128 results on '"Strapagiel, D."'
Search Results
2. The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions
- Author
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Rahmioglu, N, Mortlock, S, Ghiasi, M, Moller, PL, Stefansdottir, L, Galarneau, G, Turman, C, Danning, R, Law, MH, Sapkota, Y, Christofidou, P, Skarp, S, Giri, A, Banasik, K, Krassowski, M, Lepamets, M, Marciniak, B, Noukas, M, Perro, D, Sliz, E, Sobalska-Kwapis, M, Thorleifsson, G, Topbas-Selcuki, NF, Vitonis, A, Westergaard, D, Arnadottir, R, Burgdorf, KS, Campbell, A, Cheuk, CSK, Clementi, C, Cook, J, De Vivo, I, DiVasta, A, Dorien, O, Donoghue, JF, Edwards, T, Fontanillas, P, Fung, JN, Geirsson, RT, Girling, JE, Harkki, P, Harris, HR, Healey, M, Heikinheimo, O, Holdsworth-Carson, S, Hostettler, IC, Houlden, H, Houshdaran, S, Irwin, JC, Jarvelin, M-R, Kamatani, Y, Kennedy, SH, Kepka, E, Kettunen, J, Kubo, M, Kulig, B, Kurra, V, Laivuori, H, Laufer, MR, Lindgren, CM, MacGregor, S, Mangino, M, Martin, NG, Matalliotaki, C, Matalliotakis, M, Murray, AD, Ndungu, A, Nezhat, C, Olsen, CM, Opoku-Anane, J, Padmanabhan, S, Paranjpe, M, Peters, M, Polak, G, Porteous, DJ, Rabban, J, Rexrode, KM, Romanowicz, H, Saare, M, Saavalainen, L, Schork, AJ, Sen, S, Shafrir, AL, Siewierska-Gorska, A, Slomka, M, Smith, BH, Smolarz, B, Szaflik, T, Szyllo, K, Takahashi, A, Terry, KL, Tomassetti, C, Treloar, SA, Vanhie, A, Vincent, K, Vo, KC, Werring, DJ, Zeggini, E, Zervou, M, Stefansson, K, Nyegaard, M, Uimari, O, Yurttas-Beim, P, Tung, JY, Adachi, S, Buring, JE, Ridker, PM, D'Hooghe, T, Goulielmos, GN, Hapangama, DK, Hayward, C, Horne, AW, Low, S-K, Martikainen, H, Chasman, D, Rogers, PAW, Saunders, PT, Sirota, M, Spector, T, Strapagiel, D, Whiteman, DC, Giudice, LC, Velez-Edwards, DR, Kraft, P, Salumets, A, Nyholt, DR, Magi, R, Becker, CM, Steinthorsdottir, V, Missmer, SA, Montgomery, GW, Morris, AP, Zondervan, KT, Rahmioglu, N, Mortlock, S, Ghiasi, M, Moller, PL, Stefansdottir, L, Galarneau, G, Turman, C, Danning, R, Law, MH, Sapkota, Y, Christofidou, P, Skarp, S, Giri, A, Banasik, K, Krassowski, M, Lepamets, M, Marciniak, B, Noukas, M, Perro, D, Sliz, E, Sobalska-Kwapis, M, Thorleifsson, G, Topbas-Selcuki, NF, Vitonis, A, Westergaard, D, Arnadottir, R, Burgdorf, KS, Campbell, A, Cheuk, CSK, Clementi, C, Cook, J, De Vivo, I, DiVasta, A, Dorien, O, Donoghue, JF, Edwards, T, Fontanillas, P, Fung, JN, Geirsson, RT, Girling, JE, Harkki, P, Harris, HR, Healey, M, Heikinheimo, O, Holdsworth-Carson, S, Hostettler, IC, Houlden, H, Houshdaran, S, Irwin, JC, Jarvelin, M-R, Kamatani, Y, Kennedy, SH, Kepka, E, Kettunen, J, Kubo, M, Kulig, B, Kurra, V, Laivuori, H, Laufer, MR, Lindgren, CM, MacGregor, S, Mangino, M, Martin, NG, Matalliotaki, C, Matalliotakis, M, Murray, AD, Ndungu, A, Nezhat, C, Olsen, CM, Opoku-Anane, J, Padmanabhan, S, Paranjpe, M, Peters, M, Polak, G, Porteous, DJ, Rabban, J, Rexrode, KM, Romanowicz, H, Saare, M, Saavalainen, L, Schork, AJ, Sen, S, Shafrir, AL, Siewierska-Gorska, A, Slomka, M, Smith, BH, Smolarz, B, Szaflik, T, Szyllo, K, Takahashi, A, Terry, KL, Tomassetti, C, Treloar, SA, Vanhie, A, Vincent, K, Vo, KC, Werring, DJ, Zeggini, E, Zervou, M, Stefansson, K, Nyegaard, M, Uimari, O, Yurttas-Beim, P, Tung, JY, Adachi, S, Buring, JE, Ridker, PM, D'Hooghe, T, Goulielmos, GN, Hapangama, DK, Hayward, C, Horne, AW, Low, S-K, Martikainen, H, Chasman, D, Rogers, PAW, Saunders, PT, Sirota, M, Spector, T, Strapagiel, D, Whiteman, DC, Giudice, LC, Velez-Edwards, DR, Kraft, P, Salumets, A, Nyholt, DR, Magi, R, Becker, CM, Steinthorsdottir, V, Missmer, SA, Montgomery, GW, Morris, AP, and Zondervan, KT
- Abstract
Endometriosis is a common condition associated with debilitating pelvic pain and infertility. A genome-wide association study meta-analysis, including 60,674 cases and 701,926 controls of European and East Asian descent, identified 42 genome-wide significant loci comprising 49 distinct association signals. Effect sizes were largest for stage 3/4 disease, driven by ovarian endometriosis. Identified signals explained up to 5.01% of disease variance and regulated expression or methylation of genes in endometrium and blood, many of which were associated with pain perception/maintenance (SRP14/BMF, GDAP1, MLLT10, BSN and NGF). We observed significant genetic correlations between endometriosis and 11 pain conditions, including migraine, back and multisite chronic pain (MCP), as well as inflammatory conditions, including asthma and osteoarthritis. Multitrait genetic analyses identified substantial sharing of variants associated with endometriosis and MCP/migraine. Targeted investigations of genetically regulated mechanisms shared between endometriosis and other pain conditions are needed to aid the development of new treatments and facilitate early symptomatic intervention.
- Published
- 2023
3. 2,4-Disubstituted pyridine derivatives are effective against intracellular and biofilm-forming tubercle bacilli
- Author
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Korycka-Machała, M., primary, Kawka, M., additional, Lach, J., additional, Płocińska, R., additional, Bekier, A., additional, Dziadek, B., additional, Brzostek, A., additional, Płociński, P., additional, Strapagiel, D., additional, Szczesio, M., additional, Gobis, K., additional, and Dziadek, J., additional
- Published
- 2022
- Full Text
- View/download PDF
4. A genomic Neolithic time transect of hunter-farmer admixture in central Poland
- Author
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Fernandes, D. M., Strapagiel, D., Borówka, P., Marciniak, B., Żądzińska, E., Sirak, K., Siska, V., Grygiel, R., Carlsson, J., Manica, A., Lorkiewicz, W., and Pinhasi, R.
- Published
- 2018
- Full Text
- View/download PDF
5. Fungal Planet description sheets : 1436 –1477
- Author
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Tan, Y.P., Bishop-Hurley, S.L., Shivas, R.G., Cowan, D.A., Maggs-Kölling, G., Maharachchikumbura, S.S.N., Pinruan, U., Bransgrove, K.L., De la Peña-Lastra, S., Larsson, E., Lebel, T., Mahadevakumar, S., Mateos, A., Osieck, E.R., Rigueiro-Rodríguez, A., Sommai, S., Ajithkumar, K., Akulov, A., Anderson, F.E., Arenas, F., Balashov, S., Bañares, Berger, D.K., Bianchinotti, M.V., Bien, S., Bilański, P., Boxshall, A.G., Bradshaw, M., Broadbridge, J., Calaça, F.J.S., Campos-Quiroz, C., Carrasco-Fernández, J., Castro, J.F., Chaimongkol, S., Chandranayaka, S., Chen, Y., Comben, D., Dearnaley, J.D.W., Ferreira-Sá, A.S., Dhileepan, K., Díaz, M.L., Divakar, P.K., Xavier-Santos, S., Fernández-Bravo, A., Gené, J., Guard, F.E., Guerra, M., Gunaseelan, S., Houbraken, J., Janik-Superson, K., Jankowiak, R., Jeppson, M., Jurjević, Kaliyaperumal, M., Kelly, L.A., Kezo, K., Khalid, A.N., Khamsuntorn, P., Kidanemariam, D., Kiran, M., Lacey, E., Langer, G.J., López-Llorca, L.V., Luangsa-Ard, J.J., Lueangjaroenkit, P., Lumbsch, H.T., Maciá-Vicente, J.G., Mamatha Bhanu, L.S., Marney, T.S., Marqués-Gálvez, J.E., Morte, A., Naseer, A., Navarro-Ródenas, A., Oyedele, O., Peters, S., Piskorski, S., Quijada, L., Ramírez, G.H., Raja, K., Razzaq, A., Rico, V.J., Rodríguez, A., Ruszkiewicz-Michalska, M., Sánchez, R.M., Santelices, C., Savitha, A.S., Serrano, M., Leonardo-Silva, L., Solheim, H., Somrithipol, S., Sreenivasa, M.Y., Stępniewska, H., Strapagiel, D., Taylor, T., Torres-Garcia, D., Vauras, J., Villarreal, M., Visagie, C.M., Wołkowycki, M., Yingkunchao, W., Zapora, E., Groenewald, J.Z., Crous, P.W., Tan, Y.P., Bishop-Hurley, S.L., Shivas, R.G., Cowan, D.A., Maggs-Kölling, G., Maharachchikumbura, S.S.N., Pinruan, U., Bransgrove, K.L., De la Peña-Lastra, S., Larsson, E., Lebel, T., Mahadevakumar, S., Mateos, A., Osieck, E.R., Rigueiro-Rodríguez, A., Sommai, S., Ajithkumar, K., Akulov, A., Anderson, F.E., Arenas, F., Balashov, S., Bañares, Berger, D.K., Bianchinotti, M.V., Bien, S., Bilański, P., Boxshall, A.G., Bradshaw, M., Broadbridge, J., Calaça, F.J.S., Campos-Quiroz, C., Carrasco-Fernández, J., Castro, J.F., Chaimongkol, S., Chandranayaka, S., Chen, Y., Comben, D., Dearnaley, J.D.W., Ferreira-Sá, A.S., Dhileepan, K., Díaz, M.L., Divakar, P.K., Xavier-Santos, S., Fernández-Bravo, A., Gené, J., Guard, F.E., Guerra, M., Gunaseelan, S., Houbraken, J., Janik-Superson, K., Jankowiak, R., Jeppson, M., Jurjević, Kaliyaperumal, M., Kelly, L.A., Kezo, K., Khalid, A.N., Khamsuntorn, P., Kidanemariam, D., Kiran, M., Lacey, E., Langer, G.J., López-Llorca, L.V., Luangsa-Ard, J.J., Lueangjaroenkit, P., Lumbsch, H.T., Maciá-Vicente, J.G., Mamatha Bhanu, L.S., Marney, T.S., Marqués-Gálvez, J.E., Morte, A., Naseer, A., Navarro-Ródenas, A., Oyedele, O., Peters, S., Piskorski, S., Quijada, L., Ramírez, G.H., Raja, K., Razzaq, A., Rico, V.J., Rodríguez, A., Ruszkiewicz-Michalska, M., Sánchez, R.M., Santelices, C., Savitha, A.S., Serrano, M., Leonardo-Silva, L., Solheim, H., Somrithipol, S., Sreenivasa, M.Y., Stępniewska, H., Strapagiel, D., Taylor, T., Torres-Garcia, D., Vauras, J., Villarreal, M., Visagie, C.M., Wołkowycki, M., Yingkunchao, W., Zapora, E., Groenewald, J.Z., and Crous, P.W.
- Abstract
Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilax glyciphylla. Brazil, Preussia bezerrensis from air. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora viadrina from rhizosphere soil of Quercus robur, and Septoria krystynae on leaf spots of Viscum album. Portugal (Azores), Acrogenospora stellata on dead wood or bark. South Africa, Phyllactinia greyi
- Published
- 2022
6. Fungal Planet description sheets: 1436–1477
- Author
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Universidad de Alicante. Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante. Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Tan, Y.P., Bishop-Hurley, S.L., Shivas, R.G., Cowan, Don A., Maggs-Kölling, Gillian, Maharachchikumbura, S.S.N., Pinruan, U., Bransgrove, K.L., De la Peña-Lastra, S., Larsson, E., Lebel, T., Mahadevakumar, S., Mateos, A., Osieck, E.R., Rigueiro-Rodríguez, A., Sommai, S., Ajithkumar, K., Akulov, A., Anderson, F.E., Arenas, F., Balashov, S., Bañares Baudet, Ángel, Berger, D.K., Bianchinotti, M.V., Bien, S., Bilański, P., Boxshall, A.-G., Bradshaw, M., Broadbridge, J., Calaça, F.J.S., Campos-Quiroz, C., Carrasco-Fernández, J., Castro, J.F., Chaimongkol, S., Chandranayaka, S., Chen, Y., Comben, D., Dearnaley, J.D.W., Ferreira-Sá, A.S., Dhileepan, K., Díaz, M.L., Divakar, P.K., Xavier-Santos, S., Fernández-Bravo, A., Gené, J., Guard, F.E., Guerra, M., Gunaseelan, S., Houbraken, J., Janik-Superson, K., Jankowiak, R., Jeppson, M., Jurjević, Ž., Kaliyaperumal, M., Kelly, L.A., Kezo, K., Khalid, Abdul Nasir, Khamsuntorn, P., Kidanemariam, D., Kiran, M., Lacey, E., Langer, G.J., Lopez-Llorca, Luis Vicente, Luangsa-ard, J.J., Lueangjaroenkit, P., Lumbsch, H.T., Maciá-Vicente, Jose G., Mamatha Bhanu, L.S., Marney, T.S., Marqués-Gálvez, J.E., Morte, A., Naseer, A., Navarro-Ródenas, A., Oyedele, O., Peters, S., Piskorski, S., Quijada, L., Ramírez, G.H., Raja, K., Razzaq, A., Rico, V.J., Rodríguez, A., Ruszkiewicz-Michalska, M., Sánchez, R.M., Santelices, C., Savitha, A.S., Serrano, M., Leonardo-Silva, L., Solheim, H., Somrithipol, S., Sreenivasa, M.Y., Stępniewska, H., Strapagiel, D., Taylor, T., Torres-Garcia, D., Vauras, J., Villarreal, M., Visagie, C.M., Wołkowycki, M., Yingkunchao, W., Zapora, E., Groenewald, J.Z., Crous, P.W., Universidad de Alicante. Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante. Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Tan, Y.P., Bishop-Hurley, S.L., Shivas, R.G., Cowan, Don A., Maggs-Kölling, Gillian, Maharachchikumbura, S.S.N., Pinruan, U., Bransgrove, K.L., De la Peña-Lastra, S., Larsson, E., Lebel, T., Mahadevakumar, S., Mateos, A., Osieck, E.R., Rigueiro-Rodríguez, A., Sommai, S., Ajithkumar, K., Akulov, A., Anderson, F.E., Arenas, F., Balashov, S., Bañares Baudet, Ángel, Berger, D.K., Bianchinotti, M.V., Bien, S., Bilański, P., Boxshall, A.-G., Bradshaw, M., Broadbridge, J., Calaça, F.J.S., Campos-Quiroz, C., Carrasco-Fernández, J., Castro, J.F., Chaimongkol, S., Chandranayaka, S., Chen, Y., Comben, D., Dearnaley, J.D.W., Ferreira-Sá, A.S., Dhileepan, K., Díaz, M.L., Divakar, P.K., Xavier-Santos, S., Fernández-Bravo, A., Gené, J., Guard, F.E., Guerra, M., Gunaseelan, S., Houbraken, J., Janik-Superson, K., Jankowiak, R., Jeppson, M., Jurjević, Ž., Kaliyaperumal, M., Kelly, L.A., Kezo, K., Khalid, Abdul Nasir, Khamsuntorn, P., Kidanemariam, D., Kiran, M., Lacey, E., Langer, G.J., Lopez-Llorca, Luis Vicente, Luangsa-ard, J.J., Lueangjaroenkit, P., Lumbsch, H.T., Maciá-Vicente, Jose G., Mamatha Bhanu, L.S., Marney, T.S., Marqués-Gálvez, J.E., Morte, A., Naseer, A., Navarro-Ródenas, A., Oyedele, O., Peters, S., Piskorski, S., Quijada, L., Ramírez, G.H., Raja, K., Razzaq, A., Rico, V.J., Rodríguez, A., Ruszkiewicz-Michalska, M., Sánchez, R.M., Santelices, C., Savitha, A.S., Serrano, M., Leonardo-Silva, L., Solheim, H., Somrithipol, S., Sreenivasa, M.Y., Stępniewska, H., Strapagiel, D., Taylor, T., Torres-Garcia, D., Vauras, J., Villarreal, M., Visagie, C.M., Wołkowycki, M., Yingkunchao, W., Zapora, E., Groenewald, J.Z., and Crous, P.W.
- Abstract
Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilax glyciphylla. Brazil, Preussia bezerrensis from air. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora viadrina from rhizosphere soil of Quercus robur, and Septoria krystynae on leaf spots of Viscum album. Portugal (Azores), Acrogenospora stellata on dead wood or bark. South Africa, Phyllactinia grey
- Published
- 2022
7. Fungal Planet description sheets: 1436-1477
- Author
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Universitat Rovira i Virgili, Tan YP; Bishop-Hurley SL; Shivas RG; Cowan DA; Maggs-Kölling G; Maharachchikumbura SSN; Pinruan U; Bransgrove KL; De la Peña-Lastra S; Larsson E; Lebel T; Mahadevakumar S; Mateos A; Osieck ER; Rigueiro-Rodríguez A; Sommai S; Ajithkumar K; Akulov A; Anderson FE; Arenas F; Balashov S; Bañares ; Berger DK; Bianchinotti MV; Bien S; Bila?ski P; Boxshall AG; Bradshaw M; Broadbridge J; Calaça FJS; Campos-Quiroz C; Carrasco-Fernández J; Castro JF; Chaimongkol S; Chandranayaka S; Chen Y; Comben D; Dearnaley JDW; Ferreira-Sá AS; Dhileepan K; Díaz ML; Divakar PK; Xavier-Santos S; Fernández-Bravo A; Gené J; Guard FE; Guerra M; Gunaseelan S; Houbraken J; Janik-Superson K; Jankowiak R; Jeppson M; Jurjevi? ; Kaliyaperumal M; Kelly LA; Kezo K; Khalid AN; Khamsuntorn P; Kidanemariam D; Kiran M; Lacey E; Langer GJ; López-Llorca LV; Luangsa-Ard JJ; Lueangjaroenkit P; Lumbsch HT; Maciá-Vicente JG; Bhanu LSM; Marney TS; Marqués-Gálvez JE; Morte A; Naseer A; Navarro-Ródenas A; Oyedele O; Peters S; Piskorski S; Quijada L; Ramírez GH; Raja K; Razzaq A; Rico VJ; Rodríguez A; Ruszkiewicz-Michalska M; Sánchez RM; Santelices C; Savitha AS; Serrano M; Leonardo-Silva L; Solheim H; Somrithipol S; Sreenivasa MY; Stpniewska H; Strapagiel D; Taylor T; Torres-Garcia D; Vauras J; Villarreal M; Visagie CM; Wokowycki M; Yingkunchao W; Zapora E.; Groenewald JZ, Universitat Rovira i Virgili, and Tan YP; Bishop-Hurley SL; Shivas RG; Cowan DA; Maggs-Kölling G; Maharachchikumbura SSN; Pinruan U; Bransgrove KL; De la Peña-Lastra S; Larsson E; Lebel T; Mahadevakumar S; Mateos A; Osieck ER; Rigueiro-Rodríguez A; Sommai S; Ajithkumar K; Akulov A; Anderson FE; Arenas F; Balashov S; Bañares ; Berger DK; Bianchinotti MV; Bien S; Bila?ski P; Boxshall AG; Bradshaw M; Broadbridge J; Calaça FJS; Campos-Quiroz C; Carrasco-Fernández J; Castro JF; Chaimongkol S; Chandranayaka S; Chen Y; Comben D; Dearnaley JDW; Ferreira-Sá AS; Dhileepan K; Díaz ML; Divakar PK; Xavier-Santos S; Fernández-Bravo A; Gené J; Guard FE; Guerra M; Gunaseelan S; Houbraken J; Janik-Superson K; Jankowiak R; Jeppson M; Jurjevi? ; Kaliyaperumal M; Kelly LA; Kezo K; Khalid AN; Khamsuntorn P; Kidanemariam D; Kiran M; Lacey E; Langer GJ; López-Llorca LV; Luangsa-Ard JJ; Lueangjaroenkit P; Lumbsch HT; Maciá-Vicente JG; Bhanu LSM; Marney TS; Marqués-Gálvez JE; Morte A; Naseer A; Navarro-Ródenas A; Oyedele O; Peters S; Piskorski S; Quijada L; Ramírez GH; Raja K; Razzaq A; Rico VJ; Rodríguez A; Ruszkiewicz-Michalska M; Sánchez RM; Santelices C; Savitha AS; Serrano M; Leonardo-Silva L; Solheim H; Somrithipol S; Sreenivasa MY; Stpniewska H; Strapagiel D; Taylor T; Torres-Garcia D; Vauras J; Villarreal M; Visagie CM; Wokowycki M; Yingkunchao W; Zapora E.; Groenewald JZ
- Abstract
Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilax glyciphylla. Brazil, Preussia bezerrensis from air. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora
- Published
- 2022
8. Genomic Insights Into the Mycobacterium kansasii Complex: An Update
- Author
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Jagielski, T., Borowka, P., Bakula, Z., Lach, J., Marciniak, B., Brzostek, A., Pennings, L.J., Ingen, J. van, Zolnir-Dovc, M., Strapagiel, D., Jagielski, T., Borowka, P., Bakula, Z., Lach, J., Marciniak, B., Brzostek, A., Pennings, L.J., Ingen, J. van, Zolnir-Dovc, M., and Strapagiel, D.
- Abstract
Contains fulltext : 216651.pdf (publisher's version ) (Open Access)
- Published
- 2020
9. CD14 and IL-10 gene polymorphisms in relation to tuberculosis: P571
- Author
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Druszczynska, M., Strapagiel, D., Sadowska, B., Karhukorpi, J., Karttunen, R., Kwiatkowska, S., Rozalska, B., and Rudnicka, W.
- Published
- 2005
10. Down-Regulation of Phagocytosis of H. pylori by Mannose Binding Lectin (MBL)
- Author
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Chmiela, M., Strapagiel, D., Fol, M., Wadstrom, T., and Rudnicka, W.
- Published
- 2003
11. BioSCOOP – Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks
- Author
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Jarczak, J, primary, Lach, J, additional, Borówka, P, additional, Gałka, M, additional, Bućko, M, additional, Marciniak, B, additional, and Strapagiel, D, additional
- Published
- 2019
- Full Text
- View/download PDF
12. Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health
- Author
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Holub, P, Kohlmayer, F, Prasser, F, Mayrhofer, M, Schlünder, I, Martin, G, Casati, S, Koumakis, L, Wutte, A, Kozera, Ł, Strapagiel, D, Anton, G, Zanetti, G, Sezerman, O, Mendy, M, Valík, D, Lavitrano, M, Dagher, G, Zatloukal, K, van Ommen, G, Litton, J, Mayrhofer, MT, Martin, GM, Sezerman, OU, van Ommen, GB, Litton, JE, Holub, P, Kohlmayer, F, Prasser, F, Mayrhofer, M, Schlünder, I, Martin, G, Casati, S, Koumakis, L, Wutte, A, Kozera, Ł, Strapagiel, D, Anton, G, Zanetti, G, Sezerman, O, Mendy, M, Valík, D, Lavitrano, M, Dagher, G, Zatloukal, K, van Ommen, G, Litton, J, Mayrhofer, MT, Martin, GM, Sezerman, OU, van Ommen, GB, and Litton, JE
- Abstract
The known challenge of underutilization of data and biological material from biorepositories as potential resources for medical research has been the focus of discussion for over a decade. Recently developed guidelines for improved data availability and reusability - entitled FAIR Principles (Findability, Accessibility, Interoperability, and Reusability) - are likely to address only parts of the problem. In this article, we argue that biological material and data should be viewed as a unified resource. This approach would facilitate access to complete provenance information, which is a prerequisite for reproducibility and meaningful integration of the data. A unified view also allows for optimization of long-term storage strategies, as demonstrated in the case of biobanks. We propose an extension of the FAIR Principles to include the following additional components: (1) quality aspects related to research reproducibility and meaningful reuse of the data, (2) incentives to stimulate effective enrichment of data sets and biological material collections and its reuse on all levels, and (3) privacy-respecting approaches for working with the human material and data. These FAIR-Health principles should then be applied to both the biological material and data. We also propose the development of common guidelines for cloud architectures, due to the unprecedented growth of volume and breadth of medical data generation, as well as the associated need to process the data efficiently.
- Published
- 2018
13. Species classification of Mycobacterium avium and Mycobacterium intracellulare based on whole genome analysis
- Author
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Lach, J., Marciniak, B., and Strapagiel, D.
- Published
- 2017
- Full Text
- View/download PDF
14. Draft Genome Sequences of Mycobacterium kansasii Clinical Strains
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Borowka, P., Lach, J., Bakula, Z., Ingen, J. van, Safianowska, A., Brzostek, A., Dziadek, J., Strapagiel, D., Jagielski, T., Borowka, P., Lach, J., Bakula, Z., Ingen, J. van, Safianowska, A., Brzostek, A., Dziadek, J., Strapagiel, D., and Jagielski, T.
- Abstract
Contains fulltext : 177574.pdf (publisher's version ) (Open Access), Mycobacterium kansasii is a nontuberculous mycobacterial (NTM) pathogen, frequently isolated from clinical samples and responsible for a large part of NTM infections in the human population. Here, we report the draft genome sequences of 12 M. kansasii strains isolated from clinical and host-associated sources from the Netherlands, Germany, and Poland.
- Published
- 2017
15. Association of five SNPs with human hair colour in the Polish population
- Author
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Siewierska-Górska, A., primary, Sitek, A., additional, Żądzińska, E., additional, Bartosz, G., additional, and Strapagiel, D., additional
- Published
- 2016
- Full Text
- View/download PDF
16. Draft Genome Sequences of Mycobacterium kansasii Strains 1010001454, 1010001458, 1010001468, 1010001493, 1010001495, and 1010001469, Isolated from Environmental Sources.
- Author
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Strapagiel, D., Borówka, P., Marciniak, B., Bakuła, Z., Ingen, J. van, Safianowska, A., Brzostek, A., Dziadek, J., Jagielski, T., Strapagiel, D., Borówka, P., Marciniak, B., Bakuła, Z., Ingen, J. van, Safianowska, A., Brzostek, A., Dziadek, J., and Jagielski, T.
- Abstract
Contains fulltext : 172353.pdf (publisher's version ) (Open Access)
- Published
- 2016
17. Tuberculosis bacilli still posing a threat. Polymorphism of genes regulating anti-mycobacterial properties of macrophages
- Author
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Druszczyńska M, Strapagiel D, Kwiatkowska S, Kowalewicz-Kulbat M, Rózalska B, Magdalena Chmiela, and Rudnicka W
18. Single Nucleotide Polymorphisms (SNPs) Profile as Predictive Markers of Lifestyle Modification Outcomes in Pediatric Obesity Treatment
- Author
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KIRKGÖZ, TARIK, DEMİRCİOĞLU, SERAP, GÜRAN, TÜLAY, BEREKET, ABDULLAH, and Gawlik A., Sobalska-Kwapis M., Antosz A., Strapagiel D., Seweryn M., Shmoish M., BEREKET A., Wasniewska M., KIRKGÖZ T., DEMİRCİOĞLU S., et al.
- Subjects
Internal Diseases ,Endokrin ve Otonom Sistemler ,ENDOCRINOLOGY & METABOLISM ,Endocrinology, Diabetes and Metabolism ,Endocrinology and Metabolic Diseases ,Sağlık Bilimleri ,Endokrinoloji ,Pediatrics ,İç Hastalıkları ,Clinical Medicine (MED) ,Çocuk Sağlığı ve Hastalıkları ,Child Health and Diseases ,Endocrinology ,Health Sciences ,Yaşam Bilimleri ,Klinik Tıp (MED) ,Pediatri, Perinatoloji ve Çocuk Sağlığı ,Internal Medicine Sciences ,Klinik Tıp ,Endocrine and Autonomic Systems ,Life Sciences ,Dahili Tıp Bilimleri ,CLINICAL MEDICINE ,Tıp ,Pediatri ,Pediatrics, Perinatology and Child Health ,Endokrinoloji ve Metabolizma Hastalıkları ,ENDOKRİNOLOJİ VE METABOLİZMA ,Medicine ,PEDİATRİ ,Endokrinoloji, Diyabet ve Metabolizma - Published
- 2022
19. Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health
- Author
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Dominik Strapagiel, Sara Casati, Andrea Wutte, Irene Schlünder, Jan-Eric Litton, Osman Ugur Sezerman, Gert-Jan B. van Ommen, Petr Holub, Gillian M. Martin, Marialuisa Lavitrano, Gianluigi Zanetti, Łukasz Kozera, Dalibor Valík, Michaela Th. Mayrhofer, Georges Dagher, Florian Kohlmayer, Maimuna Mendy, Gabriele Anton, Lefteris Koumakis, Kurt Zatloukal, Fabian Prasser, Holub, P, Kohlmayer, F, Prasser, F, Mayrhofer, M, Schlünder, I, Martin, G, Casati, S, Koumakis, L, Wutte, A, Kozera, Ł, Strapagiel, D, Anton, G, Zanetti, G, Sezerman, O, Mendy, M, Valík, D, Lavitrano, M, Dagher, G, Zatloukal, K, van Ommen, G, Litton, J, and Acibadem University Dspace
- Subjects
0301 basic medicine ,Information storage and retrieval systems ,FAIR (Findable ,Databases, Factual ,Biobanks -- Management ,Process (engineering) ,Test data generation ,incentives ,privacy protection ,Interoperability ,and Reusable) principle ,Medicine (miscellaneous) ,Guidelines as Topic ,Cloud computing ,Reuse ,General Biochemistry, Genetics and Molecular Biology ,Accessible ,And Reusable) Principles ,Fair (findable ,Incentives ,Interoperable ,Open Science ,Privacy Protection ,Provenance Information Management ,Quality ,03 medical and health sciences ,0302 clinical medicine ,Resource (project management) ,open science ,Humans ,Medicine ,030212 general & internal medicine ,Biological Specimen Banks ,Data protection ,Information Dissemination ,business.industry ,MED/04 - PATOLOGIA GENERALE ,Findability ,Original Articles ,Cell Biology ,General Medicine ,Biobank ,Data science ,incentive ,3. Good health ,FAIR (Findable, Accessible, Interoperable, and Reusable) principle ,030104 developmental biology ,Privacy ,quality ,and Reusable) principles ,Freedom of information ,business ,provenance information management ,Confidentiality ,FAIR (Findable, Accessible, Interoperable, and Reusable) principles - Abstract
The known challenge of underutilization of data and biological material from biorepositories as potential resources formedical research has been the focus of discussion for over a decade. Recently developed guidelines for improved data availability and reusability—entitled FAIR Principles (Findability, Accessibility, Interoperability, and Reusability)—are likely to address only parts of the problem. In this article,we argue that biologicalmaterial and data should be viewed as a unified resource. This approach would facilitate access to complete provenance information, which is a prerequisite for reproducibility and meaningful integration of the data. A unified view also allows for optimization of long-term storage strategies, as demonstrated in the case of biobanks.Wepropose an extension of the FAIR Principles to include the following additional components: (1) quality aspects related to research reproducibility and meaningful reuse of the data, (2) incentives to stimulate effective enrichment of data sets and biological material collections and its reuse on all levels, and (3) privacy-respecting approaches for working with the human material and data. These FAIR-Health principles should then be applied to both the biological material and data. We also propose the development of common guidelines for cloud architectures, due to the unprecedented growth of volume and breadth of medical data generation, as well as the associated need to process the data efficiently., peer-reviewed
- Published
- 2018
- Full Text
- View/download PDF
20. A genomic Neolithic time transect of hunter-farmer admixture in central Poland
- Author
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Dominik Strapagiel, Jens Carlsson, Wiesław Lorkiewicz, Veronika Siska, Daniel Fernandes, Kendra Sirak, Paulina Borówka, Ryszard Grygiel, Andrea Manica, Błażej Marciniak, Ron Pinhasi, Elżbieta Żądzińska, Strapagiel, D [0000-0001-9752-4270], Żądzińska, E [0000-0003-1001-7319], Manica, A [0000-0003-1895-450X], and Apollo - University of Cambridge Repository
- Subjects
0301 basic medicine ,Steppe ,Population genetics ,Human Migration ,Population ,Pastoralism ,lcsh:Medicine ,DNA, Mitochondrial ,Article ,03 medical and health sciences ,Middle East ,0302 clinical medicine ,Bronze Age ,Humans ,DNA, Ancient ,lcsh:Science ,education ,Mesolithic ,History, Ancient ,education.field_of_study ,Multidisciplinary ,geography.geographical_feature_category ,Chromosomes, Human, Y ,Farmers ,Human migration ,business.industry ,Genome, Human ,lcsh:R ,Genetic Drift ,Agriculture ,Genomics ,Archaeology ,Europe ,030104 developmental biology ,Geography ,Ancient DNA ,Genetics, Population ,lcsh:Q ,Poland ,business ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times.
- Published
- 2018
21. Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils.
- Author
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Serwecińska L, Font-Nájera A, Strapagiel D, Lach J, Tołoczko W, Bołdak M, and Urbaniak M
- Subjects
- Bacteria genetics, Bacteria drug effects, Bacteria classification, Metagenomics methods, Drug Resistance, Microbial genetics, Poland, Sewage microbiology, Soil Microbiology, Agriculture methods, Fertilizers, Soil chemistry, Microbiota genetics, Microbiota drug effects
- Abstract
Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
22. α-Hemolysin from Staphylococcus aureus Changes the Epigenetic Landscape of Th17 Cells.
- Author
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Pastwińska J, Karwaciak I, Karaś K, Sałkowska A, Chałaśkiewicz K, Strapagiel D, Sobalska-Kwapis M, Dastych J, and Ratajewski M
- Subjects
- Humans, Staphylococcal Infections immunology, Staphylococcal Infections microbiology, DNA Methylation, Cell Differentiation, Transcriptome, Staphylococcus aureus immunology, Staphylococcus aureus genetics, Hemolysin Proteins genetics, Hemolysin Proteins immunology, Hemolysin Proteins metabolism, Th17 Cells immunology, Th17 Cells metabolism, Epigenesis, Genetic, Bacterial Toxins immunology, Bacterial Toxins genetics
- Abstract
The human body harbors a substantial population of bacteria, which may outnumber host cells. Thus, there are multiple interactions between both cell types. Given the common presence of Staphylococcus aureus in the human body and the role of Th17 cells in controlling this pathogen on mucous membranes, we sought to investigate the effect of α-hemolysin, which is produced by this bacterium, on differentiating Th17 cells. RNA sequencing analysis revealed that α-hemolysin influences the expression of signature genes for Th17 cells as well as genes involved in epigenetic regulation. We observed alterations in various histone marks and genome methylation levels via whole-genome bisulfite sequencing. Our findings underscore how bacterial proteins can significantly influence the transcriptome, epigenome, and phenotype of human Th17 cells, highlighting the intricate and complex nature of the interaction between immune cells and the microbiota., (Copyright © 2024 The Authors.)
- Published
- 2024
- Full Text
- View/download PDF
23. The whole genome sequence of Polish vaccine strain Mycobacterium bovis BCG Moreau.
- Author
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Krysztopa-Grzybowska K, Lach J, Polak M, Strapagiel D, Dziadek J, Olszewski M, Zasada AA, Darlińska A, Lutyńska A, and Augustynowicz-Kopeć E
- Subjects
- Poland, Humans, Tuberculosis prevention & control, Tuberculosis microbiology, INDEL Mutation, Mutation, BCG Vaccine genetics, BCG Vaccine immunology, Mycobacterium bovis genetics, Mycobacterium bovis classification, Genome, Bacterial, Whole Genome Sequencing, Polymorphism, Single Nucleotide
- Abstract
Currently, tuberculosis immunoprophylaxis is based solely on Bacillus Calmette-Guérin (BCG) vaccination, and some of the new potential tuberculosis vaccines are based on the BCG genome. Therefore, it is reasonable to analyze the genomes of individual BCG substrains. The aim of this study was the genetic characterization of the BCG-Moreau Polish (PL) strain used for the production of the BCG vaccine in Poland since 1955. Sequencing of different BCG lots showed that the strain was stable over a period of 59 years. As a result of comparison, BCG-Moreau PL with BCG-Moreau Rio de Janeiro (RDJ) 143 single nucleotide polymorphisms (SNPs) and 32 insertion/deletion mutations (INDELs) were identified. However, the verification of these mutations showed that the most significant were accumulated in the BCG-Moreau RDJ genome. The mutations unique to the Polish strain genome are 1 SNP and 2 INDEL. The strategy of combining short-read sequencing with long-read sequencing is currently the most optimal approach for sequencing bacterial genomes. With this approach, the only available genomic sequence of BCG-Moreau PL was obtained. This sequence will primarily be a reference point in the genetic control of the stability of the vaccine strain in the future. The results enrich knowledge about the microevolution and attenuation of the BCG vaccine substrains., Importance: The whole genome sequence obtained is the only genomic sequence of the strain that has been used for vaccine production in Poland since 1955. Sequencing of different BCG lots showed that the strain was stable over a period of 59 years. The comprehensive genomic analysis performed not only enriches knowledge about the microevolution and attenuation of the BCG vaccine substrains but also enables the utilization of identified markers as a reference point in the genetic control and identity tests of the stability of the vaccine strain in the future., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
- Full Text
- View/download PDF
24. Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds.
- Author
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Włodarczyk R, Drzewińska-Chańko J, Kamiński M, Meissner W, Rapczyński J, Janik-Superson K, Krawczyk D, Strapagiel D, Ożarowska A, Stępniewska K, and Minias P
- Subjects
- Animals, Humans, Birds microbiology, Bacteria genetics, RNA, Ribosomal, 16S genetics, Gastrointestinal Microbiome, Microbiota
- Abstract
Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)
- Published
- 2024
- Full Text
- View/download PDF
25. Association of Three Genetic Loci with Molar Incisor Hypomineralization in Polish Children.
- Author
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Milona M, Ciechanowicz A, Węsierska K, Gońda-Domin M, Zawiślak A, Jarząbek A, Sobalska-Kwapis M, Jarczak J, Gruszka R, Strapagiel D, Janiszewska-Olszowska J, and Grocholewicz K
- Abstract
Background: Molar incisor hypomineralization (MIH) is a qualitative, demarcated enamel defect of hypomineralization affecting one to four first permanent molars, often with incisor involvement. Its etiology is complex. However, evidence suggests the influence of genetic factors, potentially including the single nucleotide polymorphisms (SNPs) rs2889956, rs4811117 and rs13058467, which were previously linked to MIH in a genome-wide association study of German children. The aim was to replicate analyses of possible associations between the SNPs and molar incisor hypomineralization in Polish children., Methods: The final study group consisted of 778 children aged 126-168 months old. Saliva samples were taken, and genomic DNA was extracted and genotyped using beadchip microarrays., Results: Among the 778 subjects, there were 68 (8.7%) subjects with MIH and 710 (91.3%) subjects without MIH. There were no significant differences in distributions in age, sex, or the frequency of caries in permanent dentition between the MIH and non-MIH groups. The rs2889956, rs4811117, and rs13058467 genotype distributions in the studied group conformed to the expected Hardy-Weinberg equilibria, and there were no significant differences in the distributions of their alleles or genotypes between the MIH and non-MIH groups., Conclusion: Our replication study did not confirm highly significant associations between the single nucleotide polymorphisms rs2889956, rs4811117, and rs13058467 with molar incisor hypomineralization in Polish children.
- Published
- 2024
- Full Text
- View/download PDF
26. Publisher Correction: Analytical sensitivity of a method is critical in detection of low-level BRCA1 constitutional epimutation.
- Author
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Machaj F, Sokolowska KE, Borowski K, Retfiński S, Strapagiel D, Sobalska-Kwapis M, Huzarski T, Lubiński J, and Wojdacz TK
- Published
- 2023
- Full Text
- View/download PDF
27. rs67047829 genotypes of ERV3-1/ZNF117 are associated with lower body mass index in the Polish population.
- Author
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Clark JSC, Podsiadło K, Sobalska-Kwapis M, Marciniak B, Rydzewska K, Ciechanowicz A, van de Wetering T, and Strapagiel D
- Subjects
- Humans, Male, Female, Body Mass Index, Poland, Genotype, Weight Loss genetics, Codon, Polymorphism, Single Nucleotide, Obesity complications, Adiposity genetics
- Abstract
There is now substantial evidence that zinc-finger proteins are implicated in adiposity. Aims were to datamine for high-frequency (near-neutral selection) pretermination-codon (PTC) single-nucleotide polymorphisms (SNPs; n = 141) from a database with > 550,000 variants and analyze possible association with body mass index in a large Polish sample (n = 5757). BMI was regressed (males/females together or separately) against genetic models. Regression for rs67047829 uncovered an interaction-independent association with BMI with both sexes together: mean ± standard deviation, kg/m
2 : [G];[G], 25.4 ± 4.59 (n = 3650); [G](;)[A], 25.0 ± 4.28 (n = 731); [A];[A], 23.4 ± 3.60 (n = 44); additive model adjusted for age and sex: p = 4.08 × 10-5 ; beta: - 0.0458, 95% confidence interval (CI) - 0.0732 : - 0.0183; surviving Bonferroni correction; for males: [G];[G], 24.8 ± 4.94 (n = 1878); [G](;)[A], 24.2 ± 4.31 (n = 386); [A];[A], 22.4 ± 3.69 (n = 23); p = 4.20 × 10-4 ; beta: - 0.0573, CI - 0.0947 : - 0.0199. For average-height males the difference between [G];[G] and [A];[A] genotypes would correspond to ~ 6 kg, suggesting considerable protection against increased BMI. rs67047829 gives a pretermination codon in ERV3-1 which shares an exonic region and possibly promoter with ZNF117, previously associated with adiposity and type-2 diabetes. As this result occurs in a near-neutral Mendelian setting, a drug targetting ERV3-1/ZNF117 might potentially provide considerable benefits with minimal side-effects. This result needs to be replicated, followed by analyses of splice-variant mRNAs and protein expression., (© 2023. Springer Nature Limited.)- Published
- 2023
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28. Analytical sensitivity of a method is critical in detection of low-level BRCA1 constitutional epimutation.
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Machaj F, Sokolowska KE, Borowski K, Retfiński S, Strapagiel D, Sobalska-Kwapis M, Huzarski T, Lubiński J, and Wojdacz TK
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- Female, Humans, Pregnancy, Research Design, Genetic Profile, Health Status, BRCA1 Protein genetics, Genes, BRCA1, Labor, Obstetric
- Abstract
Recent reports based on a substantial number of cases, warrant need for population-based research to determine implications of constitutional methylation of tumor suppressor genes such as BRCA1 occurring in healthy tissue in the prediction of cancer. However, the detection of the constitutional methylation in DNA extracted from blood has already been shown to be technologically challenging, mainly because epimutations appear to be present in blood at a very low level. The analytical sensitivity required for low-level methylation detection can be provided by NGS, but this technique is still labor and cost-intensive. We assessed if PCR-based MS-HRM and BeadChip microarray technologies, which are standardized and cost-effective technologies for methylation changes screening, provide a sufficient level of analytical sensitivity for constitutional BRCA1 methylation detection in blood samples. The study included whole blood samples from 67 healthy women, 35 with previously confirmed and 32 with no detectable BRCA1 promoter methylation for which we performed both MS-HRM based BRCA1 gene methylation screening and genome wide methylation profiling with EPIC microarray. Our results shown, that low-level BRCA1 methylation can be effectively detected in DNA extracted from blood by PCR-based MS-HRM. At the same time, EPIC microarray does not provide conclusive results to unambiguously determine the presence of BRCA1 constitutional methylation in MS-HRM epimutation positive samples. The analytical sensitivity of MS-HRM is sufficient to detect low level BRCA1 constitutional epimutation in DNA extracted from blood and BeadChip technology-based microarrays appear not to provide that level of analytical sensitivity., (© 2023. Springer Nature Limited.)
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- 2023
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29. Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis.
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Górska A, Urbanowicz M, Grochowalski Ł, Seweryn M, Sobalska-Kwapis M, Wojdacz T, Lange M, Gruchała-Niedoszytko M, Jarczak J, Strapagiel D, Górska-Ponikowska M, Pelikant-Małecka I, Kalinowski L, Nedoszytko B, Gutowska-Owsiak D, and Niedoszytko M
- Subjects
- Adult, Humans, DNA Methylation, Epigenesis, Genetic, Tryptases genetics, Oncogenes, DNA, Gene Expression, CpG Islands, Forkhead Transcription Factors genetics, Mastocytosis, Systemic genetics, Mastocytosis, Systemic diagnosis, Anaphylaxis genetics
- Abstract
Mastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that are relevant to the pathology. Epigenetic alterations are responsible for regulating the expression of genes that do not modify the DNA sequence. In general, it is accepted that DNA methylation inhibits the binding of transcription factors, thereby down-regulating gene expression. However, so far, little is known about the epigenetic factors leading to the clinical onset of mastocytosis. Therefore, it is essential to identify possible epigenetic predictors, indicators of disease progression, and their link to the clinical picture to establish appropriate management and a therapeutic strategy. The aim of this study was to analyze genome-wide methylation profiles to identify differentially methylated regions (DMRs) in patients with mastocytosis compared to healthy individuals, as well as the genes located in those regulatory regions. Genome-wide DNA methylation profiling was performed in peripheral blood collected from 80 adult patients with indolent systemic mastocytosis (ISM), the most prevalent subvariant of mastocytosis, and 40 healthy adult volunteers. A total of 117 DNA samples met the criteria for the bisulfide conversion step and microarray analysis. Genome-wide DNA methylation analysis was performed using a MethylationEPIC BeadChip kit. Further analysis was focused on the genomic regions rather than individual CpG sites. Co-methylated regions (CMRs) were assigned via the CoMeBack method. To identify DMRs between the groups, a linear regression model with age as the covariate on CMRs was performed using Limma. Using the available data for cases only, an association analysis was performed between methylation status and tryptase levels, as well as the context of allergy, and anaphylaxis. KEGG pathway mapping was used to identify genes differentially expressed in anaphylaxis. Based on the DNA methylation results, the expression of 18 genes was then analyzed via real-time PCR in 20 patients with mastocytosis and 20 healthy adults. A comparison of the genome-wide DNA methylation profile between the mastocytosis patients and healthy controls revealed significant differences in the methylation levels of 85 selected CMRs. Among those, the most intriguing CMRs are 31 genes located within the regulatory regions. In addition, among the 10 CMRs located in the promoter regions, 4 and 6 regions were found to be either hypo- or hypermethylated, respectively. Importantly, three oncogenes- FOXQ1 , TWIST1 , and ERG -were identified as differentially methylated in mastocytosis patients, for the first time. Functional annotation revealed the most important biological processes in which the differentially methylated genes were involved as transcription, multicellular development, and signal transduction. The biological process related to histone H2A monoubiquitination (GO:0035518) was found to be enriched in association with higher tryptase levels, which may be associated with more aberrant mast cells and, therefore, more atypical mast cell disease. The signal in the BAIAP2 gene was detected in the context of anaphylaxis, but no significant differential methylation was found in the context of allergy. Furthermore, increased expression of genes encoding integral membrane components ( GRM2 and KRTCAP3 ) was found in mastocytosis patients. This study confirms that patients with mastocytosis differ significantly in terms of methylation levels in selected CMRs of genes involved in specific molecular processes. The results of gene expression profiling indicate the increased expression of genes belonging to the integral component of the membrane in mastocytosis patients ( GRM2 and KRTCAP3 ). Further work is warranted, especially in relation to the disease subvariants, to identify links between the methylation status and the symptoms and novel therapeutic targets.
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- 2023
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30. Novel Antimicrobial Peptides from Saline Environments Active against E. faecalis and S. aureus : Identification, Characterisation and Potential Usage.
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Lach J, Krupińska M, Mikołajczyk A, Strapagiel D, Stączek P, and Matera-Witkiewicz A
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- Humans, Antimicrobial Peptides, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Peptides, Microbial Sensitivity Tests, Staphylococcus aureus, Methicillin-Resistant Staphylococcus aureus
- Abstract
Microorganisms inhabiting saline environments have been known for decades as producers of many valuable bioproducts. These substances include antimicrobial peptides (AMPs), the most recognizable of which are halocins produced by halophilic Archaea. As agents with a different modes of action from that of most conventionally used antibiotics, usually associated with an increase in the permeability of the cell membrane as a result of a formation of channels and pores, AMPs are a currently promising object of research focused on the investigation of antibiotics with non-standard modes of action. The aim of this study was to investigate antimicrobial activity against multidrug-resistant human pathogens of three peptides, which were synthetised based on sequences identified in metagenomes from saline environments. The investigations were performed against Enterococcus faecalis , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , Escherichia coli and Candida albicans . Subsequently, the cytotoxicity and haemolytic properties of the tested peptides were verified. An in silico analysis of the interaction of the tested peptides with molecular targets for reference antibiotics was also carried out in order to verify whether or not they can act in a similar way. The P1 peptide manifested the growth inhibition of E. faecalis at a MIC
50 of 32 µg/mL and the P3 peptide at a MIC50 of 32 µg/mL was shown to inhibit the growth of both E. faecalis and S. aureus . Furthermore, the P1 and P3 peptides were shown to have no cytotoxic or haemolytic activity against human cells.- Published
- 2023
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31. Skin Microbiome in Prurigo Nodularis.
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Tutka K, Żychowska M, Żaczek A, Maternia-Dudzik K, Pawełczyk J, Strapagiel D, Lach J, and Reich A
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- Humans, RNA, Ribosomal, 16S genetics, Skin microbiology, Pruritus, Staphylococcus genetics, Prurigo, Microbiota genetics, Dermatitis, Atopic microbiology
- Abstract
Prurigo nodularis (PN) is a chronic condition characterized by the presence of nodular lesions accompanied by intense pruritus. The disease has been linked to several infectious factors, but data on the direct presence of microorganisms in the lesions of PN are scarce. The aim of this study was to evaluate the diversity and composition of the bacterial microbiome in PN lesions by targeting the region V3-V4 of 16S rRNA. Skin swabs were obtained from active nodules in 24 patients with PN, inflammatory patches of 14 patients with atopic dermatitis (AD) and corresponding skin areas of 9 healthy volunteers (HV). After DNA extraction, the V3-V4 region of the bacterial 16S rRNA gene was amplified. Sequencing was performed using the Illumina platform on the MiSeq instrument. Operational taxonomic units (OTU) were identified. The identification of taxa was carried out using the Silva v.138 database. There was no statistically significant difference in the alpha-diversity (intra-sample diversity) between the PN, AD and HV groups. The beta-diversity (inter-sample diversity) showed statistically significant differences between the three groups on a global level and in paired analyses. Staphylococcus was significantly more abundant in samples from PN and AD patients than in controls. The difference was maintained across all taxonomic levels. The PN microbiome is highly similar to that of AD. It remains unclear whether the disturbed composition of the microbiome and the domination of Staphylococcus in PN lesions may be the trigger factor of pruritus and lead to the development of cutaneous changes or is a secondary phenomenon. Our preliminary results support the theory that the composition of the skin microbiome in PN is altered and justify further research on the role of the microbiome in this debilitating condition.
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- 2023
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32. Draft genomes of halophilic Archaea strains isolated from brines of the Carpathian Foreland, Poland.
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Lach J, Strapagiel D, Matera-Witkiewicz A, and Stączek P
- Abstract
Halophilic Archaea are a unique group of microorganisms living in saline environments. They constitute a complex group whose biodiversity has not been thoroughly studied. Here, we report three draft genomes of halophilic Archaea isolated from brines, representing the genera of Halorubrum , Halopenitus, and Haloarcula . Two of these strains, Boch-26 and POP-27, were identified as members of the genera Halorubrum and Halopenitus , respectively. However, they could not be assigned to any known species because of the excessive difference in genome sequences between these strains and any other described genomes. In contrast, the third strain, Boch-26, was identified as Haloarcula hispanica . Genome lengths of these isolates ranged from 2.7 Mbp to 3.0 Mbp, and GC content was in the 63.77%-68.77% range. Moreover, functional analysis revealed biosynthetic gene clusters (BGCs) related to terpenes production in all analysed genomes and one BGC for RRE (RiPP recognition element)-dependent RiPP (post-translationally modified peptides) biosynthesis. Moreover, the obtained results enhanced the knowledge about the salt mines microbiota biodiversity as a poorly explored environment so far., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)
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- 2023
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33. A first insight into the Polish Bochnia Salt Mine metagenome.
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Lach J, Królikowska K, Baranowska M, Krupińska M, Strapagiel D, Matera-Witkiewicz A, and Stączek P
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- Humans, Poland, RNA, Ribosomal, 16S genetics, Bacteria genetics, Sodium Chloride, Dietary, Pharmaceutical Preparations, Metagenomics, Metagenome, Sodium Chloride
- Abstract
The Bochnia Salt Mine is one of the oldest mines in Europe. It was established in the thirteenth century, and actively operated until 1990. The mine has been placed on the UNESCO World Heritage List. Previous research describing Polish salt mines has been focused on bioaerosol characteristics and the identification of microorganisms potentially important for human health. The use of Polish salt mines as inhalation chambers for patients of health resorts has also been investigated. Nevertheless, the biodiversity of salt mines associated with biotechnological potential has not been well characterized. The present study paper examines the biodiversity of microorganisms in the Bochnia Salt Mine based on 16S rRNA gene and shotgun sequencing. Biodiversity studies revealed a significantly higher relative abundance of Chlamydiae at the first level of the mine (3.5%) compared to the other levels (< 0.1%). Patescibacteria microorganisms constituted a high percentage (21.6%) in the sample from site RA6. Shotgun sequencing identified 16 unique metagenome-assembled genomes (MAGs). Although one was identified as Halobacterium bonnevillei, the others have not yet been assigned to any species; it is possible that these species may be undescribed. Preliminary analyses of the biotechnological and pharmaceutical potential of microorganisms inhabiting the mine were also performed, and the biosynthetic gene cluster (BGC) profiles and antimicrobial peptide (AMP) coding genes in individual samples were characterized. Hundreds of BGCs and dozens of AMP coding genes were identified in metagenomes. Our findings indicate that Polish salt mines are promising sites for further research aimed at identifying microorganisms that are producers of potentially important substances with biotechnological and pharmaceutical applications., (© 2023. The Author(s).)
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- 2023
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34. Effect of an Intranasal Corticosteroid on Quality of Life and Local Microbiome in Young Children With Chronic Rhinosinusitis: A Randomized Clinical Trial.
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Latek M, Lacwik P, Molinska K, Blauz A, Lach J, Rychlik B, Strapagiel D, Majak J, Molinska J, Czech D, Seweryn M, Kuna P, Palczynski C, and Majak P
- Subjects
- Adult, Child, Male, Humans, Female, Child, Preschool, Quality of Life, Sodium Chloride therapeutic use, Immunity, Innate, Lymphocytes, Adrenal Cortex Hormones therapeutic use, Chronic Disease, Treatment Outcome, Nasal Polyps drug therapy, Rhinitis drug therapy, Sinusitis drug therapy
- Abstract
Importance: Intranasal corticosteroids (INCs) remain the first-line treatment of chronic rhinosinusitis (CRS) in both adults and children, despite the lack of evidence regarding their efficacy in the pediatric population. Similarly, their effect on the sinonasal microbiome has not been well documented., Objective: To assess the clinical, immunological, and microbiological effects of 12 weeks of an INC in young children with CRS., Design, Setting, and Participants: This open-label randomized clinical trial was performed in a pediatric allergy outpatient clinic in 2017 and 2018. Children aged 4 to 8 years with CRS diagnosed by a specialist were included. Data were analyzed from January 2022 to June 2022., Interventions: Patients were randomized to receive intranasal mometasone in an atomizer for 12 weeks (1 application per nostril, once per day) and supplemental 3-mL sodium chloride (NaCl), 0.9%, solution in a nasal nebulizer once a day for 12 weeks (INC group) or 3-mL NaCl, 0.9%, solution in a nasal nebulizer once a day for 12 weeks (control group)., Main Outcomes and Measures: Measures taken both before and after treatment included the Sinus and Nasal Quality of Life Survey (SN-5), a nasopharynx swab for microbiome analysis by next-generation sequencing methods, and nasal mucosa sampling for occurrence of innate lymphoid cells (ILCs)., Results: Of the 66 children enrolled, 63 completed the study. The mean (SD) age of the cohort was 6.1 (1.3) years; 38 participants (60.3%) were male and 25 (39.7%) were female. The clinical improvement reflected by reduction in SN-5 score was significantly higher in the INC group compared with the control group (INC group score before and after treatment, 3.6 and 3.1, respectively; control group score before and after treatment, 3.4 and 3.8, respectively; mean between-group difference, -0.58; 95% CI, -1.31 to -0.19; P = .009). The INC group had a greater increase in nasopharyngeal microbiome richness and larger decrease in nasal ILC3 abundance compared with the control group. A significant interaction was observed between change in microbiome richness and the INC intervention on the prediction of significant clinical improvement (odds ratio, 1.09; 95% CI, 1.01-1.19; P = .03)., Conclusions and Relevance: This randomized clinical trial demonstrated that treatment with an INC improved the quality of life of children with CRS and had a significant effect on increasing sinonasal biodiversity. Although further investigation is needed of the long-term efficacy and safety of INCs, these data may reinforce the recommendation of using INCs as a first-line treatment of CRS in children., Trial Registration: ClinicalTrials.gov Identifier: NCT03011632.
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- 2023
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35. Assessment of the Potential Role of Selected Single Nucleotide Polymorphisms (SNPs) of Genes Related to the Functioning of Regulatory T Cells in the Pathogenesis of Psoriasis.
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Purzycka-Bohdan D, Nedoszytko B, Sobalska-Kwapis M, Zabłotna M, Żmijewski MA, Wierzbicka J, Gleń J, Strapagiel D, Szczerkowska-Dobosz A, and Nowicki RJ
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- Humans, T-Lymphocytes, Regulatory metabolism, Genetic Predisposition to Disease, RNA, Messenger, Case-Control Studies, Polymorphism, Single Nucleotide, Psoriasis genetics, Psoriasis metabolism
- Abstract
Recent studies have indicated a key role of the impaired suppressive capacity of regulatory T cells (Tregs) in psoriasis (PsO) pathogenesis. However, the genetic background of Treg dysfunctions remains unknown. The aim of this study was to evaluate the association of PsO development with selected single nucleotide polymorphisms (SNPs) of genes in which protein products play a significant role in the regulation of differentiation and function of Tregs. There were three study groups in our research and each consisted of different unrelated patients and controls: 192 PsO patients and 5605 healthy volunteers in the microarray genotyping group, 150 PsO patients and 173 controls in the ARMS-PCR method group, and 6 PsO patients and 6 healthy volunteers in the expression analysis group. The DNA microarrays analysis (283 SNPs of 57 genes) and ARMS-PCR method (8 SNPs in 7 genes) were used to determine the frequency of occurrence of SNPs in selected genes. The mRNA expression of selected genes was determined in skin samples. There were statistically significant differences in the allele frequencies of four SNPs in three genes ( TNF , IL12RB2 , and IL12B) between early-onset PsO patients and controls. The lowest p -value was observed for rs3093662 ( TNF ), and the G allele carriers had a 2.73 times higher risk of developing early-onset PsO. Moreover, the study revealed significant differences in the frequency of SNPs and their influence on PsO development between early- and late-onset PsO. Based on the ARMS-PCR method, the association between some polymorphisms of four genes ( IL4 , IL10 , TGFB1 , and STAT3 ) and the risk of developing PsO was noticed. Psoriatic lesions were characterized with a lower mRNA expression of FOXP3 , CTLA4 , and IL2 , and a higher expression of TNF and IL1A in comparison with unaffected skin. In conclusion, the genetic background associated with properly functioning Tregs seems to play a significant role in PsO pathogenesis and could have diagnostic value.
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- 2023
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36. Draft Genomes of Halophilic Chromohalobacter and Halomonas Strains Isolated from Brines of The Carpathian Foreland, Poland.
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Lach J, Strapagiel D, Matera-Witkiewicz A, and Stączek P
- Abstract
Chromohalobacter and Halomonas are genera of bacterial microorganisms belonging to the group of halophiles. They are characterized by high diversity and the ability to produce bioproducts of biotechnological importance, such as ectoine, biosurfactants and carotenoids. Here, we report three draft genomes of Chromohalobacter and two draft genomes of Halomonas isolated from brines. The length of the genomes ranged from 3.6 Mbp to 3.8 Mbp, and GC content was in the 60.11%-66.46% range. None of the analysed genomes has been assigned to any previously known species of the genus Chromohalobacter or Halomonas . Phylogenetic analysis revealed that Chromohalobacter 296-RDG and Chromohalobacter 48-RD10 belonged to the same species, and Chromohalobacter 11-W is more distantly related to the other two analysed strains than to Chromohalobacter canadensis . Halomonas strains 11-S5 and 25-S5 were clustered together and located close to Halomonas ventosae. Functional analysis revealed BGCs related to ectoine production in all genomes analysed. This study increases our overall understanding of halophilic bacteria and is also consistent with the notion that members of this group have significant potential as useful natural product producers., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)
- Published
- 2023
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37. The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions.
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Rahmioglu N, Mortlock S, Ghiasi M, Møller PL, Stefansdottir L, Galarneau G, Turman C, Danning R, Law MH, Sapkota Y, Christofidou P, Skarp S, Giri A, Banasik K, Krassowski M, Lepamets M, Marciniak B, Nõukas M, Perro D, Sliz E, Sobalska-Kwapis M, Thorleifsson G, Topbas-Selcuki NF, Vitonis A, Westergaard D, Arnadottir R, Burgdorf KS, Campbell A, Cheuk CSK, Clementi C, Cook J, De Vivo I, DiVasta A, Dorien O, Donoghue JF, Edwards T, Fontanillas P, Fung JN, Geirsson RT, Girling JE, Harkki P, Harris HR, Healey M, Heikinheimo O, Holdsworth-Carson S, Hostettler IC, Houlden H, Houshdaran S, Irwin JC, Jarvelin MR, Kamatani Y, Kennedy SH, Kepka E, Kettunen J, Kubo M, Kulig B, Kurra V, Laivuori H, Laufer MR, Lindgren CM, MacGregor S, Mangino M, Martin NG, Matalliotaki C, Matalliotakis M, Murray AD, Ndungu A, Nezhat C, Olsen CM, Opoku-Anane J, Padmanabhan S, Paranjpe M, Peters M, Polak G, Porteous DJ, Rabban J, Rexrode KM, Romanowicz H, Saare M, Saavalainen L, Schork AJ, Sen S, Shafrir AL, Siewierska-Górska A, Słomka M, Smith BH, Smolarz B, Szaflik T, Szyłło K, Takahashi A, Terry KL, Tomassetti C, Treloar SA, Vanhie A, Vincent K, Vo KC, Werring DJ, Zeggini E, Zervou MI, Adachi S, Buring JE, Ridker PM, D'Hooghe T, Goulielmos GN, Hapangama DK, Hayward C, Horne AW, Low SK, Martikainen H, Chasman DI, Rogers PAW, Saunders PT, Sirota M, Spector T, Strapagiel D, Tung JY, Whiteman DC, Giudice LC, Velez-Edwards DR, Uimari O, Kraft P, Salumets A, Nyholt DR, Mägi R, Stefansson K, Becker CM, Yurttas-Beim P, Steinthorsdottir V, Nyegaard M, Missmer SA, Montgomery GW, Morris AP, and Zondervan KT
- Subjects
- Female, Humans, Genetic Predisposition to Disease, Genome-Wide Association Study, Pain, Comorbidity, Endometriosis genetics, Endometriosis metabolism
- Abstract
Endometriosis is a common condition associated with debilitating pelvic pain and infertility. A genome-wide association study meta-analysis, including 60,674 cases and 701,926 controls of European and East Asian descent, identified 42 genome-wide significant loci comprising 49 distinct association signals. Effect sizes were largest for stage 3/4 disease, driven by ovarian endometriosis. Identified signals explained up to 5.01% of disease variance and regulated expression or methylation of genes in endometrium and blood, many of which were associated with pain perception/maintenance (SRP14/BMF, GDAP1, MLLT10, BSN and NGF). We observed significant genetic correlations between endometriosis and 11 pain conditions, including migraine, back and multisite chronic pain (MCP), as well as inflammatory conditions, including asthma and osteoarthritis. Multitrait genetic analyses identified substantial sharing of variants associated with endometriosis and MCP/migraine. Targeted investigations of genetically regulated mechanisms shared between endometriosis and other pain conditions are needed to aid the development of new treatments and facilitate early symptomatic intervention., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2023
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38. Fungal Planet description sheets: 1436-1477.
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Tan YP, Bishop-Hurley SL, Shivas RG, Cowan DA, Maggs-Kölling G, Maharachchikumbura SSN, Pinruan U, Bransgrove KL, De la Peña-Lastra S, Larsson E, Lebel T, Mahadevakumar S, Mateos A, Osieck ER, Rigueiro-Rodríguez A, Sommai S, Ajithkumar K, Akulov A, Anderson FE, Arenas F, Balashov S, Bañares Á, Berger DK, Bianchinotti MV, Bien S, Bilański P, Boxshall AG, Bradshaw M, Broadbridge J, Calaça FJS, Campos-Quiroz C, Carrasco-Fernández J, Castro JF, Chaimongkol S, Chandranayaka S, Chen Y, Comben D, Dearnaley JDW, Ferreira-Sá AS, Dhileepan K, Díaz ML, Divakar PK, Xavier-Santos S, Fernández-Bravo A, Gené J, Guard FE, Guerra M, Gunaseelan S, Houbraken J, Janik-Superson K, Jankowiak R, Jeppson M, Jurjević Ž, Kaliyaperumal M, Kelly LA, Kezo K, Khalid AN, Khamsuntorn P, Kidanemariam D, Kiran M, Lacey E, Langer GJ, López-Llorca LV, Luangsa-Ard JJ, Lueangjaroenkit P, Lumbsch HT, Maciá-Vicente JG, Mamatha Bhanu LS, Marney TS, Marqués-Gálvez JE, Morte A, Naseer A, Navarro-Ródenas A, Oyedele O, Peters S, Piskorski S, Quijada L, Ramírez GH, Raja K, Razzaq A, Rico VJ, Rodríguez A, Ruszkiewicz-Michalska M, Sánchez RM, Santelices C, Savitha AS, Serrano M, Leonardo-Silva L, Solheim H, Somrithipol S, Sreenivasa MY, Stępniewska H, Strapagiel D, Taylor T, Torres-Garcia D, Vauras J, Villarreal M, Visagie CM, Wołkowycki M, Yingkunchao W, Zapora E, Groenewald JZ, and Crous PW
- Abstract
Novel species of fungi described in this study include those from various countries as follows: Argentina , Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum . Australia , Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus , Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilaxglyciphylla . Brazil , Preussia bezerrensis from air. Chile , Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis . Finland , Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana . France , Myrmecridium normannianum on dead culm of unidentified Poaceae . Germany , Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior . India , Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan , and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum . Indonesia , Penicillium ezekielii from Zea mays kernels. Namibia , Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata , and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii . Netherlands , Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus . Pakistan , Inocybe longistipitata on soil in a Quercus forest. Poland , Phytophthora viadrina from rhizosphere soil of Quercus robur , and Septoria krystynae on leaf spots of Viscum album . Portugal (Azores) , Acrogenospora stellata on dead wood or bark. South Africa , Phyllactinia greyiae on leaves of Greyia sutherlandii and Punctelia anae on bark of Vachellia karroo . Spain , Anteaglonium lusitanicum on decaying wood of Prunus lusitanica subsp. lusitanica , Hawksworthiomyces riparius from fluvial sediments, Lophiostoma carabassense endophytic in roots of Limbarda crithmoides , and Tuber mohedanoi from calcareus soils. Spain (Canary Islands) , Mycena laurisilvae on stumps and woody debris. Sweden , Elaphomyces geminus from soil under Quercus robur . Thailand , Lactifluus chiangraiensis on soil under Pinus merkusii, Lactifluus nakhonphanomensis and Xerocomus sisongkhramensis on soil under Dipterocarpus trees. Ukraine , Valsonectria robiniae on dead twigs of Robinia hispida . USA , Spiralomyces americanus (incl. Spiralomyces gen. nov.) from office air. Morphological and culture characteristics are supported by DNA barcodes. Citation: Tan YP, Bishop-Hurley SL, Shivas RG, et al. 2022. Fungal Planet description sheets: 1436-1477. Persoonia 49: 261-350. https://doi.org/10.3767/persoonia.2022.49.08., (© 2022 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute.)
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- 2022
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39. Identified in blood diet-related methylation changes stratify liver biopsies of NAFLD patients according to fibrosis grade.
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Sokolowska KE, Maciejewska-Markiewicz D, Bińkowski J, Palma J, Taryma-Leśniak O, Kozlowska-Petriczko K, Borowski K, Baśkiewicz-Hałasa M, Hawryłkowicz V, Załęcka P, Ufnal M, Strapagiel D, Jarczak J, Skonieczna-Żydecka K, Ryterska K, Machaliński B, Wojdacz TK, and Stachowska E
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- Humans, DNA Methylation, Biopsy, Liver Cirrhosis genetics, Non-alcoholic Fatty Liver Disease genetics, Diet, Mediterranean
- Abstract
Background: High caloric diet and lack of physical activity are considered main causes of NAFLD, and a change in the diet is still the only effective treatment of this disease. However, molecular mechanism of the effectiveness of diet change in treatment of NAFLD is poorly understood. We aimed to assess the involvement of epigenetic mechanisms of gene expression regulation in treatment of NAFLD. Eighteen participants with medium- to high-grade steatosis were recruited and trained to follow the Mediterranean diet modified to include fibre supplements. At three timepoints (baseline, after 30 and 60 days), we evaluated adherence to the diet and measured a number of physiological parameters such as anthropometry, blood and stool biochemistry, liver steatosis and stiffness. We also collected whole blood samples for genome-wide methylation profiling and histone acetylation assessment., Results: The diet change resulted in a decrease in liver steatosis along with statistically significant, but a minor change in BMI and weight of our study participants. The epigenetic profiling of blood cells identified significant genome-wide changes of methylation and acetylation with the former not involving regions directly regulating gene expression. Most importantly, we were able to show that identified blood methylation changes occur also in liver cells of NAFLD patients and the machine learning-based classifier that we build on those methylation changes was able to predict the stage of liver fibrosis with ROC AUC = 0.9834., Conclusion: Methylomes of blood cells from NAFLD patients display a number of changes that are most likely a consequence of unhealthy diet, and the diet change appears to reverse those epigenetic changes. Moreover, the methylation status at CpG sites undergoing diet-related methylation change in blood cells stratifies liver biopsies from NAFLD patients according to fibrosis grade., (© 2022. The Author(s).)
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- 2022
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40. Association studies between chromosomal regions 1q21.3, 5q21.3, 14q21.2 and 17q21.31 and numbers of children in Poland.
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Clark JSC, van de Wetering T, Marciniak B, Żądzińska E, Ciechanowicz A, Kaczmarczyk M, Boroń A, Rydzewska K, Posiadło K, and Strapagiel D
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- Female, Child, Humans, Male, Poland, Case-Control Studies, Genotype, Phenotype, Polymorphism, Single Nucleotide, Genetic Predisposition to Disease
- Abstract
Number of children is an important human trait and studies have indicated associations with single-nucleotide polymorphisms (SNPs). Aim: to give further evidence for four associations using a large sample of Polish subjects. Data from the POPULOUS genetic database was provided from anonymous, healthy, unrelated, Polish volunteers of both sexes (N = 5760). SNPs (n = 173) studied: (a) 69 from the chromosome 17 H1/H2 inversion; (b) six from 1q21.3, 5q21.3 and 14q21.2; and (c) 98 random negative controls. Zero-inflated negative-binomial regression (z.i.) was performed (0-3 numbers of children per individual (NCI) set as non-events; adjustors: year of birth, sex). Significance level p = 0.05 with Bonferroni correction. Statistically-significant differences (with data from both sexes combined) were obtained from highly-linked inversion SNPs: representative rs12373123 gave means: homozygotes TT: 2.31 NCI (n = 1418); heterozygotes CT: 2.35 NCI (n = 554); homozygotes CC: 2.44 NCI (n = 43) (genotype p = 0.01; TTvs.CC p = 0.004; CTvs.CC p = 0.009). (Male data alone gave similar results.) Recessive modeling indicated that H2-homozygotes had 0.118 more children than H1-homozygotes + heterozygotes (z.i.-count estimates ± standard errors: CT, - 0.508 ± 0.194; TT, - 0.557 ± 0.191). The non-over-dispersed count model detected no interactions: of importance there was no significant interaction with age. No positive results were obtained from negative-control SNPs or (b). Conclusions: association between the H1/H2 inversion and numbers of children (previously reported in Iceland) has been confirmed, albeit using a different statistical model. One limitation is the small amount of data, despite initially ~ 6000 subjects. Causal studies require further investigation., (© 2022. The Author(s).)
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- 2022
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41. Epigenetic activation of antiviral sensors and effectors of interferon response pathways during SARS-CoV-2 infection.
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Bińkowski J, Taryma-Leśniak O, Łuczkowska K, Niedzwiedź A, Lechowicz K, Strapagiel D, Jarczak J, Davalos V, Pujol A, Esteller M, Kotfis K, Machaliński B, Parczewski M, and Wojdacz TK
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- Biomarkers, Epigenesis, Genetic, Humans, Interferons genetics, Interferons immunology, SARS-CoV-2, COVID-19 genetics, COVID-19 immunology
- Abstract
Recent studies have shown that methylation changes identified in blood cells of COVID-19 patients have a potential to be used as biomarkers of SARS-CoV-2 infection outcomes. However, different studies have reported different subsets of epigenetic lesions that stratify patients according to the severity of infection symptoms, and more importantly, the significance of those epigenetic changes in the pathology of the infection is still not clear. We used methylomics and transcriptomics data from the largest so far cohort of COVID-19 patients from four geographically distant populations, to identify casual interactions of blood cells' methylome in pathology of the COVID-19 disease. We identified a subset of methylation changes that is uniformly present in all COVID-19 patients regardless of symptoms. Those changes are not present in patients suffering from upper respiratory tract infections with symptoms similar to COVID-19. Most importantly, the identified epigenetic changes affect the expression of genes involved in interferon response pathways and the expression of those genes differs between patients admitted to intensive care units and only hospitalized. In conclusion, the DNA methylation changes involved in pathophysiology of SARS-CoV-2 infection, which are specific to COVID-19 patients, can not only be utilized as biomarkers in the disease management but also present a potential treatment target., Competing Interests: Conflict of interest statement Manel Esteller is an advisor of Quimatryx and Ferrer International. The remaining authors declare no conflict of interest., (Copyright © 2022 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)
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- 2022
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42. Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells.
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Łuczkowska K, Taryma-Leśniak O, Bińkowski J, Sokołowska KE, Strapagiel D, Jarczak J, Paczkowska E, Machaliński B, and Wojdacz TK
- Abstract
Bortezomib (BTZ) is proteasome inhibitor, effectively used in the treatment of multiple myeloma, but frequently discontinued due to peripheral neuropathy, which develops in patients after consecutive treatment cycles. The molecular mechanisms affected by BTZ in neuronal cells, which result in neuropathy, remain unknown. However, BTZ is unlikely to lead to permanent morphological nerve damage, because neuropathy reverses after discontinuation of treatment, and nerve cells have very limited renewal capacity. We have previously shown that BTZ induces methylation changes in SH-SY5Y cells, which take part in the development of treatment resistance. Here, we hypothesized that BTZ affects the methylomes of mature neurons, and these changes are associated with BTZ neurotoxicity. Thus, we studied methylomes of neuronal cells, differentiated from the LUHMES cell line, after cycles of treatment with BTZ. Our results show that BTZ induces specific methylation changes in mature neurons, which are not present in SH-SY5Y cells after BTZ treatment. These changes appear to affect genes involved in morphogenesis, neurogenesis, and neurotransmission. Furthermore, identified methylation changes are significantly enriched within binding sites of transcription factors previously linked to neuron physiology, including EBF, PAX, DLX, LHX, and HNF family members. Altogether, our results indicate that methylation changes are likely to be involved in BTZ neurotoxicity.
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- 2022
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43. The Analysis of a Genome-Wide Association Study (GWAS) of Overweight and Obesity in Psoriasis.
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Kisielnicka A, Sobalska-Kwapis M, Purzycka-Bohdan D, Nedoszytko B, Zabłotna M, Seweryn M, Strapagiel D, Nowicki RJ, Reich A, Samotij D, Szczęch J, Krasowska D, Bartosińska J, Narbutt J, Lesiak A, Barasińska P, Owczarczyk-Saczonek A, Czerwińska J, Szepietowski JC, Batycka-Baran A, Czajkowski R, Górecka-Sokołowska M, Rudnicka L, Czuwara J, and Szczerkowska-Dobosz A
- Subjects
- Adaptor Proteins, Signal Transducing genetics, Alpha-Ketoglutarate-Dependent Dioxygenase FTO genetics, Body Mass Index, Genetic Predisposition to Disease, Genotype, Humans, Lectins genetics, Membrane Proteins genetics, Obesity genetics, Overweight genetics, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Psoriasis genetics
- Abstract
There is evidence that the concomitance of psoriasis and obesity may originate from the interplay between multiple genetic pathways and involve gene−gene interactions. The aim of this study was to compare the genetic background related to obesity among psoriatic patients versus healthy controls by means of a Genome-Wide Association Study (GWAS). A total of 972 psoriatic patients and a total of 5878 healthy donors were enrolled in this study. DNA samples were genotyped for over 500,000 single nucleotide polymorphisms (SNPs) using Infinium CoreExome BeadChips (Illumina, San Diego, CA, USA). Statistical analysis identified eleven signals (p < 1 × 10−5) associated with BMI across the study groups and revealed a varying effect size in each sub-cohort. Seven of the alternative alleles (rs1558902 in the FTO gene, rs696574 in the CALCRL gene, as well as rs10968110, rs4551082, rs4609724, rs9320269, and rs2338833,) are associated with increased BMI among all psoriatic patients and four (rs1556519 in the ITLN2 gene, rs12972098 in the AC003006.7 gene, rs12676670 in the PAG1 gene, and rs1321529) are associated with lower BMI. The results of our study may lead to further insights into the understanding of the pathogenesis of obesity among psoriatic patients.
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- 2022
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44. Chronic Plaque Psoriasis in Poland: Disease Severity, Prevalence of Comorbidities, and Quality of Life.
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Purzycka-Bohdan D, Kisielnicka A, Zabłotna M, Nedoszytko B, Nowicki RJ, Reich A, Samotij D, Szczęch J, Krasowska D, Bartosińska J, Narbutt J, Lesiak A, Barasińska P, Owczarczyk-Saczonek A, Czerwińska J, Szepietowski JC, Batycka-Baran A, Czajkowski R, Górecka-Sokołowska M, Rudnicka L, Czuwara J, Sobalska-Kwapis M, Strapagiel D, and Szczerkowska-Dobosz A
- Abstract
The epidemiology of psoriasis has not been widely assessed in Polish population so far. This study aimed to investigate psoriasis epidemiological situation by evaluating disease course and severity, management, comorbidities, environmental factors, and knowledge about this disorder among psoriatic patients in Poland. A cross-sectional cohort population-based study enrolled 1080 psoriatic patients and 1200 controls. The mean age of psoriasis onset was 27.6 years; 78.24% had type I psoriasis. Positive family history of psoriasis was reported in 44.81% of patients, whereas itch was reported in vast majority of patients (83.33%). Based on PASI score moderate psoriasis was the most common in studied group (mean 12.63 ± 9.33, range 0−67.2). The DLQI score (12.01 ± 7.41, range 0−30.0) indicated a very large effect of psoriasis on the quality of life. Hypertension was the most prevalent comorbidity (33.80%), followed by obesity (16.85%) and dyslipidemia (11.85%). Stress was the foremost cause of disease exacerbation (66.20%); however, infections (44.07%) and seasonal changes (45.09%) had also an impact on the course of psoriasis. Psoriatic patients were more often smokers (37.59%) vs. general population (27.50%; p < 0.0001). In conclusion, epidemiological studies help clinicians in better disease and patient understanding, which may translate into better management and patient compliance.
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- 2022
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45. House dust mite sensitization and frequent antibiotic courses may suppress remission of rhinosinusitis and asthma symptoms in young children.
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Molińska K, Latek M, Rychlik B, Lach J, Strapagiel D, Majak J, Błażowski Ł, Jerzyńska J, Kuna P, and Majak P
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- Allergens, Animals, Anti-Bacterial Agents therapeutic use, Antigens, Dermatophagoides, Child, Child, Preschool, Dermatophagoides pteronyssinus, Dust, Humans, Pyroglyphidae, Asthma diagnosis, Asthma drug therapy, Asthma etiology, Mites
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- 2022
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46. DNA methylation profile in patients with indolent systemic mastocytosis.
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Górska A, Jabłońska E, Reszka E, Niedoszytko M, Lange M, Gruchała-Niedoszytko M, Jarczak J, Strapagiel D, Górska-Ponikowska M, Bastian P, Pelikant-Małecka I, Kalinowski L, and Nedoszytko B
- Abstract
Background: Mastocytosis is a clinically heterogeneous, usually acquired disease of the mast cells with a survival time that depends on the onset of the disease and ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The crucial element in pathogenesis is the presence of oncogenic KIT somatic mutation D816V. Further epigenetic alterations are responsible for regulating the expression of genes. It is essential to identify indicators of disease progression, and the specific clinical picture to establish an appropriate therapeutic strategy., Objective: The aim of this study was to analyze the relation of mastocytosis symptoms and epigenetic changes, and to identify epigenetic predictors of the disease., Methods: Global DNA methylation profile analysis was performed in peripheral blood collected from 73 patients with indolent systemic mastocytosis (ISM) and 43 healthy adult volunteers. Levels of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) were determined using an ELISA-based method, while the methylation of the Alu and LINE-1 repeats were assayed with the quantitative methylation-specific PCR technique. A questionnaire interview was conducted among the study participants to collect data on possible epigenetic modifiers. Additionally, the methylation profile was compared between three human mast cell lines: ROSA KIT D816V, ROSA KIT WT, and HMC-1.1 KIT V560G, in order to assess the association between KIT mutations and methylation profile., Results: A significantly lower level of DNA hydroxymethylation (5-hmC) in the blood was found in patients with ISM as compared to the controls (0.022% vs. 0.042%, p = 0.0001). Differences in the markers of global DNA methylation (5-mC, Alu, LINE-1) were not statistically significant, although they did indicate generally higher DNA methylation in patients with mastocytosis. The 5-hmC level was significantly associated with allergy ( p = 0.011) in patients with ISM, showing a higher level of 5-hmC in patients with allergy as compared to patients without allergy. The in vitro study revealed significant differences between the studied cell lines at the level of 5-mC, Alu, and LINE-1., Conclusions: This study confirms that epigenetic changes are involved in mastocytosis, and suggests that allergy may be an important epigenetic modifier of the disease. A possible association between KIT mutations and methylation status observed in human mast cell lines requires further investigation in human studies., Clinical Implications: Epigenetic alterations are involved in mastocytosis pathology. The possible role of allergy as an important epigenetic modifier suggests the more impaired function of mast cells in ISM patients without allergy., Capsule Summary: Decreased DNA demethylation in the blood DNA of patients with ISM confirms that epigenetic alterations are involved in mastocytosis pathology. We observed a possible role of allergy as an important epigenetic modifier. There is a possible association between KIT mutations and the methylation status observed in human mast cell lines., Competing Interests: The funder of the study had neither a role in the design of the study, the collection, analysis, and interpretation of the data, nor in writing the manuscript. The corresponding author had full access to the results of the study and to the ECNM dataset. The corresponding author has final responsibility for all data and the content of the paper, and for the decision to submit it for publication. The corresponding author declare no conflict of interest regarding this publication., (© 2021 The Authors. Clinical and Translational Allergy published by John Wiley & Sons Ltd on behalf of European Academy of Allergy and Clinical Immunology.)
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- 2021
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47. The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools.
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Lach J, Jęcz P, Strapagiel D, Matera-Witkiewicz A, and Stączek P
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- Archaea metabolism, Bacteria metabolism, Computational Biology, Data Mining, Genome, Archaeal, Genome, Bacterial, Salt Tolerance, Archaea genetics, Bacteria genetics, Biological Products analysis, Sequence Analysis, DNA methods
- Abstract
Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.
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- 2021
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48. The Role of Lysine-Specific Demethylase 1 (LSD1) in Shaping the Endothelial Inflammatory Response.
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Wojtala M, Rybaczek D, Wielgus E, Sobalska-Kwapis M, Strapagiel D, and Balcerczyk A
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- Cell Line, Histone Demethylases genetics, Humans, Inflammation genetics, NF-kappa B metabolism, RNA Interference, Signal Transduction, Endothelial Cells metabolism, Histone Demethylases metabolism, Inflammation metabolism
- Abstract
Background/aims: Inflammation is the body's natural response to stress in the broadest sense. The regulatory mechanisms that control this process, some of which are still unclear, are needed to balance the immune response, but also when insufficient, can cause immunodeficiency resulting in infection, cancer, neurodegeneration or other serious disorders. In this study, we focused on defining the role of lysine-specific demethylase 1 (LSD1), an enzyme involved in modulating the methylation state of lysine, including histone and non-histone proteins, in shaping the inflammatory profile of endothelial cells., Methods: To determine the role of LSD1 in the inflammatory response of ECs, cells were stimulated with lipopolysaccharide (100 ng/ml LPS) in the presence and absence of an LSD1 inhibitor (2-PCPA). A transcription model of LSD1 deficient cells (HMEC-1 LSD1 KD) obtained by lentiviral shRNA transduction was also used. The indicated cellular models were analyzed by gene profiling, monitoring of p65 shuttling by Western blotting and immunofluorescence staining. Also chromatin immunoprecipitation (ChIP) was performed to identify the interactions between selected: IL-6/p65 and LSD1., Results: Analysis of both experimental models revealed an altered inflammatory response following both LSD1 inhibition and LSD1 silencing. We observed decreased U-937 monocytes recruitment to LPS-activated endothelial cells and decreased extracellular secretion of many proinflammatory cytokines, also confirmed at the transcript level by RT-qPCR. Monitoring of the LPS-induced p65 translocation revealed inhibition of the NF-kB subunit in LSD1 KD vs nonT as well as due to pretreatment of 2-PCPA cells. Gene profiling performed with RNA microarrays confirmed the obtained biochemical data at the transcript level., Conclusion: In conclusion, the conducted studies showed a proinflammatory profile of LSD1 activity in endothelial cells, revealed by the inhibition of the enzyme activity and confirmed at the transcriptional level by the inhibition of its expression. Although we found significant changes in the modification of interactions between monocytes and endothelial cells as well as in cytokine/chemokine release and expression that were consistent with the altered NF-κB-p65 translocation into the nucleus, we did not identify a direct interaction between LSD1 and the transcription factor. Our finding may have important implications for prevention of cardiovascular diseases at their first stage - activation of the endothelium as well as for tumor cell biology, providing evidence for the use of LSD1 inhibitors to reduce the inflammatory response, which enhances tumor tissue remodeling, angiogenesis and metastasis., Competing Interests: The authors have no conflicts of interest to declare., (© Copyright by the Author(s). Published by Cell Physiol Biochem Press.)
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- 2021
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49. Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe.
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Mamos T, Grabowski M, Rewicz T, Bojko J, Strapagiel D, and Burzyński A
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- Animals, Ecosystem, Europe, Genetic Markers genetics, Genetics, Population methods, Introduced Species, Microsatellite Repeats genetics, Phylogeny, Phylogeography, Amphipoda genetics, Genome, Mitochondrial genetics, Polymorphism, Single Nucleotide genetics
- Abstract
The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. However, genomic knowledge about these invaders is scarce, while phylogeography and population genetics have been based on short fragments of mitochondrial markers or nuclear microsatellites. In this study, we provide: (i) a reconstruction of six mitogenomes for four invasive gammarids ( D. villosus , D. haemobaphes , D. bispinosus , and P. robustoides ); (ii) a comparison between the structure of the newly obtained mitogenomes and those from the literature; (iii) SNP calling rates for individual D. villosus and D. haemobaphes from different invasion sites across Europe; and (iv) the first time-calibrated full mitogenome phylogeny reconstruction of several Ponto-Caspian taxa. We found that, in comparison to other gammarids, the mitogenomes of Ponto-Caspian species show a translocation between the tRNA-E and tRNA-R positions. Phylogenetic reconstruction using the mitogenomes identified that Ponto-Caspian gammarids form a well-supported group that originated in the Miocene. Our study supports paraphyly in the family Gammaridae. These provided mitogenomes will serve as vital genetic resources for the development of new markers for PCR-based identification methods and demographic studies.
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- 2021
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50. Cortisol concentration affects fat and muscle mass among Polish children aged 6-13 years.
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Pruszkowska-Przybylska P, Sitek A, Rosset I, Sobalska-Kwapis M, Słomka M, Strapagiel D, Żądzińska E, and Morling N
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- Body Mass Index, Child, Female, Humans, Muscles, Poland, Pregnancy, Body Composition, Hydrocortisone
- Abstract
Background: Cortisol is a steroid hormone acting as a stress hormone, which is crucial in regulating homeostasis. Previous studies have linked cortisol concentration to body mass and body composition., Methods: The investigations were carried out in 2016-2017. A total of 176 children aged 6-13 years in primary schools in central Poland were investigated. Three types of measurements were performed: anthropometric (body weight and height, waist and hip circumferences), body composition (fat mass FM (%), muscle mass - MM (%), body cellular mass - BCM (%), total body water - TBW (%)), and cortisol concentration using saliva of the investigated individuals. Information about standard of living, type of feeding after birth, parental education and maternal trauma during pregnancy was obtained with questionnaires., Results: The results of regression models after removing the environmental factors (parental education, standard of living, type of feeding after birth, and maternal trauma during pregnancy) indicate a statistically significant association between the cortisol concentration and fat mass and muscle mass. The cortisol concentration was negatively associated with FM (%) (Beta=-0.171; p = 0.026), explaining 2.32 % of the fat mass variability and positively associated with MM (%) (Beta = 0.192; p = 0.012) explaining 3.09 % of the muscle mass variability., Conclusions: Cortisol concentration affects fat and muscle mass among Polish children., Trial Registration: The Ethical Commission at the University of Lodz (nr 19/KBBN-UŁ/II/2016)., (© 2021. The Author(s).)
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- 2021
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