A Conserved Mammalian Protein Interaction Network

Physical interactions between proteins mediate a variety of biological functions, including signal transduction, physical structuring of the cell and regulation. While extensive catalogs of such interactions are known from model organisms, their evolutionary histories are difficult to study given the lack of interaction data from phylogenetic outgroups. Using phylogenomic approaches, we infer a upper bound on the time of origin for a large set of human protein-protein interactions, showing that most such interactions appear relatively ancient, dating no later than the radiation of placental mammals. By analyzing paired alignments of orthologous and putatively interacting protein-coding genes from eight mammals, we find evidence for weak but significant co-evolution, as measured by relative selective constraint, between pairs of genes with interacting proteins. However, we find no strong evidence for shared instances of directional selection within an interacting pair. Finally, we use a network approach to show that the distribution of selective constraint across the protein interaction network is non-random, with a clear tendency for interacting proteins to share similar selective constraints. Collectively, the results suggest that, on the whole, protein interactions in mammals are under selective constraint, presumably due to their functional roles.A˚.P.B. is supported by Ga˚lo¨stiftelsen Stipendium fo¨r ho¨gre utlandsstudier. C.M.H. is supported by a National Library of Medicine Biomedical and Health Informatics Training Fellowship [LM007089-19]. G.C.C. is supported by the Reproductive Biology Group of the Food for the 21st Century program at the University of Missouri. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Background sequence characteristics influence the occurrence and severity of disease-causing mtDNA mutations.

Inherited mitochondrial DNA (mtDNA) mutations have emerged as a common cause of human disease, with mutations occurring multiple times in the world population. The clinical presentation of three pathogenic mtDNA mutations is strongly associated with a background mtDNA haplogroup, but it is not clear whether this is limited to a handful of examples or is a more general phenomenon. To address this, we determined the characteristics of 30,506 mtDNA sequences sampled globally. After performing several quality control steps, we ascribed an established pathogenicity score to the major alleles for each sequence. The mean pathogenicity score for known disease-causing mutations was significantly different between mtDNA macro-haplogroups. Several mutations were observed across all haplogroup backgrounds, whereas others were only observed on specific clades. In some instances this reflected a founder effect, but in others, the mutation recurred but only within the same phylogenetic cluster. Sequence diversity estimates showed that disease-causing mutations were more frequent on young sequences, and genomes with two or more disease-causing mutations were more common than expected by chance. These findings implicate the mtDNA background more generally in recurrent mutation events that have been purified through natural selection in older populations. This provides an explanation for the low frequency of mtDNA disease reported in specific ethnic groups

Genetic variation in the methylenetetrahydrofolate reductase gene, MTHFR, does not alter the risk of visual failure in Leber’s hereditary optic neuropathy

Focal neurodegeneration of the optic nerve in Leber hereditary optic neuropathy (LHON) is primarily due to a maternally inherited mitochondrial DNA mutation. However, the markedly reduced penetrance of LHON and segregation pattern of visual failure within families implicates an interacting nuclear genetic locus modulating the phenotype. Folate deficiency is known to cause bilateral optic neuropathy, and defects of folate metabolism have been associated with nonarteritic ischemic optic neuropathy

Mitochondrial DNA changes in pedunculopontine cholinergic neurons in Parkinson’s disease

In Parkinson’s disease (PD), mitochondrial dysfunction associates with nigral dopaminergic neuronal loss. Cholinergic neuronal loss co-occurs, particularly within a brainstem structure, the pedunculopontine nucleus (PPN). We isolated single cholinergic neurons from post-mortem PPNs of aged controls and PD patients. Mitochondrial DNA (mtDNA) copy number and mtDNA deletions were increased significantly in PD patients compared to controls. Furthermore, compared to controls the PD patients had significantly more PPN cholinergic neurons containing mtDNA deletion levels exceeding 60%, a level associated with deleterious effects on oxidative phosphorylation. The current results differ from studies reporting mtDNA depletion in nigral dopaminergic neurons of PD patients

Does mitochondrial DNA predispose to neuromyelitis optica (Devic's disease)?

Neuromyelitis optica (NMO), or Devic's disease, is a relapsing demyelinating disease of the central nervous system characterized by optic neuritis and myelitis with distinct clinical, imaging, CSF and serological features (Wingerchuk et al. , 2006). There is increasing evidence that NMO is an antibody-mediated organ-specific autoimmune disease associated with anti-aquaporin 4 antibodies detectable in serum (Lennon et al. , 2004), supported by four recent papers in the same edition of Brain (Matsuoka et al. , 2007; Misu et al. , 2007; Roemer et al. , 2007; Takahashi et al. , 2007) and the accompanying scientific commentary (Compston, 2007). However, it is still not known why the disorder specifically targets the optic nerves and spinal cord. Several siblings with NMO have been reported (McAlpine, 1938; Keegan and Weinshenker, 2000; Yamakawa et al. , 2000), raising the possibility of a genetic predisposition, but no pathogenic mutations have been identified in the AQP4 gene on chromosome 18q11.2-q12.1 (Lu et al. , 1996). NMO has similarities with Leber hereditary optic neuropathy (LHON, MIM 535 000) which is primarily due to mutations of mitochondrial DNA (mtDNA) that disrupt complex I of the respiratory chain (Carelli et al. , 2004). Although the genetic defect in LHON is present in all tissues, the pathology also is strikingly tissue-specific. Most affected individuals develop sub-acute painless visual failure due to focal involvement of both optic nerves (Newman et al. , 1991; Riordan-Eva et al. , 1995), but some also develop a progressive myelopathy, with high signal extending over multiple spinal levels on MR imaging, and the absence of oligoclonal bands in the CSF (Johns et al. , 1991; Jaros et al. , 2007). Tissue-specific susceptibility to mitochondrial dysfunction is thought to explain why the neurodegeneration in LHON only affects specific neuronal

A critical analysis of the combined usage of protein localization prediction methods: Increasing the number of independent data sets can reduce the accuracy of predicted mitochondrial localization

In the absence of a comprehensive experimentally derived mitochondrial proteome, several bioinformatic approaches have been developed to aid the identification of novel mitochondrial disease genes within mapped nuclear genetic loci. Often, many classifiers are combined to increase the sensitivity and specificity of the predictions.Here we show that the greatest sensitivity and specificity are obtained by using a combination of seven carefully selected classifiers. We also show that increasing the number of independent prediction methods can paradoxically decrease the accuracy of predicting mitochondrial localization. This approach will help to accelerate the identification of new mitochondrial disease genes by providing a principled way for the selection for combination of appropriate prediction methods of mitochondrial localization of proteins

Variation in OPA1 does not explain the incomplete penetrance of Leber hereditary optic neuropathy

Purpose: Leber hereditary optic neuropathy (LHON) is a common cause of inherited blindness, primarily due to one of three mitochondrial DNA (mtDNA) mutations. These mtDNA pathogenic mutations have variable clinical penetrance. Recent linkage evidence raised the possibility that the nuclear gene optic atrophy 1 (OPA1) determines whether mtDNA mutation carriers develop blindness. To validate these findings we studied OPA1 in three independent LHON cohorts: sequencing the gene in discordant male sib pairs, carrying out a family-based association study of common functional genetic variants, and carrying out a population-based association study of the same genetic variants.Methods: We tested 3 hypothesis in three separate study groups. Study group 1: Direct sequencing of OPA1 coding regions was performed using sequencing methodologies (Applied Biosystems, Foster City, CA). Chromatograms were compared with the GenBank reference sequence NM_015560.1. Splice-site prediction was performed using GeneSplicer. Study group 2: Genotyping for rs166850 and rs10451941 was performed by restriction fragment length polymorphism (RFLP) analysis with specific primers for both genotypes, using The restriction enzymes RsaI and FspBI to discriminate genotypes. Study group 3: Genotyping for rs166850 and rs10451941 was performed by primer extension of allele-specific extensions products by matrix-associated laser desorption/ionisation time-of-flight (MALDI-TOF, Seqeunom, San Diego, CA) mass spectrometry. Allele and genotype frequencies were compared using Pearson's chi-square test. Multiple logistic regression was performed to look for interactions between the variables. All analyses were performed using SPSS software version 17.0 (SPSS Inc.).Results: In all three groups we were unable to find an association between OPA1 genetic variation and visual failure in LHON mtDNA mutation carriers.Conclusions: Our findings suggest that genetic variation in OPA1 is unlikely to make a major contribution to the risk of blindness in LHON mutation carriers.Medical Research Council (UK)UK Parkinson Disease SocietyUK NIHR Biomedical Research Centre for Aging and AgeTelethon-ItalyNewcastle Univ, Inst Human Genet, Newcastle Upon Tyne NE1 3BZ, Tyne & Wear, EnglandRoyal Victoria Infirm, Dept Ophthalmol, Newcastle Upon Tyne NE1 4LP, Tyne & Wear, EnglandUniv Bologna, Dept Neurol Sci, Bologna, ItalyUniv Fed Sao Paulo, UNIFESP, Dept Oftalmol, Sao Paulo, BrazilFdn Neurol Inst C Besta, Unit Mol Neurogenet, Milan, ItalyUniv Fed Sao Paulo, UNIFESP, Dept Oftalmol, Sao Paulo, BrazilTelethon-Italy: GGP06233Web of Scienc

Two-photon spectroscopy of the biphenyl chromophore. The electronic excited states of biphenyl and fluorene below 50000 cm-1

The two-photon excitation spectra of biphenyl and fluorene in dil. soln. were measured up to 50,000 cm-1. Both spectra exhibit a medium intense band system in the range 32,000-42,000 cm-1, and a strong band above 45,000 cm-1. The lowest frequency feature is assigned to a B3 symmetry transition in biphenyl and the corresponding B2 transition in fluorene. The polarization of the higher bands leads to the assignment of 2 A states at 38,000 and 47,000 cm-1. The origin of the electronically excited states of the biphenyl chromophore is discussed by simple composite mol. considerations as well as CNDO CI calcns. The latter give a semiquant. picture of transition energies and transition probabilities for 1- and 2-photon allowed excitations. A compilation of 1-photon spectra and calcns. from the literature is included in the anal. to provide a consistent picture of the electronically excited states of the biphenyl chromophore up to 50,000 cm-1

A systematic literature review of undergraduate clinical placements in underserved areas.

Context: The delivery of undergraduate clinical education in underserved areas is increasing in various contexts across the world in response to local workforce needs. A collective understanding of the impact of these placements is lacking. Previous reviews have often taken a positivist approach by only looking at outcome measures. This review addresses the question: What are the strengths and weaknesses for medical students and supervisors of community placements in underserved areas? Methods: A systematic literature review was carried out by database searching, citation searching, pearl growing, reference list checking and use of own literature. The databases included MEDLINE, EMBASE, PsycINFO, Web of Science and ERIC. The search terms used were combinations and variations of four key concepts exploring general practitioner (GP) primary care, medical students, placements and location characteristics. The papers were analysed using a textual narrative synthesis. Findings: The initial search identified 4923 results. After the removal of duplicates and the screening of titles and abstracts, 185 met the inclusion criteria. These full articles were obtained and assessed for their relevance to the research question; 54 were then included in the final review. Four main categories were identified: student performance, student perceptions, career pathways and supervisor experiences. Conclusions: This review reflects the emergent qualitative data as well as the quantitative data used to assess initiatives. Underserved area placements have produced many beneficial implications for students, supervisors and the community. There is a growing amount of evidence regarding rural, underserved areas, but little in relation to inner city, deprived areas, and none in the UK

Mitochondrial DNA and traumatic brain injury.

OBJECTIVE: Traumatic brain injury (TBI) is a multifactorial pathology with great interindividual variability in response to injury and outcome. Mitochondria contain their own DNA (mtDNA) with genomic variants that have different physiological and pathological characteristics, including susceptibility to neurodegeneration. Given the central role of mitochondria in the pathophysiology of neurological injury, we hypothesized that its genomic variants may account for the variability in outcome following TBI. METHODS: We undertook an analysis of mitochondrial haplogroups in a large, well-characterized cohort of 1,094 TBI patients. A proportional odds model including age, brain computed tomography characteristics, injury severity, pupillary reactivity, mitochondrial haplogroups, and APOE was applied to Glasgow Outcome Score (GOS) data. RESULTS: mtDNA had a significant association with 6-month GOS (p=0.008). Haplogroup K was significantly associated with favorable outcome (odds ratio=1.64, 95% confidence interval=1.08-2.51, p=0.02). There was also a significant interaction between mitochondrial genome and age (p=0.002), with a strong protective effect of both haplogroups T (p=0.015) and K (p=0.017) with advancing age. We also found a strong interaction between APOE and mitochondrial haplogroups (p=0.001), indicating a protective effect of haplogroup K in carriers of the APOE ε4 allele. INTERPRETATION: These findings reveal an interplay between mitochondrial DNA, pathophysiology of TBI, and aging. Haplogroups K and T, which share a common maternal ancestor, are shown as protective in TBI. The data also suggest that the APOE pathways interact with genetically regulated mitochondrial functions in the response to acute injury, as previously reported in Alzheimer disease