Bacterial strains and plasmids used in this study.

<p>Bacterial strains and plasmids used in this study.</p

Effects of cold shock on SW1 DNA replication and gene expression.

<p>(A) Growth of <i>S. piezotolerans</i> WP3 at 20°C and after cold shock to 4°C. The arrow indicate the time point of cold shock (OD₆₀₀ = 0.598). (B) Transcription level of <i>cspA</i>, <i>fpsA</i> and <i>fpsR</i> upon cold shock. The transcription level of these genes before cold shock (zero point) was set as 1. (C) Determination of copy numbers of SW1RF DNA and ssDNA after cold shock. (D) Relative transcription levels of <i>fpsA</i> and <i>fpsR</i> upon cold shock. As for the different copy number of SW1 RF DNA, the transcription levels of <i>fpsA</i> and <i>fpsR</i> were standardized to the copy number of transcriptional templates (RF and prophage of SW1). The transcription level of the two genes at zero point was set as 1. Standard deviations are indicated by error bars from triplicate assays. All of the data shown represent two independent experiments.</p

Primers used in this study.

<p>Primers used in this study.</p

SW1 RF DNA and ssDNA copy number variations over the life cycle of WP3 at different temperatures.

<p>The same amount of WP3 culture was inoculated in 2216E medium and then incubated at 20°C (A) and 4°C (B). The samples were taken from the cultures at different time point and the DNA copy number was determined. The data shown above represents two independent experiments and the error bars indicate standard deviations from triplicate assays. The different growth phases were represented with different colors. EP: Exponeitial phase, SP: Stationary phase and DP: Decline phase.</p

The relative transcription level (RTL) of <i>P_fpsA</i> and <i>P_fpsR</i> over the life cycle of WP3 at different temperatures.

<p>The same amount of WP3 culture was inoculated in 2216E medium and then incubated at 20°C (A) and 4°C (B). The RTL value were obtained by the calibration of the relative mRNA level of <i>fpsA</i> and <i>fpsR</i> with SW1 RF DNA copy number. The RTL of the two promoters at zero point were set as 1. The data shown above represents two independent experiments and the error bars indicate standard deviations from triplicate assays. The different growth phases were represented with different colors. EP: Exponeitial phase, SP: Stationary phase and DP: Decline phase.</p

Resting energy expenditure based on equation estimation can predict renal outcomes in patients with type 2 diabetes mellitus and biopsy-proven diabetic kidney disease

The aim of this study was to investigate the relationship between resting energy expenditure (REE) based on equation estimation and renal outcomes in patients with diabetes kidney disease (DKD). A total of 124 patients were enrolled from a retrospective cohort of Type 2 Diabetes mellitus (T2DM) patients with biopsy-proven DKD. Renal outcome defined as End-Stage Renal Disease (ESRD). To compare the predictive ability of different REE estimation equations on ESRD. Patients’ REE was assessed according to the estimating equation with the best predictive power, and then the relationship between REE and ESRD risk was fitted using a restricted cubic spline curve (RCS) plot and REE cutoff values were obtained. Grouping using cutoff values, and ultimately evaluate the relationship between REE and the risk of ESRD using a Multivariate Cox regression model. The strongest predictive validity for renal outcomes was the NDCKD-equation. The patients were divided into the higher-REE group (n = 78) and the lower-REE group (n = 46), based on the cutoff value. During the follow-up, 30 of 124 patients (24.2%) proceeded to ESRD. Multivariate Cox regression models showed that the risk of ESRD in patients with lower REE was 6.08 times increased compared with that in those with higher REE (HR = 6.08; 95% CI, 1.28–28.80, p = 0.023). These findings suggested that the lower REE was an independent risk factor for unfavorable renal outcomes in patients with DKD.</p

Image_1_Causal linkage between type 2 diabetes mellitus and inflammatory bowel disease: an integrated Mendelian randomization study and bioinformatics analysis.png

BackgroundObservational studies have indicated associations between type 2 diabetes mellitus (T2DM) and both colorectal cancer (CRC) and inflammatory bowel disease (IBD). However, the underlying causality and biological mechanisms between these associations remains unclear.MethodsWe conducted a bidirectional Mendelian randomization (MR) analysis employing summary statistics from genome-wide association studies involving European individuals. The inverse variance weighting (IVW) method was the primary method used to assess causality. Additionally, we applied MR Egger, Weighted median, Simple mode, and Weighted mode to evaluate the robustness of the results. Outliers were identified and eliminated using the MR-PRESSO, while the MR-Egger intercept was used to assess the horizontal pleiotropic effects of single nucleotide polymorphisms (SNPs). The heterogeneity was evaluated using the Cochrane Q test, and sensitivity analysis was performed using leave-one-out method. The F statistic was calculated to evaluate weak instrumental variable bias. Finally, a pilot bioinformatics analysis was conducted to explore the underlying biological mechanisms between T2DM and IBD/UC.ResultsThe IVW results demonstrated that T2DM significantly reduced risks of IBD (OR=0.885, 95% CI: 0.818–0.958, P=0.002) and ulcerative colitis (UC) (OR=0.887, 95% CI: 0.812–0.968, P=0.007). Although the 95% CIs of MR Egger, Weighted median, Simple mode, and Weighted mode were broad, the majority of their estimates were consistent with the direction of IVW. Despite significant heterogeneity among SNPs, no horizontal pleiotropy was observed. The leave-one-out analysis showed that the causality remained consistent after each SNP was removed, underscoring the reliability of the results. Reverse MR analysis indicated that genetic susceptibility to both CRC and IBD had no significant effect on the relative risk of T2DM. Ten hub genes were identified, which mainly enriched in pathways including maturity onset diabetes of the young, thyroid cancer, gastric acid secretion, longevity regulating pathway, melanogenesis, and pancreatic secretion.ConclusionThe presence of T2DM does not increase the risk of CRC or IBD. Moreover, T2DM might reduce risk of IBD, including UC. Conversely, the occurrence of CRC or IBD does not influence the risk of T2DM. The association between T2DM and IBD/UC may be related to the changes in multiple metabolic pathways and CTLA-4-mediated immune response.</p

Image_2_Causal linkage between type 2 diabetes mellitus and inflammatory bowel disease: an integrated Mendelian randomization study and bioinformatics analysis.png

BackgroundObservational studies have indicated associations between type 2 diabetes mellitus (T2DM) and both colorectal cancer (CRC) and inflammatory bowel disease (IBD). However, the underlying causality and biological mechanisms between these associations remains unclear.MethodsWe conducted a bidirectional Mendelian randomization (MR) analysis employing summary statistics from genome-wide association studies involving European individuals. The inverse variance weighting (IVW) method was the primary method used to assess causality. Additionally, we applied MR Egger, Weighted median, Simple mode, and Weighted mode to evaluate the robustness of the results. Outliers were identified and eliminated using the MR-PRESSO, while the MR-Egger intercept was used to assess the horizontal pleiotropic effects of single nucleotide polymorphisms (SNPs). The heterogeneity was evaluated using the Cochrane Q test, and sensitivity analysis was performed using leave-one-out method. The F statistic was calculated to evaluate weak instrumental variable bias. Finally, a pilot bioinformatics analysis was conducted to explore the underlying biological mechanisms between T2DM and IBD/UC.ResultsThe IVW results demonstrated that T2DM significantly reduced risks of IBD (OR=0.885, 95% CI: 0.818–0.958, P=0.002) and ulcerative colitis (UC) (OR=0.887, 95% CI: 0.812–0.968, P=0.007). Although the 95% CIs of MR Egger, Weighted median, Simple mode, and Weighted mode were broad, the majority of their estimates were consistent with the direction of IVW. Despite significant heterogeneity among SNPs, no horizontal pleiotropy was observed. The leave-one-out analysis showed that the causality remained consistent after each SNP was removed, underscoring the reliability of the results. Reverse MR analysis indicated that genetic susceptibility to both CRC and IBD had no significant effect on the relative risk of T2DM. Ten hub genes were identified, which mainly enriched in pathways including maturity onset diabetes of the young, thyroid cancer, gastric acid secretion, longevity regulating pathway, melanogenesis, and pancreatic secretion.ConclusionThe presence of T2DM does not increase the risk of CRC or IBD. Moreover, T2DM might reduce risk of IBD, including UC. Conversely, the occurrence of CRC or IBD does not influence the risk of T2DM. The association between T2DM and IBD/UC may be related to the changes in multiple metabolic pathways and CTLA-4-mediated immune response.</p

Table_3_Causal linkage between type 2 diabetes mellitus and inflammatory bowel disease: an integrated Mendelian randomization study and bioinformatics analysis.xlsx

BackgroundObservational studies have indicated associations between type 2 diabetes mellitus (T2DM) and both colorectal cancer (CRC) and inflammatory bowel disease (IBD). However, the underlying causality and biological mechanisms between these associations remains unclear.MethodsWe conducted a bidirectional Mendelian randomization (MR) analysis employing summary statistics from genome-wide association studies involving European individuals. The inverse variance weighting (IVW) method was the primary method used to assess causality. Additionally, we applied MR Egger, Weighted median, Simple mode, and Weighted mode to evaluate the robustness of the results. Outliers were identified and eliminated using the MR-PRESSO, while the MR-Egger intercept was used to assess the horizontal pleiotropic effects of single nucleotide polymorphisms (SNPs). The heterogeneity was evaluated using the Cochrane Q test, and sensitivity analysis was performed using leave-one-out method. The F statistic was calculated to evaluate weak instrumental variable bias. Finally, a pilot bioinformatics analysis was conducted to explore the underlying biological mechanisms between T2DM and IBD/UC.ResultsThe IVW results demonstrated that T2DM significantly reduced risks of IBD (OR=0.885, 95% CI: 0.818–0.958, P=0.002) and ulcerative colitis (UC) (OR=0.887, 95% CI: 0.812–0.968, P=0.007). Although the 95% CIs of MR Egger, Weighted median, Simple mode, and Weighted mode were broad, the majority of their estimates were consistent with the direction of IVW. Despite significant heterogeneity among SNPs, no horizontal pleiotropy was observed. The leave-one-out analysis showed that the causality remained consistent after each SNP was removed, underscoring the reliability of the results. Reverse MR analysis indicated that genetic susceptibility to both CRC and IBD had no significant effect on the relative risk of T2DM. Ten hub genes were identified, which mainly enriched in pathways including maturity onset diabetes of the young, thyroid cancer, gastric acid secretion, longevity regulating pathway, melanogenesis, and pancreatic secretion.ConclusionThe presence of T2DM does not increase the risk of CRC or IBD. Moreover, T2DM might reduce risk of IBD, including UC. Conversely, the occurrence of CRC or IBD does not influence the risk of T2DM. The association between T2DM and IBD/UC may be related to the changes in multiple metabolic pathways and CTLA-4-mediated immune response.</p

Table_7_Causal linkage between type 2 diabetes mellitus and inflammatory bowel disease: an integrated Mendelian randomization study and bioinformatics analysis.xlsx

BackgroundObservational studies have indicated associations between type 2 diabetes mellitus (T2DM) and both colorectal cancer (CRC) and inflammatory bowel disease (IBD). However, the underlying causality and biological mechanisms between these associations remains unclear.MethodsWe conducted a bidirectional Mendelian randomization (MR) analysis employing summary statistics from genome-wide association studies involving European individuals. The inverse variance weighting (IVW) method was the primary method used to assess causality. Additionally, we applied MR Egger, Weighted median, Simple mode, and Weighted mode to evaluate the robustness of the results. Outliers were identified and eliminated using the MR-PRESSO, while the MR-Egger intercept was used to assess the horizontal pleiotropic effects of single nucleotide polymorphisms (SNPs). The heterogeneity was evaluated using the Cochrane Q test, and sensitivity analysis was performed using leave-one-out method. The F statistic was calculated to evaluate weak instrumental variable bias. Finally, a pilot bioinformatics analysis was conducted to explore the underlying biological mechanisms between T2DM and IBD/UC.ResultsThe IVW results demonstrated that T2DM significantly reduced risks of IBD (OR=0.885, 95% CI: 0.818–0.958, P=0.002) and ulcerative colitis (UC) (OR=0.887, 95% CI: 0.812–0.968, P=0.007). Although the 95% CIs of MR Egger, Weighted median, Simple mode, and Weighted mode were broad, the majority of their estimates were consistent with the direction of IVW. Despite significant heterogeneity among SNPs, no horizontal pleiotropy was observed. The leave-one-out analysis showed that the causality remained consistent after each SNP was removed, underscoring the reliability of the results. Reverse MR analysis indicated that genetic susceptibility to both CRC and IBD had no significant effect on the relative risk of T2DM. Ten hub genes were identified, which mainly enriched in pathways including maturity onset diabetes of the young, thyroid cancer, gastric acid secretion, longevity regulating pathway, melanogenesis, and pancreatic secretion.ConclusionThe presence of T2DM does not increase the risk of CRC or IBD. Moreover, T2DM might reduce risk of IBD, including UC. Conversely, the occurrence of CRC or IBD does not influence the risk of T2DM. The association between T2DM and IBD/UC may be related to the changes in multiple metabolic pathways and CTLA-4-mediated immune response.</p