[9] TM4 Microarray Software Suite

Saeed, Alexander I.; Bhagabati, Nirmal; Braisted, John C.; Liang, Wei; Sharov, Vasily; Howe, Eleanor; Li, Jianwei; Thiagarajan, Mathangi; White, Joseph A.; Quackenbush, John

doi:10.1016/s0076-6879(06)11009-5

Cited by 1,753 publications

(1,357 citation statements)

References 51 publications

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“…To determine how bacterial community composition varied across samples, we compared microbial sequencing profiles for each sample using correspondence analysis (CoA), providing a statistical visualization for picturing the associations between the levels of a two-way contingency table [20]. MeV 4_8_1 [21] was used for statistical software and CoA analysis. Statistical analyses including outlier determinations were performed using XLSTAT-Pro (version 2014.4.06) and/or SAS Enterprise Guide® (version 6.1).…”

Section: Methodsmentioning

confidence: 99%

Clinical and microbiological parameters of naturally occurring periodontitis in the non-human primate Macaca mulatta

Colombo

Paster²,

Grimaldi

et al. 2017

Journal of Oral Microbiology

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Background: Non-human primates appear to represent the most faithful model of human disease, but to date the oral microbiome in macaques has not been fully characterized using next-generation sequencing. Objective: In the present study, we characterized the clinical and microbiological features of naturally occurring periodontitis in non-human primates (Macaca mulatta). Design: Clinical parameters of periodontitis including probing pocket depth (PD) and bleeding on probing (BOP) were measured in 40 adult macaques (7–22 yrs), at six sites per tooth. Subgingival plaque was collected from diseased and healthy sites, and subjected to 16S rDNA sequencing and identification at the species or higher taxon level. Results: All macaques had mild periodontitis at minimum, with numerous sites of PD ≥ 4 mm and BOP. A subset (14/40) had moderate-severe disease, with >2 sites with PD ≥ 5mm, deeper mean PD, and more BOP. Animals with mild vs moderate-severe disease were identical in age, suggesting genetic heterogeneity. 16S rDNA sequencing revealed that all macaques had species that were identical to those in humans or closely related to human counterparts, including Porphyromonas gingivalis which was present in all animals. Diseased and healthy sites harboured distinct microbiomes; however there were no significant differences in the microbiomes in moderate-severe vs. mild periodontitis. Conclusions: Naturally occurring periodontitis in older macaques closely resembles human adult periodontitis, thus validating a useful model to evaluate novel anti-microbial therapies.

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Section: Methodsmentioning

confidence: 99%

Clinical and microbiological parameters of naturally occurring periodontitis in the non-human primate Macaca mulatta

Colombo

Paster²,

Grimaldi

et al. 2017

Journal of Oral Microbiology

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“…The top‐1000 most variable genes were used for principle component analysis (PCA) using MultiExperimentViewer version 4.8.1 46, 47. Signal log2 ratios, which represent fold changes, and related significances of change were calculated from the mean signal intensities and differences between diet groups was analyzed using intensity based‐moderated t‐statistics implementing empirical Bayes correction 48.…”

Section: Methodsmentioning

confidence: 99%

“…Ingenuity pathway analysis (IPA, Ingenuity® Systems, http://www.ingenuity.com) was used to explore the canonical pathways affected by the 148 reversibly and 1510 consistently changed genes. Comparison of the expression patterns of the 148 irreversible changed genes in the MF, INT, and MF/INT diet switch groups was carried out by generating a heat map using MultiExperimentViewer, version 4.8.1 46, 47.…”

Section: Methodsmentioning

confidence: 99%

Intermittent calorie restriction largely counteracts the adverse health effects of a moderate‐fat diet in aging C57BL/6J mice

Lute

Boekschoten

Dijk

et al. 2017

Molecular Nutrition Food Res

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ScopeCalorie restriction (CR) has been shown to extend life‐ and health‐span in model species. For most humans, a life‐long CR diet is too arduous to adhere to. The aim of this study was to explore whether weekly intermittent CR can (1) provide long‐term beneficial effects and (2) counteract diet‐induced obesity in male aging mice.Methods and resultsIn this study, we have exposed C57Bl/6J mice for 24 months to an intermittent (INT) diet, alternating weekly between CR of a control diet and ad libitum moderate‐fat (MF) feeding. This weekly intermittent CR significantly counteracted the adverse effects of the MF diet on mortality, body weight, and liver health markers in 24‐month‐old male mice. Hepatic gene expression profiles of INT‐exposed animals appeared much more comparable to CR‐ than to MF‐exposed mice. At 12 months of age, a subgroup of MF‐exposed mice was transferred to the INT diet. Gene expression profiles in the liver of the 24‐month‐old diet switch mice were highly similar to the INT‐exposed mice. However, a small subset of genes was consistently changed by the MF diet during the first phase of life.ConclusionWeekly intermittent CR largely, but not completely, reversed adverse effects caused by a MF diet.

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“…Principal component analysis was used for visualizing differences in bacterial community profiles. All analyses were performed using the statistical software packages of Graphpad Prism 5 (San Diego, CA, USA) and MeV 4_8_1 (Saeed et al, 2006). …”

Section: Methodsmentioning

confidence: 99%

Ligature‐associated bacterial profiles are linked to type 2 diabetes mellitus in a rat model and influenced by antibody treatment against TNF‐α or RAGE

Grauballe

Belstrøm

Østergaard

et al. 2017

Clinical & Exp Dental Res

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There is a bidirectional relationship between periodontal disease (PD) and type 2 diabetes mellitus (T2D). T2D may lead to ecological perturbations in the oral environment, which may facilitate an altered microbiota. However, previous studies have been inconclusive in determining the effect of T2D on oral bacterial profiles. Therefore, we aimed to evaluate the influence of T2D on the ligature‐associated bacterial profile in a diabetic rat model with PD and investigated the impact of blocking inflammatory pathways with antibodies targeting either Tumor Necrosis Factor α (TNF‐α) or the receptor of advanced glycation end‐products (RAGE). A total of 62 Zucker obese rats (45 T2D) and 17 lean (non‐T2D) were divided into 4 treatment groups; lean with PD, obese with PD, obese with PD and anti‐TNF‐α treatment, and obese with PD with anti‐RAGE treatment. Periodontal disease was ligature induced. Ligature‐associated bacterial profiles were analyzed using Human Oral Microbe Identification Microarray (HOMIM). Ligature‐associated bacterial profiles differed between lean and obese rats. Furthermore, treatment with antibodies against TNF‐α or RAGE had an impact on subgingival bacterial profiles. T2D phenotypes are associated with different ligature‐associated bacterial profiles and influenced by treatment with antibodies against TNF‐α or RAGE.

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[9] TM4 Microarray Software Suite

Cited by 1,753 publications

References 51 publications

Clinical and microbiological parameters of naturally occurring periodontitis in the non-human primate Macaca mulatta

Clinical and microbiological parameters of naturally occurring periodontitis in the non-human primate Macaca mulatta

Intermittent calorie restriction largely counteracts the adverse health effects of a moderate‐fat diet in aging C57BL/6J mice

Ligature‐associated bacterial profiles are linked to type 2 diabetes mellitus in a rat model and influenced by antibody treatment against TNF‐α or RAGE

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