Reconstruction the feedback regulation of amino acid metabolism to develop a non-auxotrophic L-threonine producing Corynebacterium glutamicum.

L-Threonine is an important feed additive with the third largest market size among the amino acids produced by microbial fermentation. The GRAS (generally regarded as safe) industrial workhorse Corynebacterium glutamicum is an attractive chassis for L-threonine production. However, the present L-threonine production in C. glutamicum cannot meet the requirement of industrialization due to the relatively low production level of L-threonine and the accumulation of large amounts of by-products (such as L-lysine, L-isoleucine, and glycine). Herein, to enhance the L-threonine biosynthesis in C. glutamicum, releasing the aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from feedback inhibition by L-lysine and L-threonine, respectively, and overexpressing four flux-control genes were performed. Next, to reduce the formation of by-products L-lysine and L-isoleucine without the cause of an auxotrophic phenotype, the feedback regulation of dihydrodipicolinate synthase (DapA) and threonine dehydratase (IlvA) was strengthened by replacing the native enzymes with heterologous analogues with more sensitive feedback inhibition by L-lysine and L-isoleucine, respectively. The resulting strain maintained the capability of synthesizing enough amounts of L-lysine and L-isoleucine for cell biomass formation but exhibited almost no extracellular accumulation of these two amino acids. To further enhance L-threonine production and reduce the by-product glycine, L-threonine exporter and homoserine kinase were overexpressed. Finally, the rationally engineered non-auxotrophic strain ZcglT9 produced 67.63 g/L (17.2% higher) L-threonine with a productivity of 1.20 g/L/h (108.0% higher) in fed-batch fermentation, along with significantly reduced by-product accumulation, representing the record for L-threonine production in C. glutamicum. In this study, we developed a strategy of reconstructing the feedback regulation of amino acid metabolism and successfully applied this strategy to de novo construct a non-auxotrophic L-threonine producing C. glutamicum. The main end by-products including L-lysine, L-isoleucine, and glycine were almost eliminated in fed-batch fermentation of the engineered C. glutamicum strain. This strategy can also be used for engineering producing strains for other amino acids and derivatives.

Identification of common and specific fibrosis-related genes in three common chronic kidney diseases.

BACKGROUND: Kidney fibrosis is the common final pathway of virtually all advanced forms of chronic kidney disease (CKD) including diabetic nephropathy (DN), IgA nephropathy (IgAN) and membranous nephropathy (MN), with complex mechanism. Comparative gene expression analysis among these types of CKD may shed light on its pathogenesis. Therefore, we conducted this study aiming at exploring the common and specific fibrosis-related genes involved in different types of CKD. METHODS: Kidney biopsy specimens from patients with different types of CKD and normal control subjects were analyzed using the NanoString nCounter® Human Fibrosis V2 Panel. Genes differentially expressed in all fibrotic DN, IgAN and MN tissues compared to the normal controls were regarded as the common fibrosis-related genes in CKD, whereas genes exclusively differentially expressed in fibrotic DN, IgAN or MN samples were considered to be the specific genes related to fibrosis in DN, IgAN and MN respectively. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression of the selected genes. RESULTS: Protein tyrosine phosphatase receptor type C (PTPRC), intercellular cell adhesion molecule-1 (ICAM1), vascular cell adhesion molecule-1 (VCAM1), interleukin 10 receptor alpha (IL10RA) and CC chemokine receptor 2 (CCR2) were identified as the potential common genes for kidney fibrosis in different types of CKD, while peroxisome proliferator-activated receptor alpha (PPARA), lactate oxidase (LOX), secreted phosphoprotein 1 (SPP1) were identified as the specific fibrosis-associated genes for DN, IgAN and MN respectively. qRT-PCR demonstrated that the expression levels of these selected genes were consistent with the NanoString analysis. CONCLUSIONS: There were both commonalities and differences in the mechanisms of fibrosis in different types of CKD, the commonalities might be used as the common therapeutic targets for kidney fibrosis in CKD, while the differences might be used as the diagnostic markers for DN, IgAN and MN respectively. Inflammation was highly relevant to the pathogenesis of fibrosis. This study provides further insight into the pathophysiology and treatment of fibrotic kidney disease.

Knowledge mapping of UMOD of English published work from 1985 to 2022: a bibliometric analysis.

BACKGROUND: UMOD is exclusively produced by renal epithelial cells. Recent genome-wide association studies (GWAS) suggested that common variants in UMOD gene are closely connected with the risk of CKD. However, a comprehensive and objective report on the current status of UMOD research is lacking. Therefore, we aim to conduct a bibliometric analysis to quantify and identify the status quo and trending issues of UMOD research in the past. METHODS: We collected data from the Web of Science Core Collection database and used the Online Analysis Platform of Literature Metrology, the Online Analysis Platform of Literature Metrology and Microsoft Excel 2019 to perform bibliometricanalysis and visualization. RESULTS: Based on the data from the WoSCC database from 1985 to 2022, a total of 353 UMOD articles were published in 193 academic journals by 2346 authors from 50 different countries/regions and 396 institutions. The United States published the most papers. Professor Devuyst O from University of Zurich not only published the greatest number of UMOD-related papers but also is among the top 10 co-cited authors. KIDNEY INTERNATIONAL published the most necroptosis studies, and it was also the most cited journal. High-frequency keywords mainly included 'chronic kidney disease', 'Tamm Horsfall protein' and 'mutation'. CONCLUSIONS: The number of UMOD-related articles has steadily increased over the past decades Current UMOD studies focused on Biological relevance of the UMOD to kidney function and potential applications in the risk of CKD mechanisms, these might provide ideas for further research in the UMOD field.

Comparison of two surgical interventions for advanced stages pubis and pubic symphysis tuberculosis in adults: A retrospective study of 33 cases.

PURPOSE: To compare the clinical efficacy of two surgical interventions in treating advanced stages TB of the pubis and pubic symphysis. METHODS: Between June 2010 and January 2020, 33 cases of the advanced pubis and pubic symphysis TB were treated with a one-stage debridement procedure (debridement only group, n = 15) or a one-stage debridement with bone grafting and plate fixation procedure (debridement + plating group, n = 18). The visual analog scale (VAS) score, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), operation time, intraoperative blood loss, complications, time of bone graft fusion, and improvement in the mental component summary (MCS) and physical component summary (PCS) of Short Form-36 (SF-36) were compared and analyzed. RESULTS: All patients were followed for 24.9 (SD 1.6) months. All patients were completely cured of the pubis and pubic symphysis TB with no recurrence. There were no significant differences (P >0.05) between the two groups in terms of age, follow-up period and intraoperative blood loss. The post-operative VAS scores, ESR and CRP levels, PCS and MCS scores of two groups significantly improved compared to pre-therapy. The mean operation time in debridement + plating group was 140.9 (43.2) min, which was significantly longer than in debridement only group [94.9(21.8) min, P < 0.01]. The final follow-up (FFU) indices of the VAS score in debridement only group were higher than those in debridement + plating group [1.9 (0.8) vs 1.3 (0.5), P=0.012]. A satisfactory average bony fusion time of 12.2 (3.3) months was achieved in debridement + plating group . CONCLUSIONS: A one-stage debridement, bone grafting, and reconstruction plate fixation procedure achieved reconstruction of the integrity and stability of the pelvic ring, pain relief, and rapid cure of bone TB. This procedure is a safe and effective treatment option for advanced pubis and pubic symphysis TB.

Comparison of two surgical interventions for lumbar brucella spondylitis in adults: a retrospective analysis.

This retrospective study aimed to compare the clinical efficacy of the posterior procedure with the combined anterior and posterior procedure in the surgical management of lumbar Brucella spondylitis. From January 2015 to June 2020, a total of 62 patients presenting with lumbar Brucella spondylitis underwent either one-stage posterior pedicle fixation, debridement, and interbody fusion (Group A, n = 33) or anterior debridement, bone grafting, and posterior instrumentation (Group B, n = 29). All patients were followed up for an average of 25.4 ± 1.5 months and achieved complete resolution of lumbar Brucella spondylitis. No significant differences between the groups were observed in terms of age or pre-operative, three-month postoperative and final follow-up indices of the VAS, ESR, CRP, lordosis angle, ODI scores, fusion time, and time of serum agglutination test conversion to negative (P > 0.05). Each patient exhibited notable improvements in neurological function, as assessed by the JOA score rating system. Group A demonstrated significantly shorter operative duration, intraoperative blood loss, and hospital stay compared to Group B (P < 0.05). Superficial wound infection was observed in one case in Group A, whereas Group B experienced one case each of intraoperative peritoneal rupture, postoperative ileus, iliac vein injury, and superficial wound infection. This study supports the efficacy of both surgical interventions in the treatment of lumbar Brucella spondylitis, with satisfactory outcomes. However, the posterior approach demonstrated advantages, including reduced surgical time, diminished blood loss, shorter hospital stays, and fewer perioperative complications. Consequently, the one-stage posterior pedicle fixation, debridement, and interbody fusion represent a superior treatment option.

Comparing Bone Graft Techniques for Interbody Fusion through a Posterior Approach for Treating Mid-Thoracic Spinal Tuberculosis: A Retrospective Analysis.

OBJECTIVE: Mid-thoracic spinal tuberculosis is prone to kyphotic deformities and neurologic impairment. Posterior approach can effectively restore the spinal stability by reconstructing the anterior and middle spinal columns. Titanium mesh cages (TMC), allogeneic bone (ALB), and autogenous bone (AUB) are three main bone graft struts. We aimed to compare the therapeutic efficacy of three bone graft struts, for anterior and middle column reconstruction through a posterior approach in cases of mid-thoracic spinal tuberculosis. METHODS: Hundred and thirty seven patients with thoracic spinal tuberculosis who had undergone a posterior approach from June 2010 to December 2018 were enrolled. Of them, 46 patients were treated using a titanium mesh cage (TMC group), 44 with allogenic bone grafts (ALB group), and 47 using autogenous bone grafts (AUB group). The following were analyzed to evaluate clinical efficacy: visual analogue scale (VAS) values, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) levels, kyphotic Cobb's angle, operation duration, intraoperative blood loss, improvement in American Spinal Injury Association (ASIA) grade and in the mental component summary (MCS) and physical component summary (PCS) of Short Form-36 (SF-36), duration of bone graft fusion. The data of the three groups were compared by way of variance analysis, followed by the LSD⁃t test to compare each group. A repeated measures ANOVA was used to analyze the dates of pre-, postoperative and final follow-up. RESULTS: The follow-up duration was at least 3 years. All patients achieved a complete cure for spinal TB. Neurological performance and quality of life were remarkably improved at the final follow-up. The intraoperative blood loss, operation time and VAS values 1 day postoperatively for TMC group and ALB group were significantly lower than those in AUB group (P < 0.05). The duration of bone graft fusion in ALB group (18.1 ± 3.7 months) was longer than that in TMC group and AUB group (9.5 ± 2.8 and 9.2 ± 1.9 months) (P < 0.05). No significant intergroup differences were observed in terms of age or preoperative, 3-months postoperative, and final follow-up indices of ESR and CRP among the three groups (P > 0.05). At the final follow-up, the correction loss was mild (2.1 ± 0.9, 2.2 ± 1.0, 2.1 ± 0.8) and Cobb's angles of the three groups were 20.1 ± 2.9, 20.5 ± 3.2, 20.9 ± 3.4, respectively, which were remarkably rectified in comparison with the preoperative measurements (P < 0.05). CONCLUSIONS: In terms of postoperative recovery and successful fusion rate of bone graft, it seems that posterior instrumentation, debridement, and interbody fusion with titanium mesh cages are more effective and appropriate surgical methods for mid-thoracic spinal tuberculosis.

Engineering allosteric inhibition of homoserine dehydrogenase by semi-rational saturation mutagenesis screening.

Allosteric regulation by pathway products plays a vital role in amino acid metabolism. Homoserine dehydrogenase (HSD), the key enzyme for the biosynthesis of various aspartate family amino acids, is subject to feedback inhibition by l-threonine and l-isoleucine. The desensitized mutants with the potential for amino acid production remain limited. Herein, a semi-rational approach was proposed to relieve the feedback inhibition. HSD from Corynebacterium glutamicum (CgHSD) was first characterized as a homotetramer, and nine conservative sites at the tetramer interface were selected for saturation mutagenesis by structural simulations and sequence analysis. Then, we established a high-throughput screening (HTS) method based on resistance to l-threonine analog and successfully acquired two dominant mutants (I397V and A384D). Compared with the best-ever reported desensitized mutant G378E, both new mutants qualified the engineered strains with higher production of CgHSD-dependent amino acids. The mutant and wild-type enzymes were purified and assessed in the presence or absence of inhibitors. Both purified mutants maintained >90% activity with 10 mM l-threonine or 25 mM l-isoleucine. Moreover, they showed >50% higher specific activities than G378E without inhibitors. This work provides two competitive alternatives for constructing cell factories of CgHSD-related amino acids and derivatives. Moreover, the proposed approach can be applied to engineering other allosteric enzymes in the amino acid synthesis pathway.

Recent advances, challenges and metabolic engineering strategies in the biosynthesis of 3-hydroxypropionic acid.

As an attractive and valuable platform chemical, 3-hydroxypropionic acid (3-HP) can be used to produce a variety of industrially important commodity chemicals and biodegradable polymers. Moreover, the biosynthesis of 3-HP has drawn much attention in recent years due to its sustainability and environmental friendliness. Here, we focus on recent advances, challenges, and metabolic engineering strategies in the biosynthesis of 3-HP. While glucose and glycerol are major carbon sources for its production of 3-HP via microbial fermentation, other carbon sources have also been explored. To increase yield and titer, synthetic biology and metabolic engineering strategies have been explored, including modifying pathway enzymes, eliminating flux blockages due to byproduct synthesis, eliminating toxic byproducts, and optimizing via genome-scale models. This review also provides insights on future directions for 3-HP biosynthesis.

[Construction and application of a synthetic promoter library for Corynebacterium glutamicum].

Promoter is an important genetic tool for fine-tuning of gene expression and has been widely used for metabolic engineering. Corynebacterium glutamicum is an important chassis for industrial biotechnology. However, promoter libraries that are applicable to C. glutamicum have been rarely reported, except for a few developed based on synthetic sequences containing random mutations. In this study, we constructed a promoter library based on the native promoter of odhA gene by mutating the -10 region and the bystanders. Using a red fluorescent protein (RFP) as the reporter, 57 promoter mutants were screened by fluorescence imaging technology in a high-throughput manner. These mutants spanned a strength range between 2.4-fold and 19.6-fold improvements of the wild-type promoter. The strongest mutant exhibited a 2.3-fold higher strength than the widely used strong inducible promoter Ptrc. Sequencing of all 57 mutants revealed that 55 mutants share a 1-4 bases shift (4 bases shift for 68% mutants) of the conserved -10 motif "TANNNT" to the 3' end of the promoter, compared to the wild-type promoter. Conserved T or G bases at different positions were observed for strong, moderate, and weak promoter mutants. Finally, five promoter mutants with different strength were employed to fine-tune the expression of γ-glutamyl kinase (ProB) for L-proline biosynthesis. Increased promoter strength led to enhanced L-proline production and the highest L-proline titer of 6.4 g/L was obtained when a promoter mutant with a 9.8-fold higher strength compared to the wild-type promoter was used for ProB expression. The use of stronger promoter variants did not further improve L-proline production. In conclusion, a promoter library was constructed based on a native C. glutamicum promoter PodhA. The new promoter library should be useful for systems metabolic engineering of C. glutamicum. The strategy of mutating native promoter may also guide the construction of promoter libraries for other microorganisms.

CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an L-proline exporter for L-proline hyperproduction.

Development of hyperproducing strains is important for biomanufacturing of biochemicals and biofuels but requires extensive efforts to engineer cellular metabolism and discover functional components. Herein, we optimize and use the CRISPR-assisted editing and CRISPRi screening methods to convert a wild-type Corynebacterium glutamicum to a hyperproducer of L-proline, an amino acid with medicine, feed, and food applications. To facilitate L-proline production, feedback-deregulated variants of key biosynthetic enzyme γ-glutamyl kinase are screened using CRISPR-assisted single-stranded DNA recombineering. To increase the carbon flux towards L-proline biosynthesis, flux-control genes predicted by in silico analysis are fine-tuned using tailored promoter libraries. Finally, an arrayed CRISPRi library targeting all 397 transporters is constructed to discover an L-proline exporter Cgl2622. The final plasmid-, antibiotic-, and inducer-free strain produces L-proline at the level of 142.4 g/L, 2.90 g/L/h, and 0.31 g/g. The CRISPR-assisted strain development strategy can be used for engineering industrial-strength strains for efficient biomanufacturing.

Diagnostic value of LungPoint navigation combined with EBUS-GS & ROSE in peripheral pulmonary nodules.

Background & objectives: Recently, there has been a surge to develop new devices and techniques for the diagnosis of peripheral pulmonary lesions such as the combination of LungPoint navigation and endobronchial ultrasound with a guide sheath (EBUS-GS). The present study aimed to explore the diagnostic value of LungPoint navigation in combination with EBUS-GS and rapid on-site evaluation (ROSE) particularly for peripheral pulmonary nodules. Methods: Patients (n=108) with pulmonary nodules (10 mm ≤ nodal diameter ≤30 mm) presenting to Henan Provincial People's Hospital were detected using chest computed tomographic (CT) scanning and bronchoscopy. All patients were evaluated using LungPoint navigation, EBUS-GS and ROSE techniques to evaluate the positive rate of combined diagnosis using the three methods. Results: A total of 108 patients participated in this study and successfully underwent all the three procedures. Of these, 82 patients were accurately diagnosed, making the overall diagnostic rate of 75.9 per cent for combined LungPoint navigation, EBUS-GS, and ROSE analyses. Further subgroup analysis of the diagnostic rate of the three combined techniques were conducted based on the size of the nodules which showed a diagnostic rate of 65.3 per cent for 10 mm ≤ nodule diameter ≤20 mm and 85.7 per cent for 20 mm ≤ nodal diameter ≤30 mm. Of the 108 patients, 85 had solid nodules and 23 had ground-glass nodules; the positive rate of diagnosis of solid nodules was the highest. The patients ultimately were diagnosed with lung cancer with a positive rate of 83.5 per cent. The sensitivity, specificity and positive and negative predicted values for ROSE were 90.3, 78.3, 84.8 and 83.6 per cent, respectively. Interpretation & conclusions: The combined use of the three techniques can effectively shorten the duration of the total diagnosis period and improve the safety of diagnosis without affecting the detection rate.

Safety and Efficacy of Roxadustat for Anemia in Patients With Chronic Kidney Disease: A Meta-Analysis and Trial Sequential Analysis.

Background: Roxadustat, a hypoxia-inducible factor prolyl-hydroxylase inhibitor (HIF-PHI), has been used to treat anemia in patients with chronic kidney disease (CKD). However, its safety and efficacy remain controversial. Methods: The PubMed, EMBASE, Science Citation Index, Cochrane Central Register of Controlled Trials, and Clinical Trial Registries databases were searched for relevant studies published up to April 2021. We identified randomized controlled trials (RCTs) comparing roxadustat with placebo or erythropoiesis-stimulating agents (ESAs) in anemia patients with CKD with or without dialysis. Results: Eleven studies including 6,631 patients met the inclusion criteria. In non-dialysis-dependent (NDD-) and dialysis-dependent (DD-) CKD patients, the total adverse events were not significantly different between the roxadustat and control (placebo for NDD-CKD patients and ESA for DD-CKD patients) groups [relative risk (RR) = 1.02, 95% confidence interval (CI) = 1.00, 1.04, P = 0.08, and RR = 1.22, 95% CI = 0.91, 1.64, P = 0.18, respectively], and the trial sequential analysis (TSA) confirmed the result in the NDD-CKD groups. No significant differences in hyperkalemia and infection incidences were found between roxadustat and placebo in the DD-CKD groups. The pooled results showed that roxadustat significantly increased the hemoglobin response rate compared with placebo in the NDD-CKD group and had an effect similar to that of ESA in the DD-CKD group. However, iron metabolism parameters did not seem to be obviously optimized by roxadustat. Conclusion: Roxadustat can be safely used in CKD patients. Oral roxadustat was more effective than placebo as a therapy for anemia in NDD-CKD patients and non-inferior to ESA in correcting anemia in DD-CKD patients. However, additional clinical trials are still needed to further prove whether roxadustat can optimize iron metabolism.

Combination of the Archimedes Navigation System and cryobiopsy in diagnosis of diffuse lung disease.

OBJECTIVE: To evaluate the efficacy of the Archimedes Navigation System (Broncus Medical, San Jose, CA, USA) for guidance during transbronchial cryobiopsy and the incidence of complications in patients with diffuse lung disease. METHODS: High-resolution computed tomography and transbronchial cryobiopsy were used to evaluate eight patients with diffuse lung disease. The Archimedes Navigation System was used before cryobiopsy to obtain the best path with which to avoid large vessels. Three to five cryobiopsy specimens were taken from each sampled segment. RESULTS: Preoperative planning using the Archimedes Navigation System was successfully performed on all eight patients. The probe-to-pleura distance was approximately 10 mm. No cases of pneumothorax occurred, one patient developed moderate bleeding, two developed minor bleeding, and five developed minimal bleeding that stopped spontaneously. A final diagnosis was obtained for seven patients, and ongoing follow-up was being conducted for the last patient at the time of this writing. CONCLUSIONS: This is the first report of combining navigation technology with cryobiopsy to diagnose diffuse lung disease. The Archimedes Navigation System, which provides real-time guidance, is helpful in pre-cryobiopsy planning and diagnosis of diffuse lung disease. Moreover, this system can reduce the pneumothorax rate and bleeding risk by avoiding large vessels.

Mononitration of a Calix[4]arene Methylene Bridge: Synthesis and Preliminary Catalysis Performances of Bridging Chiral p-tert-Butylcalix[4]arenes with a Monoamino Bridge Substituent in a 1,3-Alternate Conformation.

In order to prepare bridging chiral p-tert-butylcalix[4]crown-5 with a mononitro bridge substituent in a 1,3-alternate conformation, a mononitration method of calix[4]arene bridging methylene has been first developed with tert-butyl nitrite as a nitration reagent. The effects of solvent, reaction temperature, reaction time, and nitration reagent dosage on bridge mononitration have been deeply explored to obtain an optimal nitration condition. The facile nitration presents a new key for calix[4]arene bridge derivatization. After further modification and diastereoisomeric resolution, a pair of bridging chiral p-tert-butylcalix[4]arenes with a monoamino bridge substituent were produced from the bridge-mono-nitrated calix[4]arene. Their preliminary catalysis results in the Henry reaction show good catalytic activities (up to 95% yield) and still low but obviously enhanced enantioselectivities (up to 22.3% ee from 7a, 6% ee from 1), which confirms that the structural transformation indeed improves asymmetric catalysis performances of bridging chiral calix[4]crown-5 amines in a 1,3-alternate conformation.

Protein expression shift and potential diagnostic markers through proteomics profiling of tuberculous pleurisy biopsy tissues.

OBJECTIVES: Tuberculous pleurisy is a common type of tuberculosis (TB), but its diagnosis is challenging. This study aimed to profile the protein expression of this disease and identify new diagnostic makers. METHODS: Biopsy tissues from patients with tuberculous pleurisy and controls were taken through thoracoscopy, and proteins were extracted for Tandem Mass Tag Mass Spectrometry. Differential protein expression was performed between patients and controls, and the identified proteins were analyzed for pathway enrichment. Selected proteins were further validated in another set of samples using a more quantitative method. RESULTS: A total of 5101 proteins were detected and quantified in a discovery set of patients and controls. Overall protein expression was quite different between patients and controls. Most proteins were down-expressed, while a minority were overly expressed in the patient samples. At p value < 0.05 and absolute fold change >2, 295 proteins were found to be up-expressed and 608 down-expressed. The top enriched pathways included ECM-receptor interaction, complement and coagulation cascades and focal adhesion. All 19 selected candidates were validated in an independent set of patient and control samples. CONCLUSION: This unbiased proteomics approach not only provided unique insights into protein expression and pathways, but also discovered potential diagnostic markers for tuberculous pleurisy.

Self-Assembled Vesicles Formed by Positional Isomers of Sodium Dodecyl Benzene Sulfonate-Based Pseudogemini Surfactants.

The construction of pseudogemini surfactants based on noncovalent interactions (such as electrostatic interaction and π-π stacking) was a powerful method to assemble well-defined aggregates in aqueous solution. The mixtures of butane-1,4-bis(methylimidazolium bromide) ([mim-C4-mim]Br2) and positional isomers of sodium dodecyl benzene sulfonate (SDBS-0,11 or SDBS-3,8) in a molar ratio of 1:2 were studied to characterize the effect of straight and branched alkyl chains on the aggregation behavior of pseudogemini surfactants. Spontaneous phase transition from micelles to vesicles was formed by these two kinds of complexes. Interestingly, a densely stacked onion-like structure (multilamellar vesicles) with more than one dozen layers was fabricated. The micelle and vesicle phases were characterized in detail by cryogenic transmission electron microscopy, polarized optical microscopy, dynamic light scattering, and rheological measurements. It can be clearly demonstrated that the structure of alkyl chain can significantly influence the surface adsorption, solution self-assembly, and aqueous two-phase system of pseudogemini surfactants. Our work provided a convenient technique to achieve controlled self-assembly by introducing positional isomers of surfactants.

Retraction Note to: Robust Model Selection and Estimation for Censored Survival Data with High Dimensional Genomic Covariates.

The authors have retracted this article [1] because they found a fundamental mistake in the methodology that is not correctable at this time. This mistake is found in the methodology and the derivation of the model with Tukey and Huber's losses. Because of the error, the findings in the article are not reliable. All authors agree to this retraction.

Robust Model Selection and Estimation for Censored Survival Data with High Dimensional Genomic Covariates.

When relating genomic data to survival outcomes, there are three main challenges that are the censored survival outcomes, the high-dimensionality of the genomic data, and the non-normality of data. We propose a method to tackle these challenges simultaneously and obtain a robust estimation of detecting significant genes related to survival outcomes based on Accelerated Failure Time (AFT) model. Specifically, we include a general loss function to the AFT model, adopt model regularization and shrinkage technique, cope with parameters tuning and model selection, and develop an algorithm based on unified Expectation-Maximization approach for easy implementation. Simulation results demonstrate the advantages of the proposed method compared with existing methods when the data has heavy-tailed errors and correlated covariates. Two real case studies on patients are provided to illustrate the application of the proposed method.

Proof-of-Concept Workflow for Establishing Reference Intervals of Human Urine Proteome for Monitoring Physiological and Pathological Changes.

Urine as a true non-invasive sampling source holds great potential for biomarker discovery. While approximately 2000 proteins can be detected by mass spectrometry in urine from healthy people, the amount of these proteins vary considerably. A systematic evaluation of a large number of samples is needed to determine the range of the variations. Current biomarker studies often measure limited number of urine samples in the discovery phase, which makes it difficult to determine whether proteins differentially expressed between control and disease groups represent actual difference, or are just physiological variations among the individuals, leads to failures in the validation phase with the increased sample numbers. Here, we report a streamlined workflow with capacity of measuring 8 urine proteomes per day at the coverage of >1500 proteins. With this workflow, we evaluated variations in 497 urine proteomes from 167 healthy donors, establishing reference intervals (RIs) that covered urine protein variations. We demonstrated that RIs could be used to monitor physiological changes by detecting transient outlier proteins. Furthermore, we provided a RIs-based algorithm for biomarker discovery and validation to screen for diseases such as cancer. This study provided a proof-of-principle workflow for the use of urine proteome for health monitoring and disease screening.

Differential Sox10 genomic occupancy in myelinating glia.

Myelin is formed by specialized myelinating glia: oligodendrocytes and Schwann cells in the central and peripheral nervous systems, respectively. While there are distinct developmental aspects and regulatory pathways in these two cell types, myelination in both systems requires the transcriptional activator Sox10. Sox10 interacts with cell type-specific transcription factors at some loci to induce myelin gene expression, but it is largely unknown how Sox10 transcriptional networks globally compare between oligodendrocytes and Schwann cells. We used in vivo ChIP-Seq analysis of spinal cord and peripheral nerve (sciatic nerve) to identify unique and shared Sox10 binding sites and assess their correlation with active enhancers and transcriptional profiles in oligodendrocytes and Schwann cells. Sox10 binding sites overlap with active enhancers and critical cell type-specific regulators of myelination, such as Olig2 and Myrf in oligodendrocytes, and Egr2/Krox20 in Schwann cells. Sox10 sites also associate with genes critical for myelination in both oligodendrocytes and Schwann cells and are found within super-enhancers previously defined in brain. In Schwann cells, Sox10 sites contain binding motifs of putative partners in the Sp/Klf, Tead, and nuclear receptor protein families. Specifically, siRNA analysis of nuclear receptors Nr2f1 and Nr2f2 revealed downregulation of myelin genes Mbp and Ndrg1 in primary Schwann cells. Our analysis highlights different mechanisms that establish cell type-specific genomic occupancy of Sox10, which reflects the unique characteristics of oligodendrocyte and Schwann cell differentiation. GLIA 2015;63:1897-1914.