Generation of a human induced pluripotent stem cell line (CSC-40) from a Parkinson's disease patient with a PINK1 p.Q456X mutation

Parkinson's disease (PD) is a neurodegenerative disease with unknown etiology. Here we show the generation of an induced pluripotent stem cell (iPSC) line, named CSC-40, from dermal fibroblasts obtained from a 59-year-old male patient with a homozygous p.Q456X mutation in the PTEN-induced putative kinase 1 (PINK/PARK6) gene and a confirmed diagnosis of PD, which could be used to model familial PD. A non-integrating Sendai virus-based delivery of the reprogramming factors OCT3/4, SOX2, c-MYC and KLF4 was employed. The CSC-40 cell line showed normal karyotyping and fingerprinting following transduction as well as sustained expression of several pluripotency markers and the ability to differentiate into all three germ layers.We thank AnnaKarin Olden and Marianne Juhlin, for their technical support. We are also thankful to the 'Cell Line and DNA Biobank from Patients affected by Genetic Diseases' (Istituto G. Gaslini, Genova, Italy) and the Parkinson Institute Biobank, members of the Telethon Network of Genetic Biobanks (http://biobanknetwork.telethon.it; project no. GTB12001) funded by Telethon Italy, for providing fibroblasts samples. This work was supported by the Strategic Research Environment MultiPark at Lund University, and the strong research environment BAGADILICO (grant 349-2007-8626), the Swedish Parkinson Foundation (Parkinsonoden; grant 889/16), the Swedish Research Council (grant 2015-03684 to LR), Finnish Cultural Foundation (grant 00161167 to YP) and the Portuguese Foundation for Science and Technology for the doctoral fellowship - PDE/BDE/113598/2015 to AM.info:eu-repo/semantics/publishedVersio

The Palomar Transient Factory Orion Project: Eclipsing Binaries and Young Stellar Objects

The Palomar Transient Factory (PTF) Orion project is an experiment within the broader PTF survey, a systematic automated exploration of the sky for optical transients. Taking advantage of the wide field of view available using the PTF camera at the Palomar 48" telescope, 40 nights were dedicated in December 2009-January 2010 to perform continuous high-cadence differential photometry on a single field containing the young (7-10Myr) 25 Ori association. The primary motivation for the project is to search for planets around young stars in this region. The unique data set also provides for much ancillary science. In this first paper we describe the survey and data reduction pipeline, and present initial results from an inspection of the most clearly varying stars relating to two of the ancillary science objectives: detection of eclipsing binaries and young stellar objects. We find 82 new eclipsing binary systems, 9 of which we are candidate 25 Ori- or Orion OB1a-association members. Of these, 2 are potential young W UMa type systems. We report on the possible low-mass (M-dwarf primary) eclipsing systems in the sample, which include 6 of the candidate young systems. 45 of the binary systems are close (mainly contact) systems; one shows an orbital period among the shortest known for W UMa binaries, at 0.2156509 \pm 0.0000071d, with flat-bottomed primary eclipses, and a derived distance consistent with membership in the general Orion association. One of the candidate young systems presents an unusual light curve, perhaps representing a semi-detached binary system with an inflated low-mass primary or a star with a warped disk, and may represent an additional young Orion member. Finally, we identify 14 probable new classical T-Tauri stars in our data, along with one previously known (CVSO 35) and one previously reported as a candidate weak-line T-Tauri star (SDSS J052700.12+010136.8).Comment: 66 pages, 27 figures, accepted to Astronomical Journal. Minor typographical corrections and update to author affiliation

The PTF Orion Project: a Possible Planet Transiting a T-Tauri Star

We report observations of a possible young transiting planet orbiting a previously known weak-lined T-Tauri star in the 7-10 Myr old Orion-OB1a/25-Ori region. The candidate was found as part of the Palomar Transient Factory (PTF) Orion project. It has a photometric transit period of 0.448413 +- 0.000040 days, and appears in both 2009 and 2010 PTF data. Follow-up low-precision radial velocity (RV) observations and adaptive optics imaging suggest that the star is not an eclipsing binary, and that it is unlikely that a background source is blended with the target and mimicking the observed transit. RV observations with the Hobby-Eberly and Keck telescopes yield an RV that has the same period as the photometric event, but is offset in phase from the transit center by approximately -0.22 periods. The amplitude (half range) of the RV variations is 2.4 km/s and is comparable with the expected RV amplitude that stellar spots could induce. The RV curve is likely dominated by stellar spot modulation and provides an upper limit to the projected companion mass of M_p sin i_orb < 4.8 +- 1.2 M_Jup; when combined with the orbital inclination, i orb, of the candidate planet from modeling of the transit light curve, we find an upper limit on the mass of the planetary candidate of M_p < 5.5 +- 1.4 M_Jup. This limit implies that the planet is orbiting close to, if not inside, its Roche limiting orbital radius, so that it may be undergoing active mass loss and evaporation.Comment: Corrected typos, minor clarifications; minor updates/corrections to affiliations and bibliography. 35 pages, 10 figures, 3 tables. Accepted to Ap

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Confirmation of a non-synonymous SNP in PNPLA8 as a candidate causal mutation for Weaver syndrome in Brown Swiss cattle

Background: Bovine progressive degenerative myeloencephalopathy (Weaver syndrome) is a neurodegenerative disorder in Brown Swiss cattle that is characterized by progressive hind leg weakness and ataxia, while sensorium and spinal reflexes remain unaffected. Although the causal mutation has not been identified yet, an indirect genetic test based on six microsatellite markers and consequent exclusion of Weaver carriers from breeding have led to the complete absence of new cases for over two decades. Evaluation of disease status by imputation of 41 diagnostic single nucleotide polymorphisms (SNPs) and a common haplotype published in 2013 identified several suspected carriers in the current breeding population, which suggests a higher frequency of the Weaver allele than anticipated. In order to prevent the reemergence of the disease, this study aimed at mapping the gene that underlies Weaver syndrome and thus at providing the basis for direct genetic testing and monitoring of today's Braunvieh/Brown Swiss herds. Results: Combined linkage/linkage disequilibrium mapping on Bos taurus chromosome (BTA) 4 based on Illumina Bovine SNP50 genotypes of 43 Weaver-affected, 31 Weaver carrier and 86 Weaver-free animals resulted in a maximum likelihood ratio test statistic value at position 49,812,384 bp. The confidence interval (0.853 Mb) determined by the 2-LOD drop-off method was contained within a 1.72-Mb segment of extended homozygosity. Exploitation of whole-genome sequence data from two official Weaver carriers and 1145 other bulls that were sequenced in Run4 of the 1000 bull genomes project showed that only a non-synonymous SNP (rs800397662) within the PNPLA8 gene at position 49,878,773 bp was concordant with the Weaver carrier status. Targeted SNP genotyping confirmed this SNP as a candidate causal mutation for Weaver syndrome. Genotyping for the candidate causal mutation in a random sample of 2334 current Braunvieh animals suggested a frequency of the Weaver allele of 0.26 %. Conclusions: Through combined use of exhaustive sequencing data and SNP genotyping results, we were able to provide evidence that supports the non-synonymous mutation at position 49,878,773 bp as the most likely causal mutation for Weaver syndrome. Further studies are needed to uncover the exact mechanisms that underlie this syndrome

Generation of a human induced pluripotent stem cell line (CSC-42) from a patient with sporadic form of Parkinson's disease

Skin fibroblasts were collected from a 44-year-old patient with sporadic case of Parkinson's disease (PD). The non-integrating Sendai virus vector encoding OCT3/4, SOX2, c-MYC and KLF4 was used to reprogram fibroblasts into induced pluripotent stem cells (iPSCs). Generated iPSCs had normal karyotypes, expressed common stem cell markers, and were capable of differentiating into all three germ layers. Generated line could be used for PD modeling to understand the mechanisms that influence the disorder.We thank AnnaKarin Oldén and Marianne Juhlin, for their technical support. We are also thankful to the ‘Cell Line and DNA Biobank from Patients affected by Genetic Diseases’ (Istituto G. Gaslini, Genova, Italy) and the ‘Parkinson Institute Biobank, members of the Telethon Network of Genetic Biobanks (http://biobanknetwork.telethon.it; project no. GTB12001) funded by Telethon Italy, for providing fibroblasts samples. This work was supported by the Strategic Research Environment MultiPark at Lund University, the strong research environment BAGADILICO (349-2007-8626), the Swedish Parkinson Foundation (Parkinsonfonden; grant 899/16), the Swedish Research Council (grant 2015-03684 to LR), Finnish Cultural Foundation (grant 00161167 to YP) and the Portuguese Foundation for Science and Technology for the doctoral fellowship - PDE/BDE/113598/2015 to AM

Cellular alterations identified in pluripotent stem cell-derived midbrain spheroids generated from a female patient with progressive external ophthalmoplegia and parkinsonism who carries a novel variation (p.Q811R) in the POLG1 gene

Variations in the POLG1 gene encoding the catalytic subunit of the mitochondrial DNA polymerase gamma, have recently been associated with Parkinson's disease (PD), especially in patients diagnosed with progressive external ophthalmoplegia (PEO). However, the majority of the studies reporting this association mainly focused on the genetic identification of the variation in POLG1 in PD patient primary cells, and determination of mitochondrial DNA copy number, providing little information about the cellular alterations existing in patient brain cells, in particular dopaminergic neurons. Therefore, through the use of induced pluripotent stem cells (iPSCs), we assessed cellular alterations in novel p.Q811R POLG1 (POLG1Q811R) variant midbrain dopaminergic neuron-containing spheroids (MDNS) from a female patient who developed early-onset PD, and compared them to cultures derived from a healthy control of the same gender. Both POLG1 variant and control MDNS contained functional midbrain regionalized TH/FOXA2-positive dopaminergic neurons, capable of releasing dopamine. Western blot analysis identified the presence of high molecular weight oligomeric alpha-synuclein in POLG1Q811R MDNS compared to control cultures. In order to assess POLG1Q811R-related cellular alterations within the MDNS, we applied mass-spectrometry based quantitative proteomic analysis. In total, 6749 proteins were identified, with 61 significantly differentially expressed between POLG1Q811R and control samples. Pro-And anti-inflammatory signaling and pathways involved in energy metabolism were altered. Notably, increased glycolysis in POLG1Q811R MDNS was suggested by the increase in PFKM and LDHA levels and confirmed using functional analysis of glycolytic rate and oxygen consumption levels. Our results validate the use of iPSCs to assess cellular alterations in relation to PD pathogenesis, in a unique PD patient carrying a novel p.Q811R variation in POLG1, and identify several altered pathways that may be relevant to PD pathogenesis

Generation of an induced pluripotent stem cell line (CSC-46) from a patient with Parkinson's disease carrying a novel p.R301C mutation in the GBA gene

Mutations in the glucocerebrosidase (GBA) gene have been associated with the development of Parkinson's disease (PD). An induced pluripotent stem cell (iPSC) line was generated from a 60-year old patient diagnosed with PD and carrying a new mutation variant p.R301C in GBA. Using non-integrating Sendai virus-based technology, we utilized OCT3/4, SOX2, c-MYC and KLF4 transcription factors to reprogram skin fibroblasts into iPSCs. The generated iPSC line retained the mutation, displayed expression of common pluripotency markers, differentiated into the three germ layers, and exhibited normal karyotype. The iPSC line can be further used for studying PD pathogenesis.We thank AnnaKarin Olden, Anna Hammarberg and Marianne Juhlin, for their technical support. We are also thankful to the 'Cell Line and DNA Biobank from Patients affected by Genetic Diseases' (Istituto G. Gaslini, Genova, Italy) and the 'Parkinson Institute Biobank, members of the Telethon Network of Genetic Biobanks (http://biobanknetwork.telethon.it; project no. GTB12001) funded by Telethon Italy, for providing fibroblast samples. This work was supported by the Strategic Research Environment MultiPark at Lund University, the Swedish Research Council (grant 2015-03684 to LR), Finnish Cultural Foundation (grant 00161167 to YP), Portuguese Foundation for Science and Technology for the doctoral fellowship - PDE/BDE/113598/2015 to AM and IF Starting and Development Grant to LP and AJS (IF/01079/2014 and IF/00111/2013)