L-Glycosidase-Cleavable Natural Glycans Facilitate the Chemical Synthesis of Correctly Folded Disulfide-Bonded D-Proteins.

D-peptide ligands can be screened for therapeutic potency and enzymatic stability using synthetic mirror-image proteins (D-proteins), but efficient acquisition of these D-proteins can be hampered by the need to accomplish their in vitro folding, which often requires the formation of correctly linked disulfide bonds. Here, we report the finding that temporary installation of natural O-linked-ß-N-acetyl-D-glucosamine (O-GlcNAc) groups onto selected D-serine or D-threonine residues of the synthetic disulfide-bonded D-proteins can facilitate their folding in vitro, and that the natural glycosyl groups can be completely removed from the folded D-proteins to afford the desired chirally inverted D-protein targets using naturally occurring O-GlcNAcase. This approach enabled the efficient chemical syntheses of several important but difficult-to-fold D-proteins incorporating disulfide bonds including the mirror-image tumor necrosis factor alpha (D-TNFα) homotrimer and the mirror-image receptor-binding domain of the Omicron spike protein (D-RBD). Our work establishes the use of O-GlcNAc to facilitate D-protein synthesis and folding and proves that D-proteins bearing O-GlcNAc can be good substrates for naturally occurring O-GlcNAcase.

An Enzyme-Cleavable Solubilizing-Tag Facilitates the Chemical Synthesis of Mirror-Image Proteins.

Mirror-image proteins (D-proteins) are useful in biomedical research for purposes such as mirror-image screening for D-peptide drug discovery, but the chemical synthesis of many D-proteins is often low yielding due to the poor solubility or aggregation of their constituent peptide segments. Here, we report a Lys-C protease-cleavable solubilizing tag and its use to synthesize difficult-to-obtain D-proteins. Our tag is easily installed onto multiple amino acids such as DLys, DSer, DThr, and/or the N-terminal amino acid of hydrophobic D-peptides, is impervious to various reaction conditions, such as peptide synthesis, ligation, desulfurization, and transition metal-mediated deprotection, and yet can be completely removed by Lys-C protease under denaturing conditions to give the desired D-protein. The efficacy and practicality of the new method were exemplified in the synthesis of two challenging D-proteins: D-enantiomers of programmed cell death protein 1 IgV domain and SARS-CoV-2 envelope protein, in high yield. This work demonstrates that the enzymatic cleavage of solubilizing tags under denaturing conditions is feasible, thus paving the way for the production of more D-proteins.

The Acyl-CoA Specificity of Human Lysine Acetyltransferase KAT2A.

Protein post-translational modifications serve to regulate a broad range of cellular functions including signal transduction, transcription, and metabolism. Protein lysine residues undergo many post-translational acylations and are regulated by a range of enzymes, such as histone acetyl transferases (HATs) and histone deacetylases (HDACs). KAT2A, well characterized as a lysine acetyltransferase for both histone and nonhistone substrates, has been reported to tolerate additional acyl-CoA substrates, such as succinyl-CoA, and shows nonacetyl transferase activity in specific biological contexts. In this work, we investigate the acyl-CoA substrate preference of KAT2A and attempt to determine whether and to what extent additional acyl-CoA substrates may be utilized by KAT2A in a cellular context. We show that while KAT2A can bind and utilize malonyl-CoA, its activity with succinyl-CoA or glutaryl-CoA is very weak, and acetylation is still the most efficient activity for KAT2A in vitro and in cells.

Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics.

Knowledge of therapeutic targets and early drug candidates is useful for improved drug discovery. In particular, information about target regulators and the patented therapeutic agents facilitates research regarding druggability, systems pharmacology, new trends, molecular landscapes, and the development of drug discovery tools. To complement other databases, we constructed the Therapeutic Target Database (TTD) with expanded information about (i) target-regulating microRNAs and transcription factors, (ii) target-interacting proteins, and (iii) patented agents and their targets (structures and experimental activity values if available), which can be conveniently retrieved and is further enriched with regulatory mechanisms or biochemical classes. We also updated the TTD with the recently released International Classification of Diseases ICD-11 codes and additional sets of successful, clinical trial, and literature-reported targets that emerged since the last update. TTD is accessible at http://bidd.nus.edu.sg/group/ttd/ttd.asp. In case of possible web connectivity issues, two mirror sites of TTD are also constructed (http://db.idrblab.org/ttd/ and http://db.idrblab.net/ttd/).

Anatomical knee variables result in worse outcomes of lateral meniscal allograft transplantation with discoid lateral menisci than with nondiscoid lateral menisci.

PURPOSE: To compare the clinical results of meniscal allograft transplantation (MAT) between patients with discoid lateral meniscus (DLM) and non-DLM (NDLM) and to analyse whether anatomical deformities cause worse clinical results in DLM patients. METHODS: Patients who underwent unilateral MAT from 2005 to 2017, including 115 patients with DLMs or NDLMs, were included in this study. Clinical outcomes [International Knee Documentation Committee (IKDC) scores, Lysholm scores, Tegner scores, and visual analogue scale (VAS) scores] and radiographic and MRI data were assessed. Clinical outcomes and anatomical knee variables were analysed by multivariate stepwise regression. RESULTS: After more than 2 years of follow-up, 9 patients were lost to follow-up, and 59 patients with DLM and 47 patients with NDLM were included. The mean postoperative results were significantly better than the preoperative data (P < 0.05) in both the DLM and NDLM groups. In addition, postoperative IKDC, Lysholm, and VAS scores but not Tegner scores were better in the NDLM group than in the DLM group. Several anatomical knee variables differed significantly between the NDLM and DLM groups and were associated with MAT outcomes. The condylar prominence ratio of the lateral and medial femoral condyles adjacent to the intercondylar notch and squaring of the lateral femoral condyle (the distance of the straight articular condylar surface) were independent factors significantly correlated with the Lysholm scores for MAT at last follow-up. CONCLUSION: MAT improved knee function in both patients with DLM and patients with NDLM, but patients NDLM had better clinical outcomes than patients with DLM. The condylar prominence ratio and squaring of the lateral femoral condyle may underlie this result. LEVEL OF EVIDENCE: III.

Integrating Target-Triggered Aptamer-Capped HRP@Metal-Organic Frameworks with a Colorimeter Readout for On-Site Sensitive Detection of Antibiotics.

Colorimetric analytical strategies exhibit great promise in developing on-site detection methods for antibiotics, while substantial recent research efforts remain problematic due to dissatisfactory sensitivity. Taking this into account, we develop a novel colorimetric sensor for in-field detection of antibiotics by using aptamer (Apt)-capped and horseradish peroxidise (HRP)-embedded zeolitic metal azolate framework-7 (MAF-7) (Apt/HRP@MAF-7) as target recognition and signal transduction, respectively. With the substrate 3,3',5,5'-tetramethylbenzidine (TMB)-impregnated chip attached on the lid, the assay can be conveniently operated in a tube and reliably quantified by a handheld colorimeter. Hydrophilic MAF-7 can not only prevent HRP aggregation but also enhance HRP activity, which would benefit its detection sensitivity. Besides, the catalytic activity of HRP@MAF-7 can be sealed through assembling with Apt and controllably released based on the bioresponsivity via forming target-Apt complexes. Consequently, a significant color signal can be observed owing to the oxidation of colorless TMB to its blue-green oxidized form oxTMB. As a proof-of-concept, portable detection of streptomycin was favorably achieved with excellent sensitivity, which is superior to most reported methods and commercial kits. The developed strategy affords a new design pattern for developing on-site antibiotics assays and immensely extends the application of enzyme embedded metal-organic framework composites.

Excitation of graphene surface plasmons polaritons by guided-mode resonances with high efficiency.

An Otto-like configuration for the excitation of graphene surface plasmon polaritons (GSPPs) is proposed. The configuration is composed of a metallic grating-dielectric-waveguide structure and a monolayer graphene with a subwavelength vacuum gap between them. The evanescent field located at the bottom surface of the dielectric waveguide corresponding to grating-coupled guided-mode resonances (GMRs) is utilized to efficiently excite the highly confined GSPPs. The finite difference time domain method is used to investigate the behaviors of the GMR-GSPP hybrid modes. The dispersion relations of GMRs and GSPPs are calculated and the numerical results further identify the excitation of GMR-GSPP hybrid modes. By changing the gap between the graphene layer and the bottom of the dielectric waveguide and the Fermi energy of graphene, the resonant frequencies of GMR-GSPP hybrid modes can be continuously tuned. When the optimized excitation condition is satisfied, the maximum energy enhancement factor in the gap can reach about 500 at the resonant frequencies. The proposed structure can be used to realize highly sensitive, compatible with planar fabrication technology, and electrically (mechanically) tunable sensors.

Late-Stage Peptide Macrocyclization by Palladium-Catalyzed Site-Selective C-H Olefination of Tryptophan.

Transition-metal-catalyzed C-H activation has shown potential in the functionalization of peptides with expanded structural diversity. Herein, the development of late-stage peptide macrocyclization methods by palladium-catalyzed site-selective C(sp2 )-H olefination of tryptophan residues at the C2 and C4 positions is reported. This strategy utilizes the peptide backbone as endogenous directing groups and provides access to peptide macrocycles with unique Trp-alkene crosslinks.

Tracing the Dynamic Changes of Element Profiles by Novel Soil Porewater Samplers with Ultralow Disturbance to Soil-Water Interface.

In flooded soils, soil-water interface (SWI) is the key zone controlling biogeochemical dynamics. Chemical species and concentrations vary greatly at micro- to cm-scales. Techniques able to track these changing element profiles both in space and over time with appropriate resolution are rare. Here, we report a patent-pending technique, the Integrated Porewater Injection (IPI) sampler, which is designed for soil porewater sampling with minimum disturbance to saturated soil environment. IPI sampler employs a single hollow fiber membrane tube to passively sample porewater surrounding the tube. When working, it can be integrated into the sample introduction system, thus the sample preparation procedure is dramatically simplified. In this study, IPI samplers were coupled to ICP-MS at data-only mode. The limits of detection of IPI-ICP-MS for Ni, As, Cd, Sb, and Pb were 0.12, 0.67, 0.027, 0.029, and 0.074 µg·L-1, respectively. Furthermore, 25 IPI samplers were assembled into an SWI profiler using 3D printing in a one-dimensional array. The SWI profiler is able to analyze element profiles at high spatial resolution (∼2 mm) every ≥24 h. When deployed in arsenic-contaminated paddy soils, it depicted the distributions and dynamics of multiple elements at anoxic-oxic transition. The results show that the SWI profiler is a powerful and robust technique in monitoring dynamics of element profile in soil porewater at high spatial resolution. The method will greatly facilitate studies of elements behaviors in sediments of wetland, rivers, lakes, and oceans.

Compound Heterozygosity for an Unstable Novel Hemoglobin Variant, Hb Dongguan [α52(E1)Ser→Cys (TCT>TGT); HBA1: c.158C>G], and the - -SEA (Southeast Asian) α-Thalassemia Deletion.

Here we report a 67-year-old Chinese male carrying an unstable novel hemoglobin (Hb) variant in compound heterozygosity with the - -SEA (Southeast Asian) α-thalassemia (α-thal) deletion. Hemoglobin analysis by capillary electrophoresis (CE) revealed a rapid degradation feature of the variant. Sanger sequencing of the Hb gene revealed a novel homozygous mutation in exon 2 of the α1-globin gene [α52(E1)Ser→Cys (TCT>TGT); HBA1: c.158C>G]. We named this novel variant Hb Dongguan for the place of origin of the proband. Additionally, gap-polymerase chain reaction (gap-PCR) indicated the presence of the heterozygous - -SEA α-thal deletion.

CSEL-BGC: A Bioinformatics Framework Integrating Machine Learning for Defining the Biosynthetic Evolutionary Landscape of Uncharacterized Antibacterial Natural Products.

The sluggish pace of new antibacterial drug development reflects a vulnerability in the face of the current severe threat posed by bacterial resistance. Microbial natural products (NPs), as a reservoir of immense chemical potential, have emerged as the most promising avenue for the discovery of next generation antibacterial agent. Directly accessing the antibacterial activity of potential products derived from biosynthetic gene clusters (BGCs) would significantly expedite the process. To tackle this issue, we propose a CSEL-BGC framework that integrates machine learning (ML) techniques. This framework involves the development of a novel cascade-stacking ensemble learning (CSEL) model and the establishment of a groundbreaking model evaluation system. Based on this framework, we predict 6,666 BGCs with antibacterial activity from 3,468 complete bacterial genomes and elucidate a biosynthetic evolutionary landscape to reveal their antibacterial potential. This provides crucial insights for interpretating the synthesis and secretion mechanisms of unknown NPs.

High-resolution short-term prediction of the COVID-19 epidemic based on spatial-temporal model modified by historical meteorological data.

In the global challenge of Coronavirus disease 2019 (COVID-19) pandemic, accurate prediction of daily new cases is crucial for epidemic prevention and socioeconomic planning. In contrast to traditional local, one-dimensional time-series data-based infection models, the study introduces an innovative approach by formulating the short-term prediction problem of new cases in a region as multidimensional, gridded time series for both input and prediction targets. A spatial-temporal depth prediction model for COVID-19 (ConvLSTM) is presented, and further ConvLSTM by integrating historical meteorological factors (Meteor-ConvLSTM) is refined, considering the influence of meteorological factors on the propagation of COVID-19. The correlation between 10 meteorological factors and the dynamic progression of COVID-19 was evaluated, employing spatial analysis techniques (spatial autocorrelation analysis, trend surface analysis, etc.) to describe the spatial and temporal characteristics of the epidemic. Leveraging the original ConvLSTM, an artificial neural network layer is introduced to learn how meteorological factors impact the infection spread, providing a 5-day forecast at a 0.01° × 0.01° pixel resolution. Simulation results using real dataset from the 3.15 outbreak in Shanghai demonstrate the efficacy of Meteor-ConvLSTM, with reduced RMSE of 0.110 and increased R 2 of 0.125 (original ConvLSTM: RMSE = 0.702, R 2 = 0.567; Meteor-ConvLSTM: RMSE = 0.592, R 2 = 0.692), showcasing its utility for investigating the epidemiological characteristics, transmission dynamics, and epidemic development.

Clinical feasibility of laparoscopic left lateral segment liver resection with magnetic anchor technique: The first clinical study from China.

BACKGROUND: Magnetic anchor technique (MAT) has been applied in laparoscopic cholecystectomy and laparoscopic appendectomy, but has not been reported in laparoscopic partial hepatectomy. AIM: To evaluate the feasibility of the MAT in laparoscopic left lateral segment liver resection. METHODS: Retrospective analysis was conducted on the clinical data of eight patients who underwent laparoscopic left lateral segment liver resection assisted by MAT in our department from July 2020 to November 2021. The Y-Z magnetic anchor devices (Y-Z MADs) was independently designed and developed by the author of this paper, which consists of the anchor magnet and magnetic grasping apparatus. Surgical time, intraoperative blood loss, intraoperative accidents, operator experience, postoperative incision pain score, postoperative complications, and other indicators were evaluated and analyzed. RESULTS: All eight patients underwent a MAT-assisted laparoscopic left lateral segment liver resection, including three patients undertaking conventional 5-port and five patients having a transumbilical single-port operation. The mean operation time was 138 ± 34.32 min (range 95-185 min) and the mean intraoperative blood loss was 123 ± 88.60 mL (range 20-300 mL). No adverse events occurred during the operation. The Y-Z MADs showed good workability and maneuverability in both tissue and organ exposure. In particular, the operators did not experience either a "chopstick" or "sword-fight" effect in the single-port laparoscopic operation. CONCLUSION: The results show that the MAT is safe and feasible for laparoscopic left lateral segment liver resection, especially, exhibits its unique abettance for transumbilical single-port laparoscopic left lateral segment liver resection.

EZH2/G9a interact to mediate drug resistance in non-small-cell lung cancer by regulating the SMAD4/ERK/c-Myc signaling axis.

Drug resistance is the leading problem in non-small-cell lung cancer (NSCLC) therapy. The contribution of histone methylation in mediating malignant phenotypes of NSCLC is well known. However, the role of histone methylation in NSCLC drug-resistance mechanisms remains unclear. Here, our data show that EZH2 and G9a, two histone methyltransferases, are involved in the drug resistance of NSCLC. Gene manipulation results indicate that the combination of EZH2 and G9a promotes tumor growth and mediates drug resistance in a complementary manner. Importantly, clinical study demonstrates that co-expression of both enzymes predicts a poor outcome in patients with NSCLC. Mechanistically, G9a and EZH2 interact and promote the silencing of the tumor-suppressor gene SMAD4, activating the ERK/c-Myc signaling pathway. Finally, SU08, a compound targeting both EZH2 and G9a, is demonstrated to sensitize resistant cells to therapeutic drugs by regulating the SMAD4/ERK/c-Myc signaling axis. These findings uncover the resistance mechanism and a strategy for reversing NSCLC drug resistance.

SpyDirect: A Novel Biofunctionalization Method for High Stability and Longevity of Electronic Biosensors.

Electronic immunosensors are indispensable tools for diagnostics, particularly in scenarios demanding immediate results. Conventionally, these sensors rely on the chemical immobilization of antibodies onto electrodes. However, globular proteins tend to adsorb and unfold on these surfaces. Therefore, self-assembled monolayers (SAMs) of thiolated alkyl molecules are commonly used for indirect gold-antibody coupling. Here, a limitation associated with SAMs is revealed, wherein they curtail the longevity of protein sensors, particularly when integrated into the state-of-the-art transducer of organic bioelectronics-the organic electrochemical transistor. The SpyDirect method is introduced, generating an ultrahigh-density array of oriented nanobody receptors stably linked to the gold electrode without any SAMs. It is accomplished by directly coupling cysteine-terminated and orientation-optimized spyTag peptides, onto which nanobody-spyCatcher fusion proteins are autocatalytically attached, yielding a dense and uniform biorecognition layer. The structure-guided design optimizes the conformation and packing of flexibly tethered nanobodies. This biolayer enhances shelf-life and reduces background noise in various complex media. SpyDirect functionalization is faster and easier than SAM-based methods and does not necessitate organic solvents, rendering the sensors eco-friendly, accessible, and amenable to scalability. SpyDirect represents a broadly applicable biofunctionalization method for enhancing the cost-effectiveness, sustainability, and longevity of electronic biosensors, all without compromising sensitivity.

The study on the effect of mercury pollution on soil microorganisms around mercury mining area.

In order to further explore the effects of soil mercury pollution on soil microbial diversity and community structure, soil samples were randomly collected from 2 m, 20 m, 30 m, 500 m and 650 m periphery of Wanshan mining area, as 5 different treatments. Each treatment had 4 replicates. Soil microbial DNA was extracted from 20 soil samples, and then high-throughput sequencing technology was used to analyse the structure and distribution of bacterial and fungal communities. The results showed that the number of bacterial and fungal communities in T0-T30 treatments was significantly larger than that in T500-T650 treatments at order, family and genus level. Whatever, the number of uniquely distributed bacterial and fungal communities among 4 replicates soil samples was quite different at order, family and genus level. The results of the effect on the microbial community structure showed that there were both the same dominant bacterial and fungal communities, and the different dominant bacterial and fungal communities at any classification level, moreover, the number of same dominant bacterial and fungal communities was larger than that of different dominant bacterial and fungal communities. The results of relationship between soil environment factors and bacterial and fungal community structure showed that distance (Hg2+), EC and pH had a high correlation with community structure, especially the distance factor, that is, the content of mercury in soil had the highest effects on community structure. The internal heterogeneity of soil caused significant differences in bacterial and fungal community structure, and the emergence of dominant bacterial and fungal communities was a manifestation of better adaptability to long-term mercury stress and other stresses in soil, which will provide a scientific reference for further exploring the mechanism of mercury enrichment between microorganisms and plants.

Clinical application of magnetic anchor technique in laparoscopic cholecystectomy: the first retrospective study in China.

Background and objectives: Magnetic anchor technique (MAT) is frequently used in laparoscopic cholecystectomy. However, there are few reports on its clinical application in China. In this study, we retrospectively analyzed the clinical application of MAT in laparoscopic cholecystectomy in China. Materials and methods: 25 patients (4 males, 21 females) who underwent laparoscopic cholecystectomy assisted by MAT at the First Affiliated Hospital of Xi'an Jiaotong University were enrolled from November 2020 to March 2021. Their records were retrospectively analyzed. The magnetic anchor device was independently designed and developed by the authors and consisted of the anchor magnet and magnetic grasping apparatus. Surgical time, intraoperative blood loss, intraoperative accidents, operator experience, postoperative incision pain score, postoperative complications, and other indicators were evaluated and analyzed. Results: All patients successfully underwent laparoscopic cholecystectomy, including 3 cases of MAT-assisted transumbilical single-port LC, 16 cases of MAT-assisted 2-port LC and 6 cases of conventional 3-port LC. The median operation time was 50 min (range 30-95 min); intraoperative bleeding was less than 30 ml. The median score of surgical incision on day 1 and 3 after the operation was 3 (range 1-4) and 1 (range 1-3), respectively. All patients had no intraoperative bile duct injury, vascular injury, postoperative bleeding, bile leakage, biliary stricture and other complications. No adverse events (such as injury to adjacent organs or failure of the magnetic anchor device) occurred either during or after the operation. Conclusions: The MAT-assisted laparoscopic cholecystectomy appears to be safe, feasible and effective and exhibits unique assistance in transumbilical single-port laparoscopic cholecystectomy.

The pattern of collagen production may contribute to the gluteal muscle contracture pathogenic process.

INTRODUCTION: Arthroscopic release is now the gold standard globally for gluteal muscle contracture (GMC) treatment. However, some patients fail to improve after the first operation and are forced to undergo a second operation. This study explores the essential role collagen fibers may play in muscle contracture in GMC. METHODS: From February 2010 to May 2018, 1041 hips of 543 GMC patients underwent arthroscopic release. Among them, 498 (91.7%) patients had bilateral GMC and were admitted to the retrospective cohort study. Pathological testing and type III collagen testing were used in contracture tissue studies. Single-cell RNA-sequencing analysis was applied to explore the role of fibroblasts in muscle repair. RESULTS: Compared with GMC II patients, GMC III patients displayed higher clinical symptoms (P < 0.05). Six weeks after the surgery, the patients in GMC II had a lower prominent hip snap rate, higher JOA score, and better hip range of motion (P < 0.05). Compared with normal muscle tissue, contracture-affected tissue tended to have more type III collagen and form shorter fibers. Recurrent GMC patients seemed to have a higher type III collagen ratio (P < 0.05). In contrast to normally repairable muscle defects, fibroblasts in non-repairable defects were shown to downregulate collagen-related pathways at the early and late stages of tissue repair. DISCUSSION: This study describes the arthroscopic release of GMC. Study findings include the suggestion that the collagen secretion function of fibroblasts and collagen pattern might influence the muscle repair ability and be further involved in the GMC pathogenic process.

Magnetic anchor technique assisted laparoscopic cholecystectomy in swine.

Magnetic anchor device based on the principle of magnet heteropolar attraction can assist laparoscopic surgery and reduce abdominal wall trauma. This study explored the feasibility of use of our self-designed magnetic anchor device for reduced-port laparoscopic cholecystectomy (LC) through animal experiments. Twelve experimental pigs (15-20 kg) were randomly divided into study group (magnetic anchor technique assisted 2-port LC, n = 6) and control group (conventional 3-port LC, n = 6). Operative time, intraoperative blood loss, and postoperative complications were compared between the two groups. LC was successfully performed in all 12 pigs. There was no significant between-group difference with respect to operative time (study group: 35.83 ± 5.12 min; control group: 34.50 ± 5.13 min, P = 0.662) or intraoperative blood loss (< 50 mL per animal in both groups). In the experimental group, there was no malfunction of the magnetic anchoring device, the use process was smooth, and the tissue traction and surgical field exposure were satisfactory. There were no perioperative complications such as bile duct injury, bile leakage, or bleeding in both groups. We demonstrated the feasibility of use of the self-designed magnetic anchor device in reduced-port LC. The device has important clinical application value.