School of Marine and Atmospheric Sciences
Stony Brook University
Stony Brook, NY 11794-5000

Site designed and maintained by
Bassem Allam

(Pr Paul Bowser's publications are available at his Cornell webpage)

Fact sheets:

Lobster calcinosis fact sheet

QPX in clams fact sheet


Scientific articles:

75. Allam B, Tanguy A, Jeffroy F, Le Bris C, Pales Espinosa E, Paillard C. (2014). Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to brown ring disease. Fish and Shellfish Immunology. In Press. pdf

74. Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, et al. (2014). The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biology, 12(6), e1001889. pdf

73. Pales Espinosa E., Corre E, Allam B. (2014). Pallial mucus of Crassostrea virginica regulates the expression of putative virulence genes of its pathogen Perkinsus marinus. International Journal for Parasitology 44: 305-317. pdf

72. Rubin E, Tanguy A, Perrigault M, Pales Espinosa E, Allam B. (2014). Characterization of the transcriptome and temperature-induced differential gene expression of in quahog parasite unknown QPX, the thraustochytrid parasite of hard clams. BMC Genomics 15: 245. pdf

71. Pales Espinosa E, Boutet I, Le Panze S, Allam B, Tanguy A. (2013). Endobacteria in Loripes lacteus: Characterization, localization and some aspect of host-symbiont regulation. Journal of Experimental Marine Biology and Ecology 448: 327-336. pdf

70. Levinton J, Doall M, Allam B. (2013). The two-year eastern oyster mortality syndrome in impacted waters. Journal of Shellfish Research 32(2): 417-427. pdf

69. Rosa M, Ward JE, Shumway SS, Wikfors GH, Pales Espinosa E, Allam B. (2013). Effects of Particle Surface Properties on Feeding Selectivity in the Eastern oyster Crassostrea virginica and the Blue mussel Mytilus edulis. Journal of Experimental Marine Biology and Ecology 446: 320-327. pdf

68. Pales Espinosa E., Winnicki S, Allam B. (2013). Early host-pathogen interactions in marine bivalves: Pallial mucus of Crassostrea virginica modulates the growth and virulence of its pathogen Perkinsus marinus. Diseases of Aquatic Organisms 104: 237-247. pdf

67. Pales Espinosa E., Allam B. (2013). Food quality and season affect the expression of the mucosal lectin MeML and food sorting abilities in the blue mussel Mytilus edulis. Marine Biology 160(6): 1441-1450. pdf

66. Allam B, Carden WE, Ward JE, Ralph G, Winnicki S, Pales Espinosa E. (2013). Early host-pathogen interactions in marine bivalves: Evidence that the alveolate parasite Perkinsus marinus infects through the oyster mantle during rejection of pseudofeces. Journal of Invertebrate Pathology 113: 26-34. pdf

65. Perrigault M., Dahl S.F., Pales-Espinosa E., Allam B. (2012). Effects of salinity on hard clam (Mercenaria mercenaria) defense parameters and QPX disease dynamics. Journal of Invertebrate Pathology 110(1): 73-82. pdf

64. Perrigault M, Allam B. (2012). Differential immune response in the hard clam (Mercenaria mercenaria) against bacteria and the protistan QPX (Quahog Parasite Unknown). Fish and Shellfish Immunology 32(6): 1124-1134. pdf

63. Homerding M, McElroy A, Taylor G, Dove A, Allam B. (2012). Investigation of epizootic shell disease in American lobsters (Homarus americanus) from Long Island Sound: II. Immune parameters in lobsters and relationships to the disease. Journal of Shellfish Research 31(2):495-504. pdf

62. Bell SL, Allam B., McElroy A, Dove A, Taylor GT. (2012). Investigation of epizootic shell disease in American lobsters (Homarus americanus) from Long Island Sound: I. Characterization of associated microbial communities. Journal of Shellfish Research 31(2):473-484. pdf

61. Sokolowski M, Allam B, Dunton K, Clark M, Kurtz E, Fast M. (2012). Spatio-temporal differences in immunophysiology of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus (Mitchill), and the relationship to parasitic copepod, Dichelesthium oblongum, (Abilgaard) infection. Journal of Fish Diseases 35(9): 649-660. pdf

60. Levinton J, Doall M, Ralston D, Starke A, Allam B. (2011). Climate change, precipitation and the loss of an estuarine refuge. PLoS One 6(4): e18849. pdf

59. Jing X, Pales Espinosa E, Perrigault M, Allam B. (2011). Identification, molecular characterization and expression analysis of a mucosal C-type lectin in the eastern oyster, Crassostrea virginica. Fish and Shellfish Immunology 30: 851-858. pdf

58. Perrigault M., Dahl S.F., Pales Espinosa E., Gambino L., Allam B. (2010). Effects of temperature on hard clam (Mercenaria mercenaria) immunity and QPX (Quahog parasite unknown) disease development: II. Defense parameters. Journal of Invertebrate Pathology 106: 322-332. pdf

57. Dahl S, Perrigault M, Liu Q, Collier JL, Barnes DA, Allam B. (2010). Effects of temperature on hard clam (Mercenaria mercenaria) immunity and QPX (Quahog parasite unknown) disease development: I. Dynamics of QPX disease. Journal of Invertebrate Pathology 106: 314-321. pdf

56. Pales Espinosa E, Hassan D, Ward JE, Shumway SE, Allam B. (2010). The blue mussel Mytilus edulis uses recognition molecules to select food particles. Biological Bulletin 219: 50-60. pdf

55. Pales Espinosa E, Perrigault M, Allam B. (2010). Identification and molecular characterization of a mucosal lectin (MeML) from Mytilus edulis and its potential role in particle capture. Comparative Biochemistry and Physiology 156:495-501. pdf

54. Perrigault M, Buggé DM., Allam B. (2010). Effect of environmental factors on survival and growth of quahog parasite unknown (QPX) in vitro. Journal of Invertebrate Pathology 104:83-89. pdf

53. Dahl S, Thiel J, Allam B. (2010). QPX disease progress in cultured and wild type hard clams in New York waters. Journal of Shellfish Research 29(1): 83-90. pdf

52. Pales Espinosa E, Perrigault M, Ward JE, Shumway S, Allam B. (2010). Lectin binding patterns of microalgae: role in particle selection in suspension feeding bivalves. Biological Bulletin 218:75-86. pdf

51. Perrigault M, Tanguy A, Allam B. (2009). Indentification and quantification of differentially expressed genes in the hard clam, Mercenaria mercenaria, in response to quahog parasite unknown (QPX). BMC Genomics 10: 377. pdf

50. Perrigault M, Allam B. (2009). Cytotoxicity of Quahog Parasite Unknown (QPX) toward hard clam (Mercenaria mercenaria) haemocytes and interactions between different pathogen isolates and host strains. Parasitology 136: 1281-1289. pdf

49. Pales Espinosa, E., Perrigault, M., Ward, J.E., Shumway, S.E., Allam, B. (2009). Lectins associated with the feeding organs of the oyster Crassostrea virginica can mediate particle selection. Biological Bulletin 217: 130-141. pdf

48. Liu Q, Allam B., Collier JL. (2009). A quantitative real-time PCR assay for QPX (Thraustochytridae), a parasite of the hard clam (Mercenaria mercenaria). Submitted to Applied and Environmental Microbiology 75:4913-4918. pdf

47. Ford SE, Allam B, Xu Z. (2009). Using PCR and bivalve “particle collectors” to investigate the environmental distribution of Haplosporidium nelsoni, the agent of MSX disease in eastern oysters. Diseases of Aquatic Organisms 83: 159-168. pdf

46. Bettencourt R, Dando P, Collins P, Costa V, Allam B, Serrão Santos R. (2009). Innate immunity in the deep sea hydrothermal vent mussel Bathymodiolus azoricus. Comparative Biochemistry and Physiology Part A 152: 278-289. pdf

45. Perrigault M, Buggé DM, Hao CC, Allam B. (2009). Modulatory effects of hard clam (Mercenaria mercenaria) tissue extracts on the in vitro growth of its pathogen QPX. Journal of Invertebrate Pathology 100: 1-8. pdf

44. Dahl, S.F., Perrigault M., Allam, B. (2008). Laboratory transmission studies of QPX disease in the hard clam: Pathogenicity of different pathogen isolates toward various clam stocks. Aquaculture 280:64-70. pdf

43. Pales Espinosa, E., Allam, B., Ford S.E. (2008). Particle selection in the ribbed mussel Geukensia demissa and the Eastern oyster Crassostrea virginica: effect of microalgae growth stage. Estuarine, Coastal and Shelf Science 79:1-6. pdf

42. Fast MD, Afonso L, Hosoya S, Johnson SC. 2008. Cortisol response and immune-related effects of Atlantic salmon (Salmo salar Linnaeus) subjected to short- and long-term stress.  Fish Shellfish Immunol Fish Shellfish Immunol. 24:194-204.

41. Gobler C.J., Berry D.L., Anderson O.R., Burson A., Koch F., Rodgers B.S., Moore L.K., Goleski J.A., Allam B., Bowser P., Tang Y., Nuzzi R. (2008). Characterization, dynamics, and ecological impacts of harmful Cochlodinium polykrikoides blooms on eastern Long Island, NY, USA. Harmful Algae 7: 293-307. pdf

40. Lyons M.M., Lau Y.-T., Carden W.E., Ward J.E., Roberts S.B., Smolowitz R., Vallino J., Allam B. (2007). Characteristics of marine aggregates in shallow ecosystems: Implications for disease ecology. Ecohealth 4: 406-420. pdf

39. Wang Z, Liu X, Dacanay A, Harrison BA, Fast M, Colquhoun DJ, Lund V, Brown LL, Li J, Altman E. (2007). Carbohydrate analysis and serological classification of typical and atypical isolates of Aeromonas salmonicida:  a rationale for the lipopolysaccharide-based classification of A. salmonicida.  Fish Shellfish Immunol. 23:1095-1106.

38. Qian H., Liu Q., Allam B., Collier J.L. (2007). Molecular genetic variation within and among isolates of QPX (Thraustochytridae), a parasite of the hard clam (Mercenaria mercenaria). Diseases of Aquatic Organisms 77: 159-168. pdf

37. Pales Espinosa E., Barillé L., Allam B. (2007). Use of encapsulated live microalgae to investigate pre-ingestive selection in Crassostrea gigas. Journal of Experimental Marine Biology and Ecology 343:118-126. pdf

36. Jones SRM, Fast MD, Johnson SC. (2007). Differential susceptibility and the responses of pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon juveniles to infection with Lepeophtheirus salmonis. Dis Aquat Org. 75: 229-238.

35. Fast MD, Johnson SC, Jones S. (2007). Differential expression of the proinflammatory cytokines IL-1β-1, TNFα-1 and IL-8 in vaccinated pink (Ocorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon juveniles. Fish Shellfish Immunol. 22: 403-407.

34. Fast MD, Johnson SC, Eddy TD, Pinto D, Ross NW. (2007). Lepeophtheirus salmonis secretory/excretory products and their effects on salmonid immune gene regulation. Parasite Immunol. 29: 179-189.

33. Dahl, S.F., Allam, B. (2007). Laboratory transmission studies of QPX disease in the hard clam: Development of an infection procedure. Journal of Shellfish Research 26: 383-389.pdf

32. Buggé D, Hégaret H, Wikfors G, Allam B. (2007). Oxidative burst in hard clam (Mercenaria mercenaria) haemocytes. Fish and Shellfish Immunology 23(1): 188-196. pdf

31. Buggé D, Allam B. (2007). Effects of starvation and macroalgae extracts on the survival and growth of Quahog Parasite Unknown (QPX). Journal of Experimental Marine Biology and Ecology 348: 60-69. pdf

30. Pales Espinosa E., Allam B. (2006). Comparative growth and survival of juvenile hard clams, Mercenaria mercenaria, fed commercially available diets. Zoo Biology 25: 513-525. pdf

29. Moss B., Allam B. (2006). Fluorometric measurement of oxidative burst in lobster hemocytes and inhibiting effect of pathogenic bacteria and hypoxia. Journal of Shellfish Research 25(3): 1051-1057. pdf

28. Fast MD, Ross NW, Muise, DM, Johnson SC. (2006). Differential gene expression in Atlantic salmon, Salmo salar, infected with Lepeophtheirus salmonis (Copepoda: Caligidae). J Aquat An Health 18:116-127.

27. Fast MD, Muise, DM, Easy RE, Ross NW, Johnson SC. (2006). The effects of successive Lepeophtheirus salmonis infections on the immunological status of Atlantic salmon (Salmo salar). Fish Shellfish Immunol 21: 228-241.

26. Fast MD, Cembella AD, Ross NW. (2006). In vitro transformation of paralytic shellfish toxins in the clams Mya arenaria and Protothaca staminea. Harmful Algae 5: 79-90.

25. Fast MD, Afonso LOB, Johnson SC. (2006). PG-3: Methods for studying the effects of sea lice infection on host physiology and health. In “A reference manual for research involving wild/cultured fish interactions with sea lice” Farrell  AP (Ed.), BC Pacific Salmon Forum commissioned reports, 2006, 73-87. (

24. Boettcher K., Smolowitz R., Lewis E., Allam B., Dickerson H., Ford S., Huq A., Reece K., Rivara G., Maloy A., Woodley C. (2006). Juvenile Oyster Disease (JOD) in Crassostrea virginica: synthesis of knowledge and recommendations. Journal of Shellfish Research 25(2): 683-686. pdf

23. Allam B., Paillard C., Auffret M., Ford S.E. (2006). Effects of the pathogenic Vibrio tapetis on different bivalve species: II. hemocyte and humoral changes following in vivo challenge. Fish and Shellfish Immunology 20: 384-397. pdf

22. Allam B., Ford S.E. (2006). Effects of the pathogenic Vibrio tapetis on different bivalve species: I. hemocyte changes following in vitro challenge. Fish and Shellfish Immunology 20: 374-383. pdf

21. Fast MD, Ross NW, Johnson SC. (2005). Prostaglandin E2 modulation of gene expression in an Atlantic salmon (Salmo salar) macrophage-like cell line (SHK-1). Dev Comp Immunol 29:  951-963.

20. Dove A.D.M., Allam B., Powers J.J., Sokolowski M.S. (2005). A prolonged thermal stress experiment on the American lobster, Homarus americanus. Journal of Shellfish Research 24: 761-765. pdf

19. Buggé D.M., Allam B. (2005). A fluorometric technique for the in vitro measurement of growth and viability in Quahog Parasite Unknown. Journal of Shellfish Research 24: 1013-1018. pdf

18. Paillard C., Allam B., Oubella R. (2004). Effect of temperature on defense parameters in Manila clam, Ruditapes philippinarum, challenged with Vibrio tapetis. Diseases of Aquatic Organisms 59: 249-262. pdf

17. Johnson, SC and Fast MD. (2004). Interactions between sea lice and their hosts. In “Host-parasite interactions”. Wiegertjes GF and Flik G (eds), BIOS Scientific Publishers Ltd. 2004, 131-161.

16. Fast MD, Ross NW, Craft CA, Locke SJ, MacKinnon SL, Johnson SC. (2004). Lepeophtheirus salmonis:  Characterization of prostaglandin E2 in secretory products of the salmon louse by RP-HPLC and Mass Spectrometry. Exp Parasitol 107: 5-13.

15. Fast MD, Burka JF, Johnson SC, Ross NW. (2003). Enzymes released from Lepeophtheirus salmonis in response to mucus from different salmonids. J Parasitol  89: 7-13.

14. Fast MD, Sims DE, Burka JF, Mustafa A, Ross NW. (2002). Skin morphology and humoral non-specific defence parameters of mucus and plasma in rainbow trout coho and Atlantic salmon. Comp Biochem Phys A 132: 645-657.

13. Fast MD, Ross NW, Mustafa A, Sims DE, Johnson SC, Conboy GA, Speare DJ, Johnson G, Burka JF. (2002). Susceptibility of rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar and coho salmon Oncorhynchus kisutch to experimental infection with sea lice Lepeophtheirus salmonis.  Dis Aquat Org 52: 57-68.

12. Allam B., Paillard C., Ford S.E. (2002). Pathogenicity of Vibrio tapetis, the etiologic agent of brown ring disease in clams. Diseases of Aquatic organisms 48: 221-231. pdf

11. Allam B., Ashton-Alcox K.A., Ford S.E. (2002). Flow cytometric measurement of hemocyte viability and phagocytic activity in the clam Ruditapes philippinarum. Journal of Shellfish Research 21: 13-19. pdf

10. Allam B., Ashton-Alcox K.A., Ford S.E. (2002). Flow cytometric characterization and separation of hemocyte in three bivalve species. Fish & Shellfish Immunology 13: 141-158. pdf

9. Allam B., Ashton-Alcox K.A., Ford S.E. (2001). Haemocyte parameters associated with resistance against brown ring disease in clams. Developmental & Comparative Immunology 25: 365-375. pdf

8. Ashton-Alcox K.A., Allam B., Ford S.E. (2000). Applications of flow cytometry to bivalve pathology. In : Recent Advances in Marine Biotechnology. Vol. 5: Immunology and Pathology. (M. Fingerman & R. Nagabhushanam, eds.) pp. 85-124. Enfield, NH, USA: Science Publishers, Inc.

7. Allam B., Paillard C., Howard A., Le Pennec M. (2000). Isolation of the pathogen Vibrio tapetis and defense parameters in Manila clam, Ruditapes philippinarum, cultured in England. Diseases of Aquatic Organisms 41: 105-113. pdf

6. Allam B., Paillard C., Auffret M. (2000). Alterations in hemolymph and extrapallial fluid parameters in the Manila clam, Ruditapes philippinarum challenged with the pathogen, Vibrio tapetis. Journal of Invertebrate Pathology 76: 63-69. pdf

5. Allam B. Auffret M. (2000).The presence of an inducible antibacterial activity in the hemolymph of the Manila clam, Ruditapes philippinarum. Lebanese Science Bulletin 1(1): 1-9.

4. Allam B., Paillard C. (1998). Defense factors in clam extrapallial fluids. Diseases of Aquatic Organisms 33: 123-128. pdf

3. Oubella R., Maes P., Allam B., Paillard C., Auffret M. (1996). Selective induction of hemocytic response in Ruditapes philippinarum (Bivalvia) by different species of Vibrio (Bacteria). Aquatic Living Ressources 9: 137-143.

2. Allam B., Paillard C., Maes P. (1996). Localization of the pathogen Vibrio P1 in clams affected by Brown Ring Disease. Diseases of Aquatic Organisms 27: 149-155. pdf

1. Allam B., Paillard C., Maes P. (1996). Effet du nouveau fluorochrome redox, le chlorure de cyanoditolyl tétrazolium (CTC), sur une souche bactérienne du genre  Vibrio. Lebanese Science Bulletin 9(1): 1-10.


Last update: June 2010