SProtP: A Web Server to Recognize Those Short-Lived Proteins Based on Sequence-Derived Features in Human Cells

Protein turnover metabolism plays important roles in cell cycle progression, signal transduction, and differentiation. Those proteins with short half-lives are involved in various regulatory processes. To better understand the regulation of cell process, it is important to study the key sequence-derived factors affecting short-lived protein degradation. Until now, most of protein half-lives are still unknown due to the difficulties of traditional experimental methods in measuring protein half-lives in human cells. To investigate the molecular determinants that affect short-lived proteins, a computational method was proposed in this work to recognize short-lived proteins based on sequence-derived features in human cells. In this study, we have systematically analyzed many features that perhaps correlated with short-lived protein degradation. It is found that a large fraction of proteins with signal peptides and transmembrane regions in human cells are of short half-lives. We have constructed an SVM-based classifier to recognize short-lived proteins, due to the fact that short-lived proteins play pivotal roles in the control of various cellular processes. By employing the SVM model on human dataset, we achieved 80.8% average sensitivity and 79.8% average specificity, respectively, on ten testing dataset (TE1-TE10). We also obtained 89.9%, 99% and 83.9% of average accuracy on an independent validation datasets iTE1, iTE2 and iTE3 respectively. The approach proposed in this paper provides a valuable alternative for recognizing the short-lived proteins in human cells, and is more accurate than the traditional N-end rule. Furthermore, the web server SProtP (http://reprod.njmu.edu.cn/sprotp) has been developed and is freely available for users

The heat shock protein family gene Hspa1l in male mice is dispensable for fertility

Background Heat shock protein family A member 1 like (Hspa1l) is a member of the 70kD heat shock protein (Hsp70) family. HSPA1L is an ancient, evolutionarily conserved gene with a highly conserved domain structure. The gene is highly abundant and constitutively expressed in the mice testes. However, the role of Hspa1l in the testes has still not been elucidated. Methods Hspa1l-mutant mice were generated using the CRISPR/Cas9 system. Histological and immunofluorescence staining were used to analyze the phenotypes of testis and epididymis. Apoptotic cells were detected through TUNEL assays. Fertility and sperm motilities were also tested. Quantitative RT-PCR was used for analyzing of candidate genes expression. Heat treatment was used to induce heat stress of the testis. Results We successfully generated Hspa1l knockout mice. Hspa1l-/- mice exhibited normal development and fertility. Further, Hspa1l-/- mice shown no significant difference in spermatogenesis, the number of apoptotic cells in testes epididymal histology, sperm count and sperm motility from Hspa1l+/+ mice. Moreover, heat stress does not exacerbate the cell apoptosis in Hspa1l-/- testes. These results revealed that HSPA1L is not essential for physiological spermatogenesis, nor is it involved in heat-induced stress responses, which provides a basis for further studies

A novel protein encoded by circRsrc1 regulates mitochondrial ribosome assembly and translation during spermatogenesis

Abstract Background Circular RNAs (circRNAs) are a large class of mammalian RNAs. Several protein products translated by circRNAs have been reported to be involved in the development of various tissues and systems; however, their physiological functions in male reproduction have yet not been explored. Results Here, we report an endogenous circRNA (circRsrc1) that encodes a novel 161-amino-acid protein which we named Rsrc1-161aa through circRNA sequencing coupled with mass spectrometry analysis on mouse testicular tissues. Deletion of Rsrc1-161aa in mice impaired male fertility with a significant decrease in sperm count and motility due to dysfunctions of mitochondrial energy metabolism. A series of in vitro rescue experiments revealed that circRsrc1 regulates mitochondrial functions via its encoded protein Rsrc1-161aa. Mechanistically, Rsrc1-161aa directly interacts with mitochondrial protein C1qbp and enhances its binding activity to mitochondrial mRNAs, thereby regulating the assembly of mitochondrial ribosomes and affecting the translation of oxidative phosphorylation (OXPHOS) proteins and mitochondrial energy metabolism. Conclusions Our studies reveal that Rsrc1-161aa protein encoded by circRsrc1 regulates mitochondrial ribosome assembly and translation during spermatogenesis, thereby affecting male fertility

The Arabidopsis SWI2/SNF2 chromatin Remodeler BRAHMA regulates polycomb function during vegetative development and directly activates the flowering repressor gene SVP.

The chromatin remodeler BRAHMA (BRM) is a Trithorax Group (TrxG) protein that antagonizes the functions of Polycomb Group (PcG) proteins in fly and mammals. Recent studies also implicate such a role for Arabidopsis (Arabidopsis thaliana) BRM but the molecular mechanisms underlying the antagonism are unclear. To understand the interplay between BRM and PcG during plant development, we performed a genome-wide analysis of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Increased H3K27me3 deposition at several hundred genes was observed in brm mutants and this increase was partially supressed by removal of the H3K27 methyltransferase CURLY LEAF (CLF) or SWINGER (SWN). ChIP experiments demonstrated that BRM directly binds to a subset of the genes and prevents the inappropriate association and/or activity of PcG proteins at these loci. Together, these results indicate a crucial role of BRM in restricting the inappropriate activity of PcG during plant development. The key flowering repressor gene SHORT VEGETATIVE PHASE (SVP) is such a BRM target. In brm mutants, elevated PcG occupancy at SVP accompanies a dramatic increase in H3K27me3 levels at this locus and a concomitant reduction of SVP expression. Further, our gain- and loss-of-function genetic evidence establishes that BRM controls flowering time by directly activating SVP expression. This work reveals a genome-wide functional interplay between BRM and PcG and provides new insights into the impacts of these proteins in plant growth and development

Development and validation of a risk-prediction nomogram for patients with ureteral calculi associated with urosepsis: A retrospective analysis

<div><p>Objectives</p><p>To develop and validate an individualized nomogram to predict probability of patients with ureteral calculi developing into urosepsis.</p><p>Methods</p><p>The clinical data of 747 patients with ureteral calculi who were admitted from June 2013 to December 2015 in Affiliated Nanhai Hospital of Southern Medical University were selected and included in the development group, while 317 ureteral calculi patients who were admitted from January 2016 to December 2016 were included in the validation group. The independent risk factors of ureteral calculi associated with urosepsis were screened using univariate and multivariate logistic regression analyses. The corresponding nomogram prediction model was drawn according to the regression coefficients. The area under the receiver operating characteristic curves and the GiViTI calibration belts were used to estimate the discrimination and calibration of the prediction model, respectively.</p><p>Results</p><p>Multivariate logistic regression analysis showed that the five risk factors of gender, mean computed tomography(CT) attenuation value of hydronephrosis, functional solitary kidney, urine white blood cell(WBC) count and urine nitrite were independent risk factors of ureteral calculi associated with urosepsis. The areas under the receiver operating characteristic curve of the development group and validation group were 0.913 and 0.874 respectively, suggesting that the new prediction model had good discrimination capacity. P-values of the GiViTI calibration test of the two groups were 0.247 and 0.176 respectively, and the 95% CIs of GiViTI calibration belt in both groups did not cross the diagonal bisector line. Therefore the predicted probability of the model was consistent with the actual probability which suggested that the calibration of the prediction model in both groups were perfect and prediction model had strong concordance performance.</p><p>Conclusion</p><p>The individualized prediction model for patients with ureteral calculi can facilitate improved screening and early identification of patients having higher risk of urosepsis.</p></div

Renewable and Superior Thermal-Resistant Cellulose-Based Composite Nonwoven as Lithium-Ion Battery Separator

A renewable and superior thermal-resistant cellulose-based composite nonwoven was explored as lithium-ion battery separator via an electrospinning technique followed by a dip-coating process. It was demonstrated that such nanofibrous composite nonwoven possessed good electrolyte wettability, excellent heat tolerance, and high ionic conductivity. The cells using the composite separator displayed better rate capability and enhanced capacity retention, when compared to those of commercialized polypropylene separator under the same conditions. These fascinating characteristics would endow this renewable composite nonwoven a promising separator for high-power lithium-ion battery

Calibration plots of the nomogram for the probability of urosepsis patients with ureteral calculi in the development group and validation group.

<p>Calibration plots of the nomogram for the probability of urosepsis patients with ureteral calculi in the development group and validation group.</p