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Готові списки джерел за темами / Homologie distante / Статті в журналах

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Статті в журналах з теми "Homologie distante"

Автор: Grafiati

Опубліковано: 14 грудня 2024

Оновлено: 31 липня 2025

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1

Patthy, László. "Detecting distant homologies of mosaic proteins." Journal of Molecular Biology 202, no. 4 (1988): 689–96. http://dx.doi.org/10.1016/0022-2836(88)90550-5.

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2

Kwessi, Eddy. "Topological Comparison of Some Dimension Reduction Methods Using Persistent Homology on EEG Data." Axioms 12, no. 7 (2023): 699. http://dx.doi.org/10.3390/axioms12070699.

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Анотація:

In this paper, we explore how to use topological tools to compare dimension reduction methods. We first make a brief overview of some of the methods often used in dimension reduction such as isometric feature mapping, Laplacian Eigenmaps, fast independent component analysis, kernel ridge regression, and t-distributed stochastic neighbor embedding. We then give a brief overview of some of the topological notions used in topological data analysis, such as barcodes, persistent homology, and Wasserstein distance. Theoretically, when these methods are applied on a data set, they can be interpreted

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3

Cruz, Sergio Manuel Serra Da, Vanessa Batista, Edno Silva, et al. "Detecting distant homologies on protozoans metabolic pathways using scientific workflows." International Journal of Data Mining and Bioinformatics 4, no. 3 (2010): 256. http://dx.doi.org/10.1504/ijdmb.2010.033520.

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4

Gardiner, John, Robyn Overall, and Jan Marc. "Distant plant homologues: don’t throw out the baby." Trends in Plant Science 17, no. 3 (2012): 126–28. http://dx.doi.org/10.1016/j.tplants.2011.12.007.

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5

Spielberg, N., Z. Luz, R. Poupko, et al. "The Crystal and Mesophase Structure of Hexakis(alkylsulfono)- benzene Homologues by X-Ray Diffractometry." Zeitschrift für Naturforschung A 41, no. 6 (1986): 855–60. http://dx.doi.org/10.1515/zna-1986-0612.

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A powder X-ray diffractometer study of hexakis(tridecylsulfono)benzene (HASB13) has been carried out over the temperature range 20 to above 80 °C. In this range three phase transitions are observed by sharp discontinuities in the diffraction pattern indicating a solid-solid, solidmesophase, and mesophase-liquid transition. The mesomorphic phase is identified as a hexagonal columnar discotic mesophase, Dhd, with intercolumnar spacing of 25.7 Å and average stacking distance of 4.9 Å. Both distances are independent of temperature but there appears to be a gradual increase in the stacking disorder

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6

Shay, C. E., P. G. Foster, and J. M. Neelin. "Predictability of sequence homologies among lysine-rich histones by immunological distance." Comparative Biochemistry and Physiology Part B: Comparative Biochemistry 86, no. 1 (1987): 193–99. http://dx.doi.org/10.1016/0305-0491(87)90197-0.

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7

SNIPAS, Scott J., Henning R. STENNICKE, Stefan RIEDL, et al. "Inhibition of distant caspase homologues by natural caspase inhibitors." Biochemical Journal 357, no. 2 (2001): 575. http://dx.doi.org/10.1042/0264-6021:3570575.

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8

SNIPAS, Scott J., Henning R. STENNICKE, Stefan RIEDL, et al. "Inhibition of distant caspase homologues by natural caspase inhibitors." Biochemical Journal 357, no. 2 (2001): 575–80. http://dx.doi.org/10.1042/bj3570575.

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Caspases play an important role in the ability of animal cells to kill themselves by apoptosis. Caspase activity is regulated in vivo by members of three distinct protease inhibitor families, two of which, baculovirus p35 and members of the inhibitor of apoptosis (IAP) family, are thought to be caspase specific. However, caspases are members of the clan of cysteine proteases designated CD, which also includes animal and plant legumains, and the bacterial proteases clostripain, gingipain-R and gingipain-K. Since these proteases have been proposed to have a common mechanism and evolutionary orig

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9

Rigden, Daniel J., Jens M. H. Thomas, Felix Simkovic, et al. "Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases inAMPLE." Acta Crystallographica Section D Structural Biology 74, no. 3 (2018): 183–93. http://dx.doi.org/10.1107/s2059798318002310.

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Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20–40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores

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10

Dorer, Douglas R., and Steven Henikoff. "Transgene Repeat Arrays Interact With Distant Heterochromatin and Cause Silencing in cis and trans." Genetics 147, no. 3 (1997): 1181–90. http://dx.doi.org/10.1093/genetics/147.3.1181.

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Tandem repeats of Drosophila transgenes can cause heterochromatic variegation for transgene expression in a copy-number and orientation-dependent manner. Here, we demonstrate different ways in which these transgene repeat arrays interact with other sequences at a distance, displaying properties identical to those of a naturally occurring block of interstitial heterochromatin. Arrays consisting of tandemly repeated white transgenes are strongly affected by proximity to constitutive heterochromatin. Moving an array closer to heterochromatin enhanced variegation, and enhancement was reverted by r

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11

Prusokiene, Alisa, Neil Boonham, Adrian Fox, and Thomas P. Howard. "Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent." PLOS ONE 19, no. 3 (2024): e0298834. http://dx.doi.org/10.1371/journal.pone.0298834.

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Current tools for estimating the substitution distance between two related sequences struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as false seeding and over-alignment, create a high barrier for the development of a stable estimator. This is especially true for viral genomes, which carry a high rate of mutation, small size, and sparse taxonomy. Developing an accurate substitution distance measure would help to elucidate the relationship between highly divergent sequences, interrogate their evolutionary history, and better facilitate the discovery of

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12

Wulandari, Isti, Kikin Hamzah Mutaqin, Giyanto Giyanto, and Sri Hendrastuti Hidayat. "Identification of Phytoplasmas on Carrot (Daucus carota L.) and Leafhopper Associated with Yellow Disease in Bogor and Bandung, West Java." Jurnal Fitopatologi Indonesia 16, no. 4 (2022): 157–65. http://dx.doi.org/10.14692/jfi.16.4.157-165.

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Gejala kuning mirip seperti infeksi fitoplasma ditemukan pada pertanaman wortel di Jawa Barat. Penelitian bertujuan mengidentifikasi fitoplasma pada tanaman wortel dan serangga wereng yang berasosiasi dengan gejala kuning di Bogor dan Bandung. Wereng yang ditemukan pada pertanaman wortel di Bogor terdiri atas 5 spesies wereng daun (Hemiptera: Cicadellidae), yaitu Balclutha incisa (Matsumura), Orosius argentatus (Evans), Cicadulina bipunctata (Matsumura), Empoascanara indica (Datta), Exitianus indicus (Distant), dan 1 spesies wereng batang (Hemiptera: Delphacidae), yaitu Sogatella furcifera (Ho

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13

Salamov, Asaf A., Makiko Suwa, Christine A. Orengo, and Mark B. Swindells. "Combining sensitive database searches with multiple intermediates to detect distant homologues." Protein Engineering, Design and Selection 12, no. 2 (1999): 95–100. http://dx.doi.org/10.1093/protein/12.2.95.

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14

Chen, Kuang-Yui M., Jiaming Sun, Jason S. Salvo, David Baker, and Patrick Barth. "High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues." PLoS Computational Biology 10, no. 5 (2014): e1003636. http://dx.doi.org/10.1371/journal.pcbi.1003636.

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15

Keegan, Ronan, Daniel Rigden, Stuart McNicholas, et al. "Ensembling for molecular replacement: making the most of your distant homologues." Acta Crystallographica Section A Foundations and Advances 74, a2 (2018): e176-e176. http://dx.doi.org/10.1107/s2053273318092586.

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16

Collier, Sarah, Alison Pendle, Kurt Boudonck, Tjeerd van Rij, Liam Dolan, and Peter Shaw. "A Distant Coilin Homologue Is Required for the Formation of Cajal Bodies in Arabidopsis." Molecular Biology of the Cell 17, no. 7 (2006): 2942–51. http://dx.doi.org/10.1091/mbc.e05-12-1157.

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Cajal bodies (CBs) are subnuclear bodies that are widespread in eukaryotes, being found in mammals, many other vertebrates and in all plant species so far examined. They are mobile structures, moving, fusing, and budding within the nucleus. Here we describe a screen for Arabidopsis mutants with altered CBs and describe mutants that have smaller Cajal bodies (ncb-2, ncb-3), lack them altogether (ncb-1), have increased numbers of CBs (pcb) or have flattened CBs (ccb). We have identified the gene affected in the ncb mutants as a distant homolog of the vertebrate gene that encodes coilin (At1g1303

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17

Orioli, Tommaso, and Daniela Dolce. "Distantly Related Homologue of UhpT in Pseudomonas aeruginosa." Bacteria 1, no. 4 (2022): 266–78. http://dx.doi.org/10.3390/bacteria1040020.

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Pseudomonas aeruginosa (PA) is an opportunistic Gram-negative bacteria that affects patients in intensive care units and chronic respiratory disease patients. Compared to other bacteria, it has a wide genome (around 6.3-Mb) that supports its metabolic versatility and antimicrobial resistance. Fosfomycin (FF) is primarily used as an oral treatment for urinary tract infections (UTIs). FF diffuses inside the cell via glycerol-3-phosphate transporter (GlpT) PA, as well as in other bacteria. In other bacteria, such as E. coli, glucose-6-phosphate transporter (UhpT) functions as FF transporter. Sinc

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18

Johnston, C. R. "A sequence sub-sampling algorithm increases the power to detect distant homologues." Nucleic Acids Research 33, no. 12 (2005): 3772–78. http://dx.doi.org/10.1093/nar/gki687.

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19

Yu, Hong-Guo, Michael G. Muszynski, and R. Kelly Dawe. "The Maize Homologue of the Cell Cycle Checkpoint Protein MAD2 Reveals Kinetochore Substructure and Contrasting Mitotic and Meiotic Localization Patterns." Journal of Cell Biology 145, no. 3 (1999): 425–35. http://dx.doi.org/10.1083/jcb.145.3.425.

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We have identified a maize homologue of yeast MAD2, an essential component in the spindle checkpoint pathway that ensures metaphase is complete before anaphase begins. Combined immunolocalization of MAD2 and a recently cloned maize CENPC homologue indicates that MAD2 localizes to an outer domain of the prometaphase kinetochore. MAD2 staining was primarily observed on mitotic kinetochores that lacked attached microtubules; i.e., at prometaphase or when the microtubules were depolymerized with oryzalin. In contrast, the loss of MAD2 staining in meiosis was not correlated with initial microtubule

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20

Chukanov, Sergey N., and Ilya S. Chukanov. "Formation of Machine Learning Features Based on the Construction of Tropical Functions." Modeling and Analysis of Information Systems 29, no. 3 (2022): 200–209. http://dx.doi.org/10.18255/1818-1015-2022-3-200-209.

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One of the main methods of computational topology and topological data analysis is persistent homology, which combines geometric and topological information about an object using persistent diagrams and barcodes. The persistent homology method from computational topology provides a balance between reducing the data dimension and characterizing the internal structure of an object. Combining machine learning and persistent homology is hampered by topological representations of data, distance metrics, and representation of data objects. The paper considers mathematical models and functions for re

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21

Henikoff, S., J. M. Jackson, and P. B. Talbert. "Distance and pairing effects on the brownDominant heterochromatic element in Drosophila." Genetics 140, no. 3 (1995): 1007–17. http://dx.doi.org/10.1093/genetics/140.3.1007.

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Abstract We examined the behavior of the brownDominant (bwD) heterochromatic insertion moved to different locations relative to centric heterochromatin. Effects were measured as the degree of silencing of a wild-type brown eye pigment gene by bwD across a tandem duplication. A series of X-ray-induced effects were recovered at high frequency. Cis-acting enhancers were obtained by relocation of the duplication closer to autosomal heterochromatin. Enhancers were also recovered on the homologous chromosome when it was similarly rearranged, revealing a novel interhomologue effect whereby interactio

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22

Peng, Changwei, and Stephen C. Jameson. "The relationship between CD4+ follicular helper T cells and CD8+ resident memory T cells: sisters or distant cousins?" International Immunology 32, no. 9 (2020): 583–87. http://dx.doi.org/10.1093/intimm/dxaa045.

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Abstract Independent studies over the last decade have characterized the properties of non-circulating CD8+ ‘resident’ memory T cells (TRM), which offer barrier protective immunity in non-lymphoid tissues and CD4+ follicular helper T cells (TFH), which mediate B-cell help in lymphoid sites. Despite their very different biological roles in the immune system, intriguing parallels have been noted between the trafficking properties and differentiation cues of these populations, parallels which have only sharpened with recent findings. In this review, we explore the features that underlie these sim

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23

Sybenga, J. "Homologous chromosome pairing in meiosis of higher eukaryotes—still an enigma?" Genome 63, no. 10 (2020): 469–82. http://dx.doi.org/10.1139/gen-2019-0154.

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Meiosis is the basis of the generative reproduction of eukaryotes. The crucial first step is homologous chromosome pairing. In higher eukaryotes, micrometer-scale chromosomes, micrometer distances apart, are brought together by nanometer DNA sequences, at least a factor of 1000 size difference. Models of homology search, homologue movement, and pairing at the DNA level in higher eukaryotes are primarily based on studies with yeast where the emphasis is on the induction and repair of DNA double-strand breaks (DSB). For such a model, the very large nuclei of most plants and animals present serio

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24

Han, Jiali, Chenyang Xu, Jun Jin, and Jicheng Hu. "PCNs, PCBs, and PCDD/Fs in Soil around a Cement Kiln Co-Processing Municipal Wastes in Northwestern China: Levels, Distribution, and Potential Human Health Risks." International Journal of Environmental Research and Public Health 19, no. 19 (2022): 12860. http://dx.doi.org/10.3390/ijerph191912860.

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To evaluate the impact of the first cement kiln co-processing municipal wastes in northwest China on the surrounding environment, the concentrations of polychlorinated naphthalenes (PCNs), polychlorinated biphenyls (PCBs), and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) were determined in 17 soil samples collected around the plant. The concentration ranges of PCNs, PCBs, and PCDD/Fs were 132–1288, 10.8–59.5, and 2.50–5.95 pg/g, and the ranges of toxic equivalents (TEQ) were 1.98–20.8, 2.36–48.0, and 73.2–418 fg/g, respectively. The concentrations of PCNs, PCBs, and PCDD/Fs in

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25

de Vries, Ida, Danique Ammerlaan, Tatjana Heidebrecht, et al. "Distant sequence regions of JBP1 contribute to J-DNA binding." Life Science Alliance 6, no. 9 (2023): e202302150. http://dx.doi.org/10.26508/lsa.202302150.

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Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it a

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26

Zarnowski, Robert, Yoshikatsu Suzuki, and J. Pietr. "Alkyl- and Alkenylresorcinols of Wheat Grains and their Chemotaxonomic Significance." Zeitschrift für Naturforschung C 59, no. 3-4 (2004): 190–96. http://dx.doi.org/10.1515/znc-2004-3-411.

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Resorcinolic lipid contents and homologue compositions in extracts isolated from soft winter, soft spring and hard (durum) wheat grains were evaluated by both instrumental and chromatography means. Resorcinol concentrations determined in wheat were diverse and varied in samples harvested within two consecutive vegetative years, whereas their homologue profiles were found to be rather invariable. The predominant alkylresorcinols identified in wheat grains were saturated 1,3-dihydroxy-5-n-heneicosylbenzene and 1,3-dihydroxy-5-nnonadecylbenzene. 1,3-Dihydroxy-5-n-heptadecylbenzene and 1,3-dihydro

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27

Ash, Kurt, Theta Brown, Tynetta Watford, LaTia E. Scott, Craig Stephens, and Bert Ely. "A comparison of the Caulobacter NA1000 and K31 genomes reveals extensive genome rearrangements and differences in metabolic potential." Open Biology 4, no. 10 (2014): 140128. http://dx.doi.org/10.1098/rsob.140128.

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The genus Caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 4°C with a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. A comparison of the K31 and the Caulobacter crescentus NA1000 genomes revealed extensive rearrangements of gene order, suggesting that the genomes had been randomly scrambled. Howeve

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28

Foster-Cuevas, Mildred, Gavin J. Wright, Michael J. Puklavec, Marion H. Brown, and A. Neil Barclay. "Human Herpesvirus 8 K14 Protein Mimics CD200 in Down-Regulating Macrophage Activation through CD200 Receptor." Journal of Virology 78, no. 14 (2004): 7667–76. http://dx.doi.org/10.1128/jvi.78.14.7667-7676.2004.

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ABSTRACT Many viral proteins limit host immune defenses, and their genes often originate from their hosts. CD200 (OX2) is a broadly distributed cell surface glycoprotein that interacts with a receptor on myeloid cells (CD200R) that is implicated in locally preventing macrophage activation. Distant, but recognizable, homologues of CD200 have been identified in many herpesviruses and poxviruses. Here, we show that the product of the K14 open reading frame from human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus) interacts with human CD200R and is expressed at the surfaces of infected ce

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29

Catcheside, D. E. A. "A restriction and modification model for the initiation and control of recombination inNeurospora." Genetical Research 47, no. 3 (1986): 157–65. http://dx.doi.org/10.1017/s0016672300023077.

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SummaryIt is hypothesized that the products of Neurosporarec+genes mask recombinators such ascogby modifying DNA and that unmodified recombinators act as recognition sites for an endonuclease with scission properties like those of the type I restriction enzymes found inE. coli. These cut the DNA in both strands at some variable distance from a recognition site. Repair of a two strand gap initiated in this way would require DNA synthesis using the information contained in the homologous DNA duplex, leading to gene conversion. Crossing over could follow from resolution of two Holliday structures

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30

Bray, J. E., A. E. Todd, F. M. G. Pearl, J. M. Thornton, and C. A. Orengo. "The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues." Protein Engineering, Design and Selection 13, no. 3 (2000): 153–65. http://dx.doi.org/10.1093/protein/13.3.153.

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31

Qachchachi, Fatima-Zahrae, Fouad Ouazzani Chahdi, Houria Misbahi, Michael Bodensteiner, and Lahcen El Ammari. "1-(Prop-2-ynyl)indoline-2,3-dione." Acta Crystallographica Section E Structure Reports Online 70, no. 3 (2014): o360. http://dx.doi.org/10.1107/s1600536814003973.

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The structure of the title compound, C11H7NO2, is isotypic to that of its homologue, 1-octylindoline-2,3-dione [Qachchachiet al.(2013).Acta Cryst.E69, o1801]. The indoline ring and the two carbonyl O atoms are approximately coplanar, the largest deviation from the mean plane being 0.021 (1) Å for one of the O atoms. The mean plane through the fused ring system is nearly perpendicular to the propynyl group, as indicated by the N—C—C—C torsion angle of 77.9 (1)°. In the crystal, molecules are linked by C—H...O hydrogen bonds and π–π interactions between benzene rings [intercentroid distance = 3.

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32

Ju, Fusong, Jianwei Zhu, Qi Zhang, et al. "Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction." Bioinformatics 38, no. 4 (2021): 990–96. http://dx.doi.org/10.1093/bioinformatics/btab777.

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Abstract Motivation Accurate prediction of protein structure relies heavily on exploiting multiple sequence alignment (MSA) for residue mutations and correlations as this information specifies protein tertiary structure. The widely used prediction approaches usually transform MSA into inter-mediate models, say position-specific scoring matrix or profile hidden Markov model. These inter-mediate models, however, cannot fully represent residue mutations and correlations carried by MSA; hence, an effective way to directly exploit MSAs is highly desirable. Results Here, we report a novel sequence s

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33

Benavente, E., and J. Sybenga. "The relation between pairing preference and chiasma frequency in tetrasomics of rye." Genome 47, no. 1 (2004): 122–33. http://dx.doi.org/10.1139/g03-134.

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The association pattern of marked tetrasomes of Secale chromosome 1R at meiotic first metaphase was analyzed. Two of the four chromosomes were identical with terminal C-bands at both arms; the other two were also identical but lacked C-bands and were homologous or homeologous with the first two. Four different types of heterozygotes for 1R were studied: (i) autotetraploid hybrids between genetic variants within Secale cereale subsp. cereale, (ii) tetraploid hybrids between subspecies of Secale cereale, (iii) tetraploid hybrids between species of Secale, and (iv) autotetrasomes of S. cereale in

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34

Thompson, Christopher W. "Determining Evolutionary Homologies of Molts and Plumages: A Commentary on Howell et al. (2003)." Condor 106, no. 1 (2004): 199–206. http://dx.doi.org/10.1093/condor/106.1.199.

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AbstractHowell et al. (2003) argue that the Humphrey-Parkes (H-P) system of molt terminology is flawed because it requires using traditional first prebasic molt as the starting point for plumage succession that results in noncorrespondence between nomenclature and presumed homology in first basic plumages. However, the H-P system does not require this. Second, they argue that plumage color can be a misleading criterion for evaluating plumage homologies. I show, however, that the timing and extent of molts, and thus their homologies, can de documented more accurately by using plumage color than

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35

Jenkins, Huw T., та Alfred A. Antson. "A nuclease cut three ways: phasing from distant homologues, an ideal α-helix and Zn-SAD". Acta Crystallographica Section A Foundations and Advances 71, a1 (2015): s197. http://dx.doi.org/10.1107/s2053273315097065.

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36

Hardy, Gail G., Melissa J. Caimano, and Janet Yother. "Capsule Biosynthesis and Basic Metabolism inStreptococcus pneumoniae Are Linked through the Cellular Phosphoglucomutase." Journal of Bacteriology 182, no. 7 (2000): 1854–63. http://dx.doi.org/10.1128/jb.182.7.1854-1863.2000.

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ABSTRACT Synthesis of the type 3 capsular polysaccharide ofStreptococcus pneumoniae requires UDP-glucose (UDP-Glc) and UDP-glucuronic acid (UDP-GlcUA) for production of the [3)-β-d-GlcUA-(1→4)-β-d-Glc-(1→] n polymer. The generation of UDP-Glc proceeds by conversion of Glc-6-P to Glc-1-P to UDP-Glc and is mediated by a phosphoglucomutase (PGM) and a Glc-1-P uridylyltransferase, respectively. Genes encoding both a Glc-1-P uridylyltransferase (cps3U) and a PGM homologue (cps3M) are present in the type 3 capsule locus, but these genes are not essential for capsule production. In this study, we cha

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37

Zhukrovska, K., and V. Fedorenko. "Comparative in silico analysis of transporters coded within biosynthetic genes clusters for ramoplanin and related antibiotics." Visnyk of Lviv University. Biological series, no. 91 (June 7, 2024): 22–35. http://dx.doi.org/10.30970/vlubs.2024.91.03.

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Glycopeptide antibiotics (GPAs), like teicoplanin and vancomycin, have been the first-line treatment for infections caused by Gram-positive multidrug-resistant pathogens. GPAs appear to be related to ramoplanin-like lipodepsipeptides (LDPs), yet another significant class of lipid II binders. Major compounds among LDPs are ramoplanin (the key representative), enduracidin, and chersinamycin; each with known biosynthetic gene clusters (BGCs). Five additional BGCs for the putative LDPs were recently described. LDP BGCs are poorly investigated; one particular aspect that deserves further investiga

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38

Kahler, C. M., E. Blum, Y. K. Miller, D. Ryan, T. Popovic, and D. S. Stephens. "exl, an Exchangeable Genetic Island in Neisseria meningitidis." Infection and Immunity 69, no. 3 (2001): 1687–96. http://dx.doi.org/10.1128/iai.69.3.1687-1696.2001.

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ABSTRACT The genetic structure and evolution of a novel exchangeable meningococcal genomic island was defined for the important human pathogen Neisseria meningitidis. In 125 meningococcal strains tested, one of three unrelated nucleotide sequences, designatedexl (exchangeable locus), was found between a gene required for heme utilization, hemO, andcol, encoding a putative Escherichia colicollagenase homologue. The 5′ boundary of each exlcassette was the stop codon of hemO, whereas the 3′ boundary was delineated by a 33-bp repeat containing neisserial uptake sequences located downstream of col.

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39

Bischof, Linnet, Franziska Schweitzer, and Jürgen J. Heinisch. "Functional Conservation of the Small GTPase Rho5/Rac1—A Tale of Yeast and Men." Cells 13, no. 6 (2024): 472. http://dx.doi.org/10.3390/cells13060472.

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Small GTPases are molecular switches that participate in many essential cellular processes. Amongst them, human Rac1 was first described for its role in regulating actin cytoskeleton dynamics and cell migration, with a close relation to carcinogenesis. More recently, the role of Rac1 in regulating the production of reactive oxygen species (ROS), both as a subunit of NADPH oxidase complexes and through its association with mitochondrial functions, has drawn attention. Malfunctions in this context affect cellular plasticity and apoptosis, related to neurodegenerative diseases and diabetes. Some

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40

Dettori, Maria Teresa, Roberta Quarta, and Ignazio Verde. "A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers." Genome 44, no. 5 (2001): 783–90. http://dx.doi.org/10.1139/g01-065.

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A linkage map was obtained using a BC1 progeny (Prunus persica × (P. persica × P. ferganensis)). The map is composed of 109 loci (74 RFLPs, 17 SSRs, 16 RAPDs, and two morphological traits) distributed in 10 linkage groups. Loci, segregating in five different ratios, were integrated in the map with JoinMap 2.0 software. The map covers 521 cM of the peach genome. The average distance between adjacent loci is 4.8 cM. Two monogenic traits, flesh adhesion (F/f) and leaf glands (E/e), were placed on the map. Thirty-two loci in common with a saturated linkage map of Prunus allowed a comparative analy

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41

Ferland1, Catherine. "Le nectar et l’ambroisie." Revue d'histoire de l'Amérique française 58, no. 4 (2006): 475–505. http://dx.doi.org/10.7202/012210ar.

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Résumé À l’époque moderne, consommer du vin et des liqueurs constitue un marqueur identitaire pour l’élite, au même titre que le bas de soie ou la perruque. Au xviiie siècle, les membres de l’élite de la Nouvelle-France boivent en se conformant aux normes en vigueur chez leur homologue métropolitaine, depuis le choix et le service des boissons jusqu’à leur absorption et, parfois, de l’ivresse qu’elles procurent. On prend également soin de respecter les prescriptions sociales liées au Boire, particulièrement celles relatives au genre. Cette façon d’afficher des manières de boire bien françaises

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42

Millán, Claudia, Massimo Domenico Sammito, Airlie J. McCoy, et al. "Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination." Acta Crystallographica Section D Structural Biology 74, no. 4 (2018): 290–304. http://dx.doi.org/10.1107/s2059798318001365.

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Macromolecular structures can be solved by molecular replacement provided that suitable search models are available. Models from distant homologues may deviate too much from the target structure to succeed, notwithstanding an overall similar fold or even their featuring areas of very close geometry. Successful methods to make the most of such templates usually rely on the degree of conservation to select and improve search models.ARCIMBOLDO_SHREDDERuses fragments derived from distant homologues in a brute-force approach driven by the experimental data, instead of by sequence similarity. The ne

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43

Chojnowski, Grzegorz, Koushik Choudhury, Philipp Heuser, et al. "The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution." Acta Crystallographica Section D Structural Biology 76, no. 3 (2020): 248–60. http://dx.doi.org/10.1107/s2059798320000455.

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The performance of automated protein model building usually decreases with resolution, mainly owing to the lower information content of the experimental data. This calls for a more elaborate use of the available structural information about macromolecules. Here, a new method is presented that uses structural homologues to improve the quality of protein models automatically constructed using ARP/wARP. The method uses local structural similarity between deposited models and the model being built, and results in longer main-chain fragments that in turn can be more reliably docked to the protein s

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44

Fabela, S., C. Domenzain, J. De la Mora, et al. "A Distant Homologue of the FlgT Protein Interacts with MotB and FliL and Is Essential for Flagellar Rotation in Rhodobacter sphaeroides." Journal of Bacteriology 195, no. 23 (2013): 5285–96. http://dx.doi.org/10.1128/jb.00760-13.

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45

Yang, Xiaofeng, and Carlos F. Quiros. "Construction of a genetic linkage map in celery using DNA-based markers." Genome 38, no. 1 (1995): 36–44. http://dx.doi.org/10.1139/g95-005.

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A F2population of two celery cultivated types (Apium graveolens L. var. rapaceum and A. graveolens L. var. secalinum) was used to construct a linkage map consisting of 29 RFLP (restriction fragment length polymorphism), 100 RAPD (random amplified polymorphic DNA), four isozyme, one disease resistance, and one growth habit markers. The map contains 11 major groups and 9 small groups and has a total length of 803 cM with an average distance of 6.4 cM between two adjacent loci. Ten percent of the RAPDs segregated as codominant markers and their allelic homologies were tested by Southern hybridiza

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46

Park, Jin-Young, Hyo Jung Kim, Chinar Pathak, et al. "Induced DNA bending by unique dimerization of HigA antitoxin." IUCrJ 7, no. 4 (2020): 748–60. http://dx.doi.org/10.1107/s2052252520006466.

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The bacterial toxin–antitoxin (TA) system regulates cell growth under various environmental stresses. Mycobacterium tuberculosis, the causative pathogen of tuberculosis (TB), has three HigBA type II TA systems with reverse gene organization, consisting of the toxin protein HigB and labile antitoxin protein HigA. Most type II TA modules are transcriptionally autoregulated by the antitoxin itself. In this report, we first present the crystal structure of the M. tuberculosis HigA3 antitoxin (MtHigA3) and MtHigA3 bound to its operator DNA complex. We also investigated the interaction between MtHig

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47

Ravin, N., and D. Lane. "Partition of the Linear Plasmid N15: Interactions of N15 Partition Functions with the sop Locus of the F Plasmid." Journal of Bacteriology 181, no. 22 (1999): 6898–906. http://dx.doi.org/10.1128/jb.181.22.6898-6906.1999.

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ABSTRACT A locus close to one end of the linear N15 prophage closely resembles the sop operon which governs partition of the F plasmid; the promoter region contains similar operator sites, and the two putative gene products have extensive amino acid identity with the SopA and -B proteins of F. Our aim was to ascertain whether the N15sop homologue functions in partition, to identify the centromere site, and to examine possible interchangeability of function with the F Sop system. When expressed at a moderate level, N15 SopA and -B proteins partly stabilize mini-F which lacks its own sopoperon b

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48

Takagi, Masakazu, Hideyuki Tamaki, Yukiko Miyamoto, et al. "Pantothenate Kinase from the Thermoacidophilic Archaeon Picrophilus torridus." Journal of Bacteriology 192, no. 1 (2009): 233–41. http://dx.doi.org/10.1128/jb.01021-09.

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ABSTRACT Pantothenate kinase (CoaA) catalyzes the first step of the coenzyme A (CoA) biosynthetic pathway and controls the intracellular concentrations of CoA through feedback inhibition in bacteria. An alternative enzyme found in archaea, pantoate kinase, is missing in the order Thermoplasmatales. The PTO0232 gene from Picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type I CoaA. The cloned gene clearly complements the poor growth of the temperature-sensitive Escherichia coli CoaA mutant strain ts9, and the recombinant protein expre

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49

Hensel, Reinhard, Peter Zwickl, Stefan Fabry, Jutta Lang, and Peter Palm. "Sequence comparison of glyceraldehyde-3-phosphate dehydrogenases from the three urkingdoms: evolutionary implication." Canadian Journal of Microbiology 35, no. 1 (1989): 81–85. http://dx.doi.org/10.1139/m89-012.

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The primary structure of the glyceraldehyde-3-phosphate dehydrogenase from the archaebacteria shows striking deviation from the known sequences of eubacterial and eukaryotic sequences, despite unequivocal homologies in functionally important regions. Thus, the structural similarity between the eubacterial and eukaryotic enzymes is significantly higher than that between the archaebacterial enzymes and the eubacterial and eukarytic enzymes. This preferred similarity of eubacterial and eukaryotic glyceraldehyde-3-phosphate dehydrogenase structures does not correspond to the phylogenetic distances

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50

Sowdhamini, R., David F. Burke, Charlotte Deane, et al. "Protein Three-Dimensional Structural Databases: Domains, Structurally Aligned Homologues and Superfamilies." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (1998): 1168–77. http://dx.doi.org/10.1107/s0907444998007148.

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This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the programDIAL[Sowdhamini & Blun

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