Complement in breast milk modifies offspring gut microbiota to promote infant health.

Breastfeeding offers demonstrable benefits to newborns and infants by providing nourishment and immune protection and by shaping the gut commensal microbiota. Although it has been appreciated for decades that breast milk contains complement components, the physiological relevance of complement in breast milk remains undefined. Here, we demonstrate that weanling mice fostered by complement-deficient dams rapidly succumb when exposed to murine pathogen Citrobacter rodentium (CR), whereas pups fostered on complement-containing milk from wild-type dams can tolerate CR challenge. The complement components in breast milk were shown to directly lyse specific members of gram-positive gut commensal microbiota via a C1-dependent, antibody-independent mechanism, resulting in the deposition of the membrane attack complex and subsequent bacterial lysis. By selectively eliminating members of the commensal gut community, complement components from breast milk shape neonate and infant gut microbial composition to be protective against environmental pathogens such as CR.

RVdb: a comprehensive resource and analysis platform for rhinovirus research.

Rhinovirus (RV), a prominent causative agent of both upper and lower respiratory diseases, ranks among the most prevalent human respiratory viruses. RV infections are associated with various illnesses, including colds, asthma exacerbations, croup and pneumonia, imposing significant and extended societal burdens. Characterized by a high mutation rate and genomic diversity, RV displays a diverse serological landscape, encompassing a total of 174 serotypes identified to date. Understanding RV genetic diversity is crucial for epidemiological surveillance and investigation of respiratory diseases. This study introduces a comprehensive and high-quality RV data resource, designated RVdb (http://rvdb.mgc.ac.cn), covering 26 909 currently identified RV strains, along with RV-related sequences, 3D protein structures and publications. Furthermore, this resource features a suite of web-based utilities optimized for easy browsing and searching, as well as automatic sequence annotation, multiple sequence alignment (MSA), phylogenetic tree construction, RVdb BLAST and a serotyping pipeline. Equipped with a user-friendly interface and integrated online bioinformatics tools, RVdb provides a convenient and powerful platform on which to analyse the genetic characteristics of RVs. Additionally, RVdb also supports the efforts of virologists and epidemiologists to monitor and trace both existing and emerging RV-related infectious conditions in a public health context.

A deep learning method to predict bacterial ADP-ribosyltransferase toxins.

MOTIVATION: ADP-ribosylation is a critical modification involved in regulating diverse cellular processes, including chromatin structure regulation, RNA transcription, and cell death. Bacterial ADP-ribosyltransferase toxins (bARTTs) serve as potent virulence factors that orchestrate the manipulation of host cell functions to facilitate bacterial pathogenesis. Despite their pivotal role, the bioinformatic identification of novel bARTTs poses a formidable challenge due to limited verified data and the inherent sequence diversity among bARTT members. RESULTS: We proposed a deep learning-based model, ARTNet, specifically engineered to predict bARTTs from bacterial genomes. Initially, we introduced an effective data augmentation method to address the issue of data scarcity in training ARTNet. Subsequently, we employed a data optimization strategy by utilizing ART-related domain subsequences instead of the primary full sequences, thereby significantly enhancing the performance of ARTNet. ARTNet achieved a Matthew's correlation coefficient (MCC) of 0.9351 and an F1-score (macro) of 0.9666 on repeated independent test datasets, outperforming three other deep learning models and six traditional machine learning models in terms of time efficiency and accuracy. Furthermore, we empirically demonstrated the ability of ARTNet to predict novel bARTTs across domain superfamilies without sequence similarity. We anticipate that ARTNet will greatly facilitate the screening and identification of novel bARTTs from bacterial genomes. AVAILABILITY: ARTNet is publicly accessible at http://www.mgc.ac.cn/ARTNet/. The source code of ARTNet is freely available at https://github.com/zhengdd0422/ARTNet/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Nanochannel Stability of Chemically Converted Graphene Oxide Membranes.

Chemically converted graphene oxide laminate membranes, which exhibit stable interlayered nanochannels in aqueous environments, are receiving increasing attention owing to their potential for selective water and ion permeation. However, how the molecular properties of conversion agents influence the stabilization of nanochannels and how effectively nanochannels are stabilized have rarely been studied. In this study, mono-, di-, and tri-saccharide molecules of glucose (Glu), maltose (Glu2), and maltotriose (Glu3) are utilized, respectively, to chemically modify graphene oxide (GO). The aim is to create nanochannels with different levels of stability and investigate how these functional conversion agents affect the separation performance. The effects of the property differences between different conversion agents on nanochannel stabilization are demonstrated. An agent with efficient chemical reduction of GO and limited intercalation in the resulting nanochannel ensures satisfactory nanochannel stability during desalination. The stabilized membrane nanochannel exhibits a permeance of 0.69 L m-2 h-1 bar-1 and excellent Na2SO4 rejection of 96.42%. Furthermore, this optimized membrane nanochannel demonstrates enhanced stability under varying external conditions compared to the original GO. This study provides useful information for the design of chemical conversion agents for GO nanochannel stabilization and the development of nanochannel membranes for precise separation.

Integrating plasma protein-centric multi-omics to identify potential therapeutic targets for pancreatic cancer.

BACKGROUND: Deciphering the role of plasma proteins in pancreatic cancer (PC) susceptibility can aid in identifying novel targets for diagnosis and treatment. METHODS: We examined the relationship between genetically determined levels of plasma proteins and PC through a systemic proteome-wide Mendelian randomization (MR) analysis utilizing cis-pQTLs from multiple centers. Rigorous sensitivity analyses, colocalization, reverse MR, replications with varying instrumental variable selections and additional datasets, as well as subsequent meta-analysis, were utilized to confirm the robustness of significant findings. The causative effect of corresponding protein-coding genes' expression and their expression pattern in single-cell types were then investigated. Enrichment analysis, between-protein interaction and causation, knock-out mice models, and mediation analysis with established PC risk factors were applied to indicate the pathogenetic pathways. These candidate targets were ultimately prioritized upon druggability and potential side effects predicted by a phenome-wide MR. RESULTS: Twenty-one PC-related circulating proteins were identified in the exploratory phase with no evidence for horizontal pleiotropy or reverse causation. Of these, 11 were confirmed in a meta-analysis integrating external validations. The causality at a transcription level was repeated for neutrophil elastase, hydroxyacylglutathione hydrolase, lipase member N, protein disulfide-isomerase A5, xyloside xylosyltransferase 1. The carbohydrate sulfotransferase 11 and histo-blood group ABO system transferase exhibited high-support genetic colocalization evidence and were found to affect PC carcinogenesis partially through modulating body mass index and type 2 diabetes, respectively. Approved drugs have been established for eight candidate targets, which could potentially be repurposed for PC therapies. The phenome-wide investigation revealed 12 proteins associated with 51 non-PC traits, and interference on protein disulfide-isomerase A5 and cystatin-D would increase the risk of other malignancies. CONCLUSIONS: By employing comprehensive methodologies, this study demonstrated a genetic predisposition linking 21 circulating proteins to PC risk. Our findings shed new light on the PC etiology and highlighted potential targets as priorities for future efforts in early diagnosis and therapeutic strategies of PC.

The association between the basal metabolic rate and cardiovascular disease: A two-sample Mendelian randomization study.

BACKGROUND: Mendelian randomization analysis was applied to elucidate the causal relationship between the basal metabolic rate (BMR) and common cardiovascular diseases. METHOD: We choose BMR as exposure. BMR is the metabolic rate of the body when the basic physiological activities (blood circulation, breathing and constant body temperature) are maintained. The normal BMR is 1507 kcal/day for men and 1276 kcal/day for women. The dataset was drawn from the public GWAS dataset (GWAS ID: ukb-a-268), collected and analysed by UK biobank, containing 331,307 European males and females. SNPs independently and strongly associated with BMR were used as instrumental variables in the inverse variance weighted analysis. MR-Egger, weighted median, MR pleiotropy residual sum, and outlier methods were also performed, and the sensitivity was evaluated using horizontal pleiotropy and heterogeneity analyses to ensure the stability of the results. RESULTS: An increased BMR is associated with a higher risk of cardiomyopathy (odds ratio [OR] = 2.00, 95% confidence interval [CI], 1.57-2.54, p = 1.87 × 10-8), heart failure (OR = 1.39, 95% CI, 1.27-2.51, p = 8.1 × 10-13), and valvular heart disease (OR = 1.18, 95% CI, 1.10-1.27, p = .00001). However, there was no clear association between BMR and the subtypes of other cardiovascular diseases, such as coronary disease (OR = .96, 95% CI, .85-1.08, p = .48651) and atrial fibrillation (AF) (OR = 1.85, 95% CI, 1.70-2.02, p = 6.28 × 10-44). CONCLUSION: Our study reveals a possible causal effect of BMR on the risk of cardiomyopathy, heart failure and valvular disease, but not for coronary disease and AF.

Two-dimensional angle measurement with sub-arcsecond precision and MHz update rate using heterodyne interferometry with optical frequency comb.

Heterodyne interferometry is a powerful tool for achieving high precision and fast measurement. We developed an angle measurement system based on heterodyne interferometry by combining discrete equal-spacing longitudinal modes of optical frequency comb with an acousto-optic modulator. Using a self-designed grating-corner-cube sensor, this method can achieve a two-dimensional angle measurement with sub-arcsecond accuracy and megahertz (MHz) update rate. We experimentally demonstrate a precision of 0.073 arcsec under a 3 MHz update rate, and comparison residuals are kept within 0.063 arcsec over 300 arcsec when compared to a piezo stage. In the dynamic measurement of a 40 Hz frequency, the continuous sinusoidal motion of 0.05 arcsec can be clearly distinguished and reconstructed.

Nesfatin-1: A Biomarker and Potential Therapeutic Target in Neurological Disorders.

Nesfatin-1 is a novel adipocytokine consisting of 82 amino acids with anorexic and anti-hyperglycemic properties. Further studies of nesfatin-1 have shown it to be closely associated with neurological disorders. Changes in nesfatin-1 levels are closely linked to the onset, progression and severity of neurological disorders. Nesfatin-1 may affect the development of neurological disorders and can indicate disease evolution and prognosis, thus informing the choice of treatment options. In addition, regulation of the expression or level of nesfatin-1 can improve the level of neuroinflammation, apoptosis, oxidative damage and other indicators. It is demonstrated that nesfatin-1 is involved in neuroprotection and may be a therapeutic target for neurological disorders. In this paper, we will also discuss the role of nesfatin-1 as a biomarker in neurological diseases and its potential mechanism of action in neurological diseases, providing new ideas for the diagnosis and treatment of neurological diseases.

Silencing of the T-type voltage-gated calcium channel α1 subunit by fungus-mediated RNAi altered the structure of F-actin and caused defective behaviors in Ditylenchus destructor.

BACKGROUND: T-type calcium channels, characterized as low-voltage activated (LVA) calcium channels, play crucial physiological roles across a wide range of tissues, including both the neuronal and nonneuronal systems. Using in situ hybridization and RNA interference (RNAi) techniques in vitro, we previously identified the tissue distribution and physiological function of the T-type calcium channel α1 subunit (DdCα1G) in the plant-parasitic nematode Ditylenchus destructor. METHODS AND RESULTS: To further characterize the functional role of DdCα1G, we employed a combination of immunohistochemistry and fungus-mediated RNAi and found that DdCα1G was clearly distributed in stylet-related tissue, oesophageal gland-related tissue, secretory-excretory duct-related tissue and male spicule-related tissue. Silencing DdCα1G led to impairments in the locomotion, feeding, reproductive ability and protein secretion of nematodes. To confirm the defects in behavior, we used phalloidin staining to examine muscle changes in DdCα1G-RNAi nematodes. Our observations demonstrated that defective behaviors are associated with related muscular atrophy. CONCLUSION: Our findings provide a deeper understanding of the physiological functions of T-type calcium channels in plant-parasitic nematodes. The T-type calcium channel can be considered a promising target for sustainable nematode management practices.

ZOVER: the database of zoonotic and vector-borne viruses.

Emerging infectious diseases significantly threaten global public health and socioeconomic security. The majority of emerging infectious disease outbreaks are caused by zoonotic/vector-borne viruses. Bats and rodents are the two most important reservoir hosts of many zoonotic viruses that can cross species barriers to infect humans, whereas mosquitos and ticks are well-established major vectors of many arboviral diseases. Moreover, some emerging zoonotic diseases require a vector to spread or are intrinsically vector-borne and zoonotically transmitted. In this study, we present a newly upgraded database of zoonotic and vector-borne viruses designated ZOVER (http://www.mgc.ac.cn/ZOVER). It incorporates two previously released databases, DBatVir and DRodVir, for bat- and rodent-associated viruses, respectively, and further collects up-to-date knowledge on mosquito- and tick-associated viruses to establish a comprehensive online resource for zoonotic and vector-borne viruses. Additionally, it integrates a set of online visualization tools for convenient comparative analyses to facilitate the discovery of potential patterns of virome diversity and ecological characteristics between/within different viral hosts/vectors. The ZOVER database will be a valuable resource for virologists, zoologists and epidemiologists to better understand the diversity and dynamics of zoonotic and vector-borne viruses and conduct effective surveillance to monitor potential interspecies spillover for efficient prevention and control of future emerging zoonotic diseases.

VFDB 2022: a general classification scheme for bacterial virulence factors.

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over 100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide.

In vivo segmental vertebral kinematics in patients with degenerative lumbar scoliosis.

PURPOSE: This study aimed to find a standard of the vertebra kinematics during functional weight-bearing activities in degenerative lumbar scoliosis (DLS) patients. METHODS: Fifty-four patients were involved into this study with forty-two in DLS group and twelve in the control group. The three-dimensional (3D) vertebral models from L1 to S1 of each participant were reconstructed by computed tomography (CT). Dual-orthogonal fluoroscopic imaging, along with FluoMotion and Rhinoceros software, was used to record segmental vertebral kinematics during functional weight-bearing activities. The primary and coupled motions of each vertebra were analyzed in patients with DLS. RESULTS: During flexion-extension of the trunk, anteroposterior (AP) translation and craniocaudal (CC) translation at L5-S1 were higher than those at L2-3 (9.3 ± 5.1 mm vs. 6.4 ± 3.5 mm; P < 0.05). The coupled mediolateral (ML) translation at L5-S1 in patients with DLS was approximately three times greater than that in the control group. During left-right bending of the trunk, the coupled ML rotation at L5-S1 was higher in patients with DLS than that in the control group (17.7 ± 10.3° vs. 8.4 ± 4.4°; P < 0.05). The AP and CC translations at L5-S1 were higher than those at L1-2, L2-3, and L3-4. During left-right torsion of the trunk, the AP translation at L5-S1 was higher as compared to other levels. CONCLUSIONS: The greatest coupled translation was observed at L5-S1 in patients with DLS. Coupled AP and ML translations at L5-S1 were higher than those in healthy participants. These data improved the understanding of DLS motion characteristics.

Preoperative and follow-up variations of psoas major muscle are related to S1 screw loosening in patients with degenerative lumbar spinal stenosis.

BACKGROUND: It was reported the paraspinal muscle played an important role in spinal stability. The preoperative paraspinal muscle was related to S1 screw loosening. But the relationship between preoperative and postoperative change of psoas major muscle (PS) and S1 pedicle screw loosening in degenerative lumbar spinal stenosis (DLSS) patients has not been reported. This study investigated the effects of preoperative and follow-up variations in the psoas major muscle (PS) on the first sacral vertebra (S1) screw loosening in patients with DLSS. METHODS: 212 patients with DLSS who underwent lumbar surgery were included. The patients were divided into the S1 screw loosening group and the S1 screw non-loosening group. Muscle parameters were measured preoperatively and at last follow-up magnetic resonance imaging. A logistic regression analysis was performed to investigate the risk factors for S1 screw loosening. RESULTS: The S1 screw loosening rate was 36.32% (77/212). The relative total cross-sectional areas and relative functional cross-sectional areas (rfCSAs) of the PS at L2-S1 were significantly higher after surgery. The increased rfCSA values of the PS at L3-S1 in the S1 screw non-loosening group were significantly higher than those in the S1 screw loosening group. The regression analysis showed male, lower CT value of L1 and longer segment fusion were independent risk factors for S1 screw loosening, and postoperative hypertrophy of the PS was a protective factor for S1 screw loosening. CONCLUSIONS: Compared to the preoperative muscle, the PS size increased and fatty infiltration decreased after surgery from L2-3 to L5-S1 in patients with DLSS after short-segment lumbar fusion surgery. Postoperative hypertrophy of the PS might be considered as a protective factor for S1 screw loosening. MRI morphometric parameters and postoperative selected exercise of PS for DLSS patients after posterior lumbar fusion surgery might contribute to improvement of surgical outcome.

Side-Chain-Dependent Functional Intercalations in Graphene Oxide Membranes for Selective Water and Ion Transport.

Subnanometer interlayer space in graphene oxide (GO) laminates is desirable for use as permselective membrane nanochannels. Although the facile modification of the local structure of GO enables various nanochannel functionalizations, precisely controlling nanochannel space is still a challenge, and the roles of confined nanochannel chemistry in selective water/ion separation have not been clearly defined. In this study, macrocyclic molecules with consistent basal plane but varying side groups were used to conjunct with GO for modified nanochannels in laminates. We demonstrated the side-group dependence of both the angstrom-precision tunability for channel free space and the energy barrier setting for ion transport, which challenges the permeability-selectivity trade-off with a slightly decreased permeance from 1.1 to 0.9 L m-2 h-1 bar-1 but an increased salt rejection from 85% to 95%. This study provides insights into the functional-group-dependent intercalation modifications of GO laminates for understanding laminate structural control and nanochannel design.

Structure basis of two nanobodies neutralizing SARS-CoV-2 Omicron variant by targeting ultra-conservative epitopes.

The evolving SARS-CoV-2 Omicron strain has repeatedly caused widespread disease epidemics, and effective antibody drugs continue to be in short supply. Here, we identified a batch of nanobodies with high affinity for receptor binding domain (RBD) of SARS-CoV-2 spike protein, separated them into three classes using high performance liquid chromatography (HPLC), and then resolved the crystal structure of the ternary complexes of two non-competing nanobodies (NB1C6 and NB1B5) with RBD using X-ray crystallography. The structures showed that NB1B5 and NB1C6 bind to the left and right flank of the RBD, respectively, and that the binding epitopes are highly conserved cryptic sites in all SARS-CoV-2 mutant strains, as well as that NB1B5 can effectively block the ACE2. These two nanobodies were covalently linked into multivalent and bi-paratopic formats, and have a high affinity and neutralization potency for omicron, potentially inhibiting viral escape. The binding sites of these two nanobodies are relatively conserved, which help guide the structural design of antibodies targeting future variants of SARS-CoV-2 to combat COVID-19 epidemics and pandemics.

Astrocyte-derived SerpinA3N promotes neuroinflammation and epileptic seizures by activating the NF-κB signaling pathway in mice with temporal lobe epilepsy.

Impaired activation and regulation of the extinction of inflammatory cells and molecules in injured neuronal tissues are key factors in the development of epilepsy. SerpinA3N is mainly associated with the acute phase response and inflammatory response. In our current study, transcriptomics analysis, proteomics analysis, and Western blotting showed that the expression level of Serpin clade A member 3N (SerpinA3N) is significantly increased in the hippocampus of mice with kainic acid (KA)-induced temporal lobe epilepsy, and this molecule is mainly expressed in astrocytes. Notably, in vivo studies using gain- and loss-of-function approaches revealed that SerpinA3N in astrocytes promoted the release of proinflammatory factors and aggravated seizures. Mechanistically, RNA sequencing and Western blotting showed that SerpinA3N promoted KA-induced neuroinflammation by activating the NF-κB signaling pathway. In addition, co-immunoprecipitation revealed that SerpinA3N interacts with ryanodine receptor type 2 (RYR2) and promotes RYR2 phosphorylation. Overall, our study reveals a novel SerpinA3N-mediated mechanism in seizure-induced neuroinflammation and provides a new target for developing neuroinflammation-based strategies to reduce seizure-induced brain injury.

Two-Dimensional Interlayer Space Induced Horizontal Transformation of Metal-Organic Framework Nanosheets for Highly Permeable Nanofiltration Membranes.

Laminar membranes comprising graphene oxide (GO) and metal-organic framework (MOF) nanosheets benefit from the regular in-plane pores of MOF nanosheets and thus can support rapid water transport. However, the restacking and agglomeration of MOF nanosheets during typical vacuum filtration disturb the stacking of GO sheets, thus deteriorating the membrane selectivity. Therefore, to fabricate highly permeable MOF nanosheets/reduced GO (rGO) membranes, a two-step method is applied. First, using a facile solvothermal method, ZnO nanoparticles are introduced into the rGO laminate to stabilize and enlarge the interlayer spacing. Subsequently, the ZnO/rGO membrane is immersed in a solution of tetrakis(4-carboxyphenyl)porphyrin (H2 TCPP) to realize in situ transformation of ZnO into Zn-TCPP in the confined interlayer space of rGO. By optimizing the transformation time and mass loading of ZnO, the obtained Zn-TCPP/rGO laminar membrane exhibits preferential orientation of Zn-TCPP, which reduces the pathway tortuosity for small molecules. As a result, the composite membrane achieves a high water permeance of 19.0 L m-2  h-1  bar-1 and high anionic dye rejection (>99% for methyl blue).

Protectin conjugates in tissue regeneration 1 alleviates sepsis-induced acute lung injury by inhibiting ferroptosis.

BACKGROUND: Acute lung injury (ALI) is a common and serious complication of sepsis with high mortality. Ferroptosis, categorized as programmed cell death, contributes to the development of lung injury. Protectin conjugates in tissue regeneration 1 (PCTR1) is an endogenous lipid mediator that exerts protective effects against multiorgan injury. However, the role of PCTR1 in the ferroptosis of sepsis-related ALI remains unknown. METHODS: A pulmonary epithelial cell line and a mouse model of ALI stimulated with lipopolysaccharide (LPS) were established in vitro and in vivo. Ferroptosis biomarkers, including ferrous (Fe2+), glutathione (GSH), malondialdehyde (MDA) and 4-Hydroxynonenal (4-HNE), were assessed by relevant assay kits. Glutathione peroxidase 4 (GPX4) and prostaglandin-endoperoxide synthase 2 (PTGS2) protein levels were determined by western blotting. Lipid peroxides were examined by fluorescence microscopy and flow cytometry. Cell viability was determined by a CCK-8 assay kit. The ultrastructure of mitochondria was observed with transmission electron microscopy. Morphology and inflammatory cytokine levels predicted the severity of lung injury. Afterward, related inhibitors were used to explore the potential mechanism by which PCTR1 regulates ferroptosis. RESULTS: PCTR1 treatment protected mice from LPS-induced lung injury, which was consistent with the effect of the ferroptosis inhibitor ferrostatin-1. PCTR1 treatment decreased Fe2+, PTGS2 and lipid reactive oxygen species (ROS) contents, increased GSH and GPX4 levels and ameliorated mitochondrial ultrastructural injury. Administration of LPS or the ferroptosis agonist RSL3 resulted in reduced cell viability, which was rescued by PCTR1. Mechanistically, inhibition of the PCTR1 receptor lipoxin A4 (ALX), protein kinase A (PKA) and transcription factor cAMP-response element binding protein (CREB) partly decreased PCTR1 upregulated GPX4 expression and a CREB inhibitor blocked the effects ofPCTR1 on ferroptosis inhibition and lung protection. CONCLUSION: This study suggests that PCTR1 suppresses LPS-induced ferroptosis via the ALX/PKA/CREB signaling pathway, which may offer promising therapeutic prospects in sepsis-related ALI.

Genome-wide dissection reveals diverse pathogenic roles of bacterial Tc toxins.

Tc toxins were originally identified in entomopathogenic bacteria, which are important as biological pest control agents. Tc toxins are heteromeric exotoxins composed of three subunit types, TcA, TcB, and TcC. The C-terminal portion of the TcC protein encodes the actual toxic domain, which is translocated into host cells by an injectosome nanomachine comprising the other subunits. Currently the pathogenic roles and distribution of Tc toxins among different bacterial genera remain unclear. Here we have performed a comprehensive genome-wide analysis, and established a database that includes 1,608 identified Tc loci containing 2,528 TcC proteins in 1,421 Gram-negative and positive bacterial genomes. Our findings indicate that TcCs conform to the architecture of typical polymorphic toxins, with C-terminal hypervariable regions (HVR) encoding more than 100 different classes of putative toxic domains, most of which have not been previously recognized. Based on further analysis of Tc loci in the genomes of all Salmonella and Yersinia strains in EnteroBase, a "two-level" evolutionary dynamics scenario is proposed for TcC homologues. This scenario implies that the conserved TcC RHS core domain plays a critical role in the taxonomical specific distribution of TcC HVRs. This study provides an extensive resource for the future development of Tc toxins as valuable agrochemical tools. It furthermore implies that Tc proteins, which are encoded by a wide range of pathogens, represent an important versatile toxin superfamily with diverse pathogenic mechanisms.

Site-Specific Modification of Single Domain Antibodies by Enzyme-Immobilized Magnetic Beads.

Nanobodies as imaging agents and drug conjugates have shown great potential for cancer diagnostics and therapeutics. However, site-specific modification of a nanobody with microbial transglutaminase (mTGase) encounters problems in protein separation and purification. Here, we describe a facile yet reliable strategy of immobilizing mTGase onto magnetic beads for site-specific nanobody modification. The mTGase immobilized on magnetic beads (MB-mTGase) exhibits catalytic activity nearly equivalent to that of the free mTGase, with good reusability and universality. Magnetic separation simplifies the protein purification step and reduces the loss of nanobody bioconjugates more effectively than size exclusion chromatography. Using MB-mTGase, we demonstrate site-specific conjugation of nanobodies with fluorescent dyes and polyethylene glycol molecules, enabling targeted immunofluorescence imaging and improved circulation dynamics and tumor accumulation in vivo. The combined advantages of MB-mTGase method, including high conjugation efficiency, quick purification, less protein loss, and recycling use, are promising for site-specific nanobody functionalization and biomedical applications.