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Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS. The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples. sgj@sanger.ac.uk
Sequences are arguably the most common biological data. An easy-to-use tool can greatly facilitate daily manipulation and analysis of biological sequences. Here, we present SEQEL, a tool providing a convenient environment for editing, formatting and rendering of DNA, RNA and protein sequences. This is accomplished by extending the commonly used text editor, Emacs, which is available for Windows, Linux and Mac OS. The unit tested ELISP source code for seqel is freely available from https://github.com/rnaer/seqel along with documentation. zhenjiang.xu@gmail.com.
Structural studies of pentachromium and pentacobalt extended metal atom chain (EMAC) systems are presented in which the metal chains are helically wrapped by either the pentadentate dianion tripyridyldiamide (tpda) or its diethyl-substituted analogue bis(4-ethyl-2-pyridylamido)pyridine (etpda). The compound Cr(5)(tpda)(4)(NCS)(2), has alternating long and short Cr-Cr distances, contrary to recent reports that describe it as symmetrical with essentially equally spaced chromium atoms. The linear Cr(5)(10+) chain is composed of two Cr(2)(4+) quadruply bonded units and an isolated high spin Cr(II) unit. The new compounds Cr(5)(etpda)(4)Cl(2), [Cr(5)(etpda)(4)FCl]PF(6), and Co(5)(etpda)(4)(NCS)(2)() employ the etpda ligand as "insulation" around a central pentametal-atom "wire." Compound, like all other oxidized pentachromium compounds, has very disparate alternating short-long-short-long Cr-Cr distances, 2.032(3) A, 2.560(6) A, 1.873(5) A, and 2.509(4) A. Compound shows a nearly uniform spacing of the Co atoms, although the outer Co-Co distances (2.279[4] A) are slightly longer than the inner ones (2.239[4] A).
The relationship between equatorial ligands structures and magnetic response of [Ni3]6+ extended metal atom chain core has been investigated. The distances between metal ions in Ni metal strings are largely predefined by framework provided through equatorial ligands. The equatorial ligands thus have primary influence on the magnitude of magnetic coupling between terminal high spin centers. Since the σ channel has greatest contribution to J, the variations in Ni–Ni bond lengths have immediate and strong effect on magnetic properties. The secondary, yet important role is played by ligand field strength and nucleophilicity. It has been shown that energy difference between singly occupied σ-type MOs composed of d(z2) of terminal ions and doubly occupied σ-type MO evolved from d(z2) of the central ion in antiferromagnetic state solution is inversely proportional to magnitude of J. Hence, the alignment between energies of d(z2) orbitals on HS and LS centers directly affected by ligand field strength governs the magnetic response. Moreover, the greater basicity of lone pairs coordinating terminal metal atoms correlates with the larger absolute value of magnetic coupling constant.
Striding to extend the length of metal-atom strings, oligo-α-pyridylamino ligands are modulated with naphthyridyl moieties leading to the undeca-nickel mixed-valence complexes [Ni11(bnatpya)4Cl2]4+ (1) and [Ni11(bnatpya)4Cl2]2+ (2). The first single-molecule conductance measurements of a linear undeca-nickel chain were performed.
Spin crossover (SCO) describes the reversible interconversion between low-spin and high-spin electronic configurations in transition metal complexes, arising from a delicate balance between ligand field splitting and electron pairing energy. Cobalt-based extended metal atom chains (EMACs) and their heterometallic analogues, HEMACs, offer a versatile platform for probing spin-state energetics and switchable magnetism through variations in metal-metal and metal-ligand interactions. Here, we report the synthesis, redox chemistry, and magnetic properties of the heterometallic chains [CoPdCo(dpa)4Cl2] (1) and [CoNiCo(dpa)4Cl2] (2, dpa = 2,2'-dipyridylamido), together with their one-electron oxidized derivatives [1][SbCl6] and [2][PF6]. Variable-temperature single-crystal X-ray diffraction, SQUID magnetometry, variable-temperature 1H NMR spectroscopy, and density functional theory reveal that redox reaction and central metal substitution can modulate the spin-state equilibria of these Co-M-Co chains. The neutral complexes 1 and 2 feature antiferromagnetically coupled high-spin Co(II) termini, with 2 displaying structure-dependent spin crossover in the solid state. Upon oxidation, [1][SbCl6] adopts a robust high-spin configuration over the entire temperature range studied, whereas [2][PF6] undergoes an incomplete, temperature-driven spin crossover between low-spin and high-spin states, as evidenced by concerted structural, magnetic, and spectroscopic signatures. DFT calculations elucidate the delicate enthalpy-entropy balance governing these behaviors and highlight the role of central metal size and Co-N bond metrics in biasing the spin-state landscape. These results provide insight into the interplay between redox state, spin-state behavior, and heterometallic chain composition in cobalt-based HEMACs.
Thermal management in molecular systems presents challenges that require a deeper understanding of phonon transport, an essential aspect of heat conduction in single-molecule junctions. Our work introduces the use of heavy atoms as a strategy for suppressing phonon transport in organic molecules. Starting with a one-dimensional (1D) force-constant model and density functional theory calculations of model chemical systems, we illustrate how increasing the mass of a central atom affects phonon transmission and conductance. Following this, we turned our attention to the chemically accessible systems of metallapolyynes and extended metal atom chains (EMACs). Our findings suggest that several of the studied EMACs exhibit thermal conductance either near or below a recently proposed threshold of 10 pW/K-a crucial step toward reaching high thermoelectric figure of merits. Specifically, we predict that the molecule MoMoNi(npo)4(NCS)2 has a thermal conductance of just 8.3 pW/K at 300 K. Our results demonstrate that conceptually simple chemical modifications can markedly reduce the thermal conductance of single molecules; these results both deepen our understanding of the mechanisms driving single-molecule phonon thermal conductance and suggest a path toward using single molecules as thermoelectric materials.
The granuloma serves not only as a physical barrier to restrict the dissemination of intracellular pathogens but also functions as a complex immune microenvironment. However, the bioenergetics and regulatory mechanisms maintaining this architecture remain elusive in vertebrates. Here, integrating multi-tissue transcriptomics, single-cell RNA sequencing (scRNA-seq), ultrastructural imaging, and fluorescence in situ hybridization (FISH) in a largemouth bass (Micropterus salmoides)-Nocardia seriolae infection model, we resolved the metabolic and functional landscape of the granuloma. We found that across multiple tissues (head kidney, spleen, liver, kidney), the host initiates a synchronized transcriptional program that promotes macrophage differentiation into specialized epithelioid macrophages (E-Macs). Notably, E-Macs concurrently upregulated specific transporters and metabolic enzymes (e.g., laao, slc6a8), as well as oxidative phosphorylation (OXPHOS) and glycolysis genes, accompanied by mitochondrial proliferation. Functionally, E-Macs shifted from a pro-inflammatory to an immunoregulatory and pro-survival phenotype, characterized by high expression of protease inhibitors (e.g., csta) and anti-apoptotic factors (e.g., bcl2l14, ywhag1). Comparative analysis in zebrafish confirmed these metabolic and regulatory signatures are evolutionarily conserved. In conclusion, this study reveals a host survival strategy of immune regulation underpinned by metabolic adaptation, providing novel perspectives for controlling chronic granulomatous diseases in aquaculture.
Four experiments in human predictive learning evaluated whether the extinction makes the acquisition context specific (EMACS) effect is attenuated when the increase in prediction error that extinction produces disappears. Participants had to evaluate the relationship between a given food (cue) that was ingested by an imaginary client of a given restaurant (context) and a potential gastric illness (outcome). The task was implemented using Gorilla online software. All participants received the relevant training in context A, and equivalent exposure to context B. Cue E was presented paired with the outcome in all groups. Cue E was then either extinguished (group E) or not extinguished (group NE), either previously or concurrently to training of the target cue (P). P was then tested in contexts A and B. When extinction was conducted concurrently, performance to P became context-dependent regardless of the number of extinction trials (12 or 24)-the EMACS effect. The EMACS effect disappeared when extinction was elongated to 24 trials, and conducted before acquisition of P. Implications of these results for attentional explanations of context processing are discussed. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
Semilocal and random phase approximation (RPA) density functional theory (DFT) and complete active space (CASSCF + NEVPT2) methodologies were applied to investigate a new class of extended metal atom chain (EMAC) complexes. A novel triferrous complex has been synthesized recently that does not utilize the usual 2,2'-dipyridylamine (dpa) ligand framework, which essentially always results in a tetragonal coordination environment and general formula M3(dpa)4X2, where X is an anion. Instead, the triferrous complex utilizes a dianionic, 2,6-bis(trimethylsilylamido)pyridine ligand (L2-) resulting in the formation of trigonal complexes with general formula Fe3L3. To better understand the electronic structure of this complex, calculations were utilized to explore the experimentally isolated Fe3L3, and a smaller theoretical complex, in order to compare and contrast with the traditional dpa-based EMACs. Due to the absence of anionic, axial ligands, the sigma nonbonding orbitals formed from the metal d orbitals are lower in energy than in the dpa complexes, and compete with the pi bonding orbitals for occupation in the Fe3L3 complex. While the idealized geometry of these complexes is D3h, a helical distortion of the ligands and subsequent electronic symmetry breaking due to Jahn-Teller distortions are predicted utilizing both semilocal and RPA DFT methods, ending in a C2 structure that closely matches the reported crystal structure. Predicted Mössbauer isomer shifts and ultraviolet/visible (UV/vis) spectra also agree with the experimental data available in the literature. Magnetic coupling constants also indicate ferromagnetic coupling between nearest neighbor irons. Two-dimensional (2D) potential energy surfaces were calculated for a range of fixed Fe-Fe bond lengths, revealing a flat potential energy surface over a wide range of Fe-Fe bond lengths and verifying the ability of RPA to act as a higher-level check on semilocal DFT results. In order to verify the predicted high-spin ground state, CASSCF + NEVPT2 was applied to selected molecular configurations and confirmed the predictions made by DFT. These calculations shed light on the physical ground state electron configuration of Fe3L3 and correlate this electronic configuration with the available experimental data.
Heterometallic extended metal atom chains (EMACs) aligned with three types of metal were rationally synthesized by forming unbridged metal-metal bonds based on the interactions between highest occupied and lowest unoccupied molecular orbitals at the d z 2 ${{_{{\rm z}{^{2}}}}}$ orbital. These chains form pentanuclear structures aligned as Rh-Pt-M-Pt-Rh with relatively large formation constants of 5.0×1013  M-2 for M=Pt and 6.3×1011  M-2 for M=Pd, while retaining their backbones in solution. In the case of M=Cu, the original Cu(+2) atoms were reduced to Cu(+1) during the synthetic process. Cu(+1) has an unprecedented trigonal bipyramidal coordination geometry. The reported synthesis based on asymmetrical dinuclear complexes provides a guideline for the synthesis of hetero-EMACs to allow several analogs through judicious combinations realized by tuning the number of metal nuclei and metal species.
Clear cell carcinoma (CCC) of the ovary is an uncommon, but an aggressive epithelial ovarian cancer (EOC), which has overlapping histopathologic features with other ovarian tumours. Lately, Napsin A has been identified as its useful diagnostic immunohistochemical (IHC) marker. Fifty-eight prospectively diagnosed ovarian CCCs, 53 high-grade serous carcinomas (HGSCs), 16 endometrioid adenocarcinomas (EMACs), six mixed carcinomas, containing components of CCC and EMAC, seven metastatic mucinous adenocarcinomas and six ovarian yolk sac tumours (YSTs) were tested for Napsin A immunostaining. Fifty ovarian CCCs, 50 HGSCs, seven ovarian EMACs and five mixed carcinomas were tested for WT1 immunostaining. Napsin A was positively expressed in all 58 (100%) CCCs; was focally positive in 1 of 6 YSTs; in 1/16 EMACs and in six cases of mixed carcinomas, while it was negative in all 53 HGSCs and in seven metastatic mucinous adenocarcinomas. Other IHC markers expressed in cases of CCC ovary were CK7 (31/31) (100%), WT1 (0/50), p53 (20/26, 'wild type'), ER (4/31, focal) (12.9%), PAX8 (14/14) (100%), glypican-3 (4/10, focal) (44.4%), p16INK4 (5/5, focal) and CK20 (0/5). Various IHC markers expressed in HGSCs were WT1 (48/50) (96%), p53 (31/31, mostly 'mutation type'), CK7 (9/9) (100%) ER (13/16, variable) (81.2%) and PAX8 (14/14) (100%). IHC markers expressed in EMACs were ER (15/16) (93.7%), CK7 (2/2) (100%) and WT1 (0/7). IHC markers expressed in mixed carcinomas were CK7 (2/2) (100%), WT1 (0/2), focal Napsin A (6/6) and focal ER (5/6). The sensitivity and specificity of Napsin A for the diagnosis of CCC ovary was 100% and 90.9%, respectively. The sensitivity and specificity of WT1 for diagnosis of HGSC ovary was found to be 96% and 100%, respectively. Napsin A and WT1 are highly sensitive and specific IHC markers for diagnosing ovarian CCCs and HGSCs, respectively, and in differentiating these tumours from their mimics. Napsin A is useful in identification of component of CCC in certain EMACs.
EMACs (extended metal-atom chains) offer a unique platform for the exploration of metal-metal interactions. There has been significant advances on the synthesis of EMACs, such as lengthening the chains up to 11 metal atoms thus far, integrating naphthyridine moieties for tuning the charge carried at metal centers, and manipulation of metal-metal interactions. However, the metal centers in EMACs hitherto are limited to first row transition metals which are more labile than those relatively inert ones with electrons filled in the 4d and 5d shells. In this Communication, the synthesis, crystallographic, magnetic, and electrical conducting studies of [Ru5(mu5-tpda)4Cl2] and [Ru5(mu5-tpda)4(NCS)2], the first pentanuclear EMACs of second-row transition metal, are reported.
To characterize serum elevations of carbohydrate antigens; DU-PAN-2, CA19-9, sialyl Lewisx and CA125 in endometrial adenocarcinomas (EMACs), particularly focusing on the clarification of DU-PAN-2 expression profiles. Sixty-four resected EMACs of endometrioid type were used. The preoperative serum values of four markers were measured and comparatively analyzed regarding the relationship between histological grade and clinicopathological stage. The overall ratios of positive cases were 26.2% for DU-PAN-2, 25.0% for CA19-9, 13.6% for sialyl Lewisx, and 35.5% for CA125. DU-PAN-2 decreased as the grading went up (G1: 410.3 +/- 243.8 to G3: 246.7 +/- 90.0 U/mL), however, the reverse was true with CA19-9 (G1: 123.9 +/- 147.4 to G3: 320.0 +/- 180.0 U/mL). Sialyl Lewisx showed a strong tendency towards high elevation in G1 (346.3 +/- 102.6 U/mL), compared to G3 (< 2.5 U/mL). CA125 increased markedly as the grading went up (G1: 43.5 +/- 6.3 to G3: 578.0 +/- 10.0 U/mL). During staging-up from I + II to III + IV, the positive ratios inclined in all four markers as follows: DU-PAN-2, 18.4-53.3%; CA19-9, 20.4-40.0%; sialyl Lewisx, 11.4-22.2%; CA125, 31.8-44.4%. Serum elevations and positive ratios were correlated for DU-PAN-2, CA19-9 and CA125, while the reverse relationship was found for sialyl Lewisx. It is suggested that DU-PAN-2 tends to be produced more in well-differentiated components of EMACs than in poorly differentiated ones. Since approximately half the cases with EMAC were serologically positive for DU-PAN-2 in stage III + IV, the marker is believed to be of much use for monitoring the cases with an extrauterine extent.
Retrieval of a flavor-illness association has been found to show contextual dependence when the association is learned after a nontarget flavor-illness association has been extinguished in what has been named as the extinction makes acquisition context-specific (EMACS) effect. Four experiments were designed to further explore the EMACS effect in conditioned taste aversion. Experiments 1 and 2 replicated the EMACS effect using rats that did not experience extinction, and rats that underwent extinction of a different flavor as controls. Experiments 3 and 4 found that the experience of extinction with the nontarget Flavor X in a given context (A) led to context-specificity of performance to the target Flavor Y both, when Y was trained in a highly familiar context (B) and tested in the context where X had been trained (Context A, Experiment 3), and when the test was conducted in a less familiar context (C) where no cues or outcomes were presented before (Experiment 4). These results are consistent with the idea that the experience of extinction encourages organism's attention to the contexts, making retrieval of new learning context-specific. (PsycINFO Database Record (c) 2018 APA, all rights reserved).
Two experiments evaluated whether the experience of extinction makes acquisition context specific (EMACS) while the extinction learning itself also becomes context dependent under ABA and ABC renewal designs in a human predictive learning situation. Two groups of participants received X-Outcome pairings in context A followed by P-Outcome pairings in context B. For participants in group E, cue X was then extinguished in context B while cue P was trained. Participants in group NE were trained with P, but they did not have the extinction experience. Testing target cues outside the context B (i.e. the context in which P was trained and X was extinguished) in group E led to an increase in responding to cue X (Renewal effect) and a decrease in responding to cue P (EMACS effect) regardless of whether the test was conducted in context A (Experiment 1) or in an alternative context C (Experiment 2). Combined results suggest that Renewal and EMACS effects may be based on the same underlying mechanism. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Recently published static DFT and CASSCF/CASPT2 calculations depicted extremely flat Potential Energy Surfaces (PESs) for the Cr-Cr flexibility of Cr3(dpa)4X2 (X = NCS-, CN-, NO3-) extended metal atom chains (EMACs) (M. Spivak, et al., Dalton Trans., 2017, 46, 6202). We herein explore the thermal and crystal packing effects on the structure of EMACs using ab initio molecular dynamics (MD). Car-Parrinello DFT-based simulations of the isolated molecules show that thermal energy favors asymmetric arrangements of the Cr3 chain due, in part, to the bending of the axial ligands (X) and the increased X-Cr distance, both of which weaken X → Cr σ-donation. This effect is even more prominent in the crystalline phase due to the interaction between the axial ligands of neighboring molecules in the unit cell. This could explain the typical discrepancies between the experimental and theoretical characterization of Cr3 EMACs observed in the literature.
Extended metal atom chains (EMACs) are promising candidates for molecular wires but their band structures remain to be explored. As a quasi-one-dimensional (Q1D) system, the incommensurate helical nature of EMACs hinders such calculations. In this work, we resolved this issue via explicit implementation of helical symmetry. Moreover, the pattern of metal d bands was rationalized by a systematic investigation on a series of related Q1D helical systems. Two critical factors, helical ligand field and chemically asymmetric ligand field, are proposed and identified. We found that the symmetry and ligand fields of the system dominate the pattern of the metal d bands, instead of specific chemical composition of ligands. The presented method and rationale are applicable to not only EMACs but also related Q1D helical systems.
Extended metal atom chains (EMACs) contain a linear metal chain wrapped by various ligands. Most complexes are of the form M(3)(dpa)(4)X(2), where M = metal, dpa = 2,2'-dipyridylamide, and X = various anions. The ligands form helical coils about the metal chain, which results in chiral EMAC complexes. The EMACs containing the metals Co and Cu were partially separated in polar organic mode using a vancomycin-based chiral stationary phase. Under similar conditions, two EMACs with Ni metal and varying anions could be baseline separated. The polar organic mode was used because of the instability of the compounds in aqueous mobile phases. Also, these conditions are more conducive to preparative separations. Polarimetric measurements on the resolved enantiomers of Ni(3)(dpa)(4)Cl(2) indicate that they have extraordinarily high specific rotations (on the order of 5000 deg cc/g dm).
Pentacobalt EMACs [Co(5)(mu(5)-dpzpda)(4)X(2)] (X = Cl(-) (), NCS(-) ()) with fine-tuning of the supporting ligand based on the tripyridyldiamine ligand, N,N'-di(pyrazin-2-yl)pyridine-2,6-diamine (H(2)dpzpda), and their reduced form (Ph(4)P)[Co(5)(mu(5)-dpzpda)(4)X(2)] (X = Cl(-) (), NCS(-) ()) were first synthesized and structurally characterized. The structures of showed direct Co-Co bonds with Co-Co distances in the range 2.2385(7)-2.2888(15) A, and valence electrons delocalized through the whole metal chain with distances of longer than 9.06 A. The distances of the inner Co-Co bonds and the Co-axial ligands became longer after reduction, whereas no significant change was observed in the distances of the outer Co-Co bonds and Co-N (supporting ligand) bonds, which was consistent with the MO analysis. Electrochemical studies on both and showed one reversible oxidation and one reversible reduction at E(1/2) = +0.82 and -0.05 V for , and at E(1/2) = +0.89 and +0.02 V for , respectively. The redox reactions of the thiocyanate complex happened at higher potentials than the chloride complex . A magnetism study of revealed anomalous magnetic behaviour similar to that of heptacobalt EMACs, and a deviation from the Curie-Weiss law was observed. The chi(M)T value at 300 K is 0.84 and 1.16 emu K mol(-1) for and , respectively, suggesting spin-equilibrium or a spin-admixture between doublet and quartet states arising from the Boltzmann distribution over different energy levels. Similar results were obtained for and , showing intermediate chi(M)T values between a diamagnetic and a triplet state of 0.15-0.96 emu K mol(-1) in the temperature range 5-300 K. The structural and magnetic results were interpreted through an EHMO study.