The Spatio-Temporal Structure of Spiral-Defect Chaos

We present a study of the recently discovered spatially-extended chaotic state known as spiral-defect chaos, which occurs in low-Prandtl-number, large-aspect-ratio Rayleigh-Benard convection. We employ the modulus squared of the space-time Fourier transform of time series of two-dimensional shadowgraph images to construct the structure factor ${S}({\vec k},\omega )$. This analysis is used to characterize the average spatial and temporal scales of the chaotic state. We find that the correlation length and time can be described by power-law dependences on the reduced Rayleigh number ${\epsilon}$. These power laws have as yet no theoretical explanation.Comment: RevTex 38 pages with 13 figures. Due to their large size, some figures are stored as separate gif images. The paper with included hi-res eps figures (981kb compressed, 3.5Mb uncompressed) is available at ftp://mobydick.physics.utoronto.ca/pub/MBCA96.tar.gz An mpeg movie and samples of data are also available at ftp://mobydick.physics.utoronto.ca/pub/. Paper submitted to Physica

LC3 and STRAP regulate actin filament assembly by JMY during autophagosome formation.

During autophagy, actin filament networks move and remodel cellular membranes to form autophagosomes that enclose and metabolize cytoplasmic contents. Two actin regulators, WHAMM and JMY, participate in autophagosome formation, but the signals linking autophagy to actin assembly are poorly understood. We show that, in nonstarved cells, cytoplasmic JMY colocalizes with STRAP, a regulator of JMY's nuclear functions, on nonmotile vesicles with no associated actin networks. Upon starvation, JMY shifts to motile, LC3-containing membranes that move on actin comet tails. LC3 enhances JMY's de novo actin nucleation activity via a cryptic actin-binding sequence near JMY's N terminus, and STRAP inhibits JMY's ability to nucleate actin and activate the Arp2/3 complex. Cytoplasmic STRAP negatively regulates autophagy. Finally, we use purified proteins to reconstitute LC3- and JMY-dependent actin network formation on membranes and inhibition of network formation by STRAP. We conclude that LC3 and STRAP regulate JMY's actin assembly activities in trans during autophagy

Principle of Maximum Entropy Applied to Rayleigh-B\'enard Convection

A statistical-mechanical investigation is performed on Rayleigh-B\'enard convection of a dilute classical gas starting from the Boltzmann equation. We first present a microscopic derivation of basic hydrodynamic equations and an expression of entropy appropriate for the convection. This includes an alternative justification for the Oberbeck-Boussinesq approximation. We then calculate entropy change through the convective transition choosing mechanical quantities as independent variables. Above the critical Rayleigh number, the system is found to evolve from the heat-conducting uniform state towards the convective roll state with monotonic increase of entropy on the average. Thus, the principle of maximum entropy proposed for nonequilibrium steady states in a preceding paper is indeed obeyed in this prototype example. The principle also provides a natural explanation for the enhancement of the Nusselt number in convection.Comment: 13 pages, 4 figures; typos corrected; Eq. (66a) corrected to remove a double counting for $k_{\perp}=0$; Figs. 1-4 replace

Effects of long-term inorganic and organic fertilizations on the soil micro and macro structures of rice paddies

The soil structure of paddy soil is very dynamic from the aggregate to the pedon scale because of intensive anthropogenic management strategies. In this study, we tested the hypothesis that long-term inorganic and organic fertilizations can affect soil structure at different scales. Microstructure assessed by soil aggregates (3–5 mm in diameter) and macrostructure assessed by small soil cores (CoreS) (5 cm in diameter, 5 cm in height) and large soil cores (CoreL) (10 cm in diameter, 10 cm in height) were sampled from three long-term fertilization treatments, including no fertilizer (CK), application of inorganic fertilizer (NPK), and a combination of inorganic fertilizer and organic manure (NPKOM), established in 1982. They were scanned at two scales with two types of micro-computed tomography (micro-CT) and quantified using image analysis. Results showed that relative to CK treatment, long-term NPKOM fertilization increased soil organic C (SOC) by 28% and available water content (AWC) by 20%, but decreased soil bulk density by 0.2 g cm− 3 whereas NPK showed no difference. Soils under CK and NPK treatments exhibited an identical dense structure at both aggregate and core scales in which pores were mainly cracks resulting from shrink/swell processes, and showed no significant difference in porosity and size distribution of the CT-identified pores (> 3.7 μm). Compared with the CK treatment, the soil in the NPKOM treatment had greater intra- and inter-aggregate pores, and increased porosity by 58.3%, 144.9%, and 65.9% at aggregate, CoreS, and CoreL scales, respectively. These were attributed to the biopores formed from decayed roots, stubble, and organic manures as a result of increased yields and direct amendment of organic manure. Overall, this study demonstrates that organic fertilization can improve the physical qualities of paddy soils across different scales but inorganic fertilization in isolation does not

Modeling the Subsurface Structure of Sunspots

While sunspots are easily observed at the solar surface, determining their subsurface structure is not trivial. There are two main hypotheses for the subsurface structure of sunspots: the monolithic model and the cluster model. Local helioseismology is the only means by which we can investigate subphotospheric structure. However, as current linear inversion techniques do not yet allow helioseismology to probe the internal structure with sufficient confidence to distinguish between the monolith and cluster models, the development of physically realistic sunspot models are a priority for helioseismologists. This is because they are not only important indicators of the variety of physical effects that may influence helioseismic inferences in active regions, but they also enable detailed assessments of the validity of helioseismic interpretations through numerical forward modeling. In this paper, we provide a critical review of the existing sunspot models and an overview of numerical methods employed to model wave propagation through model sunspots. We then carry out an helioseismic analysis of the sunspot in Active Region 9787 and address the serious inconsistencies uncovered by \citeauthor{gizonetal2009}~(\citeyear{gizonetal2009,gizonetal2009a}). We find that this sunspot is most probably associated with a shallow, positive wave-speed perturbation (unlike the traditional two-layer model) and that travel-time measurements are consistent with a horizontal outflow in the surrounding moat.Comment: 73 pages, 19 figures, accepted by Solar Physic

The CPT1C 5′UTR Contains a Repressing Upstream Open Reading Frame That Is Regulated by Cellular Energy Availability and AMPK

BACKGROUND: Translational control is utilized as a means of regulating gene expression in many species. In most cases, posttranscriptional regulatory mechanisms play an important role in stress response pathways and can lead to dysfunctional physiology if blocked by mutations. Carnitine Palmitoyltransferase 1 C (CPT1C), the brain-specific member of the CPT 1 family, has previously been shown to be involved in regulating metabolism in situations of energy surplus. PRINCIPAL FINDINGS: Sequence analysis of the CPT1C mRNA revealed that it contains an upstream open reading frame (uORF) in the 5' UTR of its mRNA. Using CPT1C 5' UTR/luciferase constructs, we investigated the role of the uORF in translational regulation. The results presented here show that translation from the CPT1C main open reading frame (mORF) is repressed by the presence of the uORF, that this repression is relieved in response to specific stress stimuli, namely glucose deprivation and palmitate-BSA treatment, and that AMPK inhibition can relieve this uORF-dependent repression. SIGNIFICANCE: The fact that the mORF regulation is relieved in response to a specific set of stress stimuli rather than general stress response, hints at an involvement of CPT1C in cellular energy-sensing pathways and provides further evidence for a role of CPT1C in hypothalamic regulation of energy homeostasis

Unlocking the biological potential of proteins from edible insects through enzymatic hydrolysis: a review

peer-reviewedThis review, focusing on studies published between 2005 and 2017, analysed the literature on the generation of bioactive peptides (BAPs) from edible insect proteins following enzymatic hydrolysis. The protein extraction and quantification methodologies used for edible insects varied considerably. While several edible insects have been evaluated for their ability to release BAPs, silkworm (Bombyx mori) is currently the most studied. Specifically, the angiotensin converting enzyme (ACE) inhibitory, antioxidant and antidiabetic properties of edible insect protein enzymatic hydrolysates have been studied. Potent in vitro ACE inhibitory and antioxidant hydrolysates/peptides have been reported. In certain instances, these properties were validated in small animal studies (i.e. hypotensive effects). Enzymatic hydrolysis of edible insect proteins may also enhance technofunctional properties (i.e. solubility). The wider application of enzymatic hydrolysis protocols to edible insect proteins may ultimately allow for the increased discovery and utilisation of novel BAPs as sustainable protein/peptide sources for human nutrition.ACCEPTEDpeer-reviewe

Enhancing methane production from lignocellulosic biomass by combined steam‑explosion pretreatment and bioaugmentation with cellulolytic bacterium Caldicellulosiruptor bescii

Background: Biogas production from lignocellulosic biomass is generally considered to be challenging due to the recalcitrant nature of this biomass. In this study, the recalcitrance of birch was reduced by applying steam-explosion (SE) pretreatment (210 °C and 10 min). Moreover, bioaugmentation with the cellulolytic bacterium Caldicellulosiruptor bescii was applied to possibly enhance the methane production from steam-exploded birch in an anaerobic digestion (AD) process under thermophilic conditions (62 °C). Results: Overall, the combined SE and bioaugmentation enhanced the methane yield up to 140% compared to untreated birch, while SE alone contributed to the major share of methane enhancement by 118%. The best methane improvement of 140% on day 50 was observed in bottles fed with pretreated birch and bioaugmentation with lower dosages of C. bescii (2 and 5% of inoculum volume). The maximum methane production rate also increased from 4-mL CH4/ g VS (volatile solids)/day for untreated birch to 9-14-mL CH4/ g VS/day for steam-exploded birch with applied bioaugmentation. Bioaugmentation was particularly effective for increasing the initial methane production rate of the pretreated birch yielding 21-44% more methane than the pretreated birch without applied bioaugmentation. The extent of solubilization of the organic matter was increased by more than twofold when combined SE pretreatment and bioaugmentation was used in comparison with the methane production from untreated birch. The beneficial effects of SE and bioaugmentation on methane yield indicated that biomass recalcitrance and hydrolysis step are the limiting factors for efficient AD of lignocellulosic biomass. Microbial community analysis by 16S rRNA amplicon sequencing showed that the microbial community composition was altered by the pretreatment and bioaugmentation processes. Notably, the enhanced methane production by pretreatment and bioaugmentation was well correlated with the increase in abundance of key bacterial and archaeal communities, particularly the hydrolytic bacterium Caldicoprobacter, several members of syntrophic acetate oxidizing bacteria and the hydrogenotrophic Methanothermobacter. Conclusion: Our findings demonstrate the potential of combined SE and bioaugmentation for enhancing methane production from lignocellulosic biomass