Graham Tebb - Academia.edu (original) (raw)
Papers by Graham Tebb
The EMBO Journal, Dec 1, 1988
The requirements for the formation of a stable transcription complex on the RNA polymerase 11-tra... more The requirements for the formation of a stable transcription complex on the RNA polymerase 11-transcribed Xenopus U2 snRNA gene have been analysed in vivo by oocyte microinjection experiments. The two elements of the U2 promoter which are located in the 5' flanking region of the gene, the DSE and the PSE, are shown to be essential but not sufficient for stable complex formation. Two additional elements are required. The first is a short gene-internal sequence; the second is the nucleotide at the normal point of initiation, which must be a purine. If this nucleotide is changed to a pyrimidine the site of initiation is altered and, concomitantly, the transcription complex formed on the mutant template remains unstable. These results suggest that there is a distinct topological requirement for complex formation which may involve an exact stereospecific alignment of RNA polymerase II with transcription factors bound to the promoter. Despite the apparent involvement of RNA polymerase, transcription per se is not required for complex stability.
Bulletin of the African Bird Club, 2015
Molecular and Cellular Biology, Apr 1, 1989
The sequences involved in enhancement of transcription of the Xenopus U2 small nuclear RNA gene b... more The sequences involved in enhancement of transcription of the Xenopus U2 small nuclear RNA gene by the distal sequence element (DSE) of its promoter were analyzed in detail by microinjection of mutant genes into Xenopus oocytes. The DSE was shown to be roughly 60 base pairs long. Within this region, four motifs were found to contribute to DSE function: an ATGCAAAT octamer sequence, an SpI binding site, and two additional motifs which, since they are related in sequence, may bind the same transcription factor. These motifs were named D2 (for DSE; U2). Both the octamer sequence and the SpI site bound nuclear factors in vitro, but no factor binding to the D2 motifs was detected. All four elements were independently capable of enhancing transcription of the U2 gene to some extent. Furthermore, when assayed under both competitive and noncompetitive conditions, the individual units of the DSE displayed functional redundancy.
The EMBO Journal, 1987
Xenopus laevis U5 snRNA genes are found in several genomic arrangements, represented by a predomi... more Xenopus laevis U5 snRNA genes are found in several genomic arrangements, represented by a predominant tandem repeat of 583 bp and other minor repeats. Several copies of the major tandem repeat have been cloned and expressed in Xenopus oocytes. The transcripts assemble into U5 snRNPs which are recognized by anti-Sm antibodies. We have identified functional elements in the U5 gene promoter. Although similar in organization to other U snRNA gene promoters, U5 contains significant differences and is more efficiently expressed than the Xenopus U2 gene in oocytes. The proximal sequence element (PSE), although homologous to a mammalian consensus for this region (Skuzeski et al., 1984), does not resemble the previously characterized Xenopus Ul and U2 PSEs closely in sequence. The ATGCAAAT (octamer) part of the distal sequence element (DSE 1) is found in U5 in the orientation opposite to that in Ul and U2 gene promoters. DNase I protection experiments led to the identification of a third element (DSE 2), situated close to the octamer motif. Analysis of deletion mutants showed that both DSE 1 and 2 are essential parts of the U5 gene enhancer, and provides evidence that U snRNA enhancers are complex structures consisting of more than one site of DNA-factor interaction.
Bulletin of the African Bird Club, Mar 1, 2000
Following an introduction describing the history of ornithological activity in La Gamba, the pres... more Following an introduction describing the history of ornithological activity in La Gamba, the present article gives an annotatedlistofallspeciesand,wherepossible,subspeciesofbirdreliablyrecordedinLaGamba,SWCostaRicauntiltheend of June 2008. The list essentially covers the gardens of the Tropical Research Station La Gamba and the Esquinas Rainforest Lodge;theprimaryandsecondaryforestsadjacenttotheTropicalResearchStationLaGambaandtheEsquinasRainforestLodge; thebanksoftheRioBonitoandtheRioLaGamba;theagriculturallycultivatedareasaroundthevillageofLaGambaandalong theroadbetweenthePanamericanHighwayandtheEsquinasRainforestLodge;andthecoast(bythePlayaJosecitobeachand by Golfito) with the mangroves of Golfito and the Rio Coto. The importance of the area is highlighted with reference to the
Nucleic Acids Research, 1987
Cancers
We review the history of the tyrosine kinase 2 (TYK2) as the founding member of the Janus kinase ... more We review the history of the tyrosine kinase 2 (TYK2) as the founding member of the Janus kinase (JAK) family and outline its structure-function relation. Gene-targeted mice and hereditary defects of TYK2 in men have established the biological and pathological functions of TYK2 in innate and adaptive immune responses to infection and cancer and in (auto-)inflammation. We describe the architecture of the main cytokine receptor families associated with TYK2, which activate signal transducers and activators of transcription (STATs). We summarize the cytokine receptor activities with well characterized dependency on TYK2, the types of cells that respond to cytokines and TYK2 signaling-induced cytokine production. TYK2 may drive beneficial or detrimental activities, which we explain based on the concepts of tumor immunoediting and the cancer-immunity cycle in the tumor microenvironment. Finally, we summarize current knowledge of TYK2 functions in mouse models of tumor surveillance. The b...
Kuppusamy Sivakumar, Salim Ali Centre for Ornithology and Natural History, Coimbatore 641108, Ind... more Kuppusamy Sivakumar, Salim Ali Centre for Ornithology and Natural History, Coimbatore 641108, India. Present address: Wildlife Institute of India, Post Box 18, Dehra Dun 248001, India. Email: ksivakumar@wii.gov.in BLACK-NAPED ORIOLE Oriolus chinensis Two cup-shaped nests were located during January and March 1997 in the subcanopy of Alstonia kurzii and Syzygium samarangense trees at a height of 40 m and 42 m. The first pair built three incomplete nests and one complete nest during a 13 day period until the first egg was laid. Clutch size was two eggs (N=2), and mean egg size was 20.4 x 28.7 mm (N=2). On 11 February 1997 an Asian Glossy Starling Aplonis panayensis (of which many nested in tree-holes in the same tree) was observed apparently sitting on the oriole nest for a few seconds. Once the adult oriole returned, it immediately left, and no further interactions were noted.
In Tebb and Ranner (2002), we detailed significant bird records from a visit to Buryatia in June ... more In Tebb and Ranner (2002), we detailed significant bird records from a visit to Buryatia in June 2001. Among these was a Slender-billed Gull Larus genei, which we claimed represented the first record from the republic and the easternmost documented occurrence of the species in mainland Russia. We have subsequently been made aware of a previous record of Slender-billed Gull from Buryatia: on 15 June 1989 an adult male was observed in the middle of a colony of Black-headed Gulls L. ridibundus in the ‘lower portion of the Selenga Delta’ (Tupitsyn and Fefelov 1995). The bird was collected and the specimen is preserved at the University of Irkutsk. Our sighting on the upper Beloye Ozera on 20 June 2001 thus represents the second record from the republic. Nevertheless, to our knowledge it remains the easternmost record from mainland Russia. ACKNOWLEDGEMENT
Ibis, 2013
The selection of a suitable nest-site is critical for successful reproduction. Species' preferenc... more The selection of a suitable nest-site is critical for successful reproduction. Species' preferences for nest-sites have presumably evolved in relation to local habitat resources and/or interactions with other species. The importance of these two components in the nest-site selection of the Eurasian Honey Buzzard Pernis apivorus was assessed in two study areas in eastern Austria. There was almost no difference in macro-and micro-habitat features between nest-sites and random plots, suggesting that Honey Buzzards did not base their choice of nest-site on habitat characteristics. However, nests were placed significantly further from nests of Northern Goshawk Accipiter gentilis than would be expected if nest-sites had been chosen at random. Furthermore, in one study area Honey Buzzards appeared to favour areas close to human settlements, perhaps indicating a mechanism to avoid Goshawks, which tend to avoid the proximity of humans. No habitat variable was significantly associated with the loss of Honey Buzzard young, but predation was higher in territories closer to breeding pairs of Goshawks at both study sites. Although Honey Buzzards are restricted to nesting in forests, their choice of nest-site therefore appears to be largely dictated by the distribution of predators. Studies of habitat association may yield misleading results if the effects of predation risk on distribution are not considered.
Nucleic Acids Research, 1987
Appl Microbiol Biotechnol, 1988
HO I~D j,~o ~ lium citrinum in the presence of varying concen-1, trations of glucose has been exa... more HO I~D j,~o ~ lium citrinum in the presence of varying concen-1, trations of glucose has been examined. Turnover "~ ~CH0 of citrinin was found to be fast even in the pres-H0 ence of high concentrations of glucose. On the basis of these experiments, a role for citrinin in primary metabolism is postulated.
Nucleic Acids Research, 1987
An analysis, performed by DNase I footprinting, of the interactions between factors present in Mo... more An analysis, performed by DNase I footprinting, of the interactions between factors present in Molt-4 nuclear extracts and a Xenopus U2 snRNA gene promoter is presented. Four distinct regions of sequence-specific DNA-factor interaction are found. Two of these correspond to the previously identified proximal and distal sequence elements (PSE and DSE) of the promoter. Both of these elements are important in U2 transcription, indicating a functional role for the observed interactions. The other two sites of interaction correspond to a sequence element conserved in many, but not all, vertebrate U snRNA gene promoters (the MSE) and to a region adjacent to the site of transcription initiation (the "cap site"). Site-directed mutants of these latter two elements are constructed which no longer bind nuclear factors. Transcriptional analysis in Xenopus oocytes reveals that these mutants are transcribed as efficiently as wild-type U2. Other possible roles for the two factors are discussed.
Cell, 1987
The structure of a Xenopus U6 gene promoter has been investigated. Three regions in the 5′-flanki... more The structure of a Xenopus U6 gene promoter has been investigated. Three regions in the 5′-flanking sequences of the gene that are important for U6 expression are defined. Deletion of the first, between positions −156 and −280 relative to the site of transcription initiation, ...
The EMBO Journal, Dec 1, 1988
The requirements for the formation of a stable transcription complex on the RNA polymerase 11-tra... more The requirements for the formation of a stable transcription complex on the RNA polymerase 11-transcribed Xenopus U2 snRNA gene have been analysed in vivo by oocyte microinjection experiments. The two elements of the U2 promoter which are located in the 5' flanking region of the gene, the DSE and the PSE, are shown to be essential but not sufficient for stable complex formation. Two additional elements are required. The first is a short gene-internal sequence; the second is the nucleotide at the normal point of initiation, which must be a purine. If this nucleotide is changed to a pyrimidine the site of initiation is altered and, concomitantly, the transcription complex formed on the mutant template remains unstable. These results suggest that there is a distinct topological requirement for complex formation which may involve an exact stereospecific alignment of RNA polymerase II with transcription factors bound to the promoter. Despite the apparent involvement of RNA polymerase, transcription per se is not required for complex stability.
Bulletin of the African Bird Club, 2015
Molecular and Cellular Biology, Apr 1, 1989
The sequences involved in enhancement of transcription of the Xenopus U2 small nuclear RNA gene b... more The sequences involved in enhancement of transcription of the Xenopus U2 small nuclear RNA gene by the distal sequence element (DSE) of its promoter were analyzed in detail by microinjection of mutant genes into Xenopus oocytes. The DSE was shown to be roughly 60 base pairs long. Within this region, four motifs were found to contribute to DSE function: an ATGCAAAT octamer sequence, an SpI binding site, and two additional motifs which, since they are related in sequence, may bind the same transcription factor. These motifs were named D2 (for DSE; U2). Both the octamer sequence and the SpI site bound nuclear factors in vitro, but no factor binding to the D2 motifs was detected. All four elements were independently capable of enhancing transcription of the U2 gene to some extent. Furthermore, when assayed under both competitive and noncompetitive conditions, the individual units of the DSE displayed functional redundancy.
The EMBO Journal, 1987
Xenopus laevis U5 snRNA genes are found in several genomic arrangements, represented by a predomi... more Xenopus laevis U5 snRNA genes are found in several genomic arrangements, represented by a predominant tandem repeat of 583 bp and other minor repeats. Several copies of the major tandem repeat have been cloned and expressed in Xenopus oocytes. The transcripts assemble into U5 snRNPs which are recognized by anti-Sm antibodies. We have identified functional elements in the U5 gene promoter. Although similar in organization to other U snRNA gene promoters, U5 contains significant differences and is more efficiently expressed than the Xenopus U2 gene in oocytes. The proximal sequence element (PSE), although homologous to a mammalian consensus for this region (Skuzeski et al., 1984), does not resemble the previously characterized Xenopus Ul and U2 PSEs closely in sequence. The ATGCAAAT (octamer) part of the distal sequence element (DSE 1) is found in U5 in the orientation opposite to that in Ul and U2 gene promoters. DNase I protection experiments led to the identification of a third element (DSE 2), situated close to the octamer motif. Analysis of deletion mutants showed that both DSE 1 and 2 are essential parts of the U5 gene enhancer, and provides evidence that U snRNA enhancers are complex structures consisting of more than one site of DNA-factor interaction.
Bulletin of the African Bird Club, Mar 1, 2000
Following an introduction describing the history of ornithological activity in La Gamba, the pres... more Following an introduction describing the history of ornithological activity in La Gamba, the present article gives an annotatedlistofallspeciesand,wherepossible,subspeciesofbirdreliablyrecordedinLaGamba,SWCostaRicauntiltheend of June 2008. The list essentially covers the gardens of the Tropical Research Station La Gamba and the Esquinas Rainforest Lodge;theprimaryandsecondaryforestsadjacenttotheTropicalResearchStationLaGambaandtheEsquinasRainforestLodge; thebanksoftheRioBonitoandtheRioLaGamba;theagriculturallycultivatedareasaroundthevillageofLaGambaandalong theroadbetweenthePanamericanHighwayandtheEsquinasRainforestLodge;andthecoast(bythePlayaJosecitobeachand by Golfito) with the mangroves of Golfito and the Rio Coto. The importance of the area is highlighted with reference to the
Nucleic Acids Research, 1987
Cancers
We review the history of the tyrosine kinase 2 (TYK2) as the founding member of the Janus kinase ... more We review the history of the tyrosine kinase 2 (TYK2) as the founding member of the Janus kinase (JAK) family and outline its structure-function relation. Gene-targeted mice and hereditary defects of TYK2 in men have established the biological and pathological functions of TYK2 in innate and adaptive immune responses to infection and cancer and in (auto-)inflammation. We describe the architecture of the main cytokine receptor families associated with TYK2, which activate signal transducers and activators of transcription (STATs). We summarize the cytokine receptor activities with well characterized dependency on TYK2, the types of cells that respond to cytokines and TYK2 signaling-induced cytokine production. TYK2 may drive beneficial or detrimental activities, which we explain based on the concepts of tumor immunoediting and the cancer-immunity cycle in the tumor microenvironment. Finally, we summarize current knowledge of TYK2 functions in mouse models of tumor surveillance. The b...
Kuppusamy Sivakumar, Salim Ali Centre for Ornithology and Natural History, Coimbatore 641108, Ind... more Kuppusamy Sivakumar, Salim Ali Centre for Ornithology and Natural History, Coimbatore 641108, India. Present address: Wildlife Institute of India, Post Box 18, Dehra Dun 248001, India. Email: ksivakumar@wii.gov.in BLACK-NAPED ORIOLE Oriolus chinensis Two cup-shaped nests were located during January and March 1997 in the subcanopy of Alstonia kurzii and Syzygium samarangense trees at a height of 40 m and 42 m. The first pair built three incomplete nests and one complete nest during a 13 day period until the first egg was laid. Clutch size was two eggs (N=2), and mean egg size was 20.4 x 28.7 mm (N=2). On 11 February 1997 an Asian Glossy Starling Aplonis panayensis (of which many nested in tree-holes in the same tree) was observed apparently sitting on the oriole nest for a few seconds. Once the adult oriole returned, it immediately left, and no further interactions were noted.
In Tebb and Ranner (2002), we detailed significant bird records from a visit to Buryatia in June ... more In Tebb and Ranner (2002), we detailed significant bird records from a visit to Buryatia in June 2001. Among these was a Slender-billed Gull Larus genei, which we claimed represented the first record from the republic and the easternmost documented occurrence of the species in mainland Russia. We have subsequently been made aware of a previous record of Slender-billed Gull from Buryatia: on 15 June 1989 an adult male was observed in the middle of a colony of Black-headed Gulls L. ridibundus in the ‘lower portion of the Selenga Delta’ (Tupitsyn and Fefelov 1995). The bird was collected and the specimen is preserved at the University of Irkutsk. Our sighting on the upper Beloye Ozera on 20 June 2001 thus represents the second record from the republic. Nevertheless, to our knowledge it remains the easternmost record from mainland Russia. ACKNOWLEDGEMENT
Ibis, 2013
The selection of a suitable nest-site is critical for successful reproduction. Species' preferenc... more The selection of a suitable nest-site is critical for successful reproduction. Species' preferences for nest-sites have presumably evolved in relation to local habitat resources and/or interactions with other species. The importance of these two components in the nest-site selection of the Eurasian Honey Buzzard Pernis apivorus was assessed in two study areas in eastern Austria. There was almost no difference in macro-and micro-habitat features between nest-sites and random plots, suggesting that Honey Buzzards did not base their choice of nest-site on habitat characteristics. However, nests were placed significantly further from nests of Northern Goshawk Accipiter gentilis than would be expected if nest-sites had been chosen at random. Furthermore, in one study area Honey Buzzards appeared to favour areas close to human settlements, perhaps indicating a mechanism to avoid Goshawks, which tend to avoid the proximity of humans. No habitat variable was significantly associated with the loss of Honey Buzzard young, but predation was higher in territories closer to breeding pairs of Goshawks at both study sites. Although Honey Buzzards are restricted to nesting in forests, their choice of nest-site therefore appears to be largely dictated by the distribution of predators. Studies of habitat association may yield misleading results if the effects of predation risk on distribution are not considered.
Nucleic Acids Research, 1987
Appl Microbiol Biotechnol, 1988
HO I~D j,~o ~ lium citrinum in the presence of varying concen-1, trations of glucose has been exa... more HO I~D j,~o ~ lium citrinum in the presence of varying concen-1, trations of glucose has been examined. Turnover "~ ~CH0 of citrinin was found to be fast even in the pres-H0 ence of high concentrations of glucose. On the basis of these experiments, a role for citrinin in primary metabolism is postulated.
Nucleic Acids Research, 1987
An analysis, performed by DNase I footprinting, of the interactions between factors present in Mo... more An analysis, performed by DNase I footprinting, of the interactions between factors present in Molt-4 nuclear extracts and a Xenopus U2 snRNA gene promoter is presented. Four distinct regions of sequence-specific DNA-factor interaction are found. Two of these correspond to the previously identified proximal and distal sequence elements (PSE and DSE) of the promoter. Both of these elements are important in U2 transcription, indicating a functional role for the observed interactions. The other two sites of interaction correspond to a sequence element conserved in many, but not all, vertebrate U snRNA gene promoters (the MSE) and to a region adjacent to the site of transcription initiation (the "cap site"). Site-directed mutants of these latter two elements are constructed which no longer bind nuclear factors. Transcriptional analysis in Xenopus oocytes reveals that these mutants are transcribed as efficiently as wild-type U2. Other possible roles for the two factors are discussed.
Cell, 1987
The structure of a Xenopus U6 gene promoter has been investigated. Three regions in the 5′-flanki... more The structure of a Xenopus U6 gene promoter has been investigated. Three regions in the 5′-flanking sequences of the gene that are important for U6 expression are defined. Deletion of the first, between positions −156 and −280 relative to the site of transcription initiation, ...