Protein-Protein Interaction Prediction via Structure-Based Deep Learning.

Protein-protein interactions (PPIs) play an essential role in life activities. Many artificial intelligence algorithms based on protein sequence information have been developed to predict PPIs. However, these models have difficulty dealing with various sequence lengths and suffer from low generalization and prediction accuracy. In this study, we proposed a novel end-to-end deep learning framework, RSPPI, combining residual neural network (ResNet) and spatial pyramid pooling (SPP), to predict PPIs based on the protein sequence physicochemistry properties and spatial structural information. In the RSPPI model, ResNet was employed to extract the structural and physicochemical information from the protein three-dimensional structure and primary sequence; the SPP layer was used to transform feature maps to a single vector and avoid the fixed-length requirement. The RSPPI model possessed excellent cross-species performance and outperformed several state-of-the-art methods based either on protein sequence or gene ontology in most evaluation metrics. The RSPPI model provides a novel strategy to develop an AI PPI prediction algorithm.

The mitochondrial carboxylase PCCA interacts with Listeria monocytogenes phospholipase PlcB to modulate bacterial survival.

Listeria monocytogenes, a prominent foodborne pathogen responsible for zoonotic infections, owes a significant portion of its virulence to the presence of the phospholipase PlcB. In this study, we performed an in-depth examination of the intricate relationship between L. monocytogenes PlcB and host cell mitochondria, unveiling a novel participant in bacterial survival: the mitochondrial carboxylase propionyl-coenzyme A carboxylase (PCCA). Our investigation uncovered previously unexplored levels of interaction and colocalization between PCCA and PlcB within host cells, with particular emphasis on the amino acids 504-508 of PCCA, which play a pivotal role in this partnership. To assess the effect of PCCA expression on L. monocytogenes proliferation, PCCA expression levels were manipulated by siRNA-si-PCCA or pCMV-N-HA-PCCA plasmid transfection. Our findings demonstrated a clear inverse correlation between PCCA expression levels and the proliferation of L. monocytogenes. Furthermore, the effect of L. monocytogenes infection on PCCA expression was investigated by assessing PCCA mRNA and protein expression in HeLa cells infected with L. monocytogenes. These results indicate that L. monocytogenes infection did not significantly alter PCCA expression. These findings led us to propose that PCCA represents a novel participant in L. monocytogenes survival, and its abundance has a detrimental impact on bacterial proliferation. This suggests that L. monocytogenes may employ PlcB-PCCA interactions to maintain stable PCCA expression, representing a unique pro-survival strategy distinct from that of other intracellular bacterial pathogens. IMPORTANCE: Mitochondria represent attractive targets for pathogenic bacteria seeking to modulate host cellular processes to promote their survival and replication. Our current study has uncovered mitochondrial carboxylase propionyl-coenzyme A carboxylase (PCCA) as a novel host cell protein that interacts with L. monocytogenes PlcB. The results demonstrate that PCCA plays a negative regulatory role in L. monocytogenes infection, as heightened PCCA levels are associated with reduced bacterial survival and persistence. However, L. monocytogenes may exploit the PlcB-PCCA interaction to maintain stable PCCA expression and establish a favorable intracellular milieu for bacterial infection. Our findings shed new light on the intricate interplay between bacterial pathogens and host cell mitochondria, while also highlighting the potential of mitochondrial metabolic enzymes as antimicrobial agents.

Investigation the mechanism of iron overload-induced colonic inflammation following ferric citrate exposure.

Iron overload occurs due to excessive iron intake compared to the body's demand, leading to iron deposition and impairment of multiple organ functions. Our previous study demonstrated that chronic oral administration of ferric citrate (FC) caused colonic inflammatory injury. However, the precise mechanism underlying this inflammatory response remains unclear. The current study aims to investigate the mechanism by which iron overload induced by FC exposure leads to colonic inflammation. To accomplish this, mice were orally exposed to three different concentrations of FC (71 mg/kg/bw (L), 143 mg/kg/bw (M) and 286 mg/kg/bw (H)) for continuous 16 weeks, with the control group receiving ultrapure water (C). Exposure to FC caused disturbances in the excretory system, altered colonic flora alpha diversity, and enriched pathogenic bacteria, such as Mucispirillum, Helicobacter, Desulfovibrio, and Shigella. These changes led to structural disorders of the colonic flora and an inflammatory response phenotype characterized by inflammatory cells infiltration, atrophy of intestinal glands, and irregular thickening of the intestinal wall. Mechanistic studies revealed that FC-exposure activated the NF-κB signaling pathway by up-regulating TLR4, MyD88, and NF-κB mRNA levels and protein expression. This activation resulted in increased production of pro-inflammatory cytokines, further contributing to the colonic inflammation. Additionally, in vitro experiments in SW480 cells confirmed the activation of NF-κB signaling pathway by FC exposure, consistent with the in vivo findings. The significance of this study lies in its elucidation of the mechanism by which iron overload caused by FC exposure leads to colonic inflammation. By identifying the role of pathogenic bacteria and the NF-κB signaling pathway, this study could potentially offer a crucial theoretical foundation for the research on iron overload, as well as provide valuable insights for clinical iron supplementation.

Physiological roles of human interleukin-17 family.

Interleukin-17 s (IL-17s) are well-known proinflammatory cytokines, and their antagonists perform excellently in the treatment of inflammatory skin diseases such as psoriasis. However, their physiological functions have not been given sufficient attention by clinicians. IL-17s can protect the host from extracellular pathogens, maintain epithelial integrity, regulate cognitive processes and modulate adipocyte activity through distinct mechanisms. Here, we present a systematic review concerning the physiological functions of IL-17s. Our goal is not to negate the therapeutic effect of IL-17 antagonists, but to ensure their safe use and reasonably explain the possible adverse events that may occur in their application.

Characterization and genomic analysis of a novel bacteriophage BUCT_49532 lysing Klebsiella pneumoniae.

Bacteriophages are a type of virus widely distributed in nature that demonstrates a remarkable aptitude for selectively recognizing and infecting bacteria. In particular, Klebsiella pneumoniae is acknowledged as a clinical pathogen responsible for nosocomial infections and frequently develops multidrug resistance. Considering the increasing prevalence of antibiotic-resistant bacteria, bacteriophages have emerged as a compelling alternative therapeutic approach. In this study, a novel phage named BUCT_49532 was isolated from sewage using K. pneumoniae K1119 as the host. Electron microscopy revealed that BUCT_49532 belongs to the Caudoviricetes class. Further analysis through whole genome sequencing demonstrated that BUCT_49532 is a Jedunavirus comprised of linear double-stranded DNA with a length of 49,532 bp. Comparative genomics analysis based on average nucleotide identity (ANI) values revealed that BUCT_49532 should be identified as a novel species. Characterized by a good safety profile, high environmental stability, and strong lytic performance, phage BUCT_49532 presents an interesting case for consideration. Although its host range is relatively narrow, its application potential can be expanded by utilizing phage cocktails, making it a promising candidate for biocontrol approaches.

TRIM67 Implicates in Regulating the Homeostasis and Synaptic Development of Mitral Cells in the Olfactory Bulb.

In recent years, olfactory dysfunction has attracted increasingly more attention as a hallmark symptom of neurodegenerative diseases (ND). Deeply understanding the molecular basis underlying the development of the olfactory bulb (OB) will provide important insights for ND studies and treatments. Now, with a genetic knockout mouse model, we show that TRIM67, a new member of the tripartite motif (TRIM) protein family, plays an important role in regulating the proliferation and development of mitral cells in the OB. TRIM67 is abundantly expressed in the mitral cell layer of the OB. The genetic deletion of TRIM67 in mice leads to excessive proliferation of mitral cells in the OB and defects in its synaptic development, resulting in reduced olfactory function in mice. Finally, we show that TRIM67 may achieve its effect on mitral cells by regulating the Semaphorin 7A/Plexin C1 (Sema7A/PlxnC1) signaling pathway.

ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells.

Alternative lengthening of telomeres (ALTs) mechanism is activated in some somatic, germ cells, and human cancer cells. However, the key regulators and mechanisms of the ALT pathway remain elusive. Here we demonstrated that ZBTB40 is a novel telomere-associated protein and binds to telomeric dsDNA through its N-terminal BTB (BR-C, ttk and bab) or POZ (Pox virus and Zinc finger) domain in ALT cells. Notably, the knockout or knockdown of ZBTB40 resulted in the telomere dysfunction-induced foci and telomere lengthening in the ALT cells. The results also show that ZBTB40 is associated with ALT-associated promyelocytic leukemia nuclear bodies, and the loss of ZBTB40 induces the accumulation of the ALT-associated promyelocytic leukemia nuclear bodies in U2OS cells. Taken together, our results implicate that ZBTB40 is a key player of telomere protection and telomere lengthening regulation in human ALT cells.

A Charge-Transfer-Induced Strategy for Enantioselective Discrimination by Potential-Regulated Surface-Enhanced Raman Scattering Spectroscopy.

A simple and efficient enantioselective discrimination method, especially the chirality-label-free discrimination method, for the recognition of chiral small molecules with high resolution and wide applicability has been urgently desired. Herein, achiral Au/p-aminothiophenol (PATP) substrates were prepared to link the enantiomers via coupling reactions for constructing the enantioselective discrimination system. The resultant Au/PATP/enantiomer systems displayed charge-transfer (CT)-induced surface-enhanced Raman scattering (SERS) spectra that offered distinguishable information for the systems with different chirality. The differentiated spectral signal can be amplified by regulating the applied electrode potential, leading to great enantioselective discrimination performance. Moreover, the relationship between the discrimination performance and the potential-regulated CT process was revealed by SERS, which enabled an accurate and effective enantiomeric determination for various chiral molecules, including aromatic and aliphatic small molecules. The aliphatic molecule with the shorter chain was discriminated with a higher resolution, since the longer-chain molecule in the discrimination system may cause a change in the molecular electronic structure of the PATP. In addition, the aromatic chiral molecule can be distinguished easier than the aliphatic molecules, which means that the generation of the conjugation of electrons in the aromatic molecule-involved enantiomeric systems facilitates CT-induced SERS discrimination. Our work provides guidance for the design and development of an effective enantioselective discrimination strategy with high discrimination performance in diverse application fields.

Characterization and Comparative Genomics Analysis of a New Bacteriophage BUCT610 against Klebsiella pneumoniae and Efficacy Assessment in Galleria mellonella Larvae.

The spread of multidrug-resistant Klebsiella pneumoniae (MDR-KP) has become an emerging threat as a result of the overuse of antibiotics. Bacteriophage (phage) therapy is considered to be a promising alternative treatment for MDR-KP infection compared with antibiotic therapy. In this research, a lytic phage BUCT610 was isolated from hospital sewage. The assembled genome of BUCT610 was 46,774 bp in length, with a GC content of 48%. A total of 83 open reading frames (ORFs) and no virulence or antimicrobial resistance genes were annotated in the BUCT610 genome. Comparative genomics and phylogenetic analyses showed that BUCT610 was most closely linked with the Vibrio phage pYD38-A and shared 69% homology. In addition, bacteriophage BUCT610 exhibited excellent thermal stability (4-75 °C) and broad pH tolerance (pH 3-12) in the stability test. In vivo investigation results showed that BUCT610 significantly increased the survival rate of Klebsiella pneumonia-infected Galleria mellonella larvae from 13.33% to 83.33% within 72 h. In conclusion, these findings indicate that phage BUCT610 holds great promise as an alternative agent with excellent stability for the treatment of MDR-KP infection.

Progress in the efficacy and mechanism of spinal cord stimulation in neuropathological pain.

Neuropathic pain (NP) is a long-term recurrent disease caused by somatosensory nervous system injury, with spontaneous pain, hyperalgesia, ectopic pain, and paresthesia as the main clinical manifestations. It adversely affects patients' quality of life. NP treatments often include medication, physical therapy, and invasive therapy; the first two therapies are generally ineffective for some NP patients. These patients sometimes rely on invasive therapy to alleviate pain. Spinal cord stimulation (SCS) is a very effective therapeutic method. SCS is a neuroregulatory method that involves placing the electrodes on the corresponding painful spinal cords. Pain is greatly alleviated after SCS. SCS has been proven to be an effective therapeutic method for the treatment of neurological pain. Furthermore, SCS provides a feasible approach for patients with unsuccessful drug treatment. This paper reviews the relevant literature of spinal cord electrical stimulation, focusing on the mechanism of action, clinical application, clinical efficacy and technical progress of spinal cord electrical stimulation. SCS is widely used in the treatment of NP diseases such as postherpetic neuralgia, back surgery failure syndrome, and phantom limb pain. With advancements in science and technology, tremendous progress has also been made in the spinal cord electrical stimulation method and good momentum has been maintained.

Heterogeneous Driving Factors of Carbon Emissions Embedded in China's Export: An Application of the LASSO Model.

With the steady growth of CO2 emissions embedded in trade, the driving forces of emissions have attracted extensive attention. Most of the literature has verified a bundle of the influential factors; however, further analyses are necessary to understand the predominant and heterogeneous driving factors in different economies and/or industries. Accordingly, by applying the multiregional input-output (MRIO) model, this article firstly evaluates the embodied carbon emissions of China's export from 1992 to 2020 in total volumes and by 14 industries. Then, the Least Absolute Shrinkage and Selection Operator (LASSO) estimations allow us to discover that urbanization, technology update and gross domestic product (GDP) are the leading three prioritizing factors in generating China's export emissions. Interestingly, this paper discovers that raising the proportion of female parliamentarians contributes to an abatement of emissions. Furthermore, the empirical results suggest that the heterogeneities of those factors do exist among industries. For example, the percentage of females in parliaments turns out to have a larger effect among labor-intensive industries only. In facing with rapid globalization and economic development of China, this paper provides important policy implications towards specific industries in terms of mitigating trade emissions. It guides policy-makers to achieve "carbon neutrality" by avoiding carbon leakage in net-export countries such as China.

A Galactosidase-Activatable Fluorescent Probe for Detection of Bacteria Based on BODIPY.

Pathogenic E. coli infection is one of the most widespread foodborne diseases, so the development of sensitive, reliable and easy operating detection tests is a key issue for food safety. Identifying bacteria with a fluorescent medium is more sensitive and faster than using chromogenic media. This study designed and synthesized a ß-galactosidase-activatable fluorescent probe BOD-Gal for the sensitive detection of E. coli. It employed a biocompatible and photostable 4,4-difluoro-3a,4a-diaza-s-indancene (BODIPY) as the fluorophore to form a ß-O-glycosidic bond with galactose, allowing the BOD-Gal to show significant on-off fluorescent signals for in vitro and in vivo bacterial detection. This work shows the potential for the use of a BODIPY based enzyme substrate for pathogen detection.

Nuclear Factor Related to KappaB Binding Protein (NFRKB) Is a Telomere-Associated Protein and Involved in Liver Cancer Development.

Alternative lengthening of telomeres (ALT) is a homologous recombination-based telomere maintenance mechanism activated in 10-15% of human cancers. Although significant progress has been made, the key regulators of the ALT pathway and its role in cancer development remain elusive. Bioinformatics methods were used to predict novel telomere-associated proteins (TAPs) by analysis of large-scale ChIP-Seq data. Immunostaining and fluorescence in situ hybridization experiments were applied to detect the subcellular location of target genes and telomeres. Western blot and reverse transcription-polymerase chain reaction (RT-PCR) were used to examine the expression of targeting genes. Overall survival (OS) analyses were used to evaluate the relationship between gene expression and survival time; immunohistochemistry was used to detect the distribution of target genes in liver cancer tissues. We found that nuclear factor related to kappaB binding protein (NFRKB), a metazoan-specific subunit of the INO80 complex, can associate with telomeres in human ALT cells. Loss of NFRKB induces dysfunction of telomeres and less PML bodies in U2OS cells. In addition, NFRKB is low/moderately expressed in cytoplasm of normal hepatocytes but heavily accumulating in the nucleus of liver cancer cells. Finally, the high expression of NFRKB is associated with short OS time and poor prognosis. NFRKB is a TAP and protects telomeres from DNA damage in ALT cells. It is highly expressed in hepatocellular carcinoma (HCC) cells and predicts a poor prognosis. NFRKB may be a promising prognostic biomarker for the treatment of HCC in the future.

Advances in clinical basic research: Performance, treatments, and mechanisms of Parkinson disease.

The loss of neuronal in the substantia nigra of the elderly contributes to striatal damage and plays a critical part in the common forms of neurodegenerative diseases such as Parkinson disease (PD). The deficit of dopamine is one of the most familiar neuropathological features of PD as well as α-Synuclein aggregation. The peripheral autonomic nervous system is also affected negatively during the course of the disease, although the subsistent of dyskinesias and else major motor characteristic deficits take significant role in the diagnostic methods during clinical practice, which is related to a number of non-motor symptoms that might increase aggregate risks. Multiple pathways and mechanisms are involved in the molecular pathogenesis: α-Synuclein, neuronal homeostasis, mitochondrial function, oxidative stress, as well as neuroinflammation. Investigations in the last few years for diagnostic biomarkers used neuroimaging, including single photon emission computed tomography  as well as cutting-edge magnetic resonance imaging techniques, which has been presented to facilitate discrepant diagnosis. Pharmacological treatment is also important and efficient in equal measure. In addition to reliance on striatal dopamine replacement therapy, many solutions that are used for motor or nonmotor symptoms in these patients are available.

Breakthroughs on the clinical management of headache and questions that need to be solved.

Headache is a common refractory disorder among adults, especially in females, which can lower the quality of life in patients and increase medical costs. Nearly 90% of people have been affected by headache disorders during their lifetime. The severe situation of headaches has drawn the attention of researchers in recent years. Although the mechanism of headache has not been fully understood by us, there are many effective preventive drugs and treatments available. This review is aimed to sum up the progress in clinical trials of headaches in the past 5 years.

Trade Impacts on Embodied Carbon Emissions-Evidence from the Bilateral Trade between China and Germany.

This article attempts to investigate the impacts of bilateral trade on the environment by estimating the embodied carbon emissions between China and Germany over the period 1999-2018. The above impacts are broadly explored in the literature both under the framework of theoretical and empirical analysis. However, there exist fewer empirical studies exploring the nonlinear relationship between trade volumes and carbon emissions between a well-developed and emerging economies. By applying the multiregional input-output (MRIO) model, this article aims to reveal the impacts of trade on the environment in the case of China-Germany. Specifically, trade amounts between China and Germany rank high with a similarly increasing trend and both of them are large net exporting countries. However, China experienced much larger carbon emissions embodied in its exports to Germany. Despite potential concerns on the carbon leakage issue of China from Germany, we find that the bilateral trades fit an inverse U-shape in the embodied carbon emissions, which suggests that the trade between the two countries can finally reduce carbon intensity without obstructing economic development particularly in the long-term. This paper guides policy-makers to quantify the issue of CO2 transfer among bilateral trades in order to achieve the target of trading sustainability.

BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS.

BACKGROUND: Whole genome bisulfite sequencing (WGBS) also known as BS-seq has been widely used to measure the methylation of whole genome at single-base resolution. One of the key steps in the assay is converting unmethylated cytosines into thymines (BS conversion). Incomplete conversion of unmethylated cytosines can introduce false positive methylation call. Developing a quick method to evaluate bisulfite conversion ratio (BCR) is benefit for both quality control and data analysis of WGBS. RESULTS: Here we provide a computational method named "BCREval" to estimate the unconverted rate (UCR) by using telomeric repetitive DNA as native spike-in control. We tested the method by using public WGBS data and found that it is very stable and most of BS conversion assays can achieve> 99.5% efficiency. The non-CpG DNA methylation at telomere fits a binomial model and may result from a random process with very low possibility (the ratio < 0.4%). And the comparison between BCREval and Bismark (Krueger and Andrews, Bioinformatics 27:1571-1572, 2011), a widely used BCR evaluator, suggests that our algorithm is much faster and more efficient than the latter. CONCLUSION: Our method is a simple but robust method to QC and speculates BCR for WGBS experiments to make sure it achieves acceptable level. It is faster and more efficient than current tools and can be easily integrated into presented WGBS pipelines.

Anomalous thermoelectricity in strained Bi2Te3 films.

Bi2Te3-based alloys have been intensively used for thermoelectric coolers and generators due to their high Seebeck coefficient S. So far, efforts to improve the S have been made mostly on changing the structures and components. Herein, we demonstrate an anomalous thermoelectricity in strained Bi2Te3 films, i.e., the value of S is obviously changed after reversing the direction of temperature gradient. Further theoretical and experimental analysis shows that it originates from the coupling of thermoelectric and flexoelectric effects caused by a stress gradient. Our finding provides a new avenue to adjust the S of Bi2Te3-based thermoelectric materials through flexoelectric polarization.

Role of the Wnt/ß-catenin signaling pathway in the response of chondrocytes to mechanical loading.

In order to better understand the mechanisms by which chondrocytes respond to mechanical stimulation, ATDC5 mouse embryonic carcinoma cells were induced to differentiate into chondrocytes and then exposed to mechanical loading. To specifically elucidate the role of this pathway, the localization and expression of proteins involved in the Wnt/ß-catenin signaling pathway were observed. Chondrogenic-differentiated ATDC5 cells were exposed to a 12% cycle tension load for 1, 2, 4, or 8 h. At each time point, immunofluorescence staining, western blot analysis, and qPCR were used to track the localization of ß-catenin and glycogen synthase kinase-3ß (GSK-3ß) expression. In addition, the mRNA expression of Wnt3a, disheveled homolog 1 (Dvl-1), GSK-3ß, and collagen type II were also detected. Activation of the Wnt/ß-catenin signaling pathway was investigated in cells treated with Dickkopf-related protein 1 (DKK-1). ß-catenin and GSK-3ß protein expression increased initially and then decreased over the mechanical loading period, and the corresponding mRNA levels followed a similar trend. After application of the inhibitor DKK-1, Wnt/ß­catenin signaling was suppressed, and the mRNA expression of collagen II was also reduced. Thus, stimulation of chondrocytes with mechanical strain loading is associated with the translocation of active ß-catenin from the cytoplasm to the nucleus.

Probing local surface conductance using current sensing atomic force microscopy.

We have analyzed correlations between surface morphology and current sensing images obtained using a current sensing atomic force microscope (CSAFM) and the implication of surface conductivity derived from the current sensing images. We found that in cases where the diameter of a CSAFM probe tip is much smaller than the correlation length of the surface morphological features, the current detected using the probe should have little correlation with the surface features imaged by the same probe. If the sample thickness is much larger than the tip size, the surface conductivity distribution of a sample can be derived from a current sensing image using the Holm resistance relation, and the current probed using a CSAFM reflects the conductance variations in a layer on the surface with the thickness comparable to the probe diameter. However, if the thickness of a sample is comparable to or smaller than the tip diameter, CSAFM measures the conductance across the entire portion of the sample sandwiched between the tip and the electrode.