CDS-DB, an omnibus for patient-derived gene expression signatures induced by cancer treatment.

Patient-derived gene expression signatures induced by cancer treatment, obtained from paired pre- and post-treatment clinical transcriptomes, can help reveal drug mechanisms of action (MOAs) in cancer patients and understand the molecular response mechanism of tumor sensitivity or resistance. Their integration and reuse may bring new insights. Paired pre- and post-treatment clinical transcriptomic data are rapidly accumulating. However, a lack of systematic collection makes data access, integration, and reuse challenging. We therefore present the Cancer Drug-induced gene expression Signature DataBase (CDS-DB). CDS-DB has collected 78 patient-derived, paired pre- and post-treatment transcriptomic source datasets with uniformly reprocessed expression profiles and manually curated metadata such as drug administration dosage, sampling time and location, and intrinsic drug response status. From these source datasets, 2012 patient-level gene perturbation signatures were obtained, covering 85 therapeutic regimens, 39 cancer subtypes and 3628 patient samples. Besides data browsing, download and search, CDS-DB also supports single signature analysis (including differential gene expression, functional enrichment, tumor microenvironment and correlation analyses), signature comparative analysis and signature connectivity analysis. This provides insights into drug MOA and its heterogeneity in patients, drug resistance mechanisms, drug repositioning and drug (combination) discovery, etc. CDS-DB is available at http://cdsdb.ncpsb.org.cn/.

MdSVWC1, a new pattern recognition receptor triggers multiple defense mechanisms against invading bacteria in Musca domestica.

BACKGROUND: Single-domain von Willebrand factor type C (SVWC) constitute a protein family predominantly identified in arthropods, characterized by a SVWC domain and involved in diverse physiological processes such as host defense, stress resistance, and nutrient metabolism. Nevertheless, the physiological mechanisms underlying these functions remain inadequately comprehended. RESULTS: A massive expansion of the SVWC gene family in Musca domestica (MdSVWC) was discovered, with a count of 35. MdSVWC1 was selected as the representative of the SVWC family for functional analysis, which led to the identification of the immune function of MdSVWC1 as a novel pattern recognition receptor. MdSVWC1 is highly expressed in both the fat body and intestines and displays acute induction upon bacterial infection. Recombinant MdSVWC1 binds to surfaces of both bacteria and yeast through the recognition of multiple pathogen-associated molecular patterns and exhibits Ca2+-dependent agglutination activity. MdSVWC1 mutant flies exhibited elevated mortality and hindered bacterial elimination following bacterial infection as a result of reduced hemocyte phagocytic capability and weakened expression of antimicrobial peptide (AMP) genes. In contrast, administration of recombinant MdSVWC1 provided protection to flies from bacterial challenges by promoting phagocytosis and AMP genes expression, thereby preventing bacterial colonization. MdSPN16, a serine protease inhibitor, was identified as a target protein of MdSVWC1. It was postulated that the interaction of MdSVWC1 with MdSPN16 would result in the activation of an extracellular proteolytic cascade, which would then initiate the Toll signaling pathway and facilitate the expression of AMP genes. CONCLUSIONS: MdSVWC1 displays activity as a soluble pattern recognition receptor that regulates cellular and humoral immunity by recognizing microbial components and facilitating host defense.

Mesenchymal Stem Cells Engineered by Multicomponent Coassembled DNA Nanofibers for Enhanced Wound Healing.

A major challenge for stem cell therapies, such as using mesenchymal stem cells to treat skin injuries, is the stable engraftment of exogenous cells and the maintenance of their regenerative capacities in the wound areas. DNA-based self-assembly strategies can be used for artificial and multifunctional cell surface engineering to stabilize and enhance their functions for therapeutic applications. Here, we developed DNA nanofiber-decorated stem cells, in which DNA-based, multivalent fiber-like structures were self-assembled in situ on the cell surfaces. These engineered stem cells have demonstrated robust reactive oxygen species (ROS) scavenging effects, specific adhesion to damaged vascular endothelial cells, and the ability to enhance angiogenesis, which were effective and safe for acute or chronic wound healing in a mouse model with excisional skin injury. This DNA nanostructure-engineered stem cell provides a novel therapeutic platform for the treatment of tissue damage.

Modulating the Coordination Environment of Carbon-Dot-Supported Fe Single-Atom Nanozymes for Enhanced Tumor Therapy.

Herein, carbon dot (CD)-supported Fe single-atom nanozymes with high content of pyrrolic N and ultrasmall size (ph-CDs-Fe SAzyme) are fabricated by a phenanthroline-mediated ligand-assisted strategy. Compared with phenanthroline-free nanozymes (CDs-Fe SAzyme), ph-CDs-Fe SAzyme exhibit higher peroxidase (POD)-like activity due to their structure similar to that of ferriporphyrin in natural POD. Aberration-corrected high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) and X-ray absorption fine structure spectroscopy (XAFS) analyses show that metal Fe is dispersed in ph-CDs-Fe SAzyme as single atoms. Steady-state kinetic studies show that the maximum velocity (Vmax ) and turnover number (kcat ) of H2 O2  homolytic cleavage catalyzed by ph-CDs-Fe SAzyme are 3.0 and 6.2 more than those of the reaction catalyzed by CDs-Fe SAzyme. Density functional theory (DFT) calculations show that the energy barrier of the reaction catalyzed by ph-CDs-Fe SAzyme is lower than that catalyzed by CDs-Fe SAzyme. Antitumor efficacy experiments show that ph-CDs-Fe SAzyme can efficiently inhibit the growth of tumor cells both in vitro and in vivo by synergistic chemodynamic and photothermal effects. Here a new paradigm is provided for the development of efficient antitumor therapeutic approaches based on SAzyme with POD-like activity.

Muscle LIM protein of Macrobrachium nipponense (MnMLP) involved in immune and stress response.

The muscle LIM protein (MLP) is a member of the cysteine and glycine-rich protein (CSRP) family, composed of CSRP1, CSRP2 and CSRP3/MLP. MLP is involved in a multitude of functional roles, including cytoskeletal organization, transcriptional regulation, and signal transduction. However, the molecular mechanisms underlying its involvement in immune and stress responses remain to be elucidated. This study identified an MnMLP in the freshwater crustacean Macrobrachium nipponense. The isothermal titration calorimetry assay demonstrated that recombinant MnMLP was capable of coordinating with Zn2+. Upon challenge by Aeromonas veronii or WSSV, and exposure to CdCl2, up-regulation was recorded in the muscle and intestinal tissues, suggesting its involvement in immune and anti-stress responses. MnMLP protein was predominantly expressed in the cytoplasm of the transfected HEK-293T cells, but after treatment with LPS, Cd2+ or H2O2, the MnMLP was observed to be transferred into the nucleus. The comet assay demonstrated that the overexpression of MnMLP could mitigate the DNA damage induced by H2O2 in HEK-293T cells, suggesting the potential involvement of MnMLP in the DNA repair process. These findings suggest that DNA repair may represent a possible mechanism by which MnMLP may be involved in the host's defense against pathogens and stress.

Peptidoglycan recognition protein SC (PGRP-SC) shapes gut microbiota richness, diversity and composition by modulating immunity in the house fly Musca domestica.

The gastrointestinal tract of all animals, including insects, is colonized by a remarkable array of microorganisms which are referred to collectively as the gut microbiota. The hosts establish mutually beneficial interactions with the gut microbiota. However, the mechanisms shaping these interactions remain to be better understood. Here, we investigated the roles of Musca domestica peptidoglycan recognition protein SC (MdPGRP-SC), a secreted pattern recognition receptor, in shaping the gut microbial community structure by using biochemical and high-throughput sequencing approaches. The recombinant MdPGRP-SC (rMdPGRP-SC) could strongly bind various pathogen-associated molecular patterns (PAMPs) including peptidoglycan, lipopolysaccharide and D-galactose, and exhibited mild affinity to ß-1, 3-glucan and D-mannose. Meanwhile, rMdPGRP-SC could also bind different kinds of microorganisms, including gram-positive bacteria (Bacillus subtilis and Staphylococcus aureus), gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) and yeast (Pichia pastoris). rMdPGRP-SC also exhibited weak antibacterial activity against Bacillus subtilis. Knockdown of MdPGRP-SC by RNAi reduced the persistence of ingested E. coli and a load of indigenous microbiota in the larval gut significantly. In addition, depleted MdPGRP-SC also altered the gut microbiota composition and led to increased ratios of Gram-negative bacteria. We hypothesize that MdPGRP-SC is involved in maintaining gut homeostasis by modulating the immune intensity of the gut through multiple mechanisms, including degrading or neutralizing various PAMPs and selectively suppressing the growth of some bacteria. Considering the functional conservation of the peptidoglycan recognition protein (PGRP) family in insects, the catalytic PGRPs might be promising candidate targets not only for pest and vector control but also for the treatment of bacterial infection in insect farming.

Ecological succession and functional characteristics of lactic acid bacteria in traditional fermented foods.

Fermented foods are important parts of traditional food culture with a long history worldwide. Abundant nutritional materials and open fermentation contribute to the diversity of microorganisms, resulting in unique product quality and flavor. Lactic acid bacteria (LAB), as important part of traditional fermented foods, play a decisive role in the quality and safety of fermented foods. Reproduction and metabolic of microorganisms drive the food fermentation, and microbial interaction plays a major role in the fermentation process. Nowadays, LAB have attracted considerable interest due to their potentialities to add functional properties to certain foods or as supplements along with the research of gut microbiome. This review focuses on the characteristics of diversity and variability of LAB in traditional fermented foods, and describes the principal mechanisms involved in the flavor formation dominated by LAB. Moreover, microbial interactions and their mechanisms in fermented foods are presented. They provide a theoretical basis for exploiting LAB in fermented foods and improving the quality of traditional fermented foods. The traditional fermented food industry should face the challenge of equipment automation, green manufacturing, and quality control and safety in the production.

E2F family play important roles in tumorigenesis.

Tumors are serious threats to human health. The transcription factors are regarded as the potential targets for tumor treatment. As an important family of transcription factors, E2F family transcription factors (E2Fs) play vital roles in cell proliferation and regulation. However, the expression feature, gene functions, and molecular interactions of E2Fs in tumorigenesis are not clear. In this study, the transcriptome data, mutation data, and protein-protein interaction data of 10 high-incidence tumors in China from the TCGA database were integrated and analyzed to explore the expression, structure, function, mutation, and phylogenetic characteristics of E2Fs. The results showed that E2F1 and E2F7 were regularly upregulated in the tumor samples. Moreover, E2Fs participated in the regulation of the cell cycle, cell aging, and other signaling pathways. As an important regulator, E2F1 interacted with more proteins than other E2Fs. At the same time, the genetic mutation types of E2Fs varied in tumor type and patient sex, of which gene amplification accounts for the largest proportion. Phylogenetic analysis showed that E2Fs were conserved in 41 species, including fruit flies, nematodes, and humans. Meanwhile, E2Fs had a tendency for gene expansion during evolution. In conclusion, this study clarified the expression pattern, mutation characteristics, and evolutionary trend of E2Fs in high-incidence tumors in China, and suggested that E2F family transcription factors could be novel diagnostic markers for tumor diseases. Furthermore, this work can provide a theoretical basis for the development of anti-tumor-targeted drugs.

Synergistic inactivation of Escherichia coli O157:H7 and Staphylococcus aureus by gallic acid and thymol and its potential application on fresh-cut tomatoes.

Antibacterial activity against Escherichia coli O157:H7 and Staphylococcus aureus of five typical plant-derived compounds [gallic acid (G.A), citral (Cit), thymol (Thy), salicylic acid (S.A), lauric acid (L.A)] were investigated by determining the minimum inhibitory concentration (MIC) and the fractional inhibitory concentration index (FICI). The results showed that only a combination of Thy and G.A (TGA), with a concentration of 0.1 and 1.25 mg/mL, respectively, had a synergistic effect (FICI = 0.5) on both E. coli O157:H7 and S. aureus. The amount of Thy and G.A in mixture were four-fold lower than the MICs of the individuals shown to cause the equivalent antimicrobial activity in trypticase soy broth (TSB). The microbial reduction obtained in TSB with addition of TGA were significantly higher (P < 0.05) than the reduction shown for the broth supplemented with the separated phenolics. TGA caused the changes of morphology and membrane integrity of bacteria. Additionally, the application of TGA on fresh-cut tomatoes are investigated. Fresh-cut tomatoes inoculated with E. coli O157:H7and S. aureus were washed for 2min, 5min, 10min at 4 °C, 25 °C, 40 °C in 0.3% NaOCl, or water containing TGA at various concentrations. Overall, the reduction of TGA achieved against S. aureus is higher than E. coli O157:H7. Same concentrations of combined antimicrobials at a temperature of 40 °C further increased the degree of microbial inactivation, with an additional 0.89-1.51 log CFU/g reduction compared to that at 25 °C. Moreover, 1/2MICThy+1/2MICG.A at 25 °C for 10min or 40 °C for 5min were generally acceptable with sensorial scores higher than 7. Our results showed that TGA could work synergistically on the inactivation of the tested bacteria and may be used as an alternative disinfectant of fresh produce.

Resveratrol inhibits HeLa cell proliferation by regulating mitochondrial function.

The beneficial roles of resveratrol (RES) in affecting proliferation of multiple cancer cells have attracted intensive attention. However, the underlying mechanism remains unclear. This study aims to bridge the knowledge gap by investigating RES-induced growth inhibition of HeLa cells. Our work focuses on the metergasis of mitochondria in the RES-exposed cells. Therefore, HeLa cells were treated with different concentrations of RES for 30 min and 24 h, respectively. As a result, concentration-dependent increases in cell growth inhibition, ROS (reactive oxygen species) triggering, and LC3-II (light chain 3-II) expression were detected in the HeLa cells exposed to RES for 24 h. Interestingly, a specific concentration-dependent effect was observed in the HeLa cells exposed to RES for 30 min, that is, low concentration RES (≤ 25 µmol/L) reduced ROS levels, inhibited transcription and expression levels of LC3-II, and stimulated mitochondrial respiratory capacities. In contrast, high concentration RES (50 and 100 µmol/L) induced ROS over-production and autophagy in the cells, resulting in decreased levels of mitochondrial membrane potential, mitochondrial DNA copy numbers, and mitochondrial respiratory capacities. Together, our data concluded that RES inhibited HeLa cell proliferation through perturbation of mitochondrial structure and function, and ROS-induced autophagy also played a critical role in the process.

Strong Light-Matter Interactions in Chiral Plasmonic-Excitonic Systems Assembled on DNA Origami.

The exploitation of strong light-matter interactions in chiral plasmonic nanocavities may enable exceptional physical phenomena and lead to potential applications in nanophotonics, information communication, etc. Therefore, a deep understanding of strong light-matter interactions in chiral plasmonic-excitonic (plexcitonic) systems constructed by a chiral plasmonic nanocavity and molecular excitons is urgently needed. Herein, we systematically studied the strong light-matter interactions in gold nanorod-based chiral plexcitonic systems assembled on DNA origami. Rabi splitting and anticrossing behavior were observed in circular dichroism spectra, manifesting chiroptical characteristic hybridization. The bisignate line shape of the circular dichroism (CD) signal allows the accurate discrimination of hybrid modes. A large Rabi splitting of ∼205/∼199 meV for left-handed/right-handed plexcitonic nanosystems meets the criterion of strong coupling. Our work deepens the understanding of light-matter interactions in chiral plexcitonic nanosystems and will facilitate the development of chiral quantum optics and chiroptical devices.

Anti-diabetic and gut microbiota modulation effects of sacha inchi (Plukenetia volubilis L.) leaf extract in streptozotocin-induced type 1 diabetic mice.

BACKGROUND: Sacha inchi (Plukenetia volubilis L.) tea has been used as an adjuvant treatment for diabetes in Pu'er, in the Yunnan province of China. The effects of sacha inchi tea on diabetes and the underlying mechanisms remain unknown. This study was conducted to investigate the influence of a water extract of sacha inchi (P. volubilis L.) leaves (PWE) on hypoglycemic activity and gut microbiota composition in mice with streptozotocin (STZ)-induced type 1 diabetes mellitus (T1DM). During the 6 weeks of the study, T1DM mice were administered PWE intragastrically at 400 mg kg-1 body weight (BW) per day. RESULTS: Treatment with PWE reduced excessive loss of BW and excessive intake of food. It significantly decreased blood glucose levels and improved oral glucose tolerance. The treatment caused protective histopathological transformations in sections of the pancreas, leading to decreased insulin resistance and improved insulin sensitivity. Treatment with PWE also significantly ameliorated disorders of the gut microbiota structure and increased the richness and diversity of intestinal microbial species in T1DM mice. At the genus level, the populations of several crucial bacteria, such as Akkermansia, Parabacteroides, and Muribaculum increased in the PWE treatment group but the abundance of Ruminiclostridium and Oscillibacter decreased. CONCLUSIONS: Treatment with PWE can ameliorate hyperglycemic symptoms in STZ-induced T1DM mice, and the anti-diabetic effect of PWE was related to the amelioration of gut microbial structural disorder and the enrichment of functional bacteria. © 2022 Society of Chemical Industry.

A DNA-Based Plasmonic Nanodevice for Cascade Signal Amplification.

Here, we describe a DNA circuit-aided, origami nanodevice-based plasmonic system, which performs DNA-regulated, cascade amplification of faint chemical/biological signals. In this system, two gold-nanorods (GNRs) are co-assembled onto a DNA lock-containing, tweezer-like DNA origami template. Logic circuits serve as recognition and amplification elements for specific messengers, producing DNA keys for driving conformational changes of the plasmonic nanodevices. In the presence of input signals including nucleic acids, adenosines, chiral tyrosinamides or specific receptors expressed by tumor cells, the plasmonic nanodevices can be activated to perform dynamic structural motions, reporting robust responses via plasmonic circular dichroism (CD) spectral changes. This DNA nanodevice-based system provides a different design to enrich the strategies for constructing synthetic nanomachines, enabling the customized bottom-up nanostructure construction for sensitive biological signaling.

A single von Willebrand factor C-domain protein acts as an extracellular pattern-recognition receptor in the river prawn Macrobrachium nipponense.

The single von Willebrand factor C-domain proteins (SVWCs) are mainly found in arthropods. Their expression may be regulated by several environmental stresses, including nutritional status and bacterial and viral infections. However, the underlying regulatory mechanism is unclear. In the present study, we identified a member of the SVWC family from the river prawn Macrobrachium nipponense as a soluble and bacteria-inducible pattern-recognition receptor (designated MnSVWC). In vitro, recombinant MnSVWC exhibited pronounced binding and Ca2+-dependent agglutinating abilities against diverse microbes, including Gram-negative bacteria (i.e. Escherichia coli and Aeromonas victoria), Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), and yeast (Pichia pastoris). ELISA assays revealed that recombinant MnSVWC recognizes a broad range of various pathogen-associated molecular patterns (PAMPs) and has high affinity to lipopolysaccharide and lysine-type and diaminopimelic acid-type peptidylglycan and d-galactose and low affinity to d-mannan and ß-1,3-glucan. Mutant MnSVWCP57A with an impaired Glu-Pro-Asn (EPN) motif displayed reduced affinity to all these PAMPs to varying extent. Moreover, MnSVWC bound to the surface of hemocytes and promoted their phagocytic activity and clearance of invasive bacteria. RNAi-mediated MnSVWC knockdown in prawn reduced the ability to clear invading bacteria, but did not block the activities of the Toll pathway or the arthropod immune deficiency (IMD) pathway, or the expression of antimicrobial peptide genes. These results indicate that MnSVWC functions as an extracellular pattern-recognition receptor in M. nipponense that mediates cellular immune responses by recognizing PAMPs, agglutinating invasive microbes, and promoting phagocytosis in hemocytes.

Hierarchical Assembly of Super-DNA Origami Based on a Flexible and Covalent-Bound Branched DNA Structure.

DNA origami technique provides a programmable way to construct nanostructures with arbitrary shapes. The dimension of assembled DNA origami, however, is usually limited by the length of the scaffold strand. Herein, we report a general strategy to efficiently organize multiple DNA origami tiles to form super-DNA origami using a flexible and covalent-bound branched DNA structure. In our design, the branched DNA structures (Bn: with a certain number of 2-6 branches) are synthesized by a copper-free click reaction. Equilateral triangular DNA origamis with different numbers of capture strands (Tn: T1, T2, and T3) are constructed as the coassembly tiles. After hybridization with the branched DNA structures, the super-DNA origami (up to 13 tiles) can be efficiently ordered in the predesigned patterns. Compared with traditional DNA junctions (Jn: J2-J6, as control groups) assembled by base pairing between several DNA strands, a higher yield and more compact structures are obtained using our strategy. The highly ordered and discrete DNA origamis can further precisely organize gold nanoparticles into different patterns. This rationally developed DNA origami ordering strategy based on the flexible and covalent-bound branched DNA structure presents a new avenue for the construction of sophisticated DNA architectures with larger molecular weights.

A Tubular DNA Nanodevice as a siRNA/Chemo-Drug Co-delivery Vehicle for Combined Cancer Therapy.

Using the DNA origami technique, we constructed a DNA nanodevice functionalized with small interfering RNA (siRNA) within its inner cavity and the chemotherapeutic drug doxorubicin (DOX), intercalated in the DNA duplexes. The incorporation of disulfide bonds allows the triggered mechanical opening and release of siRNA in response to intracellular glutathione (GSH) in tumors to knockdown genes key to cancer progression. Combining RNA interference and chemotherapy, the nanodevice induced potent cytotoxicity and tumor growth inhibition, without observable systematic toxicity. Given its autonomous behavior, exceptional designability, potent antitumor activity and marked biocompatibility, this DNA nanodevice represents a promising strategy for precise drug design for cancer therapy.

Enzyme Mimic Nanomaterials and Their Biomedical Applications.

Nanomaterials with enzyme-mimicking behavior (nanozymes) have attracted a lot of research interest recently. In comparison to natural enzymes, nanozymes hold many advantages, such as good stability, ease of production and surface functionalization. As the catalytic mechanism of nanozymes is gradually revealed, the application fields of nanozymes are also broadly explored. Beyond traditional colorimetric detection assays, nanozymes have been found to hold great potential in a variety of biomedical fields, such as tumor theranostics, antibacterial, antioxidation and bioorthogonal reactions. In this review, we summarize nanozymes consisting of different nanomaterials. In addition, we focus on the catalytic performance of nanozymes in biomedical applications. The prospects and challenges in the practical use of nanozymes are discussed at the end of this Minireview.

A fibrinogen-related protein (Mnfico3) acts as a novel pattern recognition receptor in Macrobrachium nipponense.

Fibrinogen-related proteins (FREPs) are widely found in both vertebrates as well as invertebrates, and they play a crucial role in host immunity. In this study, we isolated a novel ficolin gene (Mnfico3) from the oriental river prawn Macrobrachium nipponense. The complete cDNA sequence of Mnfico3 was 1133 bp long, containing an open reading frame of 765 bp coding for Mnfico3, a protein consisting of 254 amino acids. The Mnfico3 protein contained a putative N-terminal signal peptide and a fibrinogen-related protein domain present at the C-terminal. Phylogenetic analysis indicated that Mnfico3 had a closer evolutionary relationship with vertebrate ficolins than with its invertebrate homologues. Tissue distribution analysis indicated that Mnfico3 was predominantly expressed in muscle, in which its transcription was increased following bacterial challenge by Aeromonas veronii. Function analysis using recombinant protein revealed that rMnFico3 had broad-spectrum binding capacity to a variety of microorganisms and pathogen-associated molecular pattern (PAMP) ligands. Furthermore, rMnFico3 exhibited Ca2+-dependent agglutinating activity against microbes in vitro, and ability to attach to the hemocyte surface which promoted phagocytosis and subsequent clearance of invasive bacteria in vivo. Silencing rMnFico3 in prawn through RNAi did not alter the expression of antimicrobial peptide genes (ALF and Crustin). These results manifested that MnFico3 functioned as a potential pattern recognition receptor (PPR) to mediate cellular immune response by recognizing PAMPs, agglutinating invasive microbes, and promoting phagocytosis of hemocytes.

Recombinant expression of an oriental river prawn anti-lipopolysaccharide factor gene in Pichia pastoris and its characteristic analysis.

Anti-lipopolysaccharide factors (ALFs), as main host-defense molecules of crustaceans, form a unique family of antimicrobial peptides (AMPs). MnALF4 is one isoform of ALFs isolated from the freshwater prawn Macrobrachium nipponense. In the present study, MnALF4 gene was successfully expressed in the yeast Pichia pastoris and the recombinant MnALF4 protein exhibited efficient and broad-spectrum antimicrobial activities against both Gram-positive bacteria and Gram-negative bacteria in vitro. When prawns were injected with rMnALF4 before bacterial challenge with E. coli, the recombinant protein effectively promote the elimination of bacteria by the host. It manifested that rMnALF4 could effectively kill the invading bacteria in vivo. Treatment with rMnALF4 led to remarkable changes in bacterial morphology, such as spheroidization, oversized bacteria, and cell lysis. In addition, rMnALF4 showed weak hemolysis activity to the rabbit red blood cells. Our work suggests that MnALF4 plays an important role in Macrobrachium immunity and is worthy of further investigation as a potential antibacterial agent with high efficacy against bacterial infection and low toxicity to host cells.

Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue.

In recent years, high-throughput technologies have contributed to the development of a more precise picture of the human proteome. However, 2129 proteins remain listed as missing proteins (MPs) in the newest neXtProt release (2019-02). The main reasons for MPs are a low abundance, a low molecular weight, unexpected modifications, membrane characteristics, and so on. Moreover, >50% of the MS/MS data have not been successfully identified in shotgun proteomics. Open-pFind, an efficient open search engine, recently released by the pFind group in China, might provide an opportunity to identify these buried MPs in complex samples. In this study, proteins and potential MPs were identified using Open-pFind and three other search engines to compare their performance and efficiency with three large-scale data sets digested by three enzymes (Glu-C, Lys-C, and trypsin) with specificity on different amino acid (AA) residues. Our results demonstrated that Open-pFind identified 44.7-93.1% more peptide-spectrum matches and 21.3-61.6% more peptide sequences than the second-best search engine. As a result, Open-pFind detected 53.1% more MP candidates than MaxQuant and 8.8% more candidate MPs than Proteome Discoverer. In total, 5 (PE2) of the 124 MP candidates identified by Open-pFind were verified with 2 or 3 unique peptides containing more than 9 AAs by using a spectrum theoretical prediction with pDeep and synthesized peptide matching with pBuild after spectrum quality analysis, isobaric post-translational modification, and single amino acid variant filtering. These five verified MPs can be saved as PE1 proteins. In addition, three other MP candidates were verified with two unique peptides (one peptide containing more than 9 AAs and the other containing only 8 AAs), which was slightly lower than the criteria listed by C-HPP and required additional verification information. More importantly, unexpected modifications were detected in these MPs. All MS data sets have been deposited into ProteomeXchange with the identifier PXD015759.