A Functional Dissection of the mRNA and Locally Synthesized Protein Population in Neuronal Dendrites and Axons.

Neurons are characterized by a complex morphology that enables the generation of subcellular compartments with unique biochemical and biophysical properties, such as dendrites, axons, and synapses. To sustain these different compartments and carry a wide array of elaborate operations, neurons express a diverse repertoire of gene products. Extensive regulation at both the messenger RNA (mRNA) and protein levels allows for the differentiation of subcellular compartments as well as numerous forms of plasticity in response to variable stimuli. Among the multiple mechanisms that control cellular functions, mRNA translation is manipulated by neurons to regulate where and when a protein emerges. Interestingly, transcriptomic and translatomic profiles of both dendrites and axons have revealed that the mRNA population only partially predicts the local protein population and that this relation significantly varies between different gene groups. Here, we describe the space that local translation occupies within the large molecular and regulatory complexity of neurons, in contrast to other modes of regulation. We then discuss the specialized organization of mRNAs within different neuronal compartments, as revealed by profiles of the local transcriptome. Finally, we discuss the features and functional implications of both locally correlated-and anticorrelated-mRNA-protein relations both under baseline conditions and during synaptic plasticity.

Landscape of surfaceome and endocytome in human glioma is divergent and depends on cellular spatial organization.

Therapeutic strategies directed at the tumor surfaceome (TS), including checkpoint inhibitor blocking antibodies, antibody drug conjugates (ADCs), and chimeric antigen receptor T (CAR-T) cells, provide a new armament to fight cancer. However, a remaining bottleneck is the lack of strategies to comprehensively interrogate patient tumors for potential TS targets. Here, we have developed a platform (tumor surfaceome mapping [TS-MAP]) integrated with a newly curated TS classifier (SURFME) that allows profiling of primary 3D cultures and intact patient glioma tumors with preserved tissue architecture. Moreover, TS-MAP specifically identifies proteins capable of endocytosis as tractable targets for ADCs and other modalities requiring toxic payload internalization. In high-grade gliomas that remain among the most aggressive forms of cancer, we show that cellular spatial organization (2D vs. 3D) fundamentally transforms the surfaceome and endocytome (e.g., integrins, proteoglycans, semaphorins, and cancer stem cell markers) with general implications for target screening approaches, as exemplified by an ADC targeting EGFR. The TS-MAP platform was further applied to profile the surfaceome and endocytome landscape in a cohort of freshly resected gliomas. We found a highly diverse TS repertoire between patient tumors, not directly associated with grade and histology, which highlights the need for individualized approaches. Our data provide additional layers of understanding fundamental to the future development of immunotherapy strategies, as well as procedures for proteomics-based target identification and selection. The TS-MAP platform should be widely applicable in efforts aiming at a better understanding of how to harness the TS for personalized immunotherapy.

New Perspectives on Genomic Imprinting, an Essential and Multifaceted Mode of Epigenetic Control in the Developing and Adult Brain.

Mammalian evolution entailed multiple innovations in gene regulation, including the emergence of genomic imprinting, an epigenetic regulation leading to the preferential expression of a gene from its maternal or paternal allele. Genomic imprinting is highly prevalent in the brain, yet, until recently, its central roles in neural processes have not been fully appreciated. Here, we provide a comprehensive survey of adult and developmental brain functions influenced by imprinted genes, from neural development and wiring to synaptic function and plasticity, energy balance, social behaviors, emotions, and cognition. We further review the widespread identification of parental biases alongside monoallelic expression in brain tissues, discuss their potential roles in dosage regulation of key neural pathways, and suggest possible mechanisms underlying the dynamic regulation of imprinting in the brain. This review should help provide a better understanding of the significance of genomic imprinting in the normal and pathological brain of mammals including humans.

Ferrier Glycosylation Mediated by the TEMPO Oxoammonium Cation.

The TEMPO oxoammonium cation has been proven to be both an efficient oxidizing reagent and an electrophilic substrate frequently found in organic reactions. Here, we report that this versatile chemical reagent can also be used as an efficient promoter for C- and N-glycosylation reactions through a Ferrier rearrangement with moderate to high yields. This unprecedented reactivity is explained in terms of a Lewis acid activation of glycal by TEMPO+ forming a type of glycal-TEMPO+ mesomeric structure, which occurs through an extended vinylogous hyperconjugation toward the π*(O═N+) orbital [LP(O1) → π*(C1═C2), π*(C1═C2) → σ*(C3-O3), and LP(O6) → π*(O═N+)]. This enables the formation of the respective Ferrier glycosyl cation, which is trapped by various nucleophiles. The extended hyperconjugation (or double hyperconjugation) toward the π*(O═N+) orbital, which confers the Lewis acid character of the TEMPO cation, was supported by natural bond orbital analysis at the M06-2X/6-311+G** level of theory.

Elucidation of the Pyridine Ring-Opening Mechanism of 2,2'-Bipyridine or 1,10-Phenanthroline Ligands at Re(I) Carbonyl Complexes.

The cleavage of the C-N bonds of aromatic heterocycles, such as pyridines or quinolines, is a crucial step in the hydrodenitrogenation (HDN) industrial processes of fuels in order to minimize the emission of nitrogen oxides into the atmosphere. Due to the harsh conditions under which these reactions take place (high temperature and H2 pressure), the mechanism by which they occur is only partially understood, and any study at the molecular level that reveals new mechanistic possibilities in this area is of great interest. Herein, we unravel the pyridine ring-opening mechanism of 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen) ligands coordinated to the cis-{Re(CO)2(N-RIm)(PMe3)} (N-RIm= N-alkylimidazole) fragment under mild conditions. Computational calculations show that deprotonation of the pyridine ring, once dearomatized, is crucial to induce ring contraction, triggering extrusion of the nitrogen atom from the ring and cleavage of the C-N bond. It is noteworthy that different products (regioisomers) are obtained depending on whether the ligand used is bipy or phen due to the additional rigidity and stability conferred by the central ring of the phen ligand, an issue also addressed and clarified computationally. Strong support for the proposed mechanism is provided by the characterization and isolation, including three single-crystal X-ray diffraction structures, of several of the proposed reaction intermediates.

Salinity and pH effects on water-oil-calcite interfaces by using molecular dynamics.

Smart water injection is a technology that allows changing the wettability of the oil rock by injecting water at different salinities, in a cheap and environmentally friendly way compared to other traditional methods. In this study, the individual effect of some typical salts on the wettability of the (104) surface of calcite toward non-polar and polar crude oil models was explored by molecular dynamics as a function of the salinity and pH. The results obtained show that the electrical double layer plays a principal role in the detachment of crude oil models. The divalent ion salts, i.e., CaCl2, CaSO4, MgCl2, and MgSO4, do not form the electrical double layer on calcite, but salts of NaCl and Na2SO4 form it. Moreover, the surface affinity of calcite to the non-polar crude oil is not affected by the salinity. However, the affinity of the calcite surface toward polar crude is affected by salinity and pH conditions. This research provides new insights into the action mechanisms that could help optimize its uses in enhanced oil recovery.

Cutaneous Rosai-Dorfman disease with MAP2K1 mutation, initially mimicking an infection with parasitized histiocytes.

Rarely, Rosai-Dorfman disease (RDD) manifests exclusively in the skin, typically as nodules on the trunk and extremities. Recognition of characteristic histopathologic features enables diagnosis of RDD. A 55-year-old female presented with a 7-year history of cutaneous nodules involving the trunk and extremities. A prior skin biopsy specimen at a different institution had demonstrated a dense dermal lymphohistiocytic infiltrate with histiocytes containing GMS+ forms, favored to represent cryptococcal organisms, with a differential diagnosis including other infections with parasitized histiocytes. Despite antibiotic therapy, lesions persisted. After a presentation to our institution, a biopsy specimen showed a diffuse infiltrate, including histiocytes with voluminous pale cytoplasm with focal emperipolesis of inflammatory cells and S100 immunohistochemical positivity. Clinical and radiologic examinations did not identify significant extracutaneous involvement. A genetic study performed on the biopsy specimen identified a K57Q mutation of MAP2K1. The presence of this mutation correlated with prior reports of MAP2K1 mutation in classic RDD, thereby supporting our histopathologic diagnosis of RDD over an infectious process and further illuminating options for targeted therapies. At 3-year follow-up, the patient has been managed with a course of systemic corticosteroids and excision of bothersome lesions. Consideration of systemic therapy is ongoing.

Curvature and confinement effects on chiral liquid crystal morphologies.

Chiral liquid crystals (ChLCs) exhibit an inherent twist that originates at the molecular scale and can extend over multiple length scales when unconstrained. Under confinement, the twist is thwarted, leading to formation of defects in the molecular order that offer distinct optical responses and opportunities for colloidal driven assembly. Past studies have explored spheroidal confinement down to the nanoscopic regime, where curved boundaries produce surface defects to accommodate topological constraints and restrict the propagation of cuboidal defect networks. Similarly, strict confinement in channels and shells has been shown to give rise to escaped configurations and skyrmions. However, little is known about the role of extrinsic curvature in the development of cholesteric textures and Blue Phases (BP). In this paper, we examine the palette of morphologies that arises when ChLCs are confined in toroidal and cylindrical cavities. The equilibrium morphologies are obtained following an annealing strategy of a Landau-de Gennes free energy functional. Three dimensionless groups are identified to build phase diagrams: the natural twist, the ratio of elastic energies, and the circumscription of a BP cell. Curvature is shown to introduce helical features that are first observed as a Double Twist, and progress to Chiral Ribbons and, ultimately, Helical BP and BP. Chiral ribbons are examined as useful candidates for driven assembly given their tunability and robustness.

Raman spectroscopy and molecular dynamics simulations of aqueous two-phase systems for the purification of phosphoric acid.

In this work, Raman spectroscopy and molecular dynamics simulations were used to elucidate key interactions between polyethylene glycol (PEG) and phosphoric acid (H3PO4) in aqueous two-phase systems for the extraction of phosphoric acid. Extensive molecular dynamics simulations were performed, and radial distribution functions as well as hydrogen bonds between PEG and other molecules were measured. Experimental data were used in combination with the slope method to infer PEG-H3PO4 interactions, and the interpretation is consistent with molecular simulation results. Based on our experimental and simulation results, we propose a solvation mechanism governed by hydrogen bonding interactions: at low concentrations of H3PO4 within the polymer-rich aqueous solution, entropy dominates and phosphoric acid molecules have weak interactions with PEG; as the concentration of phosphoric acid increases above a certain critical value, enthalpy dominates with PEG molecules interacting strongly with H3PO4 molecules via hydrogen bonds.

Development of squamous cell carcinoma in the setting of chronic discoid lupus erythematosus may be associated with plasmacytoid dendritic cell inflammation.

Discoid lupus erythematosus (DLE) is the most common type of cutaneous lupus and is clinically characterized by alopecia, depigmentation, and scars on sun-exposed skin. Squamous cell carcinoma is a potential long-term complication. The most important risk factor for squamous cell carcinoma development in people with dark skin is chronic scarring and inflammation, such as those seen in long-standing discoid plaques. African Americans who develop squamous cell carcinoma in the setting of chronic scarring and inflammation have a greater risk of metastasis and recurrence compared to sun-induced squamous cell carcinoma seen in whites. Despite this, the pathogenesis of squamous cell carcinoma development in chronic DLE is not fully understood. Herein, we describe a case of an African American patient who developed squamous cell carcinoma on a long-standing discoid plaque. Analysis of the lesion revealed a null type pattern of p53 protein expression and abundant CD123+ plasmacytoid dendritic cells, as potential drivers of oncogenesis and inflammation, respectively. Dermatologists should be aware of the increased risk of squamous cell carcinoma development within long-standing discoid plaques for a prompt early diagnosis and active long-term surveillance.

Stabilizing Effect of a 4c/6e Hypervalent Bond in Dinitrodiphenyl Disulfides and Their Thermochemical Properties: Experimental and Computational Approach.

Thermochemical properties and intramolecular interactions of 2,2'-dinitrodiphenyl disulfide (2DNDPDS) and 4,4'-dinitrodiphenyl disulfide (4DNDPDS) were determined and analyzed. Their standard molar formation enthalpies in the gas phase (ΔfHm°(g)'s) were experimentally determined; theoretically, they were computed using the G4 composite method and atomization reactions. Specifically, ΔfHm°(g)'s were obtained by combining formation enthalpies in the condensed phase and enthalpies of phase change. Formation enthalpies in the condensed phase were determined experimentally through combustion energies, which in turn were found by means of a rotatory bomb combustion calorimeter. Sublimation enthalpies were derived from thermogravimetric experiments, measuring the rate of mass loss and using Langmuir and Clausius-Clapeyron equations. Fusion enthalpies and heat capacities of the solid and liquid phases were measured as functions of temperature by differential scanning calorimetry, and the heat capacities of the gas phase were calculated via molecular orbital calculations. Theoretical and experimental ΔfHm°(g)'s differed by <5.5kJ·mol-1, and isomerization enthalpies are discussed. In addition, using theoretical tools [natural bond orbitals (NBO) and quantum theory of atoms in molecules (QTAIM)], intramolecular interactions were analyzed. An uncommon hypervalent four-center six-electron interaction of type O···S-S···O was found in 2DNDPDS. This hypervalent interaction, in addition to the extent of conjugation between the aryl and NO2 moieties and the formation of intramolecular C-H···S hydrogen bonds, counteracts the repulsion caused by steric repulsions. Hydrogen bonding was confirmed through geometric parameters as well as QTAIM.

Short-term administration of tibolone reduces inflammation and oxidative stress in the hippocampus of ovariectomized rats fed high-fat and high-fructose.

Inflammation and oxidative stress are critical events involved in neurodegeneration. In animal models, it has been shown that chronic consumption of a hypercaloric diet, which leads to inflammatory processes, affects the hippocampus, a brain region fundamental for learning and memory processes. In addition, advanced age and menopause are risk factors for neurodegeneration. Hormone replacement therapy (HRT) ameliorates menopause symptoms. Tibolone (TB), a synthetic hormone, exerts estrogenic, progestogenic and androgenic effects on different tissues. We aimed to determine the effect of short-term TB administration on oxidative stress and inflammation markers in the hippocampus of ovariectomized rats fed a high-fat-and-fructose diet (HFFD). Adult female rats were ovariectomized (OVX) and fed standard diet or HFFD-consisting of 10% lard supplemented chow and 20% high-fructose syrup in the drinking water-and administered vehicle or TB (1 mg/kg for seven days). Finally, we administered hormone receptor antagonists (MPP, RU486 or FLU) to each of the OVX + HFFD + TB groups. Bodyweight, triglycerides and cholesterol, oxidative stress and inflammation markers, and the activity and expression of antioxidant enzymes were quantified in the hippocampus of each experimental group. We observed that short-term TB administration significantly reduced body weight, AGEs, MDA levels, increased SOD and GPx activity, improved GSH/GSSG ratio, and reduced IL-6 and TNF-α. Our findings suggest that short-term administration of TB decreases oxidative stress and reduces inflammation caused by HFFD and early estrogenic decline. These effects occurred via estrogen receptor alpha.

Bonding and antibonding characters of the first order reduced density matrix. A new look at two charge-shift bonds.

This article reports a new way of analyzing chemical bonds based on the use of gradient of a first order reduced density matrix (1-RDM) map to partition bonds into atomic core, valence, and dorsal regions that can be further characterized as bonding or antibonding. These classifications are directly related to the familiar language of molecular orbital analysis. Analyses based on these quantities and the critical points of the 1-RDM performed on two charge-shift bonds show that although they share common features, there are fundamental differences in these interactions that are detected neither by density-based analysis nor by valence bond theory. The results suggest the gradient of 1-RDM as a valuable tool in bond analysis.

Benign and low-grade superficial endothelial cell neoplasms in the molecular era.

Vascular tumors are the most common mesenchymal neoplasms of the skin and subcutis, and they encompass a heterogeneous group with diverse clinical, histological, and molecular features, as well as biological behavior. Over the past two decades, molecular studies have enabled the identification of pathogenic recurrent genetic alterations that can be used as additional data points to support the correct classification of these lesions. The purpose of this review is to summarize the available data related to superficially located benign and low-grade vascular neoplasms and to highlight recent molecular advances with the role of surrogate immunohistochemistry to target pathogenic proteins as diagnostic biomarkers.

Atypical Presentations of Extraparenchymal Neurocysticercosis.

BACKGROUND: Neurocysticercosis (NCC) is the most common parasitic infection of the central nervous system and is typically diagnosed through visualization of the cysts in the cerebral parenchyma by neuro-imaging. However, neuro-imaging may not detect extraparenchymal neurocysticercosis (EPNCC), which is a rare manifestation of the disease involving the subarachnoid, meningeal, and intraventricular spaces. We report 2 cases of extraparenchymal neurocysticercosis, and discuss the diagnostic challenges and management of this entity. METHODS: Two cases were identified through clinical records. RESULTS: Both patients had an insidious onset with slow progression of disease, and presented with papilledema and cerebrospinal fluid (CSF) eosinophilia. One case was diagnosed with spinal cord biopsy. The other was diagnosed with CSF serology and next-generation sequencing-based pathogen analysis. Both patients were treated with ventriculoperitoneal shunt, systemic antiparasitic agents, and immunosuppression. CONCLUSIONS: EPNCC is less common than parenchymal NCC. A high level of clinical suspicion is required given its rarity, long incubation period, and slow progression. Diagnosis and treatment can be challenging and requires a multidisciplinary approach.

Synthesis, in vitro, in silico and in vivo hypoglycemic and lipid-lowering effects of 4-benzyloxy-5-benzylidene-1,3-thiazolidine-2,4-diones mediated by dual PPAR α/γ modulation.

In current work, we prepared a series of nine 4-benzyloxy-5-benzylidene-1,3-thiazolidine-2,4-diones using a two-step pathway. Compounds 1-9 were tested in vitro using a set of three proteins recognized as important targets in diabetes and related diseases: PPARα, PPARγ, and GLUT-4. Compounds 1-3, 5, and 7 showed significant increases in the mRNA expression of PPARγ and GLUT-4, whereas compounds 1-3 did it over PPARα. Compounds 1-3 were identified as a dual PPAR α/γ modulators and were selected for evaluating the in vivo antidiabetic action at 100 mg/kg dose, being orally actives and decreasing blood glucose concentration in a hyperglycemic mice model, as well as reducing the triacylglycerides levels in normolipidemic rats. Docking and molecular dynamics studies were conducted to clarify the dual effect and binding mode of compounds 1-3 on both PPARs. Compounds 2 and 3 exhibited robust in vitro and in vivo efficacy and could be considered dual PPAR modulators with antidiabetic and antidyslipidemic effects.

Strongly Electron-Donating Triazolylidene Ligands: Cationic Metal Carbonyl Complexes of 1-Methyl-1,2,3-triazole as Triazolium Surrogates.

A new strategy for tuning the electronic properties of 1,2,3-triazol-5-ylidene metal complexes is reported using {Mo(η3-C4H7)(bipy)(CO)2} or {Re(bipy)(CO)3} fragments as substituents at the triazole N3 atom. The reaction of cationic molybdenum(II) and rhenium(I) 1-methyl-1,2,3-triazole compounds with the strong base KN(SiMe3)2 in the presence of electrophilic metal fragments, such as AgOTf (OTf = trifluoromethanesufonate) or [CuCl(IPr)] [IPr = 2,6-(diisopropyl)phenylimidazol-2-ylidene] affords a new type of 1,2,3-triazol-5-ylidene complexes. For silver(I) cationic bis(triazolylidene), [Ag(tzNHCM)2]OTf (M = [Mo], 2; [Re], 4), complexes are obtained, whereas in the case of Cu(I) mixed normal/mesoionic NHC, [Cu(IPr)(tzNHCM)]OTf (M = [Mo], 7; [Re], 8) complexes are formed. This special type of mesoionic N-heterocyclic carbenes bear a metal fragment at the N3 atom of the 1,2,3-triazole moiety, showing notable enhancement of the carbene electron donor ability compared to conventional alkyl-substituted analogues. Transmetalation from cationic silver bis(triazolylidene) complexes 2 and 4, prepared using this methodology, has proven to be very efficient toward [M'Cl(cod)]2 (M' = Rh, Ir; cod = 1,5-cyclooctadiene), affording the corresponding cationic bis(triazolylidene) [M'(cod)(tzNHCM)2]OTf (9-12) complexes. A subsequent reaction with CO(g) easily produces substitution of the diene ligand, affording the corresponding cis-dicarbonyl [M'(CO)2(tzNHCM)2]OTf (13-16) compounds.

Ribosomes: The New Role of Ribosomal Proteins as Natural Antimicrobials.

Moonlighting proteins are those capable of performing more than one biochemical or biophysical function within the same polypeptide chain. They have been a recent focus of research due to their potential applications in the health, pharmacological, and nutritional sciences. Among them, some ribosomal proteins involved in assembly and protein translation have also shown other functionalities, including inhibiting infectious bacteria, viruses, parasites, fungi, and tumor cells. Therefore, they may be considered antimicrobial peptides (AMPs). However, information regarding the mechanism of action of ribosomal proteins as AMPs is not yet fully understood. Researchers have suggested that the antimicrobial activity of ribosomal proteins may be associated with an increase in intracellular reactive oxidative species (ROS) in target cells, which, in turn, could affect membrane integrity and cause their inactivation and death. Moreover, the global overuse of antibiotics has resulted in an increase in pathogenic bacteria resistant to common antibiotics. Therefore, AMPs such as ribosomal proteins may have potential applications in the pharmaceutical and food industries in the place of antibiotics. This article provides an overview of the potential roles of ribosomes and AMP ribosomal proteins in conjunction with their potential applications.

Novel fusion genes in spindle cell rhabdomyosarcoma: The spectrum broadens.

Rhabdomyosarcoma (RMS) encompasses a heterogeneous group of tumors with striated muscle differentiation. RMSs are classified as alveolar, embryonal, spindle cell/sclerosing, and pleomorphic types and molecular analysis of these tumors has identified aberrations that are useful in their further subclassification. Spindle cell rhabdomyosarcoma (SpRMS) is uncommon and has been described with VGLL2 fusions, EWSR1/FUS-TFCP2 rearrangements, and myoD1 mutations-the mutations are associated with significantly different prognoses. In addition, the NCOA2-MEIS1 fusion gene was recently described in two primary intraosseous RMS that contained spindle cell components. Herein, we report three cases of SpRMS harboring different novel fusion genes, one possessing EP300-VGLL3, a second with NCOA2-MEIS1 and CAV1-MET, and the third case had HMGA2-NEGR1 and multiple amplified genes.

Identification of EWSR1-NFATC2 fusion in simple bone cysts.

AIMS: Simple bone cysts are benign intramedullary tumours primarily involving the long bones in skeletally immature individuals. Several mechanisms have been proposed for their pathogenesis. Although the diagnosis is typically straightforward, the interpretation can be problematic, because of superimposed fracture causing them to resemble aneurysmal bone cysts and other tumours. EWSR1-NFATC2 or FUS-NFATC2 fusions, which are characteristic of a subset of aggressive round cell sarcomas, have been recently detected in simple bone cysts. The aim of this study was to examine the clinicopathological and molecular features in a series of simple bone cysts. METHODS AND RESULTS: Using RNA-based next-generation sequencing and/or fluorescence in-situ hybridisation, we investigated the presence of EWSR1 or FUS rearrangements in nine simple bone cysts. The patients were five females and four males, aged 3-23 years (median, 14 years); the tumours ranged from 19 mm to 160 mm (median, 46 mm) in size, and involved the femur (n = 3), humerus (n = 2), fibula (n = 2), tibia (n = 1), and iliac wing (n =1). We identified three cases with EWSR1-NFATC2 fusion (showing identical breakpoints to those in EWSR1-NFATC2 sarcomas) and one additional case with FUS rearrangement. Unlike in EWSR1-NFATC2 sarcomas, immunohistochemical expression of NKX3.1 and NKX2.2 was absent in two simple bone cysts tested. CONCLUSIONS: More than 40% of simple bone cysts harbour genetic alterations confirming that they are neoplastic, investigation of EWSR1 and/or FUS rearrangement may help to distinguish simple bone cysts from mimics, and NFATC2 rearrangement is not pathognomonic of malignancy.