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Softberry Inc bprom program
Bprom Program, supplied by Softberry Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bprom+program/bprom+program/pm42118393-85-12-14
Average 86 stars, based on 1 article reviews
bprom program - by Bioz Stars, 2026-09
86/100 stars

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Article Title: Low leucine levels in the blood enhance the pathogenicity of neonatal meningitis-causing Escherichia coli.
Article Snippet: To investigate whether the administration of leucine, which targets the Lrp-NsrP-PurD regulatory pathway, could be a potential 0.0 0.5 1.0 1.5 N sr P re la tiv e ex pr es si on WT-LB WT-Blood a b c d e 0.0 0.5 1.0 1.5 Leu-H Leu-L f g 0.0 0.5 1.0 1.5 Leu-H Leu-L lrp ns 0.0 0.5 1.0 1.5 WT lrp 0 5 10 15 R el at iv e ex pr es si on rpoS Mock-ChIP Lrp-ChIP ns N sr P re la tiv e ex pr es si on N sr P re la tiv e ex pr es si on NsrP N sr P re la tiv e ex pr es si on h PromoterRNA-coding region 5’3’ Transcription start site Lrp binding site NsrPDNA WT NsrP 5S rRNA Leu-H Leu-L 0.0 0.5 1.0 1.5 N sr P re la tiv e ex pr es si on WT Leu-H Leu-L i 0.0 0.5 1.0 1.5 Leu-H Leu-L N sr P re la tiv e ex pr es si on NsrPpro-mut ns 5’- CAATATTTATTCCC -3’ NsrPpro-mut 5’- CAATATTTATTCCC -3’ -100 100 200 300 400 500 RU -500 0 500 1000 1500 2000 2500 3000 3500 R es po ns e 0 KD = 6.08 × 10-6 1.25 μM 625 nM 312.5 nM 156.3 nM 78.2 nM 39.1 nM 20 nM (s) P = 3.61 × 10-5 P = 9.56 × 10-5 244 (nt) 116 Fig. 4 | Low leucine levels repressedNsrP expression via Lrp. a qRT-PCR analysis of NsrP expression in the NMEC WT strain in LB medium and mouse blood. b The NsrP promoter region and the potential binding site of Lrp were predicted by the BProm program (SoftBerry). c qRT-PCR analysis of the NsrP expression in WT and Δlrp. d Biacore SPR kinetic analyses of Lrp binding to the promoter of NsrP. e Fold enrichment of the NsrP promoter in the Lrp-ChIP samples compared with that in the mock-ChIP samples. f qRT-PCR analysis of the NsrP expression in WT NMEC in M9 medium supplemented with 0.1mM leucine (Leu-L) or 5mM leucine (Leu-H). g Northern blotting of NsrP sRNA in WT NMEC in M9 medium supplemented with 0.1 or 5mM leucine.

Article Title: Comparative Chloroplast Genomics of Sugar Beet and Wild Relatives: Insights into Photosystem Gene Regulation and Stress Tolerance.
Article Snippet: 1 Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye 2 Centre for Innovative Food Technologies Development, Application and Research, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye 3 State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China 4 Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China 5 Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan 6 Alpha Genomics Private Limited, Islamabad 45710, Pakistan 7 Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea 8 Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, 37150 Kastamonu, Türkiye 9 SUNUM Nanotechnology Research Centre, Sabanci University, Istanbul 34956, Türkiye 10 Department of Biology, Faculty of Science and Literature, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye 11 Department of Agricultural Biotechnology, Faculty of Agriculture, Iğdır University, Iğdır, Türkiye Abstract Chloroplast genome analyses provide critical insights into plant genetic diversity, evolution, and responses to abiotic stress.. In Beta vulgaris L., a major crop contributing approximately 20% of global sugar production, breeding efforts have focused on improving root and sugar yield, including the introgression of traits from wild relatives such as Beta maritima for resistance to Rhizomania, Cercospora leaf spot, and nematodes.. Haploid and doubled haploid technologies have further accelerated the development of homozygous lines for hybrid seed production.

Article Title: Differential vasoproliferative traits of Bartonella henselae strains associated with autotransporter BafA variants
Article Snippet: Red underlines: predicted -10 and -35 box regions by the BPROM program (Softberry, Inc.).

Sequencing:

Article Title: The Two-Component System TtrRS Regulates the Expression of the 05890-05900 Operon that Promotes the Sulfur Metabolism of Vibrio parahaemolyticus.
Article Snippet: The marine bacterium Vibrio parahaemolyticus is responsible for the seafood-borne gastroenteritis in humans.. Two-component system (TCS) TtrRS plays important roles in host colonization and works as an important regulator in V. parahaemolyticus.. However, the mechanisms by which TtrRS regulates the downstream genes, as well as the function of their target genes, remain largely unknown.

Expressing:

Article Title: Low leucine levels in the blood enhance the pathogenicity of neonatal meningitis-causing Escherichia coli
Article Snippet: .. Fig. 4 Low leucine levels repressed NsrP expression via Lrp. a qRT-PCR analysis of NsrP expression in the NMEC WT strain in LB medium and mouse blood. b The NsrP promoter region and the potential binding site of Lrp were predicted by the BProm program (SoftBerry). c qRT-PCR analysis of the NsrP expression in WT and Δ lrp . d Biacore SPR kinetic analyses of Lrp binding to the promoter of NsrP. e Fold enrichment of the NsrP promoter in the Lrp-ChIP samples compared with that in the mock-ChIP samples. f qRT-PCR analysis of the NsrP expression in WT NMEC in M9 medium supplemented with 0.1 mM leucine (Leu-L) or 5 mM leucine (Leu-H). g Northern blotting of NsrP sRNA in WT NMEC in M9 medium supplemented with 0.1 or 5 mM leucine. ..

Quantitative RT-PCR:

Article Title: Low leucine levels in the blood enhance the pathogenicity of neonatal meningitis-causing Escherichia coli
Article Snippet: .. Fig. 4 Low leucine levels repressed NsrP expression via Lrp. a qRT-PCR analysis of NsrP expression in the NMEC WT strain in LB medium and mouse blood. b The NsrP promoter region and the potential binding site of Lrp were predicted by the BProm program (SoftBerry). c qRT-PCR analysis of the NsrP expression in WT and Δ lrp . d Biacore SPR kinetic analyses of Lrp binding to the promoter of NsrP. e Fold enrichment of the NsrP promoter in the Lrp-ChIP samples compared with that in the mock-ChIP samples. f qRT-PCR analysis of the NsrP expression in WT NMEC in M9 medium supplemented with 0.1 mM leucine (Leu-L) or 5 mM leucine (Leu-H). g Northern blotting of NsrP sRNA in WT NMEC in M9 medium supplemented with 0.1 or 5 mM leucine. ..

Binding Assay:

Article Title: Low leucine levels in the blood enhance the pathogenicity of neonatal meningitis-causing Escherichia coli
Article Snippet: .. Fig. 4 Low leucine levels repressed NsrP expression via Lrp. a qRT-PCR analysis of NsrP expression in the NMEC WT strain in LB medium and mouse blood. b The NsrP promoter region and the potential binding site of Lrp were predicted by the BProm program (SoftBerry). c qRT-PCR analysis of the NsrP expression in WT and Δ lrp . d Biacore SPR kinetic analyses of Lrp binding to the promoter of NsrP. e Fold enrichment of the NsrP promoter in the Lrp-ChIP samples compared with that in the mock-ChIP samples. f qRT-PCR analysis of the NsrP expression in WT NMEC in M9 medium supplemented with 0.1 mM leucine (Leu-L) or 5 mM leucine (Leu-H). g Northern blotting of NsrP sRNA in WT NMEC in M9 medium supplemented with 0.1 or 5 mM leucine. ..

SPR Assay:

Article Title: Low leucine levels in the blood enhance the pathogenicity of neonatal meningitis-causing Escherichia coli
Article Snippet: .. Fig. 4 Low leucine levels repressed NsrP expression via Lrp. a qRT-PCR analysis of NsrP expression in the NMEC WT strain in LB medium and mouse blood. b The NsrP promoter region and the potential binding site of Lrp were predicted by the BProm program (SoftBerry). c qRT-PCR analysis of the NsrP expression in WT and Δ lrp . d Biacore SPR kinetic analyses of Lrp binding to the promoter of NsrP. e Fold enrichment of the NsrP promoter in the Lrp-ChIP samples compared with that in the mock-ChIP samples. f qRT-PCR analysis of the NsrP expression in WT NMEC in M9 medium supplemented with 0.1 mM leucine (Leu-L) or 5 mM leucine (Leu-H). g Northern blotting of NsrP sRNA in WT NMEC in M9 medium supplemented with 0.1 or 5 mM leucine. ..

Northern Blot:

Article Title: Low leucine levels in the blood enhance the pathogenicity of neonatal meningitis-causing Escherichia coli
Article Snippet: .. Fig. 4 Low leucine levels repressed NsrP expression via Lrp. a qRT-PCR analysis of NsrP expression in the NMEC WT strain in LB medium and mouse blood. b The NsrP promoter region and the potential binding site of Lrp were predicted by the BProm program (SoftBerry). c qRT-PCR analysis of the NsrP expression in WT and Δ lrp . d Biacore SPR kinetic analyses of Lrp binding to the promoter of NsrP. e Fold enrichment of the NsrP promoter in the Lrp-ChIP samples compared with that in the mock-ChIP samples. f qRT-PCR analysis of the NsrP expression in WT NMEC in M9 medium supplemented with 0.1 mM leucine (Leu-L) or 5 mM leucine (Leu-H). g Northern blotting of NsrP sRNA in WT NMEC in M9 medium supplemented with 0.1 or 5 mM leucine. ..

Amplification:

Article Title: Vibrio parahaemolyticus Down-Regulates the Intracellular c-di-GMP Level to Promote Swarming Motility by Sensing Surface.
Article Snippet: Vibrio parahaemolyticus, a significant food-borne pathogen that causes economic and public health problems worldwide, can produce two types of flagella, the single polar flagellum responsible for swimming in a liquid environment and the lateral flagella (laf) that enable the bacteria to swarm on the tops of solid surfaces.. The polar flagellar genes are expressed either in liquid or on a surface, however, laf genes would only be activated by surface sensing.. In this study, the molecular mechanism of surface sensing activating laf gene expression in V. parahaemolyticus was investigated.

Polymerase Chain Reaction:

Article Title: Vibrio parahaemolyticus Down-Regulates the Intracellular c-di-GMP Level to Promote Swarming Motility by Sensing Surface.
Article Snippet: Vibrio parahaemolyticus, a significant food-borne pathogen that causes economic and public health problems worldwide, can produce two types of flagella, the single polar flagellum responsible for swimming in a liquid environment and the lateral flagella (laf) that enable the bacteria to swarm on the tops of solid surfaces.. The polar flagellar genes are expressed either in liquid or on a surface, however, laf genes would only be activated by surface sensing.. In this study, the molecular mechanism of surface sensing activating laf gene expression in V. parahaemolyticus was investigated.

Plasmid Preparation:

Article Title: Vibrio parahaemolyticus Down-Regulates the Intracellular c-di-GMP Level to Promote Swarming Motility by Sensing Surface.
Article Snippet: Vibrio parahaemolyticus, a significant food-borne pathogen that causes economic and public health problems worldwide, can produce two types of flagella, the single polar flagellum responsible for swimming in a liquid environment and the lateral flagella (laf) that enable the bacteria to swarm on the tops of solid surfaces.. The polar flagellar genes are expressed either in liquid or on a surface, however, laf genes would only be activated by surface sensing.. In this study, the molecular mechanism of surface sensing activating laf gene expression in V. parahaemolyticus was investigated.



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