Selection, identification and crystal structure of shark-derived single-domain antibodies against a green fluorescent protein.

Shark variable domain of new antigen receptors (VNARs) are the smallest naturally occurring binding domains with properties of low complexity, small size, cytoplasmic expression, and ease of engineering. Green fluorescent protein (GFP) molecules have been analyzed in conventional microscopy, but their spectral characteristics preclude their use in techniques offering substantially higher resolution. Besides, the GFP molecules can be quenched in acidic environment, which makes it necessary to develop anti-GFP antibody to solve these problems. In view of the diverse applications of GFP and unique physicochemical features of VNAR, the present study aims to generate VNARs against GFP. Here, we identified 36 VNARs targeting eCGP123, an extremely stable GFP, by phage display from three immunized sharks. These VNARs bound to eCGP123 with affinity constant KD values ranging from 6.76 to 605 nM. Among them, two lead VNARs named aGFP-14 and aGFP-15 with nanomolar eCGP123-binding affinity were selected for in-depth characterization. aGFP-14 and aGFP-15 recognized similar epitopes on eCGP123. X-ray crystallography studies clarified the mechanism by which aGFP14 interacts with eCGP123. aGFP-14 also showed cross-reaction with EGFP, with KD values of 47.2 nM. Finally, immunostaining analyses demonstrated that aGFP-14 was able to bind effectively to the EGFP expressed in both cultured cells and mouse brain tissues, and can be used as a fluorescence amplifier for EGFP. Our research demonstrates a feasible idea for the screening and production of shark-derived VNARs. The two high-affinity VNARs developed in the study contribute to the diversity of GFP sdAbs and may enhance the applications of GFP.

Properties of Pacific white shrimp (Litopenaeus vannamei) collagen and its degradation by endogenous proteinases during cold storage.

Many factors are responsible for the diminished quality of shrimp during cold storage, while the role of collagen has rarely been studied. This study therefore investigated the relationship between collagen degradation and changes of textural properties of Pacific white shrimp, and its hydrolysis by endogenous proteinases. The textural properties of shrimp decreased gradually along with disruption of shrimp muscle tissues, and the chewiness property of shrimp muscle showed a linear relationship with collagen contents in muscle during 6-day-storage at 4 °C. Pepsin-solubilized collagen in shrimp muscle consisted of one α1 chain and two α2 chains, revealing a typical tripeptide sequence (i.e., Gly-X-Y) in their molecules. In addition, collagen could be hydrolyzed by crude endogenous proteinases extracted from shrimp hepatopancreas, and serine proteinase plays a critical role in the process. These findings strongly suggested that the quality reduction of shrimp during cold storage is closely associated with collagen degradation.

Research Progresses and Applications of Fluorescent Protein Antibodies: A Review Focusing on Nanobodies.

Since the discovery of fluorescent proteins (FPs), their rich fluorescence spectra and photochemical properties have promoted widespread biological research applications. FPs can be classified into green fluorescent protein (GFP) and its derivates, red fluorescent protein (RFP) and its derivates, and near-infrared FPs. With the continuous development of FPs, antibodies targeting FPs have emerged. The antibody, a class of immunoglobulin, is the main component of humoral immunity that explicitly recognizes and binds antigens. Monoclonal antibody, originating from a single B cell, has been widely applied in immunoassay, in vitro diagnostics, and drug development. The nanobody is a new type of antibody entirely composed of the variable domain of a heavy-chain antibody. Compared with conventional antibodies, these small and stable nanobodies can be expressed and functional in living cells. In addition, they can easily access grooves, seams, or hidden antigenic epitopes on the surface of the target. This review provides an overview of various FPs, the research progress of their antibodies, particularly nanobodies, and advanced applications of nanobodies targeting FPs. This review will be helpful for further research on nanobodies targeting FPs, making FPs more valuable in biological research.

Involvement of MMP-9 in collagen degradation of sea bass (Lateolabrax japonicus): Cloning, expression, and characterization.

Disintegration of intramuscular connective tissue is responsible for postmortem tenderization of fish muscles during chilled storage. Matrix metalloproteinase-9 (MMP-9) was reported to be involved in this process, whereas the mechanism has not been revealed. In the present study, purified type I and V collagens from the connective tissues of sea bass (Lateolabrax japonicus) muscles were first prepared. These two kinds of collagens comprise three polypeptide chains (α), forming a typical triple-helical domain as determined by circular dichroism. The complete coding region of MMP-9 containing an open reading frame of 2070 bp encoding 689 amino acid residues was then cloned. The recombinant MMP-9 catalytic domain (rcMMP-9) was expressed in Escherichia coli and exhibited high hydrolyzing activity toward gelatin. Besides, rcMMP-9 was effective in degrading type V collagen rather than type I collagen at 4°C. The enzymatic activity of rcMMP-9 was highly pH-dependent, and its enzymatic activity under neutral and basic conditions was higher than that under acidic conditions. Metal ion Ca2+ was necessary for the maintenance of rcMMP-9 activity, whereas Zn2+ inhibited its activity. Our present study indicated that MMP-9 is responsible for the disintegration of intramuscular connective tissues by cleaving type V collagen during postmortem tenderization of fish muscle. PRACTICAL APPLICATION: Elucidation the involvement of MMP-9 in collagen degradation will deliver a reference for the prevention of muscular protein decomposition during chilled storage of fish fillets.

Relationships of Matrix Metalloproteinase 1 and a Tissue Inhibitor of Metalloproteinase to Collagen Metabolism in Haliotis discus hannai.

In response to physical, chemical, and/or biological stimuli, considerable tissue self-degradation occurs in abalone, causing severe post-harvest quality loss. During this process, the extracellular matrix (ECM) is greatly degraded by endogenous proteases. The main component of the ECM is collagen, primarily type I collagen. Although the activity of matrix metalloproteinases (MMPs), which can specifically degrade collagen, is precisely regulated by tissue inhibitors of MPs (TIMPs), indicating that MMPs and TIMPs play crucial roles in the regulation of tissue self-degradation, few studies have reported the interaction between MMPs and TIMPs. In this study, we reveal collagenases to participate in postmortem tissue self-degradation of Haliotis discus hannai by degrading type I collagen. The recombinant MMP-1 catalytic domain (rMMP1c) of abalone with high purity and enzyme activity is expressed using a prokaryotic expression system. The optimum temperature and pH for rMMP1c are 37 °C and 7.0, respectively. The thermal denaturation temperature of rMMP1c is 67.0 ± 0.9 °C. Ethylenediamine tetraacetic acid (EDTA) and 1,10-phenanthroline can completely inhibit rMMP1c activity, while Ba2+, Ca2+, and Mg2+ can significantly elevate it. TIMP is also expressed using HEK 293F cells. Recombinant TIMP (rTIMP) shows good inhibitory activity toward rMMP1c. Inhibition kinetics analyses reveal rTIMP to be a competitive inhibitor of rMMP1c. Biolayer interferometry reveals that rTIMP can effectively bind with rMMP1c, with an equilibrium dissociation constant value of 263 nM. rMMP1c effectively degrades type I collagen γ-ß-α chains in turn, and rTIMP can significantly inhibit rMMP1c degradation activity. These results provide a theoretical basis for the study of MMP and TIMP interaction and elucidate the possible mechanism for abalone tissue self-degradation.

The Life Cycle Transitions of Temperate Phages: Regulating Factors and Potential Ecological Implications.

Phages are viruses that infect bacteria. They affect various microbe-mediated processes that drive biogeochemical cycling on a global scale. Their influence depends on whether the infection is lysogenic or lytic. Temperate phages have the potential to execute both infection types and thus frequently switch their infection modes in nature, potentially causing substantial impacts on the host-phage community and relevant biogeochemical cycling. Understanding the regulating factors and outcomes of temperate phage life cycle transition is thus fundamental for evaluating their ecological impacts. This review thus systematically summarizes the effects of various factors affecting temperate phage life cycle decisions in both culturable phage-host systems and natural environments. The review further elucidates the ecological implications of the life cycle transition of temperate phages with an emphasis on phage/host fitness, host-phage dynamics, microbe diversity and evolution, and biogeochemical cycles.

Screening and Characterization of Shark-Derived VNARs against SARS-CoV-2 Spike RBD Protein.

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is the major target for antibody therapeutics. Shark-derived variable domains of new antigen receptors (VNARs) are the smallest antibody fragments with flexible paratopes that can recognize protein motifs inaccessible to classical antibodies. This study reported four VNARs binders (JM-2, JM-5, JM-17, and JM-18) isolated from Chiloscyllium plagiosum immunized with SARS-CoV-2 RBD. Biolayer interferometry showed that the VNARs bound to the RBD with an affinity KD ranging from 38.5 to 2720 nM, and their Fc fusions had over ten times improved affinity. Gel filtration chromatography revealed that JM-2-Fc, JM-5-Fc, and JM-18-Fc could form stable complexes with RBD in solution. In addition, five bi-paratopic VNARs, named JM-2-5, JM-2-17, JM-2-18, JM-5-18, and JM-17-18, were constructed by fusing two VNARs targeting distinct RBD epitopes based on epitope grouping results. All these bi-paratopic VNARs except for JM-5-18 showed higher RBD binding affinities than its component VNARs, and their Fc fusions exhibited further enhanced binding affinities, with JM-2-5-Fc, JM-2-17-Fc, JM-2-18-Fc, and JM-5-18-Fc having KD values lower than 1 pM. Among these Fc fusions of bi-paratopic VNARs, JM-2-5-Fc, JM-2-17-Fc, and JM-2-18-Fc could block the angiotensin-converting enzyme 2 (ACE2) binding to the RBD of SARS-CoV-2 wildtype, Delta, Omicron, and SARS-CoV, with inhibition rates of 48.9~84.3%. Therefore, these high-affinity VNAR binders showed promise as detectors and therapeutics of COVID-19.

Amelioration of Androgenetic Alopecia by Algal Oligosaccharides Prepared by Deep-Sea Bacterium Biodegradation.

Androgenetic alopecia (AGA) is a dihydrotestosterone (DHT)-mediated hair loss disorder characterized by shortened anagen hair cycle. Oligosaccharides derived from seaweeds possess diverse biological functions. However, little is known about their effects on AGA. In this study, algal oligosaccharide (AOS) was characterized for its mitigation effects on key features involved in AGA pathogenesis, such as DHT- mediated cellular signaling and shortened anagen hair cycle. AOS with varying degrees of polymerization (DP), namely, AOS (DP2), AOS (DP4-6), and AOS (DP8-12), were prepared by agar biodegradation with Flammeovirga pacifica WPAGA1, an agarolytic bacterium isolated from deep-sea sediments. In vitro results showed that AOS with varying DPs significantly ameliorated the DHT-induced alterations of regulatory factors in human hair follicle dermal papilla cells in a dose- and DP-dependent manner, as revealed by the normalization of several hair-growth-stimulating or inhibitory factors. In vivo studies showed that AOS (DP2) extended the anagen phase and thereby delayed catagen progression in mice. Furthermore, AOS (DP2) stimulated dorsal hair growth in mice by increasing hair length, density, and thickness. Therefore, our findings indicated that AOS antagonized key factors involved in AGA pathogenesis, suggesting the potential application of AOS in the prevention and the treatment of AGA.

Characterization and crystal structure of prolyl endopeptidase from abalone (Haliotis discus hannai).

Aimed to study the characteristics of prolyl endopeptidase (PEP, EC 3.4.21.26) and its possible role in the degradation of collagen, we cloned the full-length cDNA sequence of PEP from abalone (Haliotis discus hannai) (Hdh-PEP). Recombinant Hdh-PEP (rHdh-PEP) was expressed in vitro, its enzymatic properties were detected, and its secondary structure was analyzed by Circular Dichroism (CD). We for the first time determined the 1.5 Å crystal structure of rHdh-PEP. The decomposition effect of rHdh-PEP on collagen peptides was analyzed. Our data revealed that the molecular weight of rHdh-PEP is 85 kDa, consisting of a catalytic domain and a ß-propeller domain. The optimal pH and temperature of rHdh-PEP were pH 6.0 and 20 °C, respectively. Using small collagen peptides as substrates, HPLC-ESI-MS analysis confirmed that rHdh-PEP specifically cleaved at the carboxyl side of proline residues, suggesting its role in the degradation of collagen peptides during autolysis.

Caspase-3C gene from red swamp crayfish, Procambarus clarki: Characterization and expression in response to pathogenic infection.

The caspase is an essential module in the Drosophila immune deficiency (IMD) pathway, which plays a crucial role in countering pathogen infection. In this study, a gene named PcCaspase-3C was found in Procambarus clarkia with a full-length of 4684 bp, including a 1572 bp opening reading frame, which encoded a putative protein of 523 amino acids. PcCaspase-3C contained a CASc domain constituted of 237 amino acids. The PcCaspase-3C gene was primarily expressed in heart, stomach, and intestine, while less in gonad, hepatopancreas, gills, and hemocytes, with the least expression in muscle. Infection with Staphyloccocus aureus, Vibrio parahaemolyticus or white spot syndrome virus (WSSV) induced an up-regulated expression of PcCaspase-3C in intestine or stomach to varying degrees. When PcCaspase-3C was silenced by double-stranded RNA, the expression of some antimicrobial peptides such as ALF2, ALF5, ALF6, Cru3, Cru4, and Lys was significantly inhibited. In addition, silencing of PcCaspase-3C accelerated infection with WSSV in vivo. According to these results, we suggest that PcCaspase-3C might play a crucial role in the immune response of P. clarkia against pathogenic bacterial and viral infections.

Biochemical characterization of G64W mutant of acidic beta-crystallin 4.

Crystallins are structural proteins in the lens that last a lifetime with little turnover. Deviant in crystallins can cause rare but severe visual impairment, namely, congenital cataracts. It is reported that several mutations in the acidic ß-crystallin 4 (CRYBA4) are related to congenital cataracts. However, the pathogenesis of these mutants is not well understood at molecular level. Here we evaluate the biochemical properties of wild type CRYBA4 (CRYBA4WT) and a pathogenic G64W mutant (CRYBA4G64W) including protein folding, polymerization state and protein stability. Furthermore, we explore the differences in their interactions with α-crystallin A (CRYAA) and basic ß-crystallin 1 (CRYBB1) via yeast two-hybrid and pull-down assay in vitro, through which we find that G64W mutation leads to protein misfolding, decreases protein stability, blocks its interaction with CRYBB1 but maintains its interaction with CRYAA. Our results deepen our understanding of the pathogenesis of congenital cataracts.

Nucleus-translocated matrix metalloprotease 1 regulates innate immune response in Pacific abalone (Haliotis discus hannai).

As an important economical shellfish in coastal area of China, abalone is susceptible to bacterial infection, especially Vibiro parahemolyticus (V. parahemolyticus). Matrix metalloproteinases (MMPs) have been extensively investigated in the immune response of mammals. However, little is known about the involvement of MMP in abalone innate immune system against pathogen infection. In this study, the role of MMP-1 in the immune response of Pacific abalone (Haliotis discus hannai) was explored. The results showed that V. parahemolyticus infection induced significantly elevated expression of MMP-1 as well as immune related genes including allograft inflammatory factor 1 (AIF-1), macrophage expressed gene 1 (MPEG-1) and TPA-inducible sequence 11 family protein (Tis11FP). Notably, silencing of MMP-1 reduced the expression of these genes, suggesting that MMP-1 was an upstream regulatory factor in V. parahemolyticus infection. Further analysis showed that MMP-1 was engaged in the regulation of cellular (phagocytosis, apoptosis) and humoral [superoxide dismutase (SOD), alkaline phosphatase (ALP), acid phosphatase (ACP)] immunity. Interestingly, the extracellularly distributed MMP-1 could be translocated to the nuclei of hemocytes, thereby functioning as a transcriptional regulator or by selectively activating or inactivating other components through proteolysis. Hence, our study established an important role of MMP-1 in abalone innate immunity against V. parahemolyticus infection and it represented the first report on the investigation of MMP in abalone.

Purification, Characterization, and Crystal Structure of Parvalbumins, the Major Allergens in Mustelus griseus.

Fish play important roles in human nutrition and health, but also trigger allergic reactions in some population. Parvalbumin (PV) represents the major allergen of fish. While IgE cross-reactivity to PV in various bony fish species has been well characterized, little information is available about allergens in cartilaginous fish. In this study, two shark PV isoforms (named as SPV-I and SPV-II) from Mustelus griseus were purified. Their identities were further confirmed by mass spectroscopic analysis. IgE immunoblot analysis showed that sera from fish-allergic patients reacted to both SPV-I and SPV-II, but the majority of sera reacted more intensely to SPV-I than SPV-II. Thermal denaturation monitored by CD spectrum showed that both of the SPV allergens are highly thermostable. SPV-I maintained its IgE-binding capability after heat denaturation, while the IgE-binding capability of SPV-II was reduced. The results of crystal structure showed that SPV-I and SPV-II were similar in their overall tertiary structure, but their amino acid sequences shared lower similarities, indicating that the differences in the IgE-binding capabilities of SPV-I and SPV-II might be due to differential antigen epitopes in these two isoforms.

Involvement of clip-domain serine protease in the anti-Vibrio immune response of abalone (Haliotis discus hannai)-Molecular cloning, characterization and functional analysis.

Vibrio parahemolyticus (V. parahemolyticus) is a major pathogen for abalone, an important economical shellfish in coastal area of China. There is little known about the abalone innate immune system against pathogen infection. Clip-domain serine proteases (cSPs) are increasingly recognized to play important roles in host immune defense in invertebrates. In this study, we cloned a cSP (Hdh-cSP) from abalone (Haliotis discus hannai). We found out that Hdh-cSP was widely expressed in multiple tissues of abalone, with highest level in the immune-like organ, hepatopancreas. V. parahemolyticus infection induced significantly elevated expression of Hdh-cSP in addition to better-characterized innate immune component genes including Rel/NF-κB, allograft inflammatory factor (ALInFa), macrophage expressed protein (MEP) and caspase-8. Importantly, the silencing of Hdh-cSP reduced the expression of these genes, suggesting that Hdh-cSP was an upstream regulatory factor in V. parahemolyticus infection. Further analysis showed that apoptosis of hemocytes was inhibited when the transcription of Hdh-cSP was knocked down, suggesting that Hdh-cSP participated in cell apoptosis by regulation of caspase 8 expression in V. parahemolyticus infection. Therefore, our study established an important role of cSP in the innate immunity against V. parahemolyticus infection in abalone.

Conjugated polymer nanomaterials for theranostics.

Conjugated polymer nanomaterials (CPNs), as optically and electronically active materials, hold promise for biomedical imaging and drug delivery applications. This review highlights the recent advances in the utilization of CPNs in theranostics. Specifically, CPN-based in vivo imaging techniques, including near-infrared (NIR) imaging, two-photon (TP) imaging, photoacoustic (PA) imaging, and multimodal (MM) imaging, are introduced. Then, CPN-based photodynamic therapy (PDT) and photothermal therapy (PTT) are surveyed. A variety of stimuli-responsive CPN systems for drug delivery are also summarized, and the promising trends and translational challenges are discussed.

Smart conjugated polymer nanocarrier for healthy weight loss by negative feedback regulation of lipase activity.

Healthy weight loss represents a real challenge when obesity is increasing in prevalence. Herein, we report a conjugated polymer nanocarrier for smart deactivation of lipase and thus balancing calorie intake. After oral administration, the nanocarrier is sensitive to lipase in the digestive tract and releases orlistat, which deactivates the enzyme and inhibits fat digestion. It also creates negative feedback to control the release of itself. The nanocarrier smartly regulates activity of the lipase cyclically varied between high and low levels. In spite of high fat diet intervention, obese mice receiving a single dose of the nanocarrier lose weight over eight days, whereas a control group continues the tendency to gain weight. Daily intragastric administration of the nanocarrier leads to lower weight of livers or fat pads, smaller adipocyte size, and lower total cholesterol level than that of the control group. Near-infrared fluorescence of the nanocarrier reveals its biodistribution.

Conjugated Polymer Nanoparticles for Fluorescence Imaging and Sensing of Neurotransmitter Dopamine in Living Cells and the Brains of Zebrafish Larvae.

Nanoscale materials are now attracting a great deal of attention for biomedical applications. Conjugated polymer nanoparticles have remarkable photophysical properties that make them highly advantageous for biological fluorescence imaging. We report on conjugated polymer nanoparticles with phenylboronic acid tags on the surface for fluorescence detection of neurotransmitter dopamine in both living PC12 cells and brain of zebrafish larvae. The selective enrichment of dopamine and fluorescence signal amplification characteristics of the nanoparticles show rapid and high-sensitive probing such neurotransmitter with the detection limit of 38.8 nM, and minimum interference from other endogenous molecules. It demonstrates the potential of nanomaterials as a multifunctional nanoplatform for targeting, diagnosis, and therapy of dopamine-relative disease.

pH-Responsive and near-infrared-emissive polymer nanoparticles for simultaneous delivery, release, and fluorescence tracking of doxorubicin in vivo.

Dextran modified with pendant acetals is used to load doxorubicin (DOX) and a near-infrared-emissive conjugated polymer (BTTPF), and this aims to provide selective drug release at therapeutic targets including tumors. The BTTPF is applicable to tracking the anticancer drug release through the change of Förster resonance energy transfer efficiency between doxorubicin and BTTPF during degradation of the nanoparticles in vivo.

A fluorescence-Raman dual-imaging platform based on complexes of conjugated polymers and carbon nanotubes.

The present study describes a flexible nanoplatform based on electrostatic assembly of conjugated polyelectrolytes (CPEs) and carboxylated multi-walled carbon nanotubes (cMWNTs). It is demonstrated that the obtained nanocomposites inherit intrinsic optical properties of CPEs and characteristic Raman vibration modes of MWNTs, providing a fluorescence-Raman dual-imaging method for intracellular tracking and locating of MWNTs. We suggest that the cellular internalization of the CPE-cMWNT nanocomposites is a surface charge-dependent process. The strengths of this nanoplatform include satisfying biocompatibility, enhanced protein-repellent property, and ease of implementation, making it available for both in vitro and in vivo applications.