Resolutions of monomial almost complete intersections and generalizations

Let S=K[x₁,…,x_n] be a polynomial ring over a field kand let / be a monomial ideal of S. The main result of this paper is an explicit minimal resolution of kover R= S/Iwhen / is a monomial almost complete intersection ideal of S. We also compute an upper bound on the multigraded resolution of k over a generalization of monomial almost complete intersection ring.     

Divergent and Modular Synthesis of Terpenoid Scaffolds via a AuI Catalyzed One-Pot Cascade

A one-pot cascade sequence to generate synthetically challenging polycyclic scaffolds is reported utilizing a novel Lewis acid gold catalyst for the key cyclization step, enabling the divergent synthesis of both 6,6,5-tricyclic and 6,6,6,5-tetracyclic cores through both ligand and reaction condition control. We have combined the intrinsic complexity and stereoselectivity of cycloadditions with the electronic and steric properties of gold complexes to selectively generate complex polycyclic scaffolds in a single operation.     

Environmental controls of UV-B radiation in forested streams of northern Michigan

We examined UV-B radiation flux and its environmental control within and among streams of northern Michigan. UV-B flux was estimated in streams by plastic dosimetry strips, which allow for the simultaneous and repeated in situ measurement of solar radiation. During the summer of 2004, UV-B flux was measured across depth gradients and along longitudinal transects in seven streams, which were chosen to encompass a range of dissolved organic carbon (DOC) concentrations and canopy cover. Attenuation coefficients of UV-B (K(d) (UV-B)) were estimated using plastic dosimeters placed along a depth gradient. K(d UV-B) were positively correlated with DOC concentration and similar to values obtained with laboratory and in situ spectrometry. Along 100 m longitudinal transects, UV-B flux varied along all streams regardless of their canopy cover and DOC concentration. Within-stream fluxes of UV-B were correlated to canopy cover in the only two streams that both had relatively low DOC concentration and variable canopy cover. Large differences were found among streams in the average UV-B flux (corrected for incident solar flux) reaching the dosimeters at 5 cm depth. These among-stream differences were largely accounted for by the stream width, canopy cover, and DOC concentration. Our results illustrate an inherent variability in UV-B flux within and among streams of northern Michigan that is strongly tied to the interactions of DOC concentration, stream size and riparian vegetation.     

Fluorine Bonding Enhances the Energetics of Protein-Lipid Binding in the Gas Phase

This paper reports on the first experimental study of the energies of noncovalent fluorine bonding in a protein-ligand complex in the absence of solvent. Arrhenius parameters were measured for the dissociation of gaseous deprotonated ions of complexes of bovine β-lactoglobulin (Lg), a model lipid-binding protein, and four fluorinated analogs of stearic acid (SA), which contained (X =) 13, 15, 17, or 21 fluorine atoms. In all cases, the activation energies (E_a) measured for the loss of neutral XF-SA from the (Lg + XF-SA)^7– ions are larger than for SA. From the kinetic data, the average contribution of each?>?CF₂ group to E_a was found to be ~1.1 kcal mol^–1, which is larger than the ~0.8 kcal mol^–1 value reported for?>?CH₂ groups. Based on these results, it is proposed that fluorocarbon–protein interactions are inherently stronger (enthalpically) than the corresponding hydrocarbon interactions.

Phase behaviour of poly-(λ-benzyl-L-glutamate) in benzyl alcohol

Polarized optical microscopy has been used to investigate phase transitions in the poly-(λ-benzyl-L-glutamate) benzyl alcohol system and these have been compared with the predictions of Flory. All of the samples studied form gels at room temperature. The behaviour of the lowest concentration studied, 5 per cent by volume, shows transitions in the optical microscope compatible with the Flory phase diagram, becoming isotropic at elevated temperatures. Gels of higher concentrations exhibit bulk phase separation into an isotropic liquid phase and an anisotropic phase at room temperature, also in accord with the Flory predictions; the texture of the anisotropic phase varies with concentration. At higher temperatures these concentrations exhibit two coexistent anisotropic phases.     

Capillary electrophoresis as a probe of enantiospecific interactions between photoactive transition metal complexes and DNA

Recently, we have demonstrated the capacity to separate chiral transition metal (TM) complexes of the type [M(diimine)(3)](n+) using CE buffers containing chiral tartrate salts. In separate work, several chromium(III)-tris-diimine complexes in particular have been shown to bind enantioselectively with calf-thymus (CT) DNA, and a qualitative assessment of the relative strength and enantiospecificity of this interaction is of significant interest in the characterization of these complexes as potential DNA photocleavage agents. Here, we describe two convenient approaches to investigate such binding behavior using chiral CE. For complexes with lower DNA affinities exhibiting primarily surface binding, DNA itself is used as the chiral resolving agent in the electrophoretic buffer. In this approach, resolution of the TM complexes into their Lambda and Delta isomers is achieved with the isomer eluting later exhibiting superior binding affinity toward DNA. For more strongly bound TM complexes containing ligands known to intercalate with DNA, the [Cr(diimine)(3)](3+) complexes are preincubated with oligonucleotide and subsequently enantiomerically resolved in a dibenzoyl-L-tartrate buffer system that facilitates analysis of the unbound TM species only. Differences in isomer binding affinity are distinguished by the relative peak areas of the Lambda- and Delta-isomers, and relative binding strengths of different complexes can be inferred from comparison of the total amount of unbound complex at equivalent DNA/TM ratios.     

An Emergent Framework: Views of Mathematical Processes

The findings reported in this paper were generated from a case study of teacher leaders at a state‐level mathematics conference. Investigation focused on how participants viewed the mathematical processes of communication, connections, representations, problem solving, and reasoning and proof. Purposeful sampling was employed to select nine participants who were then interviewed and observed as they presented a session at the conference. Participants' statements revealed differences in their views of mathematical processes. The analysis led to an emergent framework for views of mathematical processes that includes three levels: participatory, experiential, and sense‐making. Implications are shared for mathematics methods instructors, professional learning, and research. Discussion also relates the framework to the Standards for Mathematical Practice.     

Development of Second Generation Activity-Based Chemical Probes for Sirtuins

NAD⁺ (nicotinamide adenine dinucleotide)-dependent protein deacylases, namely, the sirtuins, are important cell adaptor proteins that alter cell physiology in response to low calorie conditions. They are thought to mediate the beneficial effects of calorie restriction to extend longevity and improve health profiles. Novel chemical probes are highly desired for a better understanding of sirtuin’s roles in various biological processes. We developed a group of remarkably simple activity-based chemical probes for the investigation of active sirtuin content in complex native proteomes. These probes harbor a thioacyllysine warhead, a diazirine photoaffinity tag, as well as a terminal alkyne bioorthogonal functional group. Compared to their benzophenone-containing counterparts, these new probes demonstrated improved labeling efficiency and sensitivity, shortened irradiation time, and reduced background signal. They were applied to the labeling of individual recombinant proteins, protein mixtures, and whole cell lysate. These cell permeable small molecule probes also enabled the cellular imaging of sirtuin activity change. Taken together, our study provides new chemical biology tools and future drug discovery strategies for perturbing the activity of different sirtuin isoforms.     

Retraction: Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases

Retraction of ‘Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases’ by Ai Tran et al., Chem. Sci., 2020, 11, 11818–11826, DOI: 10.1039/D0SC04161K.

The Royal Society of Chemistry hereby wholly retracts this Chemical Science article due to concerns about the reproducibility of the data.The Royal Society of Chemistry has been contacted by the authors of this article to alert us that recent experiments by their group have shown that some results are not reproducible, especially the yields of several key intermediates. Given the focus on the easy access to epigenetically important nucleosides and related ODNs, unreliable yields significantly impact the confidence in the results. In addition, it was discovered that one of the biological samples provided to the authors was mislabelled. The human stem cells were actually mouse stem cells, hence some discussion and conclusions in the article may no longer apply. Ahead of a thorough re-examination of the entire study, in order to preserve the rigor of the scientific record, the signing authors have chosen to retract the article and they would like to apologise for any inconvenience this may have caused for readers.Signed: Ai Tran, Song Zheng, Dawanna S. White, Alyson M. Curry and Yana CenRetraction endorsed by May Copsey, Executive Editor, Chemical Science     

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the ?7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)^7– ions, compared with that of the (Lg + PA)^7– ion, it is concluded that the –OH groups of the X-OHPA ligands participate in strong (5 – 11 kcal mol^–1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the –OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the –OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (K_a) measured for 7-OHPA [(2.3 ± 0.2) × 10⁵ M^–1] is similar to the value for the PA [(3.8 ± 0.1) × 10⁵ M^–1]; K_a for 3-OHPA [(1.1 ± 0.3) × 10⁶ M^–1] is approximately three-times larger, whereas K_a for 16-OHPA [(2.3 ± 0.2) × 10⁴ M^–1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand –OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.