Maliga, P.  2014.  Chloroplast Biotechnology: Methods and Protocols. Methods in Molecular Biology. 1132Website
Book Chapter
Severinov, K, Semenova E, Kazakov T.  2011.  Class I microcins: Their structures activities, and mechanisms of resistance. Prokaryotic Antimicrobial Peptides: from Genes to Applications. :289-308.
Messing, J, Holding D.  2013.  Evolution, Structure, and Function of Prolamin Storage Proteins.. Seed Genomics. :139-158.
Li, Y., Segal, G., Wang, Q., Dooner HK.  2013.  Gene tagging with engineered Ds elements in maize. Methods in Molecular Biology: Plant Transposable Elements. :83-99.
Messing, J, Bennetzen J.  2008.  Grass Genome Structure and Evolution. Genome Dynamics. 4:41-56.
Li, Y., Dooner HK.  2012.  Helitron Proliferation and Gene-Fragment Capture. Topics in Current Genetics, 24: Plant Transposable Elements- Impact on Genome Structure and Function. :193-227.
Nasr, I, Messing J, Ciclitira PJ.  2014.  Novel and Experimental Therapies on the Horizon. Celiac Disease, Clinical Gastroenterology. :193-208.
Zhang, W, Messing J.  In Press.  PacBio RS for gene family studies. Methods in Molecular Biology. Haplotyping.
Tungsuchat-Huang, T, Maliga P.  2014.  Plastid marker gene excision in greenhouse-grown tobacco by Agrobacterium-delivered Cre recombinase. Chloroplast Biotechnology. 1132:205-220. Abstract
Uniform transformation of the thousands of plastid genome (ptDNA) copies in a cell is driven by selection for plastid markers. When each of the plastid genome copies is uniformly altered, the marker gene is no longer needed. Plastid markers have been efficiently excised by site-specific recombinases expressed from nuclear genes either by transforming tissue culture cells or introducing the genes by pollination. Here we describe a protocol for the excision of plastid marker genes directly in tobacco (Nicotiana tabacum) plants by the Cre recombinase. Agrobacterium encoding the recombinase on its T-DNA is injected at an axillary bud site of a decapitated plant, forcing shoot regeneration at the injection site. The excised plastid marker, the bar au gene, confers a visual aurea leaf phenotype; thus marker excision via the flanking recombinase target sites is recognized by the restoration of normal green color of the leaves. The bar au marker-free plastids are transmitted through seed to the progeny. PCR and DNA gel blot (Southern) protocols to confirm transgene integration and plastid marker excision are also provided herein.
Maliga, P, Tungsuchat-Huang T.  2014.  Plastid transformation in Nicotiana tabacum and Nicotiana sylvestris by biolistic DNA delivery to leaves. Chloroplast Biotechnology: Methods and Protocols. 1132:147-163. Abstract
The protocol we report here is based on biolistic delivery of the transforming DNA to tobacco leaves, selection of transplastomic clones by spectinomycin resistance and regeneration of plants with uniformly transformed plastid genomes. Because the plastid genome of Nicotiana tabacum derives from Nicotiana sylvestris, and the two genomes are highly conserved, vectors developed for N. tabacum can be used in N. sylvestris. Also, the tissue culture responses of N. tabacum cv. Petit Havana and N. sylvestris accession TW137 are similar, allowing plastid engineering protocols developed for N. tabacum to be directly applied to N. sylvestris. However, the tissue culture protocol is applicable only in a subset of N. tabacum cultivars. Here we highlight differences between the protocols for the two species. We describe updated vectors targeting insertions in the unique and repeated regions of the plastid genome as well as systems for marker excision. The simpler genetics of the diploid N. sylvestris, as opposed to the allotetraploid N. tabacum, make it an attractive model for plastid transformation.
Maliga, P.  2012.  Plastid transformation in flowering plants. Genomics of Chloroplasts and Mitochondria. 35:393-414. Abstract
The plastid genome of higher plants is relatively small, 120–230-kb in size, and present in up to 10,000 copies per cell. Standard protocols for the introduction of transforming DNA employ biolistic DNA delivery or polyethylene glycol treatment. Genetically stable, transgenic plants are obtained by modification of the plastid genome by homologous recombination, followed by selection for the transformed genome copy by the expression of marker genes that protect the cells from selective agents. Commonly used selective agents are antibiotics, including spectinomycin, streptomycin, kanamycin and chloramphenicol. Selection for resistance to amino acid analogues has also been successful. The types of plastid genome manipulations include gene deletion, gene insertion, and gene replacement, facilitated by specially designed transformation vectors. Methods are also available for post-transformation removal of marker genes. The model species for plastid genetic manipulation is Nicotiana tabacum, in which most protocols have been tested. Plastid transformation is also available in several solanaceous crops (tomato, potato, eggplant) and ornamental species (petunia, Nicotianasylvestris). Significant progress has been made with Brasssicaceae including cabbage, oilseed rape and Arabidopsis. Recent additions to the crops in which plastid transformation is reproducibly obtained are lettuce, soybean and sugar beet. The monocots are a taxonomic group recalcitrant to plastid transformation; initial inroads have been made only in rice.
Messing, J.  2009.  The Polyploid Origin of Maize. The Maize Handbook: Domestication, Genetics, and Genome. :221-238.
Pillitteri LJ, DJ.  2013.  Stomatal development in Arabidopsis.. Arabidopsis Book. :10.1199/tab.0162.
Messing, J.  2009.  The Structure of the Maize Genome. Molecular Genetic Approaches to Maize Improvement, Biotechnology in Agriculture and Forestry. 63:213-230.
Mehrotra, S, Hawley RS, McKim KS.  2007.  Synapsis, double strand breaks and domains of crossover control in females. Recombination and meiosis, crossing-over and disjunction . :125-152.
Savage-Dunn, C, Padgett RW.  2017.  The TGF-β Family in Caenorhabditis elegans. The Biology of the TGF-β Family.
Dooner, HK, Weil CF.  2013.  Transposons and gene creation. Molecular Genetics and Epigenetics of Plant Transposons. :143-167.
Wu, Y, Messing J.  In Press.  Understanding and improving protein traits in maize seeds. Achieving Sustainable Maize Cultivation.
Pougach, K, Severinov K.  2012.  Use of semi-quantitative Northern blot analysis to determine relative quantities of bacterial CRISPR transcripts. Methods in Molecular Biology on Bacterial Regulatory RNA . :73-86.
Journal Article
Bolot, S, Abrouk M, Masood-Quraishi U, Stein N, Messing J, Feuillet C, Salse J.  2009.  The 'inner circle' of the cereal genomes. Curr Opin Plant Biol. 12:119-25. AbstractWebsite
Early marker-based macrocolinearity studies between the grass genomes led to arranging their chromosomes into concentric 'crop circles' of synteny blocks that initially consisted of 30 rice-independent linkage groups representing the ancestral cereal genome structure. Recently, increased marker density and genome sequencing of several cereal genomes allowed the characterization of intragenomic duplications and their integration with intergenomic colinearity data to identify paleo-duplications and propose a model for the evolution of the grass genomes from a common ancestor. On the basis of these data an 'inner circle' comprising five ancestral chromosomes was defined providing a new reference for the grass chromosomes and new insights into their ancestral relationships and origin, as well as an efficient tool to design cross-genome markers for genetic studies.
Jiao, X, Doamekpor S, Bird JG, Nickels BE, Tong L, Hart RP, Kiledjian M.  2017.  5′-end Nicotinamide Adenine Dinucleotide cap in human cells promotes RNA decay through DXO-mediated deNADding.. Cell. 168(6):1015-1027.
McKim, KS, Jang JK, Sekelsky JJ, Laurencon A, Hawley RS.  2000.  mei-41 is required for precocious anaphase in Drosophila females. Chromosoma. 109:44-49.
Hari, KL, Santerre A, Sekelsky JJ, McKim KS, Boyd JB, Hawley RS.  1995.  The mei-41 gene of D. melanogaster is a structural and function homolog of the human ataxia telangiectasia gene. Cell. 82:815-821.
McKim, KS, Hayashi-Hagihara A.  1998.  mei-W68 in Drosophila melanogaster encodes a Spo11 homolog: evidence that the mechanism for initiating meiotic recombination is conserved. Genes & Dev.. 12:2932-42. AbstractWebsite
Meiotic recombination requires the action of several gene products in both Saccharomyces cerevisiae and Drosophila melanogaster. Genetic studies in D. melanogaster have shown that the mei-W68 gene is required for all meiotic gene conversion and crossing-over. We cloned mei-W68 using a new genetic mapping method in which P elements are used to promote crossing-over at their insertion sites. This resulted in the high-resolution mapping of mei-W68 to a 18-kb region that contains a homolog of the S. cerevisiae spo11 gene. Molecular analysis of several mutants confirmed that mei-W68 encodes an spo11 homolog. Spo11 and MEI- W68 are members of a family of proteins similar to a novel type II topoisomerase. On the basis of this and other lines of evidence, Spo11 has been proposed to be the enzymatic activity that creates the double- strand breaks needed to initiate meiotic recombination. This raises the possibility that recombination in Drosophila is also initiated by double-strand breaks. Although these homologous genes are required absolutely for recombination in both species, their roles differ in other respects. In contrast to spo11, mei-W68 is not required for synaptonemal complex formation and does have a mitotic role.