Geometric frustration of Jahn-Teller order in the infinite-layer lattice.

The Jahn-Teller effect, in which electronic configurations with energetically degenerate orbitals induce lattice distortions to lift this degeneracy, has a key role in many symmetry-lowering crystal deformations1. Lattices of Jahn-Teller ions can induce a cooperative distortion, as exemplified by LaMnO3 (refs. 2,3). Although many examples occur in octahedrally4 or tetrahedrally5 coordinated transition metal oxides due to their high orbital degeneracy, this effect has yet to be manifested for square-planar anion coordination, as found in infinite-layer copper6,7, nickel8,9, iron10,11 and manganese oxides12. Here we synthesize single-crystal CaCoO2 thin films by topotactic reduction of the brownmillerite CaCoO2.5 phase. We observe a markedly distorted infinite-layer structure, with ångström-scale displacements of the cations from their high-symmetry positions. This can be understood to originate from the Jahn-Teller degeneracy of the dxz and dyz orbitals in the d7 electronic configuration along with substantial ligand-transition metal mixing. A complex pattern of distortions arises in a [Formula: see text] tetragonal supercell, reflecting the competition between an ordered Jahn-Teller effect on the CoO2 sublattice and the geometric frustration of the associated displacements of the Ca sublattice, which are strongly coupled in the absence of apical oxygen. As a result of this competition, the CaCoO2 structure forms an extended two-in-two-out type of Co distortion following 'ice rules'13.

O-Glycome Profiling of Breast Cancer Cell Lines to Understand Breast Cancer Brain Metastasis.

Breast cancer is the second leading cause of cancer-related death among women and a major source of brain metastases. Despite the increasing incidence of brain metastasis from breast cancer, the underlying mechanisms remain poorly understood. Altered glycosylation is known to play a role in various diseases including cancer metastasis. However, profiling studies of O-glycans and their isomers in breast cancer brain metastasis (BCBM) are scarce. This study analyzed the expression of O-glycans and their isomers in human breast cancer cell lines (MDA-MB-231, MDA-MB-361, HTB131, and HTB22), a brain cancer cell line (CRL-1620), and a brain metastatic breast cancer cell line (MDA-MB-231BR) using nanoLC-MS/MS, identifying 27 O-glycan compositions. We observed significant upregulation in the expression of HexNAc1Hex1NeuAc2 and HexNAc2Hex3, whereas the expression of HexNAc1Hex1NeuAc1 was downregulated in MDA-MB-231BR compared to other cell lines. In our isomeric analysis, we observed notable alterations in the isomeric forms of the O-glycan structure HexNAc1Hex1NeuAc1 in a comparison of different cell lines. Our analysis of O-glycans and their isomers in cancer cells demonstrated that changes in their distribution can be related to the metastatic process. We believe that our investigation will contribute to an enhanced comprehension of the significance of O-glycans and their isomers in BCBM.

MS-based glycomics and glycoproteomics methods enabling isomeric characterization.

Glycosylation is one of the most significant and abundant posttranslational modifications in mammalian cells. It mediates a wide range of biofunctions, including cell adhesion, cell communication, immune cell trafficking, and protein stability. Also, aberrant glycosylation has been associated with various diseases such as diabetes, Alzheimer's disease, inflammation, immune deficiencies, congenital disorders, and cancers. The alterations in the distributions of glycan and glycopeptide isomers are involved in the development and progression of several human diseases. However, the microheterogeneity of glycosylation brings a great challenge to glycomic and glycoproteomic analysis, including the characterization of isomers. Over several decades, different methods and approaches have been developed to facilitate the characterization of glycan and glycopeptide isomers. Mass spectrometry (MS) has been a powerful tool utilized for glycomic and glycoproteomic isomeric analysis due to its high sensitivity and rich structural information using different fragmentation techniques. However, a comprehensive characterization of glycan and glycopeptide isomers remains a challenge when utilizing MS alone. Therefore, various separation methods, including liquid chromatography, capillary electrophoresis, and ion mobility, were developed to resolve glycan and glycopeptide isomers before MS. These separation techniques were coupled to MS for a better identification and quantitation of glycan and glycopeptide isomers. Additionally, bioinformatic tools are essential for the automated processing of glycan and glycopeptide isomeric data to facilitate isomeric studies in biological cohorts. Here in this review, we discuss commonly employed MS-based techniques, separation hyphenated MS methods, and software, facilitating the separation, identification, and quantitation of glycan and glycopeptide isomers.

Orbital Order Melting at Reduced Dimensions.

The orbital degree of freedom, strongly coupled with the lattice and spin, is an important factor when designing correlated functions. Whether the long-range orbital order is stable at reduced dimensions and, if not, what the critical thickness is remains a tantalizing question. Here, we report the melting of orbital ordering, observed by controlling the dimensionality of the canonical eg1 orbital system LaMnO3. Epitaxial films are synthesized with vertically aligned orbital ordering planes on an orthorhombic substrate, so that reducing film thickness changes the two-dimensional planes into quasi-one-dimensional nanostrips. The orbital order appears to be suppressed below the critical thickness of about six unit cells by changing the characteristic phonon modes and making the Mn d orbital more isotropic. Density functional calculations reveal that the electronic energy instability induced by bandwidth narrowing via the dimensional crossover and the interfacial effect causes the absence of orbital order in the ultrathin thickness.

Targeted N-Glycan Analysis with Parallel Reaction Monitoring Using a Quadrupole-Orbitrap Hybrid Mass Spectrometer.

Targeted mass spectrometric analysis is widely employed across various omics fields. The approach has been successfully employed for the structural analysis of proteins, glycans, lipids, and small molecules. Selected reaction monitoring and multiple reaction monitoring (MRM) have been a method of choice for targeted structural studies of biomolecules. However, innovations in instrument designs have led to the development of parallel reaction monitoring (PRM). PRM detects all product ions simultaneously rather than optimizing/preselecting the target glycan transitions, simplifying the analytical workflow. By reducing background interference, increasing selectivity/specificity, and improving data quality, PRM allows reliable quantification of target glycans in complex matrices. PRM can also improve sensitivity for detecting low-abundance target glycans and reduce low-level limit of quantification values with an improved S/N ratio. PRM's advantages are attributed to the development of sensitive and highly selective mass analyzers, orbitrap, and time of flight. In this study, we developed a sensitive PRM method for the quantitative analysis of permethylated N-glycans, an important class of disease biomarkers, using a quadrupole-orbitrap hybrid mass spectrometer. Pooled human cerebrospinal fluid was used for the study as a source of permethylated N-glycans. The method illustrates the fragmentation of N-glycans at different collision energies as well as the optimization of collision energy. The method also detects low-abundance N-glycans more efficiently than MRM. This study is the first attempt to develop a sensitive PRM-based method to analyze permethylated N-glycans.

Direct Comparison of N-Glycans and Their Isomers Derived from Spike Glycoprotein 1 of MERS-CoV, SARS-CoV-1, and SARS-CoV-2.

The emergence of COVID-19 pandemic has engaged the scientific community around the globe in the rapid development of effective therapeutics and vaccines. Owing to its crucial role in the invasion of the host cell, spike (S) glycoprotein is one of the major targets in these studies. The S1 subunit of the S protein (S1 protein) accommodates the receptor-binding domain, which enables the initial binding of the virus to the host cell. Being a heavily glycosylated protein, numerous studies have investigated its glycan composition. However, none of the studies have explored the isomeric glycan distribution of this protein. Furthermore, this isomeric glycan distribution has never been compared to that in S1 proteins of other coronaviruses, severe acute respiratory syndrome coronavirus 1 and Middle East respiratory syndrome coronavirus, which were responsible for past epidemics. This study explores the uncharted territory of the isomeric glycan distribution in the coronaviruses' S1 protein using liquid chromatography coupled to tandem mass spectrometry. We believe that our data would facilitate future investigations to study the role of isomeric glycans in coronavirus viral pathogenesis.

Mesoporous Graphitized Carbon Column for Efficient Isomeric Separation of Permethylated Glycans.

Post-translational modifications are vital aspects of functional proteins. Therefore, it is critical to understand their roles in biological processes. Glycosylation is particularly challenging to study among these modifications due to the heterogeneity displayed by the glycans in terms of their isomers. Thus, researchers continue to strive for the development of efficient liquid chromatography techniques for isomeric separation of glycans. Porous graphitized carbon (PGC) nano column has been one of the most widely used columns for this purpose, but poor stability and lack of reproducibility led to its discontinuation. In our endeavor to find an alternative stationary phase for isomeric glycan separation, we tested the mesoporous graphitized carbon (MGC) material. Unprecedentedly, satisfactory results were obtained with a column only 1 cm long, which was tested on permethylated N-glycans derived from model glycoproteins as well as biological samples. The column was found to be reproducible across months as well as across different column preparations. Additionally, to decrease the dead volume and attain a better resolution, MGC was utilized to pack a 1 cm length of a pulled capillary nanospray emitter and again demonstrated efficient isomeric separation. Thus, MGC proved to be a suitable stationary phase to obtain efficient isomeric separation of permethylated N-glycans with 1 cm-long packing length, in both capillary columns and packed nanospray emitters.

Using micro pillar array columns (µPAC) for the analysis of permethylated glycans.

Glycosylation is a complex and common post-translational modification of proteins. To study glycosylation, liquid chromatography-mass spectrometry (LC-MS) is often used to profile and structurally characterize the glycans in biological systems. While bed packed reverse phase columns are frequently utilized for the separation of permethylated glycans, the use of newly commercialized micro array pillar nanoLC columns (µPAC) have not been demonstrated previously. Owing to its advantages such as low back pressure, reproducibility, and durability, we have investigated the viability of the µPAC for the analysis of permethylated glycans. In this work, we demonstrate the online purification ability of µPAC trapping column compared against PepMap trapping column. We also found that the 50 cm µPAC can be used for the analysis of both permethylated N- and O-glycans. The use of 50 cm µPAC was compared against the previous method. The use of 200 cm µPAC was also investigated for the permethylated glycan analysis. 200 cm µPAC demonstrated efficient separation of oligomannose glycan isomers as well as other complex glycans.

N-Glycomics of Cerebrospinal Fluid: Method Comparison.

Cerebrospinal fluid (CSF) contains valuable biological and neurological information. However, its glycomics analysis is hampered due to the low amount of protein in the biofluid, as has been demonstrated by other glycomics studies using a substantial amount of CSF. In this work, we investigated different N-glycan sample preparation approaches to develop a more sensitive method. These methods, one with an increased amount of buffer solution during the N-glycan release step with a lower amount of sample volume and the other with Filter-Aided N-Glycan Separation (FANGS), were compared with recent work to demonstrate their effectiveness. It was demonstrated that an increased amount of buffer solution showed higher intensity in comparison to the previously published method and FANGS. This suggested that digestion efficiency during the N-glycan release step was not in an optimal condition from the previously published method, and that there is a substantial loss of sample with FANGS when preparing N-glycans from CSF.

Glucose unit index (GUI) of permethylated glycans for effective identification of glycans and glycan isomers.

Retention time is the most common and widely used criterion to report the separation of glycans using Liquid Chromatography (LC), but it varies widely across different columns, instruments and laboratories. This variation is problematic when inter-laboratory data is compared. Furthermore, it influences reproducibility and hampers efficient data interpretation. In our endeavor to overcome this variance, we propose the use of the Glucose Unit Index (GUI) on C18 and PGC column-based separation of reduced and permethylated glycans. GUI has previously been utilized for retention time normalization of native and labeled glycans. We evaluated this method with reduced and permethylated glycans derived from model glycoproteins fetuin and ribonuclease B (RNase B), and then implemented it to human blood serum to generate C18 and PGC column-based isomeric glycan libraries. GUI values for glycan compositions were calculated with respect to the glucose units derived from dextrin, which was employed as an elution standard. The GUI values were validated on three different LC systems (UltiMate 3000 Nano UHPLC systems) in two laboratories to ensure the reliability and reproducibility of the method. Applicability on real samples was demonstrated using human breast cancer cell lines. A total of 116 permethylated N-glycans separated on a C18 column and 134 glycans separated on a PGC column were compiled in a library. Overall, the established GUI method and the demonstration of reproducible inter- and intra-laboratory GUI values would aid the future development of automated glycan and isomeric glycan identification methods.

N-Glycan Profile of Cerebrospinal Fluids from Alzheimer's Disease Patients Using Liquid Chromatography with Mass Spectrometry.

Glycosylation, an essential post-translational protein modification, is known to be altered in a variety of diseases, including neurodegenerative diseases such as Alzheimer's disease (AD), which is one of the most common neurodegenerative disorders that results in cognitive and memory impairments. To investigate the progression of such a condition, cerebrospinal fluid (CSF), a unique biofluid that may possess significant biochemical and neurochemical changes due to the disease, is utilized. However, due to the low concentration of proteins in CSF, a large volume of the biofluid is often required to comprehensively characterize the glycome in CSF. In this work, a glycomic study of CSF was performed using as little as 10 µL of CSF. This approach was executed with permethylation of released N-glycans with minimal sample cleanup, in conjunction with an online purification system attached to liquid chromatography and a high-resolution mass spectrometer. This technique was then applied to clinical samples. Preliminary data suggest that fucosylated and bisecting GlcNAc structures were higher in abundances in females with AD, while both females and males exhibited lower abundances of high-mannose structures. Although there seems to be statistically significant differences between disease state and disease-free CSF, due to the lack of number of samples, further validation study should be conducted.

Advances in mass spectrometry-based glycomics.

The diversification of the chemical properties and biological functions of proteins is attained through posttranslational modifications, such as glycosylation. Glycans, which are covalently attached to proteins, play a vital role in cell activities. The microheterogeneity and complexity of glycan structures associated with proteins make comprehensive glycomic analysis challenging. However, recent advancements in mass spectrometry (MS), separation techniques, and sample preparation methods have primarily facilitated structural elucidation and quantitation of glycans. This review focuses on describing recent advances in MS-based techniques used for glycomic analysis (2012-2018), including ionization, tandem MS, and separation techniques coupled with MS. Progress in glycomics workflow involving glycan release, purification, derivatization, and separation will also be highlighted here. Additionally, the recent development of quantitative glycomics through comparative and multiplex approaches will also be described.

Characterization of isomeric glycan structures by LC-MS/MS.

The characterization of glycosylation is critical for obtaining a comprehensive view of the regulation and functions of glycoproteins of interest. Due to the complex nature of oligosaccharides, stemming from variable compositions and linkages, and ion suppression effects, the chromatographic separation of glycans, including isomeric structures, is necessary for exhaustive characterization by MS. This review introduces the fundamental principles underlying the techniques in LC utilized by modern day glycomics researchers. Recent advances in porous graphitized carbon, reverse phase, ion exchange, and hydrophilic interaction LC utilized in conjunction with MS, for the characterization of protein glycosylation, are described with an emphasis on methods capable of resolving isomeric glycan structures.

Assessing the hydrophobicity of glycopeptides using reversed-phase liquid chromatography and tandem mass spectrometry.

Retention time is one of the most important parameters that has been widely used to demonstrate the separation results obtained from liquid chromatography (LC) platforms. However, retention time can shift when samples are tested with different instruments and laboratories, which hinders the identification process of analytes when comparing data collected from different LC systems. To address this problem, hydrophobicity index was introduced for retention time normalization of the glycopeptides separated by reversed-phase LC (RPLC). Tandem MS was used for the detection and identification of glycopeptides. In addition, the influence of different types of glycans on the hydrophobicity of peptide backbones was studied by comparing the retention time of glycopeptides with their non-glycosylated counterparts. The hydrophobicity of tryptic digested glycopeptides derived from model glycoproteins, including bovine fetuin, α1-acid glycoprotein, and haptoglobin from human plasma, were evaluated based on the hydrophobicity index of the standard peptides from a peptide retention time calibration mixture. The reduction of hydrophobicity of multiple peptide backbones was observed due to the hydrophilic glycan structures. By comparing the hydrophobicity index of glycopeptides collected from different time and instruments, the day-to-day and lab-to-lab comparisons suggested high reliability and reproducibility of this approach. The RSD% of hydrophobicity index from inter-lab experiments was 1.2%, while the RSD% of retention time was 5.1%. Then, the applications of this method were demonstrated on complex glycopeptide samples extracted from human blood serum. The hydrophobicity index can be applied to address the retention time shift when using different instruments, thereby boosting confidence of the characterization of glycopeptides.

Exploring TEM Coherence Properties via Speckle Contrast Analysis in Coherent Electron Scattering of Amorphous Material.

We investigate the coherence properties of a transmission electron microscope by analyzing nano-diffraction speckles originating from bulk metallic glass. The spatial correlation function of the coherent diffraction patterns, obtained in the transmission geometry, reveals the highly coherent nature of the electron probe beam and its spatial dimension incident on the sample. Quantitative agreement between the measured speckle contrast and an analytical model yields estimates for the transverse and longitudinal coherence lengths of the source. We also demonstrate that the coherence can be controlled by changing the beam convergence angle. Our findings underscore the preservation of electron beam coherence throughout the electron optics, as evidenced by the high-contrast speckles observed in the scattering patterns of the amorphous system. This study paves the way for the application of advanced coherent diffraction methodologies to investigate local structures and dynamics occurring at atomic-length scales across a diverse range of materials.

Strong Rashba parameter of two-dimensional electron gas at CaZrO3/SrTiO3 heterointerface.

We synthesized a CaZrO3/SrTiO3 oxide heterostructure, which can serve as an alternative to LaAlO3/SrTiO3, and confirmed the generation of 2-dimensional electron gas (2-DEG) at the heterointerface. We analyzed the electrical-transport properties of the 2-DEG to elucidate its intrinsic characteristics. Based on the magnetic field dependence of resistance at 2 K, which exhibited Weak Anti-localization (WAL) behaviors, the fitted Rashba parameter values were found to be about 12-15 × 10-12 eV*m. These values are stronger than the previous reported Rashba parameters obtained from the 2-DEGs in other heterostructure systems and several layered 2D materials. The observed strong spin-orbit coupling (SOC) is attributed to the strong internal electric field generated by the lattice mismatch between the CaZrO3 layer and SrTiO3 substrate. This pioneering strong SOC of the 2-DEG at the CaZrO3/SrTiO3 heterointerface may play a pivotal role in the developing future metal oxide-based quantum nanoelectronics devices.

Time-Resolved Structural Measurement of Thermal Resistance across a Buried Semiconductor Heterostructure Interface.

The precise control and understanding of heat flow in heterostructures is pivotal for advancements in thermoelectric energy conversion, thermal barrier coatings, and efficient heat management in electronic and optoelectronic devices. In this study, we employ high-angular-resolution time-resolved X-ray diffraction to structurally measure thermal resistance in a laser-excited AlGaAs/GaAs semiconductor heterostructure. Our methodology offers femtometer-scale spatial sensitivity and nanosecond time resolution, enabling us to directly observe heat transport across a buried interface. We corroborate established Thermal Boundary Resistance (TBR) values for AlGaAs/GaAs heterostructures and demonstrate that TBR arises from material property discrepancies on either side of a nearly flawless atomic interface. This work not only sheds light on the fundamental mechanisms governing heat flow across buried interfaces but also presents a robust experimental framework that can be extended to other heterostructure systems, paving the way for optimized thermal management in next-generation devices.

Observing femtosecond orbital dynamics in ultrafast Ge melting with time-resolved resonant X-ray scattering.

Photoinduced nonequilibrium phase transitions have stimulated interest in the dynamic interactions between electrons and crystalline ions, which have long been overlooked within the Born-Oppenheimer approximation. Ultrafast melting before lattice thermalization prompted researchers to revisit this issue to understand ultrafast photoinduced weakening of the crystal bonding. However, the absence of direct evidence demonstrating the role of orbital dynamics in lattice disorder leaves it elusive. By performing time-resolved resonant X-ray scattering with an X-ray free-electron laser, we directly monitored the ultrafast dynamics of bonding orbitals of Ge to drive photoinduced melting. Increased photoexcitation of bonding electrons amplifies the orbital disturbance to expedite the lattice disorder approaching the sub-picosecond scale of the nonthermal regime. The lattice disorder time shows strong nonlinear dependence on the laser fluence with a crossover behavior from thermal-driven to nonthermal-dominant kinetics, which is also verified by ab initio and two-temperature molecular dynamics simulations. This study elucidates the impact of bonding orbitals on lattice stability with a unifying interpretation on photoinduced melting.

Heat Stress of Algal Partner Hinders Colonization Success and Alters the Algal Cell Surface Glycome in a Cnidarian-Algal Symbiosis.

Corals owe their ecological success to their symbiotic relationship with dinoflagellate algae (family Symbiodiniaceae). While the negative effects of heat stress on this symbiosis are well studied, how heat stress affects the onset of symbiosis and symbiont specificity is less explored. In this work, we used the model sea anemone, Exaiptasia diaphana (commonly referred to as Aiptasia), and its native symbiont, Breviolum minutum, to study the effects of heat stress on the colonization of Aiptasia by algae and the algal cell-surface glycome. Heat stress caused a decrease in the colonization of Aiptasia by algae that were not due to confounding variables such as algal motility or oxidative stress. With mass spectrometric analysis and lectin staining, a thermally induced enrichment of glycans previously found to be associated with free-living strains of algae (high-mannoside glycans) and a concomitant reduction in glycans putatively associated with symbiotic strains of algae (galactosylated glycans) were identified. Differential enrichment of specific sialic acid glycans was also identified, although their role in this symbiosis remains unclear. We also discuss the methods used to analyze the cell-surface glycome of algae, evaluate current limitations, and provide suggestions for future work in algal-coral glycobiology. Overall, this study provided insight into how stress may affect the symbiosis between cnidarians and their algal symbionts by altering the glycome of the symbiodinian partner. IMPORTANCE Coral reefs are under threat from global climate change. Their decline is mainly caused by the fragility of their symbiotic relationship with dinoflagellate algae which they rely upon for their ecological success. To better understand coral biology, researchers used the sea anemone, Aiptasia, a model system for the study of coral-algal symbiosis, and characterized how heat stress can alter the algae's ability to communicate to the coral host. This study found that heat stress caused a decline in algal colonization success and impacted the cell surface molecules of the algae such that it became more like that of nonsymbiotic species of algae. This work adds to our understanding of the molecular signals involved in coral-algal symbiosis and how it breaks down during heat stress.