We show that the HERA data for the inclusive structure function F2(x,Q2) for x⩽10−2 and 0.045⩽Q2⩽45 GeV2 can be well described within the color dipole picture, with a simple analytic expression for ...the dipole–proton scattering amplitude, which is an approximate solution to the non-linear evolution equations in QCD. For dipole sizes less than the inverse saturation momentum 1/Qs(x), the scattering amplitude is the solution to the BFKL equation in the vicinity of the saturation line. It exhibits geometric scaling and scaling violations by the diffusion term. For dipole sizes larger than 1/Qs(x), the scattering amplitude saturates to one. The fit involves three parameters: the proton radius R, the value x0 of x at which the saturation scale Qs equals 1 GeV, and the logarithmic derivative of the saturation momentum λ. The value of λ extracted from the fit turns out to be consistent with a recent calculation using the next-to-leading order BFKL formalism.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
A numerical simulation method and an experimental method were employed to investigate the relationships between the mineral particle sizes and spectral characteristics of the sound or vibration ...signals generated during rock drilling processes. Several rock models with different aggregates were generated by means of determining the locations of aggregates randomly. The modal analysis of the rock models was conducted to reveal their vibration characteristics. Simulation results indicated that the smaller the aggregate size, the larger the high-frequency composition of sound and vibration. Several drilling experiments were performed on the rock specimens of different aggregate sizes. By using an indoor signal acquisition and analysis system, data from the sound waves and vibrations were collected, and characteristic signals were extracted. Moreover, the spectral characteristics of the sounds and vibrations of different aggregate sizes were identified. The experiment results are consistent with the conclusion of the simulation. The study provides a possibility for developing a method to evaluate the rock structure information collected from drilling vibration or sound signals for a fine exploration of geological surveys.
Approximately one-third of the Earth's photosynthetic CO2 assimilation occurs in a pyrenoid, an organelle containing the CO2-fixing enzyme Rubisco. How constituent proteins are recruited to the ...pyrenoid and how the organelle's subcompartments-membrane tubules, a surrounding phase-separated Rubisco matrix, and a peripheral starch sheath-are held together is unknown. Using the model alga Chlamydomonas reinhardtii, we found that pyrenoid proteins share a sequence motif. We show that the motif is necessary and sufficient to target proteins to the pyrenoid and that the motif binds to Rubisco, suggesting a mechanism for targeting. The presence of the Rubisco-binding motif on proteins that localize to the tubules and on proteins that localize to the matrix-starch sheath interface suggests that the motif holds the pyrenoid's three subcompartments together. Our findings advance our understanding of pyrenoid biogenesis and illustrate how a single protein motif can underlie the architecture of a complex multilayered phase-separated organelle.
Spatiotemporal gene regulation is often driven by RNA-binding proteins that harbor long intrinsically disordered regions in addition to folded RNA-binding domains. We report that the disordered ...region of the evolutionarily ancient developmental regulator Vts1/Smaug drives self-assembly into gel-like condensates. These proteinaceous particles are not composed of amyloid, yet they are infectious, allowing them to act as a protein-based epigenetic element: a prion SMAUG+. In contrast to many amyloid prions, condensation of Vts1 enhances its function in mRNA decay, and its self-assembly properties are conserved over large evolutionary distances. Yeast cells harboring SMAUG+ downregulate a coherent network of mRNAs and exhibit improved growth under nutrient limitation. Vts1 condensates formed from purified protein can transform naive cells to acquire SMAUG+. Our data establish that non-amyloid self-assembly of RNA-binding proteins can drive a form of epigenetics beyond the chromosome, instilling adaptive gene expression programs that are heritable over long biological timescales.
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•The Vts1 IDR promotes its condensation into the non-amyloid prion SMAUG+•SMAUG+ hyperactivates Vts1 function•SMAUG+ rewires post-transcriptional gene regulation to promote proliferation•Self-assembly is conserved in the human Vts1 homolog hSmaug1
Chakravarty et al. define a new mechanism in protein-based epigenetics. Self-assembly of the evolutionarily ancient RNA-binding protein Vts1/Smaug drives formation of a non-amyloid prion, SMAUG+, that heritably activates protein function. SMAUG+ rewires post-transcriptional gene expression landscapes to favor robust mitotic growth. Its self-assembly properties are conserved across eukaryotes.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
We discuss the definition and the energy evolution of scattering amplitudes with
C-odd (“odderon”) quantum numbers within the effective theory for the color glass condensate (CGC) endowed with the ...functional, JIMWLK, evolution equation. We explicitly construct gauge-invariant amplitudes describing multiple odderon exchanges in the scattering between the CGC and two types of projectiles: a color-singlet quark–antiquark pair (or ‘color dipole’) and a system of three quarks in a colorless state. We deduce the energy evolution of these amplitudes from the general JIMWLK equation, which for this purpose is recast in a more synthetic form, which is manifestly infrared finite. For the dipole odderon, we confirm and extend the non-linear evolution equations recently proposed by Kovchegov, Szymanowski and Wallon, which couple the evolution of the odderon to that of the pomeron, and predict the rapid suppression of the odderon exchanges in the saturation regime at high energy. For the 3-quark system, we focus on the linear regime at relatively low energy, where our general equations are shown to reduce to the Bartels–Kwiecinski–Praszalowicz equation. Our gauge-invariant amplitudes, and the associated evolution equations, stay explicitly outside the Möbius representation, which is the Hilbert space where the BFKL Hamiltonian exhibits holomorphic separability.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Theory and experiments suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors, but the mechanisms ...driving pre-adaptation remain enigmatic. We report that the SMAUG+ prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, SMAUG+ regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. SMAUG+ is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct SMAUG+ variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.
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•The SMAUG+ prion allows yeast to anticipate nutrient repletion after starvation•SMAUG+ regulates the decision between cardinal growth and survival strategies•SMAUG+ is hidden in plain sight in common laboratory yeast strains•Distinct SMAUG+ variants are widespread in wild yeast populations
Itakura et al. demonstrate that we have been blind to the pervasive importance of protein-based inheritance in biology. Adaptive prediction of nutritional environments by SMAUG+ prion polymorphs modulates cardinal growth and development strategies of S. cerevisiae both in the laboratory and in the wild.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
It Pays To Be in Phase Itakura, Alan K; Futia, Raymond A; Jarosz, Daniel F
Biochemistry (Easton),
05/2018, Volume:
57, Issue:
17
Journal Article
Peer reviewed
Open access
To survive, organisms must orchestrate competing biochemical and regulatory processes in time and space. Recent work has suggested that the underlying chemical properties of some biomolecules allow ...them to self-organize and that life may have exploited this property to organize biochemistry in space and time. Such phase separation is ubiquitous, particularly among the many regulatory proteins that harbor prion-like intrinsically disordered domains. And yet, despite evident regulation by post-translational modification and myriad other stimuli, the biological significance of many phase-separated compartments remains uncertain. Many potential functions have been proposed, but far fewer have been demonstrated. A burgeoning subfield at the intersection of cell biology and polymer physics has defined the biophysical underpinnings that govern the genesis and stability of these particles. The picture is complex: many assemblies are composed of multiple proteins that each have the capacity to phase separate. Here, we briefly discuss this foundational work and survey recent efforts combining targeted biochemical perturbations and quantitative modeling to specifically address the diverse roles that phase separation processes may play in biology.
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