DNA, Bacterial

Publication Title: 
Plant Cell Reports

Resistant rootstocks offer an alternative to pesticides for the control of soil pests. In Prunus spp., resistance loci to root-knot nematodes (RKN) have been mapped and a transformation method is needed to validate candidate genes. Our efforts have focused on the generation of transformed hairy-roots and composite plants appropriate for nematode infection assays. An efficient and reliable method using the A4R strain of Agrobacterium rhizogenes for the transformation of Prunus roots with an Egfp reporter gene is given.

Author(s): 
Bosselut, Nathalie
Van Ghelder, Cyril
Claverie, Michel
Voisin, Roger
Onesto, Jean-Paul
Rosso, Marie-Noëlle
Esmenjaud, Daniel
Publication Title: 
Systematic and Applied Microbiology

Five Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from galls on different plant species in Hungary: strain 39/7(T) from Prunus cerasifera Myrobalan, strain 0 from grapevine var. Ezerjó, strain 7/1 from raspberry var. Findus and in Poland, strain C3.4.1 from Colt rootstock (Prunus avium × Prunus pseudocerasus) and strain CP17.2.2 from Prunus avium. Only one of these isolates, strain 0, is able to cause crown gall on different plant species.

Author(s): 
Pu?awska, Joanna
Willems, Anne
De Meyer, Sofie E.
Süle, Sandor
Publication Title: 
Computational Biology and Chemistry

Drug resistant tuberculosis has threatened all the advances that have been made in TB control at the global stage in the last few decades. DNA gyrase enzymes are an excellent target for antibacterial drug discovery as they are involved in essential functions like DNA replication. Here we report, a successful application of high throughput virtual screening (HTVS) to identify an inhibitor of Mycobacterium DNA gyrase targeting the wild type and the most prevalent three double mutants of quinolone resistant DNA gyrase namely A90V+D94G, A74S+D94G and A90V+S91P.

Author(s): 
Patel, Kunal
Tyagi, Chetna
Goyal, Sukriti
Jamal, Salma
Wahi, Divya
Jain, Ritu
Bharadvaja, Navneeta
Grover, Abhinav
Publication Title: 
Environmental Microbiology

Mycoplasms are known as pathogens of economic and medical interest in plants, animals and man. Here, we show a positive correlation between the presence of Mycoplasma-like symbionts in their isopod hosts and survivorship on low-quality food. Most isopods that survived feeding on a cellulose-based low-quality diet for 90 days harboured 'Candidatus Hepatoplasma' in their midgut glands, while those that died within 90 days mostly either harboured no or other bacterial symbionts.

Author(s): 
Fraune, Sebastian
Zimmer, Martin
Publication Title: 
BMC microbiology

BACKGROUND: Lactobacillus plantarum is considered as a safe and effective probiotic microorganism. Among various sources of isolation, traditionally fermented foods are considered to be rich in Lactobacillus spp., which can be exploited for their probiotic attribute. Antibacterial property of L. plantarum has been demonstrated against various enteric pathogens in both in vitro and in vivo systems. This study was aimed at characterizing L.

Author(s): 
Kumar, Himanshu
Rangrez, Ashraf Y.
Dayananda, Kannayakanahalli M.
Atre, Ashwini N.
Patole, Milind S.
Shouche, Yogesh S.
Publication Title: 
BMC microbiology

BACKGROUND: Lactobacillus plantarum is considered as a safe and effective probiotic microorganism. Among various sources of isolation, traditionally fermented foods are considered to be rich in Lactobacillus spp., which can be exploited for their probiotic attribute. Antibacterial property of L. plantarum has been demonstrated against various enteric pathogens in both in vitro and in vivo systems. This study was aimed at characterizing L.

Author(s): 
Kumar, Himanshu
Rangrez, Ashraf Y.
Dayananda, Kannayakanahalli M.
Atre, Ashwini N.
Patole, Milind S.
Shouche, Yogesh S.
Publication Title: 
Clinical Chemistry

BACKGROUND: The Human Microbiome Project has ushered in a new era for human metagenomics and high-throughput next-generation sequencing strategies. CONTENT: This review describes evolving strategies in metagenomics, with a special emphasis on the core technology of DNA pyrosequencing. The challenges of microbial identification in the context of microbial populations are discussed. The development of next-generation pyrosequencing strategies and the technical hurdles confronting these methodologies are addressed.

Author(s): 
Petrosino, Joseph F.
Highlander, Sarah
Luna, Ruth Ann
Gibbs, Richard A.
Versalovic, James
Publication Title: 
The ISME journal

Neonatal necrotizing enterocolitis (NEC) is an inflammatory intestinal disorder affecting preterm infants. Intestinal bacteria have an important function; however no causative pathogen has been identified. The purpose of this study was to determine if there are differences in microbial patterns that may be critical to the development of this disease. Fecal samples from 20 preterm infants, 10 with NEC and 10 matched controls (including 4 twin pairs) were obtained from patients in a single site level III neonatal intensive care unit.

Author(s): 
Wang, Yunwei
Hoenig, Jeanette D.
Malin, Kathryn J.
Qamar, Sanaa
Petrof, Elaine O.
Sun, Jun
Antonopoulos, Dionysios A.
Chang, Eugene B.
Claud, Erika C.
Publication Title: 
FEMS microbiology ecology

Phylogenetic microarrays present an attractive strategy to high-throughput interrogation of complex microbial communities. In this work, we present several approaches to optimize the analysis of intestinal microbiota with the recently developed Microbiota Array. First, we determined how 16S rDNA-specific PCR amplification influenced bacterial detection and the consistency of measured abundance values. Bacterial detection improved with an increase in the number of PCR amplification cycles, but 25 cycles were sufficient to achieve the maximum possible detection.

Author(s): 
Rigsbee, Laura
Agans, Richard
Foy, Brent D.
Paliy, Oleg
Publication Title: 
Bioinformatics (Oxford, England)

MOTIVATION: Many current studies of complex microbial communities rely on the isolation of community genomic DNA, amplification of 16S ribosomal RNA genes (rDNA) and subsequent examination of community structure through interrogation of the amplified 16S rDNA pool by high-throughput sequencing, phylogenetic microarrays or quantitative PCR. RESULTS: Here we describe the development of a mathematical model aimed to simulate multitemplate amplification of 16S ribosomal DNA sample and subsequent detection of these amplified 16S rDNA species by phylogenetic microarray.

Author(s): 
Paliy, Oleg
Foy, Brent D.

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