The Eukaryotic CO2-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization.

Approximately 30%-40% of global CO2 fixation occurs inside a non-membrane-bound organelle called the pyrenoid, which is found within the chloroplasts of most eukaryotic algae. The pyrenoid matrix is densely packed with the CO2-fixing enzyme Rubisco and is thought to be a crystalline or amorphous solid. Here, we show that the pyrenoid matrix of the unicellular alga Chlamydomonas reinhardtii is not crystalline but behaves as a liquid that dissolves and condenses during cell division. Furthermore, we show that new pyrenoids are formed both by fission and de novo assembly. Our modeling predicts the existence of a "magic number" effect associated with special, highly stable heterocomplexes that influences phase separation in liquid-like organelles. This view of the pyrenoid matrix as a phase-separated compartment provides a paradigm for understanding its structure, biogenesis, and regulation. More broadly, our findings expand our understanding of the principles that govern the architecture and inheritance of liquid-like organelles.

Structures of AT8 and PHF1 phosphomimetic tau: Insights into the posttranslational modification code of tau aggregation.

The microtubule-associated protein tau aggregates into amyloid fibrils in Alzheimer's disease and other neurodegenerative diseases. In these tauopathies, tau is hyperphosphorylated, suggesting that this posttranslational modification (PTM) may induce tau aggregation. Tau is also phosphorylated in normal developing brains. To investigate how tau phosphorylation induces amyloid fibrils, here we report the atomic structures of two phosphomimetic full-length tau fibrils assembled without anionic cofactors. We mutated key Ser and Thr residues to Glu in two regions of the protein. One construct contains three Glu mutations at the epitope of the anti-phospho-tau antibody AT8 (AT8-3E tau), whereas the other construct contains four Glu mutations at the epitope of the antibody PHF1 (PHF1-4E tau). Solid-state NMR data show that both phosphomimetic tau mutants form homogeneous fibrils with a single set of chemical shifts. The AT8-3E tau rigid core extends from the R3 repeat to the C terminus, whereas the PHF1-4E tau rigid core spans R2, R3, and R4 repeats. Cryoelectron microscopy data show that AT8-3E tau forms a triangular multi-layered core, whereas PHF1-4E tau forms a triple-stranded core. Interestingly, a construct combining all seven Glu mutations exhibits the same conformation as PHF1-4E tau. Scalar-coupled NMR data additionally reveal the dynamics and shape of the fuzzy coat surrounding the rigid cores. These results demonstrate that specific PTMs induce structurally specific tau aggregates, and the phosphorylation code of tau contains redundancy.

Resource theory of quantum scrambling.

Quantum chaos has become a cornerstone of physics through its many applications. One trademark of quantum chaotic systems is the spread of local quantum information, which physicists call scrambling. In this work, we introduce a mathematical definition of scrambling and a resource theory to measure it. We also describe two applications of this theory. First, we use our resource theory to provide a bound on magic, a potential source of quantum computational advantage, which can be efficiently measured in experiment. Second, we also show that scrambling resources bound the success of Yoshida's black hole decoding protocol.

A persistent major mutation in canonical jasmonate signaling is embedded in an herbivory-elicited gene network.

When insect herbivores attack plants, elicitors from oral secretions and regurgitants (OS) enter wounds during feeding, eliciting defense responses. These generally require plant jasmonate (JA) signaling, specifically, a jasmonoyl-L-isoleucine (JA-Ile) burst, for their activation and are well studied in the native tobacco Nicotiana attenuata. We used intraspecific diversity captured in a 26-parent MAGIC population planted in nature and an updated genome assembly to impute natural variation in the OS-elicited JA-Ile burst linked to a mutation in the JA-Ile biosynthetic gene NaJAR4. Experiments revealed that NaJAR4 variants were associated with higher fitness in the absence of herbivores but compromised foliar defenses, with two NaJAR homologues (4 and 6) complementing each other spatially and temporally. From decade-long seed collections of natural populations, we uncovered enzymatically inactive variants occurring at variable frequencies, consistent with a balancing selection regime maintaining variants. Integrative analyses of OS-induced transcriptomes and metabolomes of natural accessions revealed that NaJAR4 is embedded in a nonlinear complex gene coexpression network orchestrating responses to OS, which we tested by silencing four hub genes in two connected coexpressed networks and examining their OS-elicited metabolic responses. Lines silenced in two hub genes (NaGLR and NaFB67) co-occurring in the NaJAR4/6 module showed responses proportional to JA-Ile accumulations; two from an adjacent module (NaERF and NaFB61) had constitutively expressed defenses with high resistance. We infer that mutations with large fitness consequences can persist in natural populations due to compensatory responses from gene networks, which allow for diversification in conserved signaling pathways and are generally consistent with predictions of an omnigene model.

Beyond the Tricks: The Science and Comparative Cognition of Magic.

Magic is an art form that has fascinated humans for centuries. Recently, the techniques used by magicians to make their audience experience the impossible have attracted the attention of psychologists, who, in just a couple of decades, have produced a large amount of research regarding how these effects operate, focusing on the blind spots in perception and roadblocks in cognition that magic techniques exploit. Most recently, this investigation has given a pathway to a new line of research that uses magic effects to explore the cognitive abilities of nonhuman animals. This new branch of the scientific study of magic has already yielded new evidence illustrating the power of magic effects as a psychological tool for nonhuman animals. This review aims to give a thorough overview of the research on both the human and nonhuman perception of magic effects by critically illustrating the most prominent works of both fields of inquiry.

1H detection and dynamic nuclear polarization-enhanced NMR of Aß1-42 fibrils.

Several publications describing high-resolution structures of amyloid-ß (Aß) and other fibrils have demonstrated that magic-angle spinning (MAS) NMR spectroscopy is an ideal tool for studying amyloids at atomic resolution. Nonetheless, MAS NMR suffers from low sensitivity, requiring relatively large amounts of samples and extensive signal acquisition periods, which in turn limits the questions that can be addressed by atomic-level spectroscopic studies. Here, we show that these drawbacks are removed by utilizing two relatively recent additions to the repertoire of MAS NMR experiments-namely, 1H detection and dynamic nuclear polarization (DNP). We show resolved and sensitive two-dimensional (2D) and three-dimensional (3D) correlations obtained on 13C,15N-enriched, and fully protonated samples of M0Aß1-42 fibrils by high-field 1H-detected NMR at 23.4 T and 18.8 T, and 13C-detected DNP MAS NMR at 18.8 T. These spectra enable nearly complete resonance assignment of the core of M0Aß1-42 (K16-A42) using submilligram sample quantities, as well as the detection of numerous unambiguous internuclear proximities defining both the structure of the core and the arrangement of the different monomers. An estimate of the sensitivity of the two approaches indicates that the DNP experiments are currently ∼6.5 times more sensitive than 1H detection. These results suggest that 1H detection and DNP may be the spectroscopic approaches of choice for future studies of Aß and other amyloid systems.

Formation and Transformation of CdS Clusters during the Prenucleation Stage and in a Dilute Dispersion at Room Temperature.

The formation and transformation of colloidal semiconductor clusters remain poorly understood. With CdS as a model system, we show that, in the reaction of cadmium myristate (Cd(MA)2) and S powder in 1-octadecene (ODE), clusters form in the prenucleation stage of quantum dots (QDs). Called precursor compounds (PCs), the clusters can transform to magic-size clusters (MSCs) in reaction at a relatively high temperature (MSC-322 displaying optical absorption peaking at 322 nm) or in a dispersion at room temperature (MSC-360). When the reaction temperature is increased, PC-360 forms at 140 °C, while PC-322 and MSC-322 form at 180 °C. In a dispersion of cyclohexane and octylamine, MSC-322 transforms to MSC-360 via MSC-345. The MSC-345 to MSC-360 transformation displays continuous and discontinuous shifts in the optical absorption. The PCs and MSCs are a group of isomers. The present findings bring insight into the cluster formation and isomerization in the prenucleation stage of QDs and in a dispersion.

Sedimentation of large, soluble proteins up to 140 kDa for 1H-detected MAS NMR and 13C DNP NMR - practical aspects.

Solution NMR is typically applied to biological systems with molecular weights < 40 kDa whereas magic-angle-spinning (MAS) solid-state NMR traditionally targets very large, oligomeric proteins and complexes exceeding 500 kDa in mass, including fibrils and crystalline protein preparations. Here, we propose that the gap between these size regimes can be filled by the approach presented that enables investigation of large, soluble and fully protonated proteins in the range of 40-140 kDa. As a key step, ultracentrifugation produces a highly concentrated, gel-like state, resembling a dense phase in spontaneous liquid-liquid phase separation (LLPS). By means of three examples, a Sulfolobus acidocaldarius bifurcating electron transfer flavoprotein (SaETF), tryptophan synthases from Salmonella typhimurium (StTS) and their dimeric ß-subunits from Pyrococcus furiosus (PfTrpB), we show that such samples yield well-resolved proton-detected 2D and 3D NMR spectra at 100 kHz MAS without heterogeneous broadening, similar to diluted liquids. Herein, we provide practical guidance on centrifugation conditions and tools, sample behavior, and line widths expected. We demonstrate that the observed chemical shifts correspond to those obtained from µM/low mM solutions or crystalline samples, indicating structural integrity. Nitrogen line widths as low as 20-30 Hz are observed. The presented approach is advantageous for proteins or nucleic acids that cannot be deuterated due to the expression system used, or where relevant protons cannot be re-incorporated after expression in deuterated medium, and it circumvents crystallization. Importantly, it allows the use of low-glycerol buffers in dynamic nuclear polarization (DNP) NMR of proteins as demonstrated with the cyanobacterial phytochrome Cph1.

Growth and antioxidant responses to water stress in eggplant MAGIC population parents, F1 hybrids and a subset of recombinant inbred lines.

BACKGROUND: The generation of new eggplant (Solanum melongena L.) cultivars with drought tolerance is a main challenge in the current context of climate change. In this study, the eight parents (seven of S. melongena and one of the wild relative S. incanum L.) of the first eggplant MAGIC (Multiparent Advanced Generation Intercrossing) population, together with four F1 hybrids amongst them, five S5 MAGIC recombinant inbred lines selected for their genetic diversity, and one commercial hybrid were evaluated in young plant stage under water stress conditions (30% field capacity; FC) and control conditions (100% FC). After a 21-day treatment period, growth and biomass traits, photosynthetic pigments, oxidative stress markers, antioxidant compounds, and proline content were evaluated. RESULTS: Significant effects (p < 0.05) were observed for genotype, water treatments and their interaction in most of the traits analyzed. The eight MAGIC population parental genotypes displayed a wide variation in their responses to water stress, with some of them exhibiting enhanced root development and reduced foliar biomass. The commercial hybrid had greater aerial growth compared to root growth. The four F1 hybrids among MAGIC parents differed in their performance, with some having significant positive or negative heterosis in several traits. The subset of five MAGIC lines displayed a wide diversity in their response to water stress. CONCLUSION: The results show that a large diversity for tolerance to drought is available among the eggplant MAGIC materials, which can contribute to developing drought-tolerant eggplant cultivars.

Surface-Ligand Tuned Reversible Transformations in Aqueous Environments Between CdSe Magic-Size Clusters and Their Precursor Compounds.

That magic-size clusters (MSCs) have their counterpart precursor compounds (PCs) has not been generally accepted by expertise circles. Here, experimental evidence to support this new concept is presented. With aqueous-phase CdSe MSCs as a model system, it is shown that when the MSCs are dispersed in water containing a certain amount of L-cysteine (Cys), the MSCs disappear slowly. Upon the addition of CdCl2 , the MSCs recover. It is proposed that after dispersing, the MSCs transform to their quasi-isomeric, non-absorbing PCs upon Cys addition. In the presence of CdCl2 , the PCs transform back to the MSCs due to Cys elimination. The surface ligand Cys of the MSCs plays a significant role in the reversible transformations. The present study provides compelling evidence that absorbing MSCs have their non-absorbing PCs. The study findings suggest that the transformation between two MSCs that display absorption spectral shifts in a stepwise pattern is assisted by their PCs.

Pathway of Room-Temperature Formation of CdSeS Magic-Size Clusters from Mixtures of CdSe and CdS Samples.

The synthetic application of prenucleation-stage samples of colloidal semiconductor quantum dots (QDs) is in its infancy. It is shown that when two prenucleation-stage samples of binary CdSe and CdS are mixed, ternary CdSeS magic-size clusters (MSCs) grow at room temperature in dispersion. As the amount of the CdS sample increases, the optical absorption of the CdSeS MSCs blueshifts from ≈380 to ≈360 nm. It is proposed that the cluster in the CdSe sample reacts with the CdS monomer from the CdS sample. The monomer substitution reaction of CdSe by CdS can proceed continuously; thus, CdSeS MSCs with tunable compositions are obtained. The present study provides compelling evidence that clusters formed in the prenucleation stage of QDs. The clusters are precursor compounds (PCs) of MSCs, transforming at room temperature with the thermoneutrality principle of isodesmic reactions. The nucleation and growth of QDs follows a multi-step non-classical instead of one-step classical nucleation model.

First in-vivo magic angle directional imaging using dedicated low-field MRI.

PURPOSE: To report the first in-vivo results from exploiting the magic angle effect, using a dedicated low-field MRI scanner that can be rotated about two axes. The magic angle directional imaging (MADI) method is used to depict collagen microstructures with 3D collagen tractography of knee ligaments and the meniscus. METHODS: A novel low-field MRI system was developed, based on a transverse field open magnet, where the magnet can be rotated about two orthogonal axes. Sets of volume scans at various orientations were obtained in healthy volunteers. The experiments focused on the anterior cruciate ligament (ACL) and the meniscus of the knee. The images were co-registered, anatomical regions of interest (ROIs) were selected and the collagen fiber orientations in each voxel were estimated from the observed image intensity variations. The 3D collagen tractography was superimposed on conventional volume images. RESULTS: The MADI method was successfully employed for the first time producing in-vivo results comparable to those previously reported for excised animal specimens using conventional MRI. Tractography plots were generated for the ACL and the menisci. These results are consistent with the known microstructure of collagen fibers in these tissues. CONCLUSION: Images obtained using low-field MRI with 1 mm3 resolution were of sufficient quality for the MADI method, which was shown to produce high quality in-vivo information of collagen microstructures. This was achieved using a cost effective and sustainable low-field magnet making the technique potentially accessible and scalable, potentially changing the way we image injuries or disease in joints.

Exploring natural genetic diversity in a bread wheat multi-founder population: Dual imaging of photosynthesis and stomatal kinetics.

A better understanding of crop phenotype under dynamic environmental conditions will help inform the development of new cultivars with superior adaptation to constantly changing field conditions. Recent research has shown that optimising photosynthetic and stomatal conductance traits holds promise for improved crop performance. However, standard phenotyping tools such as gas-exchange systems are limited by their throughput. In this work, a novel approach based on a bespoke gas-exchange chamber allowing combined measurement of the quantum yield of photosystem II (PSII) with an estimation of stomatal conductance via thermal imaging, was used to phenotype a range of bread wheat (Triticum aestivum L.) genotypes, that were a sub-set of a multi-founder experimental population. Datasets were further supplemented by measurement of photosynthetic capacity and stomatal density. First, we showed that measurement of stomatal traits using our dual imaging system compared to standard IRGA methods showed good agreement between the two methods (R2=0.86) for the rapidity of stomatal opening (Ki), with the dual-imager method resulting in less intra-genotype variation. Using the dual-imaging methods, and traditional approaches we found broad and significant variation in key traits, including photosynthetic CO2 uptake at saturating light and ambient CO2 concentration (Asat), photosynthetic CO2 uptake at saturating light and elevated CO2 concentration (Amax), the maximum velocity of Rubisco for carboxylation (Vcmax), time for stomatal opening (Ki), and leaf evaporative cooling. Anatomical analysis revealed significant variation in flag leaf adaxial stomatal density. Associations between traits highlighted significant relationships between leaf evaporative cooling, leaf stomatal conductance under low (gsmin) and high (gsmax) light intensity, and the operating efficiency of PSII (Fq'/Fm'), highlighting the importance of stomatal conductance and stomatal rapidity in maintaining optimal leaf temperature for photosynthesis in wheat. Additionally, gsmin and gsmax were positively associated, indicating that potential combination of preferable traits (i.e. inherently high gsmax, low Ki and maintained leaf evaporative cooling) are present in wheat. This work highlights for the first time the effectiveness of thermal imaging in screening dynamic stomatal conductance in a large panel of wheat genotypes. The wide phenotypic variation observed suggested the presence of exploitable genetic variability in bread wheat for dynamic stomatal conductance traits and photosynthetic capacity for targeted optimisation within future breeding programs.

Solvent-Free Mechanosynthesis of Oligopeptides by Coupling Peptide Segments of Different Lengths - Elucidating the Role of Cesium Carbonate in Ball Mill Processes.

We report an idea for the synthesis of oligopeptides using a solvent-free ball milling approach. Our concept is inspired by block play, in which it is possible to construct different objects using segments (blocks) of different sizes and lengths. We prove that by having a library of short peptides and employing the ball mill mechanosynthesis (BMMS) method, peptides can be easily coupled to form different oligopeptides with the desired functional and biological properties. Optimizing the BMMS process we found that the best yields we obtained when TBTU and cesium carbonate were used as reagents. The role of Cs2CO3 in the coupling mechanism was followed on each stage of synthesis by 1H, 13C and 133Cs NMR employing Magic Angle Spinning (MAS) techniques. It was found that cesium carbonate acts not only as a base but is also responsible for the activation of substrates and intermediates. The unique information about the BMMS mechanism is based on the analysis of 2D NMR data. The power of BMMS is proved by the example of different peptide combinations, 2+2, 3+2, 4+2, 5+2 and 4+4. The tetra-, penta-, hexa-, hepta- and octapeptides obtained under this project were fully characterized by MS and NMR techniques.

Probing Noncovalent Interactions by Fast Magic-Angle Spinning NMR at 100†kHz and More.

Noncovalent interactions are the basis for a large number of chemical and biological molecular-recognition processes, such as those occurring in supramolecular chemistry, catalysis, solid-state reactions in mechanochemistry, protein folding, protein-nucleic acid binding, and biomolecular phase separation processes. In this perspective article, some recent developments in probing noncovalent interactions by proton-detected solid-state Nuclear Magnetic Resonance (NMR) spectroscopy at Magic-Angle Spinning (MAS) frequencies of 100 kHz and more are reviewed. The development of MAS rotors with decreasing outer diameters, combined with the development of superconducting magnets operating at high static magnetic-field strengths up to 28.2 T (1200 MHz proton Larmor frequency) improves resolution and sensitivity in proton-detected solid-state NMR, which is the fundamental requirement for shedding light on noncovalent interactions in solids. The examples reported in this article range from protein-nucleic acid binding in large ATP-fueled motor proteins to a hydrogen-π interaction in a calixarene-lanthanide complex.

Dual site reactivity of indole-3-Schiff bases with S/Se/Cl substituted ketenes for stereoselective C-4 substituted indole-ß-lactams, biological evaluations, magic chloro effect and molecular docking studies.

A convenient methodology for C-4 indole-ß-lactam hybrids with chloro, sulphur and seleno substitutions through dual site reactivity of indole-3-Schiff bases towards ketenes has been developed. The reaction proceeded in a stereospecific manner with the exclusive formation of trans-ß-lactams assigned with respect to C3-H and C4-H. The synthesized novel ß-lactams have been characterized with the help of elemental analysis (CHNS) and spectroscopic techniques viz.1H NMR, 13C NMR, DEPT 135, HSQC and IR. The trans configuration was further estabilished based on X-ray crystallographic data. Examination of antibacterial properties unveiled that only derivatives 5a and 5b, featuring chloro substitution, exhibited potent activities, underscoring the emergence of the recently coined term "magic chloro effect". Molecular docking analysis provided additional support for the observed in vitro antibacterial activities of compounds 5a-b.

There's "magic" in comparative cognition.

Among the many important empirical and theoretical contributions in her career Clayton and her colleagues advanced the idea that comparative cognition researchers would benefit from considering the role of magic and the techniques of the magician in some areas of cross-species cognitive study. They provided compelling and exciting studies using the techniques of the magician and demonstrated how those affect nonhuman animals that rely on vision, showing that there are similarities and dissimilarities in how susceptible some nonhuman species are to the magician's effects that typically work so well on human observers.

Elucidating structure and metabolism of insect biomaterials by solid-state NMR.

Among the many natural biomaterials for which information on atomic-level structure and reorientational motion can offer essential clues to function, insoluble multi-component composites with limited degrees of order are among the most challenging to study. Despite its limited sensitivity, solid-state NMR (ssNMR) is often the technique of choice to ferret out these details in carbon- and nitrogen-rich materials: this spectroscopic approach can probe many biomaterials in their native or near-native states, either with or without the introduction of stable NMR-active isotopes, or with the assistance of dynamic nuclear polarization technology. During a span of close to four decades, such research targets and ssNMR approaches have been exemplified by insects, a diverse and evolutionarily agile group of organisms with global impacts that include ecology, agriculture, and human disease. In this short review, we present case studies on insect cuticles that range from protective exoskeletons and egg capsules to the wing structures that enable flight and showcase nature's awe-inspiring beauty, highlighting the use of ssNMR spectroscopy to profile chemical composition, elucidate macromolecular architecture, and monitor metabolic development in these fascinating biological assemblies.

Carbon-detected deuterium solid-state NMR rotating frame relaxation measurements for protein methyl groups under magic angle spinning.

Deuterium rotating frame solid-state NMR relaxation measurements (2H R1ρ) are important tools in quantitative studies of molecular dynamics. We demonstrate how 2H to 13C cross-polarization (CP) approaches under 10-40 kHz magic angle spinning rates can be combined with the 2H R1ρ blocks to allow for extension of deuterium rotating frame relaxation studies to methyl groups in biomolecules. This extension permits detection on the 13C nuclei and, hence, for the achievement of site-specific resolution. The measurements are demonstrated using a nine-residue low complexity peptide with the sequence GGKGMGFGL, in which a single selective -13CD3 label is placed at the methionine residue. Carbon-detected measurements are compared with the deuterium direct-detection results, which allows for fine-tuning of experimental approaches. In particular, we show how the adiabatic respiration CP scheme and the double adiabatic sweep on the 2H and 13C channels can be combined with the 2H R1ρ relaxation rates measurement. Off-resonance 2H R1ρ measurements are investigated in addition to the on-resonance condition, as they extent the range of effective spin-locking field.

The value of synthetic MRI for quantitative analysis in the diagnosis of cervical lymph node metastasis in thyroid cancer.

BACKGROUND: Preoperative effective assessment of cervical lymph node metastasis in thyroid cancer plays an important role in formulating the surgical plan. PURPOSE: To investigate the significance of synthetic magnetic resonance imaging (MRI) for quantitatively analyzing cervical lymph node metastasis in thyroid cancer. MATERIAL AND METHODS: A retrospective analysis was conducted on 30 patients with thyroid cancer, consisting of 19 thyroid cancer nodules, 45 metastatic lymph nodes, and 47 non-metastatic lymph nodes. Regions of interest (ROIs) for each type of nodule were manually delineated using a workstation. Quantitative parameters, such as T1, T2, and proton density (PD) values, were automatically extracted from synthetic MRI scans. Statistical tests and regression analysis were performed to assess differences and correlations among the quantitative parameters. RESULTS: There were no significant differences in the quantitative parameter values between the primary tumor and metastatic lymph node tissues (P > 0.05). However, significant differences were observed in the quantitative parameters between the primary tumor and non-metastatic lymph node tissues and between the metastatic and non-metastatic lymph node tissues (P < 0.05). The diagnostic accuracy for cervical lymph node metastasis in thyroid cancer was 94.4% for the T1 and T2 combined index, 91.9% for T2, 86.8% for T1, and 71.7% for PD values. CONCLUSION: The application of quantitative parameters from synthetic MRI can assist clinicians in accurately planning surgical interventions for thyroid cancer patients before surgery.