Waksman Institute of Microbiology

Research Output 1972 2019

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2019

CRISPR–Cas molecular beacons as tool for studies of assembly of CRISPR–Cas effector complexes and their interactions with DNA

Mekler, V., Kuznedelov, K., Minakhin, L., Murugan, K., Sashital, D. G. & Severinov, K., Jan 1 2019, Methods in Enzymology. Bailey, S. (ed.). Academic Press Inc., p. 337-363 27 p. (Methods in Enzymology; vol. 616).

Research output: Chapter in Book/Report/Conference proceedingChapter

Clustered Regularly Interspaced Short Palindromic Repeats
DNA
Nucleic acid sequences
RNA
Prokaryotic Cells
2 Citations (Scopus)

Localization of Hippo Signaling Components in Drosophila by Fluorescence and Immunofluorescence

Rauskolb, C. & Irvine, K., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 61-73 13 p. (Methods in Molecular Biology; vol. 1893).

Research output: Chapter in Book/Report/Conference proceedingChapter

Drosophila
Fluorescent Antibody Technique
Fluorescence
Antibodies
Proteins

Mutagenesis and imaging studies of BMP signaling mechanisms in C. elegans

Savage-Dunn, C., Gleason, R. J., Liu, J. & Padgett, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 51-73 23 p. (Methods in Molecular Biology; vol. 1891).

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutagenesis
Signal Transduction
2018
1 Citation (Scopus)

Analysis of Bacterial Transcription by “Massively Systematic Transcript End Readout,” MASTER

Vvedenskaya, I. O., Goldman, S. R. & Nickels, B., Jan 1 2018, Methods in Enzymology. Carpousis, A. J. (ed.). Academic Press Inc., p. 269-302 34 p. (Methods in Enzymology; vol. 612).

Research output: Chapter in Book/Report/Conference proceedingChapter

Transcription
High-Throughput Nucleotide Sequencing
Gene Library
Nucleic Acids
Libraries
1 Citation (Scopus)

Plant transformation by particle bombardment

Klein, T. M. & Maliga, P., Jan 1 2018, Biotechnology for Biological Control of Pests and Vectors. CRC Press, p. 105-118 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Agrobacterium
gene transfer
Genetically Modified Plants
Genes
transgenic plants
1 Citation (Scopus)

Rewiring of cyanobacterial metabolism for hydrogen production: Synthetic biology approaches and challenges

Krishnan, A., Qian, X., Ananyev, G., Lun, D. & Dismukes, G., Jan 1 2018, Advances in Experimental Medicine and Biology. Springer New York LLC, p. 171-213 43 p. (Advances in Experimental Medicine and Biology; vol. 1080).

Research output: Chapter in Book/Report/Conference proceedingChapter

Synthetic Biology
Cyanobacteria
Hydrogen production
Metabolism
Hydrogen
2017

Interdependencies between the adaptation and interference modules guide efficient crispr-cas immunity

Semenova, E. & Severinov, K., Aug 8 2017, Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts. Springer International Publishing, p. 51-62 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Clustered Regularly Interspaced Short Palindromic Repeats
crossover interference
Interspersed Repetitive Sequences
Immunity
immunity
4 Citations (Scopus)

Maize seed storage proteins

Larkins, B. A., Wu, Y., Song, R. & Messing, J., Jan 1 2017, Maize Kernel Development. CABI International, p. 175-189 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Seed Storage Proteins
seed storage proteins
Zea mays
Seed
Proteins

PacBio for haplotyping in gene families

Zhang, W. & Messing, J., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 61-71 11 p. (Methods in Molecular Biology; vol. 1551).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genes
Glutens
Nucleic Acid Repetitive Sequences
Haplotypes
Libraries
2016

Gene Regulation By Cold Shock Proteins via Transcription Antitermination

Phadtare, S. & Severinov, K., Aug 12 2016, Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria. Wiley-Blackwell, Vol. 2. p. 827-836 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cold Shock Proteins and Peptides
Temperature
Genes
Growth
Nucleic Acids
2 Citations (Scopus)

Kymographic analysis of transport in an individual neuronal sensory cilium in caenorhabditis elegans

O’Hagan, R. & Barr, M., Jan 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 107-122 16 p. (Methods in Molecular Biology; vol. 1454).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cilia
Caenorhabditis elegans
Green Fluorescent Proteins
Kymography
Molecular Motor Proteins

Transformation in Plastids

Maliga, P., Aug 27 2016, Breeding Genetics and Biotechnology. Elsevier Inc., Vol. 2. p. 255-261 7 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Plastids
plastids
Chloroplasts
Genes
Tobacco
2015

Detection and control of gluten as a food allergen

Nasr, I., Messing, J., Nasr, I. H. & Ciclitira, P. J., Jan 1 2015, Handbook of Food Allergen Detection and Control. Elsevier Ltd, p. 367-377 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Allergens
celiac disease
Glutens
Celiac Disease
allergens

Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and staudinger-bertozzi ligation

Chakraborty, A., Mazumder, A., Lin, M., Hasemeyer, A., Xu, Q., Wang, D., Ebright, Y. W. & Ebright, R., Feb 9 2015, Bacterial Transcriptional Control: Methods and Protocols. Springer New York, p. 101-131 31 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutagenesis
DNA-Directed RNA Polymerases
Ligation
phosphine
Amino Acids
1 Citation (Scopus)

Use of RNA polymerase molecular beacon assay to measure RNA polymerase interactions with model promoter fragments

Mekler, V. & Severinov, K., Feb 9 2015, Bacterial Transcriptional Control: Methods and Protocols. Springer New York, p. 199-210 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA-Directed RNA Polymerases
Assays
DNA Probes
Transcription
Escherichia coli
2014
35 Citations (Scopus)

Control of Growth During Regeneration

Sun, G. & Irvine, K., Jan 1 2014, Current Topics in Developmental Biology. Academic Press Inc., p. 95-120 26 p. (Current Topics in Developmental Biology; vol. 108).

Research output: Chapter in Book/Report/Conference proceedingChapter

Regeneration
Growth
MAP Kinase Signaling System
Stem Cells
Catenins

Notch-ligand binding assays in Drosophila cells

Xu, A. & Irvine, K., Jan 1 2014, Notch Signaling: Methods and Protocols. Humana Press Inc., p. 277-284 8 p. (Methods in Molecular Biology; vol. 1187).

Research output: Chapter in Book/Report/Conference proceedingChapter

Drosophila
Ligands
Notch Receptors
Alkaline Phosphatase
Proteins
2013
5 Citations (Scopus)

Evolution, Structure, and Function of Prolamin Storage Proteins

Holding, D. & Messing, J., Feb 5 2013, Seed Genomics. Wiley-Blackwell, p. 138-158 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Prolamins
prolamins
storage proteins
Proteins
24 Citations (Scopus)

Fertilization

Marcello, M. R., Singaravelu, G. & Singson, A., Jan 1 2013, Germ Cell Development in C. elegans. Schedl, T. (ed.). p. 321-350 30 p. (Advances in Experimental Medicine and Biology; vol. 757).

Research output: Chapter in Book/Report/Conference proceedingChapter

Fertilization
Oocytes
Fusion reactions
Spermatozoa
Germ Cells
2012
3 Citations (Scopus)

Use of semi-quantitative northern blot analysis to determine relative quantities of bacterial CRISPR transcripts

Pougach, K. & Severinov, K., Jul 27 2012, Bacterial Regulatory RNA: Methods and Protocols. Keiler, K. C. (ed.). p. 73-86 14 p. (Methods in Molecular Biology; vol. 905).

Research output: Chapter in Book/Report/Conference proceedingChapter

Northern Blotting
RNA
Bacteriophages
RNA-Directed DNA Polymerase
Ligases
2011
11 Citations (Scopus)

EGG molecules couple the oocyte-to-embryo transition with cell cycle progression

Parry, J. M. & Singson, A., Jul 4 2011, Cell Cycle in Development. Kubiak, J. (ed.). p. 135-151 17 p. (Results and Problems in Cell Differentiation; vol. 53).

Research output: Chapter in Book/Report/Conference proceedingChapter

Oocytes
Ovum
Cell Cycle
Embryonic Structures
Genes
8 Citations (Scopus)

New insights into the mechanism of fertilization in nematodes

Singaravelu, G. & Singson, A., Jan 1 2011, International Review of Cell and Molecular Biology. Elsevier Inc., p. 211-238 28 p. (International Review of Cell and Molecular Biology; vol. 289).

Research output: Chapter in Book/Report/Conference proceedingChapter

Fertilization
Spermatozoa
Fusion reactions
Oocytes
Caenorhabditis elegans

Plastid transformation as a tool for plant- based production of vaccines and therapeutic proteins

Lenzi, P., Scotti, N., Maliga, P. & Cardi, T., Nov 1 2011, Plant-derived Vaccines: Technologies and Applications. Future Medicine Ltd., p. 57-66 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Plastids
Vaccines
Proteins
Therapeutics
11 Citations (Scopus)

The Genetics and Cell Biology of Fertilization

Geldziler, B. D., Marcello, M. R., Shakes, D. C. & Singson, A., Jan 1 2011, Methods in Cell Biology. Academic Press Inc., p. 343-375 33 p. (Methods in Cell Biology; vol. 106).

Research output: Chapter in Book/Report/Conference proceedingChapter

Fertilization
Cell Biology
Caenorhabditis elegans
Germ Cells
Fertility
4 Citations (Scopus)

Transplastomics in arabidopsis: Progress toward developing an efficient method

Lutz, K. A., Azhagiri, A. & Maliga, P., Sep 23 2011, Chloroplast Research in Arabidopsis: Methods and Protocols, Volume 1. Jarvis, P. (ed.). p. 133-147 15 p. (Methods in Molecular Biology; vol. 774).

Research output: Chapter in Book/Report/Conference proceedingChapter

Plastids
Arabidopsis
Diploidy
Tobacco
DNA
2009
7 Citations (Scopus)

Static and kinetic site-specific protein-DNA photocrosslinking: Analysis of bacterial transcription initiation complexes

Naryshkin, N., Druzhinin, S., Revyakin, A., Kim, Y., Mekler, V. & Ebright, R., Dec 1 2009, DNA-Protein Interactions: Principles and Protocols, Third Edition. Moss, T. & Leblanc, B. (eds.). p. 403-437 35 p. (Methods in Molecular Biology; vol. 543).

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA
Proteins
Multiprotein Complexes
Licensure
Lasers
5 Citations (Scopus)

The polyploid origin of maize

Messing, J., Jan 1 2009, Handbook of Maize: Genetics and Genomics. Springer New York, p. 221-238 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polyploidy
Chromosomes
polyploidy
Zea mays
chromosomes

The structure of the maize genome

Messing, J., Jan 1 2009, Biotechnology in Agriculture and Forestry. Springer International Publishing, p. 213-230 18 p. (Biotechnology in Agriculture and Forestry; vol. 63).

Research output: Chapter in Book/Report/Conference proceedingChapter

Zea mays
genome
maize
Genome
corn
2008
17 Citations (Scopus)

Grass genome structure and evolution

Messing, J. & Bennetzen, J., Dec 1 2008, Plant Genomes. Volff, J-N. (ed.). p. 41-56 16 p. (Genome Dynamics; vol. 4).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ointments
Poaceae
genome
grass
Genome
4 Citations (Scopus)

Synapsis, double-strand breaks, and domains of crossover control in drosophila females

Mehrotra, S., Hawley, R. S. & McKim, K., Jan 1 2008, Recombination and Meiosis: Crossing-Over and Disjunction. Egel, R. & Lankenau, D-H. (eds.). p. 125-151 27 p. (Genome Dynamics and Stability; vol. 2).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chromosome Pairing
Drosophila
Chromosome Structures
Genetic Recombination
Cell Biology

Time-Dependent ("Mechanical"), Nonbiological Catalysis. 1. A Fully Functional Mimic of the Water-Oxidizing Center (WOC) in Photosystem II (PSII)

Brimblecombe, R., Dismukes, G., Felton, G. A., Spiccia, L. & Swiegers, G. F., Feb 25 2008, Mechanical Catalysis: Methods of Enzymatic, Homogeneous, and Heterogeneous Catalysis. John Wiley & Sons, Inc., p. 267-295 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Photosystem II Protein Complex
Catalysis
Water
tebufenozide
2007
15 Citations (Scopus)

Transformation of the Plastid Genome to Study RNA Editing

Lutz, K. A. & Maliga, P., Jan 1 2007, RNA Editing. Academic Press Inc., p. 501-518 18 p. (Methods in Enzymology; vol. 424).

Research output: Chapter in Book/Report/Conference proceedingChapter

Plastid Genomes
RNA Editing
Plastids
Genes
RNA
2003

Toll-Dorsal Signaling in Dorsal-Ventral Patterning and Innate Immunity

Bhattacharya, A. & Steward, R., Nov 7 2003, Handbook of Cell Signaling. Elsevier Inc., Vol. 2-3. p. 779-781 3 p.

Research output: Chapter in Book/Report/Conference proceedingChapter