| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Reinius, Björn, et al.
(author)
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Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse
- 2010
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11:1, s. 614-
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Journal article (peer-reviewed)abstract
- Background: Sexual dimorphism in brain gene expression has been recognized in several animal species.However, the relevant regulatory mechanisms remain poorly understood. To investigatewhether sex-biased gene expression in mammalian brain is globally regulated or locallyregulated in diverse brain structures, and to study the genomic organisation of brain-expressedsex-biased genes, we performed a large scale gene expression analysis of distinct brainregions in adult male and female mice. Results: This study revealed spatial specificity in sex-biased transcription in the mouse brain, andidentified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampusand 31 in the eye. Genes located on sex chromosomes were consistently over-represented inall brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealedY-encoded male-biased transcripts and X-encoded female-biased transcripts known to escapeX-inactivation. In addition, we identified novel coding and non-coding X-linked genes withfemale-biased expression in multiple tissues. Interestingly, the chromosomal positions of allof the female-biased non-coding genes are in close proximity to protein-coding genes thatescape X-inactivation. This defines X-chromosome domains each of which contains a codingand a non-coding female-biased gene. Lack of repressive chromatin marks in non-codingtranscribed loci supports the possibility that they escape X-inactivation. Moreover, RNADNAcombined FISH experiments confirmed the biallelic expression of one such noveldomain. Conclusion: This study demonstrated that the amount of genes with sex-biased expression variesbetween individual brain regions in mouse. The sex-biased genes identified are localized onmany chromosomes. At the same time, sexually dimorphic gene expression that is common toseveral parts of the brain is mostly restricted to the sex chromosomes. Moreover, the studyuncovered multiple female-biased non-coding genes that are non-randomly co-localized onthe X-chromosome with protein-coding genes that escape X-inactivation. This raises thepossibility that expression of long non-coding RNAs may play a role in modulating geneexpression in domains that escape X-inactivation in mouse.
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| 4. |
- Vogel, Jacob W., et al.
(author)
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Four distinct trajectories of tau deposition identified in Alzheimer’s disease
- 2021
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In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:5, s. 871-881
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Journal article (peer-reviewed)abstract
- Alzheimer’s disease (AD) is characterized by the spread of tau pathology throughout the cerebral cortex. This spreading pattern was thought to be fairly consistent across individuals, although recent work has demonstrated substantial variability in the population with AD. Using tau-positron emission tomography scans from 1,612 individuals, we identified 4 distinct spatiotemporal trajectories of tau pathology, ranging in prevalence from 18 to 33%. We replicated previously described limbic-predominant and medial temporal lobe-sparing patterns, while also discovering posterior and lateral temporal patterns resembling atypical clinical variants of AD. These ‘subtypes’ were stable during longitudinal follow-up and were replicated in a separate sample using a different radiotracer. The subtypes presented with distinct demographic and cognitive profiles and differing longitudinal outcomes. Additionally, network diffusion models implied that pathology originates and spreads through distinct corticolimbic networks in the different subtypes. Together, our results suggest that variation in tau pathology is common and systematic, perhaps warranting a re-examination of the notion of ‘typical AD’ and a revisiting of tau pathological staging. © 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.
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| 5. |
- Zhou, XP, et al.
(author)
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Non-coding variability at the APOE locus contributes to the Alzheimer's risk
- 2019
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 3310-
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Journal article (peer-reviewed)abstract
- Alzheimer’s disease (AD) is a leading cause of mortality in the elderly. While the coding change of APOE-ε4 is a key risk factor for late-onset AD and has been believed to be the only risk factor in the APOE locus, it does not fully explain the risk effect conferred by the locus. Here, we report the identification of AD causal variants in PVRL2 and APOC1 regions in proximity to APOE and define common risk haplotypes independent of APOE-ε4 coding change. These risk haplotypes are associated with changes of AD-related endophenotypes including cognitive performance, and altered expression of APOE and its nearby genes in the human brain and blood. High-throughput genome-wide chromosome conformation capture analysis further supports the roles of these risk haplotypes in modulating chromatin states and gene expression in the brain. Our findings provide compelling evidence for additional risk factors in the APOE locus that contribute to AD pathogenesis.
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| 6. |
- Anasori, Babak, et al.
(author)
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A Tungsten-Based Nanolaminated Ternary Carbide: (W,Ti)(4)C4-x
- 2019
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In: Inorganic Chemistry. - : AMER CHEMICAL SOC. - 0020-1669 .- 1520-510X. ; 58:2, s. 1100-1106
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Journal article (peer-reviewed)abstract
- Nanolamellar transition metal carbides are gaining increasing interests because of the recent developments of their twodimensional (2D) derivatives and promising performance for a variety of applications from energy storage, catalysis to transparent conductive coatings, and medicine. To develop more novel 2D materials, new nanolaminated structures are needed. Here we report on a tungsten based nanolaminated ternary phase, (W,Ti)(4)C4-x, synthesized by an Al catalyzed reaction of W, Ti, and C powders at 1600 degrees C for 4 h, under flowing argon. X-ray and neutron diffraction, along with Z-contrast scanning transmission electron microscopy, were used to determine the atomic structure, ordering, and occupancies. This phase has a layered hexagonal structure (P6(3)/mmc) with lattice parameters, a = 3.00880(7) angstrom, and c = 19.5633(6) angstrom and a nominal chemistry of (W,Ti)(4)C4-x (actual chemistry, W2.1(1)Ti1.6(1)C2.6(1)). The structure is comprised of layers of pure W that are also twin planes with two adjacent atomic layers of mixed W and Ti, on either side. The use of Al as a catalyst for synthesizing otherwise difficult to make phases, could in turn lead to the discovery of a large family of nonstoichiometric ternary transition metal carbides, synthesized at relatively low temperatures and shorter times.
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| 7. |
- Anasori, Babak, et al.
(author)
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Experimental and theoretical characterization of ordered MAX phases Mo2TiAlC2 and Mo2Ti2AlC3
- 2015
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In: Journal of Applied Physics. - : AMER INST PHYSICS. - 0021-8979 .- 1089-7550. ; 118:9, s. 094304-
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Journal article (peer-reviewed)abstract
- Herein, we report on the phase stabilities and crystal structures of two newly discovered ordered, quaternary MAX phases-Mo2TiAlC2 and Mo2Ti2AlC3-synthesized by mixing and heating different elemental powder mixtures of mMo:(3-m) Ti:1.1Al:2C with 1.5 less than= m less than= 2.2 and 2Mo: 2Ti:1.1Al:2.7C to 1600 degrees C for 4 h under Ar flow. In general, for m greater than= 2 an ordered 312 phase, (Mo2Ti) AlC2, was the majority phase; for mless than 2, an ordered 413 phase (Mo2Ti2)AlC3, was the major product. The actual chemistries determined from X-ray photoelectron spectroscopy (XPS) are Mo2TiAlC1.7 and Mo2Ti1.9Al0.9C2.5, respectively. High resolution scanning transmission microscopy, XPS and Rietveld analysis of powder X-ray diffraction confirmed the general ordered stacking sequence to be Mo-Ti-Mo-Al-Mo-Ti-Mo for Mo2TiAlC2 and Mo-Ti-Ti-Mo-Al-Mo-Ti-Ti-Mo for Mo2Ti2AlC3, with the carbon atoms occupying the octahedral sites between the transition metal layers. Consistent with the experimental results, the theoretical calculations clearly show that M layer ordering is mostly driven by the high penalty paid in energy by having the Mo atoms surrounded by C in a face-centered configuration, i.e., in the center of the Mn+1Xn blocks. At 331 GPa and 367 GPa, respectively, the Youngs moduli of the ordered Mo2TiAlC2 and Mo2Ti2AlC3 are predicted to be higher than those calculated for their ternary end members. Like most other MAX phases, because of the high density of states at the Fermi level, the resistivity measurement over 300 to 10K for both phases showed metallic behavior. (C) 2015 AIP Publishing LLC.
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| 8. |
- Bakhit, Babak, 1983-, et al.
(author)
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Dense Ti0.67Hf0.33B1.7 thin films grown by hybrid HfB2-HiPIMS/TiB2-DCMS co-sputtering without external heating
- 2021
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In: Vacuum. - : Elsevier. - 0042-207X .- 1879-2715. ; 186
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Journal article (peer-reviewed)abstract
- There is a need for developing synthesis techniques that allow the growth of high-quality functional films at low substrate temperatures to minimize energy consumption and enable coating temperature-sensitive substrates. A typical shortcoming of conventional low-temperature growth strategies is insufficient atomic mobility, which leads to porous microstructures with impurity incorporation due to atmosphere exposure, and, in turn, poor mechanical properties. Here, we report the synthesis of dense Ti0.67Hf0.33B1.7 thin films with a hardness of ∼41.0 GPa grown without external heating (substrate temperature below ∼100 °C) by hybrid high-power impulse and dc magnetron co-sputtering (HfB2-HiPIMS/TiB2-DCMS) in pure Ar on Al2O3(0001) substrates. A substrate bias potential of −300 V is synchronized to the target-ion-rich portion of each HiPIMS pulse. The limited atomic mobility inherent to such desired low-temperature deposition is compensated for by heavy-mass ion (Hf+) irradiation promoting the growth of dense Ti0.67Hf0.33B1.7.
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| 9. |
- Bakhit, Babak, 1983-, et al.
(author)
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Multifunctional ZrB2-rich Zr1-xCrxBy thin films with enhanced mechanical, oxidation, and corrosion properties
- 2021
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In: Vacuum. - : Elsevier BV. - 0042-207X .- 1879-2715. ; 185
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Journal article (peer-reviewed)abstract
- Refractory transition-metal (TM) diborides have high melting points, excellent hardness, and good chemical stability. However, these properties are not sufficient for applications involving extreme environments that require high mechanical strength as well as oxidation and corrosion resistance. Here, we study the effect of Cr addition on the properties of ZrB2-rich Zr1-xCrxBy thin films grown by hybrid high-power impulse and dc magnetron co-sputtering (Cr-HiPIMS/ZrB2-DCMS) with a 100-V Cr-metal-ion synchronized potential. Cr metal fraction, x = Cr/(Zr+Cr), is increased from 0.23 to 0.44 by decreasing the power Pzrb2 applied to the DCMS ZrB2 target from 4000 to 2000 W, while the average power, pulse width, and frequency applied to the HiPIMS Cr target are maintained constant. In addition, y decreases from 2.18 to 1.11 as a function of Pzrb2, as a result of supplying Cr to the growing film and preferential B resputtering caused by the pulsed Cr-ion flux. ZrB2.18, Zr0.77Cr0.23B1.52, Zr0.71Cr0.29B1.42, and Zr0.68Cr0.32B1.38 2 films have hexagonal AlB2 crystal structure with a columnar nanostructure, while Zr0.64Cr0.36B1.30 and Zr0.56Cr0.44B1.11 are amorphous. All films show hardness above 30 GPa. Zr0.56Cr0.44B1.11 alloys exhibit much better toughness, wear, oxidation, and corrosion resistance than ZrB2.18. This combination of properties makes Zr0.56Cr0.44B1.11 ideal candidates for numerous strategic applications.
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| 10. |
- Bakhit, Babak, et al.
(author)
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Strategy for simultaneously increasing both hardness and toughness in ZrB2-rich Zr1-xTaxBy thin films
- 2019
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In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : A V S AMER INST PHYSICS. - 0734-2101 .- 1520-8559. ; 37:3
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Journal article (peer-reviewed)abstract
- Refractory transition-metal diborides exhibit inherent hardness. However, this is not always sufficient to prevent failure in applications involving high mechanical and thermal stress, since hardness is typically accompanied by brittleness leading to crack formation and propagation. Toughness, the combination of hardness and ductility, is required to avoid brittle fracture. Here, the authors demonstrate a strategy for simultaneously enhancing both hardness and ductility of ZrB2-rich thin films grown in pure Ar on Al2O3(0001) and Si(001) substrates at 475 degrees C. ZrB2.4 layers are deposited by dc magnetron sputtering (DCMS) from a ZrB2 target, while Zr1-xTaxBy alloy films are grown, thus varying the B/metal ratio as a function of x, by adding pulsed high-power impulse magnetron sputtering (HiPIMS) from a Ta target to deposit Zr1-xTaxBy alloy films using hybrid Ta-HiPIMS/ZrB2-DCMS sputtering with a substrate bias synchronized to the metal-rich portion of each HiPIMS pulse. The average power P-Ta (and pulse frequency) applied to the HiPIMS Ta target is varied from 0 to 1800W (0 to 300 Hz) in increments of 600W (100 Hz). The resulting boron-to-metal ratio, y = B/(Zr+Ta), in as-deposited Zr1-xTaxBy films decreases from 2.4 to 1.5 as P-Ta is increased from 0 to 1800W, while x increases from 0 to 0.3. A combination of x-ray diffraction (XRD), glancing-angle XRD, transmission electron microscopy (TEM), analytical Z-contrast scanning TEM, electron energy-loss spectroscopy, energy-dispersive x-ray spectroscopy, x-ray photoelectron spectroscopy, and atom-probe tomography reveals that all films have the hexagonal AlB2 crystal structure with a columnar nanostructure, in which the column boundaries of layers with 0 amp;lt;= x amp;lt; 0.2 are B-rich, whereas those with x amp;gt;= 0.2 are Ta-rich. The nanostructural transition, combined with changes in average column widths, results in an similar to 20% increase in hardness, from 35 to 42 GPa, with a simultaneous increase of similar to 30% in nanoindentation toughness, from 4.0 to 5.2MPa root m. Published by the AVS.
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