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Journal articles on the topic 'Gene orders'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 February 2022

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1

Perseke, Marleen, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter F. Stadler, and Martin Schlegel. "Evolution of mitochondrial gene orders in echinoderms." Molecular Phylogenetics and Evolution 47, no. 2 (May 2008): 855–64. http://dx.doi.org/10.1016/j.ympev.2007.11.034.

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2

Perrin, Amandine, Jean-Stéphane Varré, Samuel Blanquart, and Aïda Ouangraoua. "ProCARs: Progressive Reconstruction of Ancestral Gene Orders." BMC Genomics 16, Suppl 5 (2015): S6. http://dx.doi.org/10.1186/1471-2164-16-s5-s6.

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3

Yang, Ning, Fei Hu, Lingxi Zhou, and Jijun Tang. "Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches." PLoS ONE 9, no. 10 (October 10, 2014): e108796. http://dx.doi.org/10.1371/journal.pone.0108796.

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4

Markov, A. V., and I. A. Zakharov. "Evolution of gene orders in genomes of cyanobacteria." Russian Journal of Genetics 45, no. 8 (August 2009): 906–16. http://dx.doi.org/10.1134/s1022795409080031.

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5

Zhang, Yiwei, Fei Hu, and Jijun Tang. "A mixture framework for inferring ancestral gene orders." BMC Genomics 13, Suppl 1 (2012): S7. http://dx.doi.org/10.1186/1471-2164-13-s1-s7.

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6

Silander, Olin K., and Martin Ackermann. "The constancy of gene conservation across divergent bacterial orders." BMC Research Notes 2, no. 1 (2009): 2. http://dx.doi.org/10.1186/1756-0500-2-2.

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7

Markov, A. V., and I. A. Zakharov. "Evolution of gene orders in mycoplasmas (Bacteria, Firmicutes, Mollicutes)." Russian Journal of Genetics 45, no. 7 (July 2009): 781–87. http://dx.doi.org/10.1134/s1022795409070035.

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8

Kunisawa, Takashi. "Gene arrangements and branching orders of gram-positive bacteria." Journal of Theoretical Biology 222, no. 4 (June 2003): 495–503. http://dx.doi.org/10.1016/s0022-5193(03)00064-x.

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9

Perez Botero, Juliana, Lea Coon, Julie Majerus, Dong Chen, and Rajiv Pruthi. "Factor IX Gene (F9) Genotyping Trends and Spectrum of Mutations Identified: A Reference Laboratory Experience." Seminars in Thrombosis and Hemostasis 44, no. 03 (September 13, 2017): 287–92. http://dx.doi.org/10.1055/s-0037-1605567.

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AbstractIn hemophilia B (HB), factor IX gene (F9) genotyping is used for molecular confirmation of affected individuals, for carrier testing, to facilitate the identification of those at risk for anaphylaxis/inhibitors (associated with large deletions), and to assist in assigning disease severity. Owing to test costs, optimal test utilization involves pre/post-test counseling and appropriate patient and test selection (e.g., mutation screening [F9MS] vs. known mutation [F9KM] testing). This article aims to review the trends and outcomes of F9-genotyping orders and describe the spectrum of variants identified in a sample of individuals in our reference laboratory. We performed a retrospective review of consecutive orders submitted to the Special Coagulation DNA Diagnostic Laboratory, Mayo Clinic, between 2012 and 2015. A total of 133 orders (38%) were identified for men: 118 (88%) were F9MS and 15 (12%) were F9KM. Thirteen orders (10%) were cancelled. A total of 209 orders were identified for women: 178 (85%) were F9MS and 31 (15%) were F9KM. Thirty-seven orders (18%) were cancelled and 30% of the tests performed yielded negative results. A total of 164 samples (47%) were received without clinical information. Seventeen previously unreported variants were identified. F9 genotyping provides useful information for HB management; however, 18% of our orders were cancelled and almost half were received without relevant clinical information, thus reaffirming the need for ongoing scrutiny of submitted orders. Optimal patient and test selection is important as is the accurate interpretation of variants identified. Most of the pathogenic variants identified were point mutations, with very few large deletions, consistent with the literature.

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10

Hu, Fei, Jun Zhou, Lingxi Zhou, and Jijun Tang. "Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions." IEEE/ACM Transactions on Computational Biology and Bioinformatics 11, no. 4 (July 2014): 667–72. http://dx.doi.org/10.1109/tcbb.2014.2309602.

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11

Zakharov, I. A., and A. V. Markov. "Gene Orders in Genomes of Alpha-Proteobacteria: Similarity and Evolution." Russian Journal of Genetics 41, no. 12 (December 2005): 1343–51. http://dx.doi.org/10.1007/s11177-006-0005-8.

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12

McDonagh, Laura M., Helen West, James W. Harrison, and Jamie R. Stevens. "Which mitochondrial gene (if any) is best for insect phylogenetics?" Insect Systematics & Evolution 47, no. 3 (June 16, 2016): 245–66. http://dx.doi.org/10.1163/1876312x-47032142.

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Despite the benefits of whole-genome analysis, in many instances — particularly in applied entomology — mitochondrial genes continue to offer a reliable, rapid and cheap alternative. To date, most studies using insect mitochondrial DNA have analysed single genes and none have rigorously attempted to assess which genes are best suited for studying particular insect orders; here, we address this issue and use the ability of individual genes to recover ordinal monophyly of various insect orders as a metric. Phylogenies were constructed for nine insect orders and three outgroups, using 12 protein-coding genes and two rRNA genes; 153 genomes were analysed and trees were constructed using PhyML. The importance of gene length and region within the mtDNA genome were explored using correlation and sliding window analyses. No single gene appeared to outperform all others. Accordingly, we recommend that mitochondrial-based reconstructions of insect relationships use a multi-gene approach, using as many genes and taxa as possible.

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13

Kunisawa, Takashi. "Branching orders among α-proteobacteria and mitochondria inferred from gene transpositions." Journal of Theoretical Biology 234, no. 1 (May 2005): 1–5. http://dx.doi.org/10.1016/j.jtbi.2004.11.004.

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14

Marshall, E. "Varmus orders up a review of the science of gene therapy." Science 267, no. 5204 (March 17, 1995): 1588. http://dx.doi.org/10.1126/science.7886441.

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15

Bertrand, Denis, Mathieu Lajoie, and Nadia El-Mabrouk. "Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes." Journal of Computational Biology 15, no. 8 (October 2008): 1063–77. http://dx.doi.org/10.1089/cmb.2008.0025.

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16

Jenner, Ronald A., Bjoern M. von Reumont, Lahcen I. Campbell, and Eivind A. B. Undheim. "Parallel Evolution of Complex Centipede Venoms Revealed by Comparative Proteotranscriptomic Analyses." Molecular Biology and Evolution 36, no. 12 (August 8, 2019): 2748–63. http://dx.doi.org/10.1093/molbev/msz181.

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Abstract Centipedes are among the most ancient groups of venomous predatory arthropods. Extant species belong to five orders, but our understanding of the composition and evolution of centipede venoms is based almost exclusively on one order, Scolopendromorpha. To gain a broader and less biased understanding we performed a comparative proteotranscriptomic analysis of centipede venoms from all five orders, including the first venom profiles for the orders Lithobiomorpha, Craterostigmomorpha, and Geophilomorpha. Our results reveal an astonishing structural diversity of venom components, with 93 phylogenetically distinct protein and peptide families. Proteomically-annotated gene trees of these putative toxin families show that centipede venom composition is highly dynamic across macroevolutionary timescales, with numerous gene duplications as well as functional recruitments and losses of toxin gene families. Strikingly, not a single family is found in the venoms of representatives of all five orders, with 67 families being unique for single orders. Ancestral state reconstructions reveal that centipede venom originated as a simple cocktail comprising just four toxin families, with very little compositional evolution happening during the approximately 50 My before the living orders had diverged. Venom complexity then increased in parallel within the orders, with scolopendromorphs evolving particularly complex venoms. Our results show that even venoms composed of toxins evolving under the strong constraint of negative selection can have striking evolutionary plasticity on the compositional level. We show that the functional recruitments and losses of toxin families that shape centipede venom arsenals are not concentrated early in their evolutionary history, but happen frequently throughout.

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17

Bronstein, I., C. S. Martin, J. J. Fortin, C. E. Olesen, and J. C. Voyta. "Chemiluminescence: sensitive detection technology for reporter gene assays." Clinical Chemistry 42, no. 9 (September 1, 1996): 1542–46. http://dx.doi.org/10.1093/clinchem/42.9.1542.

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Abstract A series of enzyme-activated chemiluminescence-based assays of reporter gene expression, useful in many biomedical applications, has been developed. The chemiluminescence detection systems for beta-galactosidase, beta-glucuronidase (GUS), and secreted placental alkaline phosphatase (SEAP) reporter enzymes are all based on use of 1,2-dioxetane substrates. This detection technology also permits the combined luminescence detection of two different reporter enzymes in the same tube, e.g., a dual assay for beta-galactosidase and luciferase. The sensitivity of these chemiluminescence assays is several orders of magnitude greater than that of conventional colorimetric or fluorometric detection methods; e.g., the detection limit for beta-galactosidase by the chemiluminescence assay is 8 fg and by a fluorometric assay is 2 pg. Furthermore, chemiluminescence enables detection of beta-galactosidase, GUS, and SEAP enzyme concentrations over a dynamic range of more than five to six orders in magnitude. These assays offer highly sensitive, quantitative, rapid, nonisotopic detection of reporter enzymes that are widely used in both mammalian cells and plant cells.

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18

Kunisawa, Takashi. "A Method for Inferring Species Branching-Orders based on Gene-Order Comparison." Joho Chishiki Gakkaishi 14, no. 2 (2004): 53–56. http://dx.doi.org/10.2964/jsik_kj00001039569.

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19

Popova, Olga V., Kirill V. Mikhailov, Mikhail A. Nikitin, Maria D. Logacheva, Aleksey A. Penin, Maria S. Muntyan, Olga S. Kedrova, Nikolai B. Petrov, Yuri V. Panchin, and Vladimir V. Aleoshin. "Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals." PLOS ONE 11, no. 10 (October 18, 2016): e0165072. http://dx.doi.org/10.1371/journal.pone.0165072.

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20

Prohaska, Sonja J., Sarah J. Berkemer, Fabian Gärtner, Thomas Gatter, Nancy Retzlaff, Christian Höner zu Siederdissen, and Peter F. Stadler. "Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem." Journal of Mathematical Biology 77, no. 2 (December 19, 2017): 313–41. http://dx.doi.org/10.1007/s00285-017-1197-3.

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21

Kunisawa, Takashi. "The phylogenetic placement of the non-phototrophic, Gram-positive thermophile ‘Thermobaculum terrenum’ and branching orders within the phylum ‘ Chloroflexi ’ inferred from gene order comparisons." International Journal of Systematic and Evolutionary Microbiology 61, no. 8 (August 1, 2011): 1944–53. http://dx.doi.org/10.1099/ijs.0.026088-0.

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The phylogenetic position of an anaerobic, non-spore-forming thermophile ‘Thermobaculum terrenum’ was investigated on the basis of gene order data from completely sequenced bacterial genomes. Gene order data can be an excellent source of phylogenetic information. Shared gene arrangements are unlikely to have arisen by chance convergence. They are likely to reflect common ancestry. ‘Thermobaculum terrenum’ was found to share three gene arrangements that are present uniquely in genomes of members of the phylum ‘Chloroflexi’, indicating convincingly that ‘Thermobaculum terrenum’ is a member of this phylum. Branching orders within the phylum ‘Chloroflexi’ were inferred by identifying monophyletic groups of species, which were circumscribed by characteristic gene arrangements. The branching orders thus inferred were in good agreement with previously reported phylogenies based on single 16S rRNA gene sequences and on multiple protein sequences. The gene order comparisons revealed a close phylogenetic affinity of ‘Thermobaculum terrenum’ to Sphaerobacter thermophilus and Thermomicrobium roseum.

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22

Ishiwata, Keisuke, Go Sasaki, Jiro Ogawa, Takashi Miyata, and Zhi-Hui Su. "Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences." Molecular Phylogenetics and Evolution 58, no. 2 (February 2011): 169–80. http://dx.doi.org/10.1016/j.ympev.2010.11.001.

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23

Le, Thanh H., David Blair, Takeshi Agatsuma, Pierre-François Humair, Nick J. H. Campbell, Mori Iwagami, D. Timothy J. Littlewood, et al. "Phylogenies Inferred from Mitochondrial Gene Orders—A Cautionary Tale from the Parasitic Flatworms." Molecular Biology and Evolution 17, no. 7 (July 1, 2000): 1123–25. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026393.

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24

Liu, Hong, and Andrew T. Beckenbach. "Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects." Molecular Phylogenetics and Evolution 1, no. 1 (March 1992): 41–52. http://dx.doi.org/10.1016/1055-7903(92)90034-e.

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25

Da, Y., V. L. Jarrell, T. Wang, R. L. Fernando, M. B. Wheeler, and H. A. Lewin. "Multilocus analysis for gene-centromere mapping using first polar bodies and secondary oocytes." Genetics 139, no. 2 (February 1, 1995): 1091–97. http://dx.doi.org/10.1093/genetics/139.2.1091.

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Abstract Polar body and oocyte typing is a new technique for gene-centromere mapping and for generating female linkage maps. A maximum likelihood approach is presented for ordering multiple markers relative to the centromere and for estimating recombination frequencies between markers and between the centromere and marker loci. Three marker-centromere orders are possible for each pair of markers: two orders when the centromere flanks the two markers and one order when the centromere is flanked by the two markers. For each possible order, the likelihood was expressed as a function of recombination frequencies for two adjacent intervals. LOD score for recombination frequency between markers or between the centromere and a marker locus was derived based on the likelihood for each gene-centromere order. The methods developed herein provide a general solution to the problem of multilocus gene-centromere mapping that involves all theoretical crossover possibilities, including four-strand double crossovers.

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26

Ye, Fei, Hu Li, and Qiang Xie. "Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs." Genes 12, no. 8 (July 26, 2021): 1134. http://dx.doi.org/10.3390/genes12081134.

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Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

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27

Luo, Kun, and Dong Hui Luo. "A Phylogenetic Analysis for Gene ITPK1." Advanced Materials Research 466-467 (February 2012): 27–30. http://dx.doi.org/10.4028/www.scientific.net/amr.466-467.27.

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Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK1) is a pivotal enzyme in producing IP6 , a moleculae that play an essential role in many biochemistry process in mammal cells. In this paper, two phylogenetic trees are constructed based on the mRNA sequences and the protein sequences, respectively. The results indicate that the protein sequences are more conserved than mRNA sequences in primates. Although both plant and animal have an abundant distribution of ITPK1 domain, there exists a great variation in protein sequence between plant and animal. The protein-based tree reflects an evolution orders that is consistent with that of organisms evolution. Z-test of selection indicates that evolution of protein ITPK1 is caused by selection pressure.

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28

Wang, Yuyu, Xiaofan Zhou, Liming Wang, Xingyue Liu, Ding Yang, and Antonis Rokas. "Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data." International Journal of Molecular Sciences 20, no. 5 (March 1, 2019): 1072. http://dx.doi.org/10.3390/ijms20051072.

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Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.

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29

Susmita, Chatterjee. "Hierarchical Analysis of Variation in the Mitochondrial 16SrRNA Gene among Five Different Insect Orders." Agricultural Sciences 06, no. 11 (2015): 1375–80. http://dx.doi.org/10.4236/as.2015.611132.

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30

Hao, L., J. Klein, and M. Nei. "Heterogeneous but conserved natural killer receptor gene complexes in four major orders of mammals." Proceedings of the National Academy of Sciences 103, no. 9 (February 21, 2006): 3192–97. http://dx.doi.org/10.1073/pnas.0511280103.

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31

Minegishi, Hiroaki, Masahiro Kamekura, Tomomi Kitajima-Ihara, Kaoru Nakasone, Akinobu Echigo, Yasuhiro Shimane, Ron Usami, Takashi Itoh, and Kunio Ihara. "Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups." International Journal of Systematic and Evolutionary Microbiology 62, no. 1 (January 1, 2012): 188–95. http://dx.doi.org/10.1099/ijs.0.031708-0.

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In many prokaryotic species, 16S rRNA genes are present in multiple copies, and their sequences in general do not differ significantly owing to concerted evolution. At the time of writing, the genus Haloarcula of the family Halobacteriaceae comprises nine species with validly published names, all of which possess two to four highly heterogeneous 16S rRNA genes. Existence of multiple heterogeneous 16S rRNA genes makes it difficult to reconstruct a biological phylogenetic tree using their sequence data. If the orthologous gene is able to be discriminated from paralogous genes, a tree reconstructed from orthologous genes will reflect a simple biological phylogenetic relationship. At present, however, we have no means to distinguish the orthologous rRNA operon from paralogous ones in the members of the family Halobacteriaceae. In this study, we found that the dihydroorotate oxidase gene, pyrD, was present in the immediate upstream of one 16S rRNA gene in each of ten strains of the family Halobacteriaceae whose genome sequences have been determined, and the direction of the pyrD gene was opposite to that of the 16S rRNA genes. In two other strains whose genome sequences have been determined, the pyrD gene was present in far separated positions. We designed PCR primer sets to amplify DNA fragments encompassing a region from the conserved region of the pyrD gene to a conserved region of the tRNA-Ala gene or the 23S rRNA gene to determine the 16S rRNA gene sequences preceded by the pyrD gene, and to see if the pyrD gene is conserved in the immediate upstream of rRNA operon(s) in the type strains of the type species of 28 genera of the family Halobacteriaceae. Seventeen type strains, including the ten strains mentioned above, gave amplified DNA fragments of approximately 4000 bp, while eleven type strains, including the two strains mentioned above, did not give any PCR products. These eleven strains are members of the Clade I haloarchaea, originally defined by Walsh et al. (2004) and expanded by Minegishi et al. (2010). Analysis of contig sequences of three strains belonging to the Clade I haloarchaea also revealed the absence of the pyrD gene in the immediate upstream of any 16S rRNA genes. It may be scientifically sound to hypothesize that during the evolution of members of the family Halobacteriaceae, a pyrD gene transposition event happened in one group and this was followed by subsequent speciation processes in each group, yielding species/genera of the Clade I group and ‘the rest’ of the present family Halobacteriaceae.

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32

WU, CATHY H., HSI-LIEN CHEN, and SHENG-CHIH CHEN. "GENE CLASSIFICATION ARTIFICIAL NEURAL SYSTEM." International Journal on Artificial Intelligence Tools 04, no. 04 (December 1995): 501–10. http://dx.doi.org/10.1142/s0218213095000255.

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A gene classification artificial neural system has been developed for rapid annotation of the molecular sequencing data being generated by the Human Genome Project. Three neural networks have been implemented, one full-scale system to classify protein sequences according to PIR (Protein Identification Resources) superfamilies, one system to classify ribosomal RNA sequences into RDP (Ribosomal Database Project) phylogenetic classes, and one pilot system to classify proteins according to Blocks motifs. The sequence encoding schema involved an n-gram hashing method to convert molecular sequences into neural input vectors, a SVD (singular value decomposition) method to compress vectors, and a term weighting method to extract motif information. The neural networks used were three-layered, feed-forward networks that employed back-propagation or counter-propagation learning paradigms. The system runs faster by one to two orders of magnitude than existing method and has a sensitivity of 85 to 100%. The gene classification artificial neural system is available on the Internet, and may be extended into a gene identification system for classifying indiscriminately sequenced DNA fragments.

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33

Sagaram, Uma Shankar, Kristen M. DeAngelis, Pankaj Trivedi, Gary L. Andersen, Shi-En Lu, and Nian Wang. "Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing." Applied and Environmental Microbiology 75, no. 6 (January 16, 2009): 1566–74. http://dx.doi.org/10.1128/aem.02404-08.

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ABSTRACT The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria in 15 phyla were present in the citrus leaf midribs, while 20 orders in 8 phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs than in asymptomatic midribs. “Candidatus Liberibacter asiaticus” was detected at a very low level in asymptomatic plants but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis results were further verified by sequencing 16S rRNA gene clone libraries, which indicated the dominance of “Candidatus Liberibacter asiaticus” in symptomatic leaves. These data implicate “Candidatus Liberibacter asiaticus” as the pathogen responsible for HLB disease.

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34

Willemsen, Anouk, Mark P. Zwart, Nicolas Tromas, Eszter Majer, José-Antonio Daròs, and Santiago F. Elena. "Multiple Barriers to the Evolution of Alternative Gene Orders in a Positive-Strand RNA Virus." Genetics 202, no. 4 (February 11, 2016): 1503–21. http://dx.doi.org/10.1534/genetics.115.185017.

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35

Shao, Renfu, Nick J. H. Campbell, Evan R. Schmidt, and Stephen C. Barker. "Increased Rate of Gene Rearrangement in the Mitochondrial Genomes of Three Orders of Hemipteroid Insects." Molecular Biology and Evolution 18, no. 9 (September 1, 2001): 1828–32. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003970.

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36

Gunduz, Mehmet, Pinar Ataca Atilla, and Erden Atilla. "New Orders to an Old Soldier: Optimizing NK Cells for Adoptive Immunotherapy in Hematology." Biomedicines 9, no. 9 (September 11, 2021): 1201. http://dx.doi.org/10.3390/biomedicines9091201.

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NK (Natural Killer) cell-mediated adoptive immunotherapy has gained attention in hematology due to the progressing knowledge of NK cell receptor structure, biology and function. Today, challenges related to NK cell expansion and persistence in vivo as well as low cytotoxicity have been mostly overcome by pioneering trials that focused on harnessing NK cell functions. Recent technological advancements in gene delivery, gene editing and chimeric antigen receptors (CARs) have made it possible to generate genetically modified NK cells that enhance the anti-tumor efficacy and represent suitable “off-the-shelf” products with fewer side effects. In this review, we highlight recent advances in NK cell biology along with current approaches for potentiating NK cell proliferation and activity, redirecting NK cells using CARs and optimizing the procedure to manufacture clinical-grade NK and CAR NK cells for adoptive immunotherapy.

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37

Chen, Guiying, Bin Wang, Jiongyu Liu, Feng Xie, and Jianping Jiang. "Complete mitochondrial genome of Nanorana pleskei (Amphibia: Anura: Dicroglossidae) and evolutionary characteristics." Current Zoology 57, no. 6 (December 1, 2011): 785–805. http://dx.doi.org/10.1093/czoolo/57.6.785.

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Abstract The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced. It includes 17,660 base pairs, containing 13 protein-coding genes, two rRNAs and 23 tRNAs. A tandem duplication of tRNAMet gene was found in this mitochondrial genome, and the similarity between the two tRNAMet genes is 85.8%, being the highest in amphibian mitochondrial genomes sequenced thus far. Based on gene organization, 24 types were found from 145 amphibian mitochondrial genomes. Type 1 was present in 108 species, type 11 in 11 species, types 5, 16, 17, and 20 each in two species, and the others each present in one species. Fifteen types were found in Anura, being the most diversity in three orders of the Lissamphibia. Our phylogenetic results using 11 protein-coding gene sequences of 145 amphibian mitochondrial genomes strongly support the monophyly of the Lissamphibia, as well as its three orders, the Gymnophiona, Caudata, and Anura, among which the relationships were ((Gymnophiona (Caudata, Anura)). Based on the phylogenetic trees, type 1 was recognized as the ancestral type for amphibians, and type 11 was the synapomorphic type for the Neobatrachia. Gene rearrangements among lineages provide meaningful phylogenetic information. The rearrangement of the LTPF tRNA gene cluster and the translocation of the ND5 gene only found in the Neobatrachia support the monophyly of this group; similarly, the tandem duplication of the tRNAMet genes only found in the Dicroglossidae support the monophyly of this family.

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Li, Wei-Ning, and Xiao-Feng Xue. "Mitochondrial genome reorganization provides insights into the relationship between oribatid mites and astigmatid mites (Acari: Sarcoptiformes: Oribatida)." Zoological Journal of the Linnean Society 187, no. 3 (July 16, 2019): 585–98. http://dx.doi.org/10.1093/zoolinnean/zlz044.

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Abstract Oribatida s.l. represents one of the most species-rich mite lineages, including two recognized groups: oribatid mites (Oribatida s.s., non-astigmatan oribatids) and astigmatid mites (Astigmata). However, the relationship between these two groups has been debated. Here, we sequenced the complete mitochondrial (mt) genome of one oribatid mite and one astigmatid mite, retrieved complete mt genomes of three oribatid mites, and compared them with two other oribatid mites and 12 astigmatid mites sequenced previously. We find that gene orders in the mt genomes of both oribatid mites and astigmatid mites are rearranged relative to the hypothetical ancestral arrangement of the arthropods. Based on the shared derived gene clusters in each mt genome group, rearranged mt genomes are roughly divided into two groups corresponding to each mite group (oribatid mites or astigmatid mites). Phylogenetic results show that Astigmata nested in Oribatida. The monophyly of Astigmata is recovered, while paraphyly of Oribatida s.s. is observed. Our results show that rearranged gene orders in the mt genomes characterize various lineages of oribatid mites and astigmatid mites, and have potential phylogenetic information for resolving the high-level (cohort or supercohort) phylogeny of Oribatida.

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Haucke, Hans-R�diger, and Gerd Gellissen. "Different mitochondrial gene orders among insects: exchanged tRNA gene positions in the COII/COIII region between an orthopteran and a dipteran species." Current Genetics 14, no. 5 (November 1988): 471–76. http://dx.doi.org/10.1007/bf00521271.

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Wang, Dapeng, and Jun Yu. "LCGserver: A Webserver for Exploring Evolutionary Trajectory of Gene Orders in a Large Number of Genomes." OMICS: A Journal of Integrative Biology 19, no. 9 (September 2015): 574–77. http://dx.doi.org/10.1089/omi.2015.0060.

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Irisarri, Iker, Douglas J. Eernisse, and Rafael Zardoya. "Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics." Journal of Natural History 48, no. 45-48 (October 13, 2014): 2825–53. http://dx.doi.org/10.1080/00222933.2014.963721.

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Zhu, Jia-chen, Pu Tang, Bo-Ying Zheng, Qiong Wu, Shu-jun Wei, and Xue-xin Chen. "The first two mitochondrial genomes of the family Aphelinidae with novel gene orders and phylogenetic implications." International Journal of Biological Macromolecules 118 (October 2018): 386–96. http://dx.doi.org/10.1016/j.ijbiomac.2018.06.087.

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Tan, Ian H., and Louis D. Druehl. "Phylogeny of the Northeast Pacific brown algal (Phaeophycean) orders as inferred from 18S rRNA gene sequences." Hydrobiologia 260-261, no. 1 (June 1993): 699–704. http://dx.doi.org/10.1007/bf00049090.

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Gao, Zheng, Binglin Li, Chengchao Zheng, and Guangyi Wang. "Molecular Detection of Fungal Communities in the Hawaiian Marine Sponges Suberites zeteki and Mycale armata." Applied and Environmental Microbiology 74, no. 19 (August 1, 2008): 6091–101. http://dx.doi.org/10.1128/aem.01315-08.

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ABSTRACT Symbiotic microbes play a variety of fundamental roles in the health and habitat ranges of their hosts. While prokaryotes in marine sponges have been broadly characterized, the diversity of sponge-inhabiting fungi has barely been explored using molecular approaches. Fungi are an important component of many marine and terrestrial ecosystems, and they may be an ecologically significant group in sponge-microbe interactions. This study tested the feasibility of using existing fungal primers for molecular analysis of sponge-associated fungal communities. None of the eight selected primer pairs yielded satisfactory results in fungal rRNA gene or internal transcribed spacer (ITS) clone library constructions. However, 3 of 10 denaturing gradient gel electrophoresis (DGGE) primer sets, which were designed to preferentially amplify fungal rRNA gene or ITS regions from terrestrial environmental samples, were successfully amplified from fungal targets in marine sponges. DGGE analysis indicated that fungal communities differ among different sponge species (Suberites zeteki and Mycale armata) and also vary between sponges and seawater. Sequence analysis of DGGE bands identified 23 and 21 fungal species from each of the two sponge species S. zeteki and M. armata, respectively. These species were representatives of 11 taxonomic orders and belonged to the phyla of Ascomycota (seven orders) and Basidiomycota (four orders). Five of these taxonomic orders (Malasseziales, Corticiales, Polyporales, Agaricales, and Dothideomycetes et Chaetothyriomcetes incertae sedis) have now been identified for the first time in marine sponges. Seven and six fungal species from S. zeteki and M. armata, respectively, are potentially new species because of their low sequence identity (≤98%) with their references in GenBank. Phylogenetic analysis indicated sponge-derived sequences were clustered into “marine fungus clades” with those from other marine habitats. This is the first report of molecular analysis of fungal communities in marine sponges, adding depth and dimension to our understanding of sponge-associated microbial communities.

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Dornburg, R., and H. M. Temin. "Retroviral vector system for the study of cDNA gene formation." Molecular and Cellular Biology 8, no. 6 (June 1988): 2328–34. http://dx.doi.org/10.1128/mcb.8.6.2328.

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A retroviral vector system was developed to study the retrotransposition of RNAs lacking all cis-acting sequences required for normal retroviral replication. Our experiments indicate that such RNAs can be encapsidated in retroviral proteins, reverse transcribed, and integrated to form functional cDNA genes in infected cells. The frequency of this process, however, was approximately 8 orders of magnitude less than that of normal retroviral replication. The efficiency was limited at each step in this process. Investigation of seven cDNA genes by Southern blot analysis revealed that all of them were truncated at either the 3' or the 5' end or both. These truncations are not seen with natural cDNA genes and raise the question of retroviral involvement in their formation.

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Dornburg, R., and H. M. Temin. "Retroviral vector system for the study of cDNA gene formation." Molecular and Cellular Biology 8, no. 6 (June 1988): 2328–34. http://dx.doi.org/10.1128/mcb.8.6.2328-2334.1988.

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A retroviral vector system was developed to study the retrotransposition of RNAs lacking all cis-acting sequences required for normal retroviral replication. Our experiments indicate that such RNAs can be encapsidated in retroviral proteins, reverse transcribed, and integrated to form functional cDNA genes in infected cells. The frequency of this process, however, was approximately 8 orders of magnitude less than that of normal retroviral replication. The efficiency was limited at each step in this process. Investigation of seven cDNA genes by Southern blot analysis revealed that all of them were truncated at either the 3' or the 5' end or both. These truncations are not seen with natural cDNA genes and raise the question of retroviral involvement in their formation.

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Hochstein, Norbert, Dennis Webb, Marianna Hösel, Werner Seidel, Sabrina Auerochs, and Walter Doerfler. "Human CAR Gene Expression in Nonpermissive Hamster Cells Boosts Entry of Type 12 Adenovirions and Nuclear Import of Viral DNA." Journal of Virology 82, no. 8 (February 6, 2008): 4159–63. http://dx.doi.org/10.1128/jvi.02657-07.

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ABSTRACT Adenovirus type 12 (Ad12) propagation in hamster BHK21 cells is blocked prior to viral DNA replication. The amounts of Ad12 DNA in the nuclei or cytoplasm of hamster cells are about 2 orders of magnitude (2 h postinfection [p.i.]) and 4 to 5 orders of magnitude (48 h p.i.) lower than in permissive human cells. Cell line BHK21-hCAR is transgenic for and expresses the human coxsackie- and adenovirus receptor (hCAR) gene. Nuclear uptake of Ad12 DNA in BHK21-hCAR cells is markedly increased compared to that in naïve BHK21 cells. Ad12 elicits a cytopathic effect in BHK21-hCAR cells but not in BHK21 cells. Quantitative PCR or [3H]thymidine labeling followed by zone velocity sedimentation fails to detect Ad12 DNA replication in BHK21 or BHK21-hCAR cells. Newly assembled Ad12 virions cannot be detected. Thus, the block in Ad12 DNA replication in hamster cells is not released by enhanced nuclear import of Ad12 DNA.

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Sen, Arnab, Vincent Daubin, Danis Abrouk, Isaac Gifford, Alison M. Berry, and Philippe Normand. "Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov." International Journal of Systematic and Evolutionary Microbiology 64, Pt_11 (November 1, 2014): 3821–32. http://dx.doi.org/10.1099/ijs.0.063966-0.

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The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class Actinobacteria and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenation of 54 proteins. In that tree, the orders Bifidobacteriales , Coriobacteriales , ‘Coryneb acteriales’, ‘Micromonosporales’, ‘Propionibacteriales’, ‘Pseudonocardiales’, Streptomycetales and ‘Streptosporangiales’ were recovered while the orders ‘Frankiales’ and Micrococcales were not. It is thus proposed that the order ‘Frankiales’, which has an effectively but not validly published name, be split into Frankiales ord. nov. (type family Frankiaceae ), Geodermatophilales ord. nov. ( Geodermatophilaceae ), Acidothermales ord. nov. ( Acidothermaceae ) and Nakamurellales ord. nov. ( Nakamurellaceae ). The order Micrococcales should also be split into Micrococcales (genera Kocuria , Rothia , Micrococcus , Arthrobacter , Tropheryma , Microbacterium , Leifsonia and Clavibacter ), Cellulomonales ( Beutenbergia , Cellulomonas , Xylanimonas , Jonesia and Sanguibacter ) and Brachybacteriales ( Brachybacterium ) but the formal proposal for this will have to wait until more genomes become available for a significant proportion of strains in this order.

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Graham, Allie M., and Felipe S. Barreto. "Independent Losses of the Hypoxia-Inducible Factor (HIF) Pathway within Crustacea." Molecular Biology and Evolution 37, no. 5 (January 31, 2020): 1342–49. http://dx.doi.org/10.1093/molbev/msaa008.

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Abstract Metazoans respond to hypoxic stress via the hypoxia-inducible factor (HIF) pathway, a mechanism thought to be extremely conserved due to its importance in monitoring cellular oxygen levels and regulating responses to hypoxia. However, recent work revealed that key members of the HIF pathway have been lost in specific lineages (a tardigrade and a copepod), suggesting that this pathway is not as widespread in animals as previously assumed. Using genomic and transcriptomic data from 70 different species across 12 major crustacean groups, we assessed the degree to which the gene HIFα, the master regulator of the HIF pathway, was conserved. Mining of protein domains, followed by phylogenetic analyses of gene families, uncovered group-level losses of HIFα, including one across three orders within Cirripedia, and in three orders within Copepoda. For these groups, additional assessment showed losses of HIF repression machinery (EGLN and VHL). These results suggest the existence of alternative mechanisms for cellular response to low oxygen and highlight these taxa as models useful for probing these evolutionary outcomes.

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Morizot, D. C., S. A. Slaugenhaupt, K. D. Kallman, and A. Chakravarti. "Genetic linkage map of fishes of the genus Xiphophorus (Teleostei: Poeciliidae)." Genetics 127, no. 2 (February 1, 1991): 399–410. http://dx.doi.org/10.1093/genetics/127.2.399.

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Abstract Analysis of genotypes of 76 polymorphic loci in more than 2600 backcross hybrid individuals derived from intra- and interspecific genetic crosses of fishes of the genus Xiphophorus (Poeciliidae) resulted in the identification of 17 multipoint linkage groups containing 55 protein-coding loci and one sex chromosome-linked pigment pattern gene. Multipoint linkage analyses identified highly probable gene orders for 10 linkage groups. The total genome length was estimated to be approximately 18 Morgans. Comparisons of the Xiphophorus linkage map with those of other fishes, amphibians and mammals suggested that fish gene maps are remarkably similar and probably retain many syntenic groups present in the ancestor of all vertebrates.

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