Abstract: Objective More than 200 million people are visually impaired or blind worldwide. Artificial vision system has been widely studied for a long time. There are two main technical paths for the research of artificial vision system, the first is implantable artificial vision device, and the second is non-implantable and wearable device. This study demonstrates a non-implantable system prototype based on a wearable touch-vision device designed for the head that can help blind people and visually impaired people complete complex tasks in life such as walking.Methods The image information front of the subjects is collected, and transmitted wirelessly to the operator. After analyzed and processed, it is wirelessly transmitted to wearable devices such as headgears in the form of tactile coding to trigger the multi-point head tactile sensation, thus the subject’s information or precise action instructions is obtained. The system also assists the subjects with voice information, allowing them to learn more about road conditions and environmental information.Results 5 healthy volunteers (2 males and 3 females) and 1 young blind person (male) were tested with the prototype. The results show that, the prototype makes full use of the head’s natural distinguishing ability for directions including front, back, left and right, and quick response ability to the touch, and the prototype can send clear instructions such as going straight, adjusting to the left or right, and turning. The test showed that the response time of subjects to tactile commands was within 0.5 s, and the mean value of the standard deviation of the deviation of walking for about 7 m is reduced to (16± 10) cm compared with the case without wearing the device.Conclusion Experimental results show that the system can provide environmental image information in a concealed and accurate manner, and help visually impaired people complete daily activities such as walking, avoiding obstacles, going up steps, entering cafes and other public places, fetching objects on the table, which meets expectations of assisting blind people improve their quality of life. In the future, the prototype system will be further improved, especially miniaturization and smart chip. The tactile devices are made into neck rings, belts, bracelets, foot rings, etc., which will be widely used in a variety of work scenarios such as travel assistance for the blind, night field trips, and deep sea diving.
Abstract: The unique three-dimensional structure of protein is closely related to its biological function. Therefore, investigating the three-dimensional structure of protein is helpful to reveal its biological function mechanism. The study of protein three-dimensional structure in the solution state using nuclear magnetic resonance (NMR) spectroscopy can accurately reveal the relationship between protein structure and biological function. The aim of this article is to provide an effective strategy for accurate analysis of protein three-dimensional structure using NMR and combination with other biophysical means such as molecular modeling and computation methods through reviewing the research progress and latest technology in these fields. Firstly, we summarize the theory of NMR for studying protein three-dimensional structure. Secondly, we deeply review the theory and technology of NMR analysis of protein three-dimensional structure, including isotope labeling of proteins (labeling methods, expression systems, and purification techniques), NMR data acquisition and analysis software, analysis of amino acid sequence, secondary structural unit and three-dimensional structure of protein using NMR and combination with other biophysical means (F?rster/fluorescence resonance energy transfer (FRET), chemical cross-linking coupled with mass spectrometry (CXMS), small angel X-ray scattering (SAXS), and cryo-electron microscopy (Cryo-EM)), and analysis of excited state structure of protein molecules using Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG RD) and chemical exchange saturation transfer (CEST) techniques. Thirdly, we overview recent researches about application of NMR for analysis of three-dimensional structure of high molecular mass single chain protein and supramolecular protein complex. Fourthly, we elaborate the latest progress in the field of NMR combined with molecular modeling and computation methods. Lastly, we summarize challenges and prospects of application of NMR for studying protein three-dimensional structure in the future.
Abstract: The neurons can transform different spatiotemporal patterns of synaptic inputs to the action potential sequences with high temporal precision. This flexible and reliable information coding strategy plays a crucial role in the process by which the nervous system generates the specific activity patterns required by dynamical situation or specific task. The initiation of an action potential follows an all-or-none principle. When the depolarization of membrane potential exceeds a threshold value, the neuron fires an action potential. The action potential threshold is highly variable within and between cells, and its specific dynamics depends on the stimulus input and firing history. In particular, the spike threshold is sensitive to the membrane voltage changes preceding the action potential. Two primary biophysical mechanisms for such state dependence of the spike threshold are Na+ inactivation and K+ activation. In most neurons, the action potentials are initiated in the axon initial segment, and the threshold variability at this site is the crucial factor that determines how neurons transfer spatiotemporal information. However, the action potentials in electrophysiological experiments are recorded in the cell body or proximal dendrite. The threshold variability at these sites is higher than that in the axon initial segment, which mainly arises from the backpropagation of axonal action potentials. Based on somatic recordings, it is shown that the spike threshold dynamics determines the transformation principle of spatiotemporal information in the neurons, which enhances the temporal coding, feature selectivity, gain modulation, and coincidence detection. In this paper, we first introduce the conception of spike threshold and its calculation methods. Then, we present an exhaustive review on the main findings of the spike threshold variability and its origins in recent years, and mainly discuss the significance of spike threshold variability for neuronal coding. Finally, we raise several key issues on the spike threshold that need to be addressed in the future.
Abstract: Kelch-like ECH associated protein 1(Keap1), a typical substrate-recognition subunit of the Cul-RING E3 ligase, plays a significant role in ubiquitination. Ubiquitination, an important post-translational modification, enables a degradation signal in both autophagy and ubiquitin-proteasome system. Recently, several substrates can be recognized and binded by wild-type Keap1, and subsequently degraded by ubiquitin proteasome system (UPS) via Keap1-Cul3-Rbx1 complex. Additionally, Keap1 has also been widely studied as a tumor suppressor protein, and mutation or abnormally deletion of Keap1 alleles contributes to different kinds of diseases. The study of Keap1 has mainly concentrated on the Keap1-Nrf2 axis, but rarely extends to downstream substrates. Given that the great importance of Keap1 in cells, this review summarizes the current research status of Keap1, including ubiquitin-proteasome system, Keap1’s structure and function, the mutation of Keap1, the substrates of Keap1, and Keap1-related diseases. It may provide a new thought for targeted therapy of Keap1-associated diseases through discussing the challenges of Keap1-related fields in clinic.
Abstract: The interferon (IFN) signaling pathway is an important cellular defense mechanism against microorganism invasion. By sensing pathogen-associated molecular patterns (PAMPs) and transmitting signaling through the downstream cascades, IFN is robustly induced in expression and secreted to activate numerous genes’ expression in self and neighboring cells. Products of these induced genes then participate in restricting infection and modulating the immune system to further respond. This process needs to be properly regulated, for its aberrant activation under non-infectious conditions results in inflammation and onset of autoimmune diseases in the host. The correct recognition of “self” and “non-self” is the first step to control. Given the fact that nucleic acids of microorganisms are important immunogenic sources to the IFN signaling, the endogenous DNA/RNA metabolisms then must be faithfully conducted and strictly regulated. A series of enzymes, using them as substrates, work at different pathways to maintain this homeostasis. Intensive investigations on mechanisms of autoimmune diseases highlighted the protective role of these enzymes. Take Aicardi-Goutières syndrome (AGS) as an example, a monogenic type I interferonopathy, 9 mutated genes have been identified separately in patients so far, including DNA metabolism involved genes TREX1, RNASEH2A, RNASEH2B, RNASEH2C, and SAMHD1, RNA-related genes ADAR1 and IFIH1, and two recently identified genes, LSM11 and RNU7-1 whose correct activity is required for histone expression. Aberrant DNA metabolism or damaged histone expression activates IFN signaling through the cGAS-STING axis, while RNA errors sensitize the MDA5-MAVS axis. Thus, despite these 9 mutations all leading to the aberrant activation of IFN signaling, they can rely on different mechanisms, implicating that even having the same symptoms clinically the optimized treatment can be different. We thus argue the importance and necessity of diagnosing at the genetic level to the treatment of complicated symptoms and hope this review benefits the understanding of the pathogenesis of autoimmune diseases.
Abstract: Liposomes are hollow spheres composed of lipids bilayer membranes, which can encapsulate and deliver hydrophilic and hydrophobic substances. Liposomes are promising nano-drug delivery systems due to low immunogenicity, good stability, low toxicity and cost. Currently, a variety of liposome drugs for tumor treatment have been listed. Liposomes can accumulate in tumor tissues via enhanced permeability and retention effect (EPR) and are internalized into tumor cells by endocytosis or pinocytosis. Subsequently, liposomes are intracellularly cleaved to release drugs, thereby killing tumor cells. Liposomes that rely on the EPR effect are called passive targeting liposomes, which lack the ability to specifically recognize target tissues. However, active targeting liposomes can achieve targeting delivery via the specific binding between the targeting modifiers on the surface of liposomes and receptors on the surface of tumor cells. These receptors such as peptides, carbohydrates, ligands, antibodies and nucleic acid aptamers on the surface of tumor cells overexpress due to rapid growth of tumor cells and needs of nutrients and related growth factors. Thus, liposomes can be reasonably designed according to these specific receptors. Recent years, some studies have reported biomimetic liposomes by coating the cell membrane on the surface of liposomes, however, the research on biomimetic liposomes is still in its infancy, and there are still many problems to be solved. Additionally, since the length is limited, biomimetic liposomes are not reviewed in this paper. Taken together, liposomes as potential drug carriers, not only protect drugs, but also reduce side effects, importantly, they can precisely target tumor tissues through introducing targeting modifiers. In this work, we review the improvement of targeting function of liposome by five targeting modifiers including peptides, carbohydrates, ligands, antibodies and nucleic acid aptamers, and summarize the existing advantages and challenges of various targeted modifications. Finally, this review is expected to provide scientific reference for the LPs drug delivery system study and theoretical basis for the drug development.
Abstract: Chromatin accessibility refers to the level of physical compaction of chromatin, which is determined by the chromatin binding factors that hinder DNA contact, nucleosome occupancy and topological structure. The chromatin accessibility pattern will be changed dynamically with external stimuli and developmental cues. Analyzing the TF (transcription factor) binding sites in the regulatory regions within the accessible chromatin can provide insight into the lineage factors and gene regulatory networks of specific cell types. Combined with high-throughput sequencing technology, several biochemical methods have been developed to describe the accessibility of chromatin, including bulk and single-cell level analysis. Depending on the techniques, the using enzymatic cleavage (DNase/MNase), transposition (Tn5) or physical methods (FAIRE) to isolate the accessible chromatin and subsequently using the high-throughput sequencing provide a genome-wide panorama of chromatin organization. This review introduced the common techniques (DNase-seq, MNase-seq, FAIRE-seq, and ATAC-seq) for determining chromatin accessibility and nucleosome positioning. The advantages and disadvantages of these 4 chromatin accessibility analysis techniques were summarized and compared. Their principles and main experimental procedures were introduced in detail; the development and application of related technologies were briefly discussed. The ATAC-seq based single-cell chromatin accessibility analysis and the view of potential useful were specially introduced. Although the chromatin accessibility profile is very valuable for studying gene regulation, it only provides a partial view of this complex process. We envision that technological improvements including single-molecule, multi-omics and spatial methods will bring further insight into the secrets of genome regulation.
Abstract: Objective To study the anti-breast cancer effects and molecular mechanisms of syringin, and to provide a theoretical basis for the clinical application of syringin.Methods The inhibitory effect of syringin on the proliferation of breast cancer cells was measured with MTT assay. Trypan blue, TdT-mediated dUTP nick-end labeling (TUNEL), and Annexin V-FITC/PI staining were used to detect apoptosis. Caspase-3 activation was detected via Western blot to determine whether apoptosis occurred. The expression of apoptosis-associated protein B-cell lymphoma-2 (Bcl-2) was detected and the effect of syringin on the mitochondrial apoptosis pathway was investigated via JC-1 staining. The PI3K agonist Recilisib was used for comparison. qRT-PCR and Western blot were used to assess the role of syringin in regulating the PI3K/Akt/mTOR pathway and inducing the apoptosis of cancer cells.Results Syringin had a time- and dose-dependent inhibitory effect on the proliferation of breast cancer cells and induced their apoptosis. A further study showed that after syringin treatment, Caspase-3 was activated, Bcl-2 expression decreased, the mitochondrial membrane potential was significantly reduced, and the mRNA and protein expressions of PI3K, Akt, and mTOR were not significantly changed, but the protein phosphorylation levels were significantly decreased. Recilisib partially limits the effect of syringin on the apoptosis of breast cancer cells.Conclusion Syringin has a good inhibitory effect on MDA-MB-231 and MCF-7 breast cancer cells. It can inhibit cell proliferation and induce mitochondrial apoptosis by inhibiting the activation of the PI3K/Akt/mTOR signaling pathway. Syringin is a potential anti-breast cancer drug.
Abstract: As a new type of organoid model, skin organoids can reconstruct and modify different types of cells and appendages with specific functions such as umbilical cord blood stem cells, induced pluripotent stem cells, keratinocytes and fibroblasts, as well as sebaceous glands, sweat gland and hair follicles under special habitats, which can not only highly simulate the physiological structure and function of skin tissues, but also better restoring more realistic skin ecology under different in vitro environments. It can also be used in the fields of skin wound regeneration, skin tumor, immune and metabolic diseases, treatment of inflammatory diseases and drug screening. Meanwhile, skin organoids can not only make up for the deficiencies of existing in vitro skin models in terms of structure and function, but also enable high-throughput screening of drugs or raw materials, reducing the time and economic costs in the later stages of drug screening. However, due to the limitations of current technology, the types and functions of organoids cannot be fully realized to realistically simulate the physiological conditions in the body such as lipid metabolism and blood circulation. Moreover, issues such as consistency and standardization of mass-produced organoids need to be addressed, such as source cells, structure and function, which require the establishment of appropriate standards based on practical applications. Based on this, this paper details the cell sources involved in skin organoids construction and their applications in recent years and several skin appendages like organs that have been constructed and provides an outlook on the future development and optimization of skin organoids.
Abstract: With the continuous development of nanotechnology, nanoformulations show unique advantages in improving drug delivery and bioavailability. However, most nanocarriers have low drug delivery efficiency, poor therapeutic effect, potential systemic toxicity and metabolic instability. In recent years, self-assembled carrier-free nanodrugs have attracted tremendous attentions in the field of biomedicine due to their unique properties such as high drug loading capacity, low toxicity, and facile synthesis. Therefore, the self-assembled carrier-free nanodrugs exhibit broad application prospects and development potential in biomedical fields, especially in anticancer and antibacterial applications. In this review, we firstly give a brief introduction to the various intermolecular interactions of self-assembly carrier-free nanodrugs, including the hydrogen bonding, π-π stacking, hydrophobic interaction and other non-covalent forces as exemplified by electrostatic interaction and Van der Waals forces. The chemical structures of drug molecules determine the strength of non-covalent interactions. Secondly, we provide an overview of the typical methods used for self-assembly of carrier-free nanodrugs including in vitro self-assembly strategy (e.g., top-down, anti-solvent precipitation, template-assisted precipitation) and in vivo self-assembly strategy. Especially, nanodrugs prepared by in vivo self-assembly method can be targeted and self-assembled at the target location, reducing adverse reactions and achieving higher efficacy. Besides, the application of carrier-free nanodrugs in biomedical fields including anticancer, antibacterial, anti-inflammatory as well as antioxidant are comprehensively reviewed. Finally, the future challenges and development trends of carrier-free nanodrugs are also prospected, which may provide a theoretical basis for the rational design of more effective self-assembly vector free nano drugs and the feasibility of clinical application.
Abstract: Brain and muscle arnt-like protein 1 (Bmal1) is the core gene of biological clock, which belongs to the transcription factor family of bHLH-PAS (basic helix-loop-helix-per-arnt-sim) domain. It can regulate the circadian rhythm through its own expression and the transcription-translation feedback regulation of the biological clock, which plays an important role in the life activities of organism. The disorder of biological clock induces a series of chronic metabolic diseases, such as cardiovascular diseases, hepatopathy and neurodegenerative diseases, usually accompanied by abnormal expression of Bmal1. Exercise may up-regulate Bmal1 expression in peripheral tissues and organs to improve chronic metabolic diseases. Different exercise loads and types of exercise, such as aerobic exercise, resistance exercise, will lead to the differential expression of Bmal1. There are many potential mechanisms of Bmal1 in improving chronic metabolic diseases by exercise intervention, such as reducing inflammation and oxidative stress, regulating autophagy, maintaining mitochondrial quality and function, interacting with exerkines and microRNA. This article reviews the physiological function of Bmal1 in multiple tissues and organs and the relationship between corresponding chronic metabolic diseases, discussing the influence of exercise intervention on Bmal1 expression deeply and putting forward the potential mechanism of Bmal1 in improving chronic metabolic diseases by exercise, in order to provide a new perspective for exercise as a non-drug treatment to prevent and treat chronic metabolic diseases.
Abstract: Endothelial cells, as non-excitable cells, were previously thought to lack functional voltage-gated calcium channels (VGCC), such as human umbilical vein endothelial cells, bovine pulmonary artery endothelial cells, bovine aortic endothelial cells, and bovine aorta endothelial cells. With the development of patch clamp technology, fluorescence microscopy technology, and polymerase chain reaction (PCR) technology, more and more VGCC are found in various endothelial cells, such as human aortic endothelial cells, rat aortic endothelial cells, and rat pulmonary microvascular endothelial cells. At present, there are 3 main detection methods for the existence of VGCC: the detection of ion channel current by patch clamp technology, the detection of intracellular calcium ion concentration change by fluorescence microscopy technology, and the detection of ion channel gene or protein expression by PCR. Endothelial cells are not only the physical barrier between blood and other adjacent tissue cells and matrix proteins, but more importantly, exert a significant influence on the physiological changes of cell and vascular tissues through the opening and closing of VGCC on the cell membrane. On the one hand, the effect of VGCC on the change of intracellular calcium ion concentration controls the release of vasodilators such as nitric oxide (NO) and regulates the balance of vascular tone. On the other hand, VGCC, which is an important route for calcium ion inflow, affects endothelial cell migration and proliferation through the induction of a kind of small G protein (Ras) and mitogen-activated proteinkinase kinase (MEK) pathways, the phosphonic acidification of phosphatidylinositol 3 kinase (PI3K) and serine/threonine protein kinase (Akt) pathways. In addition, some physiological phenomena, such as mechanical strain generated by intravascular pressure and shear stress associated with blood flow, activate VGCC by activating mechanical bodies, causing the ATP-sensitive potassium channel () channel to close, causing endothelial cell membranes to depolarize; the binding of some receptors and ligands and the opening and closing of ion channels require the participation of VGCC, such as the opening and closing of potassium ion channels with bradykinin as activator and cation channels with histamine as activator. Hence,in view of the important functions of VGCC in regulating the excitability, secretion and migration of endothelial cells, in-depth and extensive research on VGCC is of great significance for revealing and treating endothelial functional diseases such as essential hypertension and atherosclerosis.
Abstract: Peptide∶N-glycanase (PNGase) is a deglycosylation enzyme widely presented in fungi, plants, mammals and other eukaryotics. Only two bacterial PNGase have being isolated (PNGase F and PNGase F-II) thusfar, and both are used widely as research tools in glycomics. PNGase catalyzed the hydrolysis of the amide bond between N-acetylglucosamine and an Asn residue on an N-glycoprotein, generating a de-N-glycosylated protein and a complete N-oligosaccharide. After the reaction, the N-glycosylated Asn residue was converted to Asp. Although it is known that PNGase participates in protein degradation, organ development, individual growth and other key biological processes in organisms, its impacts on health was illustrated only recently. Human PNGase (NGLY1) deficiency could lead to a genetic disease named congenital disorder of deglycosylation-NGLY1. A nematode PNGase deficiency could reduce its life span. Its defects in mice could be embryonic lethal. This article describes the distribution, protein structure, and biological function of PNGase in different species. It can serve as an important information resource to support basic research for PNGase mechanism and innovative study for PNGase applications.
Abstract: DNA damage repair (SOS response) plays an important role for bacteria to adapt to the environment, resist external pressure and repair DNA damage. In order to understand the process and comprehensively revealing the survival mechanism of bacteria, here we systematically review the studies of the process, regulation and subsequent adaptive results of DNA damage repair. The results show that both endogenous and exogenous pressures can activate the SOS response,especially antibiotics. RecA plays an important role in the process of sensing external pressure and system start-up process, and is also an important regulation target. As a repressor protein,LexA is an inhibitor of the whole response. After the SOS response starts, LexA releases a series of downstream DNA damage repair genes to complete the DNA repair.The adaptive results of SOS response are as follows: DNA precise repair,slowing down or stopping cell division, increasing of chromosome mutation rate, virulence or pathogenicity change, enhanced drug resistance or horizontal transmission of drug-resistance genes. Understanding the whole process of SOS response is helpful to reveal the survival and metabolism process of bacteria adapting to the environment, and lay a theoretical foundation for the prevention and control of pathogenic bacteria.
Abstract: Mitochondrial membrane integrity is so pivotal to cell survival that its damage can lead to apoptosis, pyroptosis or inflammation. The damage includes mitochondrial outer membrane permeabilization (MOMP), mitochondrial inner membrane permeabilization (MIMP), and mitochondrial permeability transition (MPT), which regulate different signaling pathways and thus lead to different cell fate outcomes. These signaling pathways are intersecting, which makes the involved mechanisms intricate and poorly understood. In this review, we firstly analysis the role of distinct degrees of MOMP in cell survival, tumorigenesis, and apoptosis, which may operate as a tristable switch. Then we discuss the molecular mechanism of MIMP in triggering inflammation through the release of mtDNA and envision that low order oligomers of Bak/Bax induce MOMP and promote apoptosis, while high order oligomers induce MIMP and cause inflammatory response. Furthermore, we clarify the working mechanisms of MOMP-induced apoptosis and MPT-driven pyroptosis under different stimulus intensities. Finally, we outline the intrinsic connection underlying cell-fate decision influenced by mitochondrial membrane integrity. Therefore, a deep understanding of the dynamical mechanisms of how mitochondrial membrane integrity regulates cell fate should give insight into the diagnosis and treatment of cancer and neurodegenerative diseases.
Abstract: Mass spectrometry-based proteomics aims to identify peptides and proteins to give direct proofs of gene expressions, analyze structures and functions of proteins, study the relationship between proteins and diseases, and provide targeted treatment options. All these studies are based on the credibility of identified peptides and proteins. However, it is impossible to manually check all identified peptides because a large number of identifications can be collected from one mass spectrometry experiment. Thus, target-decoy approach (TDA) is proposed and always used to control the quality of identified peptides and proteins, and has been expanded to subclasses of peptides (including ordinary subclasses of peptides, variant peptides, and modified peptides) and cross-linking peptides. However, TDA still has two limitations: (1) the estimation of false discovery rate (FDR) is inaccurate and (2) validation of single identification cannot be supported. Thus, the identification results that passed the TDA-based FDR control need to be further validated and other validation methods which are used after TDA-FDR filtration (referred to as Beyond-TDA methods) have been developed to enhance peptide validation. This paper reviews TDA and its extensions as well as Beyond-TDA methods and discusses the advantages and disadvantages of each method. In the first part of this paper, we introduce the goal of proteomics, the process of mass spectrometry acquisition and analysis, the validation problem, and the early statistical methods to evaluate the identification credibility. Then, in the second part of this paper, we describe in detail the ordinary TDA-FDR method, including the assumption that random matches are equally likely to appear in target and decoy databases, the construction methods to generate the decoy database, and the computational formula of TDA-FDR. We also introduce the extensions of TDA-FDR on ordinary subclasses of peptides, variant peptides, modified peptides, proteogenomics peptides, cross-linking peptides, and glycopeptides. However, TDA cannot model the homologous incorrect peptides, thus TDA-FDR underestimates the actual false rate. So, after TDA-FDR filtration, it is necessary to use more strict validation methods, i.e., Beyond-TDA methods, which are reviewed in detail in the third part of this paper, to control validation credibility. In this part, four kinds of methods are introduced, including validation methods based on search space (trap database validation and open search validation), spectra similarity (synthetic peptide validation and theoretical spectra prediction), chemical information (retention time prediction and stable isotopic labeling validation) and machine learning technology (Percolator, pValid, and DeepRescore). Lastly, we summarize the content of this paper and discuss the future improvement directions of validation methods.
Abstract: Plasma membrane disruptions have been documented under physiological conditions in lots of mechanically active tissues, such as in skeletal muscle, the stratified epithelium that covers our body, the endothelia that line our blood vessels, the epithelial barrier of our gastrointestinal tract. Timely and effective plasma membrane repair (PMR) mechanisms have evolved to rapidly reseal a membrane breach to ensure cell survival. Otherwise, these membrane disruption events initiate a “death cascade”. PMR is coordinated by many “tinkerers”, which have a clear division of labor and show certain timing characteristics. The endosomal sorting complexes required for transport (ESCRT) is the “tinkerer” found recently who plays a key role in the repair of plasma membrane disruptions. It is composed of ESCRT-0, ESCRT-I, ESCRT-II, ESCRT-III, VPS4-VTA1 and ALIX, which take part in the budding and the formation of multivesicular body (MVB). This paper reviews two repair methods mediated by ESCRT system with budding and the formation of MVB. The function of ESCRT complex in plasma membrane repair can improve membrane disruptions, which is able to be used as an effective prevention and treatment strategy for cancer, Alzheimer’s disease, muscle injury and muscular dystrophy.
Abstract: The vast majority of bacteria require iron for growth. Iron is an essential element required for key biological processes including amino acid synthesis, oxygen transport, respiration, nitrogen fixation, methanogenesis, the citric acid cycle, photosynthesis, and DNA biosynthesis. However, obtaining iron presents challenges for the majority of microorganisms. In the ocean, the distribution of iron in the marine environment is spatially heterogeneous, which is one of the main limiting factors affecting marine primary productivity. Dissolved iron is a scarce resource for marine creatures because it is mainly present as a less soluble trivalent state (Fe3+), which makes it prone to settling and being “removed”. Marine microorganisms are presented with unique challenges to obtain essential iron ions required to survive and thrive in the ocean. To obtain enough iron source for life metabolism, microorganisms have evolved many ways to meet the demand for iron intake, among which siderophores is the most representative one. Siderophores are low molecular mass iron-binding ligands produced by marine bacteria. Microbial siderophores are multidentate Fe3+ chelators used by microbes during siderophore-mediated assimilation. They possess high affinity and selectivity for Fe3+. Among them, marine siderophore-mediated microbial iron uptake allows marine microbes to proliferate and survive in the iron-deficient marine environments. Being an important metabolic cofactor, siderophores also strongly influences the circulation of other elements. In order to better understand the role of siderophores in marine microbial ecology and deepen our understanding of marine iron cycle dynamics, this paper summarizes the types of siderophores such as hydroxamates, catecholates and carboxylates, two main siderophores synthesis pathways of microorganism and the mechanism of regulating siderophores synthesis, describes the transmembrane transport process of siderophores and several functional protein elements, the functions of siderophores such as anti-oxidative stress, regulation of pathogen virulence, formation of multifunctional iron and sulfur polymers, and anti-pathogens and so on. Although siderophores have been studied and discussed, further research can be carried out in the following aspects, such as the interaction mechanism between siderophores and marine microorganisms, the application of synthetic biology, and the coupling ability of siderophores behavior with other elements.
Abstract: Oncolytic viruses (OVs) have been investigated for a century and have become one of the most advanced types of tumor immunotherapy. It is primarily a natural or genetically modified viruses, including DNA and RNA viruses. In recent years, with the rapid development of genetic engineering technology, the gene-modified oncolytic viruses have made great progress in the field of tumor treatment, several types of viruses (including HSV, adenovirus, poxvirus, measles virus, reovirus etc.) are currently in preclinical studies, clinical trials or have been approved in clinic, showing good safety and clinical efficacy. It is generally believed that oncolytic viruses target and kill tumor cells by selectively replicating themselves in tumor cells, and finally lysing and killing tumor cells. At the same time, they can stimulate the immune responses of the body, thus enhancing the antitumor immunity, the tumor cells can be targeted and killed with no obvious side effects. The combination of oncolytic virus and immune checkpoint by gene recombination and the breakthrough of tumor immunotherapy have made the application of oncolytic virus more extensive, however, there are still some bottleneck problems such as virus targeting, security and administration route. This review provides a comprehensive and detailed overview of the development of oncolytic viruses. We list some viruses have been used as candidates for lysis of cancer cells and the clinical trials in the field of oncolytic virotherapy. And we discuss about the immunological mechanism of oncolytic virus targeting to kill tumors, and the challenges and prospects in the future.
Abstract: The CRISPR/Cas system consists of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas). The system forms an adaptive immune system in archaea and bacteria. The inherent defense mechanism enables these microorganisms to protect themselves against the invasion of foreign genetic material. The system functions of immune response including three main stages: adaptation, expression/maturation, and interference, each stage needs specific Cas proteins encoded by Cas gene located near the CRISPR sequences, along with other auxiliary proteins. In 2015, Zhang et al. reported Cas12a (Cpf1) as a member of the Class II type V CRISPR/Cas12a system, which possesses endonuclease activity. This finding holds great promise for its application in the field of biotechnology. In 2018, Doudna’s team first applied the CRISPR/Cas12a system for detecting HPV nucleic acid. The system comprises the following essential components in vitro detection: Cas12a, the crRNA sequence complementary to the target DNA, the PAM sequence, and the ssDNA reporter. Cas12a possesses a typical RuvC domain, displaying a canonical bilobed architecture that consists of a recognition (REC) lobe and a nuclease (NUC) lobe. The REC lobe contains the REC1 and REC2 domains, and the NUC lobe includes RuvC, PAM-interacting (PI), Wedge (WED), and bridge helix (BH) domains. The mature crRNA for Cas12a has a length of 42-44 nt, consists of repeat sequence (19/ 20 nt) and spacer sequence (23-25 nt). The crRNA spacer sequence has been found to require a length of 18 nt to achieve complete cleavage activity in vitro. Additionally, mutation in the bases of crRNA can indeed affect the activity of Cas12a. The PAM sequence plays a critical role in the recognition and degradation of DNA by the CRISPR/Cas system, enabling the system to distinguish between self and non-self genomic materials. Cas12a can effectively target the spacer sequence downstream of a T-rich PAM sequence at the 5" end. LbCas12a and AsCas12a both recognize the PAM sequences of 5"-TTTN-3", while FnCas12a recognizes the PAM sequences of 5"-TTN-3". All of these PAM sequences are located upstream on the non-template strand (NTS) at the 5" end. Cas12a (Cpf1), guided by the crRNA, binds to the target DNA by recognizing the PAM sequence. It exhibits the ability to induce arbitrary cleavage of ssDNA within the system while cleaving the target ssDNA or dsDNA. According to this feature, an array of nucleic acid detection methods has been developed for tumor detection and infection diagnostics, such as the DETECTR (RPA-CRISPR/Cas12a method) and HOLMES (PCR-CRISPR/Cas12a method) in 2018. Then, in 2019, Cas12aVDet (one-step detection method), where Cas12a protein was immobilized on the upper wall of the reaction tube. This not only prevented contamination from opening the tube but also reduced the detection reaction time. In 2021, the dWS-CRISPR (digital warm-start CRISPR) was developed as a one-pot detection method. It serves as an accurate approach for quantitatively detecting SARS-CoV-2 in clinical specimens. With the innovation of scientific technology, the high-sensitivity signal transduction technology has also been integrated with the CRISPR/Cas12a system, enabling direct detection of nucleic acids, and eliminating the need for nucleic acid amplification steps. Here, we elaborated the detection principles of CRISPR/Cas12a in in vitro detection. We discussed the different stages leading to the catalytic pathway of target DNA, and the practical applications of Cas12a in nucleic acid detection. These findings revealed a target interference mechanism that originates from the binding of Cas12a-guided RNA complex to complementary DNA sequences within PAM-dependent (dsDNA) regions. The crRNA-DNA binding activates Cas12a, enabling site-specific dsDNA cleavage and non-specific ssDNA trans-cleavage. The release of Cas12a ssDNase activity provides a novel approach to enhance the sensitivity and specificity of molecular diagnostic applications. Before these CRISPR/Cas12a-based nucleic acid detection methods can be introduced into clinical use, substantial work is still required to ensure the accuracy of diagnosis. Nevertheless, we believe that these innovative detection tools based on CRISPR/Cas will revolutionize future diagnostic technologies, particularly offering significant assistance in pathogen infection diagnosis for developing countries with relatively poor healthcare conditions and high prevalence of infectious diseases.
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