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Draft Genome Sequences of Five Proteobacteria Isolated from Lechuguilla Cave, New Mexico, USA, and Insights into Taxonomy and Quorum Sensing.

Gan HM, Wengert PC, Barton HA, Hudson AO, Savka MA.

Microbiol Resour Announc. 2019 Oct 3;8(40). pii: e00913-19. doi: 10.1128/MRA.00913-19.


Computational Network Analysis Identifies Evolutionarily Conserved miRNA Gene Interactions Potentially Regulating Immune Response in Bovine Trypanosomosis.

Morenikeji OB, Hawkes ME, Hudson AO, Thomas BN.

Front Microbiol. 2019 Aug 28;10:2010. doi: 10.3389/fmicb.2019.02010. eCollection 2019.


The Arabidopsis thaliana gene annotated by the locus tag At3g08860 encodes alanine aminotransferase.

Parthasarathy A, Adams LE, Savka FC, Hudson AO.

Plant Direct. 2019 Sep 18;3(9):e00171. doi: 10.1002/pld3.171. eCollection 2019 Sep.


Insight Into the Microbial Co-occurrence and Diversity of 73 Grapevine (Vitis vinifera) Crown Galls Collected Across the Northern Hemisphere.

Gan HM, Szegedi E, Fersi R, Chebil S, Kovács L, Kawaguchi A, Hudson AO, Burr TJ, Savka MA.

Front Microbiol. 2019 Aug 13;10:1896. doi: 10.3389/fmicb.2019.01896. eCollection 2019.


The Synthesis and Role of β-Alanine in Plants.

Parthasarathy A, Savka MA, Hudson AO.

Front Plant Sci. 2019 Jul 18;10:921. doi: 10.3389/fpls.2019.00921. eCollection 2019. Review.


Isolation, Whole-Genome Sequencing, and Annotation of Yimella sp. RIT 621, a Strain That Produces Antibiotic Compounds against Escherichia coli ATCC 25922 and Bacillus subtilis BGSC 168.

Parthasarathy A, Wong NH, Burns ND, Aziz-Dickerson AH, Dweh J, Buchanan D, Savka MA, Hudson AO.

Microbiol Resour Announc. 2019 Apr 25;8(17). pii: e00329-19. doi: 10.1128/MRA.00329-19.


Structure-function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control.

Crowther JM, Cross PJ, Oliver MR, Leeman MM, Bartl AJ, Weatherhead AW, North RA, Donovan KA, Griffin MDW, Suzuki H, Hudson AO, Kasanmascheff M, Dobson RCJ.

J Biol Chem. 2019 May 24;294(21):8505-8515. doi: 10.1074/jbc.RA118.006825. Epub 2019 Apr 8.


SELfies and CELLfies: Whole Genome Sequencing and Annotation of Five Antibiotic Resistant Bacteria Isolated from the Surfaces of Smartphones, An Inquiry Based Laboratory Exercise in a Genomics Undergraduate Course at the Rochester Institute of Technology.

Parthasarathy A, Wong NH, Weiss AN, Tian S, Ali SE, Cavanaugh NT, Chinsky TM, Cramer CE, Gupta A, Jha R, Johnson LK, Tuason ED, Klafehn LM, Krishnadas V, Musich RJ, Pfaff JM, Richman SC, Shumway AJ, Hudson AO.

J Genomics. 2019 Feb 19;7:26-30. doi: 10.7150/jgen.31911. eCollection 2019.


Is Plastic Pollution in Aquatic and Terrestrial Environments a Driver for the Transmission of Pathogens and the Evolution of Antibiotic Resistance?

Parthasarathy A, Tyler AC, Hoffman MJ, Savka MA, Hudson AO.

Environ Sci Technol. 2019 Feb 19;53(4):1744-1745. doi: 10.1021/acs.est.8b07287. Epub 2019 Jan 31. No abstract available.


The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies.

Mantravadi PK, Kalesh KA, Dobson RCJ, Hudson AO, Parthasarathy A.

Antibiotics (Basel). 2019 Jan 24;8(1). pii: E8. doi: 10.3390/antibiotics8010008. Review.


Whole-Genome Sequencing and Annotation of Exiguobacterium sp. RIT 452, an Antibiotic-Producing Strain Isolated from a Pond Located on the Campus of the Rochester Institute of Technology.

Parthasarathy A, Wong NH, Cavanaugh NT, Steiner KK, Wengert PC, Savka MA, Hudson AO.

Microbiol Resour Announc. 2018 Nov 1;7(17). pii: e01341-18. doi: 10.1128/MRA.01341-18. eCollection 2018 Nov.


Isolation and genomic characterization of six endophytic bacteria isolated from Saccharum sp (sugarcane): Insights into antibiotic, secondary metabolite and quorum sensing metabolism.

Parthasarathy A, Gan HM, Wong NH, Savka MA, Steiner KK, Henry KR, Hudson AO.

J Genomics. 2018 Oct 2;6:117-121. doi: 10.7150/jgen.28335. eCollection 2018.


A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals.

Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO.

Front Mol Biosci. 2018 Apr 6;5:29. doi: 10.3389/fmolb.2018.00029. eCollection 2018. Review.


Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics.

Babbitt GA, Coppola EE, Mortensen JS, Ekeren PX, Viola C, Goldblatt D, Hudson AO.

J Mol Evol. 2018 Feb;86(2):91-102. doi: 10.1007/s00239-018-9828-x. Epub 2018 Jan 17.


Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis.

Gan HM, Thomas BN, Cavanaugh NT, Morales GH, Mayers AN, Savka MA, Hudson AO.

PeerJ. 2017 Nov 14;5:e4030. doi: 10.7717/peerj.4030. eCollection 2017.


Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains TT6675 and TT9097 Employed in the Isolation and Characterization of a Giant Phage Mutant Collection.

Gan HM, Eng WWH, Barton MK, Adams LE, Samsudin NA, Bartl AJ, Hudson AO, Savka MA, Thomas JA.

Genome Announc. 2017 Aug 24;5(34). pii: e00857-17. doi: 10.1128/genomeA.00857-17.


Dihydrodipicolinate Synthase: Structure, Dynamics, Function, and Evolution.

Grant Pearce F, Hudson AO, Loomes K, Dobson RCJ.

Subcell Biochem. 2017;83:271-289. doi: 10.1007/978-3-319-46503-6_10. Review.


Genomic characterization of eight Ensifer strains isolated from pristine caves and a whole genome phylogeny of Ensifer (Sinorhizobium).

Kumar HK, Gan HM, Tan MH, Eng WW, Barton HA, Hudson AO, Savka MA.

J Genomics. 2017 Jan 18;5:12-15. doi: 10.7150/jgen.17863. eCollection 2017.


The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution.

Cala AR, Nadeau MT, Abendroth J, Staker BL, Reers AR, Weatherhead AW, Dobson RC, Myler PJ, Hudson AO.

Acta Crystallogr F Struct Biol Commun. 2016 Dec 1;72(Pt 12):885-891. Epub 2016 Nov 25.


Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly.

Thomas JA, Benítez Quintana AD, Bosch MA, Coll De Peña A, Aguilera E, Coulibaly A, Wu W, Osier MV, Hudson AO, Weintraub ST, Black LW.

J Virol. 2016 Oct 28;90(22):10284-10298. doi: 10.1128/JVI.01492-16. Print 2016 Nov 15.


Genome sequencing-assisted identification and the first functional validation of N-acyl-homoserine-lactone synthases from the Sphingomonadaceae family.

Gan HM, Dailey LK, Halliday N, Williams P, Hudson AO, Savka MA.

PeerJ. 2016 Aug 30;4:e2332. doi: 10.7717/peerj.2332. eCollection 2016.


Identification and Partial Characterization of a Novel UDP-N-Acetylenolpyruvoylglucosamine Reductase/UDP-N-Acetylmuramate:l-Alanine Ligase Fusion Enzyme from Verrucomicrobium spinosum DSM 4136(T).

Naqvi KF, Patin D, Wheatley MS, Savka MA, Dobson RC, Gan HM, Barreteau H, Blanot D, Mengin-Lecreulx D, Hudson AO.

Front Microbiol. 2016 Mar 23;7:362. doi: 10.3389/fmicb.2016.00362. eCollection 2016.


Whole-Genome Sequencing Reveals a New Genospecies of Methylobacterium sp. GXS13, Isolated from Vitis vinifera L. Xylem Sap.

Lai WX, Gan HM, Hudson AO, Savka MA.

Genome Announc. 2016 Feb 4;4(1). pii: e01695-15. doi: 10.1128/genomeA.01695-15.


Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution.

Naqvi KF, Staker BL, Dobson RC, Serbzhinskiy D, Sankaran B, Myler PJ, Hudson AO.

Acta Crystallogr F Struct Biol Commun. 2016 Jan;72(Pt 1):2-9. doi: 10.1107/S2053230X15023213. Epub 2016 Jan 1.


Can all heritable biology really be reduced to a single dimension?

Babbitt GA, Coppola EE, Alawad MA, Hudson AO.

Gene. 2016 Mar 10;578(2):162-8. doi: 10.1016/j.gene.2015.12.043. Epub 2015 Dec 23. Review.


Whole-Genome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy (Toxicodendron radicans).

Tran PN, Tan NE, Lee YP, Gan HM, Polter SJ, Dailey LK, Hudson AO, Savka MA.

Genome Announc. 2015 Nov 19;3(6). pii: e01319-15. doi: 10.1128/genomeA.01319-15.


Isolation, Identification, Whole-Genome Sequencing, and Annotation of Four Bacillus Species, B. anthracis RIT375, B. circulans RIT379, B. altitudinis RIT380, and B. megaterium RIT381, from Internal Stem Tissue of the Insulin Plant Costus igneus.

Polter SJ, Caraballo AA, Lee YP, Eng WW, Gan HM, Wheatley MS, Savka MA, Thomas BN, Hudson AO.

Genome Announc. 2015 Jul 30;3(4). pii: e00847-15. doi: 10.1128/genomeA.00847-15.


Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344.

Eng WW, Gan HM, Gan HY, Hudson AO, Savka MA.

Genome Announc. 2015 May 14;3(3). pii: e00463-15. doi: 10.1128/genomeA.00463-15.


Chemical composition and disruption of quorum sensing signaling in geographically diverse United States propolis.

Savka MA, Dailey L, Popova M, Mihaylova R, Merritt B, Masek M, Le P, Nor SR, Ahmad M, Hudson AO, Bankova V.

Evid Based Complement Alternat Med. 2015;2015:472593. doi: 10.1155/2015/472593. Epub 2015 Apr 15.


Whole-Genome Sequencing and Annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum (Bird's Eye Chili) and Capsicum chinense (Yellow Lantern Chili), Respectively.

Gan HY, Gan HM, Savka MA, Triassi AJ, Wheatley MS, Naqvi KF, Foxhall TE, Anauo MJ, Baldwin ML, Burkhardt RN, O'Bryon IG, Dailey LK, Busairi NI, Keith RC, Khair MH, Rasul MZ, Rosdi NA, Mountzouros JR, Rhoads AC, Selochan MA, Tautanov TB, Polter SJ, Marks KD, Caraballo AA, Hudson AO.

Genome Announc. 2015 Apr 16;3(2). pii: e00288-15. doi: 10.1128/genomeA.00288-15.


Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family.

Gan HM, Gan HY, Ahmad NH, Aziz NA, Hudson AO, Savka MA.

Front Cell Infect Microbiol. 2015 Jan 8;4:188. doi: 10.3389/fcimb.2014.00188. eCollection 2014.


Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico.

Gan HY, Gan HM, Tarasco AM, Busairi NI, Barton HA, Hudson AO, Savka MA.

Genome Announc. 2014 Nov 6;2(6). pii: e01133-14. doi: 10.1128/genomeA.01133-14.


L,L-diaminopimelate aminotransferase (DapL): a putative target for the development of narrow-spectrum antibacterial compounds.

Triassi AJ, Wheatley MS, Savka MA, Gan HM, Dobson RC, Hudson AO.

Front Microbiol. 2014 Sep 26;5:509. doi: 10.3389/fmicb.2014.00509. eCollection 2014.


Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.

Babbitt GA, Alawad MA, Schulze KV, Hudson AO.

Nucleic Acids Res. 2014;42(17):10915-26. doi: 10.1093/nar/gku811. Epub 2014 Sep 8.


The purification, crystallization and preliminary X-ray diffraction analysis of two isoforms of meso-diaminopimelate decarboxylase from Arabidopsis thaliana.

Oliver MR, Crowther JM, Leeman MM, Kessans SA, North RA, Donovan KA, Griffin MD, Suzuki H, Hudson AO, Kasanmascheff M, Dobson RC.

Acta Crystallogr F Struct Biol Commun. 2014 May;70(Pt 5):663-8. doi: 10.1107/S2053230X14007699. Epub 2014 Apr 25.


Whole-genome sequences of 13 endophytic bacteria isolated from shrub willow (salix) grown in geneva, new york.

Gan HY, Gan HM, Savka MA, Triassi AJ, Wheatley MS, Smart LB, Fabio ES, Hudson AO.

Genome Announc. 2014 May 8;2(3). pii: e00288-14. doi: 10.1128/genomeA.00288-14.


High-Quality Draft Whole-Genome Sequences of Three Strains of Enterobacter Isolated from Jamaican Dioscorea cayenensis (Yellow Yam).

Gan HM, Triassi AJ, Wheatley MS, Savka MA, Hudson AO.

Genome Announc. 2014 Mar 13;2(2). pii: e00170-14. doi: 10.1128/genomeA.00170-14.


Differential response of orthologous L,L-diaminopimelate aminotransferases (DapL) to enzyme inhibitory antibiotic lead compounds.

McKinnie SM, Rodriguez-Lopez EM, Vederas JC, Crowther JM, Suzuki H, Dobson RC, Leustek T, Triassi AJ, Wheatley MS, Hudson AO.

Bioorg Med Chem. 2014 Jan 1;22(1):523-30. doi: 10.1016/j.bmc.2013.10.055. Epub 2013 Nov 9.


Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation.

Gan HM, Hudson AO, Rahman AY, Chan KG, Savka MA.

BMC Genomics. 2013 Jun 28;14:431. doi: 10.1186/1471-2164-14-431.


Biochemical characterization of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-2,6-diaminopimelate ligase (MurE) from Verrucomicrobium spinosum DSM 4136(T.).

McGroty SE, Pattaniyil DT, Patin D, Blanot D, Ravichandran AC, Suzuki H, Dobson RC, Savka MA, Hudson AO.

PLoS One. 2013 Jun 13;8(6):e66458. doi: 10.1371/journal.pone.0066458. Print 2013.


Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus.

North RA, Kessans SA, Atkinson SC, Suzuki H, Watson AJ, Burgess BR, Angley LM, Hudson AO, Varsani A, Griffin MD, Fairbanks AJ, Dobson RC.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Mar 1;69(Pt 3):306-12. doi: 10.1107/S1744309113003060. Epub 2013 Feb 27.


Whole-genome sequence of Enterobacter sp. strain SST3, an endophyte isolated from Jamaican sugarcane (Saccharum sp.) stalk tissue.

Gan HM, McGroty SE, Chew TH, Chan KG, Buckley LJ, Savka MA, Hudson AO.

J Bacteriol. 2012 Nov;194(21):5981-2. doi: 10.1128/JB.01469-12.


Genome sequence of Methylobacterium sp. strain GXF4, a xylem-associated bacterium isolated from Vitis vinifera L. grapevine.

Gan HM, Chew TH, Hudson AO, Savka MA.

J Bacteriol. 2012 Sep;194(18):5157-8. doi: 10.1128/JB.01201-12.


Genome sequence of Novosphingobium sp. strain Rr 2-17, a nopaline crown gall-associated bacterium isolated from Vitis vinifera L. grapevine.

Gan HM, Chew TH, Hudson AO, Savka MA.

J Bacteriol. 2012 Sep;194(18):5137-8. doi: 10.1128/JB.01159-12.


A novel property of propolis (bee glue): anti-pathogenic activity by inhibition of N-acyl-homoserine lactone mediated signaling in bacteria.

Bulman Z, Le P, Hudson AO, Savka MA.

J Ethnopharmacol. 2011 Dec 8;138(3):788-97. doi: 10.1016/j.jep.2011.10.029. Epub 2011 Oct 28.


L,L-diaminopimelate aminotransferase from Chlamydomonas reinhardtii: a target for algaecide development.

Dobson RC, Girón I, Hudson AO.

PLoS One. 2011;6(5):e20439. doi: 10.1371/journal.pone.0020439. Epub 2011 May 25.


Dual diaminopimelate biosynthesis pathways in Bacteroides fragilis and Clostridium thermocellum.

Hudson AO, Klartag A, Gilvarg C, Dobson RC, Marques FG, Leustek T.

Biochim Biophys Acta. 2011 Sep;1814(9):1162-8. doi: 10.1016/j.bbapap.2011.04.019. Epub 2011 May 14.


Crystallization and preliminary X-ray diffraction analysis of L,L-diaminopimelate aminotransferase (DapL) from Chlamydomonas reinhardtii.

Hudson AO, Girón I, Dobson RC.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jan 1;67(Pt 1):140-3. doi: 10.1107/S174430911004844X. Epub 2010 Dec 24.

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