81 research outputs found
Autophagy in <i>Saccharomyces cerevisiae</i> requires the monomeric GTP-binding proteins, Arl1 and Ypt6
<p>Macroautophagy/autophagy is a cellular degradation process that sequesters organelles or proteins into a double-membrane structure called the phagophore; this transient compartment matures into an autophagosome, which then fuses with the lysosome or vacuole to allow hydrolysis of the cargo. Factors that control membrane traffic are also essential for each step of autophagy. Here we demonstrate that 2 monomeric GTP-binding proteins in <i>Saccharomyces cerevisiae</i>, Arl1 and Ypt6, which belong to the Arf/Arl/Sar protein family and the Rab family, respectively, and control endosome-<i>trans-</i>Golgi traffic, are also necessary for starvation-induced autophagy under high temperature stress. Using established autophagy-specific assays we found that cells lacking either <i>ARL1</i> or <i>YPT6</i>, which exhibit synthetic lethality with one another, were unable to undergo autophagy at an elevated temperature, although autophagy proceeds normally at normal growth temperature; specifically, strains lacking one or the other of these genes are unable to construct the autophagosome because these 2 proteins are required for proper traffic of Atg9 to the phagophore assembly site (PAS) at the restrictive temperature. Using degron technology to construct an inducible <i>arl1</i>Δ <i>ypt6</i>Δ double mutant, we demonstrated that cells lacking both genes show defects in starvation-inducted autophagy at the permissive temperature. We also found Arl1 and Ypt6 participate in autophagy by targeting the Golgi-associated retrograde protein (GARP) complex to the PAS to regulate the anterograde trafficking of Atg9. Our data show that these 2 membrane traffic regulators have novel roles in autophagy.</p
Additional file 1 of Inferring RNA sequence preferences for poorly studied RNA-binding proteins based on co-evolution
Supplementary Data. The excel document contains the Supplementary Data about the performances of different methods on InVitro, InVivoRay and InVivoAURA datasets, as well as the composition of each datasets (including species and RNA-binding domain information). (XLSX 32 kb
Transparent and Superamphiphobic Surfaces from Mushroom-Like Micropillar Arrays
Transparent,
superamphiphobic surfaces that repel both water and oils are prepared
from mushroom-like micropillar arrays consisting of nanoparticles
only at the top of the pillars by controlled compartment filling of
silica nanoparticles into the bottom of the polyÂ(dimethylsiloxane)
(PDMS) mold, followed by infiltration of epoxy and UV curing. Because
silica nanoparticle decorated pillar heads are more resistant to O<sub>2</sub> plasma than the polymer pillars, we can precisely control
the head size of micropillars and nanoroughness on top of the pillar
heads by varying the O<sub>2</sub> plasma time. The combination of
nanoroughness and mushroom-like micropillars leads to superhydrophobicity
and oil repellency to different organic solvents. High transparency
is achieved by increasing the spacing ratio of micropillars. Last,
we demonstrate anisotropic wetting on the hierarchical surface can
be achieved by combining photolithography, replica molding, and self-assembly
techniques
Thermodynamic Properties of Supercritical CO<sub>2</sub>/CH<sub>4</sub> Mixtures from the Virial Equation of State
Mixture virial coefficients
to seventh order are presented for
the system CO<sub>2</sub>/CH<sub>4</sub> at four supercritical temperatures:
323.15, 373.15, 473.15, and 573.15 K. Values are evaluated via the
Mayer sampling Monte Carlo method using a three-site TraPPE model
for CO<sub>2</sub> and a one-site model for CH<sub>4</sub>. The coefficients
are used to compute seven thermodynamic properties (viz., compressibility
factor, isothermal compressibility, volume expansivity, isochoric
and isobaric heat capacities, Joule–Thomson coefficient, and
speed of sound) as a function of mole fraction and density for these
temperatures. Comparison is made with corresponding data in the literature
as obtained by molecular dynamics simulation, covering densities up
to about twice the critical density. Key conclusions are as follows,
noting that some exceptions are observed in each case: (a) The virial
equation of state (VEOS) to fourth or fifth order describes all properties
to within the simulation uncertainty for densities up to at least
the critical density, and the addition of terms up to seventh order
extends this range considerably. (b) The accuracy of the VEOS is severely
diminished for conditions approaching the critical point (the present
work extends down to a reduced temperature of 1.06 for CO<sub>2</sub>), and the study of the pure component behavior suggests the critical
singularity blocks convergence for conditions at considerably higher
temperatures, albeit at correspondingly higher pressures. (c) Comparison
of the VEOS at different orders provides a reliable guide to its accuracy
at a given order, so the VEOS can provide a self-assessment of its
accuracy when independent data for comparison are unavailable. (d)
The VEOS provides a good description of the Joule–Thomson coefficient,
including the inversion point in particular. The third-order series
is needed to obtain behavior that is qualitatively correct, and the
addition of higher-order terms steadily improves the accuracy quantitatively.
(e) Under conditions where the seventh-order series is converged,
properties can be computed to a given precision with VEOS using much
less computational effort in comparison to molecular simulation
Tailoring Pore Size, Structure, and Morphology of Hierarchical Mesoporous Silica Using Diblock and Pentablock Copolymer Templates
Mesoporous materials
of tailored pore size, structure, and morphology
are of interests for a wide range of applications. It is important
to develop synthetic methods that will allow for easy processing and
facile structure modification. Here, we present the preparation of
hierarchically structured bimodal mesoporous silicas using water-soluble
polyÂ(lactic acid-<i>co</i>-glycolic acid)-<i>b</i>-polyÂ(ethylene oxide) (PLGA-<i>b</i>-PEO) diblock copolymer
and polyÂ(lactic acid-<i>co</i>-glycolic acid)-<i>b</i>-polyÂ(ethylene oxide)-<i>b</i>-polyÂ(propylene oxide)-<i>b</i>-polyÂ(ethylene oxide)-<i>b</i>-polyÂ(lactic acid-<i>co</i>-glycolic acid) (PLGA-<i>b</i>-PEO-<i>b</i>-PPO-<i>b</i>-PEO-<i>b</i>-PLGA) pentablock copolymers
as templates. The block copolymers were synthesized through a step-growth
polymerization method using a commercial Pluronic F68 macroinitiator.
Mesoporous silica samples were obtained by sol–gel chemistry
in acidic aqueous solutions. Hexagonally (<i>p</i>6<i>mm</i>) ordered mesoporous silica particles were obtained in
the presence of a PLGA-PEO diblock copolymer and exhibited bimodal
pore size distributions in the range of 2–9 nm. Core–shell
type mesoporous silica particles were obtained in the presence of
the PLGA-PEO-PPO-PEO-PLGA pentablock copolymer and exhibited a large
pore diameter up to 20 nm with distinct bimodal pore size distributions.
The pore size increased when using a longer pentablock copolymer template
in strong acid. The physicochemical properties were investigated using
small-angle X-ray scattering (SAXS), nitrogen adsorption–desorption,
transmission electron microscope (TEM), solid-state <sup>29</sup>Si
nuclear magnetic resonance (NMR), and scanning electron microscope
(SEM), respectively
In Situ Synthesis of Hybrid Aerogels from Single-Walled Carbon Nanotubes and Polyaniline Nanoribbons as Free-Standing, Flexible Energy Storage Electrodes
Hybrid aerogels consisting of interpenetrating
single-walled carbon
nanotubes and polyaniline (SWCNT/PANI) nanoribbons were prepared as
free-standing, flexible lithium ion battery (LIB) electrodes. Assisted
by camphorsulfonic acid, the anilinium cations formed complexation
with micelles of dodecylbenzene sulfonate anions within the wet SWCNT
network. Very thin PANI nanoribbons (thickness of 10–100 nm,
width of 50–1000 nm, and length of 10–20 μm) were
formed within the network after polymerization of aniline. By varying
the concentration of aniline, we were able to fine-tune the morphologies
of final PANI nanostructures, including nanoribbons, porous nanofibers,
and nanoparticles. Specifically, SWCNT/PANI nanoribbon aerogels showed
high capacity (185 mAh/g) and good cycle performance (up to 200 times),
which could be attributed to synergistic effects of efficient ion/electron
transport within the 3D carbon nanotubes network, shortened ion diffusion
distance and optimized strain relaxation from nanoribbons and nanotubes,
and effective penetration of electrolyte within interconnected nanopores
in the network
Arrangement and SERS Applications of Nanoparticle Clusters Using Liquid Crystalline Template
Manipulation
of nanomaterials such as nanoparticles (NPs) and nanorods (NRs) to
make clusters is of significant interest in material science and nanotechnology
due to the unusual collective opto-electric properties in such structures
that cannot be found in the individual NPs. This work demonstrates
an effective way to arrange NP clusters (NPCs) to make the desired
arrays based on removable and NP-guidable liquid crystalline template
using sublimation and reconstruction phenomenon. The position of the
NPCs is precisely controlled by the defect structure of the liquid
crystal (LC), namely toric focal conic domains (TFCDs), during thermal
annealing to construct the LC and corresponding NPC structures. As
a proof of concept, the surface-enhanced Raman scattering (SERS) activity
of a fabricated array of gold nanorod (GNR) clusters is measured and
shown to have highly sensitive detection characteristics essential
for potential sensing applications
Table_1_Association between weight change and risk of metabolic abnormalities in non-overweight/obese and overweight/obese population: A retrospective cohort study among Chinese adults.docx
ObjectivesTo explore the effects of weight change on the risk of metabolic abnormalities in the Chinese population.MethodsA total of 1895 metabolically healthy adults aged 21–78 years completed anthropometric and biological measurements at baseline (2012) and at an eight year follow-up (2020). Based on absolute weight change and relative weight change, the participants were split into five classes. A Cox proportional hazards regression model was used to estimate the relative risk (RR) and 95% confidence intervals (95% CI) for the risk of metabolic abnormalities using stable weight as the reference group. Stratified analysis was used to explore this relationship in participants with different baseline body mass index (BMI) levels.ResultsDuring the follow-up period, 35.41% of the participants retained a stable weight, and 10.71% had metabolic abnormalities. After covariate adjustment, for every kilogram gained over eight years, the risk of developing metabolic abnormalities increased by 22% (RR: 1.094; 95% CI: 1.063–1.127). Compared with stable weight participants, weight gain of 2–4 Kg and weight gain ≥ 4 Kg exhibited significantly higher risks of metabolic abnormalities, with RR of 1.700 (95% CI 1.150–2.513) and 1.981 (95% CI 1.372–2.859), respectively. A weight gain of ≥ 4 Kg had an opposite effect on the overweight/obesity and non-overweight/obesity groups, with an increased risk of metabolic abnormalities only in the non-overweight/obesity group (RR, 2.291; 95% CI, 1.331–3.942). Moreover, weight loss ≥ 4 Kg significantly reduced the risk of metabolic abnormalities only among overweight/obese adults (RR 0.373; 95% CI 0.154–0.906). Similar results were observed in relative body weight change analyses.ConclusionsLong-term excessive body weight gain is positively associated with an increased risk of metabolic abnormalities among adults with non-overweight/obesity, whereas long-term body weight loss is a protective factor for metabolic health among adults with overweight/obesity.</p
MicroRNA expression profiling involved in MC-LR-induced hepatotoxicity using high-throughput sequencing analysis
<p>Microcystin-LR (MC-LR), the most common microcystin (MC) present in water is known to pose a significant threat to human health especially hepatotoxicity. However, the specific molecular mechanisms underlying MC-LR-induced hepatic cellular damage still remain to be determined. MicroRNAs (miRNAs) are known to play key roles in cellular processes including development, cell proliferation and responsiveness to stress. Thus, this study aimed to examine, whether miRNAs were involved in the observed MC-LR-mediated liver damage using miRNA profiling of a human normal liver cell line HL7702 using high-throughput sequencing techniques. Protein phosphatase 2A (PP2A) activity, an established biomarker of microcystin toxicity, was determined 24 hr following treatment with the algal toxin to confirm responsiveness. Data demonstrated that MC-LR significantly inhibited PP2A activity in a concentration-dependent manner with inhibitory concentration (IC<sub>50</sub>) value of 4.6 μM. Compared with control cells, treatment with MC-LR at concentrations of 1, 2.5, 5 or 10 μM significantly modified expression of levels of 3, 10, 9, and 99 miRNAs, respectively. Expression levels of miR-15b-3p were significantly increased in all 4 treatment groups, while miR-4521 expression levels were markedly reduced. In the case of miR-451a, 1, 5 or 10 μM also significantly lowered expression levels. However, a significant rise in miR-451a was noted in cells exposed to 2.5 μM toxin. The results obtained from miRNA differential expression levels were confirmed by real-time fluorescent quantitative PCR (qPCR). Gene Ontology (GO) enrichment analysis of hepatic cells demonstrated that miRNAs significantly altered were involved in systems development, metabolism, and protein binding. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis data showed that target genes of differentially expressed miRNAs in liver cells predominantly participated in mechanistic target of rapamycin kinase (mTOR), Ras, Ras-related protein 1 (Rap1), hypoxia inducible factor 1 (HIF-1), and cancer development. In summary, evidence indicates that MC-LR-induced hepatotoxicity may be associated with alterations in miRNAs. Evidence indicates that alterations in miR-451a, miR-4521 and miR-15b-3p may be involved in the observed MC-LR- induced hepatotoxicity</p
- …