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Alimetrics employees’ scientific contributions:Articles in peer-reviewed journals
1. Apajalahti JH, Rademacher M, Htoo JK, Redshaw M, Kettunen A (2009) Divergent modulation of swine ileal microbiota by formic acid and methionine hydroxyl analogue-free acid. Animal. 2009 3:817-25. pdf
2. Grönberg H, Hietala AM, Haahtela K. (2009) Analysing Scots pine defence-related transcripts and fungal DNA levels in seedlings single- or dual-inoculated with endophytic and pathogenic Rhizoctonia species. Forest Pathology 39:377-389.
3. Kassinen A, Rinttilä T, Nikkilä J, Krogius-Kurikka L, Kajander K, Malinen E, Mättö J, Mäkelä L, Palva A (2009) Diarrhoea-predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification. World Journal of Gastroenterology 15(47):5936-5945.
4. Rodríguez-Minguela CM, Apajalahti JH, Chai B, Cole JR, Tiedje JM. (2009) Worldwide Prevalence Patterns of Class 2 Integrases outside the Clinical Setting Relates to Human Impact. Appl Environ Microbiol. 2009 Jun 5
5. Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK (2009) Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009 Feb;3(2):179-89.
6. Vaara M, Fox J, Loidl G, Siikanen O, Apajalahti J, Hansen F, Frimodt-Møller N, Nagai J, Takano M, Vaara T (2008) Novel polymyxin derivatives carrying only three positive charges are effective antibacterial agents. Antimicrob Agents Chemother. 2008 Sep;52(9):3229-36.
7. Dicksved J, Halfvarson J, Rosenquist M, Järnerot G, Tysk C, Apajalahti J, Engstrand L, Jansson JK (2008) Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J. 2008 Jul;2(7):716-27.
8. Abbas Hilmi HT, Surakka A, Apajalahti J, Saris PE (2007) Identification of the most abundant lactobacillus species in the crop of 1- and 5-week-old broiler chickens. Appl Environ Microbiol. 2007 Dec;73(24):7867-73.
9. Kassinen A, Krogius-Kurikka L, Mäkivuokko H, Rinttilä T, Paulin L, Corander J, Malinen E, Apajalahti J, Palva A (2007) The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology. 2007 Jul;133(1):24-33.
10. Kajander K, Krogius-Kurikka L, Rinttilä T, Karjalainen H, Palva A, Korpela R (2007) Effects of multispecies probiotic supplementation on intestinal microbiota in irritable bowel syndrome. Aliment Pharmacol Ther. 26(3):463-73.
11. Mäkivuokko H, Kettunen H, Saarinen, M, Kamiwaki T, Yokoyama Y, Stowell J and Rautonen N (2007) The Effect of Cocoa and Polydextrose on Bacterial Fermentation in Gastrointestinal Tract Simulations. Biosci. Biotechnol. Biochem. 71:1834-1843
12. Ojanperä S, Tuominen S, Ojanperä I (2007) Single-calibrant quantification of drugs in plasma and whole blood by liquid chromatography-chemiluminescence nitrogen detection, J.Chrom. B 856: 293.
13. Ojanperä S, Rasanen I, Sistonen J, Pelander A, Vuori E, Ojanperä I (2007) Quantification of drugs in plasma without primary reference standards by liquid chromatographychemiluminescence nitrogen detection: application to tramadol metabolite ratios, Ther. Drug Monit. 29; 423.
14. Parker J, Oviedo-Rondon EO, Clack BA, Clemente-Hernandez S, Osborne J, Remus JC, Kettunen H, Makivuokko H, Pierson EM (2007) Enzymes as feed additive to aid in responses against Eimeria species in coccidia-vaccinated broilers fed corn-soybean meal diets with different protein levels. Poult Sci. 86:643-653
15. Grönberg H, Kaparakis G, Sen, R (2006) Binucleate Rhizoctonia (Ceratorhiza spp.) as non-mycorrhizal endophytes alter Pinus sylvestris L. seedling root architecture and affect growth of rooted cuttings. Scandinavian Journal of Forest Research. 2006 21:450-57.
16. Ojanperä S, Pelander A, Pelzing M, Krebs I, Vuori E, Ojanperä I (2006). Isotopic pattern and accurate mass determination in urine drug screening by liquid chromatography/time-offlight mass spectrometry, Rapid Commun. Mass Spectrom. 20: 1161.
17. Apajalahti J (2005) Comparative gut microflora, metabolic challenges and potential opportunities. J. Appl. Poult. Res. 14:444-453
18. Malinen E, Rinttilä T, Kajander K, Mättö J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A (2005) Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. American Journal of Gastroenterology. 100:373-382.
19. Ojanperä I, Pelander A, Laks S, Gergov M, Vuori E, Witt M (2005) Application of accurate mass measurement to urine drug screening, J. Anal. Toxicol. 29: 34.
20. Ojanperä S, Ojanperä I (2005). Forensic drug screening by LC/MS utilising accurate mass measurement, LC-GC Europe 2005; 18: 607.
21. Probert HM, Apajalahti JHA, Rautonen N, Stowell J, Gibson GR (2004) Polydextrose, lactitol, and fructo-oligosaccharide fermentation by colonic bacteria in a three-stage continuous culture system. Appl. Environ. Microbiol. 70:4505-4511
22. Rinttilä T, Kassinen A, Malinen E, Krogius L, Palva A (2004) Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in fecal samples by real-time PCR. Journal of Applied Microbiology. 97:1166-1177.
23. Apajalahti J, Kettunen A, Graham H (2004) Characteristics of the gastrointestinal microbial communities, with special reference to the chicken. World’s Poultry Science Journal 60:223-232
24. Holben WE, Feris KP, Kettunen A, Apajalahti JHA (2004) GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 70:2263-2270
25. Beasley SS, Takala TM, Reunanen J, Apajalahti J, Saris PE (2004) Characterization and electrotransformation of Lactobacillus crispatus isolated from chicken crop and intestine. Poult. Sci. 83:45-48
26. Laks S, Pelander A, Vuori E, Ali-Tolppa E, Sippola E, Ojanperä I (2004) Analysis of street drugs in seized material without primary reference standards, Anal. Chem. 76:7375.
27. Peuranen S, Tiihonen K, Apajalahti J, Kettunen A, Saarinen M, Rautonen N (2004) Combination of polydextrose and lactitol affects microbial ecosystem and immune responses in rat gastrointestinal tract. Br J. Nutr. 91: 1-11
28. Grönberg H, Paulin L, Sen R (2003) ITS probe development for specific detection of Rhizoctonia spp. and Suillus bovinus based on Southern blot and liquid hybridization-fragment length polymorphism. Mycol Res. 2003 Apr;107(Pt 4):428-38.
29. Apajalahti JHA, Kettunen A, Nurminen PH, Jatila H, Holben WE (2003) Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces. Appl. Environ. Microbiol. 69:5731-5735
30. Edelman S, Leskelä S, Ron E, Apajalahti J, Korhonen TK (2003) In-vitro adhesion of an avian pathogenic Escherichia coli O78 strain to surfaces of the chicken intestinal tract and to ileal mucus. Vet. Microbiol. 91:41-56
31. Kettunen A (2003) Connecting methane fluxes to vegetation cover and water table fluctuations at microsite level: a modelling study. Global Biogeochemical Cycles 17 (2):
32. Malinen E, Kassinen A, Rinttilä T (2003) Comparison of real-time PCR with SYBR Green I or 5´-nuclease assay and dot-blot hybridisation with rDNA targeted oligonucleotide probes in quantitation of selected faecal bacteria. Microbiology UK. 149:269-277.
33. Kettunen H, Kettunen A, Rautonen N (2003) Intestinal Immune Responses in Wild-Type and ApcMin/+ Mouse, a Model for Colon Cancer. Cancer Res. 63: 5136-5142
34. Sohail SS, Bryant MM, Roland DA, Apajalahti JHA, Pierson EEM (2003) Influence of Avizyme 1500 on performance of commercial leghorns. J. Appl. Poult. Res. 12:284-290
35. Wallace RJ, McKain N, McEwan NR, Miyagawa E, Chaudhary L, King TP, Walker ND, Apajalahti JHA, Newbold CJ (2003) Eubacterium pyruvativorans sp. nov., a novel non-saccharolytic anaerobe from the rumen that ferments pyruvate and amino acids, forms caproate and utilizes acetate and propionate. Int. J. Syst. Evol. Microbiol. 53:965-970
36. Pelander A, Ojanperä I, Laks S, Rasanen I, Vuori E (2003) Toxicological screening with formula-based metabolite identification by liquid chromatography/time-of-flight mass spectrometry, Anal. Chem. 75: 5710.
37. Apajalahti JHA, Kettunen H, Kettunen A, Holben WE, Nurminen PH, Rautonen N, Mutanen M (2002) Culture-independent microbial community analysis reveals that inulin in the diet primarily affects previously unknown bacteria in the mouse caecum. Appl. Environ. Microbiol. 68:4986-4995
38. Edelman S, Westerlund-Wikström B, Leskelä S, Kettunen H, Rautonen N, Apajalahti J, Korhonen TK (2002) In vitro adhesion specificity of indigenous lactobacilli within the avain intestinal tract. Appl. Environ. Microbiol. 68:5155-5159
39. Holben WE, Williams P, Gilbert, MA, Saarinen M, Särkilahti LK, Apajalahti JHA (2002) Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon. Microb. Ecol. 44:175-185
40. Rautonen N, Apajalahti J (2002) Improving intestinal health with antibodies. Feed Mix 10:13-15
41. Apajalahti JHA, Kettunen A, Bedford MR, Holben WE (2001) Percent G+C profiling accurately reveals diet-related differences in the gastrointestinal microbial community of broiler chickens. Appl. Env. Microbiol. 67:5656-5667
42. Kettunen A (2001) Short term carbon exchange and environmental factors in a boreal fen. In: Williams WD (ed), Verhanlungen IVL 27 (3) of Congress in Dublin 1998, VII 561 pages, E. Schweizerbart'sche Verlagsbuchhandlung, Stuttgart, Germany, pp 1446-1450
43. Kettunen H, Tiihonen K, Peuranen S, Saarinen MT, Remus JC (2001) Dietary betaine accumulates in the liver and intestinal tissue and stabilizes the intestinal epithelial structure in healthy and coccidia-infected broiler chicks. Comp. Biochem. Physiol. 130:759-769
44. Kettunen H, Peuranen S, Tiihonen K (2001) Betaine aids in the osmoregulation of duodenal epithelium of broiler chicks, and affects the movement of water across the small intestinal epithelium in vitro. Comp. Biochem. Physiol. 129:595-603
45. Kettunen H, Peuranen S, Tiihonen K, Saarinen M (2001) Intestinal uptake of betaine in vitro and the distribution of methyl groups from betaine, choline, and methionine in the body of broiler chicks. Comp. Biochem. Physiol. 128:269-278.
46. Saarinen MT, Kettunen H, Pulliainen K, Peuranen S, Tiihonen K, Remus J. (2001) A novel method to analyze betaine in chicken liver: effect of dietary betaine and choline supplementation on the hepatic betaine concentration in broiler chicks. J. Agric. Food Chem. 49:559-563
47. Hämäläinen RP, Kettunen A (2000) Stability of Fourier coefficients in relation to changes in respiratory air flow patterns. Medical Engineering and Physics 22:733-739
48. Kettunen A, Kaitala V, Alm J, Silvola J, Nykänen H, Martikainen PJ (2000) Validity of regression models to predict variations in methane emissions from boreal peatlands. Boreal Env. Res 5:115-131
49. Kettunen A, Kaitala V, Lehtinen A, Lohila A, Alm J, Silvola J, Martikainen PJ (1999) Methane production and oxidation potentials in relation to water table fluctuations in peat profiles from two Finnish mires. Soil Biology & Biogeochemistry 31:1741-1749
50. Lukinmaa S, Schildt R, Rinttilä, T, Siitonen A (1999) Salmonella Enteritidis Phage Types 1 and 4: Pheno- and Genotypic Epidemiology of Recent Outbreaks in Finland. Journal of Clinical Microbiology. 37:2176-2182.
51. Apajalahti JHA, Särkilahti LK, Mäki BR, Heikkinen JP, Nurminen PH, Holben WE (1998) Effective recovery of bacterial DNA and percent-guanine-plus-cytosine- based analysis of community structure in the gastrointestinal tract of broiler chickens. Appl. Environ. Microbiol. 64:4084-4088
52. Kerovuo J, Lauraeus M, Nurminen P, Kalkkinen N, Apajalahti J (1998) Isolation, characterization, molecular gene cloning, and sequencing of a novel phytase from Bacillus subtilis. Appl. Environ. Microbiol. 64:2079-2085
53. Kettunen A, Hämäläinen JJ, Sjöholm K, Pietilä K (1996) A model for the prediction of b-glucanase activity and b-glucan concentration during mashing. Journal of Food Engineering 29:185-200
54. Kettunen A, Kaitala V, Alm J, Silvola J, Nykänen H, Martikainen PJ (1996) Cross-correlation analysis of the dynamics of methane emissions from a boreal peatland. Global Biogeochemical Cycles 10:457-471
55. Hämäläinen RP, Kettunen A (1995) On the capability of the Fourier approximation to describe breathing patterns. J. Biol. Syst. 3:633-643
56. Uotila JS, Kitunen VH, Coote T, Saastamoinen T, Salkinoja-Salonen M, Apajalahti JH (1995) Metabolism of halohydroquinones in Rhodococcus chlorophenolicus PCP-1. Biodegradation. 6:119-126
57. Varotsis C, Babcock GT, Lauraeus M, Wikstrom M (1995) Raman detection of a peroxy intermediate in the hydroquinone-oxidizing cytochrome aa3 of Bacillus subtilis. Biochim. Biophys. Acta 1231:111-116
58. Powers L, Lauraeus M, Reddy KS, Chance B, Wikstrom M (1994) Structure of the binuclear heme iron-copper site in the quinol-oxidizing cytochrome aa3 from Bacillus subtilis. Biochim. Biophys. Acta. 1183:504-512
59. Baumann M, Lauraeus M (1993) Purification of membrane proteins using a micropreparative gel electrophoresis apparatus: purification of subunits of the integral membrane protein Bacillus subtilis aa3-type quinol oxidase for low level amino acid sequence analysis. Anal. Biochem. 214:142-148
60. Lauraeus M, Morgan JE, Wikstrom M (1993) Peroxy and ferryl intermediates of the quinol-oxidizing cytochrome aa3 from Bacillus subtilis. Biochemistry 32:2664-2670
61. Lauraeus M, Wikstrom M (1993) The terminal quinol oxidases of Bacillus subtilis have different energy conservation properties. J. Biol. Chem. 268:11470-11473
62. Lauraeus M, Wikstrom M, Varotsis C, Tecklenburg MM, Babcock GT (1992) Optical and resonance Raman spectroscopy of the heme groups of the quinol-oxidizing cytochrome aa3 of Bacillus subtilis. Biochemistry. 31:10054-10060
63. Uotila JS, Kitunen VH, Apajalahti JHA, Salkinoja-Salonen MS (1992) Environment dependent mechanism of dehalogenation by Rhodococcus chlorophenolicus PCP-1. Appl. Microbiol. Biotechnol. 38:408-412
64. Lauraeus M, Haltia T, Saraste M, Wikstrom M (1991) Bacillus subtilis expresses two kinds of haem-A-containing terminal oxidases. Eur. J. Biochem. 197:699-705
65. Saraste M, Metso T, Nakari T, Jalli T, Lauraeus M, Van der Oost J (1991) The Bacillus subtilis cytochrome-c oxidase. Variations on a conserved protein theme. Eur. J. Biochem. 195:517-525
66. Uotila JS, Salkinoja-Salonen MS, Apajalahti JH (1991) Dechlorination of pentachlorophenol by membrane bound enzymes of Rhodococcus chlorophenolicus PCP-I. Biodegradation 2:25-31
67. Häggblom MM, Apajalahti JHA, Salkinoja-Salonen MS (1988) Degradation of chlorinated phenolic compounds occurring in pulp mill effluents. Water Sci.Technol. 20:205-208
68. Häggblom MM, Apajalahti JH, Salkinoja-Salonen MS (1988) Hydroxylation and dechlorination of chlorinated guaiacols and syringols by Rhodococcus chlorophenolicus. Appl. Environ. Microbiol. 54:683-687
69. Häggblom MM, Apajalahti JHA, Salkinoja-Salonen MS (1988) O-methylation of chlorinated para-hydroquinones by Rhodococcus chlorophenolicus. Appl. Environ. Microbiol. 54:1818-1824
70. Apajalahti JH, Salkinoja-Salonen MS (1987) Complete dechlorination of tetrachlorohydroquinone by cell extracts of pentachlorophenol-induced Rhodococcus chlorophenolicus. J. Bacteriol. 169:5125-5130
71. Apajalahti JH, Salkinoja-Salonen MS (1987) Dechlorination and para-hydroxylation of polychlorinated phenols by Rhodococcus chlorophenolicus. J. Bacteriol. 169:675-681
72. Apajalahti JHA, Salkinoja-Salonen MS (1986) Degradation of polychlorinated phenols by Rhodococcus chlorophenolicus. Appl. Microbiol. Biotechnol. 25:62-67
73. Apajalahti JHA, Karpanoja P, Salkinoja-Salonen M (1986) Rhodococcus chlorophenolicus sp. nov., a chlorophenol-mineralizing actinomycete. Intern. J. Syst. Bacteriol. 36:246-251
74. Häggblom MM, Apajalahti J, Salkinoja-Salonen M (1986) Metabolism of chloroguaiacols by Rhodococcus chlorophenolicus. Appl. Microbiol. Biotechnol. 24:397-404
75. Salkinoja-Salonen M, Hakulinen R, Silakoski L, Apajalahti J, Backström V, Nurmiaho-Lassila E-L (1985) Fluidized bed technology in the anaerobic treatment of forest industry wastewaters. Water Sci. Technol. 17:77-88
76. Valo R, Apajalahti J, Salkinoja-Salonen M (1985) Studies on the physiology of microbial degradation of pentachlorophenol. Appl. Microbiol. Biotechnol. 21:313-319
77. Apajalahti JHA, Salkinoja-Salonen MS (1984) Absorption of pentachlorophenol (PCP) by bark chips and its role in microbial PCP degradation. Microb. Ecol. 10:359-367
78. Salkinoja-Salonen MS, Apajalahti J, Silakoski L, Hakulinen R (1984) Anaerobic fluidised bed purification for the effluents from chemical and mechanical pulping. Biotechnol. Adv. 2:357-375
79. Salkinoja-Salonen M, Hakulinen R, Valo R, Apajalahti J (1983) Biodegradation of recalcitrant organochlorine compounds in fixed film reactors. Water Sci. Technol. 15:309-319
Book chapters
80. Ojanperä I, Pelander A, Ojanperä S (2009). Forensic and toxicological drug screening. In I. Ferrer, Thurman EM (eds.) Time-of-flight mass spectrometry: Principles and applications. Wiley.
81. Apajalahti J, Kettunen A (2006) Microbes of the chicken gastrointestinal tract. In: G.C. Perry (ed) Avian gut function in health and disease. Poultry Science Symposium Series Vol 28. CABI Publishing, Wallingford, pp 121-137
82. Apajalahti J, Kettunen A (2006) Rational development of novel microbial modulators. In: Barug D, de Jong J, Kies AK, Verstegen MWA (eds) Antimicrobial growth promoters. Where do we go from here? Wageningen academic publishers, Wageningen. pp 165-181
83. Schmid K, Schlothauer RC, Friedrich U, Staudt C, Apajalahti J, Bech Hansen E (2005) Development of probiotic food ingredients. In: Goktepe I, Juneja VK, Ahmedna M (eds.) Probiotics In Food Safety And Human Health. Taylor & Francis CRC Press, 2005.
84. Graham H, Apajalahti J, Peuranen S (2004) Xylo-oligosaccharides alter metabolism of gut microbes and blood xylose levels in chicks. -In: van der Kamp J, W Asp, N.-G, Miller Jones, J, Schaafsma, G (eds) Dietary fibre, bio-active carbohydrates for food and feed. Wageningen Academic Publishers, pp 329-332
85. Vasander H, Kettunen A (2006) Carbon in peatlands, In: Wieder RK, Vitt DH (eds) Boreal Peatland Ecosystems, Ecological Studies, 188, Springer Verlag Berlin Heidelberg, pp 165-194
86. Bedford MR, Apajalahti J (2001) Implications of diet and enzyme supplementation on the microflora of the intestinal tract. In: van der Poel, A. F. B, Vahl, J. L, and Kwakkel, R. P. (eds) Advances in nutritional technology 2001. Wageningen Pers, Wageningen, pp 197-206
87. Bedford MR, Apajalahti J (2001) Microbial interactions in the response to exogenous enzyme utilization. In: Bedford MR and Partridge GG (eds) Enzymes in farm animal nutrition. CABI Publishing, Wallingford, pp 229-314
88. Salkinoja-Salonen MS, Valo R, Apajalahti J (1987) Anaerobic treatment potential of liquid and solid forest industry wastes. In: Ferranti MP, Ferrero GL, Hermite PL (eds) Anaerobic digestion: results of research and demonstration projects. Elsevier Applied Science, London & New York, pp 104-114
89. Salkinoja-Salonen M, Apajalahti JHA, Kitunen V, Haggblom M (1987) Bacterial and abiotic degradation of chlorinated phenols and related compounds occurring in forest industry wastes. In: Water pollution research report 6. Behaviour of organic micropollutants in biological wastewater treatment. Commission of the European Communities. EUR 11356, pp 75-80
Invited papers in scientific conferences
90. Apajalahti J, Kettunen A (2006) Microbes of the digestive tract. Proceedings of 12th European Poultry Conference, 10-14 September 2006, Verona, Italy
91. Apajalahti JHA (2005) Rational development of novel microbial modulators. Proceedings of Antimicrobial growth promoters: Worldwide ban on the horizon, Jan 1 – Feb 1, Noordwijk aan Zee, The Netherlands, pp. 39-41
92. Apajalahti JHA, Kettunen A (2003) Analysis and dietary modulation of the microbial community in the avian gastrointestinal tract. Proceedings of the 26th Technical Turkey Conference, April 23-25, Pott Shrigley, UK, pp 49-55
93. Apajalahti JHA (2003) Microbial community analysis and its application in gastrointestinal health. British Society of Animal Science, Annual Meeting, March 24-26, University of York, UK
94. Apajalahti JHA, Kettunen A (2002) Efecto de la dieta sobre la flora microbiana en el tracto gastrointestinal de aves. FEDNA avances en nutrición y alimentación animal November 2002, pp 41-51
95. Apajalahti J (2000) New methods for monitoring changes in microbial communities of the gastrointestinal tract (Uusia menetelmiä ruoansulatuskanavan mikrobiyhteisön muutosten seuraamiseen - in Finnish). Annual Veterinary Congress, Helsinki, Finland
96. Apajalahti J, Bedford M (2000) Impact of Dietary and Environmental Factors on Microbial Communities of the Avian GI Tract. Proceedings of XXI World's Poultry Congress, Montreal, Canada
97. Apajalahti J, Bedford M (1998) Nutrition effects on the microflora of the GI tract. Western Nutrition Conference, Saskatoon, Canada, pp 60-68
98. Apajalahti JHA, Särkilahti LK, Holben WE (1998) Molecular characterization of microbial communities in the gastrointestinal tract of the chicken. Eight International Symposium on Microbial Ecology, Halifax, Canada
Other articles and reports
99. Ojanperä S, Ojanperä I (2006) Laaja ympärivuorokautinen toksikologian analyysipalvelu, Kliinlab 2006; 23: 108.
100. Apajalahti J, Bedford MR (1999) Improve bird performance by feeding its microflora. World Poultry 15:20-23
101. Apajalahti J (1996) Feed enzymes are precision tools (Rehuentsyymit ovat tarkkuustyötä - in finnish). Kemia - Kemi 23:650-653
102. Hämäläinen RP, Kettunen A (1995) How to describe breathing patterns: Evaluation of the Fourier transformation approach. Helsinki University of Technology, Systems Analysis Laboratory, Research Reports A61
103. Kettunen A, Schöpp W, Klimont Z (1994) Statistical Analysis of Tropospheric Ozone Concentration, International Institute for Applied Systems Analysis, WP-94-88
104. Kettunen A, Hämäläinen J (1992) Malli glukanolyysille mäskäyksessä (in Finnish with an English abstract "A model for glucanolysis during mashing"), Mallas ja Olut 5:133-142
105. Häggblom MM, Apajalahti JHA, Salkinoja-Salonen MS (1987) Bacterial degradation of polychlorinated phenolic compounds occurring in forest industry wastes. Kemia - Kemi 14:995
106. Salkinoja-Salonen MS, Apajalahti J (1982) Biodegradability of 2,3,7,8-tetrachlorodibenzo-p-dioxine and chlorophenols, especially pentachlorophenyl, by micro-organisms. Final Report. 68-03-2936, 1-73. U.S. Environmental Protection Agency, Industrial Pollution Control Division, Industrial Environmental Research Laboratory, Cincinati Ohio.
Other presentations in scientific conferences
107. Apajalahti J, Henning PH, Horn CH, Alaja S, Kettunen A (2008) Effect of common antimicrobial agents on the growth and metabolism of Megasphaera elsdenii NCIMB 41125, a lactate utilising probiotic for ruminants. Gut Microbiome, the 6th Joint Symposium INRA-RRI. Clermont-Ferrand, France, June, 18 – 20, 2008
108. Kettunen A, Henning PH, Horn CH, Alaja S, Apajalahti J (2008) Capability of Megasphaera elsdenii strain NCIMB 41125 and other probiotics to prevent accumulation of lactic acid in a rumen model. Gut Microbiome, the 6th Joint Symposium INRA-RRI. Clermont-Ferrand, France, June, 18 – 20, 2008
109. McCracken KJ, Murphy TC, Bedford MR, Apajalahti J (2006) Chicken caecal microflora correlates with ME:GE using wheat-based diets. Proceedings of 12th European Poultry Conference, 10-14 September 2006, Verona, Italy
110. Apajalahti J, Siikanen O, Purkamo L, Lauraeus M (2006) A tool for studying adherence of intestinal pathogens on intestinal mucus – opportunities for screening products for pathogen inhibition in various hosts. Gut Microbiology: Research to Improve Health, Immune Response and Nutrition Aberdeen 21st-23rd June 2006.
111. Kettunen H, Ouwehand A, Schulze H, Rautonen N (2006) Dietary essential oil supplementation enhanced intestinal immunocompetence in young broiler chicks. Fifth Joint RRI-INRA Gastrointestinal Tract Microbiology Symposium, Jun 21 – 23, Aberdeen, Scotland
112. Ojanperä S, Tuominen S, Ojanperä I (2006) Quantification of basic lipophilic drugs in blood without reference standards by LC-CLND based on extraction recovery estimation, 44th TIAFT 2006 meeting, Ljubljana, Slovenia.
113. Ouwehand AC, Kettunen H, Schulze H, Rautonen N (2006) In vitro activity of essential oils towards intestinal microbes. Fifth Joint RRI-INRA Gastrointestinal Tract Microbiology Symposium, Jun 21 – 23, Aberdeen, Scotland
114. Schulze H, Kettunen H, Ouwehand, AC, Rautonen N (2006) Dietary essential oil supplementation can affect broiler performance and digesta microbial community. Fifth Joint RRI-INRA Gastrointestinal Tract Microbiology Symposium, Jun 21 – 23, Aberdeen, Scotland
115. Tarkkanen AM, Apajalahti J, Kettunen A, Heinonen T (2006) Ampicillin treatment shifts bacterial communities in the feces – results from phase IIa clinical trial 2006 Annual Conference on Antimicrobial Resistance", June 26-28. 2006, Hyatt Regency Bethesda, Bethesda, Maryland, USA.
116. Kettunen A, Buresh R, Pierson E, Apajalahti J (2005) Gut microflora of organically grown broiler chickens differs significantly from that of conventional birds. International Poultry Exposition, International Poultry Scientific Forum, January 24-25, Atlanta, GA, USA
117. Kettunen H, Rautonen N (2005) With betaine and exogenous enzymes towards improved intestinal health and immunity, and better performance of broiler chicks. 94th Annual Meeting of Poultry Science Association. Jul 31 – Aug 3, Auburn, Alabama, USA.
118. Kettunen H, Simmins H, Rautonen N (2005) Improved intestinal health and immunity in broiler chicks when fed a combination of Betafin® and Avizyme 1500. Antimicrobial Growth Promoters: Worldwide Ban on the Horizon? The International Debate Conference for the Feed & Food Chain. Jan 31- Feb 1, Noordwijk aan Zee, The Netherlands
119. Laks S, Pelander A, Vuori E, Ojanperä I (2005) Analysis of drugs in biological samples without primary reference standards, 43rd TIAFT 2005 meeting, Seoul, Korea.
120. Oviedo-Rondón EO, Apajalahti J, Parker J, Remus J, Pierson E (2005) Modulation of intestinal microbial communities and luminal IgA secretion by an amylase, xylanase and protease-based feed enzyme system in broiler chickens vaccinated and challenged with mixed Eimeria spp. International Poultry Exposition, International Poultry Scientific Forum, January 24-25, Atlanta, GA, USA
121. Pelzing M, Laks S, Pelander A, Vuori E, Ojanperä I (2005) Comprehensive Urine Drug Screening by LC-ESI-oaTOF based on Retention Time, Accurate Mass Determination and Isotopic Pattern Information. American Society for Mass Spectrometry, 53rd ASMS Conference, 5.-9.6.2005, San Antonio, Texas, USA. Proceedings CD.
122. Rinttilä T, Malinen E, Kajander K, Mättö J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A (2005) Comparison of the Fecal Microbial Populations of IBS Patients and Symptom-free Controls. Eigth Symposium on Lactic Acid Bacteria – genetics, metabolism and application. Egmond aan Zee, the Netherlands, 2005, August 28 - September 1.
123. Rinttilä T, Kassinen A, Malinen E, Krogius L,Palva A (2004) Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in fecal samples by real-time PCR. Biosapiens 1st Permanent School in Bioinformatics. Verona, Italy, 2004, July 7 – 13.
124. Kassinen A, Malinen E, Rinttilä T, Kajander K, Mättö J, Krogius L, Saarela M, Korpela R, Palva A (2004) Comparison of the faecal microbial populations of patients suffering from irritable bowel syndrome with symptom-free age- and sex-matched controls. International Probiotic Conference, Kosice, Slovakia, 2004, September 15-19.
125. Kettunen H, Tiihonen K, Peuranen S, Rautonen N (2004) Ferulic acid rich sugarbeet extract increased blood HDL cholesterol and enhanced immunity in rats fed with western-type diet. XXII International Conference on Polyphenols. Aug 25 – 28, Helsinki, Finland
126. Krogius L, Rinttilä T, Kassinen A, Malinen E, Palva A (2004) Real-time PCR for faecal bacteria. International Probiotic Conference, 15-19.9.2004, Kosice, Slovakia.
127. Ojanperä I, Laks S, Pelander A, Vuori E (2004) Forensic Drug Analysis Without primary Reference Standards, Joint SOFT/TIAFT Meeting 2004, Washington, USA.
128. Laks S, Pelander A, Vuori E, Pelzing M, Ojanperä I (2004) Comprehensive Urine Drug Screening by Liquid Chromatography – Time-of-Flight Mass Spectrometry Based on Accurate Mass Determination and True Isotope Patterns, 21st Montreux Symposium on Liquid Chromatography/Mass Spectrometry 2004.
129. Kettunen A, Alm J (2003) Microscale variations in methane fluxes from boreal mires, EGS - AGU - EUG Joint Assembly, April, 2003, Nice, France.
130. Malinen E, Rinttilä T, Kajander K, Mättö J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A (2003) Comparison of the faecal microbial populations of patients suffering from irritable bowel syndrome with symptom-free age- and sex-matched controls. Gut health Market: Probiotic research and product development. Scandic Hotel Kalastajatorppa, 2003, October 16.
131. Tiihonen K, Kettunen H, Saarinen MT, Peuranen S (2003) Methylation metabolism in the liver - effect of dietary betaine. 4th International Conference on Homocysteine Metabolism, Jun 29 – Jul 3, Basel, Switzerland
132. Kassinen A, Rinttilä T, Malinen E, Palva A (2002) Development of molecular biology methods for detection of lactic acid bacteria from faeces. Seventh Symposium on Lactic Acid Bacteria – genetics, metabolism and application. Egmond aan Zee, the Netherlands, 2002, September 1. – 5.
133. Rajakangas J, Salminen I, Kettunen H, Basu S, Mutanen M (2002) The trans-10, cis-12 isomer of conjugated linoleic acid (CLA) enlarge the intestinal adenomas of the APCMin mouse and causes lipid accumulation in the liver. The Proceedings of the Cell signaling, transcription and translation as therapeutic targets, Jan 30 – Feb 2, Kirchberg, Luxembourg
134. Tankka S, Westerlund-Wikström B, Kettunen H, Rautonen N, Apajalahti J, Korhonen T (2001) Adhesion of lactic acid bacteria (lab) to the epithelial surfaces and gut-associated lymphoid tissues (GALT) in the avian alimentary tract. International Conference of Intestinal Bacteriology, Japan
135. Jatila HL, Oksanen JT, Kettunen H, Apajalahti JHA (2000) Eimeria maxima, an intestinal parasite predisposes broiler chicken for the outgrowth of Clostridium perfringens in ileum and caecum. Proceedings of Anaerobe 2000, U.K.
136. Cowieson AJ, Särkilahti LK, Apajalahti JHA, Acamovic T, Bedford MR (2000) Caecal microflora in broilers fed diets containing camelina with and without enzyme supplementation. Proceedings of XXI World's Poultry Congress, Montreal, Canada
137. Gilbert C, Särkilahti L, Apajalahti J, Acamovic T, Bedford MR (2000) Microbial populations in caecal contents from chicks fed lupin-based diets, with and without enzyme supplementation. Proceedings of XXI World's Poultry Congress, Montreal, Canada
138. Kettunen A (1999) A process model describing methane flux dynamics in boreal mires. Abstracts of the Spring AGU meeting, Special Session "Carbon Sequestration and Biogeochemistry of Soils", June 1-4, Boston, p CC200
139. Kettunen A (1999) Methane flux dynamics in a Finnish mire. Abstracts of the Intenarional Peat Symposium "Chemical, Physical and Biological Processes in Peat Soils", August 23-27, Jokioinen, Finland
140. Kettunen H, Peuranen S, Apajalahti J, Jatila H, Nurminen P, Saarinen M (1999) Effects of betaine on the microbial community of broiler chick gastro-intestinal tract. 12th European Symposium on Poultry Nutrition, Veldhoven, The Netherlands
141. Kettunen H, Peuranen S, Remus JC, Tiihonen K, Virtanen E (1999) The bioefficacy of dietary betaine and choline in broiler chicks. Southern Poultry Science Society Meeting. Jan 18-19, Atlanta, GA, USA
142. Peuranen S, Kettunen H, Tiihonen K (1999) Betaine increases the water retention of broiler duodenum in vitro. Society for Experimental Biology Annual Meeting. March 22-26, Edinburgh, UK
143. Kettunen A (1998) The dependence of photosynthesis and respiration rates on environmental factors in different microsites from a boreal oligotrophic pine fen. Extended abstract, Proceedings of The Spirits of Peatlands, IPS, September 7-9, Jyväskylä, Finland, pp 234-236
144. Kettunen A (1998) The connection of environmental factors to short term carbon dynamics in different surfaces of a boreal pine fen. Abstracts of XXVII Societas Internationalis limnologiae SIL: Water of life, August 9-14, Dublin, Ireland, p 300
145. Kettunen A, Kaitala V, Alm J, Lohila A, Lehtinen A, Silvola J, Martikainen PJ (1997) Methane production and oxidation potentials during a growing season in two Finnish mires. Poster in XIII ISEB conference: Matter and Energy Fluxes in the Anthropocentric Environment, September 21-26, Monopoli, Italy, p 93
146. Tiihonen K., Kettunen H, Remus J, Saarinen M, Virtanen E (1997) Effects of dietary betaine on broiler chicks without or with mild coccidiosis challenge. Poultry Science Association. Annual Meeting. Aug 3-6, Athens, GA, USA
147. Tiihonen K., Kettunen H, Virtanen E (1996) Intestinal transport and deposition of betaine by bird. European Society for Comparative Physiology and Biochemistry. 17th Annual Conference, Adaptation to Stress in Aquatic and Terrestrial Ecosystems. Aug 27-31, Antwerpen, Belgium
148. Kettunen A, Kaitala V (1995) Modelling of methane emissions from boreal peatlands. "Northern Peatlands in Global Climatic Change", Publications of the Academy of Finland, Proceedings of the International Workshop, October 8-12, Hyytiälä, Finland, pp 277-281
149. Kettunen A, Kaitala V, Alm J, Silvola J, Nykänen H, Martikainen PJ (1995) Dynamics of methane emissions in a boreal peatland. Abstracts of 1st GAIM science conference, September 25 - 29, Garmisch-Partenkirchen, Germany, p C-23
150. Kettunen A, Kaitala V, Alm J, Silvola J, Nykänen H, Martikainen PJ (1995) Regression models for predicting methane emissions from boreal peatlands. "Environmental Research in Finland Today", Microbiological Publications, Proceedings of Second Finnish Conference of Environmental Sciences, November 16-17, Helsinki, Finland, pp 265-268
151. Kettunen A, Kaitala V, Alm J, Silvola J, Nykänen H, Martikainen PJ (1995) Regression models for predicting methane emissions from boreal peatlands. Abstracts of IBFRA Climate Change, Biodiversity and Boreal Forest Ecosystems Conference, International Boreal Forest Research Association, July 30 - August 5, Joensuu, Finland, p 37
152. Hämäläinen RP, Kettunen A (1993) On the capability of the Fourier transformation to describe breathing patterns. Second European Conference on Mathematics Applied to Biology and Medicine, December 15-17, Lyon, France
153. Koljonen T, Hämäläinen JJ, Sjöholm K, Kettunen A, Pietilä K (1993) Simulation of the degradation of starch and b-glucans during mashing. Proceedings of European Brewery Convention, 24th Congress, Oslo, Norway, pp 525-532
154. Koljonen T, Kettunen A, Sjöholm K, Pietilä K, Hämäläinen JJ (1992) Simulation of Enzyme Kinetics during Malt Mashing - a New Parameter Estimation Method. Proceedings of First IEEE Conference on Control Applications, IEEE Catalog No:92CH3000-7, pp 90-95
155. Uotila JS, Saastamoinen T, Coote T, Apajalahti JHA, Salkinoja-Salonen, MS (1991) Two different dechlorinases for polychlorinated aromatic compounds from Rhodococcus chlorophenolicus PCP-1.1st International Symposium on Environmental Biotechnology, Ostende, Belgium
156. Apajalahti J, Cole J, Tiedje J (1989) Characterization of a dechlachlorination cofactor: an essential activator for 3-chlorobenzonate dechclorination by the bacterium DCB-1. Ann. Meet. Amer. Soc. Microbiol., New Orleans, LA, USA.
157. Apajalahti J, Lauraeus M, Salkinoja-Salonen MS (1988) Characterization of tetrachlorohydroquinone dechlorinating enzymes of Rhodococcus chlorophenolicus. Ann. Meet. Amer. Soc. Microbiol., Miami Beach, Fla, USA.
158. Häggblom MM, Apajalahti JHA, Salkinoja-Salonen MS (1988) O-methylation of chlorinated hydroquinones by Rhodococcus chlorophenolicus. Ann. Meet. Amer. Soc. Microbiol., Miami Beach, Fla, USA.
159. Häggblom M, Apajalahti JHA, Salkinoja-Salonen M (1987) Degradation of chlorinated phenolic compounds occurring in pulp mill effluents. Second IAWPRC Symposium of Forest Industry Wastewaters. Tampere, Finland
160. Häggblom M, Apajalahti JHA, Salkinoja-Salonen M (1987) Metabolism of chlorinated phenols and guaiacols by Rhodococcus chlorophenolicus. Ann. Meet. Amer. Soc. Microbiol. Atlanta GA, USA.
161. Salkinoja-Salonen M, Jokela J, Pellinen J, Apajalahti J (1987) Biodegradability of lignin derived components in forest industry wastewaters. Second IAWPRC Symposium of Forest Industry Wastewaters, Tampere, Finland
162. Apajalahti J, Salkinoja-Salonen M (1986) Initial reactions in the degradation of chlorophenols by Rhodococcus chlorophenolicus. Nordiskt möte om organiska miljögifter, Bråviken, Sweden
163. Häggblom M, Apajalahti J, Salkinoja-Salonen M (1986) Degradation of chloroguaiacols. Nordiskt möte om organiska miljögifter, Bråviken, Sweden.
164. Salkinoja-Salonen MS, Valo R, Apajalahti J, Hakulinen R, Silakoski L, Jaakkola T (1984) Biodegradation of chlorophenolic compounds in wastes from wood-processsing industry. In: Klug, M. J. and Reddy, C. A. (eds) Current Perspectives in Microbial Ecology. American Society for Microbiology, Wash. D.C., pp 668-676
165. Salkinoja-Salonen M, Hakulinen R, Silakoski L, Valo R, Apajalahti J (1983) Treatment of pulp and paper industry wastewaters in an anaerobic reactor: From bench scale units to full scale operation. Third Intern. Symp. Anaerobic Digestion. Boston Ma. USA, pp 107-122
Theses
166. Ojanperä S (2009) Drug Analysis without Primary Reference Standards : Application of LC-TOFMS and LC-CLND to Biofluids and Seized Material. PhD (Doctoral) thesis. University of Helsinki.
167. Grönberg H (2008) Rhizoctonia -Scots pine interactions: detection, impact on seedling performance and host defence gene response. PhD (Doctoral) thesis. University of Helsinki.
168. Kettunen A (2002) Modeling of microscale variations in methane fluxes. Systems Analysis Laboratory Research Reports A83. PhD (Doctoral) thesis. Helsinki University of Technology.
169. Kettunen H (2001) Betaine in the nutrition of broiler chicks – absorption, methyl group metabolism, and intestinal osmoregulation, PhD (Doctoral) thesis. University of Helsinki.
170. Rinttilä T (2000) Yersinia pseudotuberculosis O:3:n O-antigeeniä määräävään geenialueeseen perustuva rfb-tyypitys. Kansanterveyslaitoksen bakteriologian osasto. M.Sc. thesis, University of Helsinki.
171. Kettunen A (1996) Statistical analyses of the dynamics of methane emissions from a boreal peatland. Lic. Thesis. Helsinki University of Technology.
172. Lauraeus M (1993) The terminal oxidases of Bacillus subtilis. PhD (Doctoral) Thesis. University of Helsinki.
173. Kettunen A (1992) A model of glucanolysis during malt mashing (Malli glukanolyysille maltaan mäskäyksessä - in Finnish). M.Sc.thesis. Helsinki University of Technology.
174. Apajalahti JHA (1987) Chlorophenol metabolism of a polychlorophenol degrader, Rhodococcus chlorophenolicus sp. nov. PhD (Doctoral) thesis.University of Helsinki.
175. Apajalahti JHA (1985) Factors affecting microbial degradation of chlorophenols (Kloorifenoleiden mikrobiologiseen hajoamiseen vaikuttavia tekijöitä - in Finnish). Lic. Thesis. University of Helsinki.
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