Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

To fully understand human biology and link genotype to phenotype, the phase of DNA variants must be known. Here we present a comprehensive analysis of haplotype-resolved genomes to assess the nature and variation of haplotypes and their pairs, diplotypes, in European population samples. We use a set of 14 haplotype-resolved genomes generated by fosmid clone-based sequencing, complemented and expanded by up to 372 statistically resolved genomes from the 1000 Genomes Project. We find immense diversity of both haploid and diploid gene forms, up to 4.1 and 3.9 million corresponding to 249 and 235 per gene on average. Less than 15% of autosomal genes have a predominant form. We describe a ‘common diplotypic proteome’, a set of 4,269 genes encoding two different proteins in over 30% of genomes. We show moreover an abundance of cis configurations of mutations in the 386 genomes with an average cis/trans ratio of 60:40, and distinguishable classes of cis- versus trans-abundant genes. This work identifies key features characterizing the diplotypic nature of human genomes and provides a conceptual and analytical framework, rich resources and novel hypotheses on the functional importance of diploidy

Significant abundance of cis configurations of coding variants in diploid human genomes

To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function

Probable multiple system atrophy in a German family. J Neurol Neurosurg Psychiatry 75: 924–925

Abstract: Mutations in LRRK2 were first reported as causing Parkinson's disease (PD) in late 2004. Since then, approximately a dozen LRRK2 substitutions have been identified that are believed to be pathogenic mutations. The substitution of adenine for guanine at nucleotide 4541 (4541G>A) in LRRK2 was recently reported. This substitution resulted in the replacement of an arginine at position 1514 with a glutamine (R1514Q). Although this substitution was not found in a large cohort of controls, its pathogenicity could not be verified. We have now genotyped the R1514Q substitution in a sample of 954 PD patients from 429 multiplex PD families. This substitution was identified in 1.8% of the PD patients; however, the majority of the PD sibships segregating this substitution were discordant for this putative mutation. In addition, the R1514Q substitution was detected in 1.4% of neurologically evaluated, control individuals. These data suggest that the R1514Q variant is not a pathogenic LRRK2 mutation. We believe it is imperative that the causative nature of any newly identified genetic variant be determined before it is included in any panel for diagnostic testing. © 2006 Movement Disorder Society Key words: Parkinson's disease; genetics; LRRK2; mutation Parkinson's disease (PD) is the second most common neurodegenerative disorder. Clinical features of PD include resting tremor, rigidity, bradykinesia, and postural instability. Although quite variable, the average age of onset is 60 years. In addition, there is a slight preponderance of affected men. Pathologically, PD is characterized by the presence of Lewy bodies and progressive degeneration of neurons in the substantia nigra, pars compacta, and other brain regions. In our ongoing effort to identify additional PD susceptibility genes, we have recruited a large cohort of PD families. The control sample was collected through three sources and provided appropriate written informed consent. One sample of controls (n ϭ 52) was ascertained in Indiana, and all control subjects were examined by a single Parkinson Study Group movement disorder specialist. These control subjects completed the identical clinical evaluation as the PD sample. Individuals were considered controls if they met the following criteria: did not have a diagnosis or symptoms of PD, Alzheimer's disease (AD), stroke, or other neurological disorder; no tremor; no other first-degree family members reported to be diagnosed with PD; and no history of polio. The average age at examination of these first control subjects was 68.3 years, with a range of 55 to 82 years. All individuals were non-Hispanic Caucasians. A second control sample (n ϭ 40) was obtained from the National Cell Repository for Alzheimer's Disease. The subjects were recruited as part of an ongoing genetic initiative to make available to the research community a sample of rigorously evaluated individuals without any evidence of neurological disease. All control subjects were evaluated, and there was no evidence for either PD or dementia. The average age at examination of the second control cohort was 76.9 years, with a range of 58 to 91 years. As was the case with the first control set, all subjects from the second control set were non-Hispanic Caucasians. DNA was prepared from peripheral blood samples collected from the PD families and control subjects. The third control sample (n ϭ 276) is composed of three neurologically normal Caucasian control panels (NDPT002, NDPT006, NDPT009) obtained from the NINDS Human Genetics Resource Center at the Coriell Institute Coriell Cell Repositories (Camden, NJ). This third control sample contains 132 males and 144 females. The average age at examination of the subjects was 69.7 years, with a range of 55 to 88 years. In total, 368 neurologically normal control samples were evaluated. The guanine to adenine substitution at nucleotide 4541 of the LRRK2 cDNA that results in the R1514Q Lrrk2 (dardarin) protein variant was screened for using a newly developed TaqMan allelic-discrimination assay (Applied Biosystems). The assay was performed with 30 ng of genomic DNA from each PD subject and control individual using conditions recommended by the manufacturer and an Applied Biosystems 7300 Real Time PCR System. Of 954 affected individuals from 12 different families, 16 (1.8%) were shown to be heterozygous carriers of the R1514Q variant. In addition, 5 (1.4%) of 368 control subjects were also found to be heterozygous for the same variant similar to the frequency observed by Zimprich and associates. Discordance for the mutation among affected individuals was observed in 10 of the 13 families in which the variant was segregating. Of the 28 affected individuals in these 12 families for whom DNA was available for study, 12 of them do not carry the R1514Q variant. This finding suggests that the R1514Q variant is not segregating with PD in these families. No statistically significant difference between the R1514Q carrier group (16) and the noncarrier group (938) was detected in our analyses of numerous parameters, including age of disease onset (61.75 years in R1514Q carriers vs. 60.9 years in noncarriers), disease duration (7.18 years carriers vs. 9.53 years noncarriers), Mini-Mental State Examination score (25.62 carriers vs. 26.48 noncarriers), Blessed Functional Activity Scale (3.66 carriers vs. 4.41 noncarriers), Hoehn & Yahr (2.2 carriers vs. 2.48 noncarriers), and ethnicity. Taken together, these data suggest that the R1514Q variant is likely a nonpathogenic variant in Lrrk2 that does not contribute to the development of Parkinson disease, confirming the report of Zimprich and coworkers

Renormalisation and fixed points in Hilbert Space

The energies of low-lying bound states of a microscopic quantum many-body system of particles can be worked out in a reduced Hilbert space. We present here and test a specific non-perturbative truncation procedure. We also show that real exceptional points which may be present in the spectrum can be identified as fixed points of coupling constants in the truncation procedure.Comment: 4 pages, 1 tabl

The state of peer-to-peer network simulators

Networking research often relies on simulation in order to test and evaluate new ideas. An important requirement of this process is that results must be reproducible so that other researchers can replicate, validate and extend existing work. We look at the landscape of simulators for research in peer-to-peer (P2P) networks by conducting a survey of a combined total of over 280 papers from before and after 2007 (the year of the last survey in this area), and comment on the large quantity of research using bespoke, closed-source simulators. We propose a set of criteria that P2P simulators should meet, and poll the P2P research community for their agreement. We aim to drive the community towards performing their experiments on simulators that allow for others to validate their results

Matrix elasticity of void-forming hydrogels controls transplanted-stem-cell-mediated bone formation

The effectiveness of stem cell therapies has been hampered by cell death and limited control over fate. These problems can be partially circumvented by using macroporous biomaterials that improve the survival of transplanted stem cells and provide molecular cues to direct cell phenotype. Stem cell behaviour can also be controlled in vitro by manipulating the elasticity of both porous and non-porous materials, yet translation to therapeutic processes in vivo remains elusive. Here, by developing injectable, void-forming hydrogels that decouple pore formation from elasticity, we show that mesenchymal stem cell (MSC) osteogenesis in vitro, and cell deployment in vitro and in vivo, can be controlled by modifying, respectively, the hydrogel’s elastic modulus or its chemistry. When the hydrogels were used to transplant MSCs, the hydrogel’s elasticity regulated bone regeneration, with optimal bone formation at 60 kPa. Our findings show that biophysical cues can be harnessed to direct therapeutic stem cell behaviours in situ

Matrix elasticity of void-forming hydrogels controls transplanted-stem-cell-mediated bone formation

The effectiveness of stem cell therapies has been hampered by cell death and limited control over fate. These problems can be partially circumvented by using macroporous biomaterials that improve the survival of transplanted stem cells and provide molecular cues to direct cell phenotype. Stem cell behaviour can also be controlled in vitro by manipulating the elasticity of both porous and non-porous materials, yet translation to therapeutic processes in vivo remains elusive. Here, by developing injectable, void-forming hydrogels that decouple pore formation from elasticity, we show that mesenchymal stem cell (MSC) osteogenesis in vitro, and cell deployment in vitro and in vivo, can be controlled by modifying, respectively, the hydrogel's elastic modulus or its chemistry. When the hydrogels were used to transplant MSCs, the hydrogel's elasticity regulated bone regeneration, with optimal bone formation at 60 kPa. Our findings show that biophysical cues can be harnessed to direct therapeutic stem cell behaviours in situ

New Insights into Mutable Collagenous Tissue: Correlations between the Microstructure and Mechanical State of a Sea-Urchin Ligament

The mutable collagenous tissue (MCT) of echinoderms has the ability to undergo rapid and reversible changes in passive mechanical properties that are initiated and modulated by the nervous system. Since the mechanism of MCT mutability is poorly understood, the aim of this work was to provide a detailed morphological analysis of a typical mutable collagenous structure in its different mechanical states. The model studied was the compass depressor ligament (CDL) of a sea urchin (Paracentrotus lividus), which was characterized in different functional states mimicking MCT mutability. Transmission electron microscopy, histochemistry, cryo-scanning electron microscopy, focused ion beam/scanning electron microscopy, and field emission gun-environmental scanning electron microscopy were used to visualize CDLs at the micro- and nano-scales. This investigation has revealed previously unreported differences in both extracellular and cellular constituents, expanding the current knowledge of the relationship between the organization of the CDL and its mechanical state. Scanning electron microscopies in particular provided a three-dimensional overview of CDL architecture at the micro- and nano-scales, and clarified the micro-organization of the ECM components that are involved in mutability. Further evidence that the juxtaligamental cells are the effectors of these changes in mechanical properties was provided by a correlation between their cytology and the tensile state of the CDLs

Advanced maturation of human cardiac tissue grown from pluripotent stem cells

Cardiac tissues generated from human induced pluripotent stem cells (iPSCs) can serve as platforms for patient-specific studies of physiology and disease1-6. However, the predictive power of these models is presently limited by the immature state of the cells1, 2, 5, 6. Here we show that this fundamental limitation can be overcome if cardiac tissues are formed from early-stage iPSC-derived cardiomyocytes soon after the initiation of spontaneous contractions and are subjected to physical conditioning with increasing intensity over time. After only four weeks of culture, for all iPSC lines studied, such tissues displayed adult-like gene expression profiles, remarkably organized ultrastructure, physiological sarcomere length (2.2 µm) and density of mitochondria (30%), the presence of transverse tubules, oxidative metabolism, a positive force-frequency relationship and functional calcium handling. Electromechanical properties developed more slowly and did not achieve the stage of maturity seen in adult human myocardium. Tissue maturity was necessary for achieving physiological responses to isoproterenol and recapitulating pathological hypertrophy, supporting the utility of this tissue model for studies of cardiac development and disease.The authors acknowledge funding support from the National Institutes of Health of the USA (NIBIB and NCATS grant EB17103 (G.V.-N.); NIBIB, NCATS, NIAMS, NIDCR and NIEHS grant EB025765 (G.V.-N.); NHLBI grants HL076485 (G.V.-N.) and HL138486 (M.Y.); Columbia University MD/PhD program (S.P.M., T.C.); University of Minho MD/PhD program (D.T.); Japan Society for the Promotion of Science fellowship (K.M.); and Columbia University Stem Cell Initiative (D.S., L.S., M.Y.). We thank S. Duncan and B. Conklin for providing human iPSCs, M.B. Bouchard for assistance with image and video analysis, and L. Cohen-Gould for transmission electron microscopy services.info:eu-repo/semantics/publishedVersio