Abstract:DNA polymerase theta (Polθ), also known as DNA polymerase θ, is the member of the DNA polymerase A family and plays a crucial role in the repair of DNA double-strand breaks (DSB). Polθ has 3 distinct structural domains: the N-terminal helicase-like domain with a conserved sequence, the C-terminal polymerase domain, and the central domain, which is a disordered sequence connecting these two regions. Notably, Polθ is the only known polymerase in eukaryotes that possesses helicase activity. However, it is also an error-prone polymerase. When DNA DSBs occur, a specialized network consisting of at least 4 pathways, including classical-non homologous end joining (C-NHEJ), homologous recombination (HR), single-strand annealing (SSA), and alternative-end joining (Alt-EJ), is responsible for repairing DNA damage caused by DSBs. In the absence of major DNA repair pathways like HR, cells rely on Alt-EJ pathway mediated by Polθ to repair damaged DNA and maintain genomic stability. Nevertheless, due to the low fidelity of Polθ, Alt-EJ repair often leads to errors. Depletion of Polθ has shown to increases DSB formation and compromise genomic stability. Conversely, overexpression of Polθ has been associated with increases DNA damage markers and impairs cell cycle progression. As a result, the impact of Polθ on genome stability remains controversial. Furthermore, overexpression of Polθ is frequently observed in cancer and is associated with a characteristic mutational signature and poor prognosis. Depleting Polθ in an HR-deficient background has been shown to impair cell viability, suggesting a synthetic lethal (SL) relationship between Polθ and HR factors. In recent years, targeted chemotherapy drugs that inhibit tumor growth have gained significant attention. However, off-target effects and drug resistance pose challenges for clinical application, particularly with poly-ADP-ribose polymerase inhibitor (PARPi). Blocking Polθ activity in HR-deficient tumor cells has been found to reverse PARPi resistance, making Polθ a very promising therapeutic target in cancer treatment. The availability of crystal structures for both helicase and polymerase domain has facilitated the design of potent inhibitors of Polθ. Currently, several highly specific and effective small molecule inhibitors targeting Polθ, such as Novobiocin, RP-6685, and ART558, have been reported to effectively block various cancers with HR deficiency. The initial success of these inhibitors points to new directions for treating BRCA1/2-mutated tumors. Additionally, reducing the Alt-EJ repair pathway mediated by Polθ can improve HR repair efficiency and increase the chance of exogenous gene target integration (TI), suggesting potential new applications for Polθ inhibitors. This article reviews the recent research progress on the molecular function of Polθ and its involvement in the Alt-EJ pathway modification mechanism, providing insights for a deeper understanding of this field.

Abstract:Mitochondrial quality control plays an important role in maintaining homeostasis of mitochondrial network and normal function of mitochondria. ATPase family AAA domain-containing protein 3A (ATAD3A) is one of the mitochondrial membrane proteins involved in the regulation of mitochondrial structure and function, mitochondrial dynamics, mitophagy and other important biological processes. Recent studies show that ATAD3A not only interacts with Mic60/Mitofilin and mitochondrial transcription factor A (TFAM) to maintain mitochondrial cristae morphology and oxidative phosphorylation, but also interacts with dynamin-related protein 1 (Drp1) to positively/negatively regulate mitochondrial fission. In addition, ATAD3A serves as a bridging factor between the translocase of the outer mitochondrial membrane (TOM) complex and translocase of the inner mitochondrial membrane (TIM) complex to facilitate the import of PTEN-induced putative kinase protein 1 (PINK1) into mitochondria and its processing displays a pro-autophagic or anti-autophagic activity. This article reviews the role and mechanism of ATAD3A in regulating mitochondrial quality control. Firstly, as an inner mitochondrial membrane protein, ATAD3A is involved in maintaining the stability of mitochondrial crista structure, and its gene deletion or mutation will cause the loss and breakage of crista. Secondly, ATAD3A is also involved in maintaining mitochondrial respiratory function and mitochondrial nucleoid homeostasis, and its gene deletion or mutation can reduce the activity of mitochondrial respiratory chain complex and enhance the size and movement of nucleoid. Thirdly, ATAD3A participates in the negative regulation of mitochondrial fusion, but its role in mitochondrial fission may dependent on specific cell types, as it can promote and/or inhibit the mitochondrial fission by increasing and/or decreasing phosphorylation or oligomerization of Drp1. Finally, ATAD3A can interact with mitophagy-related proteins (e.g. PINK1, autophagy/beclin-1 regulator 1 (AMBRA1), acylglycerol kinase (AGK)) to enhance/reduce PINK1-Parkin-dependent mitophagy.

Abstract:In prokaryotes like Escherichia coli (E. coli), transcription tends to be coupled with translation, which is usually manifested in the mutual regulation of transcription and translation such as transcription polarity, transcription attenuation and synchronization of transcription and translation rates. Indirect coupling and physical coupling are two different models of the coupling. Indirect coupling maintained by the alarmone (p)ppGpp may require the assistance of DksA and TufA proteins. Physical coupling could be divided into those mediated by NusG or RfaH factors and those induced via “collision” under non-factor condition. Changes in transcription or translation in response to pressure will lead to mutual transitions among several coupling modes. Coupling is necessary for normal gene expression, and its release will contribute to adverse events such as transcription termination, R-loop formation, conflict between replication and transcription and mRNA cleavage. The related technologies of structural biology have clearly demonstrated the structural details and characteristics of partial coupled expressomes. These technologies, combined with methods like multiomics analysis, will provide deeper insights into the coupling. Significantly, the study of the coupling may bring new ideas for development of the targeted antibiotics.

Abstract:The development of animal early embryos commences with the reprogramming of terminally differentiated gametes into totipotent zygotes following fertilization. During the initial stages of embryonic development, the transcriptional levels of zygotic genome remain silent and maternal gene products dominate the regulation of development. As embryonic development progresses, the maternal gene products undergo phased degradation while the zygotic genome gradually activates transcription, marking the transition from the maternal regulation to the zygotic genome regulation in early embryonic development, which is also referred to as the maternal-zygotic transition (MZT). Zygotic genome activation (ZGA) is a critical turning process in this transition, and its accurate occurrence is crucial for early embryonic development and cell fate decisions. However, the regulatory factors and molecular mechanisms of ZGA remain poorly understood. Studies have shown that ZGA varies greatly among different species and may be affected by a variety of regulatory factors such as DNA methylation, histone modification, non-coding RNA, chromatin remodeling and ZGA related factors. Here, we review the research progress of the above regulatory factors affecting ZGA, which can provide valuable insights for further investigations into the ZGA related mechanisms of early embryos.

Abstract:R-spondin2 (Rspo2) is a member of protein family RSPOs, which can be coupled to receptor 4/5 (leucine-rich repeat-containing g protein-coupled receptor 4/5, LGR4/5), cell surface transmembrane E3 ubiquitin ligase ZNRF3/RNF43 (zinc and ring finger 3/ring finger protein 43), heparan sulfate proteoglycan (heparan sulfate proteoglycans, HSPGs) and the IQ motif (IQ gap 1) containing GTP enzyme activating protein 1, regulating the Wnt/β-catenin signaling pathway, which is the most widely studied signaling pathway and directly related to basic bone biology. Any problem in this pathway may have an impact on bone regulation. In recent years, it has been found that Rspo2 can act on osteoblast, osteoclast and chondrocytes through Wnt/β-catenin, and take part in occureace and development of some bone diseases such as ossification of the posterior longitudinal ligament (OPLL), osteoarthritis (OA) and rheumatoid arthritis (RA), so the study of Rspo2 may become a new therapeutic direction for bone-related diseases. Based on the latest research progress, this paper reviews the structure and main functions of Rspo2, the mechanism of Rspo2 regulating Wnt/β-catenin signaling pathway and its influence on skeletal system, in order to provide new ideas and ways for the prevention and treatment of bone-related diseases.

Abstract:Di-(2-ethylhexyl) phthalate (DEHP) is currently one of the most widely used plasticizers, widely found in all kinds of items, such as children’s toys and food packaging materials, but also added to wallpaper, cable protective agents and other building decoration materials. DEHP is toxic and absorbed by the human body through respiratory tract, digestive tract and skin contact, which can cause damage to multiple systems, especially the male reproductive system, and testis is an important target organ. Oxidative stress injury is the core mechanism of spermatogenesis disorder caused by DEHP. DEHP exposure can cause oxidative stress or reactive oxygen species (ROS) increase in germ cells, and on this basis, promote cell apoptosis or cause excessive autophagy. The toxicity of DEHP to Leydig cells is mainly to interfere with the synthesis of steroid hormones. For Sertoli cells, ferroptosis and destruction of the blood-testis barrier are common injury mechanisms. In addition, gene methylation caused by DEHP not only affects the spermatogenic process, but also has epigenetic effects on offspring. In this paper, we reviewed the pathological damage, germ cell toxicity and epigenetic effects of DEHP on testis, and focused on the damage and molecular mechanism on testicular spermatogenic cells, Leydig cells and Sertoli cells. Future research is required to elucidate the body’s clearance mechanism and treatment plan after exposure to DEHP and whether DEHP will damage the function of myoid cells. It is hoped that this can provide new ideas for prevention and treatment of male reproductive disorders resulting from long-term exposure to plastic products.

Abstract:Growth/differentiation factor-5 (GDF-5) belongs to transforming growth factor-β (TGF-β) family, which is expressed in bone, cartilage, heart, brain, kidney, skeletal muscle and tendon, liver, fat and other organs and tissues as well. GDF-5 binds to receptor BMPR-I/BMPR-II and activates different signaling pathways such as smad1/5/8, PI3K/Akt, p38-MAPK. For a long time, numerous studies have shown that GDF-5 plays an important role in protecting joints. However, researchers have found GDF-5 also plays significant biological functions in other organs. For example, GDF-5 improves cardiac function by reducing oxidative stress and fibrosis in infarcted hearts. GDF-5 can also reduce oxidative stress in the brain and increase the number of neurons in effort to delay the progression of Alzheimer’s disease and Parkinson’s disease. It is a situation, research on GDF-5, at present, mainly focuses on the growth and repair of bone, cartilage and tendons, while there are few reports on its biological effects in other organs. Therefore, this article reviews and summarizes the research progress on GDF-5 and metabolic diseases in recent years in order to provide new insights and theoretical basis for the role of GDF-5 in improving metabolic diseases.

Abstract:Nanozyme is novel nanoparticle with enzyme-like activity, which can be classified into peroxidase-like nanozyme, catalase-like nanozyme, superoxide dismutase-like nanozyme, oxidase-like nanozyme and hydrolase-like nanozyme according to the type of reaction they catalyze. Since researchers first discovered Fe₃O₄ nanoparticles with peroxidase-like activity in 2007, a variety of nanoparticles have been successively found to have catalytic activity and applied in bioassays, inflammation control, antioxidant damage and tumor therapy, playing a key role in disease diagnosis and treatment. We summarize the use of nanozymes with different classes of enzymatic activity in the diagnosis and treatment of diseases and describe the main factors influencing nanozyme activity. A Mn-based peroxidase-like nanozyme that induces the reduction of glutathione in tumors to produce glutathione disulfide and Mn²⁺, which induces the production of reative oxygen species (ROS) in tumor cells by breaking down H₂O₂ in physiological media through Fenton-like action, thereby inhibiting tumor cell growth. To address the limitation of tumor tissue hypoxia during photodynamic tumor therapy, the effect of photodynamic therapy is significantly enhanced by using hydrogen peroxide nanozymes to catalyze the production of oxygen from H₂O₂. In pathological states, where excess superoxide radicals are produced in the body, superoxide dismutase-like nanozymes are able to selectively regulate intracellular ROS levels, thereby protecting normal cells and slowing down the degradation of cellular function. Based on this principle, an engineered nanosponge has been designed to rapidly scavenge free radicals and deliver oxygen in time to save nerve cells before thrombolysis. Starvation therapy, in which glucose oxidase catalyzes the hydrolysis of glucose to gluconic acid and hydrogen peroxide in cancer cells with the involvement of oxygen, attenuates glycolysis and the production of intermediate metabolites such as nucleotides, lipids and amino acids, was used to synthesize an oxidase-like nanozyme that achieved effective inhibition of tumor growth. Furthermore, by fine-tuning the Lewis acidity of the metal cluster to improve the intrinsic activity of the hydrolase nanozyme and providing a shortened ligand length to increase the density of its active site, a hydrolase-like nanozyme was successfully synthesized that is capable of cleaving phosphate bonds, amide bonds, glycosidic bonds and even biofilms with high efficiency in hydrolyzing the substrate. All these effects depend on the size, morphology, composition, surface modification and environmental media of the nanozyme, which are important aspects to consider in order to improve the catalytic efficiency of the nanozyme and have important implications for the development of nanozyme. Although some progress has been made in the research of nanozymes in disease treatment and diagnosis, there are still some problems, for example, the catalytic rate of nanozymes is still difficult to reach the level of natural enzymes in vivo, and the toxic effects of some heavy metal nanozymes material itself. Therefore, the construction of nanozyme systems with multiple functions, good biocompatibility and high targeting efficiency, and their large-scale application in diagnosis and treatment is still an urgent problem to be solved. (1) To improve the selectivity and specificity of nanozymes. By using antibody coupling, the nanoparticles are able to specifically bind to antigens that are overexpressed in certain cancer cells. It also significantly improves cellular internalization through antigen-mediated endocytosis and enhances the enrichment of nanozymes in target tissues, thereby improving targeting during tumor therapy. Some exogenous stimuli such as laser and ultrasound are used as triggers to control the activation of nanozymes and achieve specific activation of nanozyme. (2) To explore more practical and safer nanozymes and their catalytic mechanisms: biocompatible, clinically proven material molecules can be used for the synthesis of nanoparticles. (3) To solve the problem of its standardization and promote the large-scale clinical application of nanozymes in biomonitoring. Thus, it can go out of the laboratory and face the market to serve human health in more fields, which is one of the future trends of nanozyme development.

Abstract:Spatial environment includes multiple scales, which can be specifically divided into operable near-scale figural space, navigable space consisting of single-viewpoint space and environmental space, and large-scale geographic space. It is very important for human and other animal’s daily life to distinguish the spatial environment at different scales. The representation of spatial scale is related to its corresponding functional requirements. The parietal lobe is responsible for the representation of near-scale space. Navigable spatial representation in the hippocampus and cerebral cortex shows a “coarse to fine” gradient along the posterior to anterior axis. However, the scale representation of abstract social space shows a dichotomy. Future research should focus on temporal dynamics of spatial scale representation and the influence of spatial scale on the format of the cognitive map.

Abstract:Ubiquitination, a diverse post-translational modification, is carried out by enzymes including E1-activating enzymes, E2-conjugating enzymes, E3 ligases, and deubiquitinating enzymes (DUBs). Ubiquitin itself possesses 7 lysine residues and N-terminal methionine, allowing for the formation of polyubiquitin chains with different lengths and linkages. These chains exhibit various topologies that can be recognized by proteins containing ubiquitin-binding domain, thereby transmitting distinct cellular signals. To unravel the physiological mechanisms associated with ubiquitin, numerous ubiquitin probes have been developed. This review provides an overview of recent advancements in the field of ubiquitin probes, focusing on activity-based and affinity-based probes. Activity-based probes are designed to covalently bind to DUBs, E1s, or E3s, enabling the identification and characterization of these enzymes. Affinity-based probes, on the other hand, selectively bind to ubiquitin-binding domains, facilitating the identification of proteins that interact with ubiquitin. Moreover, this review comprehensively discusses the synthetic methodologies employed for the acquisition of ubiquitin probes. These includes meticulous discussions on the synthesis of individual monomeric modules, the establishment of isopeptide linkages, as well as the incorporation of reactive functional groups. Additionally, the review explores the emerging area of cell-penetrating ubiquitin probes and highlights their latest applications in living cells. These probes incorporate cell-penetrating peptides to enable their internalization into cells, allowing for direct visualization and manipulation of ubiquitin-modified proteins within their native environment. Overall, this review offers insights into the design, synthesis, and applications of ubiquitin probes, highlighting their significance in elucidating ubiquitin-mediated cellular processes.

Abstract:Blood transfusion accuracy is crucial for disease treatment and emergency rescue. Prior to a blood transfusion, it is essential to perform a number of tests to assure proper clinical treatment and reduce the risk of complications. Pre-transfusion testing refers primarily to the blood group, coagulation, and infection to assure transfusion safety and prevent cross-infection. Blood type, cross-matching blood, fibrinogen, viral hepatitis, human immunodeficiency virus, and syphilis are routine pre-transfusion tests. Immunoassay is the traditional clinical pretransfusion detection method. With the expansion of clinical treatment requirements from hospital to on-site treatment, new technologies, such as electrochemical sensing, microfluidics, and spectroscopy technology, are being developed gradually for rapid detection prior to blood transfusion. The development of technologies including colloidal gold immunity and biochips has facilitated the shift from large-scale laboratory equipment to portable testing for pre-transfusion screening. Further, the introduction of artificial intelligence technologies such as machine learning, biometric technology, and computer vision has contributed to the advancement of intelligent pre-transfusion testing. This article reviews the various application scenarios, benefits, and drawbacks of different pre-transfusion detection technologies, analyzes the application of a series of new technologies in pre-transfusion detection and its future development trend, and provides a reference for promoting the development of pre-transfusion detection and even rapid disease marker detection.

Abstract:Objective It was reported that the transthyretin (TTR) has a neuroprotective effect on Alzheimer’s disease (AD), which is manifested by the ability of TTR to inhibit the pathological aggregation of amyloid beta protein (Aβ). In this work, we investigated the mechanism of the interactions between TTR and Aβ at the molecular level to reveal the neuroprotective effect of TTR on AD.Methods Protein-protein docking was used to explore the models of interaction between different structural forms of TTR and Aβ, and molecular dynamics simulation was further applied to investigate the dynamic process of the interaction between the two.Results Both TTR tetramer and monomer can interact with Aβ monomer, and the thyroxine-binding channel of TTR tetramer is the main binding site of Aβ monomer. In addition, the EF helix and EF loop of TTR tetramer were also able to bind Aβ monomer. When the TTR tetramer dissociates, the hydrophobic site of the internal TTR monomer is exposed, which has a strong affinity for Aβ monomer. For the interaction between Aβ aggregates and TTR, a higher degree of aggregation can be formed between TTR monomer and Aβ aggregates due to the β-sheet-rich property of TTR monomer and Aβ aggregates, which may therefore reduce the cytotoxicity of Aβ aggregates.Conclusion Both TTR tetramer and monomer can inhibit Aβ aggregation by “sequestering” Aβ monomer, while TTR monomer can reduce the cytotoxicity of Aβ aggregates by forming large co-aggregation with Aβ aggregates. This work can provide an important theoretical basis for the design and discovery of anti-AD drugs based on the neuroprotective effects of TTR.

Abstract:Objective Recent successful restoration of the native conformation and function of the complementary-determining regions (CDRs) of antibodies on gold nanoparticles (AuNPs) demonstrates that the era of molecular conformational engineering is dawning. Basically, molecular conformational engineering aims to precisely tune flexible non-functional molecules into special conformations to carry out novel functions, in the same way as protein folding. In order to explore the general applicability of molecular conformational engineering, as well as to reveal the mechanism of protein structure-function relationship, the objective of this work is to restore the native conformation and function of the CDRs of an antibody on platinum nanoparticles (PtNPs).Methods The CDR fragment of the anti-lysozyme antibody cAB-lys3, which has no stable conformation or function in free state, was conjugated onto the surface of PtNPs through two Pt-S bonds. The original antigen-recognizing function of the CDR restored on PtNPs was assessed by the specific inhibition of the enzymatic activity of lysozyme by the PtNP-CDR conjugates.Results After optimization of the peptide density on the surface of PtNPs and modification of PtNPs with polyethylene glycol (PEG), the resulted PtNP-based hybrid artificial antibody (PtNP-10PEG-30P1), dubbed Platinumbody, could bind specifically to lysozyme and significantly inhibit the activity of lysozyme.Conclusion This is the first time that the fragment of a protein could refold on PtNPs. Together with the previous Goldbody and Silverbody, current work demonstrates that artificial proteins could be generally created by restoration of the native conformation of natural proteins fragments on NPs.

Abstract:Objective Gastric cancer (GC) seriously affects human health and life, and research has shown that it is closely related to the serine/glycine metabolism. The proliferation ability of tumor cells is greatly influenced by the metabolism of serine and glycine. The aim of this study was to investigate the molecular mechanism of serine/glycine metabolism can affect the proliferation of gastric cancer cells.Methods In this work, a stable metabolic dynamic model of gastric cancer cells was established via a large-scale metabolic network dynamic modeling method in terms of a potential landscape description of stochastic and non-gradient systems. Based on the regulation of the model, a quantitative analysis was conducted to investigate the dynamic mechanism of serine/glycine metabolism affecting the proliferation of gastric cancer cells. We introduced random noise to the kinetic equations of the general metabolic network, and applied stochastic kinetic decomposition to obtain the Lyapunov function of the metabolic network parameter space. A stable metabolic network was achieved by further reducing the change in the Lyapunov function tied to the stochastic fluctuations.Results Despite the unavailability of a large number of dynamic parameters, we were able to successfully construct a dynamic model for the metabolic network in gastric cancer cells. When extracellular serine is available, the model preferentially consumes serine. In addition, when the conversion rate of glycine to serine increases, the model significantly upregulates the steady-state fluxes of S-adenosylmethionine (SAM) and S-adenosyl homocysteine (SAH).Conclusion In this paper, we provide evidence supporting the preferential uptake of serine by gastric cancer cells and the important role of serine/glycine conversion rate in SAM generation, which may affect the proliferation ability of gastric cancer cells by regulating the cellular methylation process. This provides a new idea and direction for targeted cancer therapy based on serine/glycine metabolism.

Abstract:Objective Disruption of epithelial layer may instantaneously induce the generation of endogenous electric fields, which was proved to play an important role in guiding the cell migration and promoting wound healing. PIEZO1 is a kind of mechanic sensitive channel, may be regulated by voltage, is proved to involve in chemotactic migration of cells and play an important role in the process of wound healing. In this paper, the role of PIEZO1 and its downstream proteins FAK and integrin β1 in the electric field guided cell migration were investigated by HaCaT cells (human immortalized keratinocyte).Methods Cell migration was tracked by Living Cell Imaging System in directed current (DC) electric field (EF). Inhibitors and RNAi techniques were applied to study the function of PIEZO1 and other related proteins in electric fields. Western blot was used to detect the expression and phosphorylation levels of integrin β1 and FAK in electric field guided migration under EF stimulation.Results Piezo1 RNAi as well as Ruthenium red and GsMTx4 treatment all significantly inhibited the electrotaxis of HaCaT cells. Electric field stimulation with GsMTx4 treatment alone increased FAK phosphorylation level and the expression of integrin β1. Electric field promoted the expression level of integrin β1 and the phosphorylation level of FAK. Inhibiting the expression of PIEZO1 by RNAi significantly attenuated the phosphorylation level of FAK under EF stimulation. Inhibition of integrin β1 and FAK by inhibitor significantly decrease the electric field guided cell migration.Conclusion PIEZO1 as well as integrin β1 and FAK are involved in the electric field guided cell migration of HaCaT cells. Electric field signals regulate the expression of integrin β1 and the activation of FAK through PIEZO1-mediated signal pathway to orchestrate cell migration.

Abstract:Objective Phosphatidylinositol 3 kinases (PI3Ks) play an important role in cell directional movement by regulating F-actin. However, the structure and function of PI3Ks are complex. The role of PI3Ks in cell electrotaxis is not fully understood. Therefore, in this study, the model organism Dictyostelium discoideum cells were used as experimental materials to explore the role of PI3K1 and PI3K2 in electrotaxis.Methods Firstly, PI3K1 coding gene pikA knockout mutant and PI3K2 coding gene pikB knockout mutant were constructed by CRISPR/Cas9 system. Secondly, two mutants were placed in a DC electric field with a strength of 12 V/cm and the electrotaxis were analyzed.Results Data analysis showed that the direction index of wild-type cells in DC electric field was (0.86±0.03), while the direction index of pikA^- and pikB^- mutants in DC electric field was (0.95±0.02) and (0.94±0.03), respectively. In addition, the average trajectory speed of wild-type cells in the electric field was (3.34±0.08) μm/min, while the average trajectory speed of pikA^- and pikB^- mutants were (4.85±0.20) μm/min and (5.48±0.15) μm/min, respectively. The t test showed that there were significant differences in the directedness index and speed between the mutant and wild type. Western blot results showed that both phosphorylated Akt and phosphorylated ERK were significantly increased in pikA^- and pikB^- mutants.Conclusion PI3K1 and PI3K2 may inhibit the electrotaxis of Dictyostelium discoideum cells by increasing the activity of Akt and ERK.

Abstract:Objective At present, the matching reagents of commercially available rapid DNA instruments based on microfluidics chip technology are autosome short tandem repeat (STR) individual identification reagents. The non-recombining part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profile is uninformative. Y-STR loci are useful markers to identify males and male lineages in forensic practice. In order to achieve rapid and fully integrated detection of Y-STR loci, this study constructed the RTyper Y27 microfluidic chip rapid detection system and validated the performance of this system.Methods The system was verified and evaluated by sensitivity, success rate, typing accuracy, peak height balance, sizing precision and accuracy, mock case sample tests, mixture detection ability, and inhibition tolerance.Results Complete Y-STR profiles can be obtained when the template amount of DNA standard 9948 was ≥8 ng, the number of blood cards was ≥3 pieces, and the number of oral swab scrapings was ≥7 times. The success rate of fully integrated detection was 91.52%, and the concordance rates was 99.74% for 165 testing samples. The success rate of 115 blood spots in these samples was 90.43%, with a typing accuracy of 99.65%, the success rate of 50 buccal swabs was 94%, with a typing accuracy of 99.92%. There was no significant difference in typing accuracy between blood spots and buccal swab samples. The peak height ratio between different fluorescence channels was 89.81%. The standard deviation of allelic ladder for 10 runs was within 0.5 bp. The size differences between allele and corresponding allele in allelic ladder was within 0.5 bp. The maximum precision CV values within and between batches were 0.48% and 0.68%, respectively, which were lower than 15%. These data indicate that the system has good accuracy and precision. The system was capable of accurately typing oral swabs, blood cards, saliva cards, cigarette butts, blood swabs and seminal stains. Complete Y-STR profiles can be obtained and distinguish at the 1∶3 ratio of minor and major contributors in artificial male DNA mixtures. Complete Y-STR genotyping can be obtained under the interference of inhibitors, such as different concentrations of humic acid (50-400 mg/L), indigotin (20-100 nmol/L) and hemoglobin (100-500 μmol/L).Conclusion In this study, the RTyper Y27 microfluidic chip rapid amplification system is combined with the Quick TargSeq 1.0 integrated system, and the Y-STR profile can be obtained in approximately 2 h. Through a series of verification experiments, the results show that the system has good repeatability, accuracy and stability, can meet the on-site Y-STR detection requirements, and can be used in forensic practice.

Abstract:Objective Body fluid stains left at crime scenes are frequently trace amounts, while the identification of body fluids through real time fluorogenic quantitative technique often necessitates the repeated detection within the limited sample, as multiple miRNA markers are the basis for the identification. Based on the goal of both the throughput and efficiency improvement of miRNA analysis in trace samples, a duplex real time fluorogenic quantitative PCR assay system was designed to accurately quantify two miRNAs simultaneously, and the system should be further verified by actual sample for the body fluid identification.Methods The duplex real time fluorogenic quantitative PCR system of miR-451a to miR-21-5p was established with specially designed primers and probes, and the concentrations of the primers and probes were both optimized. The specificity, sensitivity and reproducibility of the system were validated, while its capability for body fluid identification was assessed using the miR-451a to miR-21-5p ratio.Results The optimized assay system exhibited excellent specificity and repeatability, with coefficients of variation consistently below 8% for both intra- and inter-batch variability. The amplification efficiency of miR-451a and miR-21-5p reached 71.77% and 74.81%, respectively, with high and relatively consistent results. By utilizing this duplex real time fluorogenic quantitative PCR assay system, a total of 58 body fluid samples were analyzed, exhibiting a discrimination rate of 100% between blood and non-blood samples, as well as between peripheral blood and menstrual blood samples. Moreover, the results, obtained from single real time fluorogenic quantitative PCR assay system and duplex real time fluorogenic quantitative PCR assay system, showed no statistically significant difference with randomly selected blood samples (n=20). Compared to previous single real time fluorogenic quantitative PCR assay system, the sensitivity of duplex real time fluorogenic quantitative PCR assay system exhibited remarkable improvement. A minimum input of only 0.1 ng total RNA was sufficient for accurate detection of peripheral blood and menstrual blood samples, while saliva, semen, and vaginal secretion required only 1 ng total RNA for precise identification purposes. Additionally, the duplex real time fluorogenic quantitative PCR assay system successfully differentiated between different types of body fluids in simulated samples under natural outdoor conditions.Conclusion The duplex real time fluorogenic quantitative PCR assay system effectively reduced both the time and material costs by half compared to the single system, especially suitable for the examination of body fluid stains left at crime scenes, solving the contradiction between the trace amount and the multiple sample volumes demand of repeated real time fluorogenic quantitative PCR. The duplex real time fluorogenic quantitative PCR assay successfully distinguished blood and other body fluid, as well as peripheral blood and menstrual blood samples, which maintains an equivalent capability for body fluid identification with half sample, time and reagent consumption. This system provides an efficient tool for identifying suspicious body fluids, as well as a foundation for more multiplexed real time fluorogenic quantitative PCR assay system research.

Abstract:Objective Molecular docking plays a critical role in predicting binding modes and affinity between molecules, serving as a pivotal method in structural biology and computer-aided drug design research. Our research team has recently developed a novel template-based docking method called FitDock, which outperforms commonly used molecular docking methods in terms of accuracy and speed, particularly when approximate protein-ligand templates are available. To enhance the accessibility of the FitDock method and promote its broader application in the field of molecular simulation, the development of a graphical software tool is imperative.Methods Utilizing Python-based graphical programming, we have created FitDockApp, a plugin software for the molecular visualization software PyMOL.Results FitDockApp enables template-based molecular docking and ligand structure alignment through an interactive graphical interface, providing real-time visualization of predicted three-dimensional structures. It also offers the convenience of uploading docking files to a laboratory server to obtain the optimal template. Additionally, FitDockApp includes batch docking functionality.Conclusion FitDockApp simplifies the docking process through its user-friendly interface and provides robust functionality to assist researchers in obtaining precise docking results. FitDockApp is a free software compatible with both Windows and Linux systems and can be downloaded from http://cao.labshare.cn/fitdock/.