PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (1077)
 

Clipboard (0)
None

Select a Filter Below

Journals
more »
Year of Publication
more »
3.  Acquisition of internal models of motor tasks in children with autism 
Brain  2008;131(11):2894-2903.
Children with autism exhibit a host of motor disorders including poor coordination, poor tool use and delayed learning of complex motor skills like riding a tricycle. Theory suggests that one of the crucial steps in motor learning is the ability to form internal models: to predict the sensory consequences of motor commands and learn from errors to improve performance on the next attempt. The cerebellum appears to be an important site for acquisition of internal models, and indeed the development of the cerebellum is abnormal in autism. Here, we examined autistic children on a range of tasks that required a change in the motor output in response to a change in the environment. We first considered a prism adaptation task in which the visual map of the environment was shifted. The children were asked to throw balls to visual targets with and without the prism goggles. We next considered a reaching task that required moving the handle of a novel tool (a robotic arm). The tool either imposed forces on the hand or displaced the cursor associated with the handle position. In all tasks, the children with autism adapted their motor output by forming a predictive internal model, as exhibited through after-effects. Surprisingly, the rates of acquisition and washout were indistinguishable from normally developing children. Therefore, the mechanisms of acquisition and adaptation of internal models in self-generated movements appeared normal in autism. Sparing of adaptation suggests that alternative mechanisms contribute to impaired motor skill development in autism. Furthermore, the findings may have therapeutic implications, highlighting a reliable mechanism by which children with autism can most effectively alter their behaviour.
doi:10.1093/brain/awn226
PMCID: PMC2577807  PMID: 18819989
reach adaptation; prism adaptation; motor control; autism
4.  Depression after status epilepticus: behavioural and biochemical deficits and effects of fluoxetine 
Brain  2008;131(8):2071-2083.
Depression represents one of the most common comorbidities in patients with epilepsy. However, the mechanisms of depression in epilepsy patients are poorly understood. Establishment of animal models of this comorbidity is critical for both understanding the mechanisms of the condition, and for preclinical development of effective therapies. The current study examined whether a commonly used animal model of temporal lobe epilepsy (TLE) is characterized by behavioural and biochemical alterations involved in depression. Male Wistar rats were subjected to LiCl and pilocarpine status epilepticus (SE). The development of chronic epileptic state was confirmed by the presence of spontaneous seizures and by enhanced brain excitability. Post-SE animals exhibited increase in immobility time under conditions of forced swim test (FST) which was indicative of despair-like state, and loss of taste preference in saccharin solution consumption test which pointed to the symptomatic equivalence of anhedonia. Biochemical studies revealed compromised serotonergic transmission in the raphe-hippocampal serotonergic pathway: decrease of serotonin (5-HT) concentration and turnover in the hippocampus, measured by high performance liquid chromatography, and decrease of 5-HT release from the hippocampus in response to raphe stimulation, measured by fast cyclic voltammetry. Administration of fluoxetine (FLX, 20 mg/kg/day for 10 days) to naive animals significantly shortened immobility time under conditions of FST, and inhibited 5-HT turnover in the hippocampus. In post-SE rats FLX treatment led to a further decrease of hippocampal 5-HT turnover; however, performance in FST was not improved. At the same time, FLX reversed SE-induced increase in brain excitability. In summary, our studies provide initial evidence that post-SE model of TLE might serve as a model of the comorbidity of epilepsy and depression. The finding that behavioural equivalents of depression were resistant to an antidepressant medication suggested that depression in epilepsy might have distinct underlying mechanisms beyond alterations in serotonergic pathways.
doi:10.1093/brain/awn117
PMCID: PMC2587254  PMID: 18559371
comorbidity; depression; epilepsy; hippocampus; serotonin
5.  Depression after status epilepticus: behavioral and biochemical deficits, and effects of fluoxetine 
Brain : a journal of neurology  2008;131(Pt 8):2071-2083.
Summary
Depression represents one of the most common comorbidities in patients with epilepsy. However, the mechanisms of depression in epilepsy patients are poorly understood. Establishment of animal models of this comorbidity is critical for both understanding the mechanisms of the condition, and for preclinical development of effective therapies. The current study examined whether a commonly used animal model of temporal lobe epilepsy (TLE) is characterized by behavioral and biochemical alterations involved in depression. Male Wistar rats were subjected to LiCl and pilocarpine status epilepticus (SE). The development of chronic epileptic state was confirmed by the presence of spontaneous seizures and by enhanced brain excitability. Post-SE animals exhibited increase in immobility time under conditions of forced swim test (FST) which was indicative of despair-like state, and loss of taste preference in saccharin solution consumption test which pointed to the symptomatic equivalence of anhedonia. Biochemical studies revealed compromised serotonergic transmission in the raphe-hippocampal serotonergic pathway: decrease of serotonin (5-HT) concentration and turnover in the hippocampus, measured by high performance liquid chromatography, and decrease of 5-HT release from the hippocampus in response to raphe stimulation, measured by fast cyclic voltammetry. Administration of fluoxetine (FLX, 20 mg/kg/day for 10 days) to naïve animals significantly shortened immobility time under conditions of FST, and inhibited 5-HT turnover in the hippocampus. In post-SE rats FLX treatment led to a further decrease of hippocampal 5-HT turnover; however, performance in FST was not improved. At the same time, FLX reversed SE-induced increase in brain excitability. In summary, our studies provide initial evidence that post-SE model of TLE might serve as a model of the comorbidity of epilepsy and depression. The finding that behavioral equivalents of depression were resistant to an antidepressant medication suggested that depression in epilepsy might have distinct underlying mechanisms beyond alterations in serotonergic pathways.
doi:10.1093/brain/awn117
PMCID: PMC2587254  PMID: 18559371
Comorbidity; depression; epilepsy; hippocampus; serotonin
6.  Acquisition of internal models of motor tasks in children with autism 
Brain : a journal of neurology  2008;131(Pt 11):2894-2903.
Children with autism exhibit a host of motor disorders including poor coordination, poor tool use, and delayed learning of complex motor skills like riding a tricycle. Theory suggests that one of the crucial steps in motor learning is the ability to form internal models: to predict the sensory consequences of motor commands and learn from errors to improve performance on the next attempt. The cerebellum appears to be an important site for acquisition of internal models, and indeed the development of the cerebellum is abnormal in autism. Here, we examined autistic children on a range of tasks that required a change in the motor output in response to a change in the environment. We first considered a prism adaptation task in which the visual map of the environment was shifted. The children were asked to throw balls to visual targets with and without the prism goggles. We next considered a reaching task that required moving the handle of a novel tool (a robotic arm). The tool either imposed forces on the hand or displaced the cursor associated with the handle position. In all tasks, the children with autism adapted their motor output by forming a predictive internal model, as exhibited through after-effects. Surprisingly, the rates of acquisition and washout were indistinguishable from normally developing children. Therefore, the mechanisms of acquisition and adaptation of internal models in self-generated movements appeared normal in autism. Sparing of adaptation suggests that alternative mechanisms contribute to impaired motor skill development in autism. Furthermore, the findings may have therapeutic implications, highlighting a reliable mechanism by which children with autism can most effectively alter their behavior.
doi:10.1093/brain/awn226
PMCID: PMC2577807  PMID: 18819989
reach adaptation; prism adaptation; motor control; autism
7.  Poxvirus Decapping Enzymes Enhance Virulence by Preventing the Accumulation of dsRNA and the Induction of Innate Antiviral Responses 
Cell host & microbe  2015;17(3):320-331.
SUMMARY
Poxvirus replication involves synthesis of double stranded RNA (dsRNA), which can trigger antiviral responses by inducing phosphorylation-mediated activation of protein kinase R (PKR) and stimulating 2’5’-oligoadenylate synthetase (OAS). PKR inactivates the translation initiation factor eIF2α via phosphorylation, while OAS induces the endonuclease RNase L to degrade RNA. We show that poxvirus decapping enzymes D9 and D10, which remove caps from mRNAs, inhibit these antiviral responses by preventing dsRNA accumulation. Catalytic site mutations of D9 and D10, but not of either enzyme alone, halt vaccinia virus late protein synthesis and inhibit virus replication. Infection with the D9-D10 mutant was accompanied by massive mRNA reduction, cleavage of ribosomal RNA and phosphorylation of PKR and eIF2α that correlated with a ~15-fold increase in dsRNA compared to wild-type virus. Additionally, mouse studies show extreme attenuation of the mutant virus. Thus, vaccinia virus decapping, in addition to targeting mRNAs for degradation, prevents dsRNA accumulation and anti-viral responses.
doi:10.1016/j.chom.2015.02.002
PMCID: PMC4359750  PMID: 25766293
8.  Meta-analysis of the independent and cumulative effects of multiple genetic modifications on pig lung xenograft performance during ex vivo perfusion with human blood 
Xenotransplantation  2014;22(2):102-111.
Background
Genetically modified pigs are a promising potential source of lung xenografts. Ex-vivo xenoperfusion is an effective platform for testing the effect of new modifications, but typical experiments are limited by testing of a single genetic intervention and small sample sizes. The purpose of this study was to analyze the individual and aggregate effects of donor genetic modifications on porcine lung xenograft survival and injury in an extensive pig lung xenoperfusion series.
Methods
Data from 157 porcine lung xenoperfusion experiments using otherwise unmodified heparinized human blood were aggregated as either continuous or dichotomous variables. Lungs were wild type in 17 perfusions (11% of the study group), while 31 lungs (20% of the study group) had 1 genetic modification, 40 lungs (39%) had 2, and 47 lungs (30%) had 3 or more modifications. The primary endpoint was functional lung survival to 4 hours of perfusion. Secondary analyses evaluated previously identified markers associated with known lung xenograft injury mechanisms. In addition to comparison among all xenografts grouped by survival status, a subgroup analysis was performed of lungs incorporating the GalTKO.hCD46 genotype.
Results
Each increase in the number of genetic modifications was associated with additional prolongation of lung xenograft survival. Lungs that exhibited survival to 4 hours generally had reduced platelet activation and thrombin generation. GalTKO and the expression of hCD46, HO-1, hCD55 or hEPCR were associated with improved survival. hTBM, HLA-E, and hCD39 were associated with no significant effect on the primary outcome.
Conclusion
This meta-analysis of an extensive lung xenotransplantation series demonstrates that increasing the number of genetic modifications targeting known xenogeneic lung injury mechanisms is associated with incremental improvements in lung survival. While more detailed mechanistic studies are needed to explore the relationship between gene expression and pathway-specific injury, and explore why some genes apparently exhibit neutral (hTBM, HLA-E) or inconclusive (CD39) effects, GalTKO, hCD46, HO-1, hCD55, and hEPCR modifications were associated with significant lung xenograft protection. This analysis supports the hypothesis that multiple genetic modifications targeting different known mechanisms of xenograft injury will be required to optimize lung xenograft survival.
doi:10.1111/xen.12149
PMCID: PMC4390422  PMID: 25470239
9.  Magnetic field dependent stability and quench behavior and degradation limits in conduction-cooled MgB2 wires and coils 
Long lengths of metal/MgB2 composite conductors with high critical current density (Jc), fabricated by the power-in-tube (PIT) process, have recently become commercially available. Owing to its electromagnetic performance in the 20 K – 30 K range and relatively low cost, MgB2 may be attractive for a variety of applications. One of the key issues for magnet design is stability and quench protection, so the behavior of MgB2 wires and magnets must be understood before large systems can emerge. In this work, the stability and quench behavior of several conduction-cooled MgB2 wires are studied. Measurements of the minimum quench energy and normal zone propagation velocity are performed on short samples in a background magnetic field up to 3 T and on coils in self-field and the results are explained in terms of variations in the conductor architecture, electrical transport behavior, operating conditions (transport current and background magnetic field) and experimental setup (short sample vs small coil). Furthermore, one coil is quenched repeatedly with increasing hot-spot temperature until Jc is decreased. It is found that degradation during quenching correlates directly with temperature and not with peak voltage; a safe operating temperature limit of 260 K at the surface is identified.
doi:10.1088/0953-2048/28/3/035015
PMCID: PMC4394391  PMID: 25883414
10.  Single genome amplification and standard bulk PCR yield HIV-1 envelope products with similar genotypic and phenotypic characteristics 
Recent studies suggest that single genome amplification (SGA) as compared to standard bulk PCR and virus stocks from 293T transfection versus short term passage in peripheral blood mononuclear cells (PBMC) yield a less biased representation of HIV-1 envelope characteristics. In 9 different subjects, genetic diversity, divergence, and population structure was not significantly different among SGA or bulk PCR amplified envelope V1–V3 segments. In these subjects, 293T transfection derived virus stocks with SGA or bulk PCR amplified envelopes had similar infectivity, replication kinetics, co-receptor usage, and neutralization susceptibility. While PBMC passage as compared to the 293T derived virus stocks had similar co-receptor usage, PBMC viruses were less neutralization susceptible to some specific antibodies. Our results suggest that the method of envelope sequence amplification, either SGA or bulk PCR, does not have a significant impact on the genotypic and phenotypic properties of the virus envelope quasispecies.
doi:10.1016/j.jviromet.2015.01.006
PMCID: PMC4394631  PMID: 25681527
HIV-1; envelope; single genome amplification; diversity; replication; neutralization
11.  Factors Predictive of Corneal Graft Survival in the Cornea Donor Study 
JAMA ophthalmology  2015;133(3):246-254.
Importance
The Cornea Donor Study (CDS) showed that donor age is not a factor in survival of most penetrating keratoplasties for endothelial disease. Secondary analyses confirm the importance of surgical indication and presence of glaucoma in outcomes at 10 years.
Objective
To assess the relationship between donor and recipient factors and corneal graft survival in the CDS.
Design
Multi-center prospective, double-masked, controlled clinical trial
Setting
105 surgeons from eighty clinical sites enrolled participants and forty-three eye banks provided corneas.
Participants
1090 subjects undergoing corneal transplantation for a moderate risk condition, principally Fuchs’ dystrophy or pseudophakic/aphakic corneal edema (PACE)
Intervention(s) for Clinical Trials or Exposure(s) for observational studies
Corneas from donors <66 years or ≥ 66 years were assigned, double-masked to donor age. Surgery and post-operative care were performed according to surgeons’ usual routines. Subjects were followed for up to twelve years.
Main Outcome Measure(s)
Graft failure defined as a regraft or a cloudy cornea for 3 consecutive months.
Results
The 10-year graft failure rate was higher in cases with PACE than with Fuchs’ dystrophy (37% versus 20%, p < 0.001) and in cases with a history of glaucoma prior to penetrating keratoplasty, particularly with prior glaucoma surgery (58% with prior glaucoma surgery and medications at time of surgery versus 22% with no history of glaucoma, p<0.001). There were trends towards increased graft failure in recipients who were older (p=0.04), African-American (p=0.11), or had a smoking history (p=0.02). Lower endothelial cell density (ECD) and higher corneal thickness (CT) at 6 months, 1 year, and 5 years were associated with subsequent graft failure (p=0.04 to <0.001).
Conclusions and Relevance
Most penetrating corneal grafts for Fuchs’ dystrophy or PACE remain clear at 10 years. The risk of failure is greater for those with PACE and when there is a history of glaucoma. ECD and CT measurements during the course of post-keratoplasty follow up are associated with risk of failure. However, even with very low ECD and high CT at 5 years, most corneas remain clear at 10 years.
doi:10.1001/jamaophthalmol.2014.3923
PMCID: PMC4394864  PMID: 25322173
12.  Tissue Engineered Constructs: Perspectives on Clinical Translation 
Annals of biomedical engineering  2015;43(3):796-804.
In this article, a “bedside to bench and back” approach for developing tissue engineered medical products (TEMPs) for clinical applications is reviewed. The driving force behind this approach is unmet clinical needs. Preclinical research, both in vitro and in vivo using small and large animal models, will help find solutions to key research questions. In clinical research, ethical issues regarding the use of cells and tissues, their sources, donor consent, as well as clinical trials are important considerations. Regulatory issues, at both institutional and government levels, must be addressed prior to the translation of TEMPs to clinical practice. TEMPs are regulated as drugs, biologics, devices, or combination products by the US Food and Drug Administration (FDA). Depending on the mode of regulation, applications for TEMP introduction must be filed with the FDA to demonstrate safety and effectiveness in premarket clinical studies, followed by 510(k) premarket clearance or premarket approval (for medical devices), biologics license application approval (for biologics), or New Drug Application approval (for drugs). A case study on nerve cuffs is presented to illustrate the regulatory process. Finally, perspectives on commercialization such as finding a company partner and funding issues, as well as physician culture change, are presented.
doi:10.1007/s10439-015-1280-0
PMCID: PMC4394896  PMID: 25711151
Tissue engineered medical products (TEMPs); bioethics; regulatory issues; Food and Drug Administration (FDA); medical devices; commercialization
13.  Human spinal locomotor control is based on flexibly organized burst generators 
Brain  2015;138(3):577-588.
Understanding the organisation of human spinal locomotor circuitry after severe CNS damage is essential for improving neurorehabilitation strategies. Danner et al. present evidence of flexibly organised burst-generating elements within the functionally isolated human lumbosacral spinal cord that generate rhythmic patterns in response to constant, repetitive epidural stimulation.
Constant drive provided to the human lumbar spinal cord by epidural electrical stimulation can cause local neural circuits to generate rhythmic motor outputs to lower limb muscles in people paralysed by spinal cord injury. Epidural spinal cord stimulation thus allows the study of spinal rhythm and pattern generating circuits without their configuration by volitional motor tasks or task-specific peripheral feedback. To reveal spinal locomotor control principles, we studied the repertoire of rhythmic patterns that can be generated by the functionally isolated human lumbar spinal cord, detected as electromyographic activity from the legs, and investigated basic temporal components shared across these patterns. Ten subjects with chronic, motor-complete spinal cord injury were studied. Surface electromyographic responses to lumbar spinal cord stimulation were collected from quadriceps, hamstrings, tibialis anterior, and triceps surae in the supine position. From these data, 10-s segments of rhythmic activity present in the four muscle groups of one limb were extracted. Such samples were found in seven subjects. Physiologically adequate cycle durations and relative extension- and flexion-phase durations similar to those needed for locomotion were generated. The multi-muscle activation patterns exhibited a variety of coactivation, mixed-synergy and locomotor-like configurations. Statistical decomposition of the electromyographic data across subjects, muscles and samples of rhythmic patterns identified three common temporal components, i.e. basic or shared activation patterns. Two of these basic patterns controlled muscles to contract either synchronously or alternatingly during extension- and flexion-like phases. The third basic pattern contributed to the observed muscle activities independently from these extensor- and flexor-related basic patterns. Each bifunctional muscle group was able to express both extensor- and flexor-patterns, with variable ratios across the samples of rhythmic patterns. The basic activation patterns can be interpreted as central drives implemented by spinal burst generators that impose specific spatiotemporally organized activation on the lumbosacral motor neuron pools. Our data thus imply that the human lumbar spinal cord circuits can form burst-generating elements that flexibly combine to obtain a wide range of locomotor outputs from a constant, repetitive input. It may be possible to use this flexibility to incorporate specific adaptations to gait and stance to improve locomotor control, even after severe central nervous system damage.
doi:10.1093/brain/awu372
PMCID: PMC4408427  PMID: 25582580
central pattern generation; epidural spinal cord stimulation; human; modular organization; spinal cord injury
15.  Continuous motion scan ptychography: characterization for increased speed in coherent x-ray imaging 
Optics Express  2015;23(5):5438-5451.
Ptychography is a coherent diffraction imaging (CDI) method for extended objects in which diffraction patterns are acquired sequentially from overlapping coherent illumination spots. The object’s complex transmission function can be reconstructed from those diffraction patterns at a spatial resolution limited only by the scattering strength of the object and the detector geometry. Most experiments to date have positioned the illumination spots on the sample using a move-settle-measure sequence in which the move and settle steps can take longer to complete than the measure step. We describe here the use of a continuous “fly-scan” mode for ptychographic data collection in which the sample is moved continuously, so that the experiment resembles one of integrating the diffraction patterns from multiple probe positions. This allows one to use multiple probe mode reconstruction methods to obtain an image of the object and also of the illumination function. We show in simulations, and in x-ray imaging experiments, some of the characteristics of fly-scan ptychography, including a factor of 25 reduction in the data acquisition time. This approach will become increasingly important as brighter x-ray sources are developed, such as diffraction limited storage rings.
doi:10.1364/OE.23.005438
PMCID: PMC4394751  PMID: 25836777
(100.5070) Phase retrieval; (100.3010) Image reconstruction techniques; (180.5810) Scanning microscopy; (180.7460) X-ray microscopy
16.  Compensation of spectral and RF errors in swept-source OCT for high extinction complex demodulation 
Optics Express  2015;23(5):5508-5520.
We provide a framework for compensating errors within passive optical quadrature demodulation circuits used in swept-source optical coherence tomography (OCT). Quadrature demodulation allows for detection of both the real and imaginary components of an interference fringe, and this information separates signals from positive and negative depth spaces. To achieve a high extinction (∼60 dB) between these positive and negative signals, the demodulation error must be less than 0.1% in amplitude and phase. It is difficult to construct a system that achieves this low error across the wide spectral and RF bandwidths of high-speed swept-source systems. In a prior work, post-processing methods for removing residual spectral errors were described. Here, we identify the importance of a second class of errors originating in the RF domain, and present a comprehensive framework for compensating both spectral and RF errors. Using this framework, extinctions >60 dB are demonstrated. A stability analysis shows that calibration parameters associated with RF errors are accurate for many days, while those associated with spectral errors must be updated prior to each imaging session. Empirical procedures to derive both RF and spectral calibration parameters simultaneously and to update spectral calibration parameters are presented. These algorithms provide the basis for using passive optical quadrature demodulation circuits with high speed and wide-bandwidth swept-source OCT systems.
doi:10.1364/OE.23.005508
PMCID: PMC4394752  PMID: 25836784
(110.4500) Optical coherence tomography; (120.3180) Interferometry; (100.0100) Image processing
17.  Sequential domain assembly of ribosomal protein S3 drives 40S subunit maturation 
Nature Communications  2016;7:10336.
Eukaryotic ribosomes assemble by association of ribosomal RNA with ribosomal proteins into nuclear precursor particles, which undergo a complex maturation pathway coordinated by non-ribosomal assembly factors. Here, we provide functional insights into how successive structural re-arrangements in ribosomal protein S3 promote maturation of the 40S ribosomal subunit. We show that S3 dimerizes and is imported into the nucleus with its N-domain in a rotated conformation and associated with the chaperone Yar1. Initial assembly of S3 with 40S precursors occurs via its C-domain, while the N-domain protrudes from the 40S surface. Yar1 is replaced by the assembly factor Ltv1, thereby fixing the S3 N-domain in the rotated orientation and preventing its 40S association. Finally, Ltv1 release, triggered by phosphorylation, and flipping of the S3 N-domain into its final position results in the stable integration of S3. Such a stepwise assembly may represent a new paradigm for the incorporation of ribosomal proteins.
Ribosome biogenesis involves the hierarchical assembly of several proteins and RNA components. Here the authors describe a mechanism for ribosomal protein S3 incorporation into 40S ribosomal subunits that involves S3 dimerization and stepwise incorporation of two distinct S3 interaction domains coupled to release of ribosomal maturation factors.
doi:10.1038/ncomms10336
PMCID: PMC4740875  PMID: 26831757
18.  Evidence that ubiquitylated H2B corrals hDot1L on the nucleosomal surface to induce H3K79 methylation 
Nature Communications  2016;7:10589.
Ubiquitylation of histone H2B at lysine 120 (H2B-Ub), a post-translational modification first discovered in 1980, plays a critical role in diverse nuclear processes including the regulation of transcription and DNA damage repair. Herein, we use a suite of protein chemistry methods to explore how H2B-Ub stimulates hDot1L-mediated methylation of histone H3 on lysine 79 (H3K79me). By using semisynthetic ‘designer' chromatin containing H2B-Ub bearing a site-specifically installed photocrosslinker, here we report an interaction between a functional hotspot on ubiquitin and the N-terminus of histone H2A. Our biochemical studies indicate that this interaction is required for stimulation of hDot1L activity and leads to a repositioning of hDot1L on the nucleosomal surface, which likely places the active site of the enzyme proximal to H3K79. Collectively, our data converge on a possible mechanism for hDot1L stimulation in which H2B-Ub physically ‘corrals' the enzyme into a productive binding orientation.
The ubiquitylation of histone H2B on lysine 120 is an important modification with roles in a diverse range of nuclear processes. Here, the authors use 'designer' chromatin to show that H2B-ub orients hDot1L into the correct position for activation.
doi:10.1038/ncomms10589
PMCID: PMC4740876  PMID: 26830124
19.  Genetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum 
Nature Communications  2016;7:10561.
DNA methylation (DNAm) levels lend themselves for defining an epigenetic biomarker of aging known as the ‘epigenetic clock'. Our genome-wide association study (GWAS) of cerebellar epigenetic age acceleration identifies five significant (P<5.0 × 10−8) SNPs in two loci: 2p22.1 (inside gene DHX57) and 16p13.3 near gene MLST8 (a subunit of mTOR complex 1 and 2). We find that the SNP in 16p13.3 has a cis-acting effect on the expression levels of MLST8 (P=6.9 × 10−18) in most brain regions. In cerebellar samples, the SNP in 2p22.1 has a cis-effect on DHX57 (P=4.4 × 10−5). Gene sets found by our GWAS analysis of cerebellar age acceleration exhibit significant overlap with those of Alzheimer's disease (P=4.4 × 10−15), age-related macular degeneration (P=6.4 × 10−6), and Parkinson's disease (P=2.6 × 10−4). Overall, our results demonstrate the utility of a new paradigm for understanding aging and age-related diseases: it will be fruitful to use epigenetic tissue age as endophenotype in GWAS.
This genome-wide association study identifies five significant SNPs in two loci which are associated with the epigenetic age of post-mortem cerebellar tissue according to a DNA methylation based biomarker of human aging.
doi:10.1038/ncomms10561
PMCID: PMC4740877  PMID: 26830004
20.  Supercurrent in van der Waals Josephson junction 
Nature Communications  2016;7:10616.
Supercurrent flow between two superconductors with different order parameters, a phenomenon known as the Josephson effect, can be achieved by inserting a non-superconducting material between two superconductors to decouple their wavefunctions. These Josephson junctions have been employed in fields ranging from digital to quantum electronics, yet their functionality is limited by the interface quality and use of non-superconducting material. Here we show that by exfoliating a layered dichalcogenide (NbSe2) superconductor, the van der Waals (vdW) contact between the cleaved surfaces can instead be used to construct a Josephson junction. This is made possible by recent advances in vdW heterostructure technology, with an atomically flat vdW interface free of oxidation and inter-diffusion achieved by eliminating all heat treatment during junction preparation. Here we demonstrate that this artificially created vdW interface provides sufficient decoupling of the wavefunctions of the two NbSe2 crystals, with the vdW Josephson junction exhibiting a high supercurrent transparency.
Van der Waals heterostructures, made of stacked two-dimensional materials, hold promise for modern electronics. Here, the authors build van der Waals junction between superconducting two-dimensional materials and reveal that the junction works as Josephson junction.
doi:10.1038/ncomms10616
PMCID: PMC4740878  PMID: 26830754
21.  Topological nodal-line fermions in spin-orbit metal PbTaSe2 
Nature Communications  2016;7:10556.
Topological semimetals can support one-dimensional Fermi lines or zero-dimensional Weyl points in momentum space, where the valence and conduction bands touch. While the degeneracy points in Weyl semimetals are robust against any perturbation that preserves translational symmetry, nodal lines require protection by additional crystalline symmetries such as mirror reflection. Here we report, based on a systematic theoretical study and a detailed experimental characterization, the existence of topological nodal-line states in the non-centrosymmetric compound PbTaSe2 with strong spin-orbit coupling. Remarkably, the spin-orbit nodal lines in PbTaSe2 are not only protected by the reflection symmetry but also characterized by an integer topological invariant. Our detailed angle-resolved photoemission measurements, first-principles simulations and theoretical topological analysis illustrate the physical mechanism underlying the formation of the topological nodal-line states and associated surface states for the first time, thus paving the way towards exploring the exotic properties of the topological nodal-line fermions in condensed matter systems.
Nodal-line shaped bands appearing near the Fermi level host unique properties in topological matter, which has yet to be confirmed in real materials. Here, the authors report the existence of topological nodal-line states in the non-centrosymmetric single-crystalline spin-orbit semimetal PbTaSe2.
doi:10.1038/ncomms10556
PMCID: PMC4740879  PMID: 26829889
22.  Joint mouse–human phenome-wide association to test gene function and disease risk 
Nature Communications  2016;7:10464.
Phenome-wide association is a novel reverse genetic strategy to analyze genome-to-phenome relations in human clinical cohorts. Here we test this approach using a large murine population segregating for ∼5 million sequence variants, and we compare our results to those extracted from a matched analysis of gene variants in a large human cohort. For the mouse cohort, we amassed a deep and broad open-access phenome consisting of ∼4,500 metabolic, physiological, pharmacological and behavioural traits, and more than 90 independent expression quantitative trait locus (QTL), transcriptome, proteome, metagenome and metabolome data sets—by far the largest coherent phenome for any experimental cohort (www.genenetwork.org). We tested downstream effects of subsets of variants and discovered several novel associations, including a missense mutation in fumarate hydratase that controls variation in the mitochondrial unfolded protein response in both mouse and Caenorhabditis elegans, and missense mutations in Col6a5 that underlies variation in bone mineral density in both mouse and human.
Phenome-wide association is a novel method that links sequence variants to a spectrum of phenotypes and diseases. Here the authors generate detailed mouse genetic and phenome data which links their phenome-wide association study (PheWAS) of mouse to corresponding PheWAS in human.
doi:10.1038/ncomms10464
PMCID: PMC4740880  PMID: 26833085
23.  A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function 
Nature Communications  2016;7:10591.
Nature has developed striking light-powered proteins such as bacteriorhodopsin, which can convert light energy into conformational changes for biological functions. Such natural machines are a great source of inspiration for creation of their synthetic analogues. However, synthetic molecular machines typically operate at the nanometre scale or below. Translating controlled operation of individual molecular machines to a larger dimension, for example, to 10–100 nm, which features many practical applications, is highly important but remains challenging. Here we demonstrate a light-driven plasmonic nanosystem that can amplify the molecular motion of azobenzene through the host nanostructure and consequently translate it into reversible chiroptical function with large amplitude modulation. Light is exploited as both energy source and information probe. Our plasmonic nanosystem bears unique features of optical addressability, reversibility and modulability, which are crucial for developing all-optical molecular devices with desired functionalities.
Controlled operation of individual molecular machines on a larger scale, 10-100 nm, remains challenging. Here, Kuzyk et al. demonstrate a light-driven plasmonic nanosystem that can amplify the molecular motion of azobenzene through a host nanostructure and translates it into reversible chiroptical response.
doi:10.1038/ncomms10591
PMCID: PMC4740900  PMID: 26830310
24.  Exceptional damage-tolerance of a medium-entropy alloy CrCoNi at cryogenic temperatures 
Nature Communications  2016;7:10602.
High-entropy alloys are an intriguing new class of metallic materials that derive their properties from being multi-element systems that can crystallize as a single phase, despite containing high concentrations of five or more elements with different crystal structures. Here we examine an equiatomic medium-entropy alloy containing only three elements, CrCoNi, as a single-phase face-centred cubic solid solution, which displays strength-toughness properties that exceed those of all high-entropy alloys and most multi-phase alloys. At room temperature, the alloy shows tensile strengths of almost 1 GPa, failure strains of ∼70% and KJIc fracture-toughness values above 200 MPa  m1/2; at cryogenic temperatures strength, ductility and toughness of the CrCoNi alloy improve to strength levels above 1.3 GPa, failure strains up to 90% and KJIc values of 275 MPa  m1/2. Such properties appear to result from continuous steady strain hardening, which acts to suppress plastic instability, resulting from pronounced dislocation activity and deformation-induced nano-twinning.
High-entropy alloys derive their properties from being multi-element systems that can crystallize as a single phase. Here, the authors examine a medium-entropy alloy, CrCoNi, which displays strength-toughness properties exceeding those of high-entropy alloys and resulting from steady strain hardening.
doi:10.1038/ncomms10602
PMCID: PMC4740901  PMID: 26830651
25.  Therapeutically engineered induced neural stem cells are tumour-homing and inhibit progression of glioblastoma 
Nature Communications  2016;7:10593.
Transdifferentiation (TD) is a recent advancement in somatic cell reprogramming. The direct conversion of TD eliminates the pluripotent intermediate state to create cells that are ideal for personalized cell therapy. Here we provide evidence that TD-derived induced neural stem cells (iNSCs) are an efficacious therapeutic strategy for brain cancer. We find that iNSCs genetically engineered with optical reporters and tumouricidal gene products retain the capacity to differentiate and induced apoptosis in co-cultured human glioblastoma cells. Time-lapse imaging shows that iNSCs are tumouritropic, homing rapidly to co-cultured glioblastoma cells and migrating extensively to distant tumour foci in the murine brain. Multimodality imaging reveals that iNSC delivery of the anticancer molecule TRAIL decreases the growth of established solid and diffuse patient-derived orthotopic glioblastoma xenografts 230- and 20-fold, respectively, while significantly prolonging the median mouse survival. These findings establish a strategy for creating autologous cell-based therapies to treat patients with aggressive forms of brain cancer.
Neural stem cells have a tropism for glioblastoma. Here the authors employ fibroblasts directly reprogrammed into induced neural stem cells and loaded with cytotoxic molecules to migrate to xenotransplanted brain tumours in mice, achieving tumour shrinkage and prolonged survival.
doi:10.1038/ncomms10593
PMCID: PMC4740908  PMID: 26830441

Results 1-25 (1077)