Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution.

Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.

Ponesimod inhibits astrocyte-mediated neuroinflammation and protects against cingulum demyelination via S1P1 -selective modulation.

Ponesimod is a sphingosine 1-phosphate (S1P) receptor (S1PR) modulator that was recently approved for treating relapsing forms of multiple sclerosis (MS). Three other FDA-approved S1PR modulators for MS-fingolimod, siponimod, and ozanimod-share peripheral immunological effects via common S1P1 interactions, yet ponesimod may access distinct central nervous system (CNS) mechanisms through its selectivity for the S1P1 receptor. Here, ponesimod was examined for S1PR internalization and binding, human astrocyte signaling and single-cell RNA-seq (scRNA-seq) gene expression, and in vivo using murine cuprizone-mediated demyelination. Studies confirmed ponesimod's selectivity for S1P1 without comparable engagement to the other S1PR subtypes (S1P2,3,4,5 ). Ponesimod showed pharmacological properties of acute agonism followed by chronic functional antagonism of S1P1 . A major locus of S1P1 expression in the CNS is on astrocytes, and scRNA-seq of primary human astrocytes exposed to ponesimod identified a gene ontology relationship of reduced neuroinflammation and reduction in known astrocyte disease-related genes including those of immediate early astrocytes that have been strongly associated with disease progression in MS animal models. Remarkably, ponesimod prevented cuprizone-induced demyelination selectively in the cingulum, but not in the corpus callosum. These data support the CNS activities of ponesimod through S1P1 , including protective, and likely selective, effects against demyelination in a major connection pathway of the brain, the limbic fibers of the cingulum, lesions of which have been associated with several neurologic impairments including MS fatigue.

Electronic Structure of Heteronuclear Cerium-Platinum Clusters.

Beyond the now well-known strong catalyst-support interactions reported for ceria-supported platinum catalysts, intermetallic Ce-Pt compounds exhibit fascinating properties such as heavy fermion behavior and magnetic instability. Small heterometallic Ce-Pt clusters, which can provide insights into the local features that govern bulk phenomena, have been less explored. Herein, the anion photoelectron spectra of three small mixed Ce-Pt clusters, Ce2OPt-, Ce2Pt-, and Ce3Pt-, are presented and interpreted with supporting density functional theory calculations. The calculations, which are readily reconciled with the experimental spectra, suggest the presence of numerous close-lying spin states, including states in which the Ce 4f electrons are ferromagnetically coupled or antiferromagnetically coupled. The Pt center is consistently in a nominal -2 charge state in all cluster neutrals and anions, giving the Ce-Pt bond ionic character. Ce-Pt bonds are stronger than Ce-Ce bonds, and the O atom in Ce2OPt- coordinates only with the Ce centers. The energy of the singly occupied Ce-local 4f orbitals relative to the Pt-local orbitals changes with cluster composition. Discussion of the results includes potential implications for Ce-rich intermetallic materials.

Lysophosphatidic acid (LPA)-antibody (504B3) engagement detected by interferometry identifies off-target binding.

BACKGROUND: Lysophosphatidic acid (LPA) is a bioactive lysophospholipid that acts through its six cognate G protein-coupled receptors. As a family, lysophospholipids have already produced medicines (e.g., sphingosine 1-phosphate) as is being pursued for LPA through the use of specific antibodies that reduce ligand availability. METHODS: The binding properties of a commercially available, reportedly specific, monoclonal LPA antibody named 504B3 that is related to the clinical candidate Lpathomab/LT3015 were reexamined using a free solution assay (FSA) measured in a compensated interferometric reader (CIR). RESULTS: Measurement of 504B3 binding properties with an FSA-CIR approach revealed similar binding affinities for 504B3 against LPA as well as the non-LPA lipids, phosphatidic acid (PA) and lysophosphatidylcholine (LPC). CONCLUSIONS: Antibody binding specificity and sensitivity, particularly involving lipid ligands, can be assessed in solution and without labels using FSA-CIR. These findings could affect interpretations of both current and past basic and clinical studies employing 504B3 and related anti-LPA antibodies.

Unlabeled lysophosphatidic acid receptor binding in free solution as determined by a compensated interferometric reader.

Native interactions between lysophospholipids (LPs) and their cognate LP receptors are difficult to measure because of lipophilicity and/or the adhesive properties of lipids, which contribute to high levels of nonspecific binding in cell membrane preparations. Here, we report development of a free-solution assay (FSA) where label-free LPs bind to their cognate G protein-coupled receptors (GPCRs), combined with a recently reported compensated interferometric reader (CIR) to quantify native binding interactions between receptors and ligands. As a test case, the binding parameters between lysophosphatidic acid (LPA) receptor 1 (LPA1; one of six cognate LPA GPCRs) and LPA were determined. FSA-CIR detected specific binding through the simultaneous real-time comparison of bound versus unbound species by measuring the change in the solution dipole moment produced by binding-induced conformational and/or hydration changes. FSA-CIR identified KD values for chemically distinct LPA species binding to human LPA1 and required only a few nanograms of protein: 1-oleoyl (18:1; KD = 2.08 ± 1.32 nM), 1-linoleoyl (18:2; KD = 2.83 ± 1.64 nM), 1-arachidonoyl (20:4; KD = 2.59 ± 0.481 nM), and 1-palmitoyl (16:0; KD = 1.69 ± 0.1 nM) LPA. These KD values compared favorably to those obtained using the previous generation back-scattering interferometry system, a chip-based technique with low-throughput and temperature sensitivity. In conclusion, FSA-CIR offers a new increased-throughput approach to assess quantitatively label-free lipid ligand-receptor binding, including nonactivating antagonist binding, under near-native conditions.

Lysophospholipid G protein-coupled receptor binding parameters as determined by backscattering interferometry.

Lysophosphatidic acid (LPA) activates cognate G protein-coupled receptors (GPCRs) to initiate biological signaling cascades. Lysophospholipid (LP) receptor binding properties remain incompletely assessed because of difficulties with ligand lipophilicity and lipid "stickiness." These inherent attributes produce high levels of nonspecific binding within cell-membrane preparations used to assess GPCRs, as has been shown in classical binding assays using radiolabeled ligands, making accurate measurements of lipid binding kinetics difficult to achieve. Backscattering interferometry (BSI) is an optical technology that measures molecular binding interactions by reporting changes in the refractive index of a solution after binding events. Here, we report the use of BSI to assess LPA1 for its ability to bind to naturally occurring lipids and a synthetic LPA1 antagonist (ONO-9780307), under both primary- and competition-binding conditions. Assessment of 12 different lipids demonstrated that the known LP ligand, 1-oleoyl-LPA, as well as an endocannabinoid metabolite, anandamide phosphate, are specific ligands for LPA1, whereas other LPs tested were not. Newly determined dissociation constants (Kd values) for orthosteric lipid ligands approximated 10-9 M, substantially lower (i.e., with higher affinity) than measured Kd values in classical binding or cell-based assays. These results demonstrate that BSI may have particular utility in assessing binding interactions between lipid receptors and their lipid ligands and could provide new screening approaches for lipid receptor identification and drug discovery.

Molybdenum Oxide Cluster Anion Reactions with C2H4 and H2O: Cooperativity and Chemifragmentation.

To probe the mechanism of sacrificial reagents in catalytic processes, product distributions from MoxOy- clusters reacting individually with C2H4 and H2O are compared with those from reactions with a C2H4 + H2O mixture, with the thermodynamics explored computationally. These molecules were chosen to model production of H2 from H2O via H2O + C2H4 → H2 + CH3CHO, mediated by MoxOy- clusters. H2O is known to sequentially oxidize MoxOy- suboxide clusters while producing H2, resulting in less reactive clusters. MoxOy- (y ∼ x) clusters undergo chemi-fragmentation reactions with C2H4, with MoxOyC2Hz- complexes forming as the cluster oxidation state increases. Unique species observed in reactions with the C2H4 + H2O mixture, Mo2O5C2H2- and MoO3C2H4-, suggest that the internal energy gained in new Mo-O bond formation from oxidation by H2O opens additional reaction channels. C2H3O- is observed uniquely in reactions with the C2H4 + H2O mixture, giving indirect evidence of CH3CHO formation via the cluster mediated H2O + C2H4 → H2 + CH3CHO reaction; C2H3O- can form via dissociative electron attachment to CH3CHO. Calculations support mechanisms that invoke participation of two ethylene molecules on thermodynamically favorable pathways leading to experimentally observed products.

Insight into ethylene interactions with molybdenum suboxide cluster anions from photoelectron spectra of chemifragments.

Recent studies on reactions between MoxOy- cluster anions and H2O/C2H4 mixtures revealed a complex web of addition, hydrogen evolution, and chemifragmentation reactions, with chemifragments unambiguously connected to cluster reactions with C2H4. To gain insight into the molecular-scale interactions along the chemifragmentation pathways, the anion photoelectron (PE) spectra of MoC2H2-, MoC4H4-, MoOC2H2-, and MoO2C2H2- formed directly in MoxOy- + C2H4 (x > 1; y ≥ x) reactions, along with supporting CCSD(T) and density functional theory calculations, are presented and analyzed. The complexes have spectra that are all consistent with η2-acetylene complexes, though for all but MoC4H4-, the possibility that vinylidene complexes are also present cannot be definitively ruled out. Structures that are consistent with the PE spectrum of MoC2H2- differ from the lowest energy structure, suggesting that the fragment formation is under kinetic control. The PE spectrum of MoO2C2H2- additionally exhibits evidence that photodissociation to MoO2- + C2H2 may be occurring. The results suggest that oxidative dehydrogenation of ethylene is initiated by Lewis acid/base interactions between the Mo centers in larger clusters and the π orbitals in ethylene.

Hydrogen evolution from water using Mo-oxide clusters in the gas phase: DFT modeling of a complete catalytic cycle using a Mo2O4-/Mo2O5- cluster couple.

Density functional theory (DFT) calculations using a small metal cluster couple, Mo2O4-/Mo2O5-, are used to model a complete catalytic cycle for H2 production from water. While Mo2O4- is known to readily react with water to form Mo2O5- and release H2, the principal challenge is in reducing Mo2O5- to Mo2O4- to complete the cycle. We investigate the role of several potential sacrificial reagents (ethylene, propylene, CO and acetylene) that can reduce Mo2O5- after the initial oxidation. DFT calculations of the free energy reaction pathways demonstrate the presence of overall kinetically accessible barriers that are below the entrance channel (separated reactants) in the Mo2O4- + H2O reaction (step I) followed by the Mo2O5- + sacrificial reagent reactions (step II). Though the overall reaction is thermodynamically favorable, the first step is highly exothermic while the second step is endothermic. The deepest part of the potential energy surface is a complex of Mo2O5- with the sacrificial reagent. If the energy gained in the first reaction and the succeeding complex formation is not lost due to collisions, the subsequent barriers can be overcome, leading to possible catalytic applications of the Mo2O4-/Mo2O5- cluster couple in H2 production reactions.

Effect of Alkyl Group on MxOy(-) + ROH (M = Mo, W; R = Me, Et) Reaction Rates.

A systematic comparison of MxOy(-) + ROH (M = Mo vs W; R = Me vs Et) reaction rate coefficients and product distributions combined with results of calculations on weakly bound MxOy(-)·ROH complexes suggest that the overall reaction mechanism has three distinct steps, consistent with recently reported results on analogous MxOy(-) + H2O reactivity studies. MxOy(-) + ROH → MxOy+1(-) + RH oxidation reactions are observed for the least oxidized clusters, and MxOy(-) + ROH → MxOyROH(-) addition reactions are observed for clusters in intermediate oxidation states, as observed previously in MxOy(-) + H2O reactions. The first step is weakly bound complex formation, the rate of which is governed by the relative stability of the MxOy(-)·ROH charge-dipole complexes and the Lewis acid-base complexes. Calculations predict that MoxOy(-) clusters form more stable Lewis acid-base complexes than WxOy(-), and the stability of EtOH complexes is enhanced relative to MeOH. Consistent with this result, MoxOy(-) + ROH rate coefficients are higher than analogous WxOy(-) clusters. Rate coefficients range from 2.7 × 10(-13) cm(3) s(-1) for W3O8(-) + MeOH to 3.4 × 10(-11) cm(3) s(-1) for Mo2O4(-) + EtOH. Second, a covalently bound complex is formed, and anion photoelectron spectra of the several MxOyROH(-) addition products observed are consistent with hydroxyl-alkoxy structures that are formed readily from the Lewis acid-base complexes. Calculations indicate that addition products are trapped intermediates in the MxOy(-) + ROH → MxOy+1(-) + RH reaction, and the third step is rearrangement of the hydroxyl group to a metal hydride group to facilitate RH release. Trapped intermediates are more prevalent in MoxOy(-) reaction product distributions, indicating that the rate of this step is higher for WxOy+1RH(-) than for MoxOy+1RH(-). This result is consistent with previous computational studies on analogous MxOy(-) + H2O reactions predicting that barriers along the pathway in the rearrangement step are higher for MoxOy(-) reactions than for WxOy(-).

Role of weakly bound complexes in temperature-dependence and relative rates of M(x)O(y)(-) + H2O (M = Mo, W) reactions.

Results of a systematic comparison of the MoxOy (-) + H2O and WxOy (-) + H2O reaction rate coefficients are reported and compared to previous experimental and computational studies on these reactions. WxOy (-) clusters undergo more direct oxidation by water to yield WxOy+1 (-) + H2, while for MoxOy (-) clusters, production of MoxOyH2 (-) (trapped intermediates in the oxidation reaction) is comparatively more prevalent. However, MoxOy (-) clusters generally have higher rate coefficients than analogous WxOy (-) clusters if MoxOy+1H2 (-) formation is included. Results of calculations on the M2Oy (-) + H2O (M = Mo, W; y = 4, 5) reaction entrance channel are reported. They include charge-dipole complexes formed from long-range interactions, and the requisite conversion to a Lewis acid-base complex that leads to MxOy+1H2 (-) formation. The results predict that the Lewis acid-base complex is more strongly bound for MoxOy (-) clusters than for WxOy (-) clusters. The calculated free energies along this portion of the reaction path are also consistent with the modest anti-Arrhenius temperature dependence measured for most MoxOy (-) + H2O reactions, and the WxOy (-) + H2O reaction rate coefficients generally being constant over the temperature range sampled in this study. For clusters that exhibit evidence of both water addition and oxidation reactions, increasing the temperature increases the branching ratio toward oxidation for both species. A more direct reaction path to H2 production may therefore become accessible at modest temperatures for certain cluster stoichiometries and structures.

Mixed cerium-platinum oxides: Electronic structure of [CeO]Ptn (n = 1, 2) and [CeO2]Pt complex anions and neutrals.

The electronic structures of several small Ce-Pt oxide complexes were explored using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. Pt and Pt2 both accept electron density from CeO diatomic molecules, in which the cerium atom is in a lower-than-bulk oxidation state (+2 versus bulk +4). Neutral [CeO]Pt and [CeO]Pt2 complexes are therefore ionic, with electronic structures described qualitatively as [CeO(+2)]Pt(-2) and [CeO(+)]Pt2 (-), respectively. The associated anions are described qualitatively as [CeO(+)]Pt(-2) and [CeO(+)]Pt2 (-2), respectively. In both neutrals and anions, the most stable molecular structures determined by calculations feature a distinct CeO moiety, with the positively charged Ce center pointing toward the electron rich Pt or Pt2 moiety. Spectral simulations based on calculated spectroscopic parameters are in fair agreement with the spectra, validating the computationally determined structures. In contrast, when Pt is coupled with CeO2, which has no Ce-localized electrons that can readily be donated to Pt, the anion is described as [CeO2]Pt(-). The molecular structure predicted computationally suggests that it is governed by charge-dipole interactions. The neutral [CeO2]Pt complex lacks charge-dipole stabilizing interactions, and is predicted to be structurally very different from the anion, featuring a single Pt-O-Ce bridge bond. The PE spectra of several of the complexes exhibit evidence of photodissociation with Pt(-) daughter ion formation. The electronic structures of these complexes are related to local interactions in Pt-ceria catalyst-support systems.

Photoelectron spectrum of PrO(-).

The photoelectron (PE) spectrum of PrO(-) exhibits a short 835 ± 20 cm(-1) vibrational progression of doublets (210 ± 30 cm(-1) splitting) assigned to transitions from the 4f(2) [(3)H4] σ6s (2) Ω = 4 anion ground state to the 4f(2) [(3)H4] σ6s Ω = 3.5 and 4.5 neutral states. This assignment is analogous to that of the recently reported PE spectrum of CeO(-), though the 82 cm(-1) splitting between the 4f [(2)F2.5] σ6s Ω = 2 and Ω = 3 CeO neutral states could not be resolved [Ray et al., J. Chem. Phys. 142, 064305 (2015)]. The origin of the transition to the Ω = 3.5 neutral ground state is 0.96 ± 0.01 eV, which is the adiabatic electron affinity of PrO. Density functional theory calculations on the anion and neutral molecules support the assignment. The appearance of multiple, irregularly spaced and low-intensity features observed ca. 1 eV above the ground state cannot be reconciled with low-lying electronic states of PrO that are accessible via one-electron detachment. However, neutral states correlated with the 4f(2) [(3)H4] 5d superconfiguration are predicted to be approximately 1 eV above the 4f(2) [(3)H4] σ6s Ω = 3.5 neutral ground state, leading to the assignment of these features to shake-up transitions to the excited neutral states. Based on tentative hot band transition assignments, the term energy of the previously unobserved 4f(2) [(3)H4] σ6s Ω = 2.5 neutral state is determined to be 1840 ± 110 cm(-1).

Low-lying electronic structure of EuH, EuOH, and EuO neutrals and anions determined by anion photoelectron spectroscopy and DFT calculations.

The anion photoelectron (PE) spectra of EuH(-) and the PE spectrum of overlapping EuOH(-) and EuO(-) anions are presented and analyzed with supporting results from density functional theory calculations on the various anions and neutrals. Results point to ionically bound, high-spin species. EuH and EuOH anions and neutrals exhibit analogous electronic structures: Transitions from (8)Σ(-) anion ground states arising from the 4f(7)σ(6s)(2) superconfiguration to the close-lying neutral (9)Σ(-) and (7)Σ(-) states arising from the 4f(7)σ(6s) superconfiguration are observed spaced by an energy interval similar to the free Eu(+) [4f(7)6s] (9)S - (7)S splitting. The electron affinities (EAs) of EuH and EuOH are determined to be 0.771 ± 0.009 eV and 0.700 ± 0.011 eV, respectively. Analysis of spectroscopic features attributed to EuO(-) photodetachment is complicated by the likely presence of two energetically competitive electronic states of EuO(-) populating the ion beam. However, based on the calculated relative energies of the close-lying anion states arising from the 4f(7)σ(6s) and 4f(6)σ(6s)(2) configurations and the relative energies of the one-electron accessible 4f(7) and 4f(6)σ(6s) neutral states based on ligand-field theory [M. Dulick, E. Murad, and R. F. Barrow, J. Chem. Phys. 85, 385 (1986)], the remaining features are consistent with the 4f(6)σ(6s)(2) (7)Σ(-) and 4f(7)σ(6s) (7)Σ(-) anion states lying very close in energy (the former was calculated to be 0.15 eV lower in energy than the latter), though the true anion ground state and neutral EA could not be established unambiguously. Calculations on the various EuO anion and neutral states suggest 4f-orbital overlap with 2p orbitals in species with 4f(6) occupancy.

Photoelectron spectra of CeO(-) and Ce(OH)2 (-).

The photoelectron spectrum of CeO(-) exhibits what appears to be a single predominant electronic transition over an energy range in which numerous close-lying electronic states of CeO neutral are well known. The photoelectron spectrum of Ce(OH)2 (-), a molecule in which the Ce atom shares the same formal oxidation state as the Ce atom in CeO(-), also exhibits what appears to be a single transition. From the spectra, the adiabatic electron affinities of CeO and Ce(OH)2 are determined to be 0.936 ± 0.007 eV and 0.69 ± 0.03 eV, respectively. From the electron affinity of CeO, the CeO(-) bond dissociation energy was determined to be 7.7 eV, 0.5 eV lower than the neutral bond dissociation energy. The ground state orbital occupancies of both CeO(-) and Ce(OH)2 (-) are calculated to have 4f 6s(2) Ce(+) superconfigurations, with open-shell states having 4f5d6s superconfiguration predicted to be over 1 eV higher in energy. Low-intensity transitions observed at higher electron binding energies in the spectrum of CeO(-) are tentatively assigned to the (1)Σ(+) (Ω = 0) state of CeO with the Ce+26s2 superconfiguration.

Ce(x)O(y)⁻ (x = 2-3) + D2O reactions: stoichiometric cluster formation from deuteroxide decomposition and anti-Arrhenius behavior.

Reactions between small cerium oxide cluster anions and deuterated water were monitored as a function of both water concentration and temperature in order to determine the temperature dependence of the rate constants. Sequential oxidation reactions of the Ce(x)O(y)⁻ (x = 2, 3) suboxide cluster anions were found to exhibit anti-Arrhenius behavior, with activation energies ranging from 0 to -18 kJ mol⁻¹. Direct oxidation of species up to y = x was observed, after which, -OD abstraction and D2O addition reactions were observed. However, the stoichiometric Ce2O4⁻ and Ce3O6⁻ cluster anions also emerge in reactions between D2O and the respective precursors, Ce2O3D⁻ and Ce3O5D2⁻. Ce2O4⁻ and Ce3O6⁻ product intensities diminish relative to deuteroxide complex intensities with increasing temperature. The kinetics of these reactions are compared to the kinetics of the previously studied Mo(x)O(y)⁻ and W(x)O(y)⁻ reactions with water, and the possible implications for the reaction mechanisms are discussed.

Comparative study of water reactivity with Mo2O(y)⁻ and W2O(y)⁻ clusters: a combined experimental and theoretical investigation.

A computational investigation of the Mo2O(y)(-) + H2O (y = 4, 5) reactions as well as a photoelectron spectroscopic probe of the deuterated Mo2O6D2(-) product have been carried out to understand a puzzling question from a previous study: Why is the rate constant determined for the Mo2O5(-) + H2O/D2O reaction, the terminal reaction in the sequential oxidation of Mo2O(y)(-) by water, higher than the W2O5(-) + H2O/D2O reaction? This disparity was intriguing because W3O(y)(-) clusters were found to be more reactive toward water than their Mo3O(y)(-) analogs. A comparison of molecular structures reveals that the lowest energy structure of Mo2O5(-) provides a less hindered water addition site than the W2O5(-) ground state structure. Several modes of water addition to the most stable molecular and electronic structures of Mo2O4(-) and Mo2O5(-) were explored computationally. The various modes are discussed and compared with previous computational studies on W2O(y)(-) + H2O reactions. Calculated free energy reaction profiles show lower barriers for the initial Mo2O(y)(-) + H2O addition, consistent with the higher observed rate constant. The terminal Mo2O(y)(-) sequential oxidation product predicted computationally was verified by the anion photoelectron spectrum of Mo2O6D2(-). Based on the computational results, this anion is a trapped dihydroxide intermediate in the Mo2O5(-) + H2O/D2O → Mo2O6(-) + H2/D2 reaction.

Direct Binding Methods to Measure Receptor-Ligand Interactions.

G-protein-coupled receptors (GPCRs) contribute to numerous physiological processes via complex network mechanisms. While indirect signaling assays (Ca2+ mobilization, cAMP production, and GTPγS binding) have been useful in identifying and characterizing downstream signaling mechanisms of GPCRs, these methods lack measurements of direct binding affinities, kinetics, binding specificity, and selectivity that are important parameters in GPCR drug discovery. In comparison to existing direct methods that use radio- or fluorescent labels, label-free techniques can closely emulate the native interactions around binding partners. Surface plasmon resonance (SPR) is a label-free technique that utilizes the refractive index (RI) property and is applied widely in quantitative GPCR-ligand binding kinetics measurement including small molecules screening. However, purified GPCRs are further embedded in a synthetic lipid environment which is immobilized through different tags to the SPR sensor surface, resulting in a non-native environment. Here, we introduced a methodology that also uses the RI property to measure binding interactions in a label-free, immobilization-free arrangement. The free-solution technique is successfully applied in quantifying the interaction of bioactive lipids to cognate lipid GPCRs, which is not purified but rather present in near-native conditions, i.e., in milieu of other cytoplasmic lipids and proteins. To further consider the wide applicability of these free-solution approaches in biomolecular interaction research, additional applications on a variety of receptor-ligand pairs are imperative.

Determination of target genes for classified molecular subtypes of triple-negative breast cancer form microarray gene expression profiling: An integrative in silico approach.

BACKGROUND: Highly heterogeneous triple-negative breast cancer (TNBC) has tough clinical features, which were gradually solving and improving in diagnosis by the molecular subtyping of TNBC. AIM: Presently, this study was focused on analyzing the genetic makeup of TNBC subtypes. SETTINGS AND DESIGN: This study explored the MicroArray expression profiling of differentially expressed genes in molecular subtypes BL1, BL2, IM, luminal androgen receptor, M, and mesenchymal stem-like of TNBC by analyzing the Gene Expression Omnibus dataset GSE167213. Various gene ontologies-based protein-protein interaction (PPI) networks were subtyped TNBC genes. The effect of genetic alteration on TNBC cases was also interpreted. MATERIALS AND METHODS: The MicroArray gene expression profiling was done through R programming and subjected to functional annotation through the database for annotation, visualization, and integrated discovery. The PPI networking of functionally associated genes was interpreted by STRING. The survival analysis was done through cBioPortal. STATISTICAL ANALYSIS USED: The t-test was used through R programming to generate the P values for a test of the significance of expressed genes. RESULTS: A total of 54,613 significant probes were analyzed in the TNBC MicroArray dataset. The functional PPI networks of BL1, BL2, and IM upregulated genes showed significant associations. The survival analysis of differentially expressed genes showed the significant prognostic effect of 32 upregulated genes of different subtypes on TNBC cases with genetic alterations, whereas the remaining genes showed no significant effects. CONCLUSION: The output of the present study provided significant target gene panels for different TNBC subtypes, which would add an informative genetic value to TNBC diagnosis.

Simple relationship between oxidation state and electron affinity in gas-phase metal-oxo complexes.

The photoelectron spectra of WO3H(-) and WO2F(-) are presented and analyzed in the context of a series of previous similar measurements on MO(y)(-) (M = Mo, W; y = 0-3), MO4H(-) and AlMOy(-) (y ≤ 4) complexes. The electronic structures of the WO3H and WO2F anion and neutral complexes were investigated using the B3LYP hybrid density functional method. The spectra of WO3H(-), WO2F(-), and previously measured AlWO3(-) photoelectron spectra show that the corresponding neutrals, in which the transition metal centers are all in a +5 oxidation state, have comparable electron affinities. In addition, the electron affinities fit the general trend of monotonically increasing electron affinity with oxidation state, in spite of the WO3H(-), WO2F(-), and AlWO3(-) having closed shell ground states, suggesting that the oxidation state of the metal atom has more influence than shell closing on the electron affinity of these transition metal-oxo complexes. Results of DFT calculations suggest that the neutrals are pyramidal and the anions are planar. However, the barriers for inversion on the neutral surface are low, and attempts to generate simple Franck-Condon simulations based on simple normal coordinate displacement, ignoring the effects of inversion, are inadequate.