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The molecular recognition properties of two pillar[n]arene sulfates (P[5]AS and P[6]AS) toward a panel of world anti-doping agency banned substances (1 – 11) were investigated by a combination of isothermal titration calorimetry, 1H NMR spectroscopy, and molecular modelling. Subsequently a sensing ensemble based on indicator displacement was created using the P[5]AS•lucigenin and P[6]AS •Hoechst 33258 complexes which allowed differentiation among the analytes with 90% accuracy. The assay was extended to allow the quantitation of pseudoephedrine in simulated urine samples with a limit of quantitation that is 30-fold below the WADA threshold. 

Honduras cuenta con 349,510 hectáreas cultivadas con café Coffea arabica, que son en su mayoría cultivos tradicionales (café sombra y café sol), y en menor escala cultivos con sistema Dosel Abierto Integrado (DAI). El sistema de café DAI consiste en plantaciones de café rodeadas por bosque en una proporción ≥ 1:1, lo que permite la preservación y la restauración de ecosistemas nativos. El objetivo de nuestra investigación fue evaluar el sistema DAI en cultivos de café como una alternativa de conservación para las aves migratorias neártico-neotropicales y aves residentes. Evaluamos características ecológicas, como la riqueza y abundancia de especies, entre los meses de noviembre de 2018 a abril de 2019. Establecimos 75 puntos de conteo de radio fijo en una zona cafetalera del departamento de Yoro, Honduras. Estadísticamente no registramos diferencias significativas en la riqueza de aves migratorias entre los sistemas de bosque, café DAI y cultivos de café tradicionales. Sin embargo, la riqueza de especies dependientes de bosque fue mayor en los sistema bosque y cultivos de café DAI que en cultivos tradicionales. Además, algunas especies dependientes de bosque, como Myioborus miniatus y Mionectes oleagineus, fueron más abundantes (P < 0.05) en bosque y cultivos de café DAI que en cultivos de café tradicionales. Nuestros resultados se suman a los reportados en Costa Rica, en donde se introdujo este agroecosistema de cultivo de café, en los que se indica que el café DAI puede ser una alternativa para la conservación de aves migratorias y residentes, en particular para especies dependientes de bosque.

 

Montane birds experience a range of challenges that may limit their breeding success, including nest predation and severe climactic conditions. The continuing effects of climate change are causing shifts in biotic and abiotic factors that may compound these threats to montane bird species. In northeastern montane forests, many bird species are shifting downslope, potentially as the result of increased precipitation and temperature at higher elevations. Although lower elevations might be more favorable in terms of climactic conditions, nest predation is higher at lower elevations. Thus, montane birds might be faced with the opposing pressures of adverse climactic conditions at higher elevations and increased predation at lower elevations. We monitored nests of Swainson's Thrush (Catharus ustulatus) along an elevation gradient in the White Mountain National Forest in New Hampshire in 2016, 2018, 2019, and 2021 to examine the effect of biotic and abiotic factors on daily nest survival rate (DSR). Linear time explained the most variation of DSR in AICc model comparison, indicating that DSR decreases across the breeding season. Rain intensity (mm/h) had a weak negative effect on DSR, indicating that heavier rain per hour decreases Swainson's Thrush DSR. Moreover, we found some support for a negative interaction effect of elevation in conjunction with minimum daily temperature: DSR of Swainson's Thrush nests at low elevations (281 m) increased with increasing minimum daily temperatures and decreased at high elevations with increasing minimum daily temperatures. Our results suggest nesting survival of montane breeding birds may be at risk as heavier precipitation events become more frequent and intense due to the changing climate and raises the possibility that other passerine species could be at risk in this system.

 

We report the synthesis of quaternary (di)cationic triamantane derivatives G1 and G3 by the permethylation of the corresponding primary ammonium ions G2 and G4. The complexation behaviors of G1–G4 toward CB[7] and CB[8] were examined by 1 H NMR spectroscopy, which reveals that CB[8] is capable of fully encapsulating G1–G4 whereas CB[7] forms inclusion complexes with G1, G2, and G4 but cannot fully encapsulate the central hydrophobic core of the bis-quaternary ammonium ion G3. The geometries of the CB[ n ]-guest complexes were determined by analyzing the complexation induced changes in chemical shifts and were further confirmed by molecular modelling using the Conformer–Rotamer Ensemble Sampling Tool (CREST) based on the GFN methods. Finally, the complexation thermodynamics were determined by a combination of 1 H NMR competitive experiments, direct isothermal titration calorimetry (ITC) measurements, and competitive ITC titrations using a tight binding ternary complex as a competitor. 

ELT-2 is the major transcription factor (TF) required for Caenorhabditis elegans intestinal development. ELT-2 expression initiates in embryos to promote development and then persists after hatching through the larval and adult stages. Though the sites of ELT-2 binding are characterized and the transcriptional changes that result from ELT-2 depletion are known, an intestine-specific transcriptome profile spanning developmental time has been missing. We generated this dataset by performing Fluorescence Activated Cell Sorting on intestine cells at distinct developmental stages. We analyzed this dataset in conjunction with previously conducted ELT-2 studies to evaluate the role of ELT-2 in directing the intestinal gene regulatory network through development. We found that only 33% of intestine-enriched genes in the embryo were direct targets of ELT-2 but that number increased to 75% by the L3 stage. This suggests additional TFs promote intestinal transcription especially in the embryo. Furthermore, only half of ELT-2's direct target genes were dependent on ELT-2 for their proper expression levels, and an equal proportion of those responded to elt-2 depletion with over-expression as with under-expression. That is, ELT-2 can either activate or repress direct target genes. Additionally, we observed that ELT-2 repressed its own promoter, implicating new models for its autoregulation. Together, our results illustrate that ELT-2 impacts roughly 20–50% of intestine-specific genes, that ELT-2 both positively and negatively controls its direct targets, and that the current model of the intestinal regulatory network is incomplete as the factors responsible for directing the expression of many intestinal genes remain unknown.

 

We report the molecular recognition properties of Pillar[ n ]MaxQ (P[ n ]MQ) toward a series of (methylated) amino acids, amino acid amides, and post-translationally modified peptides by a combination of 1 H NMR, isothermal titration calorimetry, indicator displacement assays, and molecular dynamics simulations. We find that P6MQ is a potent receptor for N -methylated amino acid side chains. P6MQ recognized the H3K4Me 3 peptide with K d = 16 nM in phosphate buffered saline. 

Abstract Pilot projects have emerged in cities globally as a way to experiment with the utilization of a suite of smart mobility and emerging transportation technologies. Automated vehicles (AVs) have become central tools for such projects as city governments and industry explore the use and impact of this emerging technology. This paper presents a large-scale assessment of AV pilot projects in U.S. cities to understand how pilot projects are being used to examine the risks and benefits of AVs, how cities integrate these potentially transformative technologies into conventional policy and planning, and how and what they are learning about this technology and its future opportunities and risks. Through interviews with planning practitioners and document analysis, we demonstrate that the approaches cities take for AVs differ significantly, and often lack coherent policy goals. Key findings from this research include: (1) a disconnect between the goals of the pilot projects and a city’s transportation goals; (2) cities generally lack a long-term vision for how AVs fit into future mobility systems and how they might help address transportation goals; (3) an overemphasis of non-transportation benefits of AV pilots projects; (4) AV pilot projects exhibit a lack of policy learning and iteration; and (5) cities are not leveraging pilot projects for public benefits. Overall, urban and transportation planners and decision makers show a clear interest to discover how AVs can be used to address transportation challenges in their communities, but our research shows that while AV pilot projects purport to do this, while having numerous outcomes, they have limited value for informing transportation policy and planning questions around AVs. We also find that AV pilot projects, as presently structured, may constrain planners’ ability to re-think transportation systems within the context of rapid technological change. 

Abstract Low complexity domains (LCDs) in proteins are regions predominantly composed of a small subset of the possible amino acids. LCDs are involved in a variety of normal and pathological processes across all domains of life. Existing methods define LCDs using information-theoretical complexity thresholds, sequence alignment with repetitive regions, or statistical overrepresentation of amino acids relative to whole-proteome frequencies. While these methods have proven valuable, they are all indirectly quantifying amino acid composition, which is the fundamental and biologically-relevant feature related to protein sequence complexity. Here, we present a new computational tool, LCD-Composer, that directly identifies LCDs based on amino acid composition and linear amino acid dispersion. Using LCD-Composer's default parameters, we identified simple LCDs across all organisms available through UniProt and provide the resulting data in an accessible form as a resource. Furthermore, we describe large-scale differences between organisms from different domains of life and explore organisms with extreme LCD content for different LCD classes. Finally, we illustrate the versatility and specificity achievable with LCD-Composer by identifying diverse classes of LCDs using both simple and multifaceted composition criteria. We demonstrate that the ability to dissect LCDs based on these multifaceted criteria enhances the functional mapping and classification of LCDs.