Статті в журналах: "Homologie distante"

1

Patthy, László. "Detecting distant homologies of mosaic proteins." Journal of Molecular Biology 202, no. 4 (August 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 (July 18, 2023): 699. http://dx.doi.org/10.3390/axioms12070699.

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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 differently. From EEG data embedded into a manifold of high dimension, we discuss these methods and we compare them across persistent homologies of dimensions 0, 1, and 2, that is, across connected components, tunnels and holes, shells around voids, or cavities. We find that from three dimension clouds of points, it is not clear how distinct from each other the methods are, but Wasserstein and Bottleneck distances, topological tests of hypothesis, and various methods show that the methods qualitatively and significantly differ across homologies. We can infer from this analysis that topological persistent homologies do change dramatically at seizure, a finding already obtained in previous analyses. This suggests that looking at changes in homology landscapes could be a predictor of seizure.

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3

Cruz, Sergio Manuel Serra Da, Vanessa Batista, Edno Silva, Frederico Tosta, Clarissa Vilela, Rafael Cuadrat, Diogo Tschoeke, Alberto M. R. Davila, Maria Luiza Machado Campos, and Marta Mattoso. "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 (March 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, K. Praefcke, B. Kohne, J. Pickardt, and K. Horn. "The Crystal and Mesophase Structure of Hexakis(alkylsulfono)- benzene Homologues by X-Ray Diffractometry." Zeitschrift für Naturforschung A 41, no. 6 (June 1, 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 as the temperature is increased. The magnitude of the intercolumnar distance suggests a considerable degree of side chain disorder. A detailed X-ray diffraction study was also performed at room temperature on a single crystal of hexakis(propylsulfono) benzene (HASB3), which is not mesogenic. The results provide detailed information on the structure of HASB 3 which is used in the interpretation of HASB 13 results.

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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 (January 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, Jan POTEMPA, James TRAVIS, Alan J. BARRETT, and Guy S. SALVESEN. "Inhibition of distant caspase homologues by natural caspase inhibitors." Biochemical Journal 357, no. 2 (July 15, 2001): 575. http://dx.doi.org/10.1042/0264-6021:3570575.

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8

SNIPAS, Scott J., Henning R. STENNICKE, Stefan RIEDL, Jan POTEMPA, James TRAVIS, Alan J. BARRETT, and Guy S. SALVESEN. "Inhibition of distant caspase homologues by natural caspase inhibitors." Biochemical Journal 357, no. 2 (July 9, 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 origin, we hypothesized that the caspase inhibitors may also regulate these other proteases. We tested this hypothesis by examining the effect of the natural caspase inhibitors on other members of protease clan CD. The IAP family proteins were found to have only a slight inhibitory effect on gingipain-R. The cowpox viral cytokine-response modifier A (CrmA) serpin had no effect on any of the proteases tested but a single point mutation of CrmA (Asp → Lys) resulted in strong inhibition of gingipain-K. More substantial, with respect to the hypothesis, was the strong inhibition of gingipain-K by wild-type p35. The site in p35, required for inhibition of gingipain-K, was mapped to Lys94, seven residues C-terminal to the caspase inhibitory site. Our data indicate that the virally encoded caspase inhibitors have adopted a mechanism that allows them to regulate disparate members of clan CD proteases.

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9

Rigden, Daniel J., Jens M. H. Thomas, Felix Simkovic, Adam Simpkin, Martyn D. Winn, Olga Mayans, and Ronan M. Keegan. "Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases inAMPLE." Acta Crystallographica Section D Structural Biology 74, no. 3 (March 1, 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 is rarely attempted and is dependent on the crystallographer's expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g.solvent accessibility) or crystallographic parameters (e.g.Bfactors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipelineAMPLEto produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways withMrBUMP, fail. Further significant performance gains result when the structure-based distance geometry methodCONCOORDis used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach.CONCOORDis freely available and computationally inexpensive, so these novel methods offer readily available new routes to solve difficult MR cases.

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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 (November 1, 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 recombination of the array onto a normal sequence chromosome. Rearrangements that lack the array enhanced variegation of white on a homologue bearing the array. Therefore, silencing of white genes within a repeat array depends on its distance from heterochromatin of the same chromosome or of its paired homologue. In addition, white transgene arrays cause variegation of a nearby gene in cis, a hallmark of classical position-effect variegation. Such spreading of heterochromatic silencing correlates with array size. Finally, white transgene arrays cause pairing-dependent silencing of a non-variegating white insertion at the homologous position.

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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 (March 21, 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 new viral genomes. To tackle these problems, we propose an approach that uses short-read mappers to create whole-genome maps, and gradient descent to isolate the homologous fraction and calculate the final distance value. We implement this approach as Mottle. With the use of simulated and biological sequences, Mottle was able to remain stable to 0.66–0.96 substitutions per base pair and identify viral outgroup genomes with 95% accuracy at the family-order level. Our results indicate that Mottle performs as well as existing programs in identifying taxonomic relationships, with more accurate numerical estimation of genomic distance over greater divergences. By contrast, one limitation is a reduced numerical accuracy at low divergences, and on genomes where insertions and deletions are uncommon, when compared to alternative approaches. We propose that Mottle may therefore be of particular interest in the study of viruses, viral relationships, and notably for viral discovery platforms, helping in benchmarking of homology search tools and defining the limits of taxonomic classification methods. The code for Mottle is available at https://github.com/tphoward/Mottle_Repo.

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12

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 (February 1999): 95–100. http://dx.doi.org/10.1093/protein/12.2.95.

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13

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 (May 22, 2014): e1003636. http://dx.doi.org/10.1371/journal.pcbi.1003636.

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14

Keegan, Ronan, Daniel Rigden, Stuart McNicholas, Eugene Krissinel, Jens Thomas, Adam Simpkin, Felix Simkovic, Martyn Winn, and Keith Wilson. "Ensembling for molecular replacement: making the most of your distant homologues." Acta Crystallographica Section A Foundations and Advances 74, a2 (August 22, 2018): e176-e176. http://dx.doi.org/10.1107/s2053273318092586.

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15

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 (November 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 (Horváth). Deteksi fitoplasma pada tanaman dan wereng dilakukan dengan nested-PCR, sikuensing, dan analisis DNA sikuen. Nested-PCR berhasil mengamplifikasi DNA target, yaitu gen 16S rRNA fitoplasma dari tanaman dan wereng. Analisis identitas matriks sikuen fitoplasma asal tanaman wortel di Bogor menunjukkan homologi tertinggi dengan fitoplasma dari grup 16SrII, yaitu Peanut witches’-broom phytoplasma; sedangkan sampel asal Bandung menunjukkan homologi tertinggi dengan fitoplasma dari grup 16SrI, yaitu Ca. Phytoplasma asteris dan Tomato big bud phytoplasma. Analisis identitas matriks sikuen fitoplasma asal wereng di Bogor (B. incisa, S. furcifera) menunjukkan homologi tertinggi dengan fitoplasma dari grup 16SrII, yaitu Cactus witches’-broom phytoplasma; sedangkan fitoplasma asal C. bipunctata dari Bogor menunjukkan homologi tertinggi dengan fitoplasma grup 16SrI, yaitu Ca. Phytoplasma asteris. Tulisan ini merupakan laporan pertama fitoplasma yang menginfeksi tanaman wortel di Bogor dan Bandung.

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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 (July 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 (At1g13030) and have termed the resulting protein Atcoilin. A T-DNA insertional mutant in this gene (ncb-4) also lacks Cajal bodies. Overexpression of Atcoilin cDNA in ncb-1 restores Cajal bodies, which recruit U2B″ as in the wild type, but which are, however, much larger than in the wild type. Thus we have shown that At1g13030 is required for Cajal body formation in Arabidopsis, and we hypothesize that the level of its expression is correlated with Cajal body size. The Atcoilin gene is unaffected in pcb and ccb, suggesting that other genes can also affect CBs.

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17

Orioli, Tommaso, and Daniela Dolce. "Distantly Related Homologue of UhpT in Pseudomonas aeruginosa." Bacteria 1, no. 4 (November 7, 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. Since mutant GlpT leads to FF resistant PA, it is assumed that GlpT is the only FF transporter. However, it is also assumed that PA uses glucose-6-phosphate and, thus, homologous proteins of UhpT may be present in its genome. Here, we present an attempt to find a distant related homologue of UhpT in PA. A Hidden Markov Model (HMM) was created to seek for Major facilitator family (MFS) domain in 21 PA genomes of 14 CF patients annotated with prokka and the statistical analysis was performed (MCC: 0.84, ACC: 0.99). Then, the HMM was applied to PA genomes. Besides the actual GlpT, annotated as glpt_1, one more GlpT protein was found in 21 out of 21 genomes, annotated as glpt_2. Since glpt_2 clusters closer to UhpT than GlpT, glpt_2 was selected to build a model. Computing a structural superimposition, the model and the template of UhpT have 0.6 Å of RMSD. The model of glpt_2 has some characteristics that are fundamental to UhpT functions. The binding site, consisting of 2 arginines (Arg46 and Arg275) and Lys45, is totally conserved, as well as the topology of the structure. Asp90 is also conserved in glpt_2 model. No studies aimed at searching for distant related homologous of UhpT. Since the high genetic exchange and high mutational rate in bacteria, it is likely that PA has a UhpT-like protein in the PA genome. The binding site is superimposable to UhpT protein as well as the overall topology. In fact, the 12 TMs are completely comparable, suggesting a well-defined folding of the protein across the bilayer lipid membrane. To enforce our hypothesis, in all 21 PA genomes, we also found a protein annotated as membrane sensor protein UhpC, important for expression and function of UhpT in E. coli. Since PA strains are wild-type, we can assume that most of the PA have proteins like this. The presence of a homologue of UhpT suggests that this protein is conserved in PA genome.

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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 (July 1, 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 (May 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 attachment but was correlated with a measure of tension: the distance between homologous or sister kinetochores (in meiosis I and II, respectively). Further, the tension-sensitive 3F3/2 phosphoepitope colocalized, and was lost concomitantly, with MAD2 staining at the meiotic kinetochore. The mechanism of spindle assembly (discussed here with respect to maize mitosis and meiosis) is likely to affect the relative contributions of attachment and tension. We support the idea that MAD2 is attachment-sensitive and that tension stabilizes microtubule attachments.

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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 (September 25, 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 representing persistent landscape objects based on the persistent homology method. The persistent landscape functions allow you to map persistent diagrams to Hilbert space. The representations of topological functions in various machine learning models are considered. An example of finding the distance between images based on the construction of persistent landscape functions is given. Based on the algebra of polynomials in the barcode space, which are used as coordinates, the distances in the barcode space are determined by comparing intervals from one barcode to another and calculating penalties. For these purposes, tropical functions are used that take into account the basic structure of the barcode space. Methods for constructing rational tropical functions are considered. An example of finding the distance between images based on the construction of tropical functions is given. To increase the variety of parameters (machine learning features), filtering of object scanning by rows from left to right and scanning by columns from bottom to top are built. This adds spatial information to topological information. The method of constructing persistent landscapes is compatible with the approach of constructing tropical rational functions when obtaining persistent homologies.

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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 (July 1, 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 interactions occur between genetic elements near opposite ends of a chromosome arm rather than between paired alleles. Cis-acting suppressors were obtained as secondary rearrangements in which the duplication was moved farther away from heterochromatin. Suppression was correlated with loss of cytological association between bwD and the polytene chromocenter. Surprisingly, the distance from bwD to the chromocenter was not correlated with the strength of enhancement or suppression. We propose that bwD fails to coalesce with the chromocenter when its position along the chromosome places it beyond a threshold distance from heterochromatin, and this threshold depends upon the configuration of both the chromosome carrying bwD and its paired homologue.

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22

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 (October 7, 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 this study were generally lower than those in soil around municipal waste incinerators and industrial parks in other areas. An exponential function equation was applied for the relationship between the concentration of the target compounds and the distance from the cement kiln stack, the results showed that PCN and PCB concentrations declined with the increasing of distance from the stack. Furthermore, it was found that the effect of the cement kiln on surrounding soil contaminations with PCNs and PCBs was stronger than that of PCDD/Fs by comparing the PCN, PCB, and PCDD/F homologue profiles in the fly ash sample from the plant and soil samples at different distances. The total carcinogenic risks (CR) of PCNs, PCBs, and PCDD/Fs for children and adults in soil were 1.65 × 10−8–8.93 × 10−8 and 1.70 × 10−8–9.16 × 10−8, respectively, which was less than the risk threshold (CR = 1 × 10−6), and there was no health risk.

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23

de Vries, Ida, Danique Ammerlaan, Tatjana Heidebrecht, Patrick HN Celie, Daan P. Geerke, Robbie P. Joosten, and Anastassis Perrakis. "Distant sequence regions of JBP1 contribute to J-DNA binding." Life Science Alliance 6, no. 9 (June 16, 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 as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.

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24

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 (July 3, 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 similarities and discuss whether these indicate meaningful homologies in the development of CD8+ TRM and CD4+ TFH or reflect resemblances which are only ‘skin-deep’.

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25

Sybenga, J. "Homologous chromosome pairing in meiosis of higher eukaryotes—still an enigma?" Genome 63, no. 10 (October 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 serious problems. Homology search without DSBs cannot be explained by models based on DSB repair. The movement of homologues to meet each other and make contact at the molecular level is not understood. These problems are discussed and the conclusion is that at present practically nothing is known of meiotic homologue pairing in higher eukaryotes up to the formation of the synaptonemal complex, and that new, necessarily speculative models must be developed. Arguments are given that RNA plays a central role in homology search and a tentative model involving RNA in homology search is presented. A role of actin in homologue movement is proposed. The primary role of DSBs in higher eukaryotes is concluded to not be in pairing but in the preparation of Holliday junctions, ultimately leading to chromatid exchange.

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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 (April 1, 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-dihydroxy-5-n-tricosylbenzene were also determined, whereas 1,3-dihydroxy-5-n-pentadecylbenzene and 1,3-dihydroxy- 5-n-pentacosylbenzene were present in these extracts only in spurious amounts. Furthermore, our results show that alk(en)ylresorcinols may be useful as chemotaxonomic markers for a distinction between soft and hard wheat plants. Cluster analysis with Ward’s amalgamation algorithm and five different distance linkage types clearly discriminated particular wheats into species- and cultivar-specific clusters, whereas the use of principal component analysis allowed us to specify, which of the variables analysed were decisive. This approach may be useful for both plant breeders and taxonomists to classify wheat species/ cultivars.

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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 (October 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. However, a careful analysis revealed that the distance from the origin of replication was conserved for the majority of the genes and that many of the rearrangements involved inversions that included the origin of replication. On a finer scale, numerous small indels were observed. K31 proteins involved in essential functions shared 80–95% amino acid sequence identity with their C. crescentus homologues, while other homologue pairs tended to have lower levels of identity. In addition, the K31 chromosome contains more than 1600 genes with no homologue in NA1000.

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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 (July 15, 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 cells solely during the lytic cycle. Despite sharing only 40% primary sequence identity, K14 and CD200 interacted with CD200R with an almost identical and low affinity (KD = 0.5 μM), in contrast to other characterized viral homologue interactions. Cells expressing CD200 or K14 on the cell surface were able to inhibit secretion by activated macrophages of proinflammatory cytokines such as tumor necrosis factor alpha, an effect that could be specifically relieved by addition of monoclonal antibodies and soluble monomeric CD200 protein. We conclude that CD200 delivers local down-modulatory signals to myeloid cells through direct cell-cell contact and that the K14 viral homologue closely mimics this.

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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 (June 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 formed during gap repair. The hypothesis explains the polarity in the frequency of conversion events across genetic loci, the observation that chromosomes carrying recombinators are more often converted than is the homologue, and how recombinators can initiate conversion at a distance, as suggested by the pattern of conversion events in thehis-3locus in crosses heterozygous for the translocation TM429.

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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 (March 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 (February 26, 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 = 3.5630 (10) Å], forming a three-dimensional structure.

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32

Ju, Fusong, Jianwei Zhu, Qi Zhang, Guozheng Wei, Shiwei Sun, Wei-Mou Zheng, and Dongbo Bu. "Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction." Bioinformatics 38, no. 4 (November 27, 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 set network (called Seq-SetNet) to directly and effectively exploit MSA for protein structure prediction. Seq-SetNet uses an ‘encoding and aggregation’ strategy that consists of two key elements: (i) an encoding module that takes a component homologue in MSA as input, and encodes residue mutations and correlations into context-specific features for each residue; and (ii) an aggregation module to aggregate the features extracted from all component homologues, which are further transformed into structural properties for residues of the query protein. As Seq-SetNet encodes each homologue protein individually, it could consider both insertions and deletions, as well as long-distance correlations among residues, thus representing more information than the inter-mediate models. Moreover, the encoding module automatically learns effective features and thus avoids manual feature engineering. Using symmetric aggregation functions, Seq-SetNet processes the homologue proteins as a sequence set, making its prediction results invariable to the order of these proteins. On popular benchmark sets, we demonstrated the successful application of Seq-SetNet to predict secondary structure and torsion angles of residues with improved accuracy and efficiency. Availability and implementation The code and datasets are available through https://github.com/fusong-ju/Seq-SetNet. Supplementary information Supplementary data are available at Bioinformatics online.

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Benavente, E., and J. Sybenga. "The relation between pairing preference and chiasma frequency in tetrasomics of rye." Genome 47, no. 1 (January 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 a wheat background. Earlier observations that heterozygous associations (banded with unbanded) had consistently higher chiasma frequencies than homozygous associations were extended and confirmed. To analyze this phenomenon more closely, the possible relations between this correlation and several other meiotic phenomena were studied. For this analysis, three genetically different autotetraploid hybrids within S. cereale were selected that differed with respect to the relation between pairing type and chiasma frequency. Special attention was given to different patterns of interference and other meiotic phenomena in the two chromosome arms of chromosome 1R. No relations between such phenomena and the relation between pairing type and chiasma frequency could be established. A hypothesis is formulated assuming that long-distance homologue attraction is concentrated in a limited number of sites and that in different genotypes, different patterns of active sites are present. Moderately weak attraction sites can pair with strong homologous sites under favorable genetic conditions, but two weak sites cannot. Then, heterozygotes have more effective pairing initiation and consequently chiasma formation than homozygotes. Under less favorable conditions, only strong sites are effective, and then, homozygotes pair better, but the chiasma frequency is lower. A model of the forces involved in homologue attraction is presented.Key words: autopolyploids, preferential pairing, chiasma frequency, homologue attraction, Secale.

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Thompson, Christopher W. "Determining Evolutionary Homologies of Molts and Plumages: A Commentary on Howell et al. (2003)." Condor 106, no. 1 (February 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 by not doing so. Howell et al. (2003) propose a revised H-P system. To follow their system, one must accept their notion that no first-cycle molts are homologous with prebasic molts in subsequent molt cycles. However, this is not so as many species have a molt in their first cycle that is homologous to definitive prebasic molt. In addition, Howell et al.'s (2003) system does not offer any new or better criteria for identifying homologies than those suggested by Humphrey and Parkes (1959) and, thus, is not an improvement on the H-P system. First-cycle molts and plumages of most birds are poorly known. Therefore, we will not have sufficient data to determine whether new molts have been evolutionarily added to the first cycle, as suggested by Howell et al. (2003), until the molts of many more species of birds are studied. Further, these studies must be done on closely related species, not phylogenetically distant ones as proposed by Howell et al. (2003).Determinación de las Homologías Evolutivas de la Muda y el Plumaje: Un Comentario sobre Howell et al. (2003)Resumen. Howell et al. (2003) aducen que el sistema Humphrey-Parkes (H-P) de terminología para la muda es erróneo porque requiere utilizar la primera muda prebásica como el punto de partida para la sucesión del plumaje, lo que resulta en falta de correspondencia entre la nomenclatura y las presuntas homologías en los primeros plumajes básicos. Sin embargo, el sistema H-P no requiere esto. Segundo, ellos argumentan que el color de plumaje puede ser un criterio engañoso para evaluar las homologías del plumaje, pero yo demuestro que el momento y la extensión de las mudas, y por tanto sus homologías, pueden documentarse con mayor exactitud utilizando el color del plumaje que no haciéndolo. Howell et al. (2003) proponen un sistema H-P revisado que implica aceptar su noción de que ninguna de las mudas del primer ciclo es homóloga con mudas prebásicas de ciclos de muda subsiguientes. Sin embargo, esto no es así, pues muchas especies tienen una muda en su primer ciclo que es homóloga a la muda prebásica definitiva. Adicionalmente, el sistema de Howell et al. (2003) no ofrece criterios nuevos o mejores para identificar las homologías que aquellos sugeridos por Humphrey and Parkes (1959), por lo que no representa un mejoramiento del sistema H-P. Las mudas y los plumajes del primer ciclo de la mayoría de las aves son poco conocidos. Por lo tanto, hasta que no se estudie la muda en muchas más especies de aves, no tendremos suficientes datos para determinar si nuevas mudas se han adicionado evolutivamente al primer ciclo como Howell et al. (2003) sugirieron. Más aún, dichos estudios deben hacerse en especies estrechamente relacionadas, no en aquellas filogenéticamente distantes como Howell et al. (2003) propusieron.

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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 (23 серпня 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 (April 1, 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 characterized a mutant that produces fourfold less capsule than the type 3 parent. The spontaneous mutation resulting in this phenotype was not contained in the type 3 capsule locus but was instead located in a distant gene (pgm) encoding a second PGM homologue. The function of this gene product as a PGM was demonstrated through enzymatic and complementation studies. Insertional inactivation ofpgm reduced capsule production to less than 10% of the parental level. The loss of PGM activity in the insertion mutants also caused growth defects and a strong selection for isolates containing second-site suppressor mutations. These results demonstrate that most of the PGM activity required for type 3 capsule biosynthesis is derived from the cellular PGM.

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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 investigation is transporters coded within BGCs. These proteins most likely take part in the export of antibiotics out of the cell, as well as in the producer’s resistance to its own secondary metabolite. In this work, we performed in silico analysis of genes encoding transporters from ramoplanin and other LDP BGCs. We investigated the domain architecture of these transporters, discovered their homologues in BGCs from MIBiG and beyond, generated models of secondary and tertiary structures, and compared the overall LDP BGCs transport genes blueprint. We were able to identify previously uncharacterized gene encoding ABC transporter within ramoplanin BGC – ramo3. Ramo1 and Ramo3 in ramoplanin BGC appear to be paralogues coding for a permease subunit of the ABC transporter. In every other LDP BGCs, except for chersinamycin BGC, we found only one corresponding homologue encoding this type of protein. Similarly, we found that Ramo2 and Ramo23 are also homologous proteins, which appear to be ATP-binding subunits of the ABC transporter; Ramo2 and Ramo23 have only one homologue in each other LDP BGCs. Next, we were able to describe Ramo8 as ATP-binding ABC transporter, containing both ATPase and transmembrane parts, similar to those encoded in GPA BGCs. For Ramo8, we modelled 3D structure as well as quaternary structure for homodimer of this protein. Finally, our in silico analysis revealed Ramo31 to be a proton membrane antiporter, having distant homologue only in chersinamycin BGC; most likely Ramo31 is not connected to ramoplanin biosynthesis.

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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 (March 1, 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. One of the three alternative exl cassettes contained the meningococcal hemoglobin receptor gene, hmbR (exl3). In other meningococcal strains, hmbR was absent from the genome and was replaced by either a nucleotide sequence containing a novel open reading frame, exl2, or a cassette containing exl3. The proteins encoded byexl2 and exl3 had no significant amino acid homology to HmbR but contained six motifs that are also present in the lipoprotein components of the lactoferrin (LbpB), transferrin (TbpB), and hemoglobin-haptoglobin (HpuA) uptake systems. To determine the evolutionary relationships among meningococci carryinghmbR, exl2, or exl3, isolates representing 92 electrophoretic types were examined.hmbR was found throughout the population structure ofN. meningitidis (genetic distance, >0.425), whereasexl2 and exl3 were found in clonal groups at genetic distances of <0.2. The commensal neisserial species were identified as reservoirs for all of the exl cassettes found in meningococci. The structure of these cassettes and their correlation with clonal groups emphasize the extensive gene pool and frequent horizontal DNA transfer events that contribute to the evolution and virulence of N. meningitidis.

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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 (March 7, 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 of these features of Rac1 are conserved in its yeast homologue Rho5. Here, we review the structural and functional similarities and differences between these two evolutionary distant proteins and propose yeast as a useful model and a device for high-throughput screens for specific drugs.

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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 (October 1, 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 analysis to be made between the two maps. Homologies were found among the respective linkage groups. No relevant differences were observed in the linear order of the common loci.Key words: peach, linkage map, Prunus persica, Prunus ferganensis, molecular markers.

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41

Ferland1, Catherine. "Le nectar et l’ambroisie." Revue d'histoire de l'Amérique française 58, no. 4 (March 6, 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 sert à marquer la distance qui les sépare des gens du peuple et ainsi de s’éloigner du spectre de la « sauvagerie », mais sert aussi à affirmer leur filiation identitaire avec la France, en perpétuant leur appartenance à la culture française et, par extension, à la « civilisation ».

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Millán, Claudia, Massimo Domenico Sammito, Airlie J. McCoy, Andrey F. Ziem Nascimento, Giovanna Petrillo, Robert D. Oeffner, Teresa Domínguez-Gil, Juan A. Hermoso, Randy J. Read, and Isabel Usón. "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 (April 1, 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 new algorithms implemented inARCIMBOLDO_SHREDDERare described in detail, illustrating its characteristic aspects in the solution of new and test structures. In an advance from the previously published algorithm, which was based on omitting or extracting contiguous polypeptide spans, model generation now uses three-dimensional volumes respecting structural units. The optimal fragment size is estimated from the expected log-likelihood gain (LLG) values computed assuming that a substructure can be found with a level of accuracy near that required for successful extension of the structure, typically below 0.6 Å root-mean-square deviation (r.m.s.d.) from the target. Better sampling is attempted through model trimming or decomposition into rigid groups and optimization throughPhaser'sgyrerefinement. Also, after model translation, packing filtering and refinement, models are either disassembled into predetermined rigid groups and refined (gimblerefinement) orPhaser's LLG-guided pruning is used to trim the model of residues that are not contributing signal to the LLG at the target r.m.s.d. value. Phase combination among consistent partial solutions is performed in reciprocal space withALIXE. Finally, density modification and main-chain autotracing inSHELXEserve to expand to the full structure and identify successful solutions. The performance on test data and the solution of new structures are described.

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43

Chojnowski, Grzegorz, Koushik Choudhury, Philipp Heuser, Egor Sobolev, Joana Pereira, Umut Oezugurel, and Victor S. Lamzin. "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 (February 28, 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 sequence. The application of the homology-based model extension method to the example of a CFA synthase at 2.7 Å resolution resulted in a more complete model with almost all of the residues correctly built and docked to the sequence. The method was also evaluated on 1493 molecular-replacement solutions at a resolution of 4.0 Å and better that were submitted to the ARP/wARP web service for model building. A significant improvement in the completeness and sequence coverage of the built models has been observed.

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44

Fabela, S., C. Domenzain, J. De la Mora, A. Osorio, V. Ramirez-Cabrera, S. Poggio, G. Dreyfus, and L. Camarena. "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 (September 20, 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 (February 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 hybridization. One-quarter of the dominant RAPDs were linked in repulsion phase, whereas the majority of them were linked to either codominant or dominant markers in coupling phase. About 10% of the markers showed significant segregation distortion. The detectable level of duplications in the celery genome was relatively low.Key words: Apium graveolens, RFLP, RAPD, linkage map.

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46

Park, Jin-Young, Hyo Jung Kim, Chinar Pathak, Hye-Jin Yoon, Do-Hee Kim, Sung Jean Park, and Bong-Jin Lee. "Induced DNA bending by unique dimerization of HigA antitoxin." IUCrJ 7, no. 4 (June 26, 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 MtHigA3 and DNA using NMR spectroscopy. The MtHigA3 antitoxin structure is a homodimer that contains a structurally well conserved DNA-binding domain at the N-terminus and a dimerization domain at the C-terminus. Upon comparing the HigA homologue structures, a distinct difference was found in the C-terminal region that possesses the β-lid, and diverse orientations of two helix–turn–helix (HTH) motifs from HigA homologue dimers were observed. The structure of MtHigA3 bound to DNA reveals that the promoter DNA is bound to two HTH motifs of the MtHigA3 dimer presenting 46.5° bending, and the distance between the two HTH motifs of each MtHigA3 monomer was increased in MtHigA3 bound to DNA. The β-lid, which is found only in the tertiary structure of MtHigA3 among the HigA homologues, causes the formation of a tight dimerization network and leads to a unique arrangement for dimer formation that is related to the curvature of the bound DNA. This work could contribute to the understanding of the HigBA system of M. tuberculosis at the atomic level and may contribute to the development of new antibiotics for TB treatment.

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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 (November 15, 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 but retains the sopC centromere. The stabilization does not depend on increased copy number. Likewise, an N15 mutant with most of its sop operon deleted is partly stabilized by F Sop proteins and fully stabilized by its own. Four inverted repeat sequences similar to those of sopC were located in N15. They are distant from the sop operon and from each other. Two of these were shown to stabilize a mini-F sop deletion mutant when N15 Sop proteins were provided. Provision of the SopA homologue to plasmids with a sopA deletion resulted in further destabilization of the plasmid. The N15 Sop proteins exert effective, but incomplete, repression at the F soppromoter. We conclude that the N15 sop locus determines stable inheritance of the prophage by using dispersed centromere sites. The SopB-centromere and SopA-operator interactions show partial functional overlap between N15 and F. SopA of each plasmid appears to interact with SopB of the other, but in a way that is detrimental to plasmid maintenance.

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48

Takagi, Masakazu, Hideyuki Tamaki, Yukiko Miyamoto, Roberta Leonardi, Satoshi Hanada, Suzanne Jackowski, and Shigeru Chohnan. "Pantothenate Kinase from the Thermoacidophilic Archaeon Picrophilus torridus." Journal of Bacteriology 192, no. 1 (October 23, 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 expressed in E. coli cells transfers phosphate to pantothenate at pH 5 and 55°C. In contrast to E. coli CoaA, the P. torridus enzyme is refractory to feedback regulation by CoA, indicating that in P. torridus cells the CoA levels are not regulated by the CoaA step. These data suggest the existence of two subtypes within the class of prokaryotic type I CoaAs.

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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 (January 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 among the three urkingdoms as deduced from comparisons of ribosomal ribonucleic acid sequences. Indications will be presented that the closer relationship of the eubacterial and eukaryotic glyceraldehyde-3-phosphate dehydrogenase resulted from a gene transfer from eubacteria to eukaryotes after the segregation of the three urkingdoms.Key words: glyceraldehyde-3-phosphate dehydrogenase, archaebacteria, protein evolution.

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50

Sowdhamini, R., David F. Burke, Charlotte Deane, Jing-fei Huang, Kenji Mizuguchi, Hampapathulu A. Nagarajaram, John P. Overington, N. Srinivasan, Robert E. Steward, and Tom L. Blundell. "Protein Three-Dimensional Structural Databases: Domains, Structurally Aligned Homologues and Superfamilies." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 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 & Blundell (1995),Protein Sci.4, 506–520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the programCOMPARER[Sali & Blundell (1990),J. Mol. Biol.212, 403–428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

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