Bacillus subtilis and Escherichia coli, as widely used microbial species, are of great significance in studying microbial community relationships, adaptive evolution in various niches, engineering ...cell factories that produce specific products, and designing genome reduction. The pan-genome analysis is an effective method for studying the characteristics and functions of genes among and within species. Many research directions and conclusions usually depend on accurate gene identification and reliable pan-genome results. However, there currently lack enough studies showing how to achieve high-quality pan-genome results between or within certain species. This chapter will take Bacillus subtilis as an example to introduce a stepwise manner for improving the quality of the pan-genome by gradually removing confounding strains step-by-step, and ultimately obtaining a reliable high-quality pan-genome landscape of Bacillus subtilis, which could be used as a quality control protocol in pan-genome analysis pipeline. Finally, we suggest further improving the pan-genome analysis results of Escherichia coli to prove the feasibility and credibility of the quality control protocol for obtaining high-quality pan-genome landscape.
Previous studies have suggested that point-of-care ultrasound could help to evaluate and diagnose pediatric skull fracture for the closed scalp hematoma from blunt trauma. However, relevant data in ...Chinese children are missing, especially in children 0–6 years old.
Our study aimed to evaluate the efficacy of point-of-care ultrasound to diagnose skull fracture in children 0–6 years old with scalp hematoma in China.
We performed a prospective observational study and screened children 0–6 years old with closed scalp hematoma and a Glasgow coma scale of 14–15 at Hospital in China. Enrolled children (N = 152) were first evaluated for skull fracture with point-of-care ultrasound by the emergency physician and then received a head computed tomography scan.
The point-of-care ultrasound examination and computed tomography scan revealed skull fracture in 13 (8.6%) and 12 (7.9%) children, respectively. The kappa test showed a satisfactory agreement between two examinations (P < 0.0001), with kappa = 0.87 (95% confidence interval, i.e., 95% CI, 0.69, 1.00) and area under the curve = 0.95 (95% CI 0.86, 1, P < 0.0001). The point-of-care ultrasound examination had the sensitivity of 91.7% (95% CI 62.5%, 100%), specificity of 98.6% (95% CI 94.6%, 100%), positive predictive value of 84.6% (95% CI 56.5%, 96.9%), negative predictive value of 99.2% (95% CI 95.6%, 100%), and accuracy of 98.0% (95% CI 94.1%, 99.6%).
While our study is preliminary in nature, our findings may guide future larger studies in assessing the utility of point-of-care ultrasound examination in diagnosing skull fractures in children with scalp hematoma from minor head trauma.
To investigate whether education level of family members predicts all-cause and cardiovascular death and initial-episode peritonitis in patients on peritoneal dialysis (PD).
A total of 2264 patients ...on chronic PD were collected from seven centers affiliated with the Socioeconomic Status on the Outcome of Peritoneal Dialysis (SSOP) Study. All demographic, socioeconomic and laboratory data of patients and the education level of all family members were recorded at baseline. Multivariate Cox regression was used to calculate the hazard ratio (HR) of all-cause and cardiovascular mortality, and initial-episode peritonitis with adjustments for recognized traditional factors.
There were no significant differences in baseline characteristics between patients with (n = 1752) and without (n = 512) complete education information. According to the highest education level of patients' family, included 1752 patients were divided into four groups, i.e. elementary or lower (15%), middle (27%), high (24%) and more than high school (34%). The family highest education (using elementary school or lower group as reference, hazard ratio and 95% confidence interval of middle school group, high school group and more than high school group was 0.680.48-0.96, 0.640.45-0.91, 0.660.48-0.91, respectively) rather than their average education level or patients' or spouse's education was significantly associated with the higher mortality. Neither patients' nor family education level did correlate to the risk for cardiovascular death or initial-episode peritonitis.
Family members' education level was found to be a novel predictor of PD outcome. Family, as the main source of health care providers, should be paid more attention in our practice.
Background/Aims: Cognitive impairment and abnormal structural neuroimaging is common in chronic kidney disease patients. We aimed to explore its association with dialysis modality and the ...relationship between cognitive impairment and abnormal structural neuroimaging. Methods: Sixty peritoneal dialysis patients and 30 hemodialysis and 30 non-dialyzed stage 3-5 chronic kidney disease patients without history of stroke were enrolled for the study. Participants were matched for age, gender, education, diabetes status, and dialysis duration (if appropriate). Cognitive functions were measured using a battery of recognized instruments. Brain features were examined with 3-dimensional magnetic resonance imaging. Results: Cognitive impairment was significantly more severe in dialysis patients than in non-dialyzed patients. The global and specific cognitive function were not significantly different between patients on peritoneal dialysis and hemodialysis. Hemodialysis patients had more severe white matter hyperintensity, sulcal and ventricular atrophy, and SVIs than other patients. In all groups, higher white matter grade, ventricular grade, and hippocampal atrophy were significantly associated with global cognitive impairment, with hazard ratios of 1.80 (1.22-2.64), 1.67 (1.09-2.57), and 2.49 (1.07-5.77), respectively. White matter grade was also significantly associated with delayed memory (hazard ratio 1.63; 1.12-2.39). Conclusion: Dialysis modality showed no association with cognitive impairment, although hemodialysis patients had more severe neuroimaging abnormalities. For the whole group, white matter hyperintensity, and ventricular and hippocampal atrophy, were independently associated with global cognitive impairment in chronic kidney disease patients.
Abstract
Motivation
In the evolution of species, a kind of special sequences, termed ultraconserved sequences (UCSs), have been inherited without any change, which strongly suggests those sequences ...should be crucial for the species to survive or adapt to the environment. However, the UCSs are still regarded as mysterious genetic sequences so far. Here, we present a systematic study of ultraconserved genomic regions in the budding yeast based on the publicly available genome sequences, in order to reveal their relationship with the adaptability or fitness advantages of the budding yeast.
Results
Our results indicate that, in addition to some fundamental biological functions, the UCSs play an important role in the adaptation of Saccharomyces cerevisiae to the acidic environment, which is backed up by the previous observation. Besides that, we also find the highly unchanged genes are enriched in some other pathways, such as the nutrient-sensitive signaling pathway. To facilitate the investigation of unique UCSs, the UCSC Genome Browser was utilized to visualize the chromosomal position and related annotations of UCSs in S.cerevisiae genome.
Availability and implementation
For more details on UCSs, please refer to the Supplementary information online, and the custom code is available on request.
Supplementary information
Supplementary data are available at Bioinformatics online.
Objectives
To identify predictors of new-onset diabetes and impaired glucose tolerance (IGT) events in patients undergoing peritoneal dialysis (PD) based on baseline and time-dependent covariates, ...respectively.
Methods
In this prospective, single center-based cohort, all non-diabetic incident PD patients between August 2003 and August 2011 were included. All demographic and laboratory data were recorded at baseline. Repeated measurements for laboratory, dialysis prescription, and nutrition parameters were recorded at regular intervals. Multivariable Cox regression models built from baseline and time-dependent variables respectively were used to calculate the hazard ratio (HR) of potential predictors for new-onset diabetes and IGT (NODI).
Results
Of the 612 PD patients, 25 (4.1%) and 7 (1.1%) patients were identified with NODI, respectively, during a mean follow-up period of 32.4 (12.9 – 60.8) months. Using multivariable Cox regression analysis, age and body mass index (BMI) at baseline were significantly associated with NODI after adjustment for potential confounders. During follow-up, time-dependent BMI and serum high-sensitive C-reactive protein (HS-CRP) independently predicted the risk for NODI. Patients with NODI had significantly elevated plasma glucose concentrations and BMI from the start of PD therapy, with serum HS-CRP maintained at high levels. Dietary/dialysate energy intake and other laboratory parameters were not correlated with NODI risk either as baseline or time-dependent variables.
Conclusions
Traditional and uremic-related risk factors, such as older age, higher BMI, and inflammation, contribute to new-onset diabetes and impaired glucose tolerance in PD patients.
BACKGROUND: Nitrogen limitation can induce neutral lipid accumulation in microalgae, as well as inhibiting their growth. Therefore, to obtain cultures with both high biomass and high lipid contents, ...and explore the lipid accumulation mechanisms, we implemented nitrogen deprivation in a model diatom Phaeodactylum tricornutum at late exponential phase. RESULTS: Neutral lipid contents per cell subsequently increased 2.4-fold, both the number and total volume of oil bodies increased markedly, and cell density rose slightly. Transcriptional profile analyzed by RNA-Seq showed that expression levels of 1213 genes (including key carbon fixation, TCA cycle, glycerolipid metabolism and nitrogen assimilation genes) increased, with a false discovery rate cut-off of 0.001, under N deprivation. However, most light harvesting complex genes were down-regulated, extensive degradation of chloroplast membranes was observed under an electron microscope, and photosynthetic efficiency declined. Further identification of lipid classes showed that levels of MGDG and DGDG, the main lipid components of chloroplast membranes, dramatically decreased and triacylglycerol (TAG) levels significantly rose, indicating that intracellular membrane remodeling substantially contributed to the neutral lipid accumulation. CONCLUSIONS: Our findings shed light on the molecular mechanisms of neutral lipid accumulation and the key genes involved in lipid metabolism in diatoms. They also provide indications of possible strategies for improving microalgal biodiesel production.
Objective:
Peritoneal dialysis (PD)-related peritonitis is independently associated with low serum 25-hydroxy vitamin D 25(OH)D levels. Our objective is to examine the feasibility of conducting a ...large, randomised controlled trial to determine the effects of vitamin D supplementation on the risk of PD-related peritonitis.
Design:
Pilot, prospective, open-label randomised controlled trial.
Setting:
Peking University First Hospital, China.
Participants:
Patients receiving PD who had recovered from a recent episode of peritonitis between 30 September 2017 and 28 May 2020.
Interventions:
Oral natural vitamin D supplementation (2000 IU per day) versus no vitamin D supplementation for 12 months.
Primary and secondary outcome measures:
Primary outcomes were feasibility (recruitment success, retention, adherence, safety) and fidelity (change in serum 25(OH)D level during follow-up) for a large, randomised controlled trial in the future to determine the effects of vitamin D on PD-related peritonitis. Secondary outcomes were time to peritonitis occurrence and outcome of subsequent peritonitis.
Results:
Overall, 60 among 151 patients were recruited (recruitment rate was 39.7%, 95% CI 31.9–47.5%, recruitment rate among eligible patients was 61.9%, 95% CI 52.2–71.5%). Retention and adherence rates were 100.0% (95% CI 100.0–100.0%) and 81.5% (95% CI 66.8–96.1%), respectively. During follow-up, serum 25(OH)D levels increased in the vitamin D (VD) group (from 19.25 ± 10.11 nmol/L to 60.27 ± 23.29 nmol/L after 6 months, p < 0.001, n = 31), and remained higher (p < 0.001) than those in the control group (n = 29). No differences were observed between the two groups with respect to time to subsequent peritonitis (hazard ratio 0.85, 95% CI 0.33–2.17) or any of the peritonitis outcomes. Adverse events were uncommon.
Conclusions:
A randomised controlled trial of the effect of vitamin D supplementation on peritonitis occurrence in patients receiving PD is feasible, safe and results in adequate serum 25(OH)D levels.
Graphical Abstract
This is a visual representation of the abstract.
Background
Uremic toxins have been suspected as potential contributors for cognitive impairment in peritoneal dialysis (PD) patients. However, associations between the clearance of serum small and ...middle molecules and the change of cognitive function were not fully explored and then we explored this issue in the present study.
Method
A total of clinically-stable 222 patients on PD were enrolled and then followed up for 2 years in this single-center prospective cohort study. Small and middle molecules clearances were examined by urea clearance (Kt/V), creatinine clearance (Ccr) and beta-2 microglobulin (B2M) clearance via dialysate and urine at baseline and after 2 years. Global and specific cognitive impairment were measured at baseline and after 2 years. Modified Mini-Mental State Examination (3MS) was assessed for global cognitive function, trail-making tests A and B for executive function and subtests of the battery for the assessment of neuropsychological status for immediate and delayed memory, visuospatial skills and language ability.
Results
The median of total Kt/V, Ccr and B2M clearance were 1.89, 53.2 l/w/1.73 m
2
and 17.5 l/w/1.73 m
2
, respectively at baseline. The prevalence of global cognitive impairment was 12.3% for 222 patients and 15.4% for the remained 130 patients after 2 years. At baseline, total Kt/V was independently positively associated with delayed memory function. Total and dialysate beta-2 microglobulin clearance was positively associated with 3MS scores and negatively with completion time on trail A after multivariate adjustment. At 2 years, we observed a significant difference in the changing trend of 3MS scores between groups divided by total B2M clearance (
P
= 0.033), which still maintained to be meaningful after multivariate adjustment (
P
= 0.024). Patients with total B2M clearance > 19.0 l/w/1.73 m
2
got significant improvement on their 3MS scores (
P
= 0.005). Patients divided by total Kt/V or Ccr were not significantly different in the trends of general and any specific cognitive function during the follow up.
Conclusion
The higher middle molecules clearance independently correlated to better performance on general cognitive and executive function in PD patients, which also predict an improvement in general cognitive function during the follow up.
The marine diatom Phaeodactylum tricornutum is attracting considerable interest as a candidate for biofuel production due to its fast growth and high lipid content. Nitrogen deficiency can increase ...the lipid content in certain microalgae species, including P. tricornutum. However, the molecular basis of such changes remains unclear without analyzing metabolism at the proteomic level. We attempted to systematically analyze protein expression level changes of P. tricornutum upon N deprivation. We observed translational level changes that could overall redirect the metabolic network from carbon flux towards lipid accumulation. N deprivation led to an increase in the expression of genes involved in nitrogen assimilation and fatty acid biosynthesis and a concomitant decrease in photosynthesis and lipid catabolism enzymes. These molecular level changes are consistent with the observed physiological changes, e.g., in photosynthesis rate and saturated lipid content. Our results provide information at the proteomic level of the key enzymes involved in carbon flux towards lipid accumulation in P. tricornutum and suggest candidates for genetic manipulation in microalgae breeding for biodiesel production.
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