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Marcel A. Behr - One of the best experts on this subject based on the ideXlab platform.
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mycobacterium avium subsp paratuberculosis and m avium subsp avium are independently evolved pathogenic clones of a much broader group of m avium organisms
Journal of Bacteriology, 2008Co-Authors: Christine Y. Turenne, David C. Alexander, Desmond M Collins, Marcel A. BehrAbstract:Mycobacterium avium comprises organisms that share the same species designation despite considerable genomic and phenotypic variability. To determine the degree and nature of variability between subspecies and strains of M. avium, we used multilocus sequencing analysis, studying 56 genetically diverse strains of M. avium that included all described subspecies. In total, 8,064 bp of sequence from 10 gene loci were studied, with 205 (2.5%) representing variable positions. The majority (149/205) of these variations were found among M. avium subsp. hominissuis organisms. Recombination was also evident in this subspecies. In contrast, there was comparatively little variability and no evidence of recombination within the pathogenic subspecies, M. avium subsp. paratuberculosis, M. avium subsp. avium, and M. avium subsp. silvaticum. Phylogenetic analysis showed that M. avium subsp. avium and M. avium subsp. silvaticum strains clustered together on one branch, while a distinct branch defined M. avium subsp. paratuberculosis organisms. Despite the independent origin of these pathogenic subspecies, an analysis of their rates of nonsynonymous (dN) to synonymous (dS) substitutions showed increased dN/dS ratios for both: 0.67 for M. avium subsp. paratuberculosis and 0.50 for M. avium subsp. avium/M. avium subsp. silvaticum, while the value was 0.08 for M. avium subsp. hominissuis organisms. In conclusion, M. avium subsp. hominissuis represents a diverse group of organisms from which two pathogenic clones (M. avium subsp. paratuberculosis and M. avium subsp. avium/M. avium subsp. silvaticum) have evolved independently.
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sequencing of hsp65 distinguishes among subsets of the mycobacterium avium complex
Journal of Clinical Microbiology, 2006Co-Authors: Christine Y. Turenne, Makeda Semret, Debby Cousins, Desmond M Collins, Marcel A. BehrAbstract:The Mycobacterium avium complex consists of epidemiologically distinct subsets. The classification of these subsets is complicated by a number of factors, including the ambiguous results obtained with phenotypic and genetic assays and the recent appreciation that human and avian strains appear to be distinct. In previous work, sequencing based on a 441-bp portion of the hsp65 gene has proven to efficiently classify isolates within the Mycobacterium genus but provides low resolution for distinguishing among members of the M. avium complex. Therefore, in this study, we have targeted the more variable 3' region of the hsp65 gene to determine whether it can effectively discriminate M. avium complex isolates at the levels of species and subspecies. Primers designed for this target consistently generated amplicons for all organisms classified as M. avium complex. Sequences obtained indicate that M. intracellulare is genetically divergent from M. avium organisms, and distinct sequevars were obtained for M. avium subsets, including M. avium subsp. avium (bird type), M. avium subsp. hominissuis, and M. avium subsp. paratuberculosis. In addition, sequence differences served to distinguish bovine from ovine strains of M. avium subsp. paratuberculosis. A unique profile for M. avium subsp. silvaticum was not obtained. These results indicate that sequencing the 3' region of the hsp65 gene can simply and unambiguously distinguish species and subspecies of the M. avium complex.
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Genomic Polymorphisms for Mycobacterium avium subsp. paratuberculosis Diagnostics
Journal of clinical microbiology, 2005Co-Authors: Makeda Semret, David C. Alexander, Christine Y. Turenne, Petra De Haas, Pieter Overduin, Dick Van Soolingen, Debby Cousins, Marcel A. BehrAbstract:Mycobacterium avium subsp. paratuberculosis is a serious pathogen of domestic ruminants, in which it causes paratuberculosis (Johne's disease), a chronic and eventually fatal inflammatory bowel disease. Its rising incidence in many regions of the world has resulted in significant economic losses to the livestock industry (13). This organism also infects free-ranging wildlife species (16). The impact of M. avium subsp. paratuberculosis in nonruminant wildlife species is largely unknown; however, the potential for interspecies transmission has important implications for paratuberculosis control programs. M. avium subsp. paratuberculosis is also being actively investigated as the possible cause of a debilitating human inflammatory bowel disease, Crohn's disease (4, 5, 18). Effective control of Johne's disease and investigation of the potential link to Crohn's disease have been hampered by the lack of effective assays to easily and accurately diagnose M. avium subsp. paratuberculosis infections. Commercially available serological assays for bovine disease are convenient but offer poor sensitivity, especially during subclinical disease. Moreover, owing to the high degree of genetic similarity between M. avium subsp. paratuberculosis and the other members of the M. avium complex, many of the proteins that are recognized during the early stages of infection are not specific for M. avium subsp. paratuberculosis (14). Since M. avium subsp. avium is highly prevalent in the environment but not associated with a similar clinical syndrome in mammals, the capacity to differentiate between these closely related organisms is essential for rational clinical and epidemiologic assessment. Previous work has identified a number of M. avium subsp. paratuberculosis genetic sequences that are absent from other mycobacteria, such as the insertion sequence IS900 (11), the F57 element (21), and the hspX gene (9), but the value of these sequences for diagnostics of M. avium subsp. paratuberculosis remains unclear. Although PCR testing for the multicopy insertion element IS900 is widely used, there are concerns about its specificity and its validity as a direct proxy for M. avium subsp. paratuberculosis. IS900-like elements have been found in unrelated organisms (10), and other M. avium complex insertion elements, including IS1311 (7) and IS1626 (22), share considerable sequence similarity. In the cases of F57 and hspX, their specificity for M. avium subsp. paratuberculosis has not to date been rigorously evaluated in a large sample of clinical isolates. More recently, data derived from genome sequencing projects have suggested a number of polymorphic genomic regions that may serve in the specific diagnosis of M. avium subsp. paratuberculosis. Our microarray-based comparisons using M. avium subsp. avium strain 104 as the reference revealed 14 large sequence polymorphisms (LSPs) that are variably present among a small collection of M. avium isolates. Three of these regions appeared to be present in M. avium subsp. avium (LSPAs) and absent from M. avium subsp. paratuberculosis isolates (23). Conversely, computational comparisons of the genome sequences of M. avium subsp. paratuberculosis strain K10 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002944","term_id":"41406098","term_text":"NC_002944"}}NC_002944) and M. avium subsp. avium strain 104 (http://www.tigr.org) have identified DNA sequences that are present in the former but missing or divergent in the latter (2, 3, 19). We have to date identified 17 regions varying in length from 2.9 to 66 kb that are unique to M. avium subsp. paratuberculosis strain K10; we call these LSPPs. Such sequences can be expected to lend themselves to nucleic acid-based diagnostic tests and, if they encode immunogenic proteins, to immunological assays as well. One of these, a 19-kb sequence that we call LSPP12, has been previously documented (8, 23). Another, a 98-kb segment of the genome that encompasses elements we call LSPP14 and LSPP15, also includes within it a 38-kb element that was recently described as an M. avium subsp. paratuberculosis-specific putative pathogenicity island (24). The objective of our study was to assess the value of these LSPs for the specific diagnosis of M. avium subsp. paratuberculosis. To be diagnostically specific for M. avium subsp. paratuberculosis, an LSPP must be found only in M. avium subsp. paratuberculosis isolates and should be absent from non-M. avium subsp. paratuberculosis isolates. Conversely, for an LSPA to serve in the molecular diagnosis of M. avium subsp. paratuberculosis, it should be consistently present in non-M. avium subsp. paratuberculosis isolates but missing from a broad collection of M. avium subsp. paratuberculosis isolates. We therefore tested the distribution of the 17 LSPPs and 3 LSPAs across a panel of 383 M. avium complex isolates. Our results indicate that many LSP regions, although distinct between prototype genome sequences, are heterogeneously distributed across geographically diverse isolates and so lack the specificity required for diagnostics. However, a subset of LSPs do appear highly specific for M. avium subsp. paratuberculosis and should prove useful in the development of effective diagnostics for Johne's disease and evaluation of the Crohn's disease hypothesis.
Saeed G Kadasah - One of the best experts on this subject based on the ideXlab platform.
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An Updated Phytopharmacological Review on Medicinal Plant of Arab Region: Apium graveolens Linn.
Pharmacognosy reviews, 2017Co-Authors: Abdulrahman K. Al-asmari, Tanwir Athar, Saeed G KadasahAbstract:Apium graveolens Linn. (Karafs) is used in traditional medicine for the treatment of the various ailments. There is a need to explore and authenticate the pharmacological profile and medicinal importance of the Karafs. In this paper, the literature and the published work on Apium were collected using online resources "Google scholar", "Web of science", "Scopus" and "PubMed". Each of the pharmacological activity was searched individually using the keywords "Apium/Karafs/Apium graveolens + individual pharmacological activity". We documented the most cited and most recent literatures. The current findings illuminate the importance Karafs in the traditional medicine and their impact in treating various diseases. This review strongly supports the fact that the Apium has emerged as a good source of medicine in treating various diseases. There is also a need to isolate the bioactive phytochemicals present in this plant.
Manfred Rösch - One of the best experts on this subject based on the ideXlab platform.
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New aspects of agriculture and diet of the early medieval period in central Europe: waterlogged plant material from sites in south-western Germany
Vegetation History and Archaeobotany, 2008Co-Authors: Manfred RöschAbstract:Archaeobotanical investigations of three waterlogged sites of the migration and the early Merovingian periods throw new light on agriculture and human diet of the Germanic tribe of the Alamanni in southwestern Germany from the 3rd to the 6th century a.d . Agriculture was based on the growing of a large variety of cereals: Hordeum , Triticum dicoccon , T. spelta , Secale cereale , T. monococcum , T. aestivum , Avena sativa and Panicum miliaceum . Hordeum was most frequent. It occurs as naked and as hulled barley. In a grave with wet preserved plant macrofossils dated to the 6th century in Trossingen, Hordeum distichon was also present. In addition, the Alamanni cultivated the oil and fibre plants Linum usitatissimum , Papaver somniferum , Cannabis sativa , Camelina and Brassica rapa , as well as the pulses Lens culinaris and Pisum sativum . More surprising were finds of vegetables and spices. Among them, Juniperus communis and Humulus lupulus could have been gathered in the wild, but Coriandrum sativum , Apium graveolens and Satureja montana must have been cultivated in gardens. In addition to wild gathered material Pyrus , Malus , Prunus avium and Ficus carica also occurred, which were most probably grown in orchards or were even imported. Therefore the Alamanni were not only farmers growing cereals and other field crops, but they also had gardens and orchards were they grew vegetables, spices and fruits. Most probably they learned horticulture from the Romans when they settled near the border of the Roman Empire. This investigation shows in an impressive way how much more information can be gathered when waterlogged plant material is available, especially concerning fruits and spices.
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Human diet and land use in the time of the Khans—Archaeobotanical research in the capital of the Mongolian Empire, Qara Qorum, Mongolia
Vegetation History and Archaeobotany, 2005Co-Authors: Manfred Rösch, Elske Fischer, Tanja MärkleAbstract:Archaeobotanical investigations at Qara Qorum (Karakorum), Mongolia, reveal information about diet and land use from the 13th to the 15th century A.D. People grew Panicum miliaceum , Hordeum vulgare , Triticum aestivum and Setaria italica in nearby irrigated fields but additionally imported all other known cereals, including Oryza sativa , in small amounts as well as oil and fibre plants and pulses. The most common oil and fibre plant was Cannabis sativa . At least ten species of vegetables and spices such as Carum carvi , Coriandrum sativum , Apium graveolens , Beta vulgaris , Lycium chinense and Piper nigrum were either gathered from the wild, grown locally or imported. Apart from some wild gathered species like Pinus sibirica and Fragaria vesca , most of the fruits and nuts as for instance Vitis vinifera , Ficus carica , Ziziphus jujuba , Prunus dulcis , P . insititia , P . avium and P . persica , Cucumis melo and Juglans regia must also have been imported from quite long distances. First pollen results from lake Ugii Nuur, 50 km north of Qara Qorum indicate a much earlier beginning of agriculture than in the high and late Medieval.
Adrian J. Gibbs - One of the best experts on this subject based on the ideXlab platform.
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potyviruses novel and known in cultivated and wild species of the family apiaceae in australia
Archives of Virology, 2002Co-Authors: J Moran, A. M. Mackenzie, B Van Rijswijk, V Traicevski, Elliot W Kitajima, Adrian J. GibbsAbstract:Three potyviruses were identified by gene sequencing and found to be widespread in species of Apiaceae in Australia. Only celery mosaic virus was found in celery crops and in one of 180 specimens of feral carrot (Daucus carota). Another related but distinct novel potyvirus, carrot virus Y, was the only virus found in carrot crops and all except one feral carrot. A more distantly related novel potyvirus, Apium virus Y, was found in plants of sea celery (Apium prostratum), cultivated parsley (Petroselinum crispum) and the immigrant weed species poison hemlock (Conium maculatum). These three potyviruses, together with celery yellow mosaic virus of South America and the closely related carrot thin leaf virus and carrot virus B of North America, form a distinct subgenus of the Potyviridae most closely related to turnip mosaic virus and two potyviruses of yam; yam mosaic virus from the Ivory Coast and Japanese yam mosaic virus. Celery mosaic and carrot virus Y are probably recent migrants to Australia, but Apium virus Y may have been endemic longer. In ELISA tests using polyclonal antibodies against virions of celery mosaic virus, some isolates of carrot virus Y were indistinguishable from celery mosaic virus, whereas others gave smaller absorbancy values, and those of Apium virus Y did not react. This study shows the value of virus identification based on gene sequencing for planning control measures.
Christine Y. Turenne - One of the best experts on this subject based on the ideXlab platform.
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mycobacterium avium subsp paratuberculosis and m avium subsp avium are independently evolved pathogenic clones of a much broader group of m avium organisms
Journal of Bacteriology, 2008Co-Authors: Christine Y. Turenne, David C. Alexander, Desmond M Collins, Marcel A. BehrAbstract:Mycobacterium avium comprises organisms that share the same species designation despite considerable genomic and phenotypic variability. To determine the degree and nature of variability between subspecies and strains of M. avium, we used multilocus sequencing analysis, studying 56 genetically diverse strains of M. avium that included all described subspecies. In total, 8,064 bp of sequence from 10 gene loci were studied, with 205 (2.5%) representing variable positions. The majority (149/205) of these variations were found among M. avium subsp. hominissuis organisms. Recombination was also evident in this subspecies. In contrast, there was comparatively little variability and no evidence of recombination within the pathogenic subspecies, M. avium subsp. paratuberculosis, M. avium subsp. avium, and M. avium subsp. silvaticum. Phylogenetic analysis showed that M. avium subsp. avium and M. avium subsp. silvaticum strains clustered together on one branch, while a distinct branch defined M. avium subsp. paratuberculosis organisms. Despite the independent origin of these pathogenic subspecies, an analysis of their rates of nonsynonymous (dN) to synonymous (dS) substitutions showed increased dN/dS ratios for both: 0.67 for M. avium subsp. paratuberculosis and 0.50 for M. avium subsp. avium/M. avium subsp. silvaticum, while the value was 0.08 for M. avium subsp. hominissuis organisms. In conclusion, M. avium subsp. hominissuis represents a diverse group of organisms from which two pathogenic clones (M. avium subsp. paratuberculosis and M. avium subsp. avium/M. avium subsp. silvaticum) have evolved independently.
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sequencing of hsp65 distinguishes among subsets of the mycobacterium avium complex
Journal of Clinical Microbiology, 2006Co-Authors: Christine Y. Turenne, Makeda Semret, Debby Cousins, Desmond M Collins, Marcel A. BehrAbstract:The Mycobacterium avium complex consists of epidemiologically distinct subsets. The classification of these subsets is complicated by a number of factors, including the ambiguous results obtained with phenotypic and genetic assays and the recent appreciation that human and avian strains appear to be distinct. In previous work, sequencing based on a 441-bp portion of the hsp65 gene has proven to efficiently classify isolates within the Mycobacterium genus but provides low resolution for distinguishing among members of the M. avium complex. Therefore, in this study, we have targeted the more variable 3' region of the hsp65 gene to determine whether it can effectively discriminate M. avium complex isolates at the levels of species and subspecies. Primers designed for this target consistently generated amplicons for all organisms classified as M. avium complex. Sequences obtained indicate that M. intracellulare is genetically divergent from M. avium organisms, and distinct sequevars were obtained for M. avium subsets, including M. avium subsp. avium (bird type), M. avium subsp. hominissuis, and M. avium subsp. paratuberculosis. In addition, sequence differences served to distinguish bovine from ovine strains of M. avium subsp. paratuberculosis. A unique profile for M. avium subsp. silvaticum was not obtained. These results indicate that sequencing the 3' region of the hsp65 gene can simply and unambiguously distinguish species and subspecies of the M. avium complex.
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Genomic Polymorphisms for Mycobacterium avium subsp. paratuberculosis Diagnostics
Journal of clinical microbiology, 2005Co-Authors: Makeda Semret, David C. Alexander, Christine Y. Turenne, Petra De Haas, Pieter Overduin, Dick Van Soolingen, Debby Cousins, Marcel A. BehrAbstract:Mycobacterium avium subsp. paratuberculosis is a serious pathogen of domestic ruminants, in which it causes paratuberculosis (Johne's disease), a chronic and eventually fatal inflammatory bowel disease. Its rising incidence in many regions of the world has resulted in significant economic losses to the livestock industry (13). This organism also infects free-ranging wildlife species (16). The impact of M. avium subsp. paratuberculosis in nonruminant wildlife species is largely unknown; however, the potential for interspecies transmission has important implications for paratuberculosis control programs. M. avium subsp. paratuberculosis is also being actively investigated as the possible cause of a debilitating human inflammatory bowel disease, Crohn's disease (4, 5, 18). Effective control of Johne's disease and investigation of the potential link to Crohn's disease have been hampered by the lack of effective assays to easily and accurately diagnose M. avium subsp. paratuberculosis infections. Commercially available serological assays for bovine disease are convenient but offer poor sensitivity, especially during subclinical disease. Moreover, owing to the high degree of genetic similarity between M. avium subsp. paratuberculosis and the other members of the M. avium complex, many of the proteins that are recognized during the early stages of infection are not specific for M. avium subsp. paratuberculosis (14). Since M. avium subsp. avium is highly prevalent in the environment but not associated with a similar clinical syndrome in mammals, the capacity to differentiate between these closely related organisms is essential for rational clinical and epidemiologic assessment. Previous work has identified a number of M. avium subsp. paratuberculosis genetic sequences that are absent from other mycobacteria, such as the insertion sequence IS900 (11), the F57 element (21), and the hspX gene (9), but the value of these sequences for diagnostics of M. avium subsp. paratuberculosis remains unclear. Although PCR testing for the multicopy insertion element IS900 is widely used, there are concerns about its specificity and its validity as a direct proxy for M. avium subsp. paratuberculosis. IS900-like elements have been found in unrelated organisms (10), and other M. avium complex insertion elements, including IS1311 (7) and IS1626 (22), share considerable sequence similarity. In the cases of F57 and hspX, their specificity for M. avium subsp. paratuberculosis has not to date been rigorously evaluated in a large sample of clinical isolates. More recently, data derived from genome sequencing projects have suggested a number of polymorphic genomic regions that may serve in the specific diagnosis of M. avium subsp. paratuberculosis. Our microarray-based comparisons using M. avium subsp. avium strain 104 as the reference revealed 14 large sequence polymorphisms (LSPs) that are variably present among a small collection of M. avium isolates. Three of these regions appeared to be present in M. avium subsp. avium (LSPAs) and absent from M. avium subsp. paratuberculosis isolates (23). Conversely, computational comparisons of the genome sequences of M. avium subsp. paratuberculosis strain K10 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002944","term_id":"41406098","term_text":"NC_002944"}}NC_002944) and M. avium subsp. avium strain 104 (http://www.tigr.org) have identified DNA sequences that are present in the former but missing or divergent in the latter (2, 3, 19). We have to date identified 17 regions varying in length from 2.9 to 66 kb that are unique to M. avium subsp. paratuberculosis strain K10; we call these LSPPs. Such sequences can be expected to lend themselves to nucleic acid-based diagnostic tests and, if they encode immunogenic proteins, to immunological assays as well. One of these, a 19-kb sequence that we call LSPP12, has been previously documented (8, 23). Another, a 98-kb segment of the genome that encompasses elements we call LSPP14 and LSPP15, also includes within it a 38-kb element that was recently described as an M. avium subsp. paratuberculosis-specific putative pathogenicity island (24). The objective of our study was to assess the value of these LSPs for the specific diagnosis of M. avium subsp. paratuberculosis. To be diagnostically specific for M. avium subsp. paratuberculosis, an LSPP must be found only in M. avium subsp. paratuberculosis isolates and should be absent from non-M. avium subsp. paratuberculosis isolates. Conversely, for an LSPA to serve in the molecular diagnosis of M. avium subsp. paratuberculosis, it should be consistently present in non-M. avium subsp. paratuberculosis isolates but missing from a broad collection of M. avium subsp. paratuberculosis isolates. We therefore tested the distribution of the 17 LSPPs and 3 LSPAs across a panel of 383 M. avium complex isolates. Our results indicate that many LSP regions, although distinct between prototype genome sequences, are heterogeneously distributed across geographically diverse isolates and so lack the specificity required for diagnostics. However, a subset of LSPs do appear highly specific for M. avium subsp. paratuberculosis and should prove useful in the development of effective diagnostics for Johne's disease and evaluation of the Crohn's disease hypothesis.