed via the original article

Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor-5

<p><b>Copyright information:</b></p><p>Taken from "Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor"</p><p>http://www.biomedcentral.com/1471-213X/7/67</p><p>BMC Developmental Biology 2007;7():67-67.</p><p>Published online 13 Jun 2007</p><p>PMCID:PMC1906760.</p><p></p>d by FIGLA. Paraformaldehyde fixed and paraffin embedded adult ovarian section were hybridized with digoxigenin (DIG) labeled antisense (A, C, E, G, I) or sense (B, D, F, H, J) synthetic oligonuclotides probes specific to [E330009P21Rik] (A, B), [E330017A01Rik] (C, D), [C330003B14Rik] (E, F), [E330034G19Rik] (G, H) and [Genbank:] (I, J) cDNAs

Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor-8

<p><b>Copyright information:</b></p><p>Taken from "Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor"</p><p>http://www.biomedcentral.com/1471-213X/7/67</p><p>BMC Developmental Biology 2007;7():67-67.</p><p>Published online 13 Jun 2007</p><p>PMCID:PMC1906760.</p><p></p>5, E17.5 and newborn. For elements in the NIA microarray, the mean intensity ratio lognull (red) over normal (blue) on X axis is plotted against the average intensity ratio lognull and normal on Y axis. Data represent mean of 3–4 independent biological samples with Cy3 and Cy5 dye reversals and spiked Ambion RNA controls. B. Same as (A) except restricted to expression profiles of 203 newborn genes regulated by FIGLA (≥ 2 fold, ρ ≤ 0.05, after analysis of variance)

Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor-2

<p><b>Copyright information:</b></p><p>Taken from "Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor"</p><p>http://www.biomedcentral.com/1471-213X/7/67</p><p>BMC Developmental Biology 2007;7():67-67.</p><p>Published online 13 Jun 2007</p><p>PMCID:PMC1906760.</p><p></p>GLA. A. qRT-PCR of total RNA isolated from somatic and reproductive tract tissues normalized to HPRT and plotted relative to 100% expression in ovary. B. qRT-PCR of total ovarian RNA isolated from normal and null mice at E12.5, E14.5, E17.5 and newborn and plotted relative to HPRT. Data is the average of two independently isolated biological samples, analyzed in triplicate at each developmental time point. (ita) and (iota)(shaded) were previously identified as ovary-specific and were not represented in microarray or SAGE data

Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor-1

<p><b>Copyright information:</b></p><p>Taken from "Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor"</p><p>http://www.biomedcentral.com/1471-213X/7/67</p><p>BMC Developmental Biology 2007;7():67-67.</p><p>Published online 13 Jun 2007</p><p>PMCID:PMC1906760.</p><p></p>regulated (B) by FIGLA. Individual genes are represented by horizontal bar. Each lane represents an independently obtained biological sample (three for E12.5, E14.5 and E17.5; four for newborn) with Cy3 and Cy5 dye reversals indicated at the bottom. Blue represents greater abundance in the presence of FIGLA and red indicates less. Four genes [NIA:551381, NIA:H330A03, NIA:H3134D03, NIA:H3058H02] up-regulated at E17.5 and newborn are indicated with dots to the left. Genes encoding transcripts characterized in greater detail are indicated by an asterisk and are labeled to the right. Both and were identified by the screen, but not characterized further