Search for: All records

The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub₂) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub₂combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub₂are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub₂modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.

 

Porous media flows are common in both natural and anthropogenic systems. Mapping these flows in a laboratory setting is challenging and often requires non-intrusive measurement techniques, such as particle image velocimetry (PIV) coupled with refractive index matching (RIM). RIM-coupled PIV allows the mapping of velocity fields around transparent solids by analyzing the movement of neutrally buoyant micron-sized seeding particles. The use of this technique in a porous medium can be problematic because seeding particles adhere to grains, which causes the grain bed to lose transparency and can obstruct pore flows. Another non-intrusive optical technique, planar laser-induced fluorescence (PLIF), can be paired with RIM and does not have this limitation because fluorescent dye is used instead of particles, but it has been chiefly used for qualitative flow visualization. Here, we propose a quantitative PLIF-based methodology to map both porous media flow fields and porous media architecture. Velocity fields are obtained by tracking the advection-dominated movement of the fluorescent dye plume front within a porous medium. We also propose an automatic tracking algorithm that quantifies 2D velocity components as the plume moves through space in both an Eulerian and a Lagrangian framework. We apply this algorithm to three data sets: a synthetic data set and two laboratory experiments. Performance of this algorithm is reported by the mean (bias error,B) and standard deviation (random error,SD) of the residuals between its results and the reference data. For the synthetic data, the algorithm produces maximum errors ofB & SD= 32% & 23% in the Eulerian framework, respectively, andB & SD= −0.04% & 3.9% in the Lagrangian framework. The small-scale laboratory experimental data requires the Eulerian framework and produce errors ofB & SD= −0.5% & 33%. The Lagrangian framework is used on the large-scale laboratory experimental data and produces errors ofB & SD= 5% & 44%. Mapping the porous media architecture shows negligible error for reconstructing calibration grains of known dimensions.

 

Understanding the mechanisms by which information and misinformation spread through groups of individual actors is essential to the prediction of phenomena ranging from coordinated group behaviors to misinformation epidemics. Transmission of information through groups depends on the rules that individuals use to transform the perceived actions of others into their own behaviors. Because it is often not possible to directly infer decision-making strategies in situ, most studies of behavioral spread assume that individuals make decisions by pooling or averaging the actions or behavioral states of neighbors. However, whether individuals may instead adopt more sophisticated strategies that exploit socially transmitted information, while remaining robust to misinformation, is unknown. Here, we study the relationship between individual decision-making and misinformation spread in groups of wild coral reef fish, where misinformation occurs in the form of false alarms that can spread contagiously through groups. Using automated visual field reconstruction of wild animals, we infer the precise sequences of socially transmitted visual stimuli perceived by individuals during decision-making. Our analysis reveals a feature of decision-making essential for controlling misinformation spread: dynamic adjustments in sensitivity to socially transmitted cues. This form of dynamic gain control can be achieved by a simple and biologically widespread decision-making circuit, and it renders individual behavior robust to natural fluctuations in misinformation exposure. 

Estimates suggest that over 4 gigatons per year of carbon dioxide (Gt-CO₂year⁻¹) be removed from the atmosphere by 2050 to meet international climate goals. One strategy for carbon dioxide removal is seaweed farming; however its global potential remains highly uncertain. Here, we apply a dynamic seaweed growth model that includes growth-limiting mechanisms, such as nitrate supply, to estimate the global potential yield of four types of seaweed. We estimate that harvesting 1 Gt year⁻¹of seaweed carbon would require farming over 1 million km²of the most productive exclusive economic zones, located in the equatorial Pacific; the cultivation area would need to be tripled to attain an additional 1 Gt year⁻¹of harvested carbon, indicating dramatic reductions in carbon harvest efficiency beyond the most productive waters. Improving the accuracy of annual harvest yield estimates requires better understanding of biophysical constraints such as seaweed loss rates (e.g., infestation, disease, grazing, wave erosion).

 

Abstract Colloidal quantum wells, or nanoplatelets, show among the lowest thresholds for amplified spontaneous emission and lasing among solution-cast materials and among the highest modal gains of any known materials. Using solution measurements of colloidal quantum wells, this work shows that under photoexcitation, optical gain increases with pump fluence before rolling off due to broad photoinduced absorption at energies lower than the band gap. Despite the common occurrence of gain induced by an electron–hole plasma found in bulk materials and epitaxial quantum wells, under no measurement conditions was the excitonic absorption of the colloidal quantum wells extinguished and gain arising from a plasma observed. Instead, like gain, excitonic absorption reaches a minimum intensity near a photoinduced carrier sheet density of 2 × 10 13  cm −2 above which the absorption peak begins to recover. To understand the origins of these saturation and reversal effects, measurements were performed with different excitation energies, which deposit differing amounts of excess energy above the band gap. Across many samples, it was consistently observed that less energetic excitation results in stronger excitonic bleaching and gain for a given carrier density. Transient and static optical measurements at elevated temperatures, as well as transient X-ray diffraction of the samples, suggest that the origin of gain saturation and reversal is a heating and disordering of the colloidal quantum wells which produces sub-gap photoinduced absorption. 

The Wilkins Peak Member (WPM) of the Green River Formation in Wyoming, USA, comprises alternating lacustrine and alluvial strata that preserve a record of terrestrial climate during the early Eocene climatic optimum. We use a Bayesian framework to develop age-depth models for three sites, based on new 40Ar/39Ar sanidine and 206Pb/238U zircon ages from seven tuffs. The new models provide two- to ten-fold increases in temporal resolution compared to previous radioisotopic age models, confirming eccentricity-scale pacing of WPM facies, and permitting their direct comparison to astronomical solutions. Starting at ca. 51 Ma, the median ages for basin-wide flooding surfaces atop six successive alluvial marker beds coincide with short eccentricity maxima in the astronomical solutions. These eccentricity maxima have been associated with hyperthermal events recorded in marine strata during the early Eocene. WPM strata older than ca. 51 Ma do not exhibit a clear relationship to the eccentricity solutions, but accumulated 31%−35% more rapidly, suggesting that the influence of astronomical forcing on sedimentation was modulated by basin tectonics. Additional high-precision radioisotopic ages are needed to reduce the uncertainty of the Bayesian model, but this approach shows promise for unambiguous evaluation of the phase relationship between alluvial marker beds and theoretical eccentricity solutions. 

Transcription factors (TF) require access to target sites within nucleosomes to initiate transcription. The target site position within the nucleosome significantly influences TF occupancy, but how is not quantitatively understood. Using ensemble and single-molecule fluorescence measurements, we investigated the targeting and occupancy of the transcription factor, Gal4, at different positions within the nucleosome. We observe a dramatic decrease in TF occupancy to sites extending past 30 base pairs (bp) into the nucleosome which cannot be explained by changes in the TF dissociation rate or binding site orientation. Instead, the nucleosome unwrapping free energy landscape is the primary determinant of Gal4 occupancy by reducing the Gal4 binding rate. The unwrapping free energy landscape defines two distinct regions of accessibility and kinetics with a boundary at 30 bp into the nucleosome where the inner region is over 100-fold less accessible. The Gal4 binding rate in the inner region no longer depends on its concentration because it is limited by the nucleosome unwrapping rate, while the frequency of nucleosome rewrapping decreases because Gal4 exchanges multiple times before the nucleosome rewraps. Our findings highlight the importance of the nucleosome unwrapping free energy landscape on TF occupancy and dynamics that ultimately influences transcription initiation.