Gel purification of gDNA for next-generation sequencing applications.

We demonstrate that gDNA can be conveniently and efficiently isolated and purified using standard agarose gel electrophoresis, band excision and gel purification. This method yields a substantial amount at microgram levels of gDNA per gel cleanup with high purity. An RNase A treatment step can be omitted.

Validation of reference genes for the normalization of RT-qPCR gene expression in 1021 grown in different culture media.

Background And Objectives: House-keeping genes are generally selected as reference genes in gene expression analysis. However, some genes may not be stably expressed across all experimental conditions. Thus, this study aimed to validate seven house-keeping genes for gene expression analysis in 1021.

sp. nov., an epiphytic bacterium isolated from rice root surfaces.

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303 and 1310. Their colonies were circular, entire, opaque, convex and yellow.

Differential effects of synthetic media on long-term growth, starch accumulation and transcription of ADP-glucosepyrophosphorylase subunit genes in Landoltia punctata.

Murashige & Skoog (MS) and Hoagland's media were previously used for in vitro culture of Landoltia punctata. During subsequent ex vitro culture, the use of MS medium resulted in a higher growth rate, compared to Hoagland's medium. Thus, a higher starch content of L.

Growth modulation effects of CBM2a under the control of AtEXP4 and CaMV35S promoters in Arabidopsis thaliana, Nicotiana tabacum and Eucalyptus camaldulensis.

The expression of cell-wall-targeted Carbohydrate Binding Modules (CBMs) can alter cell wall properties and modulate growth and development in plants such as tobacco and potato. CBM2a identified in xylanase 10A from Cellulomonas fimi is of particular interest for its ability to bind crystalline cellulose. However, its potential for promoting plant growth has not been explored.

Pseudoxanthomonas helianthi sp. nov., isolated from roots of Jerusalem artichoke (Helianthus tuberosus).

A bacterium designated as strain roo10T was isolated from roots of Jerusalem artichoke (Helianthus tuberosus). Cells were Gram-stain-negative and non-motile rods. The phylogenetic analysis of the 16S rRNA gene indicated that it represented a member of the genus Pseudoxanthomonas, and its close relatives included Pseudoxanthomonas kalamensis JA40T (97.

Antimicrobial compounds from endophytic Streptomyces sp. BCC72023 isolated from rice (Oryza sativa L.).

An endophytic actinomycete strain BCC72023 was isolated from rice (Oryza sativa L.) and identified as the genus Streptomyces, based on phenotypic, chemotaxonomic and 16S rRNA gene sequence analyses. The strain showed 99.

Micromonospora soli sp. nov., isolated from rice rhizosphere soil.

An actinomycete strain SL3-70(T) was isolated from a rice field and characterised using a polyphasic approach. The morphological and chemotaxonomical characteristics of strain SL3-70(T) indicate that it belongs to the genus Micromonospora. The phylogenetic analysis of the nearly complete 16S rRNA gene sequence revealed that strain SL3-70(T) is a member of the genus Micromonospora, and is closely related to Micromonospora echinaurantica DSM 43904(T) (99.

sp. nov., isolated from roots of upland rice.

An actinomycete strain, designated CP2R9-1, was isolated from root internal tissues of upland rice (). Based on a polyphasic approach, strain CP2R9-1 was characterized as a member of the genus Diaminopimelic acid and 3-OH-diaminopimelic acid were present in the cell-wall peptidoglycan. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unidentified phospholipids and four unidentified polar lipids.

Micromonospora endophytica sp. nov., an endophytic actinobacteria of Thai upland rice (Oryza sativa).

An actinobacterial strain, DCWR9-8-2(T), was isolated from a leaf of Thai upland rice (Oryza sativa) collected in Chumporn province, Thailand. Strain DCWR9-8-2(T) is Gram-stain-positive aerobic bacteria that produce single spores directly on the vegetative hypha. Cell wall peptidoglycan of this strain exhibits meso-diaminopimelic acid and glycine, the reducing sugars of whole-cell hydrolysate are arabinose, glucose, ribose, xylose and small amount of mannose.

Paenibacillus lemnae sp. nov., an endophytic bacterium of duckweed (Lemna aequinoctialis).

A Gram-stain-variable, rod-shaped and endospore-forming bacterium, designated strain L7-75, was isolated from duckweed (Lemna aequinoctialis). Cells were motile with a monopolar flagellum. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain L7-75(T) belonged to the genus Paenibacillus, and the closest phylogenetically related species were Paenibacillus uliginis N3/975(T) (98.

Rhizobium lemnae sp. nov., a bacterial endophyte of Lemna aequinoctialis.

Bacterial strain L6-16(T) was isolated from Lemna aequinoctialis. Cells were Gram-stain-negative, rod-shaped and motile with monopolar flagella. The phylogenetic analysis of its nearly complete 16S rRNA gene sequence revealed that strain L6-16(T) was a member of the genus Rhizobium.

Evaluations of the mutagenicity of a pigment extract from bulb culture of Hippeastrum reticulatum.

The use of anthocyanins in food products as colorants has been limited because of their instability toward alkaline pH and high temperature. This study aimed to determine color stability and mutagenicity of the anthocyanin-based pigment extract from bulb cultures of Hippeastrum (Hippeastrum reticulatum). The pigment extract retained its reddish-orange color under alkaline conditions (⩽pH 11) and was stable up to 6 h at 95 °C.

Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis).

A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8(T) during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8(T) were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8(T) was phylogenetically related to species of the genus Rhizobium.

Plastid marker gene excision by the phiC31 phage site-specific recombinase.

Marker genes are essential for selective amplification of rare transformed plastid genome copies to obtain genetically stable transplastomic plants. However, the marker gene becomes dispensable when homoplastomic plants are obtained. Here we report excision of plastid marker genes by the phiC31 phage site-specific integrase (Int) that mediates recombination between bacterial (attB) and phage (attP) attachment sites.