- Molecular biology of heterocyst differentiation in the cyanobacterium Anabaena
- Symbiotic association of cyanobacteria with plants
- Genomic analysis and molecular evolution of genomes and its components
- Molecular tools for the study of cyanobacteria

Molecular biology of heterocyst differentiation in the cyanobacterium Anabaena

• Xu X, Elhai J, Wolk CP (2007). Transcriptional and developmental responses by Anabaena to deprivation of fixed nitrogen. In: The Cyanobacteria: Molecular Biology, Genomics and Evolution (Herrero A, Flores E, eds.). Horizon Scientific Press, Norwich, UK.
   
• John C Meeks and Jeff Elhai (2002). Regulation of cellular differentiation in filamentous cyanobacteria in free-living and plant-associated symbiotic growth states. Microbiology and Molecular Biology Reviews 66:94-121. Abstract / Full Text

First part of review discusses current thinking regarding controls over patterned heterocyst differentiation. Second part discusses how plants might use these controls for their own purposes.
 
• Wolk CP, Elhai J, Kuritz T, Holland D (1993). Amplified expression of a transcriptional pattern formed during development of Anabaena. Mol Microbiol 7:441-445. Abstract

Technical advance: Using RNA polymerase from phage T7 to amplify weak transcription made visible by fusion of gene to luxAB (encoding luciferase). Peter's idea, I believe. Scientific advance: Demonstrating that a gene known to be important in heterocyst differentiation is expressed at spatially localized sites.
 
• Elhai J, Wolk CP (1990). Developmental regulation and spatial pattern of expression of the structural genes for nitrogenase in the cyanobacterium Anabaena. EMBO J 9:3379-3388. Abstract

From my post-doc days in Peter's lab. It says that genes expressed in heterocysts require developmental signals, not merely the environmental conditions that are present in differentiated cells.

• Chiu WL, Peters GA, Levieille G, Still P, Cousins S, Osborne B, Elhai J (2005). Nitrogen deprivation and symbiotic gland development. Plant Physiol (in press). Full text
   
• John C Meeks and Jeff Elhai (2002). Regulation of cellular differentiation in filamentous cyanobacteria in free-living and plant-associated symbiotic growth states. Microbiology and Molecular Biology Reviews 66:94-121. Abstract / Full Text

First part of review discusses current thinking regarding controls over patterned heterocyst differentiation. Second part discusses how plants might use these controls for their own purposes.
 
• Gantar M, Elhai J (1999). Colonization of wheat para-nodules by the N₂-fixing cyanobacterium Nostoc sp. strain 2S9B. New Phytologist 141:373-379. Abstract / Full Text

Product of my now long distance collaboration with Miro Gantar. Many nitrogen-fixers can infect artificially nodulated plants, but this strain of Nostoc is able to both infect and (unlike all the rest) fix nitrogen under fully aerobic conditions..
 
• Ow MC, Gantar M, Elhai J (1999). Reconstitution of a cycad-cyanobacterial association. Symbiosis 27:125-134. Abstract / Full Text

Maria Ow's project, completed when she was a senior undergraduate. Miro was a post-doc in my lab at the time. My interest in plant-cyanobacterial symbioses has shifted to the more tractable system of symbiosis with the bryophyte Anthoceros, in collaboration with Jack Meeks and others in the Nostoc genome project.

• Elhai J, Taton A, Massar JP, Myers JK, Travers M, Casey J, Slupesky M, Shrager J (2009). BioBIKE: A web-based, programmable, integrated biological knowledge base. Nucl Acids Res 37:W28-W32. Abstract/Full text
   
• Elhai J, Kato M, Cousins S, Lindblad P, Costa JL (2008). Very small mobile repeated elements in cyanobacterial genomes. Genome Res 18:1484-1499. Full text
   
• Massar JP, Travers M, Elhai J, and Shrager J (2005). BioLingua: a programmable knowledge environment for biologists. Bioinformatics 21:199-207. Full Text
   
• Meeks JC, Elhai J, Potts M, Thiel T, Larimer F, Lamerdin J, Predki P, Atlas R (2001) An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium. Photosyn Res 70:85-106. Abstract

First look at the genome of a cyanobacterium capable of symbiotic association with a variety of plants.
 
• Elhai J (2001). Determination of bias in the relative abundance of oligonucleotides in DNA sequences. J. Comput. Biology 8:151-175. Abstract / Full Text
• Vogel S, Hoke K, Elhai J (2001) Appendix: Simplified expressions of a measure of compositional bias. J. Comput. Biology 8:170-175. Full Text

Lays the basis for studying underrepresented and overrepresented oligonucleotides in genomic sequences.. Suzanne Vogel was an undergraduate who did as much as anyone in working out the mathematical proofs for the key relationships used in the paper. Kathy Hoke is a faculty member in the math department at University of Richmond.
 
• Matveyev, AV, Young KT, Meng A, Elhai J (2001). DNA methyltransferases of the cyanobacterium Anabaena PCC 7120. Nucl Acids Res 29:1491-1506. Abstract / Full Text

Rationally defines class of DNA modifying enzymes. Contributes to understanding of horizontal transfer of genes. KT, an undergraduate, did much of the theoretical work as well as some cloning, Another undergraduate, Andrew, cloned and characterized one of the genes. Andrey is a research associate in my lab. We have since used these cloned genes to disrupt DNA modification in Anabaena and thereby affect heterocyst differentiation.
 
• Elhai J, Cai Y, Wolk CP (1994). Conduction of pEC22, a plasmid coding for MR.EcoT22I, mediated by a resident Tn3-like transposon, Tn5396. J Bacteriol 176:5059-5067. Abstract

Ignore the obscure title. The main point of interest in this article is a model to explain the evolution of ends of transposons, and experimental support for that model. Yuping Cai was a graduate student in the lab.

• Elhai J, Vepritskiy A, Muro-Pastor AM, Flores E, Wolk CP (1997). Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120. J Bacteriol 179:1998-2005. Abstract / Full Text

Conjugation has been used by labs throughout the world to get DNA into cyanobacteria since Peter and I developed the system [Elhai & Wolk (1988)]. This paper puts the method on a sound theoretical footing. Alexey Vepritskiy did some of the functional tests, and Alicia Muro-Pastor and Enrique Flores analyzed the restriction enzymes of Anabaena.
 
• Elhai J (1993). Strong and regulated promoters in the cyanobacterium Anabaena PCC 7120. FEMS Microbiol Lett 114:179-184. Abstract

Characterizes cyanobacterial and foreign promoters that have since been used to drive expression of genes in Anabaena and other cyanobacteria.
 
• Elhai J, Wolk CP (1988). A versatile class of positive selection vectors based on the nonviability of palindrome-containing plasmids that allows cloning into long polylinkers. Gene 68:119-138. Abstract

One part of the article describes a novel vector that selects by its own viability for inserts and describes a method of making them. A second part describes several antibiotic-resistance cassettes. These tools have been used extensively by the cyanobacterial community and others.