260 results on '"Bibo, Li"'
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2. Folic Acid and Taurine Alleviate the Impairment of Redox Status, Immunity, Rumen Microbial Composition and Fermentation of Lambs under Heat Stress
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Bibo Li, Ke Wu, Guoqing Duan, Weiqi Yin, Mingkai Lei, Yining Yan, Youshe Ren, and Chunxiang Zhang
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sheep ,heat stress ,folic acid and taurine ,physiological indices ,oxidant resistance ,immunomodulation ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
The aim of this study was to investigate if the supplementation of folic acid and taurine can relieve the adverse effects of different levels of heat stress (HS) on growth performance, physiological indices, antioxidative capacity, immunity, rumen fermentation and microbiota. A total of 24 Dorper × Hu crossbred lambs (27.51 ± 0.96 kg) were divided into four groups: control group (C, 25 °C), moderate HS group (MHS, 35 °C), severe HS group (SHS, 40 °C), and the treatment group, under severe HS (RHS, 40 °C, 4 and 40 mg/kg BW/d coated folic acid and taurine, respectively). Results showed that, compared with Group C, HS significantly decreased the ADG of lambs (p < 0.05), and the ADG in the RHS group was markedly higher than in the MHS and SHS group (p < 0.05). HS had significant detrimental effects on physiological indices, antioxidative indices and immune status on the 4th day (p < 0.05). The physiological indices, such as RR and ST, increased significantly (p < 0.05) with the HS level and were significantly decreased in the RHS group, compared to the SHS group (p < 0.05). HS induced the significant increase of MDA, TNF-α, and IL-β, and the decrease of T-AOC, SOD, GPx, IL-10, IL-13, IgA, IgG, and IgM (p < 0.05). However, there was a significant improvement in these indices after the supplementation of folic acid and taurine under HS. Moreover, there were a significant increase in Quinella and Succinivibrio, and an evident decrease of the genera Rikenellaceae_RC9_gut_group and Asteroleplasma under HS (p < 0.05). The LEfSe analysis showed that the genera Butyrivibrio, Eubacterium_ventriosum_group, and f_Bifidobacteriaceae were enriched in the MHS, SHS and RHS groups, respectively. Correlated analysis indicated that the genus Rikenellaceae_RC9_gut_group was positively associated with MDA, while it was negatively involved in IL-10, IgA, IgM, and SOD (p < 0.05); The genus Anaeroplasma was positively associated with the propionate and valerate, while the genus Succinivibrio was negatively involved in TNF-α (p < 0.05). In conclusion, folic acid and taurine may alleviate the adverse effects of HS on antioxidant capacity, immunomodulation, and rumen fermentation of lambs by inducing changes in the microbiome that improve animal growth performance.
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- 2024
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3. Telomere maintenance in African trypanosomes
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Bibo Li
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telomere ,telomere end processing ,PolIE ,telomerase ,Trypanosoma brucei ,antigenic variation ,Biology (General) ,QH301-705.5 - Abstract
Telomere maintenance is essential for genome integrity and chromosome stability in eukaryotic cells harboring linear chromosomes, as telomere forms a specialized structure to mask the natural chromosome ends from DNA damage repair machineries and to prevent nucleolytic degradation of the telomeric DNA. In Trypanosoma brucei and several other microbial pathogens, virulence genes involved in antigenic variation, a key pathogenesis mechanism essential for host immune evasion and long-term infections, are located at subtelomeres, and expression and switching of these major surface antigens are regulated by telomere proteins and the telomere structure. Therefore, understanding telomere maintenance mechanisms and how these pathogens achieve a balance between stability and plasticity at telomere/subtelomere will help develop better means to eradicate human diseases caused by these pathogens. Telomere replication faces several challenges, and the “end replication problem” is a key obstacle that can cause progressive telomere shortening in proliferating cells. To overcome this challenge, most eukaryotes use telomerase to extend the G-rich telomere strand. In addition, a number of telomere proteins use sophisticated mechanisms to coordinate the telomerase-mediated de novo telomere G-strand synthesis and the telomere C-strand fill-in, which has been extensively studied in mammalian cells. However, we recently discovered that trypanosomes lack many telomere proteins identified in its mammalian host that are critical for telomere end processing. Rather, T. brucei uses a unique DNA polymerase, PolIE that belongs to the DNA polymerase A family (E. coli DNA PolI family), to coordinate the telomere G- and C-strand syntheses. In this review, I will first briefly summarize current understanding of telomere end processing in mammals. Subsequently, I will describe PolIE-mediated coordination of telomere G- and C-strand synthesis in T. brucei and implication of this recent discovery.
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- 2023
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4. Exploring the digesta- and mucosa-associated microbial community dynamics in the rumen and hindgut of goats from birth to adult
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Bibo Li, Weiqi Yin, Mingkai Lei, Xiaolong Wang, Yuxin Yang, Chunxiang Zhang, and Yulin Chen
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microbiota ,digesta ,mucosa ,gastrointestinal tract ,birth to adult ,goats ,Microbiology ,QR1-502 - Abstract
Recently, the relationship between the goat host and its gastrointestinal microbiome has emerged as a hallmark of host-microbiota symbiosis, which was indispensable for the proper physiological function that convert the plant biomass to livestock products. However, little integrative information about the establishment of gastrointestinal microflora in goats exists. Herein, we characterized the colonizing process of the bacterial community in the digesta and mucosa of the rumen, cecum, and colon of the cashmere goat from birth to adulthood to compare its spatiotemporal difference via 16S rRNA gene sequencing. A total of 1,003 genera belonging to 43 phyla were identified. Principal coordinate analysis unveiled the similarity of microbial community between or within each age group increased and gradually developed toward mature whatever in digesta or mucosa. In the rumen, the composition of the bacterial community in digesta differed significantly from in mucosa across age groups; whereas in the hindgut, there was a high similarity of bacterial composition between the in digesta and mucosa in each age group before weaning, while the bacterial community structure differed markedly between these two types of samples after weaning. Taxonomic analysis indicated that 25 and 21 core genera coexisted in digesta and mucosa of the rumen and hindgut, respectively; but their abundances differed considerably by GIT region and/or age. In digesta, as goats aged, a lower abundance of Bacillus was observed with higher abundances of Prevotella 1 and Rikenellaceae RC9 in the rumen; while in the hindgut, the genera Escherichia-Shigella, Variovorax, and Stenotrophomonas decreased and Ruminococcaceae UCG-005, Ruminococcaceae UCG-010, and Alistipes increased with age increased. In mucosa, the rumen showed microbial dynamics with increases of Butyrivibrio 2 and Prevotellaceae UCG-001 and decreases of unclassified_f_Pasteurellaceae; while the genera Treponema 2 and Ruminococcaceae UCG-010 increased and Escherichia-Shigella decreased in the hindgut as goats aged. These results shed light on the colonization process of microbiota in the rumen and hindgut, which mainly include the initial, transit, and mature phases. Furthermore, there is a significant difference in the microbial composition between in digesta and mucosa, and both these exhibit a considerable spatiotemporal specificity.
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- 2023
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5. Unwrap RAP1’s Mystery at Kinetoplastid Telomeres
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Bibo Li
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RAP1 ,telomere ,antigenic variation ,telomeric silencing ,VSG monoallelic expression ,Trypanosome brucei ,Microbiology ,QR1-502 - Abstract
Although located at the chromosome end, telomeres are an essential chromosome component that helps maintain genome integrity and chromosome stability from protozoa to mammals. The role of telomere proteins in chromosome end protection is conserved, where they suppress various DNA damage response machineries and block nucleolytic degradation of the natural chromosome ends, although the detailed underlying mechanisms are not identical. In addition, the specialized telomere structure exerts a repressive epigenetic effect on expression of genes located at subtelomeres in a number of eukaryotic organisms. This so-called telomeric silencing also affects virulence of a number of microbial pathogens that undergo antigenic variation/phenotypic switching. Telomere proteins, particularly the RAP1 homologs, have been shown to be a key player for telomeric silencing. RAP1 homologs also suppress the expression of Telomere Repeat-containing RNA (TERRA), which is linked to their roles in telomere stability maintenance. The functions of RAP1s in suppressing telomere recombination are largely conserved from kinetoplastids to mammals. However, the underlying mechanisms of RAP1-mediated telomeric silencing have many species-specific features. In this review, I will focus on Trypanosoma brucei RAP1’s functions in suppressing telomeric/subtelomeric DNA recombination and in the regulation of monoallelic expression of subtelomere-located major surface antigen genes. Common and unique mechanisms will be compared among RAP1 homologs, and their implications will be discussed.
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- 2024
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6. Proteomic analysis defines the interactome of telomerase in the protozoan parasite, Trypanosoma brucei
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Justin A. Davis, Andres V. Reyes, Nitika, Arpita Saha, Donald J. Wolfgeher, Shou-Ling Xu, Andrew W. Truman, Bibo Li, and Kausik Chakrabarti
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Trypanosoma brucei ,cell proliferation ,telomerase ,telomere ,cell growth ,parasite ,Biology (General) ,QH301-705.5 - Abstract
Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long non-coding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, and Tetrahymena models, but not in parasitic protozoa, including clinically relevant human parasites. Here, using the protozoan parasite, Trypanosoma brucei (T. brucei) as a model, we have identified the interactome of T. brucei TERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors of TbTERT, highlighting unique features of T. brucei telomerase biology. These unique interactions with TbTERT, suggest mechanistic differences in telomere maintenance between T. brucei and other eukaryotes.
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- 2023
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7. Unlocking phenotypic plasticity provides novel insights for immunity and personalized therapy in lung adenocarcinoma
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Feng Wang, Hongjuan Du, Bibo Li, Zhibin Luo, and Lei Zhu
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unlocking phenotype plasticity (UPP) ,LUAD ,drug sensitivities ,immune ,prognostic ,Genetics ,QH426-470 - Abstract
Background: Unlocking phenotype plasticity (UPP) has been shown to have an essential role in the mechanism of tumor development and therapeutic response. However, the clinical significance of unlocking phenotypic plasticity in patients with lung adenocarcinoma is unclear. This study aimed to explore the roles of unlocking phenotypic plasticity in immune status, prognosis, and treatment in patients with lung adenocarcinoma (LUAD).Methods: Differentially expressed genes (DEGs) and clinical information of UPP were selected from the cancer genome atlas (TCGA) database, and the GO, KEGG enrichment analyses were performed. The independent prognostic genes were determined by univariate and multivariate Cox regression, and the UPP signature score was constructed. Patients with LUAD were divided into high- and low-risk groups according to the median of score, and the immunocytes and immune function, the gene mutation, and drug sensitivities between the two groups were analyzed. Finally, the results were validated in the GEO database.Results: Thirty-nine significantly DEGs were determined. Enrichment analysis showed that UPP-related genes were related to protein polysaccharides and drug resistance. The prognostic results showed that the survival of patients in the high-risk group was poorer than that in the low-risk group (p < 0.001). In the high- and low-risk groups, single nucleotide polymorphism (SNP) and C > T are the most common dissent mutations. The contents of immune cells were significantly different between high- and low-risk groups. And the immune functions were also significantly different, indicating that UPP affects the immunity in LUAD. The results from TCGA were validated in the GEO.Conclusion: Our research has proposed a new and reliable prognosis indicator to predict the overall survival. Evaluation of the UPP could help the clinician to predict therapeutic responses and make individualized treatment plans in patients with LUAD.
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- 2022
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8. Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats
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Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen, and Yu Jiang
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Rumen development ,Rumen transcriptome ,Microbiome ,Rumen-microbial crosstalk ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Preweaned rumen development is vital for animal health and efficient fermentation. In this study, we integrated ruminal transcriptomic and metagenomic data to explore the dynamics of rumen functions, microbial colonization, and their functional interactions during the first 8 weeks of life in goats. Results The dynamic rumen transcriptomic and microbial profiles both exhibited two distinct phases during early rumen development. The differentially expressed genes of the rumen transcriptome between the two phases showed that the immune-related response was enriched in the first phase and nutrient-related metabolism was enriched in the second phase, whereas the differentially expressed genes of the rumen microbiome were enriched in bacteriocin biosynthesis and glycolysis/gluconeogenesis activities. The developmental shift in the rumen transcriptome (at d 21) was earlier than the feed stimulus (at d 25) and the shift in the rumen microbiome (at d 42). Additionally, 15 temporal dynamic rumen gene modules and 20 microbial modules were revealed by coexpression network analysis. Functional correlations between the rumen and its microbiome were primarily involved in rumen pH homeostasis, nitrogen metabolism and the immune response. Rumen gene modules associated with the microbial alpha diversity index were also enriched in the immune response process. Conclusions The present study touched the critical developmental process of rumen functions, microbial colonization and their functional interactions during preweaned development. Taken together, these results demonstrated that rumen development at the first phase is more likely a programmed process rather than stimulation from feed and the microbiome, while the shift of rumen metagenomes was likely regulated by both the diet and host. The intensive functional correlations between rumen genes and the microbiome demonstrated that synergistic processes occurred between them during early rumen development.
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- 2021
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9. Effect of Batch-Annealing Temperature on Oxidation of 22MnB5 Steel during Austenitizing
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Bibo Li, Yanning Liu, Ying Chen, Nan Li, Xiaolong Zhao, Jikang Li, and Maoqiu Wang
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hot stamping steel ,batch-annealing temperature ,oxidation ,austenitizing ,surface roughness ,Mining engineering. Metallurgy ,TN1-997 - Abstract
In this paper, the effect of batch-annealing temperature on the oxidation of 22MnB5 steel during austenitizing was studied. When the batch-annealing temperature was decreased from 690 to 680 °C, the surface roughness of cold-rolled 22MnB5 steel decreased, which reduced the oxide layer thickness during the subsequent austenitizing process and had little effect on the mechanical properties in the cold-rolled and quenched state. This indicated that oxidation during austenitizing could be reduced by properly reducing the batch-annealing temperature without affecting the mechanical properties.
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- 2023
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10. Assessment of Sexual Outcomes in Patients Undergoing Thulium Laser Prostate Surgery for Management of Benign Prostate Hyperplasia: A Systematic Review and Meta-analysis
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Bibo Li, PhD, MD, Lin Hao, MD, Kun Pang, PhD, MD, Guanghui Zang, PhD, MD, Jian Wang, MD, Chendi Yang, MD, Jianjun Zhang, MD, Longjun Cai, MD, Xitao Wang, MD, and Conghui Han, PhD, MD
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Thulium laser ,Prostate surgery ,Prostate hyperplasia ,Sexual outcomes ,Erectile function ,Medicine - Abstract
ABSTRACT: Background: Thulium laser (Tm:YAG) prostate surgery is a safe and effective procedure with low morbidity and comparable clinical outcomes to those of transurethral resection of the prostate (TURP). However, the sexual function outcomes (erectile and ejaculatory function) have been scarcely studied. Aim: We aimed to assess the impact of Tm:YAG prostate surgery on sexual outcomes (erectile and ejaculatory function) and compare them with those patients undergoing TURP. Material and Methods: We searched digital databases like PUBMED, SCOPUS, CENTRAL and EMBASE using relevant keywords to identify comparative studies on TURP and non-comparative studies on Tm:YAG prostate surgery that assessed sexual outcomes. We performed qualitative and quantitative analyses with the extracted data. We carried out a meta-analysis to compare postoperative International Index of Erectile Function (IIEF-5) scores and incidences of retrograde ejaculation (RE) in patients undergoing either Tm:YAG or TURP. The pre-operative and post-operative IIEF-5 scores were pooled to estimate overall scores. Results: We included 5 comparative and 8 non-comparative studies in this review. We found the postoperative IIEF-5 score improvements to be significantly higher in the Tm:YAG prostate surgery group than in the TURP group with a significant mean difference (MD) of 0.45 (95% CI, 0.18 to 0.72; P = .001). We found no significant associations between the procedures. The pooled OR for the association of RE was estimated at 0.90 (95% CI, 0.50 to 1.60; P = .71; I2 = 0%). Conclusion: Tm:YAG prostate surgery improves erectile function more than TURP, according to our findings. Tm:YAG prostate aided surgery also outperforms TURP in terms of preserving sexual function following surgery.However, We found similar or no difference in incidence of RE between Tm:YAG prostate surgery and TURP.Bibo L, Hao L, Pang K, et al. Assessment of Sexual Outcomes in Patients Undergoing Thulium Laser Prostate Surgery for Management of Benign Prostate Hyperplasia: A Systematic Review and Meta-analysis. Sex Med 2022;10:100483.
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- 2022
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11. Dietary Nutritional Level Affects Intestinal Microbiota and Health of Goats
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Hongran Guo, Bibo Li, Meiqi Gao, Qian Li, Yawei Gao, Ning Dong, Gongwei Liu, Zhichao Wang, Wenrui Gao, Yulin Chen, and Yuxin Yang
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dietary nutritional level ,cecum ,colon ,microbiota ,goats ,Biology (General) ,QH301-705.5 - Abstract
The intestine is a complex micro-ecosystem, and its stability determines the health of animals. Different dietary nutritional levels affect the intestinal microbiota and health. In this study, the nutritional levels of energy and protein in the diet of goats were changed, and the body weight was measured every 15 days. In the late feeding period, 16 S rRNA sequencing technology was used to detect the content of microorganisms. A meteorological chromatograph was used to detect volatile fatty acids in the cecum and colon of goats. In the feeding stage, reducing the nutritional level of the diet significantly reduced the weight of the lamb (p < 0.05). In the cecum, the abundance of potentially harmful bacteria, such as Sphingomonas, Marvinbryantia, and Eisenbergiella, were significantly enriched in goats fed with the standard nutritional level diets (p < 0.05). Additionally, the contents of acetate (p = 0.037) and total VFAs (p = 0.041) increased. In the colon, the abundance of SCFAs-producing bacteria, such as Ruminococcaceae, Christensenellaceae, and Papillibacter, decreased as the nutritional level in the diet increased (p < 0.05). In conclusion, the increase in nutritional level could affect the growth performance and composition of intestinal microbiota.
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- 2022
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12. Keeping Balance Between Genetic Stability and Plasticity at the Telomere and Subtelomere of Trypanosoma brucei
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Bibo Li
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telomere ,Trypanosoma brucei ,genome stability ,TRF ,RAP1 ,Biology (General) ,QH301-705.5 - Abstract
Telomeres, the nucleoprotein complexes at chromosome ends, are well-known for their essential roles in genome integrity and chromosome stability. Yet, telomeres and subtelomeres are frequently less stable than chromosome internal regions. Many subtelomeric genes are important for responding to environmental cues, and subtelomeric instability can facilitate organismal adaptation to extracellular changes, which is a common theme in a number of microbial pathogens. In this review, I will focus on the delicate and important balance between stability and plasticity at telomeres and subtelomeres of a kinetoplastid parasite, Trypanosoma brucei, which causes human African trypanosomiasis and undergoes antigenic variation to evade the host immune response. I will summarize the current understanding about T. brucei telomere protein complex, the telomeric transcript, and telomeric R-loops, focusing on their roles in maintaining telomere and subtelomere stability and integrity. The similarities and differences in functions and underlying mechanisms of T. brucei telomere factors will be compared with those in human and yeast cells.
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- 2021
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13. Trypanosoma brucei RAP1 Has Essential Functional Domains That Are Required for Different Protein Interactions
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Marjia Afrin, Hanadi Kishmiri, Ranjodh Sandhu, M. A. G. Rabbani, and Bibo Li
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RAP1 ,telomere ,Trypanosoma brucei ,protein-protein interaction ,Microbiology ,QR1-502 - Abstract
ABSTRACT RAP1 is a telomere protein that is well conserved from protozoa to mammals. It plays important roles in chromosome end protection, telomere length control, and gene expression/silencing at both telomeric and nontelomeric loci. Interaction with different partners is an important mechanism by which RAP1 executes its different functions in yeast. The RAP1 ortholog in Trypanosoma brucei is essential for variant surface glycoprotein (VSG) monoallelic expression, an important aspect of antigenic variation, where T. brucei regularly switches its major surface antigen, VSG, to evade the host immune response. Like other RAP1 orthologs, T. brucei RAP1 (TbRAP1) has conserved functional domains, including BRCA1 C terminus (BRCT), Myb, MybLike, and RAP1 C terminus (RCT). To study functions of various TbRAP1 domains, we established a strain in which one endogenous allele of TbRAP1 is flanked by loxP repeats, enabling its conditional deletion by Cre-mediated recombination. We replaced the other TbRAP1 allele with various mutant alleles lacking individual functional domains and examined their nuclear localization and protein interaction abilities. The N terminus, BRCT, and RCT of TbRAP1 are required for normal protein levels, while the Myb and MybLike domains are essential for normal cell growth. Additionally, the Myb domain of TbRAP1 is required for its interaction with T. brucei TTAGGG repeat-binding factor (TbTRF), while the BRCT domain is required for its self-interaction. Furthermore, the TbRAP1 MybLike domain contains a bipartite nuclear localization signal that is required for its interaction with importin α and its nuclear localization. Interestingly, RAP1’s self-interaction and the interaction between RAP1 and TRF are conserved from kinetoplastids to mammals. However, details of the interaction interfaces have changed throughout evolution. IMPORTANCE Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, to evade the host immune response. VSGs are expressed from subtelomeres in a monoallelic fashion. TbRAP1, a telomere protein, is essential for cell viability and VSG monoallelic expression and suppresses VSG switching. Although TbRAP1 has conserved functional domains in common with its orthologs from yeasts to mammals, the domain functions are unknown. RAP1 orthologs have pleiotropic functions, and interaction with different partners is an important means by which RAP1 executes its different roles. We have established a Cre-loxP-mediated conditional knockout system for TbRAP1 and examined the roles of various functional domains in protein expression, nuclear localization, and protein-protein interactions. This system enables further studies of TbRAP1 point mutation phenotypes. We have also determined functional domains of TbRAP1 that are required for several different protein interactions, shedding light on the underlying mechanisms of TbRAP1-mediated VSG silencing.
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- 2020
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14. Regulation of Antigenic Variation by Trypanosoma brucei Telomere Proteins Depends on Their Unique DNA Binding Activities
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Bibo Li and Yanxiang Zhao
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antigenic variation ,Trypanosoma brucei ,VSG ,telomere ,TRF ,RAP1 ,Medicine - Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, Variant Surface Glycoprotein (VSG), to evade the host immune response. Such antigenic variation is a key pathogenesis mechanism that enables T. brucei to establish long-term infections. VSG is expressed exclusively from subtelomere loci in a strictly monoallelic manner, and DNA recombination is an important VSG switching pathway. The integrity of telomere and subtelomere structure, maintained by multiple telomere proteins, is essential for T. brucei viability and for regulating the monoallelic VSG expression and VSG switching. Here we will focus on T. brucei TRF and RAP1, two telomere proteins with unique nucleic acid binding activities, and summarize their functions in telomere integrity and stability, VSG switching, and monoallelic VSG expression. Targeting the unique features of TbTRF and TbRAP1′s nucleic acid binding activities to perturb the integrity of telomere structure and disrupt VSG monoallelic expression may serve as potential therapeutic strategy against T. brucei.
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- 2021
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15. Characterization and Comparison of Microbiota in the Gastrointestinal Tracts of the Goat (Capra hircus) During Preweaning Development
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Bibo Li, Ke Zhang, Chao Li, Xiaolong Wang, Yulin Chen, and Yuxin Yang
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microbiota ,temporal-spatial specificity ,gastrointestinal tract ,preweaning ,ruminant ,Microbiology ,QR1-502 - Abstract
Bacterial communities in gastrointestinal tracts (GIT) play an important role in animal health and performance. Despite its importance, little information is available on the establishment of microbial populations in the goat GIT or on changes occurring during early development. Therefore, this study investigated the bacterial community dynamics of the rumen, duodenum, jejunum, ileum, cecum, and colon in 15 goats at five developmental stages (0, 14, 28, 42, and 56 days old) by using 16S rDNA sequencing and quantitative real-time PCR technology. 940 genera were found to belong to 44 phyla distributed along the GIT. As a whole, the microbial richness and diversity showed a clear increasing trend as the kids aged and alpha diversity differed significantly among GIT compartments mainly occurring at middle day ages (14 and 28 days). Principal coordinate analysis indicated that the bacterial community displayed distinct temporal and spatial specificity along the GIT in preweaning goats. As kids aged, the phylum Firmicutes was replaced by Bacteroidetes in rumen, whereas Proteobacteria in the large intestine was displaced by Firmicutes. The phylum Proteobacteria was mainly present in the small intestine in older animals. In the rumen, taxa, such as Bacillus and Lactococcus decreased and Prevotella, Treponema, Ruminococcus, and unclassified Prevotellaceae increased with the age of kids. Furthermore, a lower proportion of taxa, such as Lactobacillus and Bacteroides was observed with higher abundances of both Christensenellaceae_R_7 and Ruminococcus in duodenum and jejunum in older animals. In the large intestine, the microbiota displayed taxonomic dynamics with increases of Ruminococcaceae UCG 005, unclassified Lachnospiraceae, Barnesiella, and Blautia as kids aged. Predicted pathway analysis suggested that genes involved in amino acid metabolism, and translation were abundant in both rumen and duodenum, while genes involved in membrane transport and carbohydrate metabolism were enriched in the large intestine. These results indicate that both the microbial colonization process and potential function exert a temporal-spatial specificity throughout the GIT of goats. This study provides new insight into the temporal dynamics of GIT microbiota development during preweaning and will aid to develop strategies for improving animal health and downstream production.
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- 2019
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16. Effect of Austenitization Process on Oxidative Decarbonization Behavior and Mechanical Properties of 22MnB5 Steel
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Bibo Li, Ying Chen, Xiaolong Zhao, Jikang Li, Chang Wang, and Maoqiu Wang
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Mechanics of Materials ,Mechanical Engineering ,General Materials Science - Published
- 2023
17. Exploring the Spatial-Temporal Microbiota of Compound Stomachs in a Pre-weaned Goat Model
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Yu Lei, Ke Zhang, Mengmeng Guo, Guanwei Li, Chao Li, Bibo Li, Yuxin Yang, Yulin Chen, and Xiaolong Wang
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taxonomic diversity ,ruminant ,microbial community ,rumen microbiology ,gut microbiota ,Microbiology ,QR1-502 - Abstract
Ruminant animals possess a characteristic four-compartment stomach (rumen, reticulum, omasum, and abomasum) that is specialized for pre-intestinal digestion of plant materials. Of these four compartments, the rumen is the largest. The rumen’s diverse microbial community has been well studied. However, the current understanding of microbial profiles in the reticulum, omasum and abomasum are lacking. In the present study, fluid samples from the reticulum, omasum, and abomasum of goats at 3, 7, 14, 21, 28, 42, and 56 days after birth, as well as the negative controls (NC) used for microbial DNA extraction, were subjected to 16S rRNA sequencing. By filtering operational taxonomic units (OTUs) in NC, distinct temporal distributions of microbes were observed in the different compartments, we showed that the OTUs in control samples had a large effect to the samples with low microbial density. In addition, Proteobacteria gradually decreased with age from days 3 to 56 in all three compartments, and the relative abundance of Bacteroidetes increased from 24.15% (Day 3) to 52.03% (Day 56) in abomasum. Network analysis revealed that Prevotellaceae_UGG-03 and Rikenellaceae_RC9 were positively correlated with Prevotella_1, lending support to the well understood fact that cellulose is well digested in compound stomachs prior to the rumen. Pathway analysis revealed that gene expression in abomasum at Day 3 were primarily related to Glycolysis/Gluconeogenesis and Pyruvate metabolism, suggesting that colostrum digestion is the dominant function of the abomasum at an early age. These findings combined with other recent rumen microbiota data show that the microbiome landscape represents three distinct stages in ruminant stomachs. The first stage is to gain access to external microorganisms at Day 0–14, the secondary stage is for microbial transition at Day 14–28, and the third stage is for exogenous and endogenous microbial colonization beyond Day 28 of age. Our results provide insight into microbiota dynamics in ruminant stomachs, and will facilitate efforts for the maintenance of gastrointestinal balance and intervention with starter diets in juvenile ruminants during early development.
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- 2018
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18. Proteomic analysis defines the interactome of telomerase in the protozoan parasite,Trypanosoma brucei
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Justin A. Davis, Andres V. Reyes, null Nitika, Arpita Saha, Donald J. Wolfgeher, Shou-Ling Xu, Andrew W. Truman, Bibo Li, and Kausik Chakrabarti
- Abstract
Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long noncoding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, andTetrahymenamodels, but not in lower eukaryotes, including clinically relevant human parasites. Here, using the protozoan parasite,Trypanosoma brucei(T. brucei) as a model, we have identified the interactome ofT. bruceiTERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors ofTbTERT, highlighting unique features ofT. bruceitelomerase biology. These unique interactions withTbTERT, suggest mechanistic differences in telomere maintenance betweenT. bruceiand other eukaryotes.
- Published
- 2022
19. Automated handling of programmable on-product clock generation (OPCG) circuitry for delay test vector generation.
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Anis Uzzaman, Bibo Li, Thomas J. Snethen, Brion L. Keller, and Gary Grise
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- 2007
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20. Using Programmable On-Product Clock Generation (OPCG) for Delay Test.
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Brion L. Keller, Anis Uzzaman, Bibo Li, and Thomas J. Snethen
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- 2007
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21. Not all Delay Tests Are the Same - SDQL Model Shows True-Time.
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Anis Uzzaman, Mick Tegethoff, Bibo Li, Kevin McCauley, Shuji Hamada, and Yasuo Sato
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- 2006
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22. Identification of Prazosin as a Potential Flagellum Attachment Zone 1(FAZ1) Inhibitor for the Treatment of Human African Trypanosomiasis
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Cody M. Orahoske, Marjia Afrin, Yaxin Li, Jovana Hanna, Myah Marbury, Bibo Li, and Bin Su
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Proteomics ,Infectious Diseases ,Trypanosomiasis, African ,Flagella ,Animals ,Humans ,Prazosin ,Trypanocidal Agents - Abstract
Human African trypanosomiasis (HAT) remains a health threat to sub-Saharan Africa. The current treatments suffer from drug resistance and life-threatening side effects, making drug discovery for HAT still important. A high-throughput screening of the library of pharmaceutically active compounds identified prazosin, an α-adrenoceptor antagonist, that showed selective activity toward
- Published
- 2022
23. TbTRF suppresses the TERRA level and regulates the cell cycle-dependent TERRA foci number with a TERRA binding activity in its C-terminal Myb domain
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Amit Kumar Gaurav, Marjia Afrin, Arpita Saha, Unnati M. Pandya, Ranjodh Sandhu, Bibo Li, Brittny Schnur, and Vishal Nanavaty
- Subjects
biology ,AcademicSubjects/SCI00010 ,RNase P ,DNA damage ,Telomere-Binding Proteins ,Trypanosoma brucei brucei ,RNA ,Genome Integrity, Repair and Replication ,Telomere ,Trypanosoma brucei ,biology.organism_classification ,Cell biology ,Trypanosomiasis, African ,RNA interference ,parasitic diseases ,Genetics ,RNA polymerase I ,RNA, Long Noncoding ,MYB ,Variant Surface Glycoproteins, Trypanosoma - Abstract
Telomere repeat-containing RNA (TERRA) has been identified in multiple organisms including Trypanosoma brucei, a protozoan parasite that causes human African trypanosomiasis. T. brucei regularly switches its major surface antigen, VSG, to evade the host immune response. VSG is expressed exclusively from subtelomeric expression sites, and we have shown that telomere proteins play important roles in the regulation of VSG silencing and switching. In this study, we identify several unique features of TERRA and telomere biology in T. brucei. First, the number of TERRA foci is cell cycle-regulated and influenced by TbTRF, the duplex telomere DNA binding factor in T. brucei. Second, TERRA is transcribed by RNA polymerase I mainly from a single telomere downstream of the active VSG. Third, TbTRF binds TERRA through its C-terminal Myb domain, which also has the duplex DNA binding activity, in a sequence-specific manner and suppresses the TERRA level without affecting its half-life. Finally, levels of the telomeric R-loop and telomere DNA damage were increased upon TbTRF depletion. Overexpression of an ectopic allele of RNase H1 that resolves the R-loop structure in TbTRF RNAi cells can partially suppress these phenotypes, revealing an underlying mechanism of how TbTRF helps maintain telomere integrity.
- Published
- 2021
24. Microstructure evolution, mechanical properties and creep mechanisms of Mg-12Gd-1MM-0.6Zr (wt%) magnesium alloy
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Jiawei Yuan, Minglong Ma, Kui Zhang, Kaikun Wang, Li Yongjun, Li Xinggang, Guoliang Shi, and Bibo Li
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Materials science ,Scanning electron microscope ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Microstructure ,01 natural sciences ,Grain size ,0104 chemical sciences ,Creep ,Geochemistry and Petrology ,Ultimate tensile strength ,Dynamic recrystallization ,Composite material ,Magnesium alloy ,0210 nano-technology ,Eutectic system - Abstract
In this research, the microstructure evolution, mechanical properties, and creep mechanisms of Mg-12Gd-1MM-0.6Zr (wt%) alloy under different conditions were systematically studied using scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and tensile creep tests. Regarding the microstructure of the as-cast sample, the average grain size is about 42 μm, and the eutectic compounds were determined to be Mg5(Gd0.8MM0.2). During homogenization, these eutectic compounds gradually dissolve, and Mg12MM particles are precipitated. During hot extrusion, complete dynamic recrystallization (DRX) occurs, resulting in equiaxial grains with an average grain size of about 12 μm and the formation of streamlines consisting of Mg12MM particles along the extrusion direction (ED). After T5 treatment (225 °C for 7 h), a large number of β′(Mg7Gd) phases are precipitated on the {11–20}α habit plane and are interconnected, forming an interlaced network structure. The ultimate tensile strength (Rm = 405 MPa) and yield strength (RP0.2 = 288 MPa) of the T5 sample are significantly higher than those of the as-extruded sample (Rm = 289 MPa, RP0.2 = 185 MPa), but the elongation (A = 4%) was remarkably lower than that of the as-extruded sample (A = 18%). When crept at 225 °C under 100 MPa, the steady-state creep rates of the as-cast, as-extruded, and T5 samples are 1.59 × 10–8, 1.08 × 10–8, and 1.40 × 10–8 s–1, respectively, and their total strains within 100 h are respectively breaking, 0.81%, and 0.92%, indicating that the as-extruded alloy exhibits the best creep resistance. TEM analysis reveals that, during the creep process of the T5 sample, the β′ particles coarsen and the precipitate-free zones (PFZs) widen, which increase the steady-state creep rate and the total strain within 100 h as compared with the as-extruded sample.
- Published
- 2021
25. Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats
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Chen Zhao, Yu Jiang, Bibo Li, Yu Wang, Yulin Chen, Zongjun Li, and Xiangyu Pan
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Rumen-microbial crosstalk ,Rumen ,animal structures ,Biology ,QH426-470 ,Rumen transcriptome ,Rumen development ,Transcriptome ,03 medical and health sciences ,Gene expression ,Genetics ,Animals ,Microbiome ,Gene ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Goats ,Microbiota ,food and beverages ,Metabolism ,Animal Feed ,Diet ,Gluconeogenesis ,Biochemistry ,Metagenomics ,Metagenome ,TP248.13-248.65 ,Research Article ,Biotechnology - Abstract
Background Preweaned rumen development is vital for animal health and efficient fermentation. In this study, we integrated ruminal transcriptomic and metagenomic data to explore the dynamics of rumen functions, microbial colonization, and their functional interactions during the first 8 weeks of life in goats. Results The dynamic rumen transcriptomic and microbial profiles both exhibited two distinct phases during early rumen development. The differentially expressed genes of the rumen transcriptome between the two phases showed that the immune-related response was enriched in the first phase and nutrient-related metabolism was enriched in the second phase, whereas the differentially expressed genes of the rumen microbiome were enriched in bacteriocin biosynthesis and glycolysis/gluconeogenesis activities. The developmental shift in the rumen transcriptome (at d 21) was earlier than the feed stimulus (at d 25) and the shift in the rumen microbiome (at d 42). Additionally, 15 temporal dynamic rumen gene modules and 20 microbial modules were revealed by coexpression network analysis. Functional correlations between the rumen and its microbiome were primarily involved in rumen pH homeostasis, nitrogen metabolism and the immune response. Rumen gene modules associated with the microbial alpha diversity index were also enriched in the immune response process. Conclusions The present study touched the critical developmental process of rumen functions, microbial colonization and their functional interactions during preweaned development. Taken together, these results demonstrated that rumen development at the first phase is more likely a programmed process rather than stimulation from feed and the microbiome, while the shift of rumen metagenomes was likely regulated by both the diet and host. The intensive functional correlations between rumen genes and the microbiome demonstrated that synergistic processes occurred between them during early rumen development.
- Published
- 2021
26. NF-κB-Activated lncRNACASC9 Promotes Bladder Cancer Progression by Regulating the TK1 Expression
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Longjun, Cai, primary, Jianjun, Zhang, additional, Kun, Pang, additional, Lin, Hao, additional, Zhenduo, Shi, additional, Yang, Dong, additional, Bibo, Li, additional, Zhiguo, Zhang, additional, Rui, Li, additional, and Conghui, Han, additional
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- 2022
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27. Trypanosoma brucei TIF2 and TRF Suppress VSG Switching Using Overlapping and Independent Mechanisms.
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Sanaa E Jehi, Vishal Nanavaty, and Bibo Li
- Subjects
Medicine ,Science - Abstract
Trypanosoma brucei causes debilitating human African trypanosomiasis and evades the host's immune response by regularly switching its major surface antigen, VSG, which is expressed exclusively from subtelomeric loci. We previously showed that two interacting telomere proteins, TbTRF and TbTIF2, are essential for cell proliferation and suppress VSG switching by inhibiting DNA recombination events involving the whole active VSG expression site. We now find that TbTIF2 stabilizes TbTRF protein levels by inhibiting their degradation by the 26S proteasome, indicating that decreased TbTRF protein levels in TbTIF2-depleted cells contribute to more frequent VSG switching and eventual cell growth arrest. Surprisingly, although TbTIF2 depletion leads to more subtelomeric DNA double strand breaks (DSBs) that are both potent VSG switching inducers and detrimental to cell viability, TbTRF depletion does not increase the amount of DSBs inside subtelomeric VSG expression sites. Furthermore, expressing an ectopic allele of F2H-TbTRF in TbTIF2 RNAi cells allowed cells to maintain normal TbTRF protein levels for a longer frame of time. This resulted in a mildly better cell growth and partially suppressed the phenotype of increased VSG switching frequency but did not suppress the phenotype of more subtelomeric DSBs in TbTIF2-depleted cells. Therefore, TbTIF2 depletion has two parallel effects: decreased TbTRF protein levels and increased subtelomeric DSBs, both resulting in an acute increased VSG switching frequency and eventual cell growth arrest.
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- 2016
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28. Orally Active and Selective Tubulin Inhibitors as Anti-Trypanosome Agents.
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Vishal Nanavaty, Rati Lama, Ranjodh Sandhu, Bo Zhong, Daniel Kulman, Viharika Bobba, Anran Zhao, Bibo Li, and Bin Su
- Subjects
Medicine ,Science - Abstract
OBJECTIVES:There is an urgent need to develop a safe, effective, orally active, and inexpensive therapy for African trypanosomiasis due to the drawbacks of current drugs. Selective tubulin inhibitors have the potential to be promising drug candidates for the treatment of this disease, which is based on the tubulin protein structural difference between mammalian and trypanosome cells. We propose to identify novel tubulin inhibitors from a compound library developed based on the lead compounds that selectively target trypanosomiasis. METHODS:We used Trypanosoma brucei brucei as the parasite model, and human normal kidney cells and mouse microphage cells as the host model. Growth rates of both trypanosomes and mammalian cells were determined as a means to screen compounds that selectively inhibit the proliferation of parasites. Furthermore, we examined the cell cycle profile of the parasite and compared tubulin polymerization dynamics before and after the treatment using identified compounds. Last, in vivo anti-parasite activities of these compounds were determined in T. brucei-infected mice. RESULTS:Three compounds were selected that are 100 fold more effective against the growth of T. brucei cells than mammalian cells. These compounds caused cell cycle progression defects in T. brucei cells. Western analyses indicated that these compounds decreased tubulin polymerization in T. brucei cells. The in vivo investigation revealed that these compounds, when admitted orally, inhibited T. brucei cell proliferation in mouse blood. However, they were not potent enough to clear up the infection completely. CONCLUSIONS:These compounds are promising lead compounds as orally active agents for drug development of anti-trypanosome agents. A more detail structure activity relationship (SAR) was summarized that will be used to guide future lead optimization to improve the selectivity and potency of the current compounds.
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- 2016
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29. Synthesis and biological evaluation of imidamide analogs as selective anti-trypanosomal agents
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Viharika Bobba, Yaxin Li, Marjia Afrin, Raina Dano, Wenjing Zhang, Bibo Li, and Bin Su
- Subjects
Mammals ,Organic Chemistry ,Clinical Biochemistry ,Trypanosoma brucei brucei ,Pharmaceutical Science ,Biochemistry ,Trypanocidal Agents ,Tubulin Modulators ,Article ,Trypanosomiasis, African ,Tubulin ,Drug Discovery ,Molecular Medicine ,Animals ,Humans ,Molecular Biology - Abstract
Human African trypanosomiasis is caused by a protozoan parasite Trypanosoma brucei majorly infecting people living in sub-Saharan Africa. Current limited available treatments suffer from drug resistance, severe adverse effects, low efficacy, and costly administrative procedures in African countries with limited medical resources. Therefore, there is always a perpetual demand for advanced drug development and invention of new strategies to combat the disease. Previous work in our lab generated a library of sulfonamide analogs as selective tubulin inhibitors, based on the structural difference between mammalian and trypanosome tubulin proteins. Further lead derivatization was performed in the current study and generated 25 potential drug candidates to improve the drug efficacy and uptake by selectively targeting the parasite’s P2 membrane transporter protein with imidamide moiety. One of the newly synthesized analogs, compound 25 with a di-imidamide moiety, has shown greater potency with an IC(50) of 1 nM to selectively inhibit the growth of trypanosome cells without affecting the viability of mammalian cells. Western blot analyses reveal that the compound suppressed tubulin polymerization in T. brucei cells. A detailed structure-activity relationship (SAR) was summarized that will be used to guide future lead optimization.
- Published
- 2022
30. Regulatory Role of ECM Biophysical Signals in Cell and Nuclear Mechanics: A Bibliometric and Visualized Study
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Chengyao Zhang, Fei Teng, Daoxi Lei, Bibo Li, Wenhua Yan, Junyang Huang, Shuang Liang, and Guixue Wang
- Published
- 2022
31. In vivo Architecture of the Telomerase RNA Catalytic Core in Trypanosoma brucei
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Kausik Chakrabarti, Kaitlin Klotz, Justin Davis, Abhishek Dey, Bibo Li, Arpita Saha, Anaïs Monroy-Eklund, and Alain Laederach
- Subjects
Telomerase ,RNA Folding ,AcademicSubjects/SCI00010 ,Green Fluorescent Proteins ,Trypanosoma brucei brucei ,Protozoan Proteins ,Trypanosoma brucei ,RNA Prot Comp ,chemistry.chemical_compound ,Telomerase RNA ,Procyclic Form (PF) ,Catalytic Domain ,Catalytic Core ,parasitic diseases ,Genetics ,Trypanosoma Brucei ,Bloodstream Form (BF) ,Helix IV ,Ribonucleoprotein ,Enzyme Assays ,biology ,Base Sequence ,DMS ,RNA ,NAI ,biology.organism_classification ,Reverse transcriptase ,Cell biology ,Telomere ,chemistry ,Mutation ,Biocatalysis ,Nucleic Acid Conformation ,Thermodynamics ,RNA Chemical probing and mutational profiling ,Ex vivo ,DNA ,RNA, Protozoan ,Protein Binding - Abstract
Telomerase is a unique ribonucleoprotein (RNP) reverse transcriptase that utilizes its cognate RNA molecule as a template for telomere DNA repeat synthesis. Telomerase contains the reverse transcriptase protein, TERT and the template RNA, TR, as its core components. The 5’-half of TR forms a highly conserved catalytic core comprising of the template region and adjacent domains necessary for telomere synthesis. However, how telomerase RNA folding takes place in vivo has not been fully understood due to low abundance of the native RNP. Here, using unicellular pathogen Trypanosoma brucei as a model, we reveal important regional folding information of the native telomerase RNA core domains, i.e. TR template, template boundary element, template proximal helix and Helix IV (eCR4-CR5) domain. For this purpose, we uniquely combined in-cell probing with targeted high-throughput RNA sequencing and mutational mapping under three conditions: in vivo (in WT and TERT−/− cells), in an immunopurified catalytically active telomerase RNP complex and ex vivo (deproteinized). We discover that TR forms at least two different conformers with distinct folding topologies in the insect and mammalian developmental stages of T. brucei. Also, TERT does not significantly affect the RNA folding in vivo, suggesting that the telomerase RNA in T. brucei exists in a conformationally preorganized stable structure. Our observed differences in RNA (TR) folding at two distinct developmental stages of T. brucei suggest that important conformational changes are a key component of T. brucei development.
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- 2021
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32. Reviews on Selected Topics of Telomere Biology
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Bibo Li
- Published
- 2012
33. Preparation, Characterization, and In Vitro pH-sensitivity Evaluation of Superparamagnetic Iron Oxide Nanoparticle- Misonidazole pH-sensitive Liposomes
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Bibo Li, He Mei, Zhibin Luo, Daiying He, Biqiang Li, and Changyan Feng
- Subjects
Radiosensitizer ,Misonidazole ,Drug Compounding ,Metal Nanoparticles ,Pharmaceutical Science ,Antineoplastic Agents ,02 engineering and technology ,010402 general chemistry ,Ferric Compounds ,01 natural sciences ,chemistry.chemical_compound ,Drug Delivery Systems ,Spectrophotometry ,medicine ,Zeta potential ,Humans ,Liposome ,medicine.diagnostic_test ,Chemistry ,Magnetic Phenomena ,Hydrogen-Ion Concentration ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Targeted drug delivery ,A549 Cells ,Liposomes ,Particle size ,0210 nano-technology ,Superparamagnetism ,Nuclear chemistry - Abstract
Background: The use of Misonidazole (MISO), the first and a potential hypoxic tumor cell radiosensitizer, has been limited by peripheral neurotoxicity, thus discouraging phase III clinical trials. Objective: To develop a targeted drug delivery and tracing System with pH-sensitive liposomes (SpHLs) and Superparamagnetic Iron Oxide Nanoparticles (SPIONs) to counter MISO-related adverse effects and to enable tracing under magnetic resonance. Methods: SPION-MISO-SpHLs were prepared by a reverse evaporation and freeze-thawing method. HPLC and phenanthroline spectrophotometry were established for MISO and Fe determination. The characterization and in vitro pH-sensitivity of SPION-MISO-SpHLs were evaluated. Results: The maximal entrapment efficiencies of MISO and SPIONs in SPION-MISO-SpHLs were 30.2% and 23.7%, respectively. The cumulative release rates of MISO and SPIONs were respectively 2.49 and 2.47 times higher in pH 5.5 than in pH 7.4 buffer. The mean particle size of SPION-MISOSpHLs was 950 nm. The zeta potential was -58.9 mV in pH 7.4 buffer and 36.3 mV in pH 5.5 buffer. SEM imaging showed that SPION-MISO-SpHLs had similar spherical morphologies. SPIONs were packed in the center of liposomes and were well dispersed in a TEM graph. Magnetization curve showed that SPION-MISO-SpHLs retained superparamagnetic properties. SPION-MISO-SpHLs were compared with MISO+SPION+blank liposome in hypoxia and control groups of A549 cells. MISO and SPION concentrations in culture medium showed significant differences between the same concentration groups (P < 0.0001) and at different times (P < 0.0001). Conclusion: SPION-MISO-SpHLs possess pH-dependent release ability and superparamagnetism, and thus provides a system for targeted delivery and tracing under magnetic resonance.
- Published
- 2019
34. Pharmacokinetic study of an anti‐trypanosome agent with different formulations and administration routes in mice by HPLC–MS/MS
- Author
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Raina Dano, Wenjing Zhang, Bin Su, Yaxin Li, Cody M. Orahoske, and Bibo Li
- Subjects
Glycerol ,Male ,Formic acid ,medicine.medical_treatment ,Electrospray ionization ,Clinical Biochemistry ,Intraperitoneal injection ,Administration, Oral ,Mass spectrometry ,Sensitivity and Specificity ,030226 pharmacology & pharmacy ,01 natural sciences ,Biochemistry ,Article ,Analytical Chemistry ,Mice ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Pharmacokinetics ,Tandem Mass Spectrometry ,In vivo ,Drug Discovery ,medicine ,Animals ,Protein precipitation ,Molecular Biology ,Chromatography, High Pressure Liquid ,Pharmacology ,Chromatography ,010401 analytical chemistry ,Selected reaction monitoring ,Reproducibility of Results ,General Medicine ,Trypanocidal Agents ,0104 chemical sciences ,chemistry ,Linear Models ,Injections, Intraperitoneal ,Sesame Oil - Abstract
Previously compound 12 showed great anti-trypanosome activity without toxicity in the in vivo study. In the current study, a sensitive and rapid high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method was developed and validated to investigate the pharmacokinetics of compound 12 in mouse plasma. Protein precipitation method was applied to extract the compound, and it was then separated by using a Kinetex C(18) column with a mobile phase consisting of acetonitrile-0.1% formic acid water (50:50, v/v) at a flow rate of 300 μL/min. The analytes were detected with the multiple reaction monitoring (MRM) in negative electrospray ionization source for quantitative response of the compounds. Compound 12 was detected at m/z 477.0→367.2, while the internal standard compound 14 was detected at m/z 499.2→268.2. Precision of the inter- and intra-day was less than 5.22% and 2.79% respectively, while the accuracy range was within ±9.65%. The method was successfully applied to evaluate the pharmacokinetic of compound 12 in mouse plasma with two formulations (20% Cremophor EL or sesame oil) and drug administration routes (oral and intraperitoneal injection). We observed a better drug serum concentration with the Cremophor formulation, and the two different drug administration routes did not show significant difference to the drug distribution.
- Published
- 2021
35. Trypanosoma bruceiPolIE suppresses telomere recombination
- Author
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Tonini M, Rabbani Mag, Marjia Afrin, and Bibo Li
- Subjects
Telomere Recombination ,Telomerase ,DNA synthesis ,biology ,DNA damage ,Antigenic variation ,Trypanosoma brucei ,Subtelomere ,biology.organism_classification ,Cell biology ,Telomere - Abstract
Telomeres are essential for genome integrity and stability. InT. bruceithat causes human African trypanosomiasis, the telomere structure and telomere proteins also influence the virulence of the parasite, as its major surface antigen involved in the host immune evasion is expressed exclusively from loci immediately upstream of the telomere repeats. However, telomere maintenance mechanisms are still unclear except that telomerase-mediated telomere synthesis is a major player. We now identify PolIE as an intrinsic telomere complex component. We find that depletion of PolIE leads to an increased amount of telomere/subtelomere DNA damage, an elevated rate of antigenic variation, and an increased amount of telomere T-circles and C-circles, indicating that PolIE suppresses telomere recombination and helps maintain telomere integrity. In addition, we observe much longer telomere G-rich 3’ overhangs in PolIE-depleted cells, which is not dependent on telomerase. Furthermore, the level of telomere DNA synthesis is slightly increased in PolIE-depleted cells, which is dependent on telomerase. Therefore, we identify PolIE as a major player for telomere maintenance inT. brucei.
- Published
- 2021
36. miR-219-5p targets TBXT and inhibits breast cancer cell EMT and cell migration and invasion
- Author
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Bibo Li, Mei Yuan, Xing Wang, Qin Ye, Zhaodi Hu, Dahu Chen, Shuaishuai Cui, Yuanyuan Chen, Conghui Han, and Dandan Liu
- Subjects
Untranslated region ,Epithelial-Mesenchymal Transition ,cell migration ,Biophysics ,Breast Neoplasms ,TBXT ,Biology ,Biochemistry ,law.invention ,law ,Cell Movement ,microRNA ,Humans ,Inducer ,Neoplasm Invasiveness ,Molecular Biology ,Gene ,Research Articles ,Cancer ,miRNA ,Transition (genetics) ,EMT ,Cell migration ,Cell Biology ,cell invasion ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,Cancer research ,MCF-7 Cells ,Neoplastic Stem Cells ,Suppressor ,Female ,Breast cancer cells ,T-Box Domain Proteins ,Signal Transduction - Abstract
miR-219-5p has been reported to act as either a tumor suppressor or a tumor promoter in different cancers by targeting different genes. In the present study, we demonstrated that miR-219-5p negatively regulated the expression of TBXT, a known epithelial–mesenchymal transition (EMT) inducer, by directly binding to TBXT 3′-untranslated region. As a result of its inhibition on TBXT expression, miR-219-5p suppressed EMT and cell migration and invasion in breast cancer cells. The re-introduction of TBXT in miR-219-5p overexpressing cells decreased the inhibitory effects of miR-219 on EMT and cell migration and invasion. Moreover, miR-219-5p decreased breast cancer stem cell (CSC) marker genes expression and reduced the mammosphere forming capability of cells. Overall, our study highlighted that TBXT is a novel target of miR-219-5p. By suppressing TBXT, miR-219-5p plays an important role in EMT and cell migration and invasion of breast cancer cells.
- Published
- 2021
37. Hedgehog signaling regulates telomerase reverse transcriptase in human cancer cells.
- Author
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Tapati Mazumdar, Ranjodh Sandhu, Maha Qadan, Jennifer DeVecchio, Victoria Magloire, Akwasi Agyeman, Bibo Li, and Janet A Houghton
- Subjects
Medicine ,Science - Abstract
The Hedgehog (HH) signaling pathway is critical for normal embryonic development, tissue patterning and cell differentiation. Aberrant HH signaling is involved in multiple human cancers. HH signaling involves a multi-protein cascade activating the GLI proteins that transcriptionally regulate HH target genes. We have previously reported that HH signaling is essential for human colon cancer cell survival and inhibition of this signal induces DNA damage and extensive cell death. Here we report that the HH/GLI axis regulates human telomerase reverse transcriptase (hTERT), which determines the replication potential of cancer cells. Suppression of GLI1/GLI2 functions by a C-terminus truncated GLI3 repressor mutant (GLI3R), or by GANT61, a pharmacological inhibitor of GLI1/GLI2, reduced hTERT protein expression in human colon cancer, prostate cancer and Glioblastoma multiforme (GBM) cell lines. Expression of an N-terminus deleted constitutively active mutant of GLI2 (GLI2ΔN) increased hTERT mRNA and protein expression and hTERT promoter driven luciferase activity in human colon cancer cells while GANT61 inhibited hTERT mRNA expression and hTERT promoter driven luciferase activity. Chromatin immunoprecipitation with GLI1 or GLI2 antibodies precipitated fragments of the hTERT promoter in human colon cancer cells, which was reduced upon exposure to GANT61. In contrast, expression of GLI1 or GLI2ΔN in non-malignant 293T cells failed to alter the levels of hTERT mRNA and protein, or hTERT promoter driven luciferase activity. Further, expression of GLI2ΔN increased the telomerase enzyme activity, which was reduced by GANT61 administration in human colon cancer, prostate cancer, and GBM cells. These results identify hTERT as a direct target of the HH signaling pathway, and reveal a previously unknown role of the HH/GLI axis in regulating the replication potential of cancer cells. These findings are of significance in understanding the important regulatory mechanisms that determine the functions of HH/GLI signaling in cancer cells.
- Published
- 2013
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38. Tb RAP1 has an unusual duplex DNA binding activity required for its telomere localization and VSG silencing
- Author
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Marjia Afrin, Amit Kumar Gaurav, Yanxiang Zhao, Xuehua Pan, Bibo Li, and Xian Yang
- Subjects
Telomere localization ,viruses ,cells ,Repressor ,Trypanosoma brucei ,environment and public health ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,parasitic diseases ,Molecular Biology ,Research Articles ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,biology ,Chemistry ,030302 biochemistry & molecular biology ,SciAdv r-articles ,biology.organism_classification ,Subtelomere ,Cell biology ,Telomere ,health occupations ,Rap1 ,biological phenomena, cell phenomena, and immunity ,DNA ,Nuclear localization sequence ,Research Article - Abstract
The electrostatics-based dsDNA binding activity in TbRAP1 NLS can be diminished by phosphorylation of NLS-adjacent S residues., Localization of Repressor Activator Protein 1 (RAP1) to the telomere is essential for its telomeric functions. RAP1 homologs either directly bind the duplex telomere DNA or interact with telomere-binding proteins. We find that Trypanosoma brucei RAP1 relies on a unique double-stranded DNA (dsDNA) binding activity to achieve this goal. T. brucei causes human sleeping sickness and regularly switches its major surface antigen, variant surface glycoprotein (VSG), to evade the host immune response. VSGs are monoallelically expressed from subtelomeres, and TbRAP1 is essential for VSG regulation. We identify dsDNA and single-stranded DNA binding activities in TbRAP1, which require positively charged 737RKRRR741 residues that overlap with TbRAP1’s nuclear localization signal in the MybLike domain. Both DNA binding activities are electrostatics-based and sequence nonspecific. The dsDNA binding activity can be substantially diminished by phosphorylation of two 737RKRRR741-adjacent S residues and is essential for TbRAP1’s telomere localization, VSG silencing, telomere integrity, and cell proliferation.
- Published
- 2020
39. Resveratrol inhibits hypertrophic scars formation by activating autophagy via the miR-4654/Rheb axis
- Author
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Long-jun Cai, Lin Hao, Rui Li, Jicun Ding, Jianjun Zhang, Kun Pang, Zhenduo Shi, Wen Yang, Conghui Han, Bibo Li, Ying Liu, Qian Lv, and Zhiming Tang
- Subjects
0301 basic medicine ,Cancer Research ,Programmed cell death ,Cicatrix, Hypertrophic ,Rheb ,hypertrophic scar-derived fibroblasts ,Cell ,Resveratrol ,Models, Biological ,Biochemistry ,Cell Line ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Autophagy ,Genetics ,medicine ,Humans ,MTT assay ,Viability assay ,Molecular Biology ,miR-4654 ,Dose-Response Relationship, Drug ,Oncogene ,biology ,Chemistry ,Articles ,hypertrophic scar ,Fibroblasts ,MicroRNAs ,HEK293 Cells ,030104 developmental biology ,medicine.anatomical_structure ,Gene Expression Regulation ,Oncology ,030220 oncology & carcinogenesis ,Cancer research ,biology.protein ,Molecular Medicine ,Ras Homolog Enriched in Brain Protein ,RHEB - Abstract
Hypertrophic scars (HSs) are a type of pathological scar which are induced by surgery, burn injuries or trauma during the healing process. Due to the high recurrence rates and strong invasive properties, HSs have become a major clinical issue. Resveratrol has been identified as a potential agent to suppress scar formation; however, the underlying mechanism of action remains unclear. Therefore, the present study aimed to investigate the effect of resveratrol on HS-derived fibroblasts (HSFBs) in vitro. MTT assay was performed to evaluate cell viability following the resveratrol treatment. Western blot and RT-qPCR analysis was used to identify the expression levels and the relationship among autophagic markers, miR-4654 and resveratrol treatment. Finally, GFP-LC3 stable HSFBs cells were generated to further assess the effect of resveratrol. The results revealed that resveratrol significantly induced cell death in a dose-dependent manner and induced autophagy by downregulating the expression levels of Rheb in HSFBs. Notably, microRNA-4654 (miR-4654) was significantly decreased in the HSFBs and re-upregulated by resveratrol treatment dose-dependently. Through the bioinformatic analysis and luciferase assay, miR-4654 was identified to directly target Rheb. Transfection studies showed that miR-4654 negative correlated with Rheb expression, suggesting that the autophagic process may be altered by the miR-4654/Rheb axis under the control of resveratrol. In conclusion, the results of the present study suggested that resveratrol may promote autophagy by upregulating miR-4654, which in turn may suppress Rheb expression via directly binding to the 3′-untranslated region of Rheb. These findings provided a novel insight into the development of potential therapeutic targets for HSs.
- Published
- 2020
40. <named-content content-type='genus-species'>Trypanosoma brucei</named-content> RAP1 Has Essential Functional Domains That Are Required for Different Protein Interactions
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Marjia Afrin, M. A. G. Rabbani, Hanadi Kishmiri, Ranjodh Sandhu, and Bibo Li
- Subjects
Molecular Biology and Physiology ,Telomere-Binding Proteins ,Trypanosoma brucei brucei ,Protozoan Proteins ,lcsh:QR1-502 ,Trypanosoma brucei ,Microbiology ,lcsh:Microbiology ,Protein–protein interaction ,protein-protein interaction ,03 medical and health sciences ,0302 clinical medicine ,parasitic diseases ,Antigenic variation ,Point Mutation ,Protein Interaction Domains and Motifs ,MYB ,Gene Silencing ,Molecular Biology ,Alleles ,030304 developmental biology ,0303 health sciences ,RAP1 ,telomere ,Membrane Glycoproteins ,biology ,biology.organism_classification ,Subtelomere ,Antigenic Variation ,QR1-502 ,Cell biology ,BRCT domain ,Rap1 ,030217 neurology & neurosurgery ,Nuclear localization sequence ,Research Article - Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, to evade the host immune response. VSGs are expressed from subtelomeres in a monoallelic fashion. TbRAP1, a telomere protein, is essential for cell viability and VSG monoallelic expression and suppresses VSG switching. Although TbRAP1 has conserved functional domains in common with its orthologs from yeasts to mammals, the domain functions are unknown. RAP1 orthologs have pleiotropic functions, and interaction with different partners is an important means by which RAP1 executes its different roles. We have established a Cre-loxP-mediated conditional knockout system for TbRAP1 and examined the roles of various functional domains in protein expression, nuclear localization, and protein-protein interactions. This system enables further studies of TbRAP1 point mutation phenotypes. We have also determined functional domains of TbRAP1 that are required for several different protein interactions, shedding light on the underlying mechanisms of TbRAP1-mediated VSG silencing., RAP1 is a telomere protein that is well conserved from protozoa to mammals. It plays important roles in chromosome end protection, telomere length control, and gene expression/silencing at both telomeric and nontelomeric loci. Interaction with different partners is an important mechanism by which RAP1 executes its different functions in yeast. The RAP1 ortholog in Trypanosoma brucei is essential for variant surface glycoprotein (VSG) monoallelic expression, an important aspect of antigenic variation, where T. brucei regularly switches its major surface antigen, VSG, to evade the host immune response. Like other RAP1 orthologs, T. brucei RAP1 (TbRAP1) has conserved functional domains, including BRCA1 C terminus (BRCT), Myb, MybLike, and RAP1 C terminus (RCT). To study functions of various TbRAP1 domains, we established a strain in which one endogenous allele of TbRAP1 is flanked by loxP repeats, enabling its conditional deletion by Cre-mediated recombination. We replaced the other TbRAP1 allele with various mutant alleles lacking individual functional domains and examined their nuclear localization and protein interaction abilities. The N terminus, BRCT, and RCT of TbRAP1 are required for normal protein levels, while the Myb and MybLike domains are essential for normal cell growth. Additionally, the Myb domain of TbRAP1 is required for its interaction with T. brucei TTAGGG repeat-binding factor (TbTRF), while the BRCT domain is required for its self-interaction. Furthermore, the TbRAP1 MybLike domain contains a bipartite nuclear localization signal that is required for its interaction with importin α and its nuclear localization. Interestingly, RAP1’s self-interaction and the interaction between RAP1 and TRF are conserved from kinetoplastids to mammals. However, details of the interaction interfaces have changed throughout evolution. IMPORTANCE Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, to evade the host immune response. VSGs are expressed from subtelomeres in a monoallelic fashion. TbRAP1, a telomere protein, is essential for cell viability and VSG monoallelic expression and suppresses VSG switching. Although TbRAP1 has conserved functional domains in common with its orthologs from yeasts to mammals, the domain functions are unknown. RAP1 orthologs have pleiotropic functions, and interaction with different partners is an important means by which RAP1 executes its different roles. We have established a Cre-loxP-mediated conditional knockout system for TbRAP1 and examined the roles of various functional domains in protein expression, nuclear localization, and protein-protein interactions. This system enables further studies of TbRAP1 point mutation phenotypes. We have also determined functional domains of TbRAP1 that are required for several different protein interactions, shedding light on the underlying mechanisms of TbRAP1-mediated VSG silencing.
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- 2020
41. The NRP1 gene regulates proliferation, apoptosis, migration, and invasion in T24 and 5637 bladder cancer cells
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Conghui Han, Yang Dong, Lin Hao, Kun Pang, Xiaoying Zhang, Zhenduo Shi, Bibo Li, Zhiguo Zhang, Rongsheng Zhou, Wenda Zhang, Tao Fan, Guangyuan Zhu, Qian Lv, Ying Liu, and Rui Li
- Abstract
Background Bladder urothelial carcinoma (BC) is a fatal invasive malignancy and the most common malignancy of the urinary system. In the current study, we investigate the function and mechanisms of Neuropilin-1 (NRP1), the co-receptor for vascular endothelial growth factor, in BC pathogenesis and progression. Methods The expression of NRP1 was assessed in several BC cell lines. Additionally, the biological function of NRP1 in proliferation, apoptosis, angiogenesis, migration, and invasion of BC were validated in vitro by silencing NRP1. Moreover, gene expression profiling chip analysis was conducted, and the related signalling pathways were confirmed by Western blot to reveal the potential molecular mechanisms by which NRP1 promotes the malignant progression of BC. Results Overexpression of NRP1 was observed in several human BC cell lines. NRP1 knockdown inhibited cell proliferation, promoted apoptosis, and decreased angiogenesis, migration, and invasion in T24 and 5637 human BC cells. Microarray analysis results indicated that the expression of NRP1 was correlated with the levels of cyclin dependent kinase (CDK) 4, baculoviral IAP repeat containing 3, Cyclin E 2, CDK2, and AP-1 transcription factor subunit in BC. We also demonstrated that the biological function of NRP1was associated with activation of the mitogen-activated protein kinase (MAPK) signalling pathway. Conclusions Our findings provide evidence that NRP1, as a potential tumour promoter, contributes to the metastasis and invasion of BC, which is associated with the activation of the MAPK pathway. Targeting NRP1 has the potential to become a new therapeutic strategy to benefit more patients with BC or other cancers.
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- 2020
42. Regulation of Antigenic Variation by Trypanosoma brucei Telomere Proteins Depends on Their Unique DNA Binding Activities
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Yanxiang Zhao and Bibo Li
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Microbiology (medical) ,Trypanosoma brucei ,Review ,antigenic variation ,Myb domain ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,parasitic diseases ,Antigenic variation ,Immunology and Allergy ,Molecular Biology ,030304 developmental biology ,chemistry.chemical_classification ,telomere ,RAP1 ,0303 health sciences ,General Immunology and Microbiology ,biology ,VSG ,biology.organism_classification ,Subtelomere ,Telomere ,Cell biology ,Infectious Diseases ,chemistry ,Nucleic acid ,Medicine ,Rap1 ,TRF ,Glycoprotein ,DNA binding activity ,030217 neurology & neurosurgery ,DNA - Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, Variant Surface Glycoprotein (VSG), to evade the host immune response. Such antigenic variation is a key pathogenesis mechanism that enables T. brucei to establish long-term infections. VSG is expressed exclusively from subtelomere loci in a strictly monoallelic manner, and DNA recombination is an important VSG switching pathway. The integrity of telomere and subtelomere structure, maintained by multiple telomere proteins, is essential for T. brucei viability and for regulating the monoallelic VSG expression and VSG switching. Here we will focus on T. brucei TRF and RAP1, two telomere proteins with unique nucleic acid binding activities, and summarize their functions in telomere integrity and stability, VSG switching, and monoallelic VSG expression. Targeting the unique features of TbTRF and TbRAP1′s nucleic acid binding activities to perturb the integrity of telomere structure and disrupt VSG monoallelic expression may serve as potential therapeutic strategy against T. brucei.
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- 2021
43. Abnormal creep behavior of Mg–12Gd–1MM–0.6Zr (wt.%) alloy at 300°C
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Li Yongjun, Shi Guoliang, Jiawei Yuan, Kaikun Wang, Minglong Ma, Zhang Kui, Bibo Li, and Li Xinggang
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Materials science ,Mechanical Engineering ,Alloy ,02 engineering and technology ,engineering.material ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Grain size ,0104 chemical sciences ,Creep ,Mechanics of Materials ,Creep rate ,Phase (matter) ,engineering ,Fracture (geology) ,General Materials Science ,Composite material ,0210 nano-technology - Abstract
The creep behavior of extrusion-solution treated (T4) Mg–12Gd–1MM–0.6Zr (wt.%) alloys with different grain sizes at 300 °C was evaluated. Results showed that the creep rate curves presented an abnormal decelerated–accelerated–decelerated evolution in the initial stage, which was caused by creep aging. The accelerated creep rate is caused by the transformation from thin β' phase into coarse β1 and β phases; and the transformation of the 3D distribution β phase from the initial single variant to network containing three variants is a key reason for the secondary deceleration of creep rate. On the other hand, as the average grain size increased from 44 μm to 90 μm, the steady-state creep rate gradually decreased, but fracture time continuously increased, so coarse grain is beneficial to creep resistance of the present alloy.
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- 2021
44. Trypanosoma brucei RAP1 maintains telomere and subtelomere integrity by suppressing TERRA and telomeric RNA:DNA hybrids
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Unnati M. Pandya, Ranjodh Sandhu, Vishal Nanavaty, Sanaa E. Jehi, and Bibo Li
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0301 basic medicine ,Transcription, Genetic ,Base pair ,Ribonuclease H ,Trypanosoma brucei brucei ,Protozoan Proteins ,Biology ,03 medical and health sciences ,chemistry.chemical_compound ,Transcription (biology) ,parasitic diseases ,Genetics ,DNA Breaks, Double-Stranded ,RNA, Messenger ,Base Pairing ,Gene ,Telomere-binding protein ,030102 biochemistry & molecular biology ,Gene regulation, Chromatin and Epigenetics ,Nucleic Acid Hybridization ,rap1 GTP-Binding Proteins ,RNA ,DNA, Protozoan ,Telomere ,Subtelomere ,030104 developmental biology ,chemistry ,RNA, Long Noncoding ,RNA, Protozoan ,Variant Surface Glycoproteins, Trypanosoma ,DNA - Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, thereby evading the host's immune response. VSGs are monoallelically expressed from subtelomeric expression sites (ESs), and VSG switching exploits subtelomere plasticity. However, subtelomere integrity is essential for T. brucei viability. The telomeric transcript, TERRA, was detected in T. brucei previously. We now show that the active ES-adjacent telomere is transcribed. We find that TbRAP1, a telomere protein essential for VSG silencing, suppresses VSG gene conversion-mediated switching. Importantly, TbRAP1 depletion increases the TERRA level, which appears to result from longer read-through into the telomere downstream of the active ES. Depletion of TbRAP1 also results in more telomeric RNA:DNA hybrids and more double strand breaks (DSBs) at telomeres and subtelomeres. In TbRAP1-depleted cells, expression of excessive TbRNaseH1, which cleaves the RNA strand of the RNA:DNA hybrid, brought telomeric RNA:DNA hybrids, telomeric/subtelomeric DSBs and VSG switching frequency back to WT levels. Therefore, TbRAP1-regulated appropriate levels of TERRA and telomeric RNA:DNA hybrid are fundamental to subtelomere/telomere integrity. Our study revealed for the first time an important role of a long, non-coding RNA in antigenic variation and demonstrated a link between telomeric silencing and subtelomere/telomere integrity through TbRAP1-regulated telomere transcription.
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- 2017
45. Telomere and Subtelomere R-loops and Antigenic Variation in Trypanosomes
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Vishal Nanavaty, Arpita Saha, and Bibo Li
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R-loop ,Cell Plasticity ,Trypanosoma brucei brucei ,Trypanosoma brucei ,Article ,03 medical and health sciences ,0302 clinical medicine ,RNA, Transfer ,Structural Biology ,Transcription (biology) ,parasitic diseases ,Antigenic variation ,Molecular Biology ,Gene ,030304 developmental biology ,Genetics ,0303 health sciences ,biology ,RNA ,Genetic Variation ,Telomere ,biology.organism_classification ,Subtelomere ,Antigenic Variation ,R-Loop Structures ,030217 neurology & neurosurgery ,Variant Surface Glycoproteins, Trypanosoma - Abstract
Trypanosoma brucei is a kinetoplastid parasite that causes African trypanosomiasis, which is fatal if left untreated. T. brucei regularly switches its major surface antigen, VSG, to evade the host immune responses. VSGs are exclusively expressed from subtelomeric expression sites (ESs) where VSG genes are flanked by upstream 70 bp repeats and downstream telomeric repeats. The telomere downstream of the active VSG is transcribed into a long-noncoding RNA (TERRA), which forms RNA:DNA hybrids (R-loops) with the telomeric DNA. At an elevated level, telomere R-loops cause more telomeric and subtelomeric Double-Strand Breaks (DSBs) and increase VSG switching rate. In addition, stabilized R-loops are observed at the 70 bp repeats and immediately downstream of ES-linked VSGs in RNase H-defective cells, which also have an increased amount of subtelomeric DSBs and more frequent VSG switching. Although subtelomere plasticity is expected to be beneficial to antigenic variation, severe defects in subtelomere integrity and stability increase cell lethality. Therefore, regulation of the telomere and 70 bp repeat R-loop levels is important for the balance between antigenic variation and cell fitness in T. brucei. Additionally, the high level of the active ES transcription favors accumulation of R-loops at the telomere and 70 bp repeats, providing an intrinsic mechanism for local DSB formation, which is a strong inducer of VSG switching.
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- 2019
46. Effect of dietary concentrate to forage ratios on ruminal bacterial and anaerobic fungal populations of cashmere goats
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Xiaolong Wang, Bibo Li, Yulin Chen, Yuxin Yang, and Xufeng Han
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Rumen ,Animal food ,Microbiology ,Actinobacteria ,Neocallimastix ,03 medical and health sciences ,Bacteria, Anaerobic ,Nutrient ,Animal science ,Prevotella ,Animals ,Anaerobiosis ,030304 developmental biology ,0303 health sciences ,biology ,030306 microbiology ,Goats ,Fungi ,Bacteroidetes ,biology.organism_classification ,Biota ,Diet ,Infectious Diseases ,Piromyces ,Female - Abstract
The rumen contains a highly complex microbial ecosystem that plays an important role in converting solar energy in plants into nutrients for ruminants and generates animal food products, such as meat and milk for humans. Therefore, understanding the effect of the dietary concentrate to forage (C:F) ratio on ruminal microbiota is of great significance for the growth and development of ruminants. In this study, changes in the ruminal bacterial and anaerobic fungal populations of Shaanbei white-cashmere (SWC) goats that were reared under different dietary C:F ratios were evaluated by high-throughput sequencing analysis. It was found that dietary C:F ratio has a significant impact on the composition of the ruminal bacteria in SWC goats. The levels of Actinobacteria and Proteobacteria were significantly increased (P
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- 2019
47. Lead optimization of selective tubulin inhibitors as anti-trypanosomal agents
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Yaxin Li, Abboud Sabbagh, Bin Su, Cody M. Orahoske, Wenjing Zhang, Anran Zhao, Brittny Schnur, and Bibo Li
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Clinical Biochemistry ,Trypanosoma brucei brucei ,Pharmaceutical Science ,Trypanosoma brucei ,01 natural sciences ,Biochemistry ,Article ,Mice ,Western blot ,Drug Discovery ,medicine ,Structure–activity relationship ,Animals ,Humans ,Molecular Biology ,Ligand efficiency ,biology ,medicine.diagnostic_test ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,biology.organism_classification ,Trypanocidal Agents ,In vitro ,Tubulin Modulators ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,Tubulin ,HEK293 Cells ,RAW 264.7 Cells ,Trypanosomiasis, African ,Cell culture ,Drug Design ,biology.protein ,Molecular Medicine ,Function (biology) - Abstract
Previously synthesized tubulin inhibitors showed promising in vitro selectivity and activity against Human African Trypanosomiasis. Current aim is to improve the ligand efficiency and reduce overall hydrophobicity of the compounds, by lead optimization. Via combinatorial chemistry, 60 new analogs were synthesized. For biological assay Trypanosoma brucei brucei Lister 427 cell line were used as the parasite model and for the host model human embryonic kidney cell line HEK-293 and mouse macrophage cell line RAW 264.7 were used to test efficacy. Of the newly synthesized compounds 5, 39, 40, and 57 exhibited IC50s below 5 µM inhibiting the growth of trypanosome cells and not harming the mammalian cells at equipotent concentration. Comparably, the newly synthesized compounds have a reduced amount of aromatic moieties resulting in a decrease in molecular weight. Due to importance of tubulin polymerization during protozoan life cycle its activity was assessed by western blot analyses. Our results indicated that compound 5 had a profound effect on tubulin function. A detailed structure activity relationship (SAR) was summarized that will be used to guide future lead optimization.
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- 2019
48. miR-219-5p targets TBXT and inhibits breast cancer cell EMT and cell migration and invasion.
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Qin Ye, Xing Wang, Mei Yuan, Shuaishuai Cui, Yuanyuan Chen, Zhaodi Hu, Dandan Liu, Conghui Han, Bibo Li, and Dahu Chen
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BREAST cancer ,CANCER cells ,CELL migration ,CANCER stem cells ,CARCINOGENS ,EPITHELIAL-mesenchymal transition - Abstract
miR-219-5p has been reported to act as either a tumor suppressor or a tumor promoter in different cancers by targeting different genes. In the present study, we demonstrated that miR-219-5p negatively regulated the expression of TBXT, a known epithelial-mesenchymal transition (EMT) inducer, by directly binding to TBXT 3'-untranslated region. As a result of its inhibition on TBXT expression, miR-219-5p suppressed EMT and cell migration and invasion in breast cancer cells. The re-introduction of TBXT in miR-219-5p overexpressing cells decreased the inhibitory effects of miR-219 on EMT and cell migration and invasion. Moreover, miR-219-5p decreased breast cancer stem cell (CSC) marker genes expression and reduced the mammosphere forming capability of cells. Overall, our study highlighted that TBXT is a novel target of miR-219-5p. By suppressing TBXT, miR-219-5p plays an important role in EMT and cell migration and invasion of breast cancer cells. [ABSTRACT FROM AUTHOR]
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- 2021
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- View/download PDF
49. Exploring the Spatial-Temporal Microbiota of Compound Stomachs in a Pre-weaned Goat Model
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Xiaolong Wang, Mengmeng Guo, Yuxin Yang, Guanwei Li, Ke Zhang, Yulin Chen, Yu Lei, Chao Li, and Bibo Li
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0301 basic medicine ,Microbiology (medical) ,Rikenellaceae ,animal structures ,030106 microbiology ,lcsh:QR1-502 ,ruminant ,Abomasum ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Rumen ,Animal science ,Ruminant ,Microbiome ,Original Research ,biology ,Omasum ,gut microbiota ,biology.organism_classification ,taxonomic diversity ,rumen microbiology ,030104 developmental biology ,microbial community ,Digestion ,Reticulum - Abstract
Ruminant animals possess a characteristic four-compartment stomach (rumen, reticulum, omasum, and abomasum) that is specialized for pre-intestinal digestion of plant materials. Of these four compartments, the rumen is the largest. The rumen’s diverse microbial community has been well studied. However, the current understanding of microbial profiles in the reticulum, omasum and abomasum are lacking. In the present study, fluid samples from the reticulum, omasum, and abomasum of goats at 3, 7, 14, 21, 28, 42, and 56 days after birth, as well as the negative controls (NC) used for microbial DNA extraction, were subjected to 16S rRNA sequencing. By filtering operational taxonomic units (OTUs) in NC, distinct temporal distributions of microbes were observed in the different compartments, we showed that the OTUs in control samples had a large effect to the samples with low microbial density. In addition, Proteobacteria gradually decreased with age from days 3 to 56 in all three compartments, and the relative abundance of Bacteroidetes increased from 24.15% (Day 3) to 52.03% (Day 56) in abomasum. Network analysis revealed that Prevotellaceae_UGG-03 and Rikenellaceae_RC9 were positively correlated with Prevotella_1, lending support to the well understood fact that cellulose is well digested in compound stomachs prior to the rumen. Pathway analysis revealed that gene expression in abomasum at Day 3 were primarily related to Glycolysis/Gluconeogenesis and Pyruvate metabolism, suggesting that colostrum digestion is the dominant function of the abomasum at an early age. These findings combined with other recent rumen microbiota data show that the microbiome landscape represents three distinct stages in ruminant stomachs. The first stage is to gain access to external microorganisms at Day 0–14, the secondary stage is for microbial transition at Day 14–28, and the third stage is for exogenous and endogenous microbial colonization beyond Day 28 of age. Our results provide insight into microbiota dynamics in ruminant stomachs, and will facilitate efforts for the maintenance of gastrointestinal balance and intervention with starter diets in juvenile ruminants during early development.
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- 2018
50. Use of green fluorescent protein to monitor Lactobacillus plantarum in the gastrointestinal tract of goats
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Lei Wang, Wei Li, Bibo Li, Yulin Chen, Hailong Yan, Xufeng Han, Lei Qu, and Yuxin Yang
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Gastrointestinal tract ,biology ,Electroporation ,food and beverages ,biology.organism_classification ,Microbiology ,Green fluorescent protein ,Rumen ,In vivo ,Lactobacillus ,Media Technology ,bacteria ,Bacteria ,Lactobacillus plantarum - Abstract
The experiment aimed to specifically monitor the passage of lactobacilli in vivo after oral administration. The green fluorescent protein (GFP) gene was cloned downstream from the constitutive p32 promoter from L. lactis subsp. cremoris Wg2. The recombinant expression vector, pLEM415-gfp-p32, was electroporated into Lactobacillus plantarum (L. plantarum) isolated from goat. Green fluorescent protein (GFP) was successfully expressed in L. plantarum. After 2 h post-administration, transformed Lactobacillus could be detectable in all luminal contents. In the rumen, bacteria concentration initially decreased, reached the minimum at 42 h post-oral administration and then increased. However, this concentration decreased constantly in the duodenum. This result indicated that L. plantarum could colonize in the rumen but not in the duodenum.
- Published
- 2015
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