Search

As the primary domain of ideological and political education in higher education institutions, ideological and political courses must align with principles rooted in human psychology and education. Integrating educational psychology into ideological and political teaching in universities enhances the scientific, targeted, and forward-thinking nature of such education. The burgeoning exploration of knowledge graph applications has extended to machine translation, semantic search, and intelligent question answering. Diverging from traditional text matching, the knowledge spectrum graph transforms information acquisition in search engines. This paper pioneers a predictive system for delineating the relationship between educational psychology and ideological and political education in universities. Initially, it extracts diverse psychological mapping relationships of students, constructing a knowledge graph. By employing the KNN algorithm, the system analyzes psychological characteristics to effectively forecast the relationship between educational psychology and ideological and political education in universities. The system's functionality is meticulously detailed in this paper, and its performance is rigorously tested. The results demonstrate high accuracy, recall rates, and F1 values. The F1 score can reach 0.95enabling precise sample classification. The apex of the average curve for system response time peaks at approximately 2.5 s, maintaining an average response time of less than 3 s. This aligns seamlessly with the demands of practical online teaching requirements. The system adeptly forecasts the relationship between educational psychology and ideological and political education in universities, meeting response time requirements and thereby fostering the scientific and predictive nature of ideological and political teaching in higher education institutions., (© 2024. The Author(s).)

Background: Aortic involvement in patients with Behcet's disease (BD) is rare, but it is one of the most severe manifestations. Open surgical repair of aortic aneurysm is challenging considering the high risk of postoperative recurrent anastomotic pseudoaneurysms and is associated with a much higher mortality rate. Recently, endovascular treatment has proven to be a feasible, less invasive alternative to surgery for these patients., Case Presentation: We report a total endovascular repair of a paravisceral abdominal aortic pseudoaneurysm in a 25-year-old male patient with BD. The pseudoaneurysm was successfully excluded, and the blood supply of visceral arteries was preserved with a physician-modified three-fenestration endograft under 3D image fusion guidance. Immunosuppressive therapy was continued for 1 year postoperatively. At 18 months, the patient was asymptomatic without abdominal pain. Computed tomography angiography demonstrated the absence of pseudoaneurysm recurrence, good patency of visceral vessels., Discussion and Conclusions: Endovascular repair using physician-modified fenestrated endografts is a relatively safe and effective approach for treating paravisceral aortic pseudoaneurysm in BD patients. This technique enables the preservation of the visceral arteries and prevents aneurysm recurrence at the proximal and distal landing zones, which are common complications of open surgical repair in these patients. Furthermore, we emphasize the importance of adequate immunosuppressive therapy before and after surgical repair in BD patients, which is a major risk factor for recurrence and poor prognosis., (© 2024. The Author(s).)

Background: Andrographolide (Andro) is a diterpenoid derived from Andrographis paniculate, which has anti-inflammatory, antibacterial, antiviral and hepatoprotective activities. Gram-negative bacterial infections can cause varying degrees of liver injury in chickens, although Andro has been shown to have a protective effect on the liver, its underlying mechanism of action and effects on liver proteins are not known., Methods: The toxicity of Andro on the viability of leghorn male hepatoma (LMH) cells at different concentrations and times was analyzed by CCK-8 assays. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities in the culture supernatants were measured using an automatic biochemical analyzer to evaluate the protective effect of androscopolide on LPS-induced injury of LMH cells. Subsequently, TMT proteomics analysis were performed on the negative control group (NC group), LPS, and LPS-Andro groups, and bioinformatics analysis was performed on the differentially expressed proteins (DEPs)., Results: It was found that Andro reduced ALT and AST levels in the cell supernatant and alleviated LPS-induced injury in LMH cells. Proteomic analysis identified 50 and 166 differentially expressed proteins in the LPS vs. NC group and LPS-Andro vs. LPS group, respectively. Andro may be involved in steroid metabolic processes, negative regulation of MAPK cascade, oxidative stress, and other processes to protect against LPS-induced liver injury., Conclusions: Andro protects against LPS-induced liver injury, HMGCS1, HMGCR, FDPS, PBK, CAV1, PRDX1, PRDX4, and PRDX6, which were identified by differential proteomics, may be the targets of Andro. Our study may provide new theoretical support for Andro protection against liver injury., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Background: Cesarean birth is associated with a higher prevalence of delayed onset of lactogenesis II (DOLII) than vaginal birth. DOLII refers to the delayed initiation of copious milk production beyond 72 h after birth. This study aimed to determine the prevalence of, and factors associated with, DOLII among women who delivered via Cesarean section in China., Methods: This prospective longitudinal cohort study recruited 468 women who delivered via Cesarean section at a tertiary hospital in China from 9 October 2021 to 17 May 2022. Face-to-face interviews were conducted during their delivery hospital stay to obtain information about demographic, medical, and breastfeeding factors. We assessed the onset of lactogenesis on postpartum day four, based on the maternal perception of changes in breast fullness. The Edinburgh Postnatal Depression Scale (EPDS) was used to screen for postpartum depression. Women with DOLII were interviewed via telephone or WeChat daily for one week postpartum to determine the timing of the onset of lactogenesis II. Univariate and multivariable logistic regression analyses were used to identify the determinants of DOLII., Results: DOLII was experienced by 156 of 468 participants (33.3%). After adjusting for potential confounders, the odds of DOLII were 95% higher in primiparous women than multiparous women (adjusted odds ratio [aOR] 1.95; 95% confidence interval [CI] 1.29, 2.98), 75% higher in women with a serum albumin concentration < 35 g / L than women with normal serum albumin concentrations (aOR 1.78; 95% CI 1.09, 2.99), increased by 2.03-fold in women with an EPDS score ≥ 10 than women with an EPDS score < 10 (aOR 2.03; 95% CI 1.35, 3.07), and decreased in women with a higher number of breastfeeding sessions in the first 48 h postpartum (aOR 0.88; 95% CI 0.83, 0.93)., Conclusions: One-third of women with Cesarean section delivery experienced DOLII. DOLII was more likely in women who were primiparous, had a serum albumin concentration < 35 g / L, had a lower frequency of breastfeeding sessions, and had an EPDS score ≥ 10. Women with these risk factors who deliver via Cesarean section may need early breastfeeding support to ensure successful lactation., (© 2022. The Author(s).)

Objective: To compare the breakage risk of lengthened sacroiliac screws and ordinary sacroiliac screws to treat unilateral vertical sacral fractures and provide a reference for clinical application., Methods: A finite element model of Tile C pelvic ring injury (unilateral type Denis II fracture of the sacrum) was produced. The sacral fractures were fixed with a lengthened sacroiliac screw and ordinary sacroiliac screw in 6 types of models. The maximal von Mises stresses and stress distributions of the two kinds of screws when standing on both feet were measured and compared., Results: The maximal von Mises stress of the lengthened screw was less than that of the ordinary screw. Compared with ordinary screw, the stress distribution in the lengthened screw was more homogeneous., Conclusions: The breakage risk of screws fixed in double segments is lower than that of screws fixed in single segments, the breakage risk of lengthened screws is lower than that of ordinary screws, and the breakage risk of screws fixed in S2 segments is lower than that of screws fixed in S1 segments., (© 2022. The Author(s).)

Background: Extracellular vesicles (EVs) could mediate embryo-maternal communication to affect embryo implantation by delivering biology information, including microRNA (miRNA), protein, lipid. Our previous research shows that miR-92b-3p was differentially expressed in EVs of uterine flushing fluids during the embryo implantation period. However, the role of miR-92b-3p from EVs in embryo implantation remains elusive., Materials and Methods: EVs were isolated from porcine endometrial epithelial cells (EECs) by ultracentrifugation. MiR-92b-3p mimics and EVs were used to regulate the expression of miR-92b-3p in porcine trophoblast cells (PTr2 cells). Cell proliferation, migration and adhesion analyses were used to observe the phenotype. RT-qPCR, western blot and dual-luciferase reporter assay were used to assess the targets of miR-92b-3p., Results: In this study, EVs derived from porcine EECs were identified and could be taken up by PTr2 cells. We found that the EVs derived from EECs transfected with miR-92b-3p mimic (EVs-miR-92b-3p) significantly promoted the proliferation, migration and adhesion of PTr2 cells. We verified that Tuberous sclerosis complex subunit (TSC1) and Dickkopf 3 (DKK3) were the target genes of miR-92b-3p. Moreover, our study showed that miR-92b-3p plays a vital role in PTr2 cells via targeting TSC1 and DKK3. Furthermore, the 3'UTR vectors of TSC1 and DKK3 can rescue the effect of miR-92b-3p on PTr2 cells., Conclusions: Taken together, this study reveals a novel mechanism that EVs derived from porcine EECs treated with miR-92b-3p crosstalk with trophoblasts by targeting TSC1 and DKK3, leading to an enhanced ability for implantation., (© 2022. The Author(s).)

Background: Appropriate antibiotic prescribing is key to combating antimicrobial resistance. Upper respiratory tract infections (URTIs) are common reasons for emergency department (ED) visits and antibiotic use. Differentiating between bacterial and viral infections is not straightforward. We aim to provide an evidence-based clinical decision support tool for antibiotic prescribing using prediction models developed from local data., Methods: Seven hundred-fifteen patients with uncomplicated URTI were recruited and analysed from Singapore's busiest ED, Tan Tock Seng Hospital, from June 2016 to November 2018. Confirmatory tests were performed using the multiplex polymerase chain reaction (PCR) test for respiratory viruses and point-of-care test for C-reactive protein. Demographic, clinical and laboratory data were extracted from the hospital electronic medical records. Seventy percent of the data was used for training and the remaining 30% was used for validation. Decision trees, LASSO and logistic regression models were built to predict when antibiotics were not needed., Results: The median age of the cohort was 36 years old, with 61.2% being male. Temperature and pulse rate were significant factors in all 3 models. The area under the receiver operating curve (AUC) on the validation set for the models were similar. (LASSO: 0.70 [95% CI: 0.62-0.77], logistic regression: 0.72 [95% CI: 0.65-0.79], decision tree: 0.67 [95% CI: 0.59-0.74]). Combining the results from all models, 58.3% of study participants would not need antibiotics., Conclusion: The models can be easily deployed as a decision support tool to guide antibiotic prescribing in busy EDs.

Background: Diabetes is associated with the dysfunction of endothelial progenitor cells (EPCs), characterized as impaired angiogenesis, a phenomenon thought to be involved in the development of diabetic foot. lncRNA plays an essential role in microvascular dysfunction and signaling pathways in patients with diabetes. lncRNA taurine upregulated gene 1 (TUG1) participates in angiogenesis in various cells. However, the mechanisms of TUG1 activity in EPCs have not been elucidated., Methods: We isolated and then characterized EPCs from the peripheral blood of mice using immunofluorescence and flow cytometry. Western blot detected the wnt/β-catenin pathway in high glucose-treated EPCs. Bioinformatics analysis predicted a putative binding site for TUG1 on miR-29c-3p. The interactions among TUG1, platelet-derived growth factor-BB (PDGF-BB), and miR-29c-3p were analyzed by luciferase assays. In vivo, diabetic mouse ischemic limb was treated with normal saline or TUG1 overexpression lentiviruses., Results: We found that EPC migration, invasion, and tube formation declined after treatment with high glucose, but improved with TUG1 overexpression. Mechanically, wnt/β-catenin pathway and autophagy were involved in the function of TUG1 overexpression in high glucose-treated EPCs. Moreover, TUG1 regulates the PDGF-BB/wnt pathway and function of high glucose-treated EPCs via miR-29c-3p. In vivo, injection of TUG1 lentivirus in a diabetic mouse ischemic limb model stimulated angiogenesis., Conclusions: Our findings suggest that TUG1 restores high glucose-treated EPC function by regulating miR-29c-3p/PDGF-BB/Wnt signaling.

Background: To compare the mechanical characteristics of a percutaneous superior pubic intramedullary screw, percutaneous bridging plate and percutaneous screw-rod system of the anterior ring for the treatment of unilateral vertical pubic fractures to provide a reference for clinical application., Methods: A finite element model of pelvic anterior ring injury (unilateral vertical pubic fracture) was produced. The fractures were fixed with a percutaneous superior pubic intramedullary screw, percutaneous bridging plate and percutaneous screw-rod system of the anterior ring and their combinations in 5 types of models. The fracture stabilities under vertical, bilateral and anterior-posterior load were quantified and compared based on the displacement of the hip joints' midpoint as quantificational index of fracture stability., Results: In the condition of bilateral and anterior-posterior load, the vertical, bilateral and anterior-posterior displacements of the hip joints' midpoint of different models were significantly different respectively. In general, the displacements of the 5 pelvic anterior ring fixations were ranked from maximum to minimum as follows: bridging plate, pelvic anterior screw-rod system, combination of bridging plate and pelvic anterior screw-rod system, superior pubic intramedullary screw and combination of superior pubic intramedullary screw and pelvic anterior screw-rod system., Conclusion: For the fixation in unilateral pubic fractures of pelvic ring injury, the percutaneous superior pubic intramedullary screw is optimal, the percutaneous pelvic anterior screw-rod system is the second choice, and percutaneous bridging plate ranks the third. The percutaneous pelvic anterior screw-rod system can significantly increase fixation stability of the percutaneous superior pubic intramedullary screw and the percutaneous bridging plate.

Background: Tumor progression and distant metastasis are the main causes of deaths in colorectal cancer (CRC) patients, and the molecular mechanisms in CRC metastasis have not been completely discovered., Methods: We identified differentially expressed genes (DEGs) and lncRNAs (DELs) of CRC from The Cancer Genome Atlas (TCGA) database. Then we conducted the weighted gene co-expression network analysis (WGCNA) to investigate co-expression modules related with CRC metastasis. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, DEG-DEL co-expression network and survival analyses of significant modules were also conducted. Finally, the expressions of selected biomarkers were validated in cell lines by quantitative real-time PCR (qRT-PCR)., Results: 2032 DEGs and 487 DELs were involved the construction of WGCNA network, and greenyellow, turquoise and brown module were identified to have more significant correlation with CRC metastasis. GO and KEGG pathway analysis of these three modules have proven that the functions of DEGs were closely involved in many important processes in cancer pathogenesis. Through the DEG-DEL co-expression network, 12 DEGs and 2 DELs were considered as hub nodes. Besides, survival analysis showed that 30 DEGs were associated with the overall survival of CRC. Then 10 candidate biomarkers were chosen for validation and the expression of CA2, CHP2, SULT1B1, MOGAT2 and C1orf115 were significantly decreased in CRC cell lines when compared to normal human colonic epithelial cells, which were consistent with the results of differential expression analysis. Especially, low expression of SULT1B1, MOGAT2 and C1orf115 were closely correlated with poorer survival of CRC., Conclusion: This study identified 5 genes as new biomarkers affecting the metastasis of CRC. Besides, SULT1B1, MOGAT2 and C1orf115 might be implicated in the prognosis of CRC patients., Competing Interests: Competing interestsThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© The Author(s) 2020.)

Objectives: Mesenchymal stem cells (MSCs) have been intensively investigated as to their therapeutic potentials. However, the full chemical-defined medium supporting the isolation and expansion of human MSCs has not been developed yet., Materials and Methods: Here, we developed the full chemical-defined medium, NBVbe medium, via RNA sequencing, bioinformatic analysis, and growth factor screening., Results: The NBVbe medium contains N2B27 medium with the BSA (bovine serum albumin) replaced by the recombinant human albumin, bFGF (basic fibroblast growth factor), vitamin C, and EGF (epidermal growth factor). The NBVbe medium could support the isolation and expansion of human MSCs from the umbilical cords., Conclusions: The full chemical-defined medium supporting the isolation and expansion of human MSCs has been developed. This would be helpful for further optimization of the MSC medium, their clinical applications, and molecular characterization.

Background: Kashin-Beck disease (KBD) is an endemic osteoarthropathy, and its pathogenesis is still not entirely clear. Pathologically, many KBD changes are similar to those of osteoarthritis (OA). Therefore, this study aimed to identify changes in the levels of potential urinary biomarkers for OA, including C-telopeptide of type II collagen (uCTX-II), type II collagen cleavage neoepitope (uC2C), pyridinoline (uPYD), and uHelix-II, among adults with KBD., Methods: Urinary samples of 83 external control (EC) subjects, 91 KBD patients, and 86 internal control (IC) subjects were tested by ELISA after the subjects completed a questionnaire and X-ray examination., Results: The medians of the four markers in the KBD group were higher than those in the EC group and those in the IC group. The medians in the grade II KBD group were higher than those in the grade I group but were not statistically significant (P = 0.301, P = 0.408, P = 0.204, and P = 0.898 for uCTX-II, uC2C, uPYD, and uHelix-II, respectively). The area under the curve (AUC) of uCTX-II (0.775) was higher than that of the others (0.672, 0.639, and 0.628 for uC2C, uPYD, and uHelix-II, respectively)., Conclusion: The levels of uCTX-II, uC2C, uPYD, and uHelix-II were elevated in adults with KBD and showed an increasing trend as the severity of KBD increased. The prediction accuracy of uCTX-II was more useful than that of the others for assisting in the diagnosis of KBD.

Background: Lung adenocarcinoma (LUAD), largely remains a primary cause of cancer-related death worldwide. The molecular mechanisms in LUAD metastasis have not been completely uncovered., Methods: In this study, we identified differentially expressed genes (DEGs), miRNAs (DEMs) and lncRNAs (DELs) underlying metastasis of LUAD from The Cancer Genome Atlas database. Intersection mRNAs were used to perform gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and co-expression network analysis. In addition, survival analyses of intersection mRNAs were conducted. Finally, intersection mRNAs, miRNAs and lncRNAs were subjected to construct miRNA-mRNA-lncRNA network., Results: A total of 1015 DEGs, 54 DEMs and 22 DELs were identified in LUAD metastasis and non-metastasis samples. GO and KEGG pathway analysis had proven that the functions of intersection mRNAs were closely related with many important processes in cancer pathogenesis. Among the co-expression interactions network, 22 genes in the co-expression network were over the degree 20. These genes imply that they have connections with many other gene nodes. In addition, 14 target genes (ARHGAP11A, ASPM, HELLS, PRC1, TMPO, ARHGAP30, CD52, IL16, IRF8, P2RY13, PRKCB, PTPRC, SASH3 and TRAF3IP3) were found to be associated with survival in patients with LUAD significantly (log-rank P < 0.05). Two lncRNAs (LOC96610 and ADAM6) acting as ceRNAs were identified based on the miRNA-mRNA-lncRNA network., Conclusions: Taken together, the results may provide a novel perspective to develop a multiple gene diagnostic tool for LUAD prognosis, which might also provide potential biomarkers or therapeutic targets for LUAD.

Background: Kashin-Beck disease (KBD) is an endemic, chronic, degenerative osteoarthropathy. KBD is usually diagnosed by using X-ray image and clinical symptoms, lacking of serological biomarkers. The serum level of PIICP, PIIANP, and PIIBNP can specifically reflect the damage of the cartilage. So, in this study, the serum levels of PIICP, PIIANP, and PIIBNP were detected in order to determine whether they can be used as potential biomarkers for the diagnosis of KBD., Method: Using a status survey, the survey sites were selected in the KBD historical endemic areas and non-endemic areas in Jilin and Heilongjiang provinces. All local residents have undergone clinical examination, X-ray examination of the hands and knees, and questionnaire survey. A total of 554 people were surveyed, and 184 residents who are eligible for inclusion criteria were selected as our subjects. Fifty-six cases were diagnosed as KBD and 63 individuals were included as internal control and 65 subjects were included as external control. And blood samples of surveyed subjects were collected, and the serum was separated to detect the levels of PIICP, PIIANP, and PIIBNP by ELISA. Statistical analysis was performed using the SPSS software., Results: There were no statistically significant differences in age and sex among the three groups. The Kruskal-Wallis H test showed that the serum levels of PIICP, PIIANP, and PIIBNP were significantly different among the three groups. Multiple comparisons using Dunnett's T3 test revealed that serum levels of PIICP, PIIANP, and PIIBNP were significantly lower in KBD patients than in internal and external control. However, there was no significant difference between the internal and external control., Conclusions: The results preliminarily indicated that the levels of PIICP, PIIANP, and PIIBNP in serum could reflect the abnormal synthesis of type II collagen in KBD patients and suggested that these indicators might be used as potential biomarkers for the diagnosis of KBD.

Background: To conduct radiologic anatomical study on the relation between S1 sacroiliac screws' entry points and the route of the pelvic outer superior gluteal artery branches with the aim to provide the anatomical basis and technical reference for the avoidance of damage to the superior gluteal artery during the horizontal sacroiliac screw placement., Methods: Superior gluteal artery CTA (CT angiography) vascular imaging of 74 healthy adults (37 women and 37 men) was done with 128-slice spiral CT (computed tomography). The CT attendant-measuring software was used to portray the "safe bony entrance area" (hereinafter referred to as "Safe Area") of the S1 segment in the standard lateral pelvic view of three-dimensional reconstruction. The anatomical relation between S1 sacroiliac screws' Safe Area and the pelvic outer superior gluteal artery branches was observed and recorded. The number of cases in which artery branches intersected the Safe Area was counted. The cases in which superior gluteal artery branches disjointed from the Safe Area were identified, and the shortest distance between the Safe Area and the superior gluteal artery branch closest to the Safe Area was measured., Results: Three cases out of the 74 sample cases were excluded from this study as they were found to have no bony space for horizontal screw placement in S1 segment. Among the remaining 71 sample cases, there are 32 cases (45.1%) where the deep superior branch of superior gluteal artery passes through the Safe Area of S1 entrance point. There was no distinguishing feature and rule on how the deep superior branches and the Safe Area overlapped. In the 39 cases in which superior gluteal artery branches disjointed from the Safe Area, the deep superior branches of superior gluteal artery were the branches closest to the Safe Area and the part of the branch closest to the Safe Area was located in front of the widest part of the Safe Area. The shortest distance between the deep superior branch and the Safe Area is 0.86 ± 0.84 cm., Conclusion: There is a high risk of accidental injury of the deep superior branches of superior gluteal artery in the process of S1 sacroiliac screw placement. Even if the entry points are located in the safe bony entrance area, the absolute secure placement cannot be assured. We suggest that great attention should be paid to make thorough preoperative plans.

Background: Fish, rich in ω-3 polyunsaturated fatty acids, has been found to be associated with lower risk of several types of cancer risk, and beneficial for brain development. However, the association between fish intake and brain tumor risk is still inconsistent. Therefore, we conducted a meta-analysis to clarify the association., Methods: Relevant studies were identified from PubMed and EMBASE databases. The pooled relative risks were obtained by the fixed-effects model when no substantial heterogeneity was observed. Otherwise, the random-effects model was employed. Subgroup and publication bias analyses were also performed., Results: Nine observational studies were included in the meta-analysis. The pooled relative risk of brain cancer for the highest vs. lowest category of fish intake was 0.83 (95% confidence interval [CI]: 0.70-0.99). No significant heterogeneity was detected. Dose-response analysis showed that the RR per 100 g/day increase in fish intake was 0.95 (95% CI: 0.91-0.98). The results remained unchanged in subgroup and sensitivity analyses., Conclusions: The results of our meta-analysis suggest that fish intake might be associated with lower risk of brain cancer risk. The finding should be further confirmed by future cohort studies with validated questionnaires and strict control of confounders.

Background: A recessive mutation "c" in the Mexican axolotl, Ambystoma mexicanum, results in the failure of normal heart development. In homozygous recessive embryos, the hearts do not have organized myofibrils and fail to beat. In our previous studies, we identified a noncoding Myofibril-Inducing RNA (MIR) from axolotls which promotes myofibril formation and rescues heart development., Results: We randomly cloned RNAs from fetal human heart. RNA from clone #291 promoted myofibril formation and induced heart development of mutant axolotls in organ culture. This RNA induced expression of cardiac markers in mutant hearts: tropomyosin, troponin and α-syntrophin. This cloned RNA matches in partial sequence alignment to human microRNA-499a and b, although it differs in length. We have concluded that this cloned RNA is unique in its length, but is still related to the microRNA-499 family. We have named this unique RNA, microRNA-499c. Thus, we will refer to this RNA derived from clone #291 as microRNA-499c throughout the rest of the paper., Conclusions: This new form, microRNA-499c, plays an important role in cardiac development.

Background: A small "sigma-like" protein, AfsS, pleiotropically regulates antibiotic biosynthesis in Streptomyces coelicolor. Overexpression of afsS in S. coelicolor and certain related species causes antibiotic stimulatory effects in the host organism. Although recent studies have uncovered some of the upstream events activating this gene, the mechanisms through which this signal is relayed downstream leading to the eventual induction of antibiotic pathways remain unclear., Results: In this study, we employed whole-genome DNA microarrays and quantitative PCRs to examine the transcriptome of an afsS disruption mutant that is completely deficient in the production of actinorhodin, a major S. coelicolor antibiotic. The production of undecylprodigiosin, another prominent antibiotic, was, however, perturbed only marginally in the mutant. Principal component analysis of temporal gene expression profiles identified two major gene classes each exhibiting a distinct coordinate differential expression pattern. Surprisingly, nearly 70% of the >117 differentially expressed genes were conspicuously associated with nutrient starvation response, particularly those of phosphate, nitrogen and sulfate. Furthermore, expression profiles of some transcriptional regulators including at least two sigma factors were perturbed in the mutant. In almost every case, the effect of afsS disruption was not observed until the onset of stationary phase., Conclusion: Our data suggests a comprehensive role for S. coelicolor AfsS as a master regulator of both antibiotic synthesis and nutritional stress response, reminiscent of alternative sigma factors found in several bacteria.

Background: The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of synteny. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle differences between these two chromosomes., Results: We identified five large S. coelicolor genomic islands (larger than 25 kb) and 18 smaller islets absent in S. lividans chromosome. Many of these regions show anomalous GC bias and codon usage patterns. Six of them are in close vicinity of tRNA genes while nine are flanked with near perfect repeat sequences indicating that these are probable recent evolutionary acquisitions into S. coelicolor. Embedded within these segments are at least four DNA methylases and two probable methyl-sensing restriction endonucleases. Comparison with S. coelicolor transcriptome and proteome data revealed that some of the missing genes are active during the course of growth and differentiation in S. coelicolor. In particular, a pair of methylmalonyl CoA mutase (mcm) genes involved in polyketide precursor biosynthesis, an acyl-CoA dehydrogenase implicated in timing of actinorhodin synthesis and bldB, a developmentally significant regulator whose mutation causes complete abrogation of antibiotic synthesis belong to this category., Conclusion: Our findings provide tangible hints for elucidating the genetic basis of important phenotypic differences between these two streptomycetes. Importantly, absence of certain genes in S. lividans identified here could potentially explain the relative ease of DNA transformations and the conditional lack of actinorhodin synthesis in S. lividans.

Background: DNA microarray is an invaluable tool for gene expression explorations. In the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. To compare a large number of samples, the 'reference design' is widely used, in which all RNA samples are hybridized to a common reference. Genomic DNA is an attractive candidate for use as a universal reference, especially for bacterial systems with a low percentage of non-coding sequences. However, genomic DNA, comprising of both the sense and anti-sense strands, is unlike the single stranded cDNA usually used in microarray hybridizations. The presence of the antisense strand in the 'reference' leads to reactions between complementary labeled strands in solution and may cause the assay result to deviate from true values., Results: We have developed a mathematical model to predict the validity of using genomic DNA as a reference in the microarray assay. The model predicts that the assay can accurately estimate relative concentrations for a wide range of initial cDNA concentrations. Experimental results of DNA microarray assay using genomic DNA as a reference correlated well to those obtained by a direct hybridization between two cDNA samples. The model predicts that the initial concentrations of labeled genomic DNA strands and immobilized strands, and the hybridization time do not significantly affect the assay performance. At low values of the rate constant for hybridization between immobilized and mobile strands, the assay performance varies with the hybridization time and initial cDNA concentrations. For the case where a microarray with immobilized single strands is used, results from hybridizations using genomic DNA as a reference will correspond to true ratios under all conditions., Conclusion: Simulation using the mathematical model, and the experimental study presented here show the potential utility of microarray assays using genomic DNA as a reference. We conclude that the use of genomic DNA as reference DNA should greatly facilitate comparative transcriptome analysis.