Jeff Elhai (Research)
Selected Publications

- Molecular biology of patterned differentiation in cyanobacteria
- Comparative genomic analysis of repetitive elements
- Symbiotic association of cyanobacteria with plants
- Molecular tools for the study of cyanobacteria
- Personal programming by computationally naive researchers

Molecular biology of patterned differentiation in cyanobacteria

  • Elhai J, Khudyakov IY (to be submitted). Ancient association of the regulator HetR and an RGSGR pentapeptide-containing protein (PatX) with multicellularity in cyanobacteria. Abstract
    Identifies a previously unrecognized protein, PatX, that appeared at the dawn of multicellularity along with a transcriptional activator, HetR. The PatX/HetR system was taken over and expanded by heterocyst-forming cyanobacteria to regulate differentiation.
     
  • Corrales-Guerrero L, Mariscal V, Nürnberg DJ, Elhai J, Mullineaux CW, Flores E, Herrero A (2014). Subcellular localization and clues for the function of the HetN factor influencing heterocyst distribution in Anabaena sp. strain PCC 7120. J Bacteriol 196:3452-3460. Abstract / Full Text
    Characterizes HetN, a negative regulator of heterocyst differentiation. My major contribution was to establish that HetN is confined to a small group of cyanobacteria and is absent in most that differentiate spaced heterocysts.
     
  • 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. Abstract
    Scientific advance: Shows how expression of carbon metabolism genes during differentiation fits with physiological needs.
    Technical advance: Addresses special problems in normalizing cyanobacterial microarrays
     
  • Meeks JC, Elhai J (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 and proposes models that encompass what is known.
    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 / Full Text
    Scientific advance: Demonstrating that a gene, hepA, known to be important in heterocyst differentiation is expressed at spatially localized sites.
    Technical advance: Using RNA polymerase from phage T7 to amplify weak transcription made visible by fusion of gene to luxAB (encoding luciferase) -- Peter Wolk's idea, I believe.
     
  • 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 / Full Text
    Scientific advance: The expression nitrogenase genes depends on developmental signals, not merely the environmental conditions that prevail in differentiated cells.
    Technical advance: Established a means to determine gene expression in individual bacterial cells, through transcriptional fusions to luciferase genes.
Comparative genomic analysis of repetitive elements
  • Elhai J (2015). Highly iterated palindromic sequences (HIPs) and their relationship to DNA methyltransferases. Life 5:921-948. Abstract / Full Text
    Proposes functional explanation for the occurrence of the most highly iterated dispersed repeat known in bacterial genomes, based on biased mismatch repair.
     
  • Elhai J, Liu H, Taton A (2012). Detection of horizontal transfer of individual genes by anomalous oligomer frequencies. BMD Genomics 13:245. Abstract / Full Text
    Describes improved method for detecting genes arising in genome by horizontal gene transfer.
     
  • Elhai J, Kato M, Cousins S, Lindblad P, Costa JL (2008). Very small mobile repeated elements in cyanobacterial genomes. Genome Res 18:1484-1499. Abstract / Full Text
    Describes and characterizes what are probably the smallest known mobile elements
     
  • 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 / Full Text
    My contribution was an analysis of methylation sites and repeated sequences in 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.
    Vogel S, Hoke K, Elhai J (2001) Appendix: Simplified expressions of a measure of compositional bias. J. Comput. Biology 8:170-175. Abstract / Full Text
    Provides a simplified method for calculating the total compositional bias of an oligonucleotide in a genome, including bias of non-contiguous subsequences, proves that the commonly used measure of bias -- calculated from the maximal order Markov model -- is simply the total compositional bias when non-contiguous subsequences are non-biased, and finally shows that in real genomes, non-contiguous subsequences are significantly biased, so the common measure is often misleading.
     
  • 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 a class of DNA modifying enzymes unassociated with restriction enzymes and characterizes all methyltransferases within the genome of a cyanobacterium. Provides evidence for large scale horizontal gene transfer amongst cyanobacteria.
     
  • 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 / Full Text
    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.
Symbiotic association of cyanobacteria with plants
  • Khamar HJ, Breathwaite EK, Prasse CE, Fraley ER, Secor CR, Chibane FL, Elhai J, Chiu WL (2010). Multiple roles of soluble sugars in the establishment of Gunnera-Nostoc endosymbiosis. Plant Physiol 154:1381-1389. Abstract / Full Text
    Signaling roles of simple sugars in communication between plant host and symbiotic cyanobacterium.
     
  • Chiu WL, Peters GA, Levieille G, Still P, Cousins S, Osborne B, Elhai J (2005). Nitrogen deprivation and symbiotic gland development. Plant Physiol 139:224-230. Abstract / Full Text
    The formation of symbiotic cavities occurs in response to environmental conditions, independent of the presence of the symbiotic cyanobacterium
     
  • Meeks JC, Elhai J (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 and proposes models that encompass what is known.
    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
    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, and it does so with a plant of agronomic importance.
     
  • Ow MC, Gantar M, Elhai J (1999). Reconstitution of a cycad-cyanobacterial association. Symbiosis 27:125-134. Abstract / Full Text
    Established that the symbiosis between a cyanobacterium and a gymnosperm could be reconstituted in the laboratory. Second instance of a reconstitution of any cyanobacterial symbiosis with a seed plant. Maria Ow's project, completed when she was a senior undergraduate.
Molecular tools for the study of cyanobacteria
  • 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
    For years, conjugatal transfer of DNA into filamentous cyanobacteria was the only reliable way to manipulate the genomes of these strains. This work put the technique on a sound theoretical footing, quantitating the effect of restriction on conjugal efficiency.
     
  • Elhai J (1993). Strong and regulated promoters in the cyanobacterium Anabaena PCC 7120. FEMS Microbiol Lett 114:179-184. Abstract / Full Text
    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 / Full Text
    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.
     
  • Elhai J, Wolk CP (1988). Conjugal transfer of DNA to cyanobacteria. Methods Enzymol 167:747-754. Abstract / Full Text
    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.
Personal programming by computationally naive researchers
  • Elhai J (2010). Humans, computers, and the route to biological insights: Retaining our capacity for surprise. J Comput Biol 18:857-878. Full Text
    Argues that researchers in biology must embrace computer programming for themselves in order to maintain creativity. An alliance between researchers and programmers is not enough.
     
  • 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
    Presents a graphical programming interface integrated with the data useful to defined communities of researchers.
     
  • Massar JP, Travers M, Elhai J, and Shrager J (2005). BioLingua: a programmable knowledge environment for biologists. Bioinformatics 21:199-207. Abstract / Full Text
    Presents a text-based web interface that integrates a rich set of bioinformatic tools with the genomic data.