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1
Yang, Jin, Can Weng, Jun Lai, Tao Ding, and Hao Wang. "Molecular Dynamics Simulation on the Influences of Nanostructure Shape, Interfacial Adhesion Energy, and Mold Insert Material on the Demolding Process of Micro-Injection Molding." Polymers 11, no. 10 (September 27, 2019): 1573. http://dx.doi.org/10.3390/polym11101573.
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In micro-injection molding, the interaction between the polymer and the mold insert has an important effect on demolding quality of nanostructure. An all-atom molecular dynamics simulation method was performed to study the effect of nanostructure shape, interfacial adhesion energy, and mold insert material on demolding quality of nanostructures. The deformation behaviors of nanostructures were analyzed by calculating the non-bonded interaction energies, the density distributions, the radii of gyration, the potential energies, and the snapshots of the demolding stage. The nanostructure shape had a direct impact on demolding quality. When the contact areas were the same, the nanostructure shape did not affect the non-bonded interaction energy at PP-Ni interface. During the demolding process, the radii of gyration of molecular chains were greatly increased, and the overall density was decreased significantly. After assuming that the mold insert surface was coated with an anti-stick coating, the surface burrs, the necking, and the stretching of nanostructures were significantly reduced after demolding. The deformation of nanostructures in the Ni and Cu mold inserts were more serious than that of the Al2O3 and Si mold inserts. In general, this study would provide theoretical guidance for the design of nanostructure shape and the selection of mold insert material.
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Kômoto, Natuo, Kenji Yukuhiro, and Shuichiro Tomita. "Novel gene rearrangements in the mitochondrial genome of a webspinner, Aposthonia japonica (Insecta: Embioptera)." Genome 55, no. 3 (March 2012): 222–33. http://dx.doi.org/10.1139/g2012-007.
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Webspinners (order Embioptera) are polyneopteran insects characterized by enlarged foretarsi with silk glands, whose silk is used to produce galleries in which the insects live gregariously. The phylogenetic position of webspinners has been debated. In the present study, an almost complete mitochondrial DNA (mtDNA) sequence of Embioptera is reported for the first time. The mtDNA of a webspinner, Aposthonia japonica , has the 13 protein-coding genes (PCGs) generally found in metazoan mtDNA sequences. There is a translocation of a large region including atp6, atp8, cox3, nad3, and nad5 as well as a duplication of the 12S rRNA gene. The rearrangement does not seem to affect nucleotide composition, although amino acid composition in some parts of the mtDNA is biased compared with other Polyneoptera species. Based on phylogenetic analyses using nucleotide sequences of all PCGs concatenated with two rRNA genes and the amino acid sequences of all PCGs, A. japonica is sister to Verophasmatodea, a suborder of typical stick and leaf insects.
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Sánchez, Maximo, Martha-Helena Ramírez-Bahena, Alvaro Peix, María J. Lorite, Juan Sanjuán, Encarna Velázquez, and Jorge Monza. "Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus." International Journal of Systematic and Evolutionary Microbiology 64, Pt_3 (March 1, 2014): 781–86. http://dx.doi.org/10.1099/ijs.0.052993-0.
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Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).
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Makhdom, Asim M., and Javad Parvizi. "Modular versus nonmodular tibial inserts in total knee arthroplasty: what are the differences?" Annals of Translational Medicine 5, no. 10 (May 2017): 225. http://dx.doi.org/10.21037/atm.2017.02.25.
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Álvarez-Rodríguez, Lucía, Javier Brugos, Javier A. Cabeza, Pablo García-Álvarez, Enrique Pérez-Carreño, and Diego Polo. "Synthesis and initial transition metal chemistry of the first PGeP pincer-type germylene." Chemical Communications 53, no. 5 (2017): 893–96. http://dx.doi.org/10.1039/c6cc09283g.
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The first PGeP pincer-type germylene has been synthesized. Its divalent Ge atom easily inserts into M–M and M–Cl bonds, giving rise to products that contain a PGeP bridging germylene or a PGeP pincer chlorogermyl ligand.
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Begam, V. M. Thoulath, and S. Baulkani. "Ring Counter Based ATPG for Low Transition Test Pattern Generation." Scientific World Journal 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/729165.
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In test mode test patterns are applied in random fashion to the circuit under circuit. This increases switching transition between the consecutive test patterns and thereby increases dynamic power dissipation. The proposed ring counter based ATPG reduces vertical switching transitions by inserting test vectors only between the less correlative test patterns. This paper presents the RC-ATPG with an external circuit. The external circuit consists of XOR gates, full adders, and multiplexers. First the total number of transitions between the consecutive test patterns is determined. If it is more, then the external circuit generates and inserts test vectors in between the two test patterns. Test vector insertion increases the correlation between the test patterns and reduces dynamic power dissipation. The results prove that the test patterns generated by the proposed ATPG have fewer transitions than the conventional ATPG. Experimental results based on ISCAS’85 and ISCAS’89 benchmark circuits show 38.5% reduction in the average power and 50% reduction in the peak power attained during testing with a small size decoding logic.
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Liu, Zhen-Kai, Peng Gao, Muhammad Aqeel Ashraf, and Jun-Bao Wen. "The complete mitochondrial genomes of two weevils, Eucryptorrhynchus chinensis and E. brandti: conserved genome arrangement in Curculionidae and deficiency of tRNA-Ile gene." Open Life Sciences 11, no. 1 (January 1, 2016): 458–69. http://dx.doi.org/10.1515/biol-2016-0060.
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AbstractThe weevils Eucryptorrhynchus chinensis and Eucryptorrhynchus brandti (Coleoptera: Curculionidae), are two of the most important pests of the tree-of-heaven, Ailanthus altissima, which is found throughout China. In this study, the complete mitogenomes of the two weevils have been sequenced using Illumina HiSeqTM 2000. The mitogenomes of E. chinensis and E. brandti are 15,628bp and 15,597bp long with A+T contents of 77.7% and 76.6%, respectively. Both species have typical circular mitochondrial genomes that encode 36 genes. Except the deficiency of tRNA-Ile, the gene composition and order of E. chinensis and E. brandti are identical to the inferred ancestral gene arrangement of insects. In both mitochondrial genomes, the start codons for COI and ND1 are AAT and TTG, respectively. A5bp motif (TACTA) is detected in intergenic region between the tRNA-Ser (UCN) and ND1 genes. The ATP8/ATP6 and ND4L/ND4 gene pairs appear to overlap four or seven nucleotides (ATAA/ATGATAA) in different reading frames. The complete sequences of AT-rich region have two regions including tandem repeats. The study identifies useful genetic markers for studying the population genetics, molecular identification and phylogeographics of Eucryptorrhynchus weevils. The features of the mitochondrial genomes are expected to be valuable in
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Bogo, Amauri, and Peter Mantle. "Oligosaccharides in the honeydew of Coccoidea scale insects: Coccus hesperidum L. and a new Stigmacoccus sp. in Brazil." Anais da Sociedade Entomológica do Brasil 29, no. 3 (September 2000): 589–95. http://dx.doi.org/10.1590/s0301-80592000000300022.
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Analysis of the honeydew from an as yet undescribed, though distinctive, Brazilian Stigmacoccus sp. (near S. asper Hempel) by paper chromatography, Fast atom bombardment (FAB-MS) and Gas chromatography-mass spectrometry (GC-MS) identified fructose and glucose as monosaccharides and sucrose, maltose, trehalulose, trehalose and a hexose-hexitol as disaccharides. Erlose and glucosyl erlose have been identified as the tri- and tetra-saccharides in Stigmacoccus sp. and characterised for the first time in scale insects by modern techniques of linkage analysis. The same erlose oligosaccharides were recognised in honeydew of the common scale insect Coccus hesperidum L., together with the pentamer of this series, maltosyl erlose, therefore recognising that specific metabolic transformations of sugars into this oligomeric series occur rather widely in Coccoidea scale insects.
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Bisono, Robertus Suryo. "STUDI BANDING PELAPISAN MATERIAL SKD11 DENGAN METODE PHYSICAL VAPOUR DEPOSITION DAN THERMAL DIFUSION PADA KOMPONEN INSERT DIES MESIN STAMPING PRESS." Jurnal Teknik Mesin 6, no. 1 (February 20, 2017): 21. http://dx.doi.org/10.22441/jtm.v6i1.1202.
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Telah dilakukan pelapisan menggunakan Titanium Alumunium Nitrid (TIAlN) dengan metode PVD Coating (Physical Vapour Diposition) dan TD (Thermal Difusion) untuk perlakuan permukaan baja perkakas SKD11 sebagai material Insert Die komponen mesin Stamping Press setelah perlakuan hardening. Perlakuan permukaan dimaksudkan untuk meningkatkan kualitas permukaan khususnya kekerasan dan perubahan struktur mikro yang terjadi. Untuk mengetahui tingkat keberhasilan dari perlakuan permukaan tersebut dilakukan dengan memvariasi waktu proses, masing masing 2 sample diproses pada 4 jam, 5 jam dan 6 jam dengan temperatur proses masing-masing 400ᴼ C. Kemudian satu dari tiap variable sample tersebut di panaskan pada suhu 1000ᴼ C selama 1 jam, pendinginan dilalukan dengan udara bebas tanpa proses quenching Untuk mengetahui hasilnya dilakukan uji kekerasan mikro Vickers, pengamatan struktur mikro Scanning Eectron Microscope (SEM), dan pengujian komposisi dengan Energy Defersif Sepectroscopy (EDS) untuk mengetahui tingkat penyerapan material terdifusi. Hasil menunjukan bahwa SKD11 yang dilapisi TiAlN dengan metode PVD selama 6 jam menghasilkan lapisan yang paling keras yaitu 1363 HV dengan ketebalan lapisan 5,3µm. Proses pemanasan 1000⁰C selama 1 jam pada sample mengakibatkan penurunan kekerasan sample dan lapisan permukaan sample menjadi lebih tebal hingga 50µm. Penambahan lapisan diakibatkan oleh terdifusinya atom atom yang menyusun lapisan TiAlN ke dalam substrat serta keluarnya atom atom penyusun lapisan hingga membentuk lapisan kompleks.
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Weng, Can, Jiachen Chen, Jin Yang, Mingyong Zhou, and Bingyan Jiang. "Experimental Investigation and Molecular Dynamics Simulation on the Anti-Adhesion Behavior of Alkanethiols on Nickel Insert in Micro Injection Molding." Nanomaterials 11, no. 7 (July 14, 2021): 1834. http://dx.doi.org/10.3390/nano11071834.
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Due to the adhesion between the polymer melt and nickel (Ni) mold insert in the micro injection molding process, deformation defects frequently occur when the microstructures are demolded from the insert. In this study, self-assembled alkanethiols were applied to modify the surface of Ni mold insert to reduce its surface energy. Experimental trials were undertaken to explore the effect of alkanethiols coating on the replication quality. After that, molecular dynamics (MD) simulation was then used to investigate the adhesion behavior between the self-assembled coating and polypropylene (PP) by establishing three different types of alkanethiol material. The interaction energy, the potential energy change and radial distribution function were calculated to study the anti-adhesion mechanism. Experimental results show that all the three coatings can effectively decrease the adhesion and therefore promote the replication fidelity. It is demonstrated in MD simulation that the adhesion mainly comes from the van der Waals (vdW) force at the interface. The arrangement of sulfur atom on the Ni surface results in different absorbing behaviors. Compared with that of the PP–Ni interface, the interfacial energy and adhesion work after surface treatment is significantly reduced.
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Li, Rongrong, Min Li, Jiang Yan, Ming Bai, and Hufang Zhang. "Five Mitochondrial Genomes of the Genus Eysarcoris Hahn, 1834 with Phylogenetic Implications for the Pentatominae (Hemiptera: Pentatomidae)." Insects 12, no. 7 (June 30, 2021): 597. http://dx.doi.org/10.3390/insects12070597.
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Four complete mitogenomes of Eysarcoris rosaceus, E. montivagus, E. gibbosus, E. annamita and one near-complete mitochondrial genome of E. ventralis were sequenced and used to explore the phylogenetic relationships of tribes within the subfamily Pentatominae. The mitogenomes range from 15,422 to 16,043 base pairs (bp) in length and encode 37 genes, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes (21 in E. ventralis), and a control region. Similar to other heteropteran species, the AT contents of the sequenced species were higher than their GC contents. The most frequently used start/stop codon was ATN/TAA. GTG was only found in atp6 and atp8 of E. gibbosus. All transfer RNA genes (tRNAs) exhibit the typical cloverleaf secondary structure, except for the trnS1 and trnV, which lacks the stem of the DHU arm. The length and copy number of repeat units were conserved within Eysarcoris, with the exception of E. gibbosus. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods strongly supported the relationship among tribes within Pentatominae and confirmed that Graphosoma should be an intermediate lineage of Pentatominae. The relationship between Eysarcoris and Carbula was strongly supported and combined with our previous geometric morphometrics and chromosomal studies, suggest the Eysarcoris should belong to the tribe Eyasrcorini. This work will help to enhance our understanding of mitochondrial genomic evolution and phylogenetic relationships in Pentatominae.
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Song, Sang Jun, Kang Il Kim, and Cheol Hee Park. "Comparison of the contact stress between the sensor and real polyethylene insert in total knee arthroplasty: a finite element analysis." Annals of Translational Medicine 8, no. 21 (November 2020): 1424. http://dx.doi.org/10.21037/atm-20-3011.
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GROZEA, D., E. BENGU, C. COLLAZO-DAVILA, and L. D. MARKS. "STRUCTURE DETERMINATION OF THE Ge(111)-(3×1)Ag SURFACE RECONSTRUCTION." Surface Review and Letters 06, no. 06 (December 1999): 1061–65. http://dx.doi.org/10.1142/s0218625x99001153.
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For the first time, during the investigation of the Ag submonolayer on the Ge(111) system, large, independent domains of the Ge (111)-(3×1) Ag phase were imaged and investigated. Previous studies have reported it only as small insets between Ge (111)-(4×4) Ag and Ge (111)- c (2×8) domains. The transmission electron diffraction data were analyzed using a Direct Methods approach and "heavy-atom holography," with the result of an atomic model of the structure similar to that of Ge (111)-(3×1) Ag .
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Suto, Koshun. "Derivation of a Relativistic Wave Equation more Profound than Dirac’s Relativistic Wave Equation." Applied Physics Research 10, no. 6 (November 30, 2018): 102. http://dx.doi.org/10.5539/apr.v10n6p102.
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The author has previously derived an energy-momentum relationship applicable in a hydrogen atom. Since this relationship is taken as a departure point, there is a similarity with the Dirac’s relativistic wave equation, but an equation more profound than the Dirac equation is derived. When determining the coefficients and β of the Dirac equation, Dirac assumed that the equation satisfies the Klein-Gordon equation. The Klein-Gordon equation is an equation which quantizes Einstein's energy-momentum relationship. This paper derives an equation similar to the Klein-Gordon equation by quantizing the relationship between energy and momentum of the electron in a hydrogen atom. By looking to the Dirac equation, it is predicted that there is a relativistic wave equation which satisfies that equation, and its coefficients are determined. With the Dirac equation it is necessary to insert a term for potential energy into the equation when describing the state of the electron in a hydrogen atom. However, in this paper, a potential energy term is not introduced into the relativistic wave equation. Instead, potential energy is incorporated into the equation by changing the coefficient of the Dirac equation.
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Li, Ran, Xiaoli Ying, Weian Deng, Wantao Rong, and Xiaodong Li. "Mitochondrial genomes of eight Scelimeninae species (Orthoptera) and their phylogenetic implications within Tetrigoidea." PeerJ 9 (February 2, 2021): e10523. http://dx.doi.org/10.7717/peerj.10523.
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Scelimeninae is a key member of the pygmy grasshopper community, and an important ecological indicator. No mitochondrial genomes of Scelimeninae have been reported to date, and the monophyly of Scelimeninae and its phylogenetic relationship within Tetrigidae is still unclear. We sequenced and analyzed eight nearly complete mitochondrial genomes representing eight genera of Scelimeninae. These mitogenomes ranged in size from 13,112 to 16,380 bp and the order of tRNA genes between COII and ATP8 was reversed compared with the ancestral order of insects. The protein-coding genes (PCGs) of tetrigid species mainly with the typical ATN codons and most terminated with complete (TAA or TAG) stop codons. Analyses of pairwise genetic distances showed that ATP8 was the least conserved gene within Tetrigidae, while COI was the most conserved. The longest intergenic spacer (IGS) region in the mitogenomes was always found between tRNASer(UCN) and ND1. Additionally, tandem repeat units were identified in the longest IGS of three mitogenomes. Maximum likelihood (ML) and Bayesian Inference (BI) analyses based on the two datasets supported the monophyly of Tetriginae. Scelimeninae was classified as a non-monophyletic subfamily.
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Li, Yan Ling, and Qiang Ru. "First-Principle Calculation on Lithium Insertion of NiSn3Sb4 Alloy." Advanced Materials Research 268-270 (July 2011): 881–85. http://dx.doi.org/10.4028/www.scientific.net/amr.268-270.881.
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The first-principle calculation method with plane-wave basis and pseudo-potentials was employed to investigate the intercalation/extraction mechanism of lithium in NiSn3Sb4. The insertion/substitution formation energies and the electronic structures of NiSn3Sb4 as well as its lithiated products were studied in order to research the migration path of lithium intercalation. The results show that lithium would firstly occupy interstitial sites, then Ni and Sn atoms are replaced gradually by additional lithium. The dissociated Ni atom can relieve the volume expansion and improve the recycling performance of the crystal. It can be also found that as lithium atoms insert into host material, intense electron transport from Li2s to Sn5p and Sb5p occurs at the Fermi level.
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Uhl, Werner, Katja Martinewski, Julia Silissa Bruchhage, Alexander Hepp, Marcus Layh, Fabian Dielmann, and Paul Mehlmann. "Cooperative activation of azides by an Al/N-based active Lewis pair – unexpected insertion of nitrogen atoms into C–Si bonds and formation of AlCN3 heterocycles." Zeitschrift für Naturforschung B 75, no. 1-2 (February 25, 2020): 63–71. http://dx.doi.org/10.1515/znb-2019-0138.
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AbstractThe active Lewis pairs (ALPs) 2,6-Me2H8C5N–C(H) = C(SiMe3)–AlR2 (1a: R = tBu, 1b, R = iBu) have strained AlC2N heterocycles and relatively weak Al–N bonds. They react readily with a series of organic azides R′N3 [R′ = Ph, CH2C6H4(4-tBu), tBu, SiMe3, CH2Ph] by cleavage of the heterocycles and addition of the azides with their α-N atoms to the Al atom. The Al–N interactions result in an activation of the azide groups which insert into the C–Si bonds of the vinyl groups with their terminal γ-N atoms. Compounds with approximately planar five-membered AlCN3 heterocycles and intact N3 groups are formed in highly selective reactions.
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GONÇALVES, LEONARDO TRESOLDI, PEDRO HENRIQUE PEZZI, and FILIPE MICHELS BIANCHI. "Four new stink bug mitogenomes corroborate the internal inconsistencies in the classification of Pentatomidae (Hemiptera)." Zootaxa 5120, no. 1 (March 24, 2022): 128–42. http://dx.doi.org/10.11646/zootaxa.5120.1.8.
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Stink bugs (Pentatomidae) are a speciose group of insects that feed mostly on plants. Many species are considered agricultural pests of economically important crops around the globe. Mitochondrial genomes are valuable for evolutionary and phylogenetic studies, but have been little explored for Pentatomidae. Here, we characterized the mitochondrial genomes of four pentatomid species (Diceraeus melacanthus, Euschistus heros, Piezodorus guildinii, and Stiretrus anchorago) and performed a comparative analysis for this family and its subfamilies. Stink bug mitogenomes disclosed a conserved gene order and content, although we detected two uncommon armless tRNAs in E. heros and D. melacanthus. Phylogenetic results indicate that Pentatominae is polyphyletic, showing that internal relationships of Pentatomidae should be further investigated. Stink bug mitochondrial genes are under strong purifying selection, except for ATP8 which showed signs of positive selection.
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Yu, Tinghao, and Yalin Zhang. "Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis." Insects 12, no. 8 (July 22, 2021): 668. http://dx.doi.org/10.3390/insects12080668.
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More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.
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Veiga-Crespo, P., M. Poza, M. Prieto-Alcedo, and T. G. Villa. "Ancient genes of Saccharomyces cerevisiae." Microbiology 150, no. 7 (July 1, 2004): 2221–27. http://dx.doi.org/10.1099/mic.0.27000-0.
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Amber is a plant resin mainly produced by coniferous trees that, after entrapping a variety of living beings, was subjected to a process of fossilization until it turned into yellowish, translucent stones. It is also one of the best sources of ancient DNA on which to perform studies on evolution. Here a method for the sterilization of amber that allows reliable ancient DNA extraction with no actual DNA contamination is described. Working with insects taken from amber, it was possible to amplify the ATP9, PGU1 and rRNA18S ancient genes of Saccharomyces cerevisiae corresponding to samples from the Miocene and Oligocene. After comparison of the current genes with their ancient (up to 35–40 million years) counterparts it was concluded that essential genes such as rRNA18S are highly conserved and that even normal ‘house-keeping’ genes, such as PGU1, are strikingly conserved along the millions of years that S. cerevisiae has evolved.
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Glaum, Marcus, Wolfgang Kläaui, Brian W. Skelton, and Allan H. White. "Synthesis, X-Ray Crystal Structure and Reactivity of [(tmeda)(p-tolyl)Pd(μ2-I)AgL], an Unusual Silver Iodide Complex; Reversible CO Insertion into the Pd-C Bond of [Pd(PPh3)(p-tolyl)L] (L - = [(C5H5)Co{P(OR)2O}3] - , R = Me, Pri)." Australian Journal of Chemistry 50, no. 11 (1997): 1047. http://dx.doi.org/10.1071/c97074.
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The palladium complexes [Pd(PPh3)(aryl)LOR] (aryl = Ph, p-tolyl; LOR¯ = [(C5H5)Co{P(OR)2O}3]¯, R = Me, Pri) have been prepared by reaction of [PdI(aryl)(tmeda)] (tmeda = N,N,N′,N′-tetramethyl-ethylenediamine) with the silver salts AgLOR in the presence of PPh3. The complexes [Pd(PPh3)(aryl)LOR] rapidly and reversibly insert carbon monoxide to yield the aroyl palladium complexes [Pd(PPh3)(C(O)- p-tolyl)LOR] (R = Me, Pri ). The palladium iodide complex [PdI(p-tolyl)(tmeda)] and the silver salt AgLOR in the absence of PPh3 form an unusual adduct [(p-tolyl)(tmeda)Pd(µ2-I)AgLOMe] that contains a short silver-iodide bond (Ag-I 2 · 703(1) Å). The silver-palladium bond is bridged by iodine (Pd-Ag 3 · 011(1), Pd{I 2 · 5934(9) Å) and the silver atom is coordinated by the tris-chelating oxygen ligand LOMe.
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McGrath, Connor F., James S. Buckman, Tracy D. Gagliardi, William J. Bosche, Lori V. Coren, and Robert J. Gorelick. "Human Cellular Nucleic Acid-Binding Protein Zn2+ Fingers Support Replication of Human Immunodeficiency Virus Type 1 When They Are Substituted in the Nucleocapsid Protein." Journal of Virology 77, no. 15 (August 1, 2003): 8524–31. http://dx.doi.org/10.1128/jvi.77.15.8524-8531.2003.
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ABSTRACT A family of cellular nucleic acid binding proteins (CNBPs) contains seven Zn2+ fingers that have many of the structural characteristics found in retroviral nucleocapsid (NC) Zn2+ fingers. The sequence of the NH2-terminal NC Zn2+ finger of the pNL4-3 clone of human immunodeficiency virus type 1 (HIV-1) was replaced individually with sequences from each of the seven fingers from human CNBP. Six of the mutants were normal with respect to protein composition and processing, full-length genomic RNA content, and infectivity. One of the mutants, containing the fifth CNBP Zn2+ finger (CNBP-5) packaged reduced levels of genomic RNA and was defective in infectivity. There appear to be defects in reverse transcription in the CNBP-5 infections. Models of Zn2+ fingers were constructed by using computational methods based on available structural data, and atom-atom interactions were determined by the hydropathic orthogonal dynamic analysis of the protein method. Defects in the CNBP-5 mutant could possibly be explained, in part, by restrictions of a set of required atom-atom interactions in the CNBP-5 Zn2+ finger compared to mutant and wild-type Zn2+ fingers in NC that support replication. The present study shows that six of seven of the Zn2+ fingers from the CNBP protein can be used as substitutes for the Zn2+ finger in the NH2-terminal position of HIV-1 NC. This has obvious implications in antiviral therapeutics and DNA vaccines employing NC Zn2+ finger mutants.
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Matar, Samir F., and Jean Etourneau. "Electronic and Magnetic Structures of New Interstitial Boron Sub-Oxides B12O2:X (X = B, C, N, O)." Molecules 26, no. 1 (December 29, 2020): 123. http://dx.doi.org/10.3390/molecules26010123.
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The boron-rich boron sub-oxide rhombohedral B6O considered in B12O2 full formulation has a large O-O spacing of ~3 Å and a central vacant position that can receive interstitial atoms X, forming a central O-X-O alignment in the dodecaboron cage as observed in well-known triatomic B12 compounds as B12{C-C-C}, B12{N-B-N}, etc. Plane wave density functional theory (DFT) based calculations of unrestricted geometry relaxation of B12{O-X-O}, X = B, C, N, and O let one identify new ternary sub-oxides, all found cohesive while showing different d(X-O) distances ranging from d(B-O) = 1.95 Å down to d(O-O) = 1.73 Å with intermediate d(C-O) = 1.88 Å. The different magnitudes were assigned to the chemical affinities of X-inserts versus host oxygen with the increasing development of X-O bonding along the series with larger cohesive B12{O-O-O}. From the atom projected charge density, B presents none, while significant magnitudes are shown on C and N, the latter developing bonding with terminal oxygen atoms especially N. The presence of unpaired valence electrons leaves nonbonding charge density on X = C, N interstitial compounds, which, besides the relative isolation of the central C and N lead to the onset of magnetic moments: M(C) = 1.9 μB, and M(N) = 1 μB in a ferromagnetic ground state. Atom-resolved assessments are provided with the magnetic charge density and electron localization function electron localization function (ELF) projections on one hand and the site and spin projected density of states and the chemical bonding based on the overlap integral Sij within the COOP criterion, on the other hand.
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Niichter, W., A. L. Weickenmeier, and J. Mayer. "High precision measurement of Debye-Waller factors for NiAl." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 140–41. http://dx.doi.org/10.1017/s0424820100137070.
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Motivation Quantitative convergent beam electron diffraction (CBED) is increasingly appreciated as a tool to determine bonding charge densities of crystalline materials. Simulated CBED patterns are fitted to experimental ones to derive the structure factors. These are converted by means of the Mott formula to yield the total charge density. Finally a neutral atom total charge density is subtracted and the difference is interpreted as the bonding charge density. Accounting for the temperature by a Debye-Waller factor (DWF) the g-th Fourier coefficient of the bonding charge density is then given by where u denotes the thermal root mean square atomic displacement. Here we have assumed thesimplest case of identical isotropic atomic vibrations for all atoms in the crystal. In order to estimate the error in due to the uncertainty in u we insert the results obtained by Fox and Tabbernor for NiAl at room temperature. They found differences between atomic and measured values of in the order of 2 percent.
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Jiang, Yan, Hao-Xi Li, Xiao-Fei Yu, and Mao-Fa Yang. "Characterization of Two Complete Mitochondrial Genomes of Atkinsoniella (Hemiptera: Cicadellidae: Cicadellinae) and the Phylogenetic Implications." Insects 12, no. 4 (April 11, 2021): 338. http://dx.doi.org/10.3390/insects12040338.
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The complete mitochondrial genomes of Atkinsoniella grahami and Atkinsoniella xanthonota were sequenced. The results showed that the mitogenomes of these two species are 15,621 and 15,895 bp in length, with A+T contents of 78.6% and 78.4%, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (CR). For all PCGs, a standard start ATN codon (ATT, ATG, or ATA) was found at the initiation site, except for ATP8, for which translation is initiated with a TTG codon. All PCGs terminate with a complete TAA or TAG stop codon, except for COX2, which terminates with an incomplete stop codon T. All tRNAs have the typical cloverleaf secondary structure, except for trnS, which has a reduced dihydrouridine arm. Furthermore, these phylogenetic analyses were reconstructed based on 13 PCGs and two rRNA genes of 73 mitochondrial genome sequences, with both the maximum likelihood (ML) and Bayesian inference (BI) methods. The obtained mitogenome sequences in this study will promote research into the classification, population genetics, and evolution of Cicadellinae insects in the future.
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WANG, MENG-QI, YAO DENG, DE-LONG GUAN, BEN-YONG MAO, and MIAO LI. "A new species of the genus Tuberfemurus (Orthoptera: Tetrigoidea: Cladonotinae) with comments on the characters of mitochondrial genome." Zootaxa 5071, no. 3 (November 24, 2021): 437–46. http://dx.doi.org/10.11646/zootaxa.5071.3.9.
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A new species, Tuberfemurus viridulus sp. nov. is described and illustrated with photographs. The new species is similar to T. torulisinotus Deng, 2019, but differs from the latter by broader vertex, invisible frontal costa in profile, distinctly truncate apex of hind pronotal process, and two large triangular projections on lower outer carinae of hind femur. An updated key to species of Tuberfemurus is provided. Simultaneously, the complete mitochondrial genome of Tuberfemurus viridulus sp. nov. is sequenced and analyzed. The total length of the assembled mitogenome is 15,060 bp with 37 typical mitochondrial genes and a non-coding region (A + T-rich region). The order and orientation of the gene arrangement pattern are identical to that of most Tetrigoidea species. All PCGs initiate with the standard start codon of ATN, except ATP6 with GAC and ND1 with TTG; and terminate with the complete stop codon (TAA/TAG) or with an incomplete T- codon. This data could provide the genome information available for Tetrigoidea and facilitate phylogenetic studies of related insects.
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Takayanagi, Toshiyuki, Yuzuru Kurosaki, and Keiichi Yokoyama. "Ab initio calculations for the N(2D) + CH4 reaction: Does the N(2D) atom really insert into CH bonds of alkane molecules?" International Journal of Quantum Chemistry 79, no. 3 (2000): 190–97. http://dx.doi.org/10.1002/1097-461x(2000)79:3<190::aid-qua4>3.0.co;2-0.
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LIU, LI, HU LI, FAN SONG, WEN SONG, XUN DAI, JIAN CHANG, and Wanzhi Cai. "The mitochondrial genome of Coridius chinensis (Hemiptera: Dinidoridae)." Zootaxa 3537, no. 1 (November 2, 2012): 29. http://dx.doi.org/10.11646/zootaxa.3537.1.2.
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The nearly complete mitochondrial genome of Coridius chinensis (Dallas) is reported in this study. The mitogenome is a double-stranded circular molecule of more than 14,648 bp in length with an A+T content of 75.1%. It encoded 37 genes as in other insect mtDNAs, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region (unsuccessful sequencing), and the gene order is the same as most other known heteropteran mitogenomes. All of the 22 transfer RNAs can be folded into the typical cloverleaf structure except tRNASer(AGN), which can only form a simple loop at the site of dihydrouridine (DHU) arm as known in other metazoans. The secondary structures of the large and small ribosomal RNAs of C. chinensis are similar to other presented insects. The rrnL consisted of six structural domains and 40 helices, and the rrnS consisted of three structural domains and 26 helices. Nine PCGs are initiated with the standard initiation codons (ATN), while ND6 and ND1 use GTG, and COI and ATP8 use TTG. All PCGs stopped with TAA/TAG termination codons except the COII terminated with a single T residue. Asymmetry in the nucleotide composition between J-strand and N-strand was observed in this mitogenome.
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Zhao, Ling, Jiufeng Wei, Wanqing Zhao, Chao Chen, Xiaoyun Gao, and Qing Zhao. "The complete mitochondrial genome of Pentatoma rufipes (Hemiptera, Pentatomidae) and its phylogenetic implications." ZooKeys 1042 (June 8, 2021): 51–72. http://dx.doi.org/10.3897/zookeys.1042.62302.
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Pentatoma rufipes (Linnaeus, 1758) is an important agroforestry pest widely distributed in the Palaearctic region. In this study, we sequence and annotate the complete mitochondrial genome of P. rufipes and reconstruct the phylogenetic trees for Pentatomoidea using existing data for eight families published in the National Center for Biotechnology Information database. The mitogenome of P. rufipes is 15,887-bp-long, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region, with an A+T content of 77.7%. The genome structure, gene order, nucleotide composition, and codon usage of the mitogenome of P. rufipes were consistent with those of typical Hemiptera insects. Among the protein-coding genes of Pentatomoidea, the evolutionary rate of ATP8 was the fastest, and COX1 was found to be the most conservative gene in the superfamily. Substitution saturation assessment indicated that neither transition nor transversion substitutions were saturated in the analyzed datasets. Phylogenetic analysis using the Bayesian inference method showed that P. rufipes belonged to Pentatomidae. The node support values based on the dataset concatenated from protein-coding and RNA genes were the highest. Our results enrich the mitochondrial genome database of Pentatomoidea and provide a reference for further studies of phylogenetic systematics.
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Lin, Shuanghu, Min Huang, and Yalin Zhang. "Structural Features and Phylogenetic Implications of 11 New Mitogenomes of Typhlocybinae (Hemiptera: Cicadellidae)." Insects 12, no. 8 (July 28, 2021): 678. http://dx.doi.org/10.3390/insects12080678.
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To explore the characteristics of mitogenomes and discuss the phylogenetic relationships and molecular evolution of the six tribes within Typhlocybinae, 11 complete mitogenomes are newly sequenced and comparatively analyzed. In all of these complete mitogenomes, the number and order of the genes are highly conserved in overall organization. The PCGs initiate with ATN/TTG/GTG and terminate with TAA/TAG/T. Almost all tRNAs are folded into the typical clover-leaf secondary structure. The control region is always variable in length and in numbers of multiple tandem repeat units. The atp8 and nad2 exhibits the highest evolution rate among all the PCGs. Phylogenetic analyses based on whole mitogenome sequences, with three different datasets, using both maximum likelihood and Bayesian methods, indicate the monophyly of Typhlocybinae and its inner tribes, respectively, except for Typhlocybini and Zyginellini that are paraphyletic. Finally, we confirm that Erythroneurini is a subtribe of Dikraneurini.
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Tellinghuisen, Timothy L., Matthew S. Paulson, and Charles M. Rice. "The NS5A Protein of Bovine Viral Diarrhea Virus Contains an Essential Zinc-Binding Site Similar to That of the Hepatitis C Virus NS5A Protein." Journal of Virology 80, no. 15 (August 1, 2006): 7450–58. http://dx.doi.org/10.1128/jvi.00358-06.
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ABSTRACT The recent demonstration that the NS5A protein of hepatitis C virus (HCV) contains an unconventional zinc-binding site with the format Cx17CxCx20C and the presence of a similar sequence element in the NS5A proteins of members of the Pestivirus genus has led to the hypothesis that the NS5A protein of the pestivirus bovine viral diarrhea virus (BVDV) is a zinc-binding protein. A method for the expression and partial purification of BVDV NS5A was developed, and the partially purified protein was analyzed for zinc content by atomic absorption spectroscopy. BVDV NS5A was found to coordinate a single zinc atom per protein molecule. Mutation of any of the four cysteines of the predicted zinc-binding motif eliminated zinc coordination. Furthermore, analysis of mutations at these cysteine residues in the context of a BVDV replicon system indicated that these residues were absolutely essential for RNA replication. The recently determined crystal structure of the N-terminal zinc-binding domain of the HCV NS5A protein, combined with secondary structure predictions of the region surrounding the mapped BVDV zinc-binding region, indicates that the BVDV zinc-binding motif fits the general template Cx22CxCx24C and likely comprises a three-stranded antiparallel β-sheet fold. These data highlight the similarities between the Hepacivirus and Pestivirus NS5A proteins and suggest that both proteins perform a not-yet-defined function in RNA replication that requires coordination of a single zinc atom.
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Liu, Ning, Lijun Fang, and Yalin Zhang. "The Complete Mitochondrial Genomes of Four Species in the Subfamily Limenitidinae (Lepidoptera, Nymphalidae) and a Phylogenetic Analysis." Insects 13, no. 1 (December 22, 2021): 16. http://dx.doi.org/10.3390/insects13010016.
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The complete mitogenomes of four species, Neptis thisbe, Neptis obscurior, Athyma zeroca, and Aldania raddei, were sequenced with sizes ranging from 15,172 bp (N. obscurior) to 16,348 bp (Al. raddei). All four mitogenomes display similar nucleotide content and codon usage of protein-coding genes (PCGs). Typical cloverleaf secondary structures are identified in 21 tRNA genes, while trnS1 (AGN) lacks the dihydrouridine (DHC) arm. The gene orientation and arrangement of the four mitogenomes are similar to that of other typical mitogenomes of Lepidoptera. The Ka/Ks ratio of 13 PCGs among 58 Limenitidinae species reveals that cox1 had the slowest evolutionary rate, while atp8 and nad6 exhibited a higher evolutionary rate. The phylogenetic analysis reveals that tribe-levels are well-supported monophyletic groups. Additionally, Maximum Likelihood analysis recovered the relationship (Parthenini + ((Chalingini + (Cymothoini + Neptini)) + (Adoliadini + Limenitidini))). However, a Bayesian analysis based on the same dataset recovered the relationship (Parthenini + (Adoliadini + ((Cymothoini + Neptini) + (Chalingini + Limenitidini)))). These results will offer valuable data for the future study of the phylogenetic relationships for Limenitidinae.
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Selvaraj, Brinda, Wolfgang Buckel, Bernard T. Golding, G. Matthias Ullmann, and Berta M. Martins. "Structure and Function of 4-Hydroxyphenylacetate Decarboxylase and Its Cognate Activating Enzyme." Journal of Molecular Microbiology and Biotechnology 26, no. 1-3 (2016): 76–91. http://dx.doi.org/10.1159/000440882.
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4-Hydroxyphenylacetate decarboxylase (4Hpad) is the prototype of a new class of Fe-S cluster-dependent glycyl radical enzymes (Fe-S GREs) acting on aromatic compounds. The two-enzyme component system comprises a decarboxylase responsible for substrate conversion and a dedicated activating enzyme (4Hpad-AE). The decarboxylase uses a glycyl/thiyl radical dyad to convert 4-hydroxyphenylacetate into <i>p</i>-cresol (4-methylphenol) by a biologically unprecedented Kolbe-type decarboxylation. In addition to the radical dyad prosthetic group, the decarboxylase unit contains two [4Fe-4S] clusters coordinated by an extra small subunit of unknown function. 4Hpad-AE reductively cleaves S-adenosylmethionine (SAM or AdoMet) at a site-differentiated [4Fe-4S]<sup>2+/+</sup> cluster (RS cluster) generating a transient 5′-deoxyadenosyl radical that produces a stable glycyl radical in the decarboxylase by the abstraction of a hydrogen atom. 4Hpad-AE binds up to two auxiliary [4Fe-4S] clusters coordinated by a ferredoxin-like insert that is C-terminal to the RS cluster-binding motif. The ferredoxin-like domain with its two auxiliary clusters is not vital for SAM-dependent glycyl radical formation in the decarboxylase, but facilitates a longer lifetime for the radical. This review describes the 4Hpad and cognate AE families and focuses on the recent advances and open questions concerning the structure, function and mechanism of this novel Fe-S-dependent class of GREs.
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Zhou, Nan, Yanling Dong, Pingping Qiao, and Zhaofu Yang. "Complete Mitogenomic Structure and Phylogenetic Implications of the Genus Ostrinia (Lepidoptera: Crambidae)." Insects 11, no. 4 (April 7, 2020): 232. http://dx.doi.org/10.3390/insects11040232.
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To understand mitogenome characteristics and reveal phylogenetic relationships of the genus Ostrinia, including several notorious pests of great importance for crops, we sequenced the complete mitogenomes of four species: Ostrinia furnacalis (Guenée, 1854), Ostrinia nubilalis (Hübner, 1796), Ostrinia scapulalis (Walker, 1859) and Ostrinia zealis (Guenée, 1854). Results indicate that the four mitogenomes—O. furnacalis, O. nubilalis, O. scapulalis, and O. zealis—are 15,245, 15,248, 15,311, and 15,208 bp in size, respectively. All four mitogenomes are comprised of 37 encoded genes and a control region. All 13 protein-coding genes (PCGs) initiate with ATN and terminate with TAN, with the exception of cox1 that starts with CGA, and cox1, cox2, and nad5 that terminate with an incomplete codon T. All transfer RNA genes (tRNAs) present the typical clover-leaf secondary structure except for the trnS1 (AGN) gene. There are some conserved structural elements in the control region. Our analyses indicate that nad6 and atp6 exhibit higher evolution rates compared to other PCGs. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods revealed the relationship (O. palustralis + (O. penitalis + (O. zealis + (O. furnacalis + (O. nubilalis + O. scapulalis))))) within Ostrinia.
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Zhou, Xian, Christopher H. H. Dietrich, and Min Huang. "Characterization of the Complete Mitochondrial Genomes of Two Species with Preliminary Investigation on Phylogenetic Status of Zyginellini (Hemiptera: Cicadellidae: Typhlocybinae)." Insects 11, no. 10 (October 10, 2020): 684. http://dx.doi.org/10.3390/insects11100684.
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To explore the characteristics of mitogenomes and reveal phylogenetic relationships of the tribes of Zyginellini and Typhlocybini in Typhlocybinae, mitogenomes of two species of the Zyginellini, Parazyginella tiani and Limassolla sp., were sequenced. Mitogenomes of both species contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a large non-coding region (A + T-rich region). These characteristics are similar to other Membracoidea mitogenomes. All PCGs initiate with the standard start codon of ATN and terminate with the complete stop codon of TAA/G or with an incomplete T codon. All tRNAs have the typical clover-leaf structure, except trnS1 which has a reduced DHU arm and the acceptor stem of trnR is 5 or 6 bp in some species, an unusual feature here reported for the first time in Typhlocybinae. The A + T-rich region is highly variable in length and in numbers of tandem repeats present. Our analyses indicate that nad6 and atp6 exhibit higher evolutionary rates compared to other PCGs. Phylogenetic analyses by both maximum likelihood and Bayesian methods based on 13 protein-coding genes of 12 species of Typhlocybinae suggest that Zyginellini are paraphyletic with respect to Typhlocybini.
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Xu, Deliang, Tinghao Yu, and Yalin Zhang. "Characterization of the Complete Mitochondrial Genome of Drabescus ineffectus and Roxasellana stellata (Hemiptera: Cicadellidae: Deltocephalinae: Drabescini) and Their Phylogenetic Implications." Insects 11, no. 8 (August 14, 2020): 534. http://dx.doi.org/10.3390/insects11080534.
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To explore the mitogenome characteristics and shed light on the phylogenetic relationships and molecular evolution of Drabescini species, we sequenced and analyzed the complete mitochondrial genome of two species including Drabescus ineffectus and Roxasellana stellata. The complete mitogenomes of D. ineffectus and R. stellata are circular, closed and double-stranded molecules with a total length of 15744 bp and 15361 bp, respectively. These two newly sequenced mitogenomes contain the typical 37 genes. Most protein-coding genes (PCGs) began with the start codon ATN and terminated with the terminal codon TAA or TAG, with an exception of a special initiation codon of ND5, which started with TTG, and an incomplete stop codon T-- was found in the Cytb, COX2, ND1 and ND4. All tRNAs could be folded into the canonical cloverleaf secondary structure except for the trnS1, which lacks the DHU arm and is replaced by a simple loop. The multiple tandem repeat units were found in A + T-control region. The sliding window, Ka/Ks and genetic distance analyses indicated that the ATP8 presents a high variability and fast evolutionary rate compared to other PCGs. Phylogenetic analyses based on three different datasets (PCG123, PCG12R and AA) using both Bayesian inference (BI) and maximum likelihood (ML) methods showed strong support for the monophyly of Drabescini.
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Huang, Weijian, and Yalin Zhang. "Characterization of Two Complete Mitochondrial Genomes of Ledrinae (Hemiptera: Cicadellidae) and Phylogenetic Analysis." Insects 11, no. 9 (September 8, 2020): 609. http://dx.doi.org/10.3390/insects11090609.
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Mitochondrial genomes are widely used for investigations into phylogeny, phylogeography, and population genetics. More than 70 mitogenomes have been sequenced for the diverse hemipteran superfamily Membracoidea, but only one partial and two complete mtgenomes mitochondrial genomes have been sequenced for the included subfamily Ledrinae. Here, the complete mitochondrial genomes (mitogenomes) of two additional Ledrinae species are newly sequenced and comparatively analyzed. Results show both mitogenomes are circular, double-stranded molecules, with lengths of 14,927 bp (Tituria sagittata) and 14,918 bp (Petalocephala chlorophana). The gene order of these two newly sequenced Ledrinae is highly conserved and typical of members of Membracoidea. Similar tandem repeats in the control region were discovered in Ledrinae. Among 13 protein-coding genes (PCGs) of reported Ledrinae mitogenomes, analyses of the sliding window, nucleotide diversity, and nonsynonymous substitution (Ka)/synonymous substitution (Ks) indicate atp8 is a comparatively fast-evolving gene, while cox1 is the slowest. Phylogenetic relationships were also reconstructed for the superfamily Membracoidea based on expanded sampling and gene data from GenBank. This study shows that all subfamilies (sensu lato) are recovered as monophyletic. In agreement with previous studies, these results indicate that leafhoppers (Cicadellidae) are paraphyletic with respect to the two recognized families of treehoppers (Aetalionidae and Membracidae). Relationships within Ledrinae were recovered as (Ledra + (Petalocephala + Tituria)).
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Tang, Jiu, Weijian Huang, and Yalin Zhang. "The Complete Mitochondrial Genome of Four Hylicinae (Hemiptera: Cicadellidae): Structural Features and Phylogenetic Implications." Insects 11, no. 12 (December 7, 2020): 869. http://dx.doi.org/10.3390/insects11120869.
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To reveal mtgenome characterizations and reconstruct phylogenetic relationships of Hylicinae, the complete mtgenomes of four hylicine species, including Nacolus tuberculatus, Hylica paradoxa, Balala fujiana, and Kalasha nativa, were sequenced and comparatively analyzed for the first time. We also carried out the richest (11) subfamily sampling of Cicadellidae to date, and reconstructed phylogenetic relationships of Membracoidea among 61 species based on three datasets using maximum likelihood and Bayesian inference analyses. All new sequenced mtgenomes are molecules ranging from 14,918 to 16,221 bp in length and are double stranded, circular in shape. The gene composition and arrangement of these mtgenomes are consistent with members of Membracoidea. Among 13 protein-coding genes, most show typical ATN start codons and TAR (TAA/TAG) or an incomplete stop codon T–, and several genes start by TTG/GTG. Results of the analysis for sliding window, nucleotide diversity, and nonsynonymous substitution/synonymous substitution indicate cox1 is a comparatively slower-evolving gene while atp8 is the fastest gene. In line with previous researches, phylogenetic results indicate that treehopper families are paraphyletic with respect to family Cicadellidae and also support the monophyly of all involved subfamilies including Hylicinae. Relationships among the four hylicine genera were recovered as (Hylica + (Nacolus + (Balala + Kalasha))).
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Liu, Jing, Yuyu Wang, Ruyue Zhang, Chengmin Shi, Weicheng Lu, Jing Li, and Ming Bai. "Three Complete Mitochondrial Genomes of Erotylidae (Coleoptera: Cucujoidea) with Higher Phylogenetic Analysis." Insects 12, no. 6 (June 5, 2021): 524. http://dx.doi.org/10.3390/insects12060524.
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The family Erotylidae belongs to the superfamily Cucujoidea, which are phytophagous and mycophagous. So far, only two representative complete mitochondrial (mt) genomes of Erotylidae have been sequenced. Mitochondrial genomes of Tritoma metasobrina, Neotriplax arisana, and Episcapha opaca, which all belong to the subfamily Erotylinae, were sequenced using next-generation sequencing technology to better understand the diversity of mt genomes of Erotylidae. A comparative mt genomic analysis was conducted on the three sequenced representatives of Erotylinae and Languriinae sp. (Languriinae). The size of the complete mt genome of the 4 species ranged from 15,581 bp to 16,502 bp in length, including 37 genes (13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs) and the control region. The arrangements of their mt genomes are highly consistent with other Coleoptera species. The start codons of two PCGs (ND1 and ND5) and the stop codons of one PCG (ATP8) were illustrated differences between Languriinae sp. and the other three species. All tRNAs of these 4 species exhibited cloverleaf secondary structures except that the dihydorouridine (DHU) arm of tRNASer(AGN) was absent. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods all supported that Erotylidae as monophyletic. Erotylinae was monophyletic being the sister group to Xenocelinae. Languriinae was closely related to ‘Erotylinae-Xenocelinae’. Our results recovered Languriinae nested within Erotylidae.
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Sarbu, Ioan, Cristian Adrian Dinu, Cristian Constantin Budacu, Mihaela Gabriela Luca, constantin Mihai, Camelia Ana Grigore, and Dana Tutunaru. "Surgical Therapeutic Decision in Cases of Acrylic Resins Use in Achievieng Total Removable Prosthetics." Materiale Plastice 56, no. 3 (September 30, 2019): 605–10. http://dx.doi.org/10.37358/mp.19.3.5238.
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Materials used in additive techniques are initially in a plastic state to be inserted into different cavities or easily molded (a blunt, for example), after which they pass into a rigid phase. This process is carried out by various methods depending on the material nature. The process can be purely physical (solidifying the alloy melt, the termoplasticized macromolecular compounds), modification and rearrangement of the internal structure (sintering of ceramic masses, crystallization of glasses, amalgam intake), a process of evaporation of some components (lacquers, plasticizing polymers) or a chemical process. This latter process can be an acid-base reaction between two inorganic substances (PCZ, CIS cements), a chelating reaction (ZOE cements) between a phenolic range (organic compound, usually eugenol or orthoethoxybenzoic acid) and an inorganic powder (ZnO) or a reaction in which a macromolecular compound is formed. After the type of the reaction, the macromolecules are classified into polymers (the formation reaction is called polymerization, the compounds of which are obtained by monomers, the main chain is formed by the carbon atom only), polycondensates (the formation reaction is called polycondensation, the chain also formed from heteroatom-ON, depending on the type of material) or substances that are obtained by polyaddition ( a repeated addition, the mechanism being different from the polymerization. Our study was conducted in the Dental Clinic and comprises a total of 17 patients. The group was represented by patients aged 50-85 years. Clinical observations have been made on cases of fracture of acrylic bases, with the analysis and assessment of some clinical aspects with increased risk of fracture (jaw / mandible, median / paramedian fracture line, etc.), which increase the risk to and fracture when associated. Clinical observations have shown the presence of the risk of fracture in acrylic prostheses, with the need first of all for the proper design and realization of mobile prostheses, but also for the use of inserts.
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Zhang, Shengdi, Lukáš Sekerka, Chengqing Liao, Chengpeng Long, Jiasheng Xu, Xiaohua Dai, and Qingyun Guo. "The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships." Insects 12, no. 11 (November 8, 2021): 1005. http://dx.doi.org/10.3390/insects12111005.
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The taxonomic classification of Dactylispa, a large genus of leaf-mining beetles, is problematic because it is currently based on morphology alone. Here, the first eight mitochondrial genomes of Dactylispa species, which were used to construct the first molecular phylogenies of this genus, are reported. The lengths of the eight mitogenomes range from 17,189 bp to 20,363 bp. All of the mitochondrial genomes include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 1 A + T-rich region. According to the nonsynonymous/synonymous mutation ratio (Ka/Ks) of all PCGs, the highest and the lowest evolutionary rates were found for atp8 and cox1, respectively, which is a common phenomenon among animals. According to relative synonymous codon usage, UUA(L) has the highest frequency. With two Gonophorini species as the outgroup, mitogenome-based phylogenetic trees of the eight Dactylispa species were constructed using maximum likelihood (ML) and Bayesian inference (BI) methods based on the PCGs, tRNAs, and rRNAs. Two DNA-based phylogenomic inferences and one protein-based phylogenomic inference support the delimitation of the subgenera Dactylispa s. str. and Platypriella as proposed in the system of Chen et al. (1986). However, the subgenus Triplispa is not recovered as monophyletic. The placement of Triplispa species requires further verification and testing with more species. We also found that both adult body shape and host plant relationship might explain the subgeneric relationships among Dactylispa beetles to a certain degree.
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Das, Kalyan, Xiaofeng Xiong, Huiling Yang, Christopher E. Westland, Craig S. Gibbs, Stefan G. Sarafianos, and Edward Arnold. "Molecular Modeling and Biochemical Characterization Reveal the Mechanism of Hepatitis B Virus Polymerase Resistance to Lamivudine (3TC) and Emtricitabine (FTC)." Journal of Virology 75, no. 10 (May 15, 2001): 4771–79. http://dx.doi.org/10.1128/jvi.75.10.4771-4779.2001.
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ABSTRACT Success in treating hepatitis B virus (HBV) infection with nucleoside analog drugs like lamivudine is limited by the emergence of drug-resistant viral strains upon prolonged therapy. The predominant lamivudine resistance mutations in HBV-infected patients are Met552IIe and Met552Val (Met552Ile/Val), frequently in association with a second mutation, Leu528Met. The effects of Leu528Met, Met552Ile, and Met552Val mutations on the binding of HBV polymerase inhibitors and the natural substrate dCTP were evaluated using an in vitro HBV polymerase assay. Susceptibility to lamivudine triphosphate (3TCTP), emtricitabine triphosphate (FTCTP), adefovir diphosphate, penciclovir triphosphate, and lobucavir triphosphate was assessed by determination of inhibition constants (Ki ). Recognition of the natural substrate, dCTP, was assessed by determination ofKm values. The results from the in vitro studies were as follows: (i) dCTP substrate binding was largely unaffected by the mutations, with Km changing moderately, only in a range of 0.6 to 2.6-fold; (ii)Ki s for 3TCTP and FTCTP against Met552Ile/Val mutant HBV polymerases were increased 8- to 30-fold; and (iii) the Leu528Met mutation had a modest effect on direct binding of these β-l-oxathiolane ring-containing nucleotide analogs. A three-dimensional homology model of the catalytic core of HBV polymerase was constructed via extrapolation from retroviral reverse transcriptase structures. Molecular modeling studies using the HBV polymerase homology model suggested that steric hindrance between the mutant amino acid side chain and lamivudine or emtricitabine could account for the resistance phenotype. Specifically, steric conflict between the Cγ2-methyl group of Ile or Val at position 552 in HBV polymerase and the sulfur atom in the oxathiolane ring (common to both β-l-nucleoside analogs lamivudine and emtricitabine) is proposed to account for the resistance observed upon Met552Ile/Val mutation. The effects of the Leu528Met mutation, which also occurs near the HBV polymerase active site, appeared to be less direct, potentially involving rearrangement of the deoxynucleoside triphosphate-binding pocket residues. These modeling results suggest that nucleotide analogs that are β-d-enantiomers, that have the sulfur replaced by a smaller atom, or that have modified or acyclic ring systems may retain activity against lamivudine-resistant mutants, consistent with the observed susceptibility of these mutants to adefovir, lobucavir, and penciclovir in vitro and adefovir in vivo.
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Zhang, Zi-Yi, Jia-Yin Guan, Yu-Rou Cao, Xin-Yi Dai, Kenneth B. Storey, Dan-Na Yu, and Jia-Yong Zhang. "Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus." Insects 12, no. 5 (May 14, 2021): 453. http://dx.doi.org/10.3390/insects12050453.
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We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4–5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.
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Zhao, Huifeng, Ye Chen, Zitong Wang, Haifeng Chen, and Yaoguang Qin. "Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications." Insects 12, no. 12 (November 23, 2021): 1049. http://dx.doi.org/10.3390/insects12121049.
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The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable “backbone” of relationships among families.
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Aoki, Manabu, Hironori Hayashi, Ravikiran S. Yedidi, Cuthbert D. Martyr, Yuki Takamatsu, Hiromi Aoki-Ogata, Teruya Nakamura, et al. "C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir." Journal of Virology 90, no. 5 (November 18, 2015): 2180–94. http://dx.doi.org/10.1128/jvi.01829-15.
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ABSTRACTWe identified three nonpeptidic HIV-1 protease inhibitors (PIs), GRL-015, -085, and -097, containing tetrahydropyrano-tetrahydrofuran (Tp-THF) with a C-5 hydroxyl. The three compounds were potent against a wild-type laboratory HIV-1 strain (HIV-1WT), with 50% effective concentrations (EC50s) of 3.0 to 49 nM, and exhibited minimal cytotoxicity, with 50% cytotoxic concentrations (CC50) for GRL-015, -085, and -097 of 80, >100, and >100 μM, respectively. All the three compounds potently inhibited the replication of highly PI-resistant HIV-1 variants selected with each of the currently available PIs and recombinant clinical HIV-1 isolates obtained from patients harboring multidrug-resistant HIV-1 variants (HIVMDR). Importantly, darunavir (DRV) was >1,000 times less active against a highly DRV-resistant HIV-1 variant (HIV-1DRVRP51); the three compounds remained active against HIV-1DRVRP51with only a 6.8- to 68-fold reduction. Moreover, the emergence of HIV-1 variants resistant to the three compounds was considerably delayed compared to the case of DRV. In particular, HIV-1 variants resistant to GRL-085 and -097 did not emerge even when two different highly DRV-resistant HIV-1 variants were used as a starting population. In the structural analyses, Tp-THF of GRL-015, -085, and -097 showed strong hydrogen bond interactions with the backbone atoms of active-site amino acid residues (Asp29 and Asp30) of HIV-1 protease. A strong hydrogen bonding formation between the hydroxyl moiety of Tp-THF and a carbonyl oxygen atom of Gly48 was newly identified. The present findings indicate that the three compounds warrant further study as possible therapeutic agents for treating individuals harboring wild-type HIV and/or HIVMDR.IMPORTANCEDarunavir (DRV) inhibits the replication of most existing multidrug-resistant HIV-1 strains and has a high genetic barrier. However, the emergence of highly DRV-resistant HIV-1 strains (HIVDRVR) has recently been observedin vivoandin vitro. Here, we identified three novel HIV-1 protease inhibitors (PIs) containing a tetrahydropyrano-tetrahydrofuran (Tp-THF) moiety with a C-5 hydroxyl (GRL-015, -085, and -097) which potently suppress the replication of HIVDRVR. Moreover, the emergence of HIV-1 strains resistant to the three compounds was considerably delayed compared to the case of DRV. The C-5 hydroxyl formed a strong hydrogen bonding interaction with the carbonyl oxygen atom of Gly48 of protease as examined in the structural analyses. Interestingly, a compound with Tp-THF lacking the hydroxyl moiety substantially decreased activity against HIVDRVR. The three novel compounds should be further developed as potential drugs for treating individuals harboring wild-type and multi-PI-resistant HIV variants as well as HIVDRVR.
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Mapelli, Marina, Martin Mühleisen, Giorgia Persico, Hans van der Zandt, and Paul A. Tucker. "The 60-Residue C-Terminal Region of the Single-Stranded DNA Binding Protein of Herpes Simplex Virus Type 1 Is Required for Cooperative DNA Binding." Journal of Virology 74, no. 19 (October 1, 2000): 8812–22. http://dx.doi.org/10.1128/jvi.74.19.8812-8822.2000.
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ABSTRACT ICP8 is the major single-stranded DNA (ssDNA) binding protein of the herpes simplex virus type 1 and is required for the onset and maintenance of viral genomic replication. To identify regions responsible for the cooperative binding to ssDNA, several mutants of ICP8 have been characterized. Total reflection X-ray fluorescence experiments on the constructs confirmed the presence of one zinc atom per molecule. Comparative analysis of the mutants by electrophoretic mobility shift assays was done with oligonucleotides for which the number of bases is approximately that occluded by one protein molecule. The analysis indicated that neither removal of the 60-amino-acid C-terminal region nor Cys254Ser and Cys455Ser mutations qualitatively affect the intrinsic DNA binding ability of ICP8. The C-terminal deletion mutants, however, exhibit a total loss of cooperativity on longer ssDNA stretches. This behavior is only slightly modulated by the two-cysteine substitution. Circular dichroism experiments suggest a role for this C-terminal tail in protein stabilization as well as in intermolecular interactions. The results show that the cooperative nature of the ssDNA binding of ICP8 is localized in the 60-residue C-terminal region. Since the anchoring of a C- or N-terminal arm of one protein onto the adjacent one on the DNA strand has been reported for other ssDNA binding proteins, this appears to be the general structural mechanism responsible for the cooperative ssDNA binding by this class of protein.
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Erk, Inge, Jean-Claude Huet, Mariela Duarte, Stéphane Duquerroy, Felix Rey, Jean Cohen, and Jean Lepault. "A Zinc Ion Controls Assembly and Stability of the Major Capsid Protein of Rotavirus." Journal of Virology 77, no. 6 (March 15, 2003): 3595–601. http://dx.doi.org/10.1128/jvi.77.6.3595-3601.2003.
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ABSTRACT The recent determination of the crystal structure of VP6, the major capsid protein of rotavirus, revealed a trimer containing a central zinc ion coordinated by histidine 153 from each of the three subunits. The role of the zinc ion in the functions of VP6 was investigated by site-directed mutagenesis. The mutation of histidine 153 into a serine (H153S and H153S/S339H) did not prevent the formation of VP6 trimers. At pH <7.0, about the pK of histidine, wild-type and mutated VP6 proteins display similar properties, giving rise to identical tubular and spherical assemblies. However, at pH >7.0, histidine 153 mutant proteins did not assemble into the characteristic 45-nm-diameter tubes, in contrast to wild-type VP6. These observations showed that under conditions in which histidine residues are not charged, the properties of VP6 depended on the presence of the centrally coordinated zinc atom in the trimer. Indeed, wild-type VP6 depleted of the zinc ion by a high concentration (100 mM) of a metal-chelating agent behaved like the H153 mutant proteins. The susceptibility of wild-type VP6 to proteases is greatly increased in the absence of zinc. NH2-terminal sequencing of the proteolytic fragments showed that they all contained the β-sheet-rich VP6 head domain, which appeared to be less sensitive to protease activity than the α-helical basal domain. Finally, the mutant proteins assembled well on cores, as demonstrated by both electron microscopy and rescue of transcriptase activity. Zinc is thus not necessary for the transcription activity. All of these observations suggest that, in solution, VP6 trimers present a structural flexibility that is controlled by the presence of a zinc ion.
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Kaluza, J. F., and H. Breer. "Responsiveness of olfactory neurons to distinct aliphatic aldehydes." Journal of Experimental Biology 203, no. 5 (March 1, 2000): 927–33. http://dx.doi.org/10.1242/jeb.203.5.927.
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The responsiveness of isolated olfactory sensory neurons to stimulation with aliphatic aldehydes of varying chain length (5–10 hydrogenated carbon atoms) was investigated by means of Ca(2+)imaging. More than half the cells examined were responsive to aliphatic aldehydes. Individual cells did not react or reacted to one or multiple aldehydes; in the latter case, cells only reacted to aldehydes of consecutive carbon chain lengths. The largest proportion of cells responded to octanal. It was also demonstrated that a structural difference as small as one hydrogenated carbon atom was detectable by the olfactory neurons. Neurons were increasingly able to discriminate between two aldehydes as the difference in chain length between the two increased. Discrimination between aldehydes with longer carbon chains was reduced. Although the odorants examined belong to a distinct chemical class and differ only slightly in structure, individual olfactory sensory neurons showed quite different receptive properties.
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NOGUCHI, MUNENORI, HIROSHI INOUÉ, and KAZUMI KUBO. "Control of the Orientation of Cilia by ATP and Divalent Cations in Triton-Glycerol-Extracted Paramecium Caudatum." Journal of Experimental Biology 120, no. 1 (January 1, 1986): 105–17. http://dx.doi.org/10.1242/jeb.120.1.105.
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The ciliary responses of Paramecium caudatum, extracted in Triton X-100 andglycerol, to the external application of ATP and various divalent cations wereexamined. Ciliary beating could not be reactivated, but changes in the pointing direction of the cilia (the reorientation response) could be reactivated. The free Ca2+ concentration determined the final orientation of the cilia, which was towards the front when the Ca2+ concentration was above 10−6 moll−1, and towards the rear when below 10−7 moll−1. The reorientation response was inhibited by vanadate. These results indicate that the mechanism for the reorientation response is separable into two components. One is the movement of cilia to change their pointing direction, which, like normal ciliary beating, is energized by Mg-ATP2-. The other is the determination of the final pointing direction of the cilia, which is Ca2+ -dependent. Divalent cations can be classified into two groups according to their mode of action on the Ca2+ -dependent component. Sr2+ is an agonist and Ba2+, Zn2+ and Co2+ are antagonists to Ca2+ for the component.
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Uesaka, Toshihiro, Keiichi Yano, Seiji Sugimoto, and Masaaki Ando. "Glucagon-like peptide isolated from the eel intestine: effects on atrial beating." Journal of Experimental Biology 204, no. 17 (September 1, 2001): 3019–26. http://dx.doi.org/10.1242/jeb.204.17.3019.
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SUMMARYA new glucagon-like peptide was isolated from the intestine of the eel Anguilla japonica. The primary structure was determined by sequence analysis after cleavage with lysyl endopeptidase, quantitative amino acid analysis and fast atom bombardment mass spectrometry as HSQGTFTNDY10SKYLETRRAQ20DFVQWLMNSK30RSGGPT. Since its structure is similar to that of oxyntomodulins (OXMs) reported in various vertebrates, we named this peptide eel oxyntomodulin (eOXM). We found that eOXM enhanced the contractile force and the beating rate of the eel atrium in a dose-dependent manner. These effects of eOXM were not inhibited by betaxolol, a β1-adrenoceptor antagonist, indicating that the actions of eOXM were independent of those of adrenaline. eOXM enhanced the intracellular Ca2+ concentration of the myocardium. The contractility of the eel atrium was greatly reduced after omitting Ca2+ from the bathing medium or after treatment with verapamil, a Ca2+ channel blocker. After inhibiting Ca2+ entry under these conditions, the inotropic effect of eOXM was markedly reduced, but the chronotropic effect was not altered significantly. These results indicate that the inotropic effect of eOXM is via a stimulation of Ca2+ influx but that the chronotropic effect may be independent of extracellular Ca2+.