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gene","volume":"4","author":"B Kunkel","year":"1990","journal-title":"Genes Dev"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/MMBR.57.1.1-33.1993","article-title":"<italic>Bacillus subtilis<\/italic> sporulation: regulation of gene expression and control of morphogenesis","volume":"57","author":"J Errington","year":"1993","journal-title":"Microbiol Rev"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/0378-1119(94)00822-A","article-title":"Cloning and characterization of a <italic>Bacillus thuringiensis<\/italic> homolog of the <italic>spoIIID<\/italic> gene from <italic>Bacillus subtilis<\/italic>","volume":"154","author":"H Yoshisue","year":"1995","journal-title":"Gene"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"7341","DOI":"10.1128\/jb.175.22.7341-7347.1993","article-title":"Multilevel regulation of the sporulation transcription factor sigma K in <italic>Bacillus subtilis<\/italic>","volume":"175","author":"V Oke","year":"1993","journal-title":"J Bacteriol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"4590","DOI":"10.1128\/AEM.00304-12","article-title":"Involvement of <italic>Clostridium botulinum<\/italic> ATCC 3502 sigma factor K in early-stage sporulation","volume":"78","author":"DG Kirk","year":"2012","journal-title":"Appl Environ Microbiol"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"8063","DOI":"10.1073\/pnas.140209597","article-title":"The transcriptional profile of early to middle sporulation in <italic>Bacillus subtilis<\/italic>","volume":"97","author":"P Fawcett","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"5226","DOI":"10.1128\/jb.171.9.5226-5228.1989","article-title":"Influence of <italic>spo<\/italic> mutations on sigma E synthesis in <italic>Bacillus subtilis<\/italic>","volume":"171","author":"RM Jonas","year":"1989","journal-title":"J Bacteriol"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"2012","DOI":"10.1073\/pnas.92.6.2012","article-title":"Identification of a gene, <italic>spoIIR<\/italic>, that links the activation of sigma E to the transcriptional activity of sigma F during sporulation in <italic>Bacillus subtilis<\/italic>","volume":"92","author":"ML Karow","year":"1995","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1038\/nature08150","article-title":"Partial penetrance facilitates developmental evolution in bacteria","volume":"460","author":"A Eldar","year":"2009","journal-title":"Nature"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"2813","DOI":"10.1128\/jb.178.10.2813-2817.1996","article-title":"Analysis of the role of prespore gene expression in the compartmentalization of mother cell-specific gene expression during sporulation of <italic>Bacillus subtilis<\/italic>","volume":"178","author":"L Zhang","year":"1996","journal-title":"J Bacteriol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"7181","DOI":"10.1128\/JB.00915-07","article-title":"Essential internal promoter in the spoIIIA locus of <italic>Bacillus subtilis<\/italic>","volume":"189","author":"C Guillot","year":"2007","journal-title":"J Bacteriol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/0092-8674(90)90362-I","article-title":"A forespore checkpoint for mother cell gene expression during development in <italic>B. subtilis<\/italic>","volume":"62","author":"S Cutting","year":"1990","journal-title":"Cell"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1128\/JB.01778-12","article-title":"Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in <italic>Bacillus subtilis<\/italic>","volume":"195","author":"B Traag","year":"2013","journal-title":"J Bacteriol"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.cell.2005.02.032","article-title":"Developmental commitment in a bacterium","volume":"121","author":"J Dworkin","year":"2005","journal-title":"Cell"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1111\/j.1365-2958.2005.04811.x","article-title":"Engulfment-regulated proteolysis of SpoIIQ: evidence that dual checkpoints control sigma activity","volume":"58","author":"X Jiang","year":"2005","journal-title":"Mol Microbiol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1046\/j.1365-2958.1997.2091573.x","article-title":"SpoIVB has two distinct functions during spore formation in <italic>Bacillus subtilis<\/italic>","volume":"23","author":"V Oke","year":"1997","journal-title":"Mol Microbiol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/1471-2164-13-102","article-title":"Genome-wide dynamic transcriptional profiling in <italic>Clostridium beijerinckii<\/italic> NCIMB 8052 using single-nucleotide resolution RNA-Seq","volume":"13","author":"Y Wang","year":"2012","journal-title":"BMC Genomics"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1128\/JCM.15.3.443-446.1982","article-title":"Use of sodium taurocholate to enhance spore recovery on a medium selective for <italic>Clostridium difficile<\/italic>","volume":"15","author":"KH Wilson","year":"1982","journal-title":"J Clin Microbiol"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.mimet.2007.05.021","article-title":"The ClosTron: a universal gene knock-out system for the genus Clostridium","volume":"70","author":"JT Heap","year":"2007","journal-title":"J Microbiol Methods"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1099\/jmm.0.45790-0","article-title":"Generation of an erythromycin-sensitive derivative of <italic>Clostridium difficile<\/italic> strain 630 (630Delta<italic>erm<\/italic>) and demonstration that the conjugative transposon Tn916DeltaE enters the genome of this strain at multiple sites","volume":"54","author":"HA Hussain","year":"2005","journal-title":"J Med Microbiol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.mimet.2009.05.004","article-title":"A modular system for Clostridium shuttle plasmids","volume":"78","author":"JT Heap","year":"2009","journal-title":"J Microbiol Methods"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(\u2212Delta Delta C(T)) Method","volume":"25","author":"KJ Livak","year":"2001","journal-title":"Methods"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/S1046-2023(03)00155-5","article-title":"Normalization of cDNA microarray data","volume":"31","author":"GK Smyth","year":"2003","journal-title":"Methods"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","author":"Y Benjamini","year":"1995","journal-title":"J Roy Statist Soc Ser"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/BF02759643","article-title":"GenomeExplorer: software for analysis of complete bacterial genomes","volume":"34","author":"A Mironov","year":"2000","journal-title":"Mol Biol (Mosk)"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"D93","DOI":"10.1093\/nar\/gkm910","article-title":"DBTBS: a database of transcriptional regulation in <italic>Bacillus subtilis<\/italic> containing upstream intergenic conservation information","volume":"36","author":"N Sierro","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"3632","DOI":"10.1128\/JB.181.12.3632-3643.1999","article-title":"A <italic>Bacillus subtilis<\/italic> secreted protein with a role in endospore coat assembly and function","volume":"181","author":"M Serrano","year":"1999","journal-title":"J Bacteriol"}],"container-title":["PLoS 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