Biology subjects

Zang, L.

Publications and source records attributed to Zang, L..

10 recordsLinked to original sources

bioRxiv2026

A Scalable and Robust Workflow for Cost-Effective Post-Translational Modifications Profiling by Chemical Proteomics

Mass spectrometry-based chemical proteomics is a powerful method to analyze proteins labelled by small molecules to identify protein targets of active compounds and to profile protein post-translational modifications. The throughput and high protein input for chemical proteomics workflows has been often a limiting factor for application of the technology for specialized and difficult to culture cell lines. The high protein input was necessary to gain significant difference of noise to signal ratio in proteomics readout. Here, we describe a general chemical proteomics workflow, which is performed in 96-well plate and necessitate only 25 g of protein input to profile post-translationally modified proteins including abundant O-GlcNAcylated proteins as well as low abundant AMPylated proteins. The workflow integrates advances in Cu(I)-catalyzed azide-alkyne cycloaddition to minimize chemical side-reactivity of the click reaction and data-independent acquisition mode during LC-MS/MS measurement. An iterative optimization of protein clean-up on carboxylate-coated paramagnetic beads led to significant saving of the beads usage and lowers the unspecific protein background that resulted in sensitivity gain.

biochemistry↗

bioRxiv2026

Globin digest and its constituent peptides promote skeletal muscle hypertrophy and enhance physical performance

Globin digest (GD), an acidic protease hydrolysate of hemoglobin, has been recognized for its anti-obesity and glucose-modulating effects; however, its direct anabolic potential in skeletal muscle remains uncharacterized. We evaluated the effects of GD and its constituent peptides on muscle hypertrophy and motor function using zebrafish, mice, and C2C12 myoblasts. Adult zebrafish administered GD (400 mg/kg BW/d) for 1 week showed significantly increased swimming distance (p < 0.05). Similarly, oral administration of GD (1 g/kg BW/d) to C57BL/6J mice for 4 weeks enhanced grip strength and rotarod performance, accompanied by a 1.5-fold increase in myofiber diameter and upregulation of fast-twitch Myh1 (1.9-fold) and Myh2 (1.8-fold) mRNA levels. In vitro, GD dose-dependently (1-100 g/mL) stimulated C2C12 differentiation and MyHC accumulation. Notably, GD did not merely serve as a nutritional nitrogen source; instead, it functioned as a signaling modulator via a specific "relay-like" peptide orchestration. Among six identified sequences, Peptides 3 (WTQR) and 5 (WGK) primarily initiated early-stage commitment by upregulating MyoD and Myf5, whereas Peptides 2 (VVYP) and 6 (FES) accelerated mid-stage maturation. This stage-specific synergy achieved robust myotube hypertrophy that exceeded the efficacy of individual components. These findings demonstrate that GD promotes skeletal muscle hypertrophy and motor function through direct myogenic signaling, establishing a novel foundation for precision sports nutrition to optimize muscle maintenance and physical performance. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/728339v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@94675borg.highwire.dtl.DTLVardef@10dbbfaorg.highwire.dtl.DTLVardef@b026eforg.highwire.dtl.DTLVardef@cc4058_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2026

Impairment of bacteriophage activity in blood: a case study revealing constraints in phage isolation and translation

BackgroundPhage therapy is increasingly considered a promising alternative for treating multidrug-resistant (MDR) infections. However, its clinical application remains limited by challenges in isolating effective phages against resistant clinical strains and by the limited ability of in vitro assays to predict performance in real biological environments. While biological matrices are known to influence phage activity, these effects are not well characterised. MethodsA phage-resistant Pseudomonas aeruginosa isolate from a patient with recurrent MDR urinary tract infection was used as the model organism. Conventional isolation methods failed to recover effective phages, leading to the development of TEASER-i (Transient EDTA- and Ion-Assisted Sequential Enrichment & Recovery). Recovered phages were characterised using adsorption assays, one-step growth kinetics, and time-kill experiments. Their antibacterial activity was evaluated both in vitro and in ex vivo human matrices (whole blood, serum, plasma, and urine). Phage efficacy was quantified using maximum log reduction (Emax), area under the curve (AUC), and phage-to-bacteria ratio (PBR). ResultsA novel TEASER-i method optimised for difficult-to-treat Gram-negative infections, enabled recovery of a functionally effective Osewage-derived P. aeruginosa phage, which outperformed a Ourine-derived P. aeruginosa phage that showed slower replication and lower burst size. Phage activity varied significantly in blood, serum, and plasma. Urine supported the most sustained antibacterial effect. In many cases, early bacterial reduction was followed by regrowth. Sustained activity was associated with maintenance of favourable PBR values, while negative PBR corresponded to treatment failure. At 96 h, only two conditions maintained favourable phage load (log 10 PBR > 0): the S. aureus phage in urine (+1.66) and the sewage-derived P. aeruginosa phage in serum (+1.32). ConclusionsPhage efficacy depends not only on intrinsic lytic capacity but also on the ability to persist and amplify within specific biological environments. Conventional isolation and in vitro screening may therefore overestimate therapeutic potential. Combining optimised isolation strategies with ex vivo evaluation provides a more realistic framework for phage selection and clinical translation.

microbiology↗

bioRxiv2026

Histo-anatomical atlas and thermal tolerance of Garra rufa: A novel small teleost model adaptable to human body temperature

Garra rufa, commonly known as the doctor fish, is a small freshwater cyprinid notable for its exceptional tolerance to high temperatures, surviving even at around the human body temperature of 37 {degrees}C, and has emerging potential as a novel laboratory model for human cancer xenotransplantation and infectious disease research. To establish a foundation for its experimental use, we conducted comprehensive anatomical and histological analyses across major organ systems. The overall body organization and tissue architecture of G. rufa are broadly similar to those of zebrafish (Danio rerio), indicating a conserved cyprinid body plan. However, several organ systems in G. rufa exhibited species-specific differences compared with zebrafish, including a well-developed adhesive disc around the oral region, a long and coiled intestine, and a distinct dark pigmentation of the peritoneum. These species-specific traits may reflect ecological and behavioral adaptations of G. rufa, including benthic scraping in warm, flowing habitats. Physiological assays confirmed that G. rufa maintains high survival rates and normal swimming activity at 37 {degrees}C, whereas zebrafish exhibit significant mortality and reduced locomotion under the same conditions. Collectively, this work provides a comprehensive histo-anatomical atlas of G. rufa, highlighting its unique morphological specializations while establishing an essential reference for the development of this species as a novel experimental fish model.

zoology↗

bioRxiv2026

Systems-level Investigation of the Anxiolytic Gut-Brain Interactions induced by Paraprobiotic Lactobacillus brevis SBC8803 in Zebrafish

Anxiety disorders are among the most prevalent mental health conditions worldwide, and interest in psychobiotics--live or inactivated microorganisms that beneficially modulate the microbiota-gut-brain axis--is increasing. Heat-killed Lactobacillus brevis SBC8803 enhances serotonin (5-hydroxytryptamine; 5-HT) signaling and ameliorates stress-related phenotypes in mammals, although the gut-brain pathways mediating these effects remain incompletely defined. Here, we investigated the anxiolytic effects and underlying molecular mechanisms of oral SBC8803 administration in adult zebrafish. Adult male AB-strain zebrafish were fed a diet containing heat-killed SBC8803 for 4 weeks, and anxiety-like behavior was evaluated using the novel tank test. SBC8803-treated fish exhibited a shorter latency to enter the upper half of the tank and more frequent transitions into the upper half, consistent with reduced anxiety-like behavior. To explore underlying mechanisms, we performed brain RNA sequencing and 16S rRNA gene sequencing of intestinal contents, followed by integrative multi-omics analyses. Brain transcriptomic profiling identified differentially expressed genes and enrichment of serotonin receptor, CREB, and oxytocin signaling pathways, suggesting enhanced monoaminergic and plasticity-related signaling. Microbiome functional prediction indicated SBC8803-associated shifts in lipid and vitamin metabolism, including pathways related to riboflavin (vitamin B2) and tryptophan. Gene set variation analysis combined with DIABLO-based data integration revealed coordinated changes between microbial metabolic and brain signaling pathways, consistent with a vitamin B-serotonin-anti-inflammatory axis linking gut metabolism to neural regulation. Furthermore, residual correlation analysis showed innate gut-brain coordination independent of SBC8803 effect, such as the coupling between brain arachidonic acid and gut histidine metabolism. These findings support the biological validity of SBC8803 administration-associated interactions observed in the multi-omics analyses. Collectively, these findings indicate that the paraprobiotic SBC8803 exerts anxiolytic-like effects in zebrafish and reshapes gut-brain network states at behavioral, microbial, and transcriptomic levels, providing a mechanistic framework for considering heat-killed SBC8803 as a candidate psychobiotic for anxiety-related conditions.

microbiology↗

bioRxiv2025

Chromosome-level genome assembly of the doctor fish (Garra rufa)

Garra rufa, commonly known as doctor fish, is a small freshwater cyprinid fish recognized for its high-temperature tolerance. G. rufa is primarily known for its role in ichthyotherapy, in which it helps remove keratinized skin from human hands and feet. However, in recent years, its high-temperature tolerance has attracted attention owing to its potential use as a model for human disease research, including infectious diseases and cancer xenograft models. Despite this interest, the genomic basis underlying high-temperature tolerance remains largely unexplored, primarily because of the limited availability of genomic resources, which hinders its development as an experimental model. In the present study, a high-quality chromosome-level genome assembly of G. rufa was generated using a combination of PacBio HiFi long-read sequencing and Hi-C technology. We generated a chromosome-level genome assembly with 25 chromosomes, 1.38 Gb in total length, and scaffold N50 of 49.3 Mb. Approximately 59% of the genome comprises repetitive elements, with DNA and LTR elements being particularly abundant. In total, 27,352 protein-coding genes were annotated, of which 26,900 genes (98.3%) were functionally annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark for genome assembly and gene annotation demonstrated 94.5% and 94.7% of complete BUSCOs, respectively. We identified two heat shock transcription factor (HSF) and 239 heat shock protein (HSP)-related genes. Heat shock elements, which are HSF-binding motifs, were present within 3 kb upstream of 944 genes, with statistically significant enrichment of HSP-related genes in this set. Furthermore, molecular phylogenetic analysis and whole-genome comparisons revealed that G. rufa is evolutionarily closely related to species in the Labeoninae subfamily of the Cyprinidae family. This chromosome-level reference genome provides a valuable resource for future research aimed at elucidating the molecular mechanisms underlying high-temperature tolerance in G. rufa and establishing it as a model organism for human biomedical studies.

genomics↗

bioRxiv2023

Overexpression of ZmSTOP1-A Enhances Aluminum Tolerance in Arabidopsis by Stimulating Organic Acid Secretion and Reactive Oxygen Species Scavenging

Aluminum (Al) toxicity and low pH are major factors limiting plant growth in acidic soils. Sensitive to Proton Rhizotoxicity 1 (STOP1) transcription factor respond to these stresses by regulating the expression of multiple Al- or low pH-responsive genes. ZmSTOP1-A, a STOP1-like protein from maize (Zea mays), was localized to the nucleus and had transactivation activity. ZmSTOP1-A was expressed moderately in both roots and shoots of maize seedlings, but was not induced by Al stress or low pH. Overexpression of ZmSTOP1-A in Arabidopsis Atstop1 mutant partially restored Al tolerance and completely low pH tolerance with respect to root growth. Regarding Al tolerance, ZmSTOP1-A/Atstop1 plants showed clear upregulation of organic acid transporter genes, and leading to increased organic acid secretion and reduced Al accumulation in roots. Besides, the antioxidant enzyme activity in roots and shoots of ZmSTOP1-A/Atstop1 plants was significantly enhanced, ultimately alleviating Al toxicity via scavenging reactive oxygen species. Similarly, ZmSTOP1-A could directly activate ZmMATE1 expression in maize, positively correlated with the number of Al-responsive GGNVS cis-element in the ZmMATE1 promoter. Our results revealed that ZmSTOP1-A antagonizes Al toxicity by enhancing organic acid secretion and reactive oxygen species scavenging in Arabidopsis, demonstrating that it is an important transcription factor conferring Al tolerance. Our findings help to comprehensively elucidate the role of STOP1-like transcript factor in enabling plants to detoxifying Al.

molecular biology↗

bioRxiv2023

Haplotype-phased genome revealed the butylphthalide biosynthesis and hybrid origin of Ligusticum chuanxiong

Butylphthalide, one type of phthalides, is one of the first-line drugs for ischemic stroke therapy, while no enzyme involved in its biosynthesis pathway has been reported. Here, we present the first haplotype-resolved genome of Ligusticum chuanxiong Hort., a long-cultivated and phthalide-rich medicinal plant in Apiaceae. Based on comprehensive candidate gene screening, four Fe (II)- and 2-oxoglutarate-dependent dioxygenases (2OGDs) and two CYPs were mined and further biochemically verified as phthalide C-4/C-5 desaturase (P4,5Ds) that converts senkyunolide A to l-n-butylphthalide (l-NBP) and ligustilide to butylidenephthalide. The substrate promiscuity and functional redundancy featured for P4,5Ds may contribute to the high phthalide diversity in L. chuanxiong. Notably, comparative genomic evidence supported L. chuanxiong as a diploid hybrid with L. sinense as a potential parent. The two haplotypes demonstrated exceptional structure variance and diverged around 3.42 million years ago (Ma). Our study is an icebreaker for the dissection of phthalide biosynthesis pathway and reveals the hybrid origin of L. chuanxiong. These findings will facilitate the future metabolic engineering for l-NBP production and breeding efforts for L. chuanxiong.

synthetic biology↗

bioRxiv2022

The Respiratory Syncytial Virus G Protein Enhances the Immune Responses to the RSV F Protein in an Enveloped Virus-like Particle Vaccine Candidate

Respiratory syncytial virus (RSV) is a serious human respiratory pathogen, but no RSV vaccine has been licensed. Many of the vaccine candidates are focused on the viral F protein. However, it is the G protein that binds the likely receptor, CX3CR1, in human alveolar lung cells raising the question of the importance of the G protein in vaccine candidates. Using virus-like particle (VLP) vaccine candidates, we have directly compared VLPs containing only the pre-fusion F protein, only the G protein, or both glycoproteins. We report that VLPs containing both glycoproteins bind to anti-F protein specific monoclonal antibodies differently than VLPs containing only the pre-fusion F protein. Using RSV naive cotton rats as an animal model, we have found that VLPs assembled only with the pre-F protein stimulated extremely weak neutralizing antibody (NAb) titers as did VLPs assembled with G protein. However, VLPs assembled with both glycoproteins stimulated quite robust neutralizing antibody titers, titers that were significantly higher than the combined titers induced by pre-F only or G only VLPs. VLPs assembled with both glycoproteins induced improved protection of the animals from RSV challenge compared to pre-F VLPs and induced significantly higher levels of antibodies specific for F protein antigenic sites 0, site III, and AM14 binding site compared with VLPs containing only the pre-F protein. These combined results indicate that assembly of pre-F protein with G protein in VLPs further stabilized the pre-fusion conformation or otherwise altered the conformation of the F protein increasing the induction of protective antibodies. ImportanceRSV causes significant disease in infants, young children, and the elderly. Thus, development of an effective vaccine for these populations is a priority. Most ongoing efforts in RSV vaccine development have focused on the viral fusion (F) protein, however, the importance of inclusion of G in vaccine candidates is unclear. Here, using VLPs assembled with only the F protein or only the G protein or both glycoproteins, we show that VLPs assembled with both glycoproteins are a far superior vaccine, in a cotton rat model, than VLPs containing only F protein or only G protein. The results show that the presence of G protein in the VLPs influences the conformation of the F protein and the immune responses to F protein resulting in significantly higher neutralizing antibody titers and better protection from RSV challenge. These results suggest that inclusion of G protein in a vaccine candidate may improve its effectiveness.

microbiology↗

bioRxiv2022

Vitamin C is an efficient natural product for prevention of SARS-CoV-2 infection by targeting ACE2 in both cell and in vivo mouse models

ACE2 is a major receptor for cell entry of SARS-CoV-2. Despite advances in targeting ACE2 to inhibit SARS-CoV-2s binding, how to efficiently and flexibly control ACE2 levels for prevention of SARS-CoV-2 infection has not been explored. Here, we revealed Vitamin C (VitC) administration as an effective strategy to prevent SARS-CoV-2 infection. VitC reduced ACE2 protein levels in a dose-dependent manner, while partial reduction of ACE2 can greatly restrict SARS-CoV-2 infection. Further studies uncovered that USP50 is a crucial regulator of ACE2 protein levels, and VitC blocks the USP50-ACE2 interaction, thus promoting K48-linked polyubiquitination at Lys788 and degradation of ACE2, without disrupting ACE2 transcriptional expression. Importantly, VitC administration reduced host ACE2 and largely blocked SARS-CoV-2 infection in mice. This study identified an in vivo ACE2 balance controlled by both USP50 and an essential nutrient VitC, and revealed a critical role and application of VitC in daily protection from SARS-CoV-2 infection. HighlightsO_LIVitC reduces ACE2 protein levels in a dose-dependent manner C_LIO_LIVitC and USP50 regulate K48-linked ubiquitination at Lys788 of ACE2 C_LIO_LIVitC blocks the interaction between USP50 and ACE2 C_LIO_LIVitC administration lowers host ACE2 and prevents SARS-CoV-2 infection in vivo C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/499651v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@196682borg.highwire.dtl.DTLVardef@190f14dorg.highwire.dtl.DTLVardef@d22b59org.highwire.dtl.DTLVardef@1c0faa_HPS_FORMAT_FIGEXP M_FIG C_FIG The deubiquitinase USP50 controls ACE2 protein stability and levels, while Vitamin C blocks the USP50-ACE2 interaction and therefore results in ACE2 degradation, offering a flexible and efficient approach to protection of the host from SARS-CoV-2 infection.

microbiology↗