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1.
Simple repetitive DNA sequences from primates: Compilation and analysis 总被引:25,自引:0,他引:25
Simple repeats composed of tandemly repeated units 1–6 nucleotides (nt) long have been extracted from a selected set of primate genomic DNA sequences. Of the 501 theoretically possible, different types of repeats only 67 were present in the analyzed database in at least two different size ranges over 12 nt. They include all simple repeats known to be polymorphic in the primate genome. A list of moderately expanding and nonexpanding oligonucleotide patterns has also been included. Furthermore, we have compiled statistical data with emphasis on the overall variability of the most abundant 67 types of repeats. We have demonstrated that the expandability of at least some simple repeats may be affected by the overall base composition and by flanking sequences. In particular, the occurrence of tandemly repeated CAG and GCC triplets in exons positively correlates with their G+C content. We also noted that in the vicinity of Alu sequences tetrameric repeats are more abundant than in the total genomic DNA. This paper can be used as a comprehensive guide in identification of the most abundant and potentially polymorphic simple repeats. It is also of broader significance as a step toward understanding the contribution of flanking sequences and the overall sequence composition to variability of simple repeats.
Correspondence to: J. Jurka 相似文献
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Saldamli Gokay Upadhyay Charit Jadhav Devika Shrishrimal Rohit Patil Bapugouda Tawalbeh Loai 《Cluster computing》2022,25(3):1915-1926
Cluster Computing - Blockchain is a distributed digital ledger consisting of sequence of blocks. These blocks are groups of transactions that make up a sequence where each block contains the... 相似文献
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Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome 总被引:2,自引:2,他引:0 下载免费PDF全文
Cameron MJ Ran L Xu L Danesh A Bermejo-Martin JF Cameron CM Muller MP Gold WL Richardson SE Poutanen SM Willey BM DeVries ME Fang Y Seneviratne C Bosinger SE Persad D Wilkinson P Greller LD Somogyi R Humar A Keshavjee S Louie M Loeb MB Brunton J McGeer AJ;Canadian SARS Research Network Kelvin DJ 《Journal of virology》2007,81(16):8692-8706
It is not understood how immune inflammation influences the pathogenesis of severe acute respiratory syndrome (SARS). One area of strong controversy is the role of interferon (IFN) responses in the natural history of SARS. The fact that the majority of SARS patients recover after relatively moderate illness suggests that the prevailing notion of deficient type I IFN-mediated immunity, with hypercytokinemia driving a poor clinical course, is oversimplified. We used proteomic and genomic technology to systematically analyze host innate and adaptive immune responses of 40 clinically well-described patients with SARS during discrete phases of illness from the onset of symptoms to discharge or a fatal outcome. A novel signature of high IFN-alpha, IFN-gamma, and IFN-stimulated chemokine levels, plus robust antiviral IFN-stimulated gene (ISG) expression, accompanied early SARS sequelae. As acute illness progressed, SARS patients entered a crisis phase linked to oxygen saturation profiles. The majority of SARS patients resolved IFN responses at crisis and expressed adaptive immune genes. In contrast, patients with poor outcomes showed deviated ISG and immunoglobulin gene expression levels, persistent chemokine levels, and deficient anti-SARS spike antibody production. We contend that unregulated IFN responses during acute-phase SARS may culminate in a malfunction of the switch from innate immunity to adaptive immunity. The potential for the use of the gene signatures we describe in this study to better assess the immunopathology and clinical management of severe viral infections, such as SARS and avian influenza (H5N1), is therefore worth careful examination. 相似文献
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Stern CD Charité J Deschamps J Duboule D Durston AJ Kmita M Nicolas JF Palmeirim I Smith JC Wolpert L 《The International journal of developmental biology》2006,50(1):3-15
When, where and how is the head-tail axis of the embryo set up during development? These are such fundamental and intensely studied questions that one might expect them to have been answered long ago. Not so; we still understand very little about the cellular or molecular mechanisms that lead to the orderly arrangement of body elements along the head-tail axis in vertebrates. In this paper, we outline some of the major outstanding problems and controversies and try to identify some reasons why it has been so difficult to resolve this important issue. 相似文献
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Macey JR Schulte JA Larson A Ananjeva NB Wang Y Pethiyagoda R Rastegar-Pouyani N Papenfuss TJ 《Systematic biology》2000,49(2):233-256
A phylogenetic tree for acrodont lizards (Chamaeleonidae and Agamidae) is established based on 1434 bases (1041 informative) of aligned DNA positions from a 1685-1778 base pair region of the mitochondrial genome. Sequences from three protein-coding genes (ND1, ND2, and COI) are combined with sequences from eight intervening tRNA genes for samples of 70 acrodont taxa and two outgroups. Parsimony analysis of nucleotide sequences identifies eight major clades in the Acrodonta. Most agamid lizards are placed into three distinct clades. One clade is composed of all taxa occurring in Australia and New Guinea; Physignathus cocincinus from Southeast Asia is the sister taxon to the Australia-New Guinea clade. A second clade is composed of taxa occurring from Tibet and the Indian Subcontinent east through South and East Asia. A third clade is composed of taxa occurring from Africa east through Arabia and West Asia to Tibet and the Indian Subcontinent. These three clades contain all agamid lizards except Uromastyx, Leiolepis, and Hydrosaurus, which represent three additional clades of the Agamidae. The Chamaeleonidae forms another clade weakly supported as the sister taxon to the Agamidae. All eight clades of the Acrodonta contain members occurring on land masses derived from Gondwanaland. A hypothesis of agamid lizards rafting with Gondwanan plates is examined statistically. This hypothesis suggests that the African/West Asian clade is of African or Indian origin, and the South Asian clade is either of Indian or Southeast Asian origin. The shortest tree suggests a possible African origin for the former and an Indian origin for the latter, but this result is not statistically robust. The Australia-New Guinea clade rafted with the Australia-New Guinea plate and forms the sister group to a Southeast Asian taxon that occurs on plates that broke from northern Australia-New Guinea. Other acrodont taxa are inferred to be associated with the plates of Afro-Arabia and Madagascar (Chameleonidae), India (Uromastyx), or southeast Asia (Hydrosaurus and Leiolepis). Introduction of different biotic elements to Asia by way of separate Gondwanan plates may be a major theme of Asian biogeography. Three historical events may be responsible for the sharp faunal barrier between Southeast Asia and Australia-New Guinea, known as Wallace's line: (1) primary vicariance caused by plate separations; (2) secondary contact of Southeast Asian plates with Eurasia, leading to dispersal from Eurasia into Southeast Asia, and (3) dispersal of the Indian fauna (after collision of that subcontinent) to Southeast Asia. Acrodont lizards show the first and third of these biogeographic patterns and anguid lizards exhibit the second pattern. Modern faunal diversity may be influenced primarily by historical events such as tectonic collisions and land bridge connections, which are expected to promote episodic turnover of continental faunas by introducing new faunal elements into an area. Repeated tectonic collisions may be one of the most important phenomena promoting continental biodiversity. Phylogenetics is a powerful method for investigating these processes. 相似文献
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Glu-69 of the D2 protein in photosystem II is a potential ligand to Mn involved in photosynthetic oxygen evolution 总被引:5,自引:0,他引:5
To probe the involvement of amino acid residues of the D2 protein in the water-splitting process in photosystem II, site-directed mutagenesis was applied to identify D2 residues that might contribute to binding the Mn cluster involved in oxygen evolution. Mutation of Glu-69 to Gln or Val in D2 of the cyanobacterium Synechocystis sp. PCC 6803 was found to lead to a loss of photoautotrophic growth. However, in cells of the Gln mutant (E69Q) a significant Hill reaction rate could be observed upon the start of illumination, but the oxygen evolution rate declined with a half-time of approximately 1 min. Addition of 1 mM Mn2+ stabilized oxygen evolution in E69Q thylakoids. Other divalent cations were ineffective in specific stabilization. When the water-splitting system was bypassed, the rate of electron transport remained stable during illumination, indicating that the inactivation of oxygen evolution is localized in the water-splitting complex. We interpret these observations to indicate that Glu-69 is a Mn ligand and that the loss of oxygen evolution in the E69Q mutant upon turnover of PS II is initiated by changes in the Mn cluster, possibly leading to Mn release from the water-splitting complex. The addition of exogenous Mn to E69Q thylakoids may help to keep the Mn cluster active for a longer time, perhaps by providing Mn to rebind in the cluster after release of one Mn and before the Mn cluster had disintegrated.(ABSTRACT TRUNCATED AT 250 WORDS) 相似文献
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Hiranya Sudasinghe Rohan Pethiyagoda Rajeev Raghavan Neelesh Dahanukar Lukas Rüber Madhava Meegaskumbura 《Zoologica scripta》2020,49(6):710-731
The South and South-East Asian freshwater fish genus Systomus (Cyprinidae) comprises 17 valid species. Six nominal species, including three endemics, have been reported from Sri Lanka, a continental island separated from India by a shallow-shelf sea. The species diversity of Systomus on the island has until now not been assessed; neither has an evaluation been made of their phylogenetic history. Here, based on an analysis of the nuclear recombination activating protein 1 (rag1), and mitochondrial cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) gene markers, and a morphological examination of 143 specimens from 49 locations in Sri Lanka, we reassess the diversity of Systomus on the island and analyse patterns of their evolution and biogeography. Divergence-time estimates, based on a substitution rate calibration, date the basal split between Systomus and its sister group, the Afrotropical small barbs, to 30.0 Ma (95% highest posterior density: 25.4–35.2 Ma). The species of Systomus belong to two distinct clades. The first includes the Sri Lankan endemics S. asoka, S. martenstyni and S. pleurotaenia, which comprise an insular diversification following the immigration of a common ancestor during the Oligocene. The second, which includes the remaining species of Indian, Sri Lankan and South-East Asian Systomus, has a crown age dating to the Late Miocene. Morphological and molecular species delimitation analyses failed to validate the two nominal species, S. spilurus and S. timbiri, previously reported from Sri Lanka: both are considered synonyms of S. sarana, as are the nomina S. chryseus, S. chrysopoma, S. laticeps, S. rufus, S. pinnauratus and S. subnasutus. Four genetically and geographically discrete lineages of S. sarana occur in the island, and three in India. Molecular species delimitation analysis suggests these all belong to a single species, S. sarana. The genetically distinct Sri Lankan populations of S. sarana result from Plio-Pleistocene dispersal or vicariance events between India and Sri Lanka—as a result of emergence and inundation of the now submerged isthmus connecting the two landmasses—as well as autochthonous insular diversification. 相似文献
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Hiranya Sudasinghe Rohan Pethiyagoda Ranasinghe Hettiarachchige Tharindu Ranasinghe Rajeev Raghavan Neelesh Dahanukar Madhava Meegaskumbura 《Journal of Zoological Systematics and Evolutionary Research》2020,58(4):1076-1110
The diversity of the freshwater-fish genus Rasbora (Cyprinidae) on Sri Lanka (five species) is high compared with the four species reported from the peninsula of India, from which the island's cyprinid fauna is derived. The paucity of characters by which species of Rasbora can be phenotypically distinguished renders field identification difficult, adversely affecting the estimation of populations and distributions, with consequences for conservation and management, increasing also the risk of taxonomic inflation. From a sampling of 90 sites across Sri Lanka and based on phylogenetic and haplotype analyses of sequences of cox1 and cytb mitochondrial, and rag1 and irbp nuclear markers, we review the species diversity and phylogeography of Rasbora on the island. Molecular analyses recover, in addition to the five species previously reported, a new (cryptic) species: Rasbora adisi sp. nov. Uncorrected pairwise cox1 genetic distances between species range from 2.0 to 12.3 percent. The Sri Lankan diversification derives from a common ancestor which arrived from India during a sea-level low-stand in the mid-Miocene (15.1 Ma [95% HPD: 11.5–19.8 Ma]), when the present-day island was subaerially connected to the Indian subcontinent by a broad isthmus. This gave rise to a clade comprising five species—R. adisi sp. nov.,Rasbora armitagei, Rasbora microcephalus, Rasbora naggsi and Rasbora wilpita—with a crown age of 9.9 Ma (95% HPD: 7.1–13.3 Ma) and to a clade comprising Indian and Sri Lankan populations of Rasbora dandia, which themselves are reciprocally monophyletic. Morphological analysis of 334 specimens discriminates between most species which, however, are most reliably diagnosed by chromatic characters. The four endemic species exhibit a pattern of inter-basin dispersal via headwater capture, followed by vicariance, explaining the high diversity of the genus on the island. 相似文献