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Proteins provide the molecular basis for cellular structure, catalytic activity, signal transduction, and molecular transport in biological systems. Recombinant protein expression is widely used to prepare and manufacture novel proteins that serve as the foundation of many biopharmaceutical products. However, protein translation bioprocesses are inherently prone to low-level errors. These sequence variants caused by amino acid misincorporation have been observed in both native and recombinant proteins. Protein sequence variants impact product quality, and their presence can be exacerbated through cellular stress, overexpression, and nutrient starvation. Therefore, the cell line selection process, which is used in the biopharmaceutical industry, is not only directed towards maximizing productivity, but also focuses on selecting clones which yield low sequence variant levels, thereby proactively avoiding potentially inauspicious patient safety and efficacy outcomes. Here, we summarize a number of hallmark studies aimed at understanding the mechanisms of amino acid misincorporation, as well as exacerbating factors, and mitigation strategies. We also describe key advances in analytical technologies in the identification and quantification of sequence variants, and some practical considerations when using LC-MS/MS for detecting sequence variants. [ABSTRACT FROM AUTHOR]

Therapeutic IgG mAbs have shown presence of three variations of their heavy chain C-termini, including the unprocessed C-terminal lysine, the processed C-terminal lysine, and C-terminal amidation. These variants are also present in endogenous human IgGs, although the level of unprocessed C-terminal lysine is very low. Here we report a new heavy-chain C-terminal variant, i.e., the des-GK truncation, which exists in both recombinant and endogenous human IgG4. The des-GK truncation was found in negligible amount in IgG1, IgG2 and IgG3 subclasses. Observation of a significant level of heavy-chain C-terminal des-GK truncation in endogenous human IgG4 suggests that low level of this variant present in therapeutic IgG4 is unlikely to be a safety concern. [ABSTRACT FROM AUTHOR]

Therapeutic IgG mAbs expressed from Chinese hamster ovary (CHO) cells are known to contain three C-terminal variants in their heavy chains, namely, the unprocessed C-terminal lysine, the processed C-terminal lysine, and C-terminal amidation. Although the presence of C-terminal amidation in CHO-expressed IgGs is well studied, the biological impact of the variant on the safety and efficacy of biotherapeutics has not been well understood. To further our biological understanding of C-terminal amidation, we analyzed a series of IgG samples, including both endogenous human IgGs as well as recombinant IgGs of different subclasses expressed from both CHO and murine cell lines, for their heavy-chain C-terminal variants by LC-MS/MS based peptide mapping. The results demonstrate that heavy-chain C-terminal amidation is a common variant occurring in IgG of all four subclasses (IgG1, IgG2, IgG3 and IgG4). The variant is generally present in recombinant IgG mAbs expressed from CHO cell lines but not in IgG mAbs expressed from murine cell lines, whereas the IgGs expressed from murine cell lines contain a much larger amount of unprocessed C-terminal lysine. Additionally, a significant amount of heavy-chain C-terminal amidation is observed in endogenous human IgGs, indicating that small amount of the variant present in therapeutic IgGs does not pose a safety concern. [ABSTRACT FROM AUTHOR]

What Is Known and Objective: Propofol is widely used in painless gastroscopy. However, sedation with propofol alone might increase the risk of respiratory and circulatory complications. This randomized clinical study compares the efficacy and safety of esketamine or dezocine combined with intravenous (IV) propofol in patients undergoing gastroscopy. Methods: A total of 102 patients were enrolled in this study and randomized into two groups. All patients were adults aged 18–64 years who underwent upper gastrointestinal gastroscopy. Patients were randomly assigned to two groups to receive esketamine (0.3 mg/kg) combined with propofol (group E) or dezocine (0.05 mg/kg) combined with propofol (group D). In both groups, the drugs were administered intravenously. The primary outcome was the dose of propofol which provided a satisfactory sedative effect, both to the endoscopist and the patients. Secondary outcomes included recovery time, side effects (such as hypotension, nausea and vomiting and agitation), and the number of adverse circulatory and respiratory events. Results: Data of 83 patients were analysed in the present study. Dosage of propofol required in group E (1.44 mg/kg ± 0.67 mg/kg) was significantly lower compared with that in group D (2.12 mg/kg ± 0.37 mg/kg) (p < 0.0001). There was no statistically significant difference in recovery time, side effects, and the frequency of sedation‐related adverse events between the two groups. What Is New and Conclusion: The study indicates that intravenous injection of propofol and esmketamine is more effective for gastroscopy. Use of esketamine reduces the total amount of propofol required in ASA I–II patients undergoing gastroscopy compared with single use of dezocine. It also provides more stable hemodynamics, without affecting the recovery time and side effects such as respiratory and circulatory adverse events. Trial Registration: The study was registered at the Chinese Clinical Trial Registry (www.chictr.org.cn; registration number: ChiCTR2100051814) on 05/10/2021. [ABSTRACT FROM AUTHOR]

Ethylene oxide (EtO) is widely used in sterilization of drug product primary containers and medical devices. The impact of residual EtO on protein therapeutics is of significant interest in the biopharmaceutical industry. The potential for EtO to modify individual amino acids in proteins has been previously reported. However, specific identification of EtO adducts in proteins and the effect of residual EtO on the stability of therapeutic proteins has not been reported to date. This paper describes studies of residual EtO with two therapeutic proteins, a PEGylated form of the recombinant human granulocyte colony-stimulating factor (Peg- GCSF) and recombinant human erythropoietin ( EPO) formulated with human serum albumin ( HSA). Peg- GCSF was filled in an EtO sterilized delivery device and incubated at accelerated stress conditions. Glu-C peptide mapping and LC- MS analyses revealed residual EtO reacted with Peg- GCSF and resulted in EtO modifications at two methionine residues (Met-127 and Met-138). In addition, tryptic peptide mapping and LC- MS analyses revealed residual EtO in plastic vials reacted with HSA in EPO formulation at Met-328 and Cys-34. This paper details the work conducted to understand the effects of residual EtO on the chemical stability of protein therapeutics. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:731-739, 2015 [ABSTRACT FROM AUTHOR]

Tetraspanins (TSPANs) play crucial roles in cell adhesion, migration, and metastasis of human cancer. However, there is no study in revealing the aspects of TSPAN9 traits and its functions in hepatocellular carcinoma (HCC) prognosis. Our study is the first to portray the TSPAN9 expression in HCC tissues with immunohistochemistry (IHC) analysis. Subsequently, a series of bioinformatics analyses such as expression estimation, survival assessment, and correlation analysis were implemented to dig out the possible upstream noncoding RNAs (ncRNAs) for TSPAN9 in HCC. In this way, the relevance within TSPAN9 and tumor immunity was then explored. We found that the TSPAN9 was downregulated in HCC tissues and had a correlation with HCC prognosis. Furthermore, we identified that the AL139383.1-hsa-miR-9-5p axis was the upstream ncRNA-related pathway most associated with TSPAN9 in HCC. Besides that, expression of TSPAN9 held a significantly negative correlation with tumor immunocyte infiltration as well as immune checkpoint CTLA4. TSPAN9-related immunomodulators were mainly enriched in T cell activation, leukocyte cell-cell adhesion, regulation of T cell activation, and regulation of leukocyte cell-cell adhesion signaling pathway. In conclusion, our results indicated that hsa-miR-9-5p-mediated downregulation of TSPAN9 was associated with poor HCC prognosis, immune-related signaling pathway, and tumor immune infiltration. [ABSTRACT FROM AUTHOR]

Battery-powered drug delivery devices are widely used as primary containers for storing and delivering therapeutic protein products to improve patient compliance and quality of life. Compared to conventional delivery approaches such as pre-filled syringes, battery-powered devices are more complex in design requiring new materials/components for proper functionality, which could cause potential product safety and quality concerns from the extractable and leachables (E&L) of the new materials/components. In this study, E&L assessments were performed on a battery-powered delivery device during the development and qualification of the device, where novel compound 2‑hydroxy-2-methylpropiophenone (HMPP) and related compounds were observed in both E&L. The source of the HMPP and related compounds was identified to be the nonproduct contact device batteries, in which HMPP photo-initiator was used as a curing agent in the battery sealant to prevent leakage of the battery electrolytes. Toxicology assessment was performed, which showed the levels of HMPP observed in the device lots were acceptable relative to the permitted daily exposure. A drug product HMPP spike study was also performed, where no product impact was observed. Based on these assessments, an action threshold and specification limits could be established as a control strategy, if needed, to mitigate the potential risks associate with the observed leachables. As a full resolution, seven battery candidates from different suppliers were screened and one new battery was successfully qualified for the delivery devices. Overall, the holistic E&L approach was fully successful in the development and qualification of the battery-powered devices for biotherapeutic products delivery ensuring product quality and patient safety. Non-product contact materials are commonly rated as low or no risk and typically considered as out of scope of E&L activities for delivery systems following industry benchmark and regulatory agency guidance. This case study is novel as it brings into attention the materials that might not normally be in consideration during the development process. It is highly recommended to understand materials in the context of intended use on a case-by-case basis and not to generalize to ensure successful development and qualification. [ABSTRACT FROM AUTHOR]

Rapid technological advances have significantly improved the capability, versatility, and robustness of mass spectrometers which has led to them playing a central role in the development, characterization, and regulatory filings of biopharmaceuticals. Their application spans the entire continuum of drug development, starting with discovery research through product development, characterization, and marketing authorization and continues well into product life cycle management. The scope of application extends beyond traditional protein characterization and includes elements like clone selection, cell culture physiology and bioprocess optimization, investigation support, and process analytical technology. More recently, advances in the MS-based multi-attribute method are enabling the introduction of MS in a cGMP environment for routine release and stability testing. While most applications of MS to date have been for monoclonal antibodies, the successes and learnings should translate to the characterization of next-gen biotherapeutics where modalities like multispecifics could be more prevalent. In this review, we describe the most significant advances in MS and correlate them to the broad spectrum of applications to biotherapeutic development. We anticipate rapid technological improvements to continue that will further accelerate widespread deployment of MS, thereby elevating our overall understanding of product quality and enabling attribute-focused product development. [ABSTRACT FROM AUTHOR]

Purpose: A high‐precision rotated elliptical beam profiling method based on pixel ion chamber is proposed in this paper. This method aims to improve the accuracy by modeling the transverse profile of rotated beam as an ellipse with additional correlation coefficient and eliminating the fitting error due to the volume averaging effect of pixel ion chamber. Methods: In pencil beam scanning (PBS) proton therapy systems, the transverse beam profile model is generally represented as a standard Gaussian distribution. Considering the elliptical spots, two‐dimensional (2D) joint Gaussian distribution characterized with the correlation coefficient ρ is adopted in this study. Gaussian‐type particle distribution with white noise was generated and processed in MATLAB to simulate the secondary particle collection in the pixel ion chamber. The simulated pixel ion chamber is a commercially available ion chamber which consists of 12 × 12 small square pixels (3.75 × 3.75 mm2) with a 0.05 mm interval. The simulated signals were preprocessed by filtering with the noise threshold and extracting the maximum simply connected domain (MSCD) of the signal. Then, five geometric parameters that identify the transverse beam profiles were fitted under different signal‐to‐noise ratio (SNR) conditions: the center of the beam (x0, y0), the spot size (σmajor, σminor), and the rotation angle θ formed between the major axes of elliptical spot and the x axes of the ion chamber. First, the simulated signals were preprocessed by filtering with the noise threshold and extracting the MSCD of the signal. Second, a rectification curve of systematic error in fitted spot size versus the prescribed spot size was used to predict the systematic error due to the volume averaging effect. Finally, the effects of fitting errors on therapeutic dose were evaluated in terms of gamma index and relative dose difference. Results: When the SNR is not less than 20 dB, the relative fitting error of spot size and the absolute fitting error of angle θ are less than 1% and 6.1°, respectively. The fitting error of beam center increases with spot size and will not exceed 0.22 mm when spot size reaches up to 12 mm. At a SNR equal to 20 dB, neither cold nor hot spots were presented in dose distribution calculated with the fitted spot parameters. Conclusion: The improved Gaussian fitting algorithm performs well when SNR is not less than 20 dB. This method can effectively distinguish the nominal beam and rotated elliptical beam. An ideal systematic error curve can be predicted and used to correct the fitted spot size, thus eliminating the systematic error due to the volume averaging effect of the pixel ion chamber. The fitting error of spot size cannot be fully corrected, but it is negligible and shows little effect on the overall therapeutic dose. [ABSTRACT FROM AUTHOR]

Soil organic carbon (SOC) is a major component of the global carbon cycle and has a potentially large impact on the greenhouse effect. Paddy soils are important agricultural soils worldwide, especially in Asia. Thus, a better understanding of the relationship between SOC of paddy soils and climate variables is crucial to a robust understanding of the potential effect of climate change on the global carbon cycle. A soil profile data set ( n = 1490) from the Second National Soil Survey of China conducted from 1979 to 1994 was used to explore the relationships of SOC density with mean annual temperature (MAT) and mean annual precipitation (MAP) in six soil regions and eight paddy soil subgroups. Results showed that SOC density of paddy soils was negatively correlated with MAT and positively correlated with MAP ( P < 0.01). The relationships of SOC density with MAT and MAP were weak and varied among the six soil regions and eight paddy soil subgroups. A preliminary assessment of the response of SOC in Chinese paddy soils to climate indicated that climate could lead to a 13% SOC loss from paddy soils. Compared to other soil regions, paddy soils in Northern China will potentially more sensitive to climate change over the next several decades. Paddy soils in Middle and Lower Yangtze River Basin could be a potential carbon sink. Reducing the climate impact on paddy soil SOC will mitigate the positive feedback loop between SOC release and global climate change. [ABSTRACT FROM AUTHOR]

In a pencil beam scanning proton therapy system, critical beam parameters, including the spot size, spot center position, and tilt angle, are monitored for security by beam profile detectors such as two-dimensional (2D) pixel-segmented ionization chambers. A method, named lines-based beam profiling (LBBP), is proposed to identify the five geometric parameters μ x , μ y , σ x , σ y , θ of rotating elliptical beam profiles using several lines (rows and columns) in the 2D detector data. The method provides solid results even in the presence of dead pixels, which can be located using a wavelet analysis. Simulation experiments were used to define the number of lines used by the LBBP method and to characterize its performance as a function of the signal-to-noise (SNR). For SNR greater than 30, the root mean square errors (RMSEs) of the beam spot size, spot center position, and rotation angle obtained with the LBBP method are less than 0.16 mm, 0.05 mm, and 0.78 degrees, respectively. The LBBP method was applied to the data collected by a pixel chamber illuminated by an X-ray source, demonstrating the capability of identifying dead pixels and providing more accurate measurements of the beam spot size and center position than the standard Gaussian fitting. [ABSTRACT FROM AUTHOR]

Insufficient copper level in the mammalian cell culture medium resulted in lactate accumulation while maintaining similar growth and culture viability profiles. Label-free, LC-MS/MS-based shotgun proteomics method was applied to compare the protein expression profiles obtained from the cultures exposed to suboptimal copper level to those provided with sufficient amount of copper. Under copper deficient condition, a substantial reduction of the protein levels of the multiple subunits of Complex IV, also known as cytochrome c oxidase, of the mitochondrial electron transport chain was observed for all three different Chinese Hamster Ovary (CHO) cell lines expressing therapeutic monoclonal antibodies tested. Additional proteins affected by suboptimal copper level included peroxiredoxin (PRDX) and hepatocyte-derived growth factor (HDGF), which were affected during early phase of the fed-batch production, several days prior to initiation of lactate accumulation. In contrast, proteins such as syntenin (SDCBP) and integral membrane 2C (ITM2C) showed altered expression patterns toward the end of culture duration, after lactate divergence had occurred. For all conditions tested, time was the most predominant factor facilitating the direction of global protein expression trend, with substantial number of proteins subjected to time-dependent changes in expression, independent of copper. [ABSTRACT FROM AUTHOR]

Protein N-Glycan analysis is traditionally performed by high pH anion exchange chromatography (HPAEC), reversed phase liquid chromatography (RPLC), or hydrophilic interaction liquid chromatography (HILIC) on fluorescence-labeled glycans enzymatically released from the glycoprotein. These methods require time-consuming sample preparations and do not provide site-specific glycosylation information. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide mapping is frequently used for protein structural characterization and, as a bonus, can potentially provide glycan profile on each individual glycosylation site. In this work, a recently developed glycopeptide fragmentation model was used for automated identification, based on their MS/MS, of N-glycopeptides from proteolytic digestion of monoclonal antibodies (mAbs). Experimental conditions were optimized to achieve accurate profiling of glycoforms. Glycan profiles obtained from LC-MS/MS peptide mapping were compared with those obtained from HPAEC, RPLC, and HILIC analyses of released glycans for several mAb molecules. Accuracy, reproducibility, and linearity of the LC-MS/MS peptide mapping method for glycan profiling were evaluated. The LC-MS/MS peptide mapping method with fully automated data analysis requires less sample preparation, provides site-specific information, and may serve as an alternative method for routine profiling of N-glycans on immunoglobulins as well as other glycoproteins with simple N-glycans. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Abstract: High resolution glycan mapping was performed on human immunoglobulin G (IgG) obtained from individual healthy subjects and from a combined sample of healthy subjects. In addition to the commonly known complex glycans, a variety of minor glycans are described and quantified, including high mannose forms and several previously unreported hybrid forms. Fc specific glycan analysis was also performed through peptide mapping with LC/MS/MS. Differences in the glycan linked Fc peptide masses allowed glycan profiles to be analyzed and quantified from IgG1 and IgG2 simultaneously for each subject within the same sample. Glycan profiles differed between subtypes, with greater levels of more fully galactosylated species found on IgG1 (e.g. G2F, SG2F) than IgG2. These results also show that Gal attachment on G1F is biased to the Man (α1→6) arm for IgG1 and on the Man (α1→3) arm for IgG2 from individual healthy subjects. [Copyright &y& Elsevier]

Mass and top-down analyses of 150-kDa monoclonal immunoglobulin gamma (IgG) antibodies were performed on an Orbitrap analyzer. Three different sample delivery methods were tested including (1) infusion of an off-line desalted IgG sample using nano-electrospray; (2) on-line desalting followed by a step elution with a high percentage of organic solvent; and (3) reversed-phase HPLC separation and on-line mass and top-down analyses of disulfide isoforms of an IgG2 antibody. The accuracy of mass measurements of intact antibody was within ±2 Da (15 ppm). The glycoforms of intact IgG antibodies separated by 162 Da were baseline resolved. In-source fragmentation of the intact antibodies produced mainly 115 residue fragments including N-terminal variable domains of heavy and light chains. The sequence coverage (the number of cleavages) was greatly increased after reduction of disulfide bonds and HPLC/MS/MS analysis of light and heavy chains using collision-induced dissociation in the ion trap of the LTQ-Orbitrap. This is an attractive alternative to peptide mapping for characterization and monitoring of post-translational modifications attributed to minimal sample preparation, high speed of the mass/top-down analysis, and relatively minor method-induced sample modifications. [ABSTRACT FROM AUTHOR]

Soil nitrogen (N) plays a central role in soil quality and biogeochemical cycles. However, little is known about the distribution and spatial variability of the different fractions of soil N within entire soil profiles. This study aimed to investigate the potential of laboratory-based hyperspectral imaging (HSI) spectroscopy to retrieve and map total N (TN), available N (AvailN), ammonium N (NH 4 -N), nitrate N (NO 3 -N), and microbial biomass N (MBN) in soil profiles at a high resolution. HSI images of eleven intact soil profiles of 100 ± 5 cm depth from three typical soil types were recorded. A variety of nonlinear machine learning techniques, such as artificial neural networks (ANN), cubist regression tree (Cubist), k-nearest neighbour (KNN), support vector machine regression (SVMR) and extreme gradient boosting (XGBoost), were compared with a partial least squares regression (PLSR) to determine the most suitable model for the prediction of the various soil N fractions. Overall, the results showed that nonlinear techniques performed better than PLSR in most cases, with a high coefficient of determination (R 2) and low root mean square error (RMSE). Among the models, SVMR was found to be superior to the other tested models for TN (R 2 P = 0.94, RMSE P = 0.17 g kg−1), AvailN (R 2 P = 0.94, RMSE P = 13.35 mg kg−1), NO 3 -N (R 2 P = 0.82, RMSE P = 7.31 mg kg−1), and NH 4 -N (R 2 P = 0.70, RMSE P = 1.51 mg kg−1) based on independent validation, whereas MBN (R 2 P = 0.63, RMSE P = 6.62 mg kg−1) was predicted best by KNN. In addition, SVMR required less computational time and was less sensitive to spectral noise. It can therefore be concluded that HSI spectroscopy combined with SVMR is suitable for the high-resolution mapping of various soil N fractions in soil profiles. Unlabelled Image • Hyperspectral imaging was used to map soil N fractions in intact soil profiles. • Multiple machine learning models are compared to select the most suitable model. • Nonlinear techniques outperformed the linear PLSR model. • SVMR exhibited higher comprehensive performance than other models. • Hyperspectral imaging coupled with SVMR is recommended for N element mapping. [ABSTRACT FROM AUTHOR]

(1) GhVLN4 is required for cotton resistance to Verticillium wilt, Verticillium dahliae can preferentially colonize in stem phloem of VIGS silenced GhVLN4 cotton. (2) Ectopic overexpression of GhVLN4 significantly lessens V. dahliae conidia attachment, germination, and colonization in roots, amplifying SA-mediated systemic acquired resistance. • The expression of GhVLN4 is responsive to Verticillium dahliae , salt, and drought stress, in addition to a variety of phytohormones. • GhVLN4 is required for cotton resistance to Verticillium wilt, V. dahliae preferentially colonize in the stem phloem of GhVLN4 -silenced cotton. • Ectopic expression of GhVLN4 greatly reduces V. dahliae conidia attachment, germination, and colonization in roots. • Ectopic expression of GhVLN4 amplifies SA signal pathway but attenuates JA pathway components in response to V. dahliae. • Ectopic overexpression of GhVLN4 significantly enhances tolerance to salt and drought stress. As structural and signaling platform in plant cell, the actin cytoskeleton is regulated by diverse actin binding proteins (ABPs). Villins are one type of major ABPs responsible for microfilament bundling, which have proved to play important roles in plant growth and development. However, the function of villins in stress tolerance is poorly understood. Here, we report the function of cotton GhVLN4 in Verticillium wilt resistance and abiotic stress tolerance. The expression of GhVLN4 was up-regulated by gibberellin, ethylene, ABA, salicylic acid, jasmonate, NaCl, PEG, and Verticillium dahliae treatment, suggesting the involvement of GhVLN4 in multiple stress and hormone responses and signaling. Virus-induced gene silencing GhVLN4 made cotton more susceptible to V. dahliae characterized by the preferential colonization and rapid growth of the fungus in both phloem and xylem of the infected stems. Arabidopsis overexpressing GhVLN4 exhibited higher resistance to V. dahliae , salt and drought than the wild-type plants. The enhanced resistance to V. dahliae is likely related to the upregulated components in SA signaling pathway; the improved tolerance to salt and drought is characterized by upregulation of the components both in ABA- related and ABA-independent signal pathways, along with altered stomatal aperture under drought. Our findings demonstrate that GhVLN4 may play important roles in regulating plant tolerance to both biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

Surface trafficking of AMPA receptors (AMPARs) is one of the important mechanisms mediating synaptic plasticity which is essential for cognitive functions such as learning and memory. Spastin, as a novel binding partner for the AMPAR, has been reported to regulate AMPAR surface expression and synaptic function. Additionally, Spastin undergoes two posttranslational modifications, phosphorylation and SUMOylation, both of which are crucial for synaptic function. However, gaps exist in our knowledge of how Spastin phosphorylation cross-talks with its SUMOylation in the regulation of AMPAR surface expression and synaptic function. Here, we reported that deSUMOylation of Spastin at Lys427 increased the surface level of AMPAR GluA2 subunit, the amplitude and frequency of miniature excitatory synaptic currents (mEPSC), and facilitated the morphological maturation of dendritic spines in cultured hippocampal neurons. Further studies demonstrated that Spastin phosphorylation at Ser210 further increased the enhancement of GluA2 surface expression and synaptic function by deSUMOylated Spastin, while dephosphorylation had the opposite effect. Simultaneously, deSUMOylation at Lys427 significantly increased the promoting effect of Spastin phosphorylation on synaptic function. In conclusion, our study suggests that cooperative interactions between phosphorylated and deSUMOylated Spastin are novel pathways to enhance synaptic function., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: Previous observational studies have established the high prevalence of bacterial pneumonia in diabetic patients, which in turn leads to increased mortality. However, the presence of a causal connection between bacterial pneumonia and diabetes remains unobserved., Methods: We chose genome-wide significant (Ρ < 1 × 10 -5 and Ρ < 1 × 10 -6 ) and independent (r 2 < 0.001) single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs) to proceed a bidirectional two-sample MR study. The extracted SNPs explored the relationship between bacterial pneumonia and diabetes by Inverse variance weighted (IVW), MR-Egger, and weighted median methods. In addition, we conducted the Heterogeneity test, the Pleiotropy test, MR-presso and the Leave-one-out (LOO) sensitivity test to validate the reliability of results., Results: In an MR study with bacterial pneumonia as an exposure factor, four different types of diabetes as outcome. It was observed that bacterial pneumonia increases the incidence of GDM (OR = 1.150 (1.027-1.274, P  = 0.011) and T1DM (OR = 1.277 (1.024-1.531), P  = 0.016). In the reverse MR analysis, it was observed that GDM (OR = 1.112 (1.023-1.201, P  = 0.009) is associated with an elevated risk of bacterial pneumonia. However, no significant association was observed bacterial pneumonia with T1DM and other types of diabetes ( P  > 0.05)., Conclusion: This study utilizing MR methodology yields robust evidence supporting a bidirectional causal association between bacterial pneumonia and GDM. Furthermore, our findings suggest a plausible causal link between bacterial pneumonia and T1DM.

The present study utilized the spared nerve injury (SNI) to create a mouse model of depression to investigate the impact of esketamine on depressive-like behaviors, on the expression of PSD-95 and CRMP2 proteins, and on changes in neuronal dendritic spine plasticity in the prefrontal cortex (PFC). Depressive-like behavioral tests were performed 1 h after esketamine treatment, and the PFC tissues were obtained on the fourth day after completing the behavioral tests. Then, dendritic spine density and morphology in the PFC were measured using Golgi staining, and CRMP2 and PSD-95 proteins were obtained from PFC tissue by western blotting. The results of this study showed that esketamine significantly increased the immobility time in the forced swimming test and tail suspension test. In the open field test, esketamine increased the time spent in the open arms, the time spent in the central area, and the total distance covered. It also increased the protein expression levels of CRMP2 and PSD-95 in addition to the total and mature dendritic spine density of the PFC in SNI-depressed mice. Esketamine can significantly improve depression-like behaviors in SNI-depressed mice and promote an increase in dendritic spine density and maturation in the PFC. These effects may be associated with changes in CRMP2 and PSD-95 expression.

Objective: Propofol and etomidate are the most commonly used sedative agents in procedural sedation, each with its own advantages and disadvantages. However, there remains considerable controversy regarding the optimal ratio for the mixture of these two drugs, warranting further investigation. Therefore, this study aims to investigate the optimal ratio for combining propofol and etomidate during gastroscopy., Methods: This study is a prospective, double-blinded, randomized controlled clinical trial. One hundred and sixty-two patients from July 2019 to December 2022 were evenly classified into three groups using a random number table as follows: (1) P group (propofol); (2) EP1 group (5 mL etomidate +10 mL propofol); (3) EP2 group (10 mL etomidate +10 mL), 54 patients per group. The medications, including a pre-sedation dose of 50 μg/kg dezocine followed by sedatives, ceasing when the patient's eyelash reflex vanished, indicating adequate sedation. Mean arterial pressure (MAP), heart rate (HR), and peripheral oxygen saturation (SpO 2 ) measurements taken before anesthesia (T1), immediately after the administration of sedatives (T2), immediately gastroscopic insertion (T3) and immediately recovery (T4) were determined. Additional, perioperative related outcomes and adverse events were also recorded., Results: The EP2 group exhibited a higher MAP at T2 compared to the P and EP1 groups ( p < 0.05). Calculated decreases in MAP revealed values of 19.1, 18.8, and 13.8% for the P, EP1, and EP2 groups at T2, respectively. Adverse events: Group EP2 exhibited a significantly lower hypotension incidence (11.1%) compared to the Propofol group (50%) and EP1 (31.5%). Concerning injection pain, Group EP2 also showing a significant decrease in comparison to P and EP1 groups ( p  < 0.05)., Conclusion: The use of a mixture of 10 mL etomidate and 10 mL propofol (at a 1:1 ratio) combined with dezocine for painless gastroscopy demonstrates hemodynamic stability, a low incidence of adverse reactions., Clinical Trial Registration: https://www.chictr.org.cn/showproj.html?proj=39874., Competing Interests: The 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., (Copyright © 2024 Tang, Zheng, Li, Zhang and Zhang.)

Stop codon readthroughs were examined in 48 recombinant therapeutic protein candidates produced from multiple clones of Chinese hamster ovary cells, using peptide mapping with LC-MS/MS detection. We found that stop codon readthrough is a common phenomenon occurring in most of these candidates, with levels varying from below the detection limit of ∼0.001 % to ∼1 %. The readthrough propensity depends on the stop codon being used, as well as the nucleotides surrounding it. The amino acids misincorporated into the stop position can be well-predicted by a third-base wobble mismatch and a first-base U/G mismatch during codon recognition, i.e., tyrosine or glutamine insertion for the UAA and UAG stop codons, and tryptophan, cysteine or arginine insertion for the UGA stop codon. Data shown in this report demonstrate the importance of optimizing the DNA sequence near the stop codon, and the importance of detecting stop codon readthroughs during the development of a therapeutic product., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

A dual Multi-Dimensional Integration (dMDI) method was proposed and demonstrated for T 2 * and R 2 * mapping. By constructing and jointly using both the original MDI term and an inversed MDI term, T 2 * and R 2 * mapping can be performed independently with intrinsic background noise suppression and spike elimination, allowing for high quantitative accuracy and robustness over a wide range of T 2 *. dMDI was compared to original MDI and curve fitting methods in terms of quantitative specificity, accuracy, reliability and computational efficiency. All methods were tested and compared via simulation and in vivo data. With high signal-to-noise-ratio (SNR), the proposed dMDI method yielded T 2 *and R 2 * values similar to curve fitting methods. For low SNR and background noise signals, the dMDI yielded low T 2 * and R 2 * values, thus effectively suppressing all background noise. Virtually zero spikes were observed in dMDI T 2 * and R 2 * maps in all simulation and imaging results. The dMDI method has the potential to provide improved and reliable T 2 * and R 2 * mapping results in routine and SNR-challenging scenarios., Competing Interests: Declaration of competing interest The following authors are employees of the UIH America, Inc., Houston, TX, United States: Yongquan Ye, Jian Xu and Zhongqi Zhang. The following authors are employees of the Beijing United Imaging Intelligent Imaging Technology Research Institute: Yan Zhang., (Copyright © 2024. Published by Elsevier Inc.)

The programmed synthesis of sequence-defined biomaterials whose monomer backbones diverge from those of canonical α-amino acids represents the next frontier in protein and biomaterial evolution. Such next-generation molecules provide otherwise nonexistent opportunities to develop improved biologic therapies, bioremediation tools, and biodegradable plastic-like materials. One monomer family of particular interest for biomaterials includes β-hydroxy acids. Many natural products contain isolated β-hydroxy acid monomers, and polymers of β-hydroxy acids (β-esters) are found in polyhydroxyalkanoate (PHA) polyesters under development as bioplastics and drug encapsulation/delivery systems. Here we report that β 2 -hydroxy acids possessing both ( R ) and ( S ) absolute configuration are substrates for pyrrolysyl-tRNA synthetase (PylRS) enzymes in vitro and that ( S )-β 2 -hydroxy acids are substrates in cellulo . Using the orthogonal Ma PylRS/ Ma tRNA Pyl synthetase/tRNA pair, in conjunction with wild-type E. coli ribosomes and EF-Tu, we report the cellular synthesis of model proteins containing two ( S )-β 2 -hydroxy acid residues at internal positions. Metadynamics simulations provide a rationale for the observed preference for the ( S )-β 2 -hydroxy acid and provide mechanistic insights that inform future engineering efforts. As far as we know, this finding represents the first example of an orthogonal synthetase that acylates tRNA with a β 2 -hydroxy acid substrate and the first example of a protein hetero-oligomer containing multiple expanded-backbone monomers produced in cellulo ., Competing Interests: The authors declare the following competing financial interest(s): N.X.H. and A.S. are coinventors on an international patent application that incorporates methods outlined in this manuscript., (© 2024 The Authors. Published by American Chemical Society.)

Introduction: Remimazolam (RMZ) is a novel intravenous sedative drug of ultra-short benzodiazepine. The optimal dose of RMZ plus butorphanol for sedation during first trimester artificial abortion is unknown. Therefore, the present study aimed to evaluate the median effective dose (ED 50 ) of RMZ combined with different doses of butorphanol on the sedative effect for first-trimester artificial abortion., Methods: Sixty-one female patients were randomly assigned to Group B10 (31 patients) and Group B15 (30 patients). RMZ was administered 5 min after IV butorphanol at doses of 10 μg/kg (Group B10) and 15 μg/kg (Group B15). Cervical dilatation at the time of using a cervical dilating rod, if the patient has body movement and affects the gynecologist's operation, we define it as "Ineffective." Therefore, the dose of RMZ was increased in the next patient. Otherwise, it was defined as "Effective," and the dose of RMZ was reduced in the next patient. According to the pre-experiment, the first dose of RMZ in the first patient was 0.35 mg/kg, and the adjacent geometric dose ratio was 0.9. The centered isotonic regression was performed to determine the ED 50 of RMZ. The total RMZ dose administered, recovery time, and anesthesia-related adverse events were all recorded., Results: The ED 50 (90% CI) of RMZ was 0.263 (0.215-0.310) mg/kg in Group B10, and 0.224 (0.191-0.261) mg/kg in Group B15, respectively. The recovery time in Group B10 was significantly shorter than in Group B15 (9.8 ± 2.3 vs. 12.5 ± 3.6 min, p  ≤ 0.001). There was no significant difference in the incidence rate of all anesthesia-related adverse events between the two groups ( p  > 0.05)., Conclusion: The ED50 of RMZ combined with a 10 μg/kg or 15 μg/kg dose of butorphanol was 0.263 and 0.224 mg/kg during painless first trimester artificial abortion. However, RMZ combined with a 10 μg/kg dose of butorphanol seems to have a shorter recovery time., Clinical Trial Registration: https://www.chictr.org.cn/bin/project/edit?pid=166623., Competing Interests: The 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., (Copyright © 2024 Chen, Li, Hu, Zheng, Mai and Zhang.)

Objective: This study evaluated the predictive value of the vasoactive-ventilation-renal (VVR) score in identifying the risk of weaning failure after cardiac surgery and developing a nomogram model to help physicians improve the success rate of weaning from mechanical ventilation in adult patients undergoing postoperative cardiac surgery., Methods: Clinical data were retrospectively collected from adult patients who underwent extracorporeal circulation cardiac surgery at the First Affiliated Hospital of Nanjing Medical University between August 2022 and April 2023 and who were subsequently transferred to the Intensive Care Unit (ICU) and treated with vasoactive drugs. Patients were divided into successful and unsuccessful weaning groups based on first-attempt weaning success. Variable selection was regularized using univariate logistic regression and Least absolute shrinkage and selection operator (LASSO) regularization. Multivariate logistic regression was performed to identify predictors and a nomogram was created to predict the risk of weaning failure., Results: A total of 519 patients were included in the study. After selecting multiple stepwise variables, the VVR score before weaning, the modified Sequential Organ Failure Assessment (mSOFA) score on weaning day, and mechanical ventilation duration before weaning were determined as predictive indicators of weaning failure in adult patients after cardiac surgery. The optimal cut-off values for these indicators were 18.46 points, 4.33 points, and 20.50 h, respectively. The predictive model constructed using these three factors demonstrated good predictive performance., Conclusions: The VVR score before weaning accurately predicts the probability of weaning failure in adult patients after cardiac surgery. The weaning risk-predictive nomogram model, established based on the VVR score, mSOFA score, and mechanical ventilation duration before weaning, demonstrated robust predictive ability., Competing Interests: The 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., (© 2024 Zhang, Tang, Ren, Zhao, You, Wang, Zhao and Zuo.)

Background and Objectives: Colorectal cancer remains an important public health problem in the context of the COVID-19 (Corona virus disease 2019) pandemic. The decline in detection rates and delayed diagnosis of the disease necessitate the exploration of novel approaches to identify individuals with a heightened risk of developing colorectal cancer. The study aids clinicians in the rational allocation and utilization of healthcare resources, thereby benefiting patients, physicians, and the healthcare system., Methods: The present study retrospectively analyzed the clinical data of colorectal cancer cases diagnosed at the Affiliated Hospital of Guilin Medical University from September 2022 to September 2023, along with a control group. The study employed univariate and multivariate logistic regression as well as LASSO (Least absolute shrinkage and selection operator) regression to screen for predictors of colorectal cancer risk. The optimal predictors were selected based on the area under the curve (AUC) of the receiver operating characteristic (ROC) curve. These predictors were then utilized in constructing a Nomogram Model for predicting colorectal cancer risk. The accuracy of the risk prediction Nomogram Model was assessed through calibration curves, ROC curves, and decision curve analysis (DCA) curves., Results: Clinical data of 719 patients (302 in the case group and 417 in the control group) were included in this study. Based on univariate logistic regression analysis, there is a correlation between Body Mass Index (BMI), red blood cell count (RBC), anemia, Mean Corpuscular Volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), platelet count (PLT), Red Cell Distribution Width-Standard Deviation (RDW-SD), and the incidence of colorectal cancer. Based on the findings of multivariate logistic regression analysis, the variables of BMI and RBC exhibit a decrease, while anemia and PLT demonstrate an increase, all of which are identified as risk factors for the occurrence of colorectal cancer. LASSO regression selected BMI, RBC, anemia, and PLT as prediction factors. LASSO regression and multivariate logistic regression analysis yielded the same results. A nomogram was constructed based on the 4 prediction factors identified by LASSO regression analysis to predict the risk of colorectal cancer. The AUC of the nomogram was 0.751 (95% CI, OR: 0.708-0.793). The calibration curves in the validation and training sets showed good performance, indicating that the constructed nomogram model has good predictive ability. Additionally, the DCA demonstrated that the nomogram model has diagnostic accuracy., Conclusion: The Nomogram Model offers precise prognostications regarding the likelihood of Colorectal Cancer in patients, thereby helping healthcare professionals in their decision-making processes and promoting the rational categorization of patients as well as the allocation of medical resources., Competing Interests: The 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., (Copyright © 2024 Zhang, Zhang, Zhang, Zhu, Wu, Tan and Jian.)

Formins or formin homology 2 (FH2) proteins, evolutionarily conserved multi-domain proteins in eukaryotes, serve as pivotal actin organizers, orchestrating the structure and dynamics of the actin cytoskeleton. However, a comprehensive investigation into the formin family and their plausible involvement in abiotic stress remains undocumented in soybean ( Glycine max ). In the current study, 34 soybean FH ( GmFH )family members were discerned, their genomic distribution spanning the twenty chromosomes in a non-uniform pattern. Evolutionary analysis of the FH gene family across plant species delineated five discernible groups (Group I to V) and displayed a closer evolutionary relationship within Glycine soja , Glycine max , and Arabidopsis thaliana . Analysis of the gene structure of GmFH unveiled variable sequence lengths and substantial diversity in conserved motifs. Structural prediction in the promoter regions of GmFH gene suggested a large set of cis-acting elements associated with hormone signaling, plant growth and development, and stress responses. The investigation of the syntenic relationship revealed a greater convergence of GmFH genes with dicots, indicating a close evolutionary affinity. Transcriptome data unveiled distinctive expression patterns of several GmFH genes across diverse plant tissues and developmental stages, underscoring a spatiotemporal regulatory framework governing the transcriptional dynamics of GmFH gene. Gene expression and qRT-PCR analysis identified many GmFH genes with a dynamic pattern in response to abiotic stresses, revealing their potential roles in regulating plant stress adaptation. Additionally, protein interaction analysis highlighted an intricate web of interactions among diverse GmFH proteins. These findings collectively underscore a novel biological function of GmFH proteins in facilitating stress adaptation in soybeans.

Purpose: In recent years, the continuous advancement of convolutional neural networks (CNNs) has led to the widespread integration of deep neural networks as a mainstream approach in clinical diagnostic support. Particularly, the utilization of CNN-based medical image segmentation has delivered favorable outcomes for aiding clinical diagnosis. Within this realm, network architectures based on the U-shaped structure and incorporating skip connections, along with their diverse derivatives, have gained extensive utilization across various medical image segmentation tasks. Nonetheless, two primary challenges persist. First, certain organs or tissues present considerable complexity, substantial morphological variations, and size discrepancies, posing significant challenges for achieving highly accurate segmentation. Second, the predominant focus of current deep neural networks on single-resolution feature extraction limits the effective extraction of feature information from complex medical images, thereby contributing to information loss via continuous pooling operations and contextual information interaction constraints within the U-shaped structure., Approach: We proposed a five-layer pyramid segmentation network (PS5-Net), a multiscale segmentation network with diverse resolutions that is founded on the U-Net architecture. Initially, this network effectively leverages the distinct features of images at varying resolutions across different dimensions, departing from prior single-resolution feature extraction methods to adapt to intricate and variable segmentation scenarios. Subsequently, to comprehensively integrate feature information from diverse resolutions, a kernel selection module is proposed to assign weights to features across different dimensions, enhancing the fusion of feature information from various resolutions. Within the feature extraction network denoted as PS-UNet, we preserve the classical structure of the traditional U-Net while enhancing it through the incorporation of dilated convolutions., Results: PS5-Net attains a Dice score of 0.9613 for liver segmentation on the CHLISC dataset and 0.8587 on the ISIC2018 dataset for skin lesion segmentation. Comparative analysis with diverse medical image segmentation methodologies in recent years reveals that PS5-Net has achieved the highest scores and substantial advancements., Conclusions: PS5-Net effectively harnesses the rich semantic information available at different resolutions, facilitating a comprehensive and nuanced understanding of the input medical images. By capitalizing on global contextual connections, the network adeptly captures the intricate interplay of features and dependencies across the entire image, resulting in more accurate and robust segmentation outcomes. The experimental validation of PS5-Net underscores its superior performance in medical image segmentation tasks, offering promising prospects for enhancing diagnostic and analytical processes within clinical settings. These results highlight the potential of PS5-Net to significantly contribute to the advancement of medical imaging technologies and ultimately improve patient care through more precise and reliable image analysis., (© 2024 Society of Photo-Optical Instrumentation Engineers (SPIE).)

Non-small cell lung cancer (NSCLC) is the most prevalent histology type of lung cancer worldwide, accounting for 18% of total cancer-related deaths estimated by GLOBOCAN in 2020. CircRNAs have emerged as potent regulators of NSCLC development. CircRANGAP1 (hsa&#95;circ&#95;0001235/hsa&#95;circ&#95;0063526) is a potential biomarker for NSCLC identified by microarray dataset analysis. Here, we investigated the biological functions of circRANGAP1 in NSCLC development and elucidated the associated competing endogenous RNA (ceRNA) mechanisms. We found that circRANGAP1 expression was upregulated in NSCLC tissues and cells, which was inversely correlated with carcinogenesis and poor clinical outcome of NSCLC patients. CircRANGAP1 knockdown inhibited NSCLC migration by regulating miR-512-5p/SOD2 axis. In conclusion, circRANGAP1 facilitated NSCLC tumorigenesis and development by sponging miR-512-5p to upregulate SOD2 expression. Suppression of circRANGAP1 expression by si-circRANGAP1 treatment could be a strategy to inhibit NSCLC development and metastasis., (© 2023. The Author(s).)

Background: Existing data suggests a potential link between human blood metabolites and sepsis, yet the precise cause-and-effect relationship remains elusive. By using a two-sample Mendelian randomization (MR) analysis, this study aims to establish a causal link between human blood metabolites and sepsis., Methods: A two-sample MR analysis was employed to investigate the relationship between blood metabolites and sepsis. To assess the causal connection between sepsis and human blood metabolites, five different MR methods were employed, A variety of sensitivity analyses were conducted, including Cochrane's Q test, MR-Egger intercept test, MR-PRESSO and leave-one-out (LOO) analysis. In order to ensure the robustness of the causal association between exposure and outcome, the Bonferroni adjustment was employed. Additionally, we conducted analyses of the metabolic pathways of the identified metabolites using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Small Molecule Pathway Database (SMPDB) database., Results: The MR analysis revealed a total of 27 metabolites (16 known and 11 unknown) causally linked to the development and progression of sepsis. After applying the Bonferroni correction, 3-carboxy-4-methyl-5-propyl-2-furanpropanoate (CMPF) remained significant in relation to 28-day all-cause mortality in sepsis. By pathway enrichment analysis, we identified four significant metabolic pathways. Notably, the Alpha Linolenic Acid and Linoleic Acid metabolism pathway emerged as a pivotal contributor to the occurrence and progression of sepsis., Conclusion: This study provides preliminary evidence of causal associations between human blood metabolites and sepsis, as ascertained by MR analysis. The findings offer valuable insights into the pathogenesis of sepsis and may provide insight into preventive and therapeutic approaches., Competing Interests: The 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., (Copyright © 2023 Zhang, Yin, Chen, You, Zhang, Zhao, Ren, Wang, Chen and Zuo.)

Objective: Propofol-opioids are the most common drug combination and can reduce the dose of propofol and the incidence of adverse events in painless artificial abortion. We hypothesized that butorphanol may reduce the median effective dose (ED 50 ) of propofol, propofol injection pain, and postoperative uterine contraction pain., Methods: This was a randomized, double-blind, controlled study. A total of 54 female patients, who had ASA I or II, aged 18-49 years, undergoing painless artificial abortion, were randomly assigned into two groups, namely, Group P (propofol) and Group PB (propofol plus 10 μg/kg butorphanol). According to the pre-experiment, the initial dose of propofol for the P and PB groups was 3 and 2.5 mg/kg, respectively, with a dose gradient of 0.25 mg/kg. The ED 50 of propofol was analyzed using probit regression analysis. The total propofol dose consumed, recovery time, and anesthesia-related adverse events were also recorded., Results: There were 25 and 29 patients in the P and PB groups, respectively. The ED 50 (95% CI) of propofol for artificial abortion were 2.477 (2.186-2.737) and 1.555 (1.173-1.846) mg/kg in the P and PB groups, respectively. The total propofol dose consumed was (150.7 ± 21.7) mg and (110.4 ± 28.2) mg in the P and PB groups, respectively ( P < 0.001). Compared with the P group, injection-site pain (76 vs. 20.7%) and uterine contraction pain (72 vs. 6.9%) in the PB group had a significant decrease ( P < 0.001)., Conclusion: Combination of propofol with 10 μg/kg butorphanol reduced the ED 50 of propofol and decreased the incidence of propofol injection-site pain and postoperative uterine contraction pain during painless artificial abortion compared with propofol alone., Clinical Trial Registration: https://www.chictr.org.cn/showproj.html?proj=166610, identifier: ChiCTR2200059795., Competing Interests: The 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., (Copyright © 2023 Zheng, Huang, Mai, Li and Zhang.)

LC-MS based peptide mapping, i.e., proteolytic digestion followed by LC-MS/MS analysis, is the method of choice for protein primary structural characterization. Manual proteolytic digestion is usually a labor-intensive procedure. In this work, a novel method was developed for fully automated online protein digestion and LC-MS peptide mapping. The method generates LC-MS data from undigested protein samples without user intervention by utilizing the same HPLC system that performs the chromatographic separation with some additional modules. Each sample is rapidly digested immediately prior to its LC-MS analysis, minimizing artifacts that can grow over longer digestion times or digest storage times as in manual or automated offline digestion methods. In this report, we implemented the method on an Agilent 1290 Infinity II LC system equipped with a Multisampler. The system performs a complete digestion workflow including denaturation, disulfide reduction, cysteine alkylation, buffer exchange, and tryptic digestion. We demonstrated that the system is capable of digesting monoclonal antibodies and other proteins with excellent efficiency and is robust and reproducible and produces fewer artifacts than manually prepared digests. In addition, it consumes only a few micrograms of material as most of the digested sample protein is subjected to LC-MS analysis.

In recent years, many studies have attempted to clarify the formation, structure and biological function of migrasomes, which are defined as specialized organelles formed by the tips and intersections of Retraction Fibrils during cell migration. It has confirmed that migrasomes were involved in various critical biological processes and diseases, and has became a new research hotspot. In this paper, we reviewed the formation and biological functions of migrasomes, explored the relationship between migrasomes, tetraspanins and hepatocellular carcinoma and discussed the potential applications of migrasomes in hepatocellular carcinoma., Competing Interests: The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed., (© 2023 Zhongqi Zhang; Tianmiao Zhang; Rongcheng Zhang; Zhengbao Zhang; Shengkui Tan.)

LC-MS based multi-attribute methods (MAM) have drawn substantial attention due to their capability of simultaneously monitoring a large number of quality attributes of a biopharmaceutical product. For successful implementation of MAM, it is usually considered a requirement that the method is capable of detecting any new or missing peaks in the sample when compared to a control. Comparing a sample to a control for rare differences is also commonly practiced in many fields for investigational purpose. Because MS signal variability differs greatly between signals of different intensities, this type of comparison is often challenging, especially when the comparison is made without enough replicates. In this report we describe a statistical method for detecting rare differences between two very similar samples without replicate analyses. The method assumes that an overwhelming majority of components have equivalent abundance between the two samples, and signals with similar intensities have similar relative variability. By analyzing several monoclonal antibody peptide mapping datasets, we demonstrated that the method is suitable for new-peak detection for MAM as well as for other applications when rare differences between two samples need to be detected. The method greatly reduced false positive rate without a significant increase of false negative rate., Competing Interests: Declaration of competing interest None., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers., (© 2023. The Author(s).)

Introduction: Oligopeptides exhibit great prospects for clinical application and its separation is of great importance in new drug development. Methods: To accurately predict the retention of pentapeptides with analogous structures in chromatography, the retention times of 57 pentapeptide derivatives in seven buffers at three temperatures and four mobile phase compositions were measured via reversed-phase high-performance liquid chromatography. The parameters ( k H A , k A , and p K a ) of the acid-base equilibrium were obtained by fitting the data corresponding to a sigmoidal function. We then studied the dependence of these parameters on the temperature (T), organic modifier composition (φ, methanol volume fraction), and polarity ( P m N parameter). Finally, we proposed two six-parameter models with (1) pH and T and (2) pH and φ or P m N as the independent variables. These models were validated for their prediction capacities by linearly fitting the predicted retention factor k-value and the experimental k-value. Results: The results showed that log k H A and log k A exhibited linear relationships with 1 / T , φ or P m N for all pentapeptides, especially for the acid pentapeptides. In the model of pH and T, the correlation coefficient (R 2 ) of the acid pentapeptides was 0.8603, suggesting a certain prediction capability of chromatographic retention. Moreover, in the model of pH and φ or P m N , the R 2 values of the acid and neutral pentapeptides were greater than 0.93, and the average root mean squared error was approximately 0.3, indicating that the k-values could be effectively predicted. Discussion: In summary, the two six-parameter models were appropriate to characterize the chromatographic retention of amphoteric compounds, especially the acid or neutral pentapeptides, and could predict the chromatographic retention of pentapeptide compounds., Competing Interests: ZZ and JZ were employed by the company Active Protein and Polypeptide Engineering Center of Shaanxi Huikang Biotechnology Co., Ltd. XY was employed by the company Kangya of Ningxia Pharmaceutical Co., Ltd. The remaining 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., (Copyright © 2023 Peng, Yang, Fang, Zhang, Zhao, Zhao, Liu and Li.)

Objective: This study aimed to determine the optimal dose of propofol combined with esketamine to inhibit the response to gastroscope insertion in elderly patients. Methods: This is a prospective, non-controlled, non-randomized, single-center study. Elderly patients aged 65-80 years were enrolled in the study with the American society of anesthesiologists (ASA) physical status I or II undergoing elective gastroscopy. All patients were administered propofol after an intravenous esketamine at the dosage of 0.3 mg/kg 30 s, the subsequent dose of propofol was determined by the response of the previous patient to gastroscope insertion (choking, body movement, etc.) using Dixon's up-and-down method. The initial dose of propofol administered to the first elderly patient was 3.0 mg/kg, and the standard ratio of propofol dose in adjacent patients was 0.9. At least six crossover points were obtained before the conclusion of the study. By using Probit analysis the median effective dose (ED 50 ), 95% effective dose (ED 95 ), and the corresponding 95% confidence interval (CI) for propofol were determined. Results: The study continued until we obtained seven crossover points and 32 elderly patients (17 males and 15 females) were collected. The ED 50 of propofol combined with esketamine inhibiting response to gastroscope insertion in elderly patients were found to be 1.479 mg/kg (95% CI 1.331-1.592 mg/kg), and ED 95 was found to be 1.738 mg/kg (95% CI 1.614-2.487 mg/kg). Conclusion: According to the present study, propofol combined with 0.3 mg/kg esketamine is safe and effective for elderly patients undergoing gastroscopy. The ED 50 and ED 95 doses of propofol inhibiting response to gastroscope insertion in elderly patients when combined with 0.3 mg/kg esketamine were 1.479 and 1.738 mg/kg, respectively, without apparent adverse effects., Competing Interests: The 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., (Copyright © 2022 Zheng, Xu, Huang, Mai, Zhang and Zhang.)

T 1 contrasts obtained using short-TR incoherent steady state gradient echo (GRE) methods are generally suboptimal, to which non-T 1 factors in the signals play a major part. In this work, we proposed an augmented T 1 -weighted (aT 1 W) method to extract the signal ratio between routine GRE T 1 W and proton density-weighted signals that effectively removes the non-T 1 effects from the original T 1 W signals, including proton density, T 2 * decay, and coil sensitivity. A recently proposed multidimensional integration (MDI) technique was incorporated in the aT 1 W calculation for better signal-to-noise ratio (SNR) performance. For comparison between aT 1 W and T 1 W results, Monte Carlo noise analysis was performed via simulation and on scanned data, and region-of-interest (ROI) analysis and comparison was performed on the system phantom. For brain scans, the image contrast, noise behavior, and SNR of aT 1 W images were compared with routine GRE and inversion-recovery-based T 1 W images. The proposed aT 1 W method yielded saliently improved T 1 contrasts (potentially > 30% higher contrast-to-noise ratio [CNR]) than routine GRE T 1 W images. Good spatial homogeneity and signal consistency as well as high SNR/CNR were achieved in aT 1 W images using the MDI technique. For contrast-enhanced (CE) imaging, aT 1 W offered stronger post-CE contrast and better boundary delineation than T 1 MPRAGE images while using a shorter scan time., (© 2022 John Wiley & Sons, Ltd.)

During the development of a therapeutic protein, its quality attributes that pertain to the primary structure must be appropriately characterized, commonly by LC-MS/MS peptide mapping experiments. Extracting attribute information from LC-MS/MS data requires knowledge of the attribute of interest. Therefore, it is important to understand all potential modifications on the therapeutic proteins. In this work, we performed UV and visible light irradiation experiments on several therapeutic proteins, with or without the presence of a photosensitizer. Light-induced modifications were detected and characterized by tryptic digestion followed by LC-MS/MS analysis. A list of potential light-induced modifications, with their respective mass changes, was obtained. These modifications are primarily on methionine, tryptophan, histidine, cysteine, tyrosine and phenylalanine residues. Many of these modifications have not been previously reported on therapeutic proteins. Our findings therefore provide a database of potential light-induced modifications that would enable the routine characterization of light-induced modifications on therapeutic proteins., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

A stable molecular structure is important in the development of a protein candidate into a therapeutic product. A therapeutic protein often contains many different variants; some of them may have an impact on the conformational stability of the protein. Conventionally, to evaluate the impact of a variant on stability, the variant must be enriched to a reasonable purity, and then its stability characterized by chromatographic or biophysical techniques. However, it is often impractical to purify and characterize each variant in a therapeutic protein. A workflow, based on limited proteolysis followed by MS detection, was established to simultaneously assess the impact of a large number of variants on conformational stability without enrichment. Because a less stable domain is more susceptible to proteolytic degradation, conformational stability of the domain can be reported from the release rate of a proteolytic peptide. A kinetic model is established to quantitatively determine the extent of domain stabilization/destabilization of different variants. The methodology is demonstrated by examining variants known to affect the stability of immunoglobulin domains, such as different N -glycoforms, methionine oxidations, and sequence variants. With this methodology, near 100 variants may be evaluated within 2 days in a single experiment. Insights into the sequence-stability relationship will be obtained by monitoring the large number of low-level sequence variants, facilitating engineering of more stable molecules.

Soil acidification has always been a substantial eco-environmental problem restricting agricultural development in the red soil region of southern China. It is necessary to determine the dynamic change in soil pH in this area to formulate regional agricultural and environmental management measures. Yujiang County, a typical county with red soil acidification in southern China, was selected as the study area. Based on soil data from 1982, 2007, and 2018, the spatiotemporal variation characteristics and the latest changes in soil pH in the county were analyzed. The results show that the soil pH in Yujiang County decreased from 5.66 to 4.74 and then increased to 4.96 from 1982 to 2018, showing a trend of first decreasing and then increasing. According to the spatial distribution characteristics of soil pH, the low soil pH values in the three periods were mainly distributed in the northern mountainous areas with more forestland and dry land area and some southern hilly areas, while the paddy soil pH values in the middle low hilly areas were relatively higher. The soil pH decreased rapidly from 1982 to 2007, showing a large area of acidification. In 2007, the proportions of acidic (4.5 < pH < 5.5) and strongly acidic (pH < 4.5) soils increased by 67.37% and 10.6%, respectively, compared with that in 1982. However, from 2007 to 2018, the soil pH of the whole county increased, and the acidification trend was alleviated, which is of great significance to the regional red soil ecological environment. Through the analysis of the main factors affecting the change in soil pH, it was found that the sharp decline in soil pH in Yujiang County during 1982-2007 was mainly caused by acid rain and excessive nitrogen application. From 2007 to 2018, no significant reduction in nitrogen fertilizer in this area occurred, and although the increase in soil organic matter contributed to alleviating soil acidification, the analysis showed that the decrease in acid rain was the main reason for the rise in soil pH in Yujiang County. At the same time, notably, there is a large area of soil in the area that is still acidic, and effective control of soil acidification is still an important ecological and environmental issue in this area. In order to further improve the pH value of soil in red soil region, it is suggested that on the basis of continuous improvement of acid rain, in addition to increasing soil organic matter by returning straw to field and other measures, appropriate amount of lime or alkaline biochar can be applied to better improve the soil ecological environment in red soil hilly region.

Ketamine is widely used in infants and young children for anesthesia, and subanesthetic doses of ketamine make neurons form new protrusions and promote synapse formation. However, the precise pathological mechanisms remain to be elucidated. In this study, we demonstrated that ketamine administration significantly increased dendritic spine density and maturity in rat cortical neurons in vivo and in vitro. Western blot analysis showed that CRMP2 protein expression was significantly increased in cerebral cortex of ketamine group, and phosphorylation levels of CRMP at Thr514 and Ser522 were significantly reduced. Furthermore, overexpression of CRMP2 promoted the growth of cortical neuron processes and dendritic spines. Although the dendritic field was more complex after adding ketamine and the density of dendritic spines increased, there was no statistical difference and no obvious superposition effect was observed. Moreover, both Ser522 mutant construction of CRMP2, GFP-CRMP2-522D, and mcherry-CDK5 showed similar inhibitory effects on neurite outgrowth, which could be rescued by ketamine. The frequency and amplitude of miniature excitatory postsynaptic currents (mEPSCs) were significantly inhibited when GFP-CRMP2-522D and mCherry-CDK5 were transfected into cortical neurons and this trend could also be rescued by ketamine. In general, this study reveals a new mechanism by which ketamine promotes the growth and development of dendritic spines in developing cortical neurons.

Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.

Main Conclusion: GhVLN4 exhibited activity of cross-linking actin filaments into bundles. Overexpression of GhVLN4 increased the abundance of thick actin bundles and resulted in longer cell phenotypes. Actin bundle is a dynamic, higher-order cytoskeleton structure that is essential for cell expansion. Villin is one of the major proteins responsible for crosslinking actin filaments into bundles. However, this kind of actin binding protein has rarely been investigated in cotton. In the present work, a cotton villin gene was molecularly cloned from Upland cotton and denominated as GhVLN4. This gene was more highly expressed in fiber-bearing wild-type cotton TM-1 (Texas Marker-1) than in Ligon lintless-1 mutant (Li-1). Biochemical analysis combined with subcellular localization revealed that GhVLN4 is an actin-binding protein performing actin filament bundling activity in vitro. In line with these findings, a greater abundance of thick actin filament bundles were observed in GhVLN4-overexpressing transgenic plants compared with those in wild-type control. Moreover, ectopic expression of GhVLN4 significantly enhanced the cell length-width ratio of Schizosaccharomyces pombe yeast and increased the length of various Arabidopsis cells, including root cells, root hairs and pollen tubes. Taken together, our results demonstrate that GhVLN4 is involved in the generation of actin filament bundles, suggesting that GhVLN4 may play important roles in regulating plant cell morphogenesis and expansion by remodeling actin cytoskeleton.

High mannose (HM) glycan levels on secreted monoclonal antibodies can be influenced by external factors, including osmolality and copper deficiency, and by intrinsic factors determined by different cell lines. In order to identify the metabolic markers associated with HM glycan levels, metabolomics analysis was performed to assess the changes in the extracellular metabolites of recombinant cell lines at different time points during fed-batch production process. Ornithine was identified as the common metabolic marker influenced by both external and intrinsic factors when eight different medium conditions and eight different cell lines exhibiting different levels of HM were compared. A strong correlation was also observed between HM and mRNA expression levels of arginase 1, an enzyme that catalyzes the conversion of arginine to ornithine. The results from functional validation study showed that the supplementation of ornithine to the culture medium leads to an increased level of HM, while reduced concentration of spermine, a downstream product of ornithine metabolism, leads to a decreased level of HM. Additional metabolic markers correlating with HM glycan levels were identified from eight-cell line comparison analysis. A common feature shared by these identified markers is their previously described roles as contributors of cellular redox regulation., (Copyright © 2015 Elsevier B.V. All rights reserved.)