Journal: Journal of Bacteriology

Article Title: Transcription of clpP Is Enhanced by a Unique Tandem Repeat Sequence in Streptococcus mutans

doi: 10.1128/jb.01436-08

Figure Lengend Snippet: FIG. 1. Characterization of the clpP locus in S. mutans UA159. (A) Schematic representation of the clpP locus and the surrounding genes. Open reading frames are represented by block arrows, and their orientations indicate the transcriptional direction. (B) The intergenic region between upp and clpP. The sequence of the clpP promoter region is also shown with putative 35, 10, and Shine-Dalgarno (SD) sequences. The transcription start site determined by primer extension assay is indicated by an asterisk. Underlined sequences denote putative CtsR repressor binding sites. Symbols: bent arrow, promoter region; lollipop, transcription termination site; shaded triangles, repeat sequences. (C) Multiple- sequence alignment of the different repeat sequences. The intergenic region of upp and clpP from S. mutans UA159 was PCR amplified by the Smu-clpP-F2 and Smu-clpP-Rout2 primers, and the PCR products were sequenced using the Smu-clpP-F1 and Smu-clpP-Rout1 primers (Table 1). Repeat sequences derived from DNA sequence analysis were aligned by ClustalW software. At least three different types of repeat sequences were observed (RS1, RS2, and RS3). (D) Detection of the clpP transcript. Northern blot analysis of total RNA isolated from S. mutans UA159 for detection of the clpP transcript. (E) RT-PCR analysis of the upp and clpP genes. RNA, isolated from the UA159 strain, was used as a template to produce cDNA. PCR was then performed on RNA (control mRNA), cDNA, and chromosomal DNA (K-DNA), using the primer pairs as described in Table 1. M, marker.

Article Snippet: For that, we performed PCR analysis using the primers Smu-clpP-1 and Smu-clpP-Rout1 (Table 1) with the genomic DNA isolated from 13 S. mutans isolates (109c, 8Vs3, GS-5, NG-8, OMZ175, SJ32, SM3209, SP-2, T8, UA130, UA159, V100, and V403), two Streptococcus rattus isolates (BHT and FA-1), and one Streptococcus cristatus isolate (ATCC 51100).

Techniques: Blocking Assay, Sequencing, Primer Extension Assay, Binding Assay, Derivative Assay, Software, Northern Blot, Isolation, Reverse Transcription Polymerase Chain Reaction, Control, Marker

Journal: Journal of Bacteriology

Article Title: Transcription of clpP Is Enhanced by a Unique Tandem Repeat Sequence in Streptococcus mutans

doi: 10.1128/jb.01436-08

Figure Lengend Snippet: FIG. 2. Stability of the clpP transcript in S. mutans. The stability of the clpP transcript was measured from cultures at mid-exponential- growth phase (70 Klett units). RNA was extracted from UA159 at the times (min) indicated above each lane, following the addition of ri- fampin to block the synthesis of new mRNA. Northern blot analyses (A) were performed with 4 g of total RNA, using the clpP sequence as a probe. Decay kinetics (B) for clpP transcripts were determined from the Northern blot. Half-lives of the transcripts were estimated from the curve. Experiments were repeated at least twice with two different amounts of RNA, and a representative Northern blot and quantitation are shown.

Article Snippet: For that, we performed PCR analysis using the primers Smu-clpP-1 and Smu-clpP-Rout1 (Table 1) with the genomic DNA isolated from 13 S. mutans isolates (109c, 8Vs3, GS-5, NG-8, OMZ175, SJ32, SM3209, SP-2, T8, UA130, UA159, V100, and V403), two Streptococcus rattus isolates (BHT and FA-1), and one Streptococcus cristatus isolate (ATCC 51100).

Techniques: Blocking Assay, Northern Blot, Sequencing, Quantitation Assay

Journal: Journal of Bacteriology

Article Title: Transcription of clpP Is Enhanced by a Unique Tandem Repeat Sequence in Streptococcus mutans

doi: 10.1128/jb.01436-08

Figure Lengend Snippet: FIG. 3. Expression of clpP at different stages of growth. (A) Total RNA was isolated from S. mutans UA159 cells grown in THY broth at the indicated time points. (B) sqRT-PCR analysis of RNA isolated at various time points. Two different amounts of RNA, 5 ng and 25 ng, were subjected to RT-PCR with primers specific for the clpP gene as described in the text. RT-PCR results with the 25 ng RNA are shown here. The growth points are as follows: 1, 31 Klett units; 2, 47 Klett units; 3, 63 Klett units; 4, 89 Klett units; 5, 120 Klett units; 6, 140 Klett units; 7, 140 Klett units (6 h); 8, 140 Klett units (8 h); 9, 140 Klett units (10 h); and 10, 139 Klett units (12 h). The gyrA gene was included to ensure that equal amounts of RNA were used for all reactions.

Article Snippet: For that, we performed PCR analysis using the primers Smu-clpP-1 and Smu-clpP-Rout1 (Table 1) with the genomic DNA isolated from 13 S. mutans isolates (109c, 8Vs3, GS-5, NG-8, OMZ175, SJ32, SM3209, SP-2, T8, UA130, UA159, V100, and V403), two Streptococcus rattus isolates (BHT and FA-1), and one Streptococcus cristatus isolate (ATCC 51100).

Techniques: Expressing, Isolation, Reverse Transcription Polymerase Chain Reaction

Journal: Journal of Bacteriology

Article Title: Transcription of clpP Is Enhanced by a Unique Tandem Repeat Sequence in Streptococcus mutans

doi: 10.1128/jb.01436-08

Figure Lengend Snippet: FIG. 4. (A) Schematic representation of the intergenic regions flanking the clpP locus in different S. mutans strains. The intergenic region between upp and clpP was PCR amplified from different S. mutans strains using Smu-clpP-F2 (arrowhead 1) and Smu-clpP-Rout2 primers (arrowhead 2). The intergenic region between clpP and SMU.1671 was PCR amplified from different S. mutans strains using L-ClpPF (arrowhead 3) and L-Smu1523R primers (arrowhead 4). (B) PCR amplification of the 5 intergenic region (5IGS) of clpP. The S. mutans strains used were UA159, 8Vs3, NG8, and V100. Length variation in the regions is due to different numbers of repeat se- quences. At least three different types of repeat sequences were ob- served—RS1, RS2, and RS3. (C) PCR amplification of the 3 inter- genic (3IGS) region of clpP.

Article Snippet: For that, we performed PCR analysis using the primers Smu-clpP-1 and Smu-clpP-Rout1 (Table 1) with the genomic DNA isolated from 13 S. mutans isolates (109c, 8Vs3, GS-5, NG-8, OMZ175, SJ32, SM3209, SP-2, T8, UA130, UA159, V100, and V403), two Streptococcus rattus isolates (BHT and FA-1), and one Streptococcus cristatus isolate (ATCC 51100).

Techniques:

Journal: Journal of Bacteriology

Article Title: Transcription of clpP Is Enhanced by a Unique Tandem Repeat Sequence in Streptococcus mutans

doi: 10.1128/jb.01436-08

Figure Lengend Snippet: FIG. 5. Role of the repeat sequences in clpP expression. (A) Gus activity. Reporter strains IBS514 and IBS515, which contain the promoter region of clpP with (PclpP) or without (PclpPRS) the repeat sequences, respectively, fused to the gusA gene, were grown in THY medium. Expression from PclpP or PclpPRS from cultures grown to mid-exponential phase was quantified by determining the level of Gus activity, as described in the text. (B) Deletion of repeat sequences. Repeat sequences upstream of clpP were deleted by the Cre-loxP method. PCR amplification was performed with Smu- clpP-F2 (arrowhead 1) and Smu-clpP-Rout2 (arrowhead 2) primers to verify the deletion. (C) Induction of clpP transcription under thermal stress in UA159. S. mutans strains UA159 and IBS517 were grown to mid-exponential phase and exposed to heat shock (45°C) treatment, as described in the text. RNA was isolated from the bacterial cells and subjected to RT-PCR with primers specific for clpP gene. The gyrA gene was included to ensure that equal amounts of RNA were used for all reactions. Control samples refer to RNA isolated from bacterial cells without any thermal shock (37°C).

Article Snippet: For that, we performed PCR analysis using the primers Smu-clpP-1 and Smu-clpP-Rout1 (Table 1) with the genomic DNA isolated from 13 S. mutans isolates (109c, 8Vs3, GS-5, NG-8, OMZ175, SJ32, SM3209, SP-2, T8, UA130, UA159, V100, and V403), two Streptococcus rattus isolates (BHT and FA-1), and one Streptococcus cristatus isolate (ATCC 51100).

Techniques: Expressing, Activity Assay, Isolation, Reverse Transcription Polymerase Chain Reaction, Control

Journal: Frontiers in Genetics

Article Title: Scale Drop Disease Virus (SDDV) and Lates calcarifer Herpes Virus (LCHV) Coinfection Downregulate Immune-Relevant Pathways and Cause Splenic and Kidney Necrosis in Barramundi Under Commercial Farming Conditions

doi: 10.3389/fgene.2021.666897

Figure Lengend Snippet: Summary of molecular tests employed to detect and/or quantify pathogens present in kidney and liver of barramundi.

Article Snippet: Tenacibaculum maritimum , Single PCR , 16S rDNA gene , A 20-μl PCR reaction contained the DNA template, 200 nM of each primer, 2 units of Taq polymerase (PCR Biosystems), and 1 × supplied buffer , 94°C for 1 min and 35 cycles of 94°C for 30 s, 50°C for 30 s and 72°C for 1 min, and an extension step at 72°C for 5 min , Plasmid containing the T. maritimum insert target , .

Techniques: SYBR Green Assay, Infection, Plasmid Preparation

Journal: Research in nursing & health

Article Title: A systematic review of illness representation clusters in chronic conditions

doi: 10.1002/nur.22013

Figure Lengend Snippet: Study and cluster characteristics

Article Snippet: Aujla et al. (2018) , Post-stroke; United Kingdom; n = 44; age 66.9 (±14.5); 32% female , Disability (NEADL), mood (PHQ-9), quality of life (EQ-5D-5L) [longitudinal] , STATA version 13.0 Cluster analysis Hierarchical agglomerative cluster analysis (Ward’s method) Partitioned into clusters using ((-medians , Three clusters Low adjusters (30%) a Moderate adjusters (25%) High adjusters (45%) a , High adjusters were older, more educated, and more likely to have a previous stroke Low adjusters were more likely to have had a severe stroke, and worse quality of life, mood, and disability during stroke recovery , Strengths: longitudinal design, performed a priori power calculations, reliability and validity of variables reported Quality rating: 8.13 (high).

Techniques: Standard Deviation, Functional Assay, Software, Activity Assay

Journal: Aging Cell

Article Title: Expression of p16 INK 4a is a biomarker of chondrocyte aging but does not cause osteoarthritis

doi: 10.1111/acel.12771

Figure Lengend Snippet: Expression of candidate aging biomarkers in human articular chondrocytes. An initial cohort of 37 cadaveric donors ranging in age from 21 to 70 years old were evaluated for gene expression. Expression was normalized to YWHAZ (custom assay) as a housekeeping gene and analyzed in log 2 format. Linear regression analysis to age was performed with r 2 and p values shown. Significant correlations are indicated by as asterisk (*) and ampersand (&) notes that 11 samples with C t values higher than 37 were set to 37 for analysis. CDKN, Cyclin‐dependent kinase inhibitor

Article Snippet: Taqman primer probes for Mmp13 (Mm00439491_m1) and Igfbp3 (Mm01187817_m1) were used for SASP analysis.

Techniques: Expressing, Gene Expression, TaqMan Assay, Variant Assay, Binding Assay