Merge branch 'master' of http://pakal.ccg.unam.mx/bioNLP-UNAM/useless

@@ -21,7 +21,7 @@ The main method follows the next pipeline:
 For filtering unknown abstracts run
 For filtering unknown abstracts run
 
 
 ```bash
 ```bash
-$ python filter_abstracts.py --input data/ecoli_abstracts/useful_abstracts.txt
+$ python filter_abstracts.py --input data/test_abstracts.txt
 ```
 ```
 The predictions will be stored by default at `filter_output/`, unless a different directory is specified by means of the `--out` option. The default names containing the predicitons are 
 The predictions will be stored by default at `filter_output/`, unless a different directory is specified by means of the `--out` option. The default names containing the predicitons are 
 
 

+
+1. Methods Mol Biol. 2018;1737:77-88. doi: 10.1007/978-1-4939-7634-8_5.
+
+Identification of New Bacterial Small RNA Targets Using MS2 Affinity Purification
+Coupled to RNA Sequencing.
+
+Carrier MC(1), Laliberté G(1), Massé E(2).
+
+Author information: 
+(1)Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke,
+QC, Canada.
+(2)Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke,
+QC, Canada. eric.masse@usherbrooke.ca.
+
+Small regulatory RNAs (sRNAs) are ubiquitous regulatory molecules expressed in
+living cells. In prokaryotes, sRNAs usually bind to target mRNAs to either
+promote their degradation or interfere with translation initiation. Because a
+single sRNA can regulate a considerable number of target mRNAs, we seek to
+identify those targets rapidly and reliably. Here, we present a robust method
+based on the co-purification of target mRNAs bound to MS2-tagged sRNAs expressed 
+in vivo. After purification of the tagged-sRNA, we use RNAseq to determine the
+identity of all RNA interacting partners and their enrichment level. We describe 
+how to analyze the RNAseq data through the Galaxy Project Platform bioinformatics
+tools to identify new mRNA targets. This technique is applicable to most sRNAs of
+E. coli and Salmonella.
+
+DOI: 10.1007/978-1-4939-7634-8_5 
+PMID: 29484588 
+
+
+2. BMC Evol Biol. 2018 Feb 12;18(1):21. doi: 10.1186/s12862-018-1134-0.
+
+A novel short L-arginine responsive protein-coding gene (laoB) antiparallel
+overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 
+Sakai originated by overprinting.
+
+Hücker SM(1)(2), Vanderhaeghen S(1), Abellan-Schneyder I(1)(3), Wecko R(1), Simon
+S(4), Scherer S(1)(5), Neuhaus K(6)(7).
+
+Author information: 
+(1)Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische
+Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
+(2)Fraunhofer ITEM-R, Am Biopark 9, 93053, Regensburg, Germany.
+(3)Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische
+Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
+(4)Department of Computer and Information Science, University of Konstanz, Box
+78, 78457, Konstanz, Germany.
+(5)ZIEL - Institute for Food & Health, Technische Universität München,
+Weihenstephaner Berg 3, 85354, Freising, Germany.
+(6)Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische
+Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
+neuhaus@tum.de.
+(7)Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische
+Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
+neuhaus@tum.de.
+
+BACKGROUND: Due to the DNA triplet code, it is possible that the sequences of two
+or more protein-coding genes overlap to a large degree. However, such non-trivial
+overlaps are usually excluded by genome annotation pipelines and, thus, only a
+few overlapping gene pairs have been described in bacteria. In contrast,
+transcriptome and translatome sequencing reveals many signals originated from the
+antisense strand of annotated genes, of which we analyzed an example gene pair in
+more detail.
+RESULTS: A small open reading frame of Escherichia coli O157:H7 strain Sakai
+(EHEC), designated laoB (L-arginine responsive overlapping gene), is embedded in 
+reading frame -2 in the antisense strand of ECs5115, encoding a CadC-like
+transcriptional regulator. This overlapping gene shows evidence of transcription 
+and translation in Luria-Bertani (LB) and brain-heart infusion (BHI) medium based
+on RNA sequencing (RNAseq) and ribosomal-footprint sequencing (RIBOseq). The
+transcriptional start site is 289 base pairs (bp) upstream of the start codon and
+transcription termination is 155 bp downstream of the stop codon. Overexpression 
+of LaoB fused to an enhanced green fluorescent protein (EGFP) reporter was
+possible. The sequence upstream of the transcriptional start site displayed
+strong promoter activity under different conditions, whereas promoter activity
+was significantly decreased in the presence of L-arginine. A strand-specific
+translationally arrested mutant of laoB provided a significant growth advantage
+in competitive growth experiments in the presence of L-arginine compared to the
+wild type, which returned to wild type level after complementation of laoB in
+trans. A phylostratigraphic analysis indicated that the novel gene is restricted 
+to the Escherichia/Shigella clade and might have originated recently by
+overprinting leading to the expression of part of the antisense strand of
+ECs5115.
+CONCLUSIONS: Here, we present evidence of a novel small protein-coding gene laoB 
+encoded in the antisense frame -2 of the annotated gene ECs5115. Clearly, laoB is
+evolutionarily young and it originated in the Escherichia/Shigella clade by
+overprinting, a process which may cause the de novo evolution of bacterial genes 
+like laoB.
+
+DOI: 10.1186/s12862-018-1134-0 
+PMCID: PMC5810103
+PMID: 29433444 
+
+
+3. PLoS One. 2017 Sep 13;12(9):e0184119. doi: 10.1371/journal.pone.0184119.
+eCollection 2017.
+
+Discovery of numerous novel small genes in the intergenic regions of the
+Escherichia coli O157:H7 Sakai genome.
+
+Hücker SM(1)(2), Ardern Z(1)(2), Goldberg T(3), Schafferhans A(3), Bernhofer
+M(3), Vestergaard G(4), Nelson CW(5), Schloter M(4), Rost B(3), Scherer S(1)(2), 
+Neuhaus K(1)(6).
+
+Author information: 
+(1)Chair for Microbial Ecology, Technische Universität München, Freising,
+Germany.
+(2)ZIEL - Institute for Food & Health, Technische Universität München, Freising, 
+Germany.
+(3)Department of Informatics-Bioinformatics & TUM-IAS, Technische Universität
+München, Garching, Germany.
+(4)Research Unit Environmental Genomics, Helmholtz Zentrum München, Neuherberg,
+Germany.
+(5)Sackler Institute for Comparative Genomics, American Museum of Natural History
+New York, New York, United States of America.
+(6)Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische
+Universität München, Freising, Germany.
+
+In the past, short protein-coding genes were often disregarded by genome
+annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of
+annotated genes have usually been interpreted to indicate either ncRNA or
+pervasive transcription. Therefore, in addition to the transcriptome, the
+translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain
+Sakai was determined at two optimal growth conditions and a severe stress
+condition combining low temperature and high osmotic pressure. All intergenic
+open reading frames potentially encoding a protein of ≥ 30 amino acids were
+investigated with regard to coverage by transcription and translation signals and
+their translatability expressed by the ribosomal coverage value. This led to
+discovery of 465 unique, putative novel genes not yet annotated in this E. coli
+strain, which are evenly distributed over both DNA strands of the genome. For 255
+of the novel genes, annotated homologs in other bacteria were found, and a
+machine-learning algorithm, trained on small protein-coding E. coli genes,
+predicted that 89% of these translated open reading frames represent bona fide
+genes. The remaining 210 putative novel genes without annotated homologs were
+compared to the 255 novel genes with homologs and to 250 short annotated genes of
+this E. coli strain. All three groups turned out to be similar with respect to
+their translatability distribution, fractions of differentially regulated genes, 
+secondary structure composition, and the distribution of evolutionary constraint,
+suggesting that both novel groups represent legitimate genes. However, the
+machine-learning algorithm only recognized a small fraction of the 210 genes
+without annotated homologs. It is possible that these genes represent a novel
+group of genes, which have unusual features dissimilar to the genes of the
+machine-learning algorithm training set.
+
+DOI: 10.1371/journal.pone.0184119 
+PMCID: PMC5597208
+PMID: 28902868  [Indexed for MEDLINE]
+
+
+4. Int J Genomics. 2017;2017:6489383. doi: 10.1155/2017/6489383. Epub 2017 Jul 16.
+
+Differential MicroRNA Analyses of Burkholderia pseudomallei- and Francisella
+tularensis-Exposed hPBMCs Reveal Potential Biomarkers.
+
+Cer RZ(1)(2), Herrera-Galeano JE(1)(2)(3), Frey KG(1)(2), Schully KL(1)(2), Luu
+TV(1)(2), Pesce J(1)(2)(4), Mokashi VP(1)(5), Keane-Myers AM(1)(2)(6),
+Bishop-Lilly KA(1)(2).
+
+Author information: 
+(1)Genomics and Bioinformatics Department, Biological Defense Research
+Directorate, Naval Medical Research Center, Frederick, MD, USA.
+(2)Henry M. Jackson Foundation for the Advancement of Military Medicine,
+Bethesda, MD, USA.
+(3)KCE Services and Consulting LLC, Columbia, MD, USA.
+(4)Division of Microbiology and Infectious Diseases, National Institute of
+Allergy and Infectious Diseases, Bethesda, MD, USA.
+(5)Navy Drug Screening Laboratory, Jacksonville, FL, USA.
+(6)Immunology, National Institute of Health, Bethesda, MD, USA.
+
+Increasing evidence that microRNAs (miRNAs) play important roles in the immune
+response against infectious agents suggests that miRNA might be exploitable as
+signatures of exposure to specific infectious agents. In order to identify
+potential early miRNA biomarkers of bacterial infections, human peripheral blood 
+mononuclear cells (hPBMCs) were exposed to two select agents, Burkholderia
+pseudomallei K96243 and Francisella tularensis SHU S4, as well as to the
+nonpathogenic control Escherichia coli DH5α. RNA samples were harvested at three 
+early time points, 30, 60, and 120 minutes postexposure, then sequenced. RNAseq
+analyses identified 87 miRNAs to be differentially expressed (DE) in a linear
+fashion. Of these, 31 miRNAs were tested using the miScript miRNA qPCR assay.
+Through RNAseq identification and qPCR validation, we identified differentially
+expressed miRNA species that may be involved in the early response to bacterial
+infections. Based upon its upregulation at early time points postexposure in two 
+different individuals, hsa-mir-30c-5p is a miRNA species that could be studied
+further as a potential biomarker for exposure to these gram-negative
+intracellular pathogens. Gene ontology functional analyses demonstrated that
+programmed cell death is the first ranking biological process associated with
+miRNAs that are upregulated in F. tularensis-exposed hPBMCs.
+
+DOI: 10.1155/2017/6489383 
+PMCID: PMC5534298
+PMID: 28791299 
+
+
+5. PLoS One. 2017 Jun 14;12(6):e0178966. doi: 10.1371/journal.pone.0178966.
+eCollection 2017.
+
+Intestinal organoids model human responses to infection by commensal and Shiga
+toxin producing Escherichia coli.
+
+Karve SS(1), Pradhan S(1), Ward DV(2), Weiss AA(1).
+
+Author information: 
+(1)Department of Molecular Genetics, Biochemistry, and Microbiology, University
+of Cincinnati, Cincinnati, Ohio, United States of America.
+(2)Center for Microbiome Research and Department of Microbiology and
+Physiological Systems, University of Massachusetts Medical School, Worcester,
+Massachusetts, United States of America.
+
+Infection with Shiga toxin (Stx) producing Escherichia coli O157:H7 can cause the
+potentially fatal complication hemolytic uremic syndrome, and currently only
+supportive therapy is available. Lack of suitable animal models has hindered
+study of this disease. Induced human intestinal organoids (iHIOs), generated by
+in vitro differentiation of pluripotent stem cells, represent differentiated
+human intestinal tissue. We show that iHIOs with addition of human neutrophils
+can model E. coli intestinal infection and innate cellular responses. Commensal
+and O157:H7 introduced into the iHIO lumen replicated rapidly achieving high
+numbers. Commensal E. coli did not cause damage, and were completely contained
+within the lumen, suggesting defenses, such as mucus production, can constrain
+non-pathogenic strains. Some O157:H7 initially co-localized with cellular actin. 
+Loss of actin and epithelial integrity was observed after 4 hours. O157:H7 grew
+as filaments, consistent with activation of the bacterial SOS stress response.
+SOS is induced by reactive oxygen species (ROS), and O157:H7 infection increased 
+ROS production. Transcriptional profiling (RNAseq) demonstrated that both
+commensal and O157:H7 upregulated genes associated with gastrointestinal
+maturation, while infection with O157:H7 upregulated inflammatory responses,
+including interleukin 8 (IL-8). IL-8 is associated with neutrophil recruitment,
+and infection with O157:H7 resulted in recruitment of human neutrophils into the 
+iHIO tissue.
+
+DOI: 10.1371/journal.pone.0178966 
+PMCID: PMC5470682
+PMID: 28614372  [Indexed for MEDLINE]
+
+
+6. BMC Genet. 2017 Mar 7;18(1):21. doi: 10.1186/s12863-017-0488-4.
+
+Deciphering alternative splicing and nonsense-mediated decay modulate expression 
+in primary lymphoid tissues of birds infected with avian pathogenic E. coli
+(APEC).
+
+Sun H(1).
+
+Author information: 
+(1)College of Animal Science and Technology, Yangzhou University, Yangzhou,
+Jiangsu, 225009, China. hongyans2392@163.com.
+
+BACKGROUND: Avian pathogenic E. coli (APEC) can lead to a loss in millions of
+dollars in poultry annually because of mortality and produce contamination.
+Studies have verified that many immune-related genes undergo changes in
+alternative splicing (AS), along with nonsense mediated decay (NMD), to regulate 
+the immune system under different conditions. Therefore, the splicing profiles of
+primary lymphoid tissues with systemic APEC infection need to be comprehensively 
+examined.
+RESULTS: Gene expression in RNAseq data were obtained for three different immune 
+tissues (bone marrow, thymus, and bursa) from three phenotype birds
+(non-challenged, resistant, and susceptible birds) at two time points.
+Alternative 5' splice sites and exon skipping/inclusion were identified as the
+major alternative splicing events in avian primary immune organs under systemic
+APEC infection. In this study, we detected hundreds of
+differentially-expressed-transcript-containing genes (DETs) between different
+phenotype birds at 5 days post-infection (dpi). DETs, PSAP and STT3A, with NMD
+have important functions under systemic APEC infection. DETs, CDC45, CDK1, RAG2, 
+POLR1B, PSAP, and DNASE1L3, from the same transcription start sites (TSS)
+indicate that cell death, cell cycle, cellular function, and maintenance were
+predominant in host under systemic APEC.
+CONCLUSIONS: With the use of RNAseq technology and bioinformatics tools, this
+study provides a portrait of the AS event and NMD in primary lymphoid tissues,
+which play critical roles in host homeostasis under systemic APEC infection.
+According to this study, AS plays a pivotal regulatory role in the immune
+response in chicken under systemic APEC infection via either NMD or alternative
+TSSs. This study elucidates the regulatory role of AS for the immune complex
+under systemic APEC infection.
+
+DOI: 10.1186/s12863-017-0488-4 
+PMCID: PMC5341183
+PMID: 28270101  [Indexed for MEDLINE]
+
+
+7. BMC Genomics. 2017 Feb 28;18(1):216. doi: 10.1186/s12864-017-3586-9.
+
+Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933
+(EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and 
+a peptide, RyhP.
+
+Neuhaus K(1)(2), Landstorfer R(3), Simon S(4), Schober S(5), Wright PR(6), Smith 
+C(6), Backofen R(6), Wecko R(3), Keim DA(4), Scherer S(3).
+
+Author information: 
+(1)Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan,
+Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising,
+Germany. neuhaus@tum.de.
+(2)Core Facility Microbiome/NGS, ZIEL Institute for Food & Health,
+Weihenstephaner Berg 3, D-85354, Freising, Germany. neuhaus@tum.de.
+(3)Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan,
+Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising,
+Germany.
+(4)Informatik und Informationswissenschaft, Universität Konstanz, D-78457,
+Konstanz, Germany.
+(5)Institut für Nachrichtentechnik, Universität Ulm, Albert-Einstein-Allee 43,
+D-89081, Ulm, Germany.
+(6)Bioinformatics Group, Department of Computer Science and BIOSS Centre for
+Biological Signaling Studies, Cluster of Excellence, University of Freiburg,
+D-79110, Freiburg, Germany.
+
+BACKGROUND: While NGS allows rapid global detection of transcripts, it remains
+difficult to distinguish ncRNAs from short mRNAs. To detect potentially
+translated RNAs, we developed an improved protocol for bacterial ribosomal
+footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A
+high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV)
+is expected to indicate a translated RNA, while a low RCV should point to a
+non-translated RNA.
+RESULTS: Based on their low RCV, 150 novel non-translated EHEC transcripts were
+identified as putative ncRNAs, representing both antisense and intergenic
+transcripts, 74 of which had expressed homologs in E. coli MG1655. Bioinformatics
+analysis predicted statistically significant target regulons for 15 of the
+intergenic transcripts; experimental analysis revealed 4-fold or higher
+differential expression of 46 novel ncRNA in different growth media. Out of 329
+annotated EHEC ncRNAs, 52 showed an RCV similar to protein-coding genes, of
+those, 16 had RIBOseq patterns matching annotated genes in other
+enterobacteriaceae, and 11 seem to possess a Shine-Dalgarno sequence, suggesting 
+that such ncRNAs may encode small proteins instead of being solely non-coding. To
+support that the RIBOseq signals are reflecting translation, we tested the
+ribosomal-footprint covered ORF of ryhB and found a phenotype for the encoded
+peptide in iron-limiting condition.
+CONCLUSION: Determination of the RCV is a useful approach for a rapid first-step 
+differentiation between bacterial ncRNAs and small mRNAs. Further, many known
+ncRNAs may encode proteins as well.
+
+DOI: 10.1186/s12864-017-3586-9 
+PMCID: PMC5331693
+PMID: 28245801  [Indexed for MEDLINE]
+
+
+8. ACS Appl Mater Interfaces. 2017 Mar 22;9(11):10047-10060. doi:
+10.1021/acsami.7b02380. Epub 2017 Mar 10.
+
+Transcriptome Analysis Reveals Silver Nanoparticle-Decorated Quercetin
+Antibacterial Molecular Mechanism.
+
+Sun D(1), Zhang W(1), Mou Z(1), Chen Y(1), Guo F(1), Yang E(1), Wang W(1).
+
+Author information: 
+(1)School of Life Sciences, Anhui Agricultural University , Hefei 230036, China.
+
+Facile and simple method is developed to synthesize silver-nanoparticle-decorated
+quercetin nanoparticles (QA NPs). Modification suggests that synergistic
+quercetin (Qe) improves the antibacterial effect of silver nanoparticles (Ag
+NPs). Characterization experiment indicates that QA NPs have a diameter of
+approximately 10 nm. QA NPs show highly effective antibacterial activities
+against drug-resistant Escherichia coli (E. coli) and Staphylococcus aureus (S.
+aureus). We explore antibacterial mechanisms using S. aureus and E. coli treated 
+with QA NPs. Through morphological changes in E. coli and S. aureus, mechanisms
+are examined for bacterial damage caused by particulate matter from local
+dissociation of silver ion and Qe from QA NPs trapped inside membranes. Moreover,
+we note that gene expression profiling methods, such as RNA sequencing, can be
+used to predict discover mechanisms of toxicity of QA NPs. Gene ontology (GO)
+assay analyses demonstrate the molecular mechanism of the antibacterial effect of
+QA NPs. Regarding cellular component ontology, "cell wall organization or
+biogenesis" (GO: 0071554) and "cell wall macromolecule metabolic process" (GO:
+0044036) are the most represented categories. The present study reports that
+transcriptome analysis of the mechanism offers novel insights into the molecular 
+mechanism of antibacterial assays.
+
+DOI: 10.1021/acsami.7b02380 
+PMID: 28240544 
+
+
+9. Biotechnol Biofuels. 2017 Feb 3;10:32. doi: 10.1186/s13068-017-0720-5.
+eCollection 2017.
+
+Development of a genetically programed vanillin-sensing bacterium for
+high-throughput screening of lignin-degrading enzyme libraries.
+
+Sana B(1), Chia KHB(2), Raghavan SS(1), Ramalingam B(3), Nagarajan N(2), Seayad
+J(3), Ghadessy FJ(1).
+
+Author information: 
+(1)p53 Laboratory, Agency for Science Technology And Research (ASTAR), 8A
+Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648 Singapore.
+(2)Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 
+138672 Singapore.
+(3)Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros,
+#07-01, Singapore, 138665 Singapore.
+
+BACKGROUND: Lignin is a potential biorefinery feedstock for the production of
+value-added chemicals including vanillin. A huge amount of lignin is produced as 
+a by-product of the paper industry, while cellulosic components of plant biomass 
+are utilized for the production of paper pulp. In spite of vast potential, lignin
+remains the least exploited component of plant biomass due to its extremely
+complex and heterogenous structure. Several enzymes have been reported to have
+lignin-degrading properties and could be potentially used in lignin biorefining
+if their catalytic properties could be improved by enzyme engineering. The much
+needed improvement of lignin-degrading enzymes by high-throughput selection
+techniques such as directed evolution is currently limited, as robust methods for
+detecting the conversion of lignin to desired small molecules are not available.
+RESULTS: We identified a vanillin-inducible promoter by RNAseq analysis of
+Escherichia coli cells treated with a sublethal dose of vanillin and developed a 
+genetically programmed vanillin-sensing cell by placing the 'very green
+fluorescent protein' gene under the control of this promoter. Fluorescence of the
+biosensing cell is enhanced significantly when grown in the presence of vanillin 
+and is readily visualized by fluorescence microscopy. The use of
+fluorescence-activated cell sorting analysis further enhances the sensitivity,
+enabling dose-dependent detection of as low as 200 µM vanillin. The biosensor is 
+highly specific to vanillin and no major response is elicited by the presence of 
+lignin, lignin model compound, DMSO, vanillin analogues or non-specific toxic
+chemicals.
+CONCLUSIONS: We developed an engineered E. coli cell that can detect vanillin at 
+a concentration as low as 200 µM. The vanillin-sensing cell did not show
+cross-reactivity towards lignin or major lignin degradation products including
+vanillin analogues. This engineered E. coli cell could potentially be used as a
+host cell for screening lignin-degrading enzymes that can convert lignin to
+vanillin.
+
+DOI: 10.1186/s13068-017-0720-5 
+PMCID: PMC5291986
+PMID: 28174601 
+
+
+10. PLoS Negl Trop Dis. 2017 Jan 6;11(1):e0005273. doi: 10.1371/journal.pntd.0005273.
+eCollection 2017 Jan.
+
+Transcriptome Sequencing Reveals Large-Scale Changes in Axenic Aedes aegypti
+Larvae.
+
+Vogel KJ(1), Valzania L(1), Coon KL(1), Brown MR(1), Strand MR(1).
+
+Author information: 
+(1)Department of Entomology, The University of Georgia, Athens, Georgia, United
+States of America.
+
+Mosquitoes host communities of microbes in their digestive tract that consist
+primarily of bacteria. We previously reported that Aedes aegypti larvae colonized
+by a native community of bacteria and gnotobiotic larvae colonized by only
+Escherichia coli develop very similarly into adults, whereas axenic larvae never 
+molt and die as first instars. In this study, we extended these findings by first
+comparing the growth and abundance of bacteria in conventional, gnotobiotic, and 
+axenic larvae during the first instar. Results showed that conventional and
+gnotobiotic larvae exhibited no differences in growth, timing of molting, or
+number of bacteria in their digestive tract. Axenic larvae in contrast grew
+minimally and never achieved the critical size associated with molting by
+conventional and gnotobiotic larvae. In the second part of the study we compared 
+patterns of gene expression in conventional, gnotobiotic and axenic larvae by
+conducting an RNAseq analysis of gut and nongut tissues (carcass) at 22 h
+post-hatching. Approximately 12% of Ae. aegypti transcripts were differentially
+expressed in axenic versus conventional or gnotobiotic larvae. However, this
+profile consisted primarily of transcripts in seven categories that included the 
+down-regulation of select peptidases in the gut and up-regulation of several
+genes in the gut and carcass with roles in amino acid transport, hormonal
+signaling, and metabolism. Overall, our results indicate that axenic larvae
+exhibit alterations in gene expression consistent with defects in acquisition and
+assimilation of nutrients required for growth.
+
+DOI: 10.1371/journal.pntd.0005273 
+PMCID: PMC5245907
+PMID: 28060822  [Indexed for MEDLINE]
+
+Conflict of interest statement: The authors have declared that no competing
+interests exist.
+
+
+11. Methods. 2017 Mar 15;117:28-34. doi: 10.1016/j.ymeth.2016.11.011. Epub 2016 Nov
+19.
+
+Identification of unknown RNA partners using MAPS.
+
+Lalaouna D(1), Prévost K(1), Eyraud A(1), Massé E(2).
+
+Author information: 
+(1)Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke,
+Québec J1E 4K8, Canada.
+(2)Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke,
+Québec J1E 4K8, Canada. Electronic address: eric.masse@usherbrooke.ca.
+
+Recent advances in high-throughput sequencing have led to an explosion in the
+rate of small regulatory RNAs (sRNAs) discovery among bacteria. However, only a
+handful of them are functionally characterized. Most of the time, little to no
+targets are known. In Lalaouna et al. (2015), we proposed a new technology to
+uncover sRNAs targetome, which is based on the MS2-affinity purification (MAPS). 
+We were able to prove its efficiency by applying it on well-characterized sRNAs
+of Escherichia coli. Thereafter, we adapted the procedure to other kind of RNA
+(mRNAs and tRNA-derived RNA fragments) and bacteria (pathogenic or Gram-positive 
+strains). Here, we clearly report all improvements and adjustments made to MAPS
+technology since it was originally reported.
+
+Copyright © 2016 Elsevier Inc. All rights reserved.
+
+DOI: 10.1016/j.ymeth.2016.11.011 
+PMID: 27876680  [Indexed for MEDLINE]
+
+
+12. FEMS Microbiol Lett. 2017 Jan;364(2). pii: fnw262. doi: 10.1093/femsle/fnw262.
+Epub 2016 Nov 16.
+
+Transcriptional and translational regulation by RNA thermometers, riboswitches
+and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and
+osmotic stress adaptation.
+
+Hücker SM(1), Simon S(2), Scherer S(1), Neuhaus K(3).
+
+Author information: 
+(1)Chair for Microbial Ecology, Technische Universität München, Weihenstephaner
+Berg 3, 85354 Freising, Germany.
+(2)Chair for Data Analysis and Visualization, Department of Computer and
+Information Science, University of Konstanz, Box 78, 78457 Konstanz, Germany.
+(3)Chair for Microbial Ecology, Technische Universität München, Weihenstephaner
+Berg 3, 85354 Freising, Germany neuhaus@wzw.tum.de.
+
+The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at
+lower temperatures compared to commensal E. coli Growth at environmental
+conditions displays complex challenges different to those in a host. EHEC was
+grown at 37°C and at 14°C with 4% NaCl, a combination of cold and osmotic stress 
+as present in the food chain. Comparison of RNAseq and RIBOseq data provided a
+snap shot of ongoing transcription and translation, differentiating
+transcriptional and post-transcriptional gene regulation, respectively. Indeed,
+cold and osmotic stress related genes are simultaneously regulated at both
+levels, but translational regulation clearly dominates. Special emphasis was
+given to genes regulated by RNA secondary structures in their 5'UTRs, such as RNA
+thermometers and riboswitches, or genes controlled by small RNAs encoded in trans
+The results reveal large differences in gene expression between short-time shock 
+compared to adaptation in combined cold and osmotic stress. Whereas the majority 
+of cold shock proteins, such as CspA, are translationally downregulated after
+adaptation, many osmotic stress genes are still significantly upregulated mainly 
+translationally, but several also transcriptionally.
+
+© FEMS 2016. All rights reserved. For permissions, please e-mail:
+journals.permissions@oup.com.
+
+DOI: 10.1093/femsle/fnw262 
+PMID: 27856567  [Indexed for MEDLINE]
+
+
+13. Poult Sci. 2016 Dec 1;95(12):2803-2814. Epub 2016 Jul 27.
+
+Thymus transcriptome reveals novel pathways in response to avian pathogenic
+Escherichia coli infection.
+
+Sun H(1)(2), Liu P(3), Nolan LK(4), Lamont SJ(5).
+
+Author information: 
+(1)College of Animal Science and Technology, Yangzhou University, Yangzhou,
+Jiangsu, China, 225009.
+(2)Department of Animal Science, Iowa State University, Ames 50011.
+(3)Department of Statistics, Iowa State University, Ames 50011.
+(4)Department of Veterinary Microbiology and Preventive Medicine, Iowa State
+University, Ames 50011.
+(5)Department of Animal Science, Iowa State University, Ames 50011
+sjlamont@iastate.edu.
+
+Avian pathogenic Escherichia coli (APEC) can cause significant morbidity in
+chickens. The thymus provides the essential environment for T cell development;
+however, the thymus transcriptome has not been examined for gene expression in
+response to APEC infection. An improved understanding of the host genomic
+response to APEC infection could inform future breeding programs for disease
+resistance and APEC control. We therefore analyzed the transcriptome of the
+thymus of birds challenged with APEC, contrasting susceptible and resistant
+phenotypes. Thousands of genes were differentially expressed in birds of the
+5-day post infection (dpi) challenged-susceptible group vs. 5 dpi non-challenged,
+in 5 dpi challenged-susceptible vs. 5 dpi challenged-resistant birds, as well as 
+in 5 dpi vs. one dpi challenged-susceptible birds. The Toll-like receptor
+signaling pathway was the major innate immune response for birds to respond to
+APEC infection. Moreover, lysosome and cell adhesion molecules pathways were
+common mechanisms for chicken response to APEC infection. The T-cell receptor
+signaling pathway, cell cycle, and p53 signaling pathways were significantly
+activated in resistant birds to resist APEC infection. These results provide a
+comprehensive assessment of global gene networks and biological functionalities
+of differentially expressed genes in the thymus under APEC infection. These
+findings provide novel insights into key molecular genetic mechanisms that
+differentiate host resistance from susceptibility in this primary lymphoid
+tissue, the thymus.
+
+© The Author 2016. Published by Oxford University Press on behalf of Poultry
+Science Association.
+
+DOI: 10.3382/ps/pew202 
+PMCID: PMC5144662
+PMID: 27466434  [Indexed for MEDLINE]
+
+
+14. Sci Rep. 2016 Jul 18;6:30025. doi: 10.1038/srep30025.
+
+Systematic analysis of an evolved Thermobifida fusca muC producing malic acid on 
+organic and inorganic nitrogen sources.
+
+Deng Y(1)(2), Lin J(3), Mao Y(1)(2), Zhang X(4).
+
+Author information: 
+(1)National Engineering Laboratory for Cereal Fermentation Technology (NELCF),
+Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
+(2)The Key Laboratory of Industrial Biotechnology, Ministry of Education,
+Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
+(3)College of Life Science, North China University of Science and Technology,
+Tangshan 063000, China.
+(4)School of pharmaceutical science, Jiangnan University, 1800 Lihu Road, Wuxi,
+Jiangsu 214122, China.
+
+Thermobifida fusca is a thermophilic actinobacterium. T. fusca muC obtained by
+adaptive evolution preferred yeast extract to ammonium sulfate for accumulating
+malic acid and ammonium sulfate for cell growth. We did transcriptome analysis of
+T. fusca muC on Avicel and cellobiose with addition of ammonium sulfate or yeast 
+extract, respectively by RNAseq. The transcriptional results indicate that
+ammonium sulfate induced the transcriptions of the genes related to carbohydrate 
+metabolisms significantly more than yeast extract. Importantly, Tfu_2487,
+encoding histidine-containing protein (HPr), didn't transcribe on yeast extract
+at all, while it transcribed highly on ammonium sulfate. In order to understand
+the impact of HPr on malate production and cell growth of the muC strain, we
+deleted Tfu_2487 to get a mutant strain: muCΔ2487, which had
+1.33 mole/mole-glucose equivalent malate yield, much higher than that on yeast
+extract. We then developed an E. coli-T. fusca shuttle plasmid for
+over-expressing HPr in muCΔ2487, a strain without HPr background, forming the
+muCΔ2487S strain. The muCΔ2487S strain had a much lower malate yield but faster
+cell growth than the muC strain. The results of both mutant strains confirmed
+that HPr was the key regulatory protein for T. fusca's metabolisms on nitrogen
+sources.
+
+DOI: 10.1038/srep30025 
+PMCID: PMC4948018
+PMID: 27424527 
+
+
+15. PLoS One. 2016 Jun 23;11(6):e0157480. doi: 10.1371/journal.pone.0157480.
+eCollection 2016.
+
+The Impact of Intramammary Escherichia coli Challenge on Liver and Mammary
+Transcriptome and Cross-Talk in Dairy Cows during Early Lactation Using RNAseq.
+
+Moyes KM(1), Sørensen P(2), Bionaz M(3).
+
+Author information: 
+(1)Department of Animal and Avian Sciences, University of Maryland, College Park,
+Maryland, United States of America.
+(2)Center for Quantitative Genetics and Genomics, Department of Molecular Biology
+and Genetics, Aarhus University, 8830 Tjele, Denmark.
+(3)Department of Animal and Rangeland Sciences, Oregon State University,
+Corvallis, Oregon, United States of America.
+
+Our objective was to identify the biological response and the cross-talk between 
+liver and mammary tissue after intramammary infection (IMI) with Escherichia coli
+(E. coli) using RNAseq technology. Sixteen cows were inoculated with live E. coli
+into one mammary quarter at ~4-6 weeks in lactation. For all cows, biopsies were 
+performed at -144, 12 and 24 h relative to IMI in liver and at 24 h post-IMI in
+infected and non-infected (control) mammary quarters. For a subset of cows (n =
+6), RNA was extracted from both liver and mammary tissue and sequenced using a
+100 bp paired-end approach. Ingenuity Pathway Analysis and the Dynamic Impact
+Approach analysis of differentially expressed genes (overall effect False
+Discovery Rate≤0.05) indicated that IMI induced an overall activation of
+inflammation at 12 h post-IMI and a strong inhibition of metabolism, especially
+related to lipid, glucose, and xenobiotics at 24 h post-IMI in liver. The data
+indicated in mammary tissue an overall induction of inflammatory response with
+little effect on metabolism at 24 h post-IMI. We identified a large number of
+up-stream regulators potentially involved in the response to IMI in both tissues 
+but a relatively small core network of transcription factors controlling the
+response to IMI for liver whereas a large network in mammary tissue.
+Transcriptomic results in liver and mammary tissue were supported by changes in
+inflammatory and metabolic mediators in blood and milk. The analysis of potential
+cross-talk between the two tissues during IMI uncovered a large communication
+from the mammary tissue to the liver to coordinate the inflammatory response but 
+a relatively small communication from the liver to the mammary tissue. Our
+results indicate a strong induction of the inflammatory response in mammary
+tissue and impairment of liver metabolism 24h post-IMI partly driven by the
+signaling from infected mammary tissue.
+
+DOI: 10.1371/journal.pone.0157480 
+PMCID: PMC4919052
+PMID: 27336699  [Indexed for MEDLINE]
+
+
+16. BMC Genomics. 2016 Feb 24;17:133. doi: 10.1186/s12864-016-2456-1.
+
+Translatomics combined with transcriptomics and proteomics reveals novel
+functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).
+
+Neuhaus K(1), Landstorfer R(2), Fellner L(3), Simon S(4), Schafferhans A(5),
+Goldberg T(6), Marx H(7), Ozoline ON(8), Rost B(9), Kuster B(10)(11), Keim
+DA(12), Scherer S(13).
+
+Author information: 
+(1)Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und
+Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität
+München, Weihenstephaner Berg 3, 85354, Freising, Germany. neuhaus@wzw.tum.de.
+(2)Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und
+Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität
+München, Weihenstephaner Berg 3, 85354, Freising, Germany. r.landstorfer@gmx.de.
+(3)Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und
+Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität
+München, Weihenstephaner Berg 3, 85354, Freising, Germany.
+fellnerlea@hotmail.com.
+(4)Lehrstuhl für Datenanalyse und Visualisierung, Fachbereich Informatik und
+Informationswissenschaft, Universität Konstanz, Box 78, 78457, Konstanz, Germany.
+simon@dbvis.inf.uni-konstanz.de.
+(5)Department of Informatics - Bioinformatics & TUM-IAS, Technische Universität
+München, Boltzmannstraße 3, 85748, Garching, Germany.
+andrea.schafferhans@rostlab.org.
+(6)Department of Informatics - Bioinformatics & TUM-IAS, Technische Universität
+München, Boltzmannstraße 3, 85748, Garching, Germany. goldberg@rostlab.org.
+(7)Chair of Proteomics and Bioanalytics, Wissenschaftszentrum Weihenstephan,
+Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising,
+Germany. h4r4ld.marx@googlemail.com.
+(8)Institute of Cell Biophysics, Russian Academy of Sciences, Moscow Region,
+142290, Pushchino, Russia. ozoline@rambler.ru.
+(9)Department of Informatics - Bioinformatics & TUM-IAS, Technische Universität
+München, Boltzmannstraße 3, 85748, Garching, Germany. rost@rostlab.org.
+(10)Chair of Proteomics and Bioanalytics, Wissenschaftszentrum Weihenstephan,
+Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising,
+Germany. kuster@wzw.tum.de.
+(11)Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische
+Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany.
+kuster@wzw.tum.de.
+(12)Lehrstuhl für Datenanalyse und Visualisierung, Fachbereich Informatik und
+Informationswissenschaft, Universität Konstanz, Box 78, 78457, Konstanz, Germany.
+keim@informatik.uni-konstanz.de.
+(13)Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und
+Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität
+München, Weihenstephaner Berg 3, 85354, Freising, Germany.
+siegfried.scherer@wzw.tum.de.
+
+BACKGROUND: Genomes of E. coli, including that of the human pathogen Escherichia 
+coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which,
+apparently, have escaped annotation due to their small size and non-essential
+function. To find such genes, global gene expression of EHEC EDL933 was examined,
+using strand-specific RNAseq (transcriptome), ribosomal footprinting
+(translatome) and mass spectrometry (proteome).
+RESULTS: Using the above methods, 72 short, non-annotated protein-coding genes
+were detected. All of these showed signals in the ribosomal footprinting assay
+indicating mRNA translation. Seven were verified by mass spectrometry.
+Fifty-seven genes are annotated in other enterobacteriaceae, mainly as
+hypothetical genes; the remaining 15 genes constitute novel discoveries. In
+addition, protein structure and function were predicted computationally and
+compared between EHEC-encoded proteins and 100-times randomly shuffled proteins. 
+Based on this comparison, 61 of the 72 novel proteins exhibit predicted
+structural and functional features similar to those of annotated proteins. Many
+of the novel genes show differential transcription when grown under eleven
+diverse growth conditions suggesting environmental regulation. Three genes were
+found to confer a phenotype in previous studies, e.g., decreased cattle
+colonization.
+CONCLUSIONS: These findings demonstrate that ribosomal footprinting can be used
+to detect novel protein coding genes, contributing to the growing body of
+evidence that hypothetical genes are not annotation artifacts and opening an
+additional way to study their functionality. All 72 genes are taxonomically
+restricted and, therefore, appear to have evolved relatively recently de novo.
+
+DOI: 10.1186/s12864-016-2456-1 
+PMCID: PMC4765031
+PMID: 26911138  [Indexed for MEDLINE]
+
+
+17. Sci Rep. 2016 Jan 28;6:19899. doi: 10.1038/srep19899.
+
+Global transcriptomic responses of Escherichia coli K-12 to volatile organic
+compounds.
+
+Yung PY(1), Grasso LL(1), Mohidin AF(1), Acerbi E(1), Hinks J(1), Seviour T(1),
+Marsili E(1)(2)(3), Lauro FM(1)(4).
+
+Author information: 
+(1)Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60
+Nanyang Drive, SBS-01N-27, Singapore 637551.
+(2)School of Chemical and Biomedical Engineering, Nanyang Technological
+University, 62 Nanyang Drive, Singapore 637459.
+(3)School of Biotechnology, Dublin City University, Collins Avenue, Dublin 9,
+Ireland.
+(4)Asian School of the Environment, Nanyang Technological University, 50 Nanyang 
+Avenue, N2-01C-45, Singapore 639798.
+
+Volatile organic compounds (VOCs) are commonly used as solvents in various
+industrial settings. Many of them present a challenge to receiving environments, 
+due to their toxicity and low bioavailability for degradation. Microorganisms are
+capable of sensing and responding to their surroundings and this makes them ideal
+detectors for toxic compounds. This study investigates the global transcriptomic 
+responses of Escherichia coli K-12 to selected VOCs at sub-toxic levels. Cells
+grown in the presence of VOCs were harvested during exponential growth, followed 
+by whole transcriptome shotgun sequencing (RNAseq). The analysis of the data
+revealed both shared and unique genetic responses compared to cells without
+exposure to VOCs. Results suggest that various functional gene categories, for
+example, those relating to Fe/S cluster biogenesis, oxidative stress responses
+and transport proteins, are responsive to selected VOCs in E. coli. The
+differential expression (DE) of genes was validated using GFP-promoter fusion
+assays. A variety of genes were differentially expressed even at non-inhibitory
+concentrations and when the cells are at their balanced-growth. Some of these
+genes belong to generic stress response and others could be specific to VOCs.
+Such candidate genes and their regulatory elements could be used as the basis for
+designing biosensors for selected VOCs.
+
+DOI: 10.1038/srep19899 
+PMCID: PMC4730218
+PMID: 26818886  [Indexed for MEDLINE]
+
+
+18. MBio. 2015 Aug 25;6(4). pii: e00998-15. doi: 10.1128/mBio.00998-15.
+
+A New Noncoding RNA Arranges Bacterial Chromosome Organization.
+
+Qian Z(1), Macvanin M(1), Dimitriadis EK(2), He X(3), Zhurkin V(4), Adhya S(5).
+
+Author information: 
+(1)Laboratory of Molecular Biology, National Cancer Institute, National
+Institutes of Health, Bethesda, Maryland, USA.
+(2)Biomedical Engineering and Physical Science, National Institute of Biomedical 
+Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland,
+USA.
+(3)Laboratory of Metabolism, National Cancer Institute, National Institutes of
+Health, Bethesda, Maryland, USA.
+(4)Laboratory of Cell Biology, National Cancer Institute, National Institutes of 
+Health, Bethesda, Maryland, USA.
+(5)Laboratory of Molecular Biology, National Cancer Institute, National
+Institutes of Health, Bethesda, Maryland, USA sadhya@helix.nih.gov.
+
+Repeated extragenic palindromes (REPs) in the enterobacterial genomes are usually
+composed of individual palindromic units separated by linker sequences. A total
+of 355 annotated REPs are distributed along the Escherichia coli genome. RNA
+sequence (RNAseq) analysis showed that almost 80% of the REPs in E. coli are
+transcribed. The DNA sequence of REP325 showed that it is a cluster of six
+repeats, each with two palindromic units capable of forming cruciform structures 
+in supercoiled DNA. Here, we report that components of the REP325 element and at 
+least one of its RNA products play a role in bacterial nucleoid DNA condensation.
+These RNA not only are present in the purified nucleoid but bind to the bacterial
+nucleoid-associated HU protein as revealed by RNA IP followed by microarray
+analysis (RIP-Chip) assays. Deletion of REP325 resulted in a dramatic increase of
+the nucleoid size as observed using transmission electron microscopy (TEM), and
+expression of one of the REP325 RNAs, nucleoid-associated noncoding RNA 4
+(naRNA4), from a plasmid restored the wild-type condensed structure.
+Independently, chromosome conformation capture (3C) analysis demonstrated
+physical connections among various REP elements around the chromosome. These
+connections are dependent in some way upon the presence of HU and the REP325
+element; deletion of HU genes and/or the REP325 element removed the connections. 
+Finally, naRNA4 together with HU condensed DNA in vitro by connecting REP325 or
+other DNA sequences that contain cruciform structures in a pairwise manner as
+observed by atomic force microscopy (AFM). On the basis of our results, we
+propose molecular models to explain connections of remote cruciform structures
+mediated by HU and naRNA4.IMPORTANCE: Nucleoid organization in bacteria is being 
+studied extensively, and several models have been proposed. However, the
+molecular nature of the structural organization is not well understood. Here we
+characterized the role of a novel nucleoid-associated noncoding RNA, naRNA4, in
+nucleoid structures both in vivo and in vitro. We propose models to explain how
+naRNA4 together with nucleoid-associated protein HU connects remote DNA elements 
+for nucleoid condensation. We present the first evidence of a noncoding RNA
+together with a nucleoid-associated protein directly condensing nucleoid DNA.
+
+Copyright © 2015 Qian et al.
+
+DOI: 10.1128/mBio.00998-15 
+PMCID: PMC4550694
+PMID: 26307168  [Indexed for MEDLINE]
+
+
+19. PLoS One. 2015 Jun 30;10(6):e0130902. doi: 10.1371/journal.pone.0130902.
+eCollection 2015.
+
+Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by
+Genomic/Transcriptomic Analysis.
+
+Zhang Y(1), Rowehl L(2), Krumsiek JM(3), Orner EP(2), Shaikh N(4), Tarr PI(5),
+Sodergren E(6), Weinstock GM(6), Boedeker EC(7), Xiong X(8), Parkinson J(9),
+Frank DN(10), Li E(2), Gathungu G(3).
+
+Author information: 
+(1)Department of Applied Mathematics and Statistics, Stony Brook University,
+Stony Brook, New York, United States of America.
+(2)Department of Medicine, Stony Brook University, Stony Brook, New York, United 
+States of America.
+(3)Department of Pediatrics, Stony Brook University, Stony Brook, New York,
+United States of America.
+(4)Department of Pediatrics, Washington University St. Louis, St. Louis,
+Missouri, United States of America.
+(5)Department of Pediatrics, Washington University St. Louis, St. Louis,
+Missouri, United States of America; Department of Molecular Microbiology,
+Washington University St. Louis, St. Louis, Missouri, United States of America.
+(6)The Genome Institute, Washington University St. Louis, St. Louis, Missouri,
+United States of America.
+(7)Department of Medicine, University of New Mexico, Albuquerque, New Mexico,
+United States of America.
+(8)Program in Molecular Structure and Function, The Hospital for Sick Children,
+Toronto, Canada.
+(9)Department of Biochemistry & Molecular and Medical Genetics, University of
+Toronto, Toronto, Canada.
+(10)Department of Medicine, University of Colorado, Denver, Colorado, United
+States of America.
+
+Erratum in
+    PLoS One. 2015;10(7):e0134759.
+
+Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently
+within mucosal lesions of patients with Crohn's disease (CD). The AIEC phenotype 
+consists of adherence and invasion of intestinal epithelial cells and survival
+within macrophages of these bacteria in vitro. Our aim was to identify candidate 
+transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and
+might be useful for rapid and accurate identification of AIEC by
+culture-independent technology. We performed comparative RNA-Sequence (RNASeq)
+analysis using AIEC strain LF82 and NIEC strain HS during exponential and
+stationary growth. Differential expression analysis of coding sequences (CDS)
+homologous to both strains demonstrated 224 and 241 genes with increased and
+decreased expression, respectively, in LF82 relative to HS. Transition metal
+transport and siderophore metabolism related pathway genes were up-regulated,
+while glycogen metabolic and oxidation-reduction related pathway genes were
+down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82
+during the exponential phase, but flagellum-dependent motility pathway genes were
+down-regulated in LF82 during the stationary phase. CDS that mapped only to the
+LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics
+approach to identify CDS specific to AIEC by incorporating the genomes of 10
+other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 
+genome and lacked homology to any of the 11 human NIEC strains. We compared these
+CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci
+belonging to clustered regularly interspaced short palindromic repeats region
+(CRISPR)--CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent
+from all non-pathogenic bacteria. As previously reported, AIEC strains were
+enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 
+AIEC strains. Reverse transcription quantitative polymerase chain reaction assays
+for 6 genes were conducted on fecal and ileal RNA samples from 22 inflammatory
+bowel disease (IBD), and 32 patients without IBD (non-IBD). The expression of Cas
+loci was detected in a higher proportion of CD than non-IBD fecal and ileal RNA
+samples (p <0.05). These results support a comparative genomic/transcriptomic
+approach towards identifying candidate AIEC signature transcripts.
+
+DOI: 10.1371/journal.pone.0130902 
+PMCID: PMC4509574
+PMID: 26125937  [Indexed for MEDLINE]
+
+
+20. Front Microbiol. 2014 Aug 13;5:402. doi: 10.3389/fmicb.2014.00402. eCollection
+2014.
+
+Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder
+bacterial ethanologenesis by activating regulatory circuits controlling inhibitor
+efflux and detoxification.
+
+Keating DH(1), Zhang Y(1), Ong IM(1), McIlwain S(1), Morales EH(2), Grass JA(3), 
+Tremaine M(1), Bothfeld W(1), Higbee A(1), Ulbrich A(4), Balloon AJ(4), Westphall
+MS(5), Aldrich J(6), Lipton MS(6), Kim J(7), Moskvin OV(1), Bukhman YV(1), Coon
+JJ(8), Kiley PJ(2), Bates DM(1), Landick R(9).
+
+Author information: 
+(1)Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
+Madison, WI, USA.
+(2)Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
+Madison, WI, USA ; Department of Biomolecular Chemistry, University of
+Wisconsin-Madison Madison, WI, USA.
+(3)Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
+Madison, WI, USA ; Department of Biochemistry, University of Wisconsin-Madison
+Madison, WI, USA.
+(4)Department of Chemistry, University of Wisconsin-Madison Madison, WI, USA.
+(5)Department of Biomolecular Chemistry, University of Wisconsin-Madison Madison,
+WI, USA ; Department of Chemistry, University of Wisconsin-Madison Madison, WI,
+USA.
+(6)Pacific Northwest National Laboratory Richland, WA, USA.
+(7)Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
+Madison, WI, USA ; Department of Chemical and Biological Engineering, University 
+of Wisconsin-Madison Madison, WI, USA.
+(8)Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
+Madison, WI, USA ; Department of Biomolecular Chemistry, University of
+Wisconsin-Madison Madison, WI, USA ; Department of Chemistry, University of
+Wisconsin-Madison Madison, WI, USA.
+(9)Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
+Madison, WI, USA ; Department of Biochemistry, University of Wisconsin-Madison
+Madison, WI, USA ; Department of Bacteriology, University of Wisconsin-Madison
+Madison, WI, USA.
+
+Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a
+key barrier to the economically viable deployment of lignocellulosic biofuels. A 
+chief contributor to this barrier is the impact on microbial processes and energy
+metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates,
+phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and
+furfurals. To understand the bacterial pathways induced by inhibitors present in 
+ammonia-pretreated biomass hydrolysates, which are less well studied than
+acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics
+of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory
+responses to the inhibitors normally present in ACSH, we measured transcript and 
+protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative 
+proteomics during fermentation to ethanol of synthetic hydrolysates containing or
+lacking the inhibitors. Our study identified four major regulators mediating
+these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of
+these regulons was correlated with a reduced rate of ethanol production, buildup 
+of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose
+conversion. The aromatic aldehyde inhibitor 5-hydroxymethylfurfural appeared to
+be reduced to its alcohol form by the ethanologen during fermentation, whereas
+phenolic acid and amide inhibitors were not metabolized. Together, our findings
+establish that the major regulatory responses to lignocellulose-derived
+inhibitors are mediated by transcriptional rather than translational regulators, 
+suggest that energy consumed for inhibitor efflux and detoxification may limit
+biofuel production, and identify a network of regulators for future synthetic
+biology efforts.
+
+DOI: 10.3389/fmicb.2014.00402 
+PMCID: PMC4132294
+PMID: 25177315 
+
+
+21. BMC Microbiol. 2014 Aug 1;14:206. doi: 10.1186/s12866-014-0206-6.
+
+Characterization and analysis of the Burkholderia pseudomallei BsaN virulence
+regulon.
+
+Chen Y, Schröder I, French CT, Jaroszewicz A, Yee XJ, Teh BE, Toesca IJ, Miller
+JF, Gan YH(1).
+
+Author information: 
+(1)Department of Biochemistry, Yong Loo Lin School of Medicine, National
+University of Singapore, Singapore 117597, Singapore. yunn_hwen_gan@nuhs.edu.sg.
+
+BACKGROUND: Burkholderia pseudomallei is a facultative intracellular pathogen and
+the causative agent of melioidosis. A conserved type III secretion system (T3SS3)
+and type VI secretion system (T6SS1) are critical for intracellular survival and 
+growth. The T3SS3 and T6SS1 genes are coordinately and hierarchically regulated
+by a TetR-type regulator, BspR. A central transcriptional regulator of the BspR
+regulatory cascade, BsaN, activates a subset of T3SS3 and T6SS1 loci.
+RESULTS: To elucidate the scope of the BsaN regulon, we used RNAseq analysis to
+compare the transcriptomes of wild-type B. pseudomallei KHW and a bsaN deletion
+mutant. The 60 genes positively-regulated by BsaN include those that we had
+previously identified in addition to a polyketide biosynthesis locus and genes
+involved in amino acid biosynthesis. BsaN was also found to repress the
+transcription of 51 genes including flagellar motility loci and those encoding
+components of the T3SS3 apparatus. Using a promoter-lacZ fusion assay in E. coli,
+we show that BsaN together with the chaperone BicA directly control the
+expression of the T3SS3 translocon, effector and associated regulatory genes that
+are organized into at least five operons (BPSS1516-BPSS1552). Using a mutagenesis
+approach, a consensus regulatory motif in the promoter regions of BsaN-regulated 
+genes was shown to be essential for transcriptional activation.
+CONCLUSIONS: BsaN/BicA functions as a central regulator of key virulence clusters
+in B. pseudomallei within a more extensive network of genetic regulation. We
+propose that BsaN/BicA controls a gene expression program that facilitates the
+adaption and intracellular survival of the pathogen within eukaryotic hosts.
+
+DOI: 10.1186/s12866-014-0206-6 
+PMCID: PMC4236580
+PMID: 25085508  [Indexed for MEDLINE]
+
+
+22. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):E2576-85. doi:
+10.1073/pnas.1401853111. Epub 2014 Jun 9.
+
+Correcting direct effects of ethanol on translation and transcription machinery
+confers ethanol tolerance in bacteria.
+
+Haft RJ(1), Keating DH(1), Schwaegler T(1), Schwalbach MS(1), Vinokur J(1),
+Tremaine M(1), Peters JM(2), Kotlajich MV(3), Pohlmann EL(1), Ong IM(1), Grass
+JA(1), Kiley PJ(4), Landick R(5).
+
+Author information: 
+(1)Great Lakes Bioenergy Research Center and.
+(2)Departments of Biochemistry,Genetics.
+(3)Departments of Biochemistry.
+(4)Great Lakes Bioenergy Research Center andBiomolecular Chemistry, and.
+(5)Great Lakes Bioenergy Research Center andDepartments of
+Biochemistry,Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
+landick@biochem.wisc.edu.
+
+The molecular mechanisms of ethanol toxicity and tolerance in bacteria, although 
+important for biotechnology and bioenergy applications, remain incompletely
+understood. Genetic studies have identified potential cellular targets for
+ethanol and have revealed multiple mechanisms of tolerance, but it remains
+difficult to separate the direct and indirect effects of ethanol. We used
+adaptive evolution to generate spontaneous ethanol-tolerant strains of
+Escherichia coli, and then characterized mechanisms of toxicity and resistance
+using genome-scale DNAseq, RNAseq, and ribosome profiling coupled with specific
+assays of ribosome and RNA polymerase function. Evolved alleles of metJ, rho, and
+rpsQ recapitulated most of the observed ethanol tolerance, implicating
+translation and transcription as key processes affected by ethanol. Ethanol
+induced miscoding errors during protein synthesis, from which the evolved rpsQ
+allele protected cells by increasing ribosome accuracy. Ribosome profiling and
+RNAseq analyses established that ethanol negatively affects transcriptional and
+translational processivity. Ethanol-stressed cells exhibited ribosomal stalling
+at internal AUG codons, which may be ameliorated by the adaptive inactivation of 
+the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant
+intragenic transcription termination for mRNAs with low ribosome density, which
+was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol
+inhibited transcript elongation by RNA polymerase in vitro. We propose that
+ethanol-induced inhibition and uncoupling of mRNA and protein synthesis through
+direct effects on ribosomes and RNA polymerase conformations are major
+contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ,
+rho, and rpsQ help protect these central dogma processes in the presence of
+ethanol.
+
+DOI: 10.1073/pnas.1401853111 
+PMCID: PMC4078849
+PMID: 24927582  [Indexed for MEDLINE]
+
+
+23. Nucleic Acids Res. 2013 Jan;41(Database issue):D1-7. doi: 10.1093/nar/gks1297.
+Epub 2012 Nov 30.
+
+The 2013 Nucleic Acids Research Database Issue and the online molecular biology
+database collection.
+
+Fernández-Suárez XM(1), Galperin MY.
+
+Author information: 
+(1)nardatabase@gmail.com
+
+The 20th annual Database Issue of Nucleic Acids Research includes 176 articles,
+half of which describe new online molecular biology databases and the other half 
+provide updates on the databases previously featured in NAR and other journals.
+This year's highlights include two databases of DNA repeat elements; several
+databases of transcriptional factors and transcriptional factor-binding sites;
+databases on various aspects of protein structure and protein-protein
+interactions; databases for metagenomic and rRNA sequence analysis; and four
+databases specifically dedicated to Escherichia coli. The increased emphasis on
+using the genome data to improve human health is reflected in the development of 
+the databases of genomic structural variation (NCBI's dbVar and EBI's DGVa), the 
+NIH Genetic Testing Registry and several other databases centered on the genetic 
+basis of human disease, potential drugs, their targets and the mechanisms of
+protein-ligand binding. Two new databases present genomic and RNAseq data for
+monkeys, providing wealth of data on our closest relatives for comparative
+genomics purposes. The NAR online Molecular Biology Database Collection,
+available at http://www.oxfordjournals.org/nar/database/a/, has been updated and 
+currently lists 1512 online databases. The full content of the Database Issue is 
+freely available online on the Nucleic Acids Research website
+(http://nar.oxfordjournals.org/).
+
+DOI: 10.1093/nar/gks1297 
+PMCID: PMC3531151
+PMID: 23203983  [Indexed for MEDLINE]
+
+
+24. Nucleic Acids Res. 2012 Nov 1;40(20):e156. doi: 10.1093/nar/gks680. Epub 2012 Jul
+19.
+
+RNAsnap™: a rapid, quantitative and inexpensive, method for isolating total RNA
+from bacteria.
+
+Stead MB(1), Agrawal A, Bowden KE, Nasir R, Mohanty BK, Meagher RB, Kushner SR.
+
+Author information: 
+(1)Department of Genetics, University of Georgia, Athens, GA 30602, USA.
+
+RNAsnap™ is a simple and novel method that recovers all intracellular RNA
+quantitatively (>99%), faster (<15 min) and less expensively (∼3 cents/sample)
+than any of the currently available RNA isolation methods. In fact, none of the
+bacterial RNA isolation methods, including the commercial kits, are effective in 
+recovering all species of intracellular RNAs (76-5700 nt) with equal efficiency, 
+which can lead to biased results in genome-wide studies involving microarray or
+RNAseq analysis. The RNAsnap™ procedure yields ∼60 µg of RNA from 10(8)
+Escherichia coli cells that can be used directly for northern analysis without
+any further purification. Based on a comparative analysis of specific transcripts
+ranging in size from 76 to 5700 nt, the RNAsnap™ method provided the most
+accurate measure of the relative amounts of the various intracellular RNAs.
+Furthermore, the RNAsnap™ RNA was successfully used in enzymatic reactions such
+as RNA ligation, reverse transcription, primer extension and reverse
+transcriptase-polymerase chain reaction, following sodium acetate/ethanol
+precipitation. The RNAsnap™ method can be used to isolate RNA from a wide range
+of Gram-negative and Gram-positive bacteria as well as yeast.
+
+DOI: 10.1093/nar/gks680 
+PMCID: PMC3488207
+PMID: 22821568  [Indexed for MEDLINE]
+
+
+25. Nucleic Acids Res. 2012 Sep;40(16):7870-84. doi: 10.1093/nar/gks503. Epub 2012
+Jun 11.
+
+Altered tRNA characteristics and 3' maturation in bacterial symbionts with
+reduced genomes.
+
+Hansen AK(1), Moran NA.
+
+Author information: 
+(1)Department of Ecology and Evolutionary Biology, West Campus, Yale University, 
+PO Box 27388 West Haven, CT 06516-7388, USA. allison.hansen@yale.edu
+
+Translational efficiency is controlled by tRNAs and other genome-encoded
+mechanisms. In organelles, translational processes are dramatically altered
+because of genome shrinkage and horizontal acquisition of gene products. The
+influence of genome reduction on translation in endosymbionts is largely unknown.
+Here, we investigate whether divergent lineages of Buchnera aphidicola, the
+reduced-genome bacterial endosymbiont of aphids, possess altered translational
+features compared with their free-living relative, Escherichia coli. Our RNAseq
+data support the hypothesis that translation is less optimal in Buchnera than in 
+E. coli. We observed a specific, convergent, pattern of tRNA loss in Buchnera and
+other endosymbionts that have undergone genome shrinkage. Furthermore, many
+modified nucleoside pathways that are important for E. coli translation are lost 
+in Buchnera. Additionally, Buchnera's A + T compositional bias has resulted in
+reduced tRNA thermostability, and may have altered aminoacyl-tRNA synthetase
+recognition sites. Buchnera tRNA genes are shorter than those of E. coli, as the 
+majority no longer has a genome-encoded 3' CCA; however, all the expressed,
+shortened tRNAs undergo 3' CCA maturation. Moreover, expression of tRNA
+isoacceptors was not correlated with the usage of corresponding codons. Overall, 
+our data suggest that endosymbiont genome evolution alters tRNA characteristics
+that are known to influence translational efficiency in their free-living
+relative.
+
+DOI: 10.1093/nar/gks503 
+PMCID: PMC3439896
+PMID: 22689638  [Indexed for MEDLINE]
+