DeepKa Web Server: High-Throughput Protein pKa Prediction.

DeepKa is a deep-learning-based protein pKa predictor proposed in our previous work. In this study, a web server was developed that enables online protein pKa prediction driven by DeepKa. The web server provides a user-friendly interface where a single step of entering a valid PDB code or uploading a PDB format file is required to submit a job. Two case studies have been attached in order to explain how pKa's calculated by the web server could be utilized by users. Finally, combining the web server with post processing as described in case studies, this work suggests a quick workflow of investigating the relationship between protein structure and function that are pH dependent. The web server of DeepKa is freely available at http://www.computbiophys.com/DeepKa/main.

SARS-CoV-2 Omicron infection in a cohort of hospitalized kidney transplant recipients: Risk factors of severity.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is a major coronavirus variant, which was prevalent in China at the end of 2022 and caused widespread infection. As an immunosuppressed group, renal transplant recipients with SARS-CoV-2 infection are prone to developing serious pneumonia or an adverse outcome event if the infection is not treated in time. Here, we analyze the possible risk factors of infection severity. MATERIALS AND METHODS: 92 cases of moderate and severe SARS-CoV-2 infection after renal transplantation were collected. Statistical methods, including Fisher's tests, F test, Spearman relative values, and multi-parameter logistic regression models, were used to analyze the risk factors for severe SARS-CoV-2 infection in renal transplant recipients. RESULTS: 44 cases complicated with hypertension were observed in the study cohort, among whom 30 were severe (OR: 4.63, p < 0.001). Out of 51 male patients infected with Omicron, 30 male patients presented with severe SARS-CoV-2 (OR: 2.45, p = 0.039). In renal transplant patients, hypertension comorbidity was closely correlated with clinical presentation (R = 0.369, p < 0.001). Blood routine test, chemistries, and additional indices showed increased neutrophils and C-reactive protein in patients with severe disease compared with the moderate group according to one-way analysis of variance (p = 0.004), while CD3 (p = 0.02) and CD4 (p = 0.04) showed lower expressional levels. We also observed meaningful correlations between neutrophil levels and hypertension comorbidity (R = 0.222, p = 0.034) and between interleukin-6 (IL-6) levels and diabetes comorbidity (R = 0.315, p = 0.011), with IL-6 considered a key factor in the context of coronavirus disease. CONCLUSION: Renal transplant recipients were generally susceptible to infection with the Omicron variant, with a more pronounced incidence of severe illness observed in the group with hypertension comorbidity.

Transcription Factor ATF3 Mediating SOCS3 Expression Aggravates Renal Ischemia-Reperfusion Injury by Activating Mitophagy.

INTRODUCTION: Suppressor of cytokine signaling 3 (SOCS3) is highly expressed in mice with renal ischemia/reperfusion (RI/R) injury and has the potential to regulate mitophagy. On this basis, this study further investigates the possible mechanism via which SOCS3 affects RI/R by regulating mitophagy. METHOD: After establishing a RI/R injury mouse model and a hypoxia/reoxygenation (H/R) cell model, the effects of silenced SOCS3 on injury and mitophagy in the above models were analyzed by ELISA, quantitative real-time polymerase chain reaction, Western blot, pathological sections, CCK-8 assay, flow cytometry, and JC-1 assay. Mechanistic studies were carried out with the help of database analysis and binding validation experiments (chromatin immunoprecipitation, dual-luciferase reporter assay, and co-immunoprecipitation). After the binding target was identified, the regulatory relationship between the target gene and SOCS3 was verified by rescue experiments. RESULT: The large increase in blood urea nitrogen (BUN) and creatinine (Cr) levels verified the success of the RI/R model. SOCS3 expression was up-regulated in RI/R mice. Silenced SOCS3 alleviated kidney damage and mitochondrial abnormalities in RI/R mice and inhibited mitophagy at the molecular level. Likewise, silenced SOCS3 alleviated H/R-induced cell damage and mitophagy. Finally, activating transcription factor 3 (ATF3) was determined to bind to the promoter of SOCS3, which interacted with insulin-like growth factor 1 receptor (IGF1R). Rescue experiments confirmed the effect of ATF3 on SOCS3 expression and the underlying regulatory mechanism. CONCLUSION: ATF3 mediates SOCS3 expression to promote the activation of mitophagy, thereby aggravating renal ischemia-reperfusion injury.

The Effect of Splenic Irradiation on Mean Fluorescence Intensity Values of HLA Antibody in Presensitized Patients Waiting for Kidney Transplantation.

To explore the desensitization treatment of patients waiting for kidney transplantation, this article comparative analysis of the effect of splenic irradiation on mean fluorescence intensity (MFI) values of HLA antibodies of 4 presensitized patients. After splenic irradiation, the mean MFI values of HLA-I antibody in 4 patients all decreased (P ≤ .001, P ≤ .001, P ≤ .001, P ≤ .001), and 3 patients had a decrease in intensity level (P ≤ .001, P = .001, P ≤ .001); as for HLA-II antibody, the mean MFI values in 3 patients also decreased (P ≤ .001, P = .025, P = .016), 1 patient had a decrease in intensity level (P ≤ .001) and the other 2 cases had no significant changes (P = 1.000, P = .564). On the other hand, splenic irradiation reduces MFI values in different levels of HLA antibody. So, splenic irradiation can reduce the MFI values of HLA antibodies.

Basis for Accurate Protein pKa Prediction with Machine Learning.

pH regulates protein structures and the associated functions in many biological processes via protonation and deprotonation of ionizable side chains where the titration equilibria are determined by pKa's. To accelerate pH-dependent molecular mechanism research in the life sciences or industrial protein and drug designs, fast and accurate pKa prediction is crucial. Here we present a theoretical pKa data set PHMD549, which was successfully applied to four distinct machine learning methods, including DeepKa, which was proposed in our previous work. To reach a valid comparison, EXP67S was selected as the test set. Encouragingly, DeepKa was improved significantly and outperforms other state-of-the-art methods, except for the constant-pH molecular dynamics, which was utilized to create PHMD549. More importantly, DeepKa reproduced experimental pKa orders of acidic dyads in five enzyme catalytic sites. Apart from structural proteins, DeepKa was found applicable to intrinsically disordered peptides. Further, in combination with solvent exposures, it is revealed that DeepKa offers the most accurate prediction under the challenging circumstance that hydrogen bonding or salt bridge interaction is partly compensated by desolvation for a buried side chain. Finally, our benchmark data qualify PHMD549 and EXP67S as the basis for future developments of protein pKa prediction tools driven by artificial intelligence. In addition, DeepKa built on PHMD549 has been proven an efficient protein pKa predictor and thus can be applied immediately to, for example, pKa database construction, protein design, drug discovery, and so on.

Updating emission inventories for vehicular organic gases: Indications from cold-start and temperature effects on advanced technology cars.

How would the organic gas emission inventories of future urban vehicles change with new features of advanced technology cars? Here, volatile organic compounds (VOCs) and intermediate volatile organic compounds (IVOCs) from a fleet of Chinese light-duty gasoline vehicles (LDGVs) were characterized by chassis dynamometer experiments to grasp the key factors affecting future inventory accuracy. Subsequently, the VOC and IVOC emissions of LDGVs in Beijing, China, from 2020 to 2035, were calculated and the spatial-temporal variations were recognized under a scenario of fleet renewal. With the tightening of emission standards (ESs), cold start contributed a larger fraction of the total unified cycle VOC emissions due to the imbalanced emission reductions between operating conditions. It took 757.47 ± 337.75 km of hot running to equal one cold-start VOC emission for the latest certified vehicles. Therefore, the future tailpipe VOC emissions would be highly dependent on discrete cold start events rather than traffic flows. By contrast, the equivalent distance was shorter and more stable for IVOCs, with an average of 8.69 ± 4.59 km across the ESs, suggesting insufficient controls. Furthermore, there were log-linear relationships between temperatures and cold-start emissions, and the gasoline direct-injection vehicles performed better adaptability under low temperatures. In the updated emission inventories, the VOC emissions were more effectively reduced than the IVOC emissions. The start emissions of VOCs were estimated to be increasingly dominant, especially in wintertime. By winter 2035, the contribution of VOC start emissions could reach 98.98 % in Beijing, while the fraction of IVOC start emissions would decrease to 59.23 %. Spatially allocation showed that the high emission regions of tailpipe organic gases from LDGVs have transferred from road networks to regions of intense human activities. Our results provide new insights into tailpipe organic gas emissions of gasoline vehicles, and can support future emission inventories and refined assessment of air quality and human health risk.

Primary organic gas emissions in vehicle cold start events: Rates, compositions and temperature effects.

Identification of air toxics emitted from light-duty gasoline vehicles (LDGVs) is expected to better protect human health. Here, the volatile organic compound (VOC) and intermediate VOC (IVOC) emissions in the high-emitted start stages were measured on a chassis dynamometer under normal and extreme temperatures for China 6 LDGVs. Low temperature enhanced the emission rates (ERs) of both VOCs and IVOCs. The VOC ERs were averaged 5.19 ± 2.74 times higher when the temperature dropped from 23 °C to 0 °C, and IVOCs were less sensitive to temperature change with an enlargement of 2.27 ± 0.19 times. Aromatics (46.75 ± 2.83%) and alkanes (18.46 ± 1.21%) dominated the cold start VOC emissions under normal temperature, which was quite different from hot running emission profiles. From the perspective of emission inventories, changes in the speciated composition of VOCs and IVOCs were less important than that in the actual magnitude of ERs under cold conditions. However, changes in the ERs and emission profiles were equally important at high temperatures. Furthermore, high time-resolved measurements revealed that low temperature enhanced both the emission peak and peak duration of fuel components and incomplete combustion products during cold start, while high temperature only increased the peak concentration of fuel components.

Protein pK a Prediction with Machine Learning.

Protein pK a prediction is essential for the investigation of the pH-associated relationship between protein structure and function. In this work, we introduce a deep learning-based protein pK a predictor DeepKa, which is trained and validated with the pK a values derived from continuous constant-pH molecular dynamics (CpHMD) simulations of 279 soluble proteins. Here, the CpHMD implemented in the Amber molecular dynamics package has been employed (Huang Y.J. Chem. Inf. Model.2018, 58, 1372-1383). Notably, to avoid discontinuities at the boundary, grid charges are proposed to represent protein electrostatics. We show that the prediction accuracy by DeepKa is close to that by CpHMD benchmarking simulations, validating DeepKa as an efficient protein pK a predictor. In addition, the training and validation sets created in this study can be applied to the development of machine learning-based protein pK a predictors in the future. Finally, the grid charge representation is general and applicable to other topics, such as the protein-ligand binding affinity prediction.

Primary hyperoxaluria diagnosed after kidney transplantation: a case report and literature review.

BACKGROUND: Primary hyperoxaluria (PH) is a rare inherited autosomal recessive disease caused by disturbed glyoxylate metabolism. The disease is characterized by calcium oxalate crystal deposition in various organs, especially in the kidney. Due to the lack of current understanding of PH, nearly all patients are only initially diagnosed with PH when recurrent lithiasis and progressive end-stage renal disease occur. Many cases are not diagnosed in patients until renal allograft insufficiency occurs after renal transplantation. This case report and literature review aim to emphasize the need for careful pre-transplant PH screening of patients with bilateral nephrocalcinosis or nephrolithiasis. CASE PRESENTATION: Renal allograft insufficiency was diagnosed as PH after kidney transplantation. Here, we detail the complete clinical course, including computed tomography images of the original kidney and renal graft, histopathological images of a biopsy of the transplanted kidney, the results of laboratory and molecular genetic tests, and the treatment. In addition, we reviewed the literature from 2000 to 2021 and analyzed 19 reported cases of PH diagnosed after kidney transplantation, and provide a summary of the characteristics, complications, treatment, and prognosis of these cases. CONCLUSIONS: By reviewing and analyzing these cases, we concluded that patients with a history of nephrocalcinosis or nephrolithiasis in both kidneys need preoperative screening for PH and appropriate treatment before kidney transplantation. Delayed graft function caused by PH is easily misdiagnosed as acute rejection, and needle biopsy should be performed at an early stage.

An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis.

Long noncoding RNAs (lncRNAs) are persistently expressed and have been described as potential biomarkers and therapeutic targets in various diseases. However, there is limited information regarding lncRNA expression in the tissue of kidney exhibiting lupus nephritis (LN)a serious complication of systemic lupus erythematosus (SLE). In this study, RNA sequencing (RNA-seq) was performed to characterize the lncRNA and mRNA expression in kidney tissues from LN (MRL/lpr) and control mice. We identified 12,979 novel lncRNAs in mouse. The expression profiles of both mRNAs and lncRNAs were differed significantly between LN and control mice. In particular, there were more upregulated lncRNAs and mRNAs than downregulated ones in the kidney tissues of LN mice. However, GO analysis showed that more downregulated genes were enriched in immune and inflammatory response-associated pathways. KEGG analysis showed that both downregulated and upregulated genes were enriched in a number of pathways, including the SLE pathway, and approximately half of these SLE-associated genes encoded inflammatory factors. Moreover, we observed that 2,181 DElncRNAs may have targeted and regulated the expression of 778 mRNAs in LN kidney tissues. The results of this study showed that 11 DElncRNAs targeted and were co-expressed with six immune and SLE-associated genes. qPCR analysis confirmed that lncRNA Gm20513 positively regulated the expression of the SLE-associated gene H2-Aa. In conclusion, the results of our study demonstrates that lncRNAs influence the progression of LN and provide some cues for further study of lncRNAs in LN. These results regarding the lncRNA-mRNAregulatory network may have important value in LN diagnosis and therapy.

PARP1-RNA interaction analysis: PARP1 regulates the expression of extracellular matrix-related genes in HK-2 renal proximal tubular epithelial cells.

Recent studies suggest that Poly(ADP-ribose) polymerase 1 (PARP1) acts as an RNA-binding protein in a majority of renal diseases with tubular cell injury. However, detailed knowledge of RNA targets and the RNA-binding regions for PARP1 is unknown. Herein, mapping of iRIP-seq reads in HK-2 renal tubular epithelial cells showed a biased distribution at coding sequence (CDS) and intron regions that is specific to these cells. A total of 1708 differentially expressed genes were identified after PARP1 knockdown using RNA-seq. Furthermore, transcriptome analysis also showed that selective variable splicing was globally regulated by PARP1 in HK-2 cells. By comparison of PARP1 RNA-seq and iRIP-seq data, we found 68 overlapping genes that are enriched in 'extracellular matrix' pathway. Follow-up identification of their interactions may contribute vital insights into the regulatory role of PARP1 as an RNA-binding protein in HK-2 cells.

Recommended prophylactic and management strategies for severe acute respiratory syndrome coronavirus 2 infection in transplant recipients.

Since December 2019, increasing attention has been paid to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in Wuhan, China. SARS-CoV-2 primarily invades the respiratory tract and lungs, leading to pneumonia and other systemic disorders. The effect of SARS-CoV-2 in transplant recipients has raised significant concerns, especially because there is a large population of transplant recipients in China. Based on the current epidemic situation, this study reviewed publications on this virus and coronavirus disease 2019 (COVID-19), analyzed common features of respiratory viral pneumonias, and presented the currently reported clinical characteristics of COVID-19 in transplant recipients to improve strategies regarding the diagnosis and treatment of COVID-19 in this special population.

Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells.

BACKGROUND: Tristetraprolin (TTP) is an RNA binding protein that plays a critical role in regulating proinflammatory immune responses by destabilizing target mRNAs via binding to their AU-rich elements (AREs) in the 3'-UTRs of mRNAs. A recent CLIP-seq study revealed that TTP-binding sites are enriched in the intronic regions of RNA. TTP is also a nuclear protein that exhibits putative DNA-binding activity. These features suggested that TTP might regulate gene transcription and/or alternative splicing of pre-mRNAs in the absence of stimulation. RESULTS: To elucidate the regulatory pattern of TTP, we cloned and overexpressed the human TTP-encoding gene, ZFP36, in HeLa cells in the absence of inflammatory stimuli. The transcriptomes of the control and ZFP36-overexpressing cells were sequenced and subjected to analysis and validation. Upon ZFP36 overexpression, the expression of genes associated with innate immunity, including those in the type I interferon signaling pathway and viral response, were specifically upregulated, implying a transcriptional regulatory mechanism associated with the predicted DNA binding activity of TTP. TTP preferentially regulated the alternative splicing of genes involved in the positive regulation of the I-κB/NF-κB cascade and the TRIF-dependent toll-like receptor, MAPK, TNF, and T cell receptor signaling pathways. CONCLUSIONS: Our findings indicated that TTP may regulate the immune response via the regulation of alternative splicing and potentially transcription, which greatly expands the current understanding of the mechanisms of TTP-mediated gene regulation.

Forkhead-box transcription factor 1 affects the apoptosis of natural regulatory T cells by controlling Aven expression.

BACKGROUND: Regulatory T (Treg) cells play important roles in autoimmune diseases, cancer, and organ transplantation. Forkhead box protein o1 (Foxo1) and IL-7Rα(CD127) are closely related to the homeostasis of Treg cells. However, the mechanism underlying Treg proliferation and activation remains unclear. Here, we evaluated how the over-expression of Foxo1 affects Treg cell proliferation via intracellular signaling. nTreg cells were transfected separately with Foxo1 and Aven small-interfering RNA (siRNA) or over-expression plasmid. The expression of signaling pathway genes and CD127 was confirmed using RT-qPCR and western blot analysis. The expression of cell surface molecules and apoptosis was confirmed by Flow Cytometry 3-(4, 5-Dimethylthiazol-2-yl) 2,5- diphenyltetrazolium bromide for cell proliferation assays. RESULTS: Foxo1 strengthened the proliferative ability of Treg cells by activating IL-7/CD127 signaling. In addition, Foxo1 suppressed Treg cell apoptosis by regulating Aven expression. CONCLUSIONS: The results in this study indicated that Foxo1 is a positive regulatory factor for the proliferation and activity of Treg cells. Foxo1 might be a potential target for the activation of nTreg cells in vivo and in vitro.

[Clinical significance of parameters of prostate volume measured by transabdominal ultrasonography in evaluating bladder outlet obstruction].

OBJECTIVE: To explore the correlation between the parameters of prostate volume (PV) measured by transabdominal ultrasonography and urodynamic results in diagnosing bladder outlet obstruction (BOO). METHODS: 112 BPH patients aged 45-85 underwent transabdominal ultrasonography to measure the superior-inferior diameter (R1) anterior-posterior diameter (R2), and left-right diameter (R3). Urodynamic examination was conducted to record the maximum flow rate (Qmax), detrusor pressure at maximum urinary flow rate (Pdet. Qmax), and detrusor pressure at minimum urinary flow rate (Pdet. Qmin), Schafer grading and international prostate symptom score (IPSS) scores were calculated. Correlation analysis was performed. RESULTS: The PV, R1, R2, and R3 were (48 +/- 29) ml, (4.3 +/- 1.0) cm, (3.7 +/- 0.9) cm, and (5.2 +/- 0.8) cm respectively. The Qmax, Pdet. Qmax, Schafer score, and IPSS score were (6.2 +/- 3.2) ml/s, (56 +/- 41) cm H2O, 3.1 +/- 1.8 (0-6) and 23 +/- 2 (15-31) respectively. Logistic regression analysis showed that R1 (OR = 22.662, P = 0.000), PV (OR = 0.946, P = 0.008) , and Qmax (OR = 0.760, P = 0.013) were positively correlated with Schafer grading value. CONCLUSION: The parameters of PV measured by transabdominal ultrasonography are reliable to diagnose BOO due to BPH.