Biomedical subjects

Li Qian

Publications and source records attributed to Li Qian.

At least 19 recordsLinked to original sources

PubMed2026

Spatially guided in vivo single-cell functional genomics of postnatal heart.

Understanding how spatial organization and cell-cell interactions shape gene regulatory programs is central to decoding tissue development and function. The transition at birth, marked by increased circulatory demands and rapid tissue growth, requires precise spatiotemporal coordination of cardiac maturation. In this study, we generated a high-resolution spatial and temporal atlas of the postnatal mouse heart by integrating single-nucleus RNA sequencing with image-based spatial transcriptomics. This framework revealed dynamic cellular interactions, niche-specific signaling and transcriptional programs guiding cardiomyocyte maturation. To functionally test prioritized regulators in vivo and at scale, we developed PIP-seq (probe-based indel-detectable Perturb-seq), a high-throughput platform that detects single guide RNA identity, infers gene editing and profiles transcription from fixed nuclei. Applying PIP-seq to the developing postnatal heart, we identified 21 previously uncharacterized regulators of cardiomyocyte maturation, including genes essential for sarcomere assembly, metabolic reprogramming and electrophysiological transitions. Together, our findings define how microenvironmental signals and intrinsic gene programs cooperate to guide heart maturation and establish a broadly applicable framework for functional genomics in complex tissues.

Animals↗

PubMed2026

PGS-GS: a framework integrating polygenic scores and genomic selection in animal breeding.

Genomic prediction has become a central paradigm in biology, enabling quantitative inference of genetic contributions to complex traits across humans, animals, and plants. Although genomic research in human genetics and animal breeding shares a highly homologous methodological foundation, significant barriers persist in their analytical paradigms and application scenarios. This study aims to promote cross-disciplinary integration by introducing human-derived polygenic scores (PGS) algorithms into animal genomic selection (GS) and proposing a PGS-GS framework with a preliminary weighting-based implementation. We systematically benchmarked the predictive performance and computational efficiency of 20 algorithms, including classical linear models, machine learning, PGS, and PGS-GS using both array and whole-genome sequencing (WGS) data across four major agricultural species: beef cattle, sheep, pigs, and chickens. Our results demonstrate that PGS and PGS-GS algorithms achieve predictive accuracy competitive with genomic best linear unbiased prediction (GBLUP) while offering markedly higher computational efficiency. Moreover, incorporating PGS-derived prior information into weighted linear and non-linear models outperformed conventional weighted GBLUP. The results provide empirical evidence to inform algorithm selection and highlight the potential of integrating human-derived PGS methodologies into animal genomic prediction frameworks.

Animals↗

PubMed2025

Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomics.

The transition at birth, marked by increased circulatory demands and rapid growth, necessitates extensive remodeling of the heart's structure, function, and metabolism. This transformation requires precise spatial and temporal coordination among diverse cardiac cell types; central to this process is cardiomyocyte maturation, yet the regulatory mechanisms driving these changes remain poorly understood. Here, we present a temporal and spatial atlas of postnatal hearts by integrating single-nucleus transcriptomics with image-based spatial transcriptomics, which uncovers the dynamic regulatory networks of cardiomyocyte maturation. To functionally interrogate candidate regulators in vivo , we developed Probe-based Indel-detectable Perturb-seq (PIP-seq), a high-throughput platform that uses probe-based chemistry to directly capture sgRNA expression, perturbation status, and transcriptomic profiles at single-nucleus resolution. Applying PIP-seq to postnatal cardiac development identified 21 novel regulators of cardiomyocyte maturation, highlighting critical nodal points in this process. Our study establishes a high-resolution framework for dissecting postnatal heart development, underscoring the integrative and highly ordered roles of microenvironment and intercellular communication in cardiomyocyte maturation. Importantly, PIP-seq enables systematic, high-throughput exploration of gene function and networks underlying complex biological processes in their native in vivo context.

Journal Article↗

PubMed2006

Cardioblast-intrinsic Tinman activity controls proper diversification and differentiation of myocardial cells in Drosophila.

The NK homeobox gene tinman (tin) is required for the specification of the cardiac, visceral muscle and somatic muscle progenitors in the early dorsal mesoderm of Drosophila. Like its vertebrate counterpart Nkx2.5, the expression of tin is maintained in cardiac cells during cardiac maturation and differentiation; however, owing to the complete lack of a dorsal vessel in tin mutant embryos, the function of tin in these cells has not been defined. Here we show that myocardial cells and dorsal vessels can form even though they lack Tin, and that viable adults can develop, as long as Tin is provided in the embryonic precardiac mesoderm. However, embryos in which tin expression is specifically missing from cardial cells show severe disruptions in the normal diversification of the myocardial cells, and adults exhibit severe defects in cardiac remodeling and function. Our study reveals that the normal expression and activity of Tin in four of the six bilateral cardioblasts within each hemisegment of the heart allows these cells to adopt a cell fate as ;working' myocardium, as opposed to a fate as inflow tract (ostial) cells. This function of tin involves the repression of Dorsocross (Doc) T-box genes and, hence, the restriction of Doc to the Tin-negative cells that will form ostia. We conclude that tin has a crucial role within myocardial cells that is required for the proper diversification, differentiation, and post-embryonic maturation of cardiomyocytes, and we present a pathway involving regulatory interactions among seven-up, midline, tinman and Dorsocross that establishes these developmental events upon myocardial cell specification.

Animals↗

PubMed2006

Antioxidants protect PINK1-dependent dopaminergic neurons in Drosophila.

Parkinson's disease (PD) is the most frequent neurodegenerative movement disorder. Mutations in the PINK1 gene are linked to the autosomal recessive early onset familial form of PD. The physiological function of PINK1 and pathological abnormality of PD-associated PINK1 mutants are largely unknown. We here show that inactivation of Drosophila PINK1 (dPINK1) using RNAi results in progressive loss of dopaminergic neurons and in ommatidial degeneration of the compound eye, which is rescued by expression of human PINK1 (hPINK1). Expression of human SOD1 suppresses neurodegeneration induced by dPINK1 inactivation. Moreover, treatment of dPINK1 RNAi flies with the antioxidants SOD and vitamin E significantly inhibits ommatidial degeneration. Thus, dPINK1 plays an essential role in maintaining neuronal survival by preventing neurons from undergoing oxidative stress, thereby suggesting a potential mechanism by which a reduction in PINK1 function leads to PD-associated neurodegeneration.

Animals↗

PubMed2006

The role of titanium surface topography on J774A.1 macrophage inflammatory cytokines and nitric oxide production.

A role for monocyte/macrophage modulation of wound healing at endosseous implants is proposed. The modification of the endosseous implant surface topography can alter cell adhesion and resultant cell behavior. The aim of this study was to define the effect of increased cpTitanium surface topography on adherent J744A.1 macrophage phenotype in culture. The J744A.1 cells were cultured on 20mm diameter cpTitanium disks prepared with smooth and grit-blasted/acid rough surface topographies for 24-72 h. Following culture in growth media with or without lipopolysaccharide (LPS), total RNA was isolated and real-time polymerase chain reaction (PCR) was used to measure the steady-state levels of the pro-inflammatory cytokines interleukin 1-beta (IL-1beta) and interleukin 6 (IL-6) and the anti-inflammatory cytokine interleukin-10 (IL-10). Additional evidence of pro-inflammatory signaling was sought by measurement of cellular nitric oxide (NO) production. In the absence of LPS, IL-1beta levels were increased on grit-blasted/acid rough surfaces during the first 48 h. In contrast, IL-6 levels were reduced on the grit-blasted/acid rough surfaces. When cultures were treated with LPS, high levels of IL-1beta and IL-6 expression were measured, irrespective of surface topography. The responses of J744A.1 cells to surface and superimposed LPS stimulation suggest only modest effects of the modeled endosseous implant surface on adherent cell pro-inflammatory cytokine expression and NO signaling.

Animals↗

PubMed2006

Interleukin-10 protects lipopolysaccharide-induced neurotoxicity in primary midbrain cultures by inhibiting the function of NADPH oxidase.

The role of anti-inflammatory cytokines in Parkinson's disease is not completely understood. In this study, using mesencephalic neuron-glia cultures, we report that both pretreatment and post-treatment of rat mesencephalic neuron-glia cultures with interleukin (IL)-10, a natural immune modulator, reduced lipopolysaccharide (LPS)-induced DA neurotoxicity. The main purpose of this study was to elucidate the molecular mechanism underlying IL-10-elicited neuroprotection. IL-10 significantly inhibited LPS-induced production of tumor necrosis factor-alpha, nitric oxide, and extracellular superoxide in microglia cells. In addition, using reconstituted neuron and glia cell cultures, IL-10 was shown to be neuroprotective only in the presence of microglia. More importantly, IL-10 failed to protect DA neurons in cultures from mice lacking NADPH oxidase (PHOX), a key enzyme for extracellular superoxide production in immune cells, suggesting the critical role of PHOX in IL-10 neuroprotection. This conclusion was further supported by the finding that IL-10 inhibited LPS-induced translocation of the cytosolic subunit of NADPH oxidase p47(phox) to the membrane. When the Janus tyrosine kinase (JAK) 1 signaling pathway was blocked, IL-10 failed to attenuate LPS-induced superoxide production, indicating that the JAK1 signaling cascade mediates the inhibitory effect of IL-10. Together, our results suggest that IL-10 inhibits LPS-induced DA neurotoxicity through the inhibition of PHOX activity in a JAK1-dependent mechanism.

Animals↗

PubMed2006

Experimental quantum key distribution with decoy states.

To increase dramatically the distance and the secure key generation rate of quantum key distribution (QKD), the idea of quantum decoys--signals of different intensities--has recently been proposed. Here, we present the first experimental implementation of decoy state QKD. By making simple modifications to a commercial quantum key distribution system, we show that a secure key generation rate of 165 bit/s, which is 1/4 of the theoretical limit, can be obtained over 15 km of a telecommunication fiber. We also show that with the same experimental parameters, not even a single bit of secure key can be extracted with a non-decoy-state protocol. Compared to building single photon sources, decoy state QKD is a much simpler method for increasing the distance and key generation rate of unconditionally secure QKD.

Journal Article↗

PubMed2006

Establishment and characterization of a novel genetic hybrid cell line for propagation of four pathogens.

Chromosomal DNAs were purified from human epidermoid carcinoma (HEP-2) cells and transfected into human embryonic lung (HEL) cells to establish a genetic hybrid cell line susceptible to infections by toxoplasma, rubella virus, cytomegalovirus, and herpes simplex virus. Karyotype analysis showed that the resultant hybrid cells, designated D3, had a chromosome number of 96, which was stable after passage for 100 generations. Direct microscopy and immunofluorescence showed that the D3 cells could be infected by the four pathogens with overt cytopathic effects. The toxoplasma and three viruses were purified from infected D3 cells by sucrose gradient centrifugation and used as the antigens for detection of specific IgG and/or IgM in serum samples from pregnant women with suspicious infections by the four pathogens, the results of which were consistent with those of commercial kits. These data indicate that a stable genetic hybrid cell line has been generated, which is a valuable tool for the isolation of the four intrauterine pathogens and for the preparation of antigens for serological tests.

Animals↗

PubMed2006

Hedgehog and RAS pathways cooperate in the anterior-posterior specification and positioning of cardiac progenitor cells.

The Drosophila heart is a highly ordered structure with only a limited number of cell types, which are arranged in a stereotyped metameric pattern. Ras signaling has previously been implicated in contributing to heart formation, but how positional information is integrated with this pathway to specify, distinguish and precisely position individual cardiac progenitors within the presumptive heart-forming region are not known. Here, we present evidence that the striped pattern of the secreted factor Hedgehog (Hh), in combination with the RAS pathway, specifies and positions neighboring groups of cardiac progenitors within each segment: the anterior ladybird (lbe)- and the posterior even skipped (eve)-expressing cardiac progenitors. Loss of hh function (while maintaining wg activity) results in the absence of the Eve cells, whereas the Lbe cells are expanded within the cardiac mesoderm. Overexpressing the repressor form of Cubitus interruptus (Ci), a Hh pathway antagonist, also results in expansion of Lbe at the expense of Eve, as does lowering Ras signaling. Conversely, overexpression of Hh or increasing Ras signaling eliminates Lbe expression while expanding Eve within the cardiogenic mesoderm. Increasing Ras signaling in the absence of Hh suggests that the Ras pathway is in part epistatic to Hh. Hh controls dorsal mesodermal Ras signaling by transcriptional regulation of the EGF receptor ligand protease, encoded by rhomboid (rho). Conversely, Hh overexpression can fully inhibit Lbe even when Ras signaling is much reduced, suggesting that Hh also acts in parallel to Ras. We propose that the Eve precursors next to the Hh stripe are distinguished from more distant Lbe precursors by locally augmenting Ras signaling via elevating rho transcripts. Thus, the spatial precision of cell type specification within an organ depends on multiple phases of inductive interaction between the ectoderm and the mesoderm.

Animals↗

PubMed2006

Cloning and sequence analysis of the gene encoding (6-4)photolyase from Dunaliella salina.

DNA photolyase can repair UV-induced DNA damage in a light-dependent manner. A cDNA of (6-4)photolyase from Dunaliella salina (GenBank accession number: AY845324) was cloned, sequenced and its amino acid sequence was deduced. The derived amino acid sequence showed high homology with other (6-4)photolyases and a predicted 3D model was constructed by homology modeling.

Amino Acid Sequence↗

PubMed2006

[Recombinant eukaryotic expression plasmid of bcr-abl gene fragment induces specific immune response in mice].

OBJECTIVE: To study the specific immune response induced by a recombinant eukaryotic expression plasmid encoding bcr-abl fusion gene fragment so as to explore new immunotherapy in mouse. METHODS: A recombinant eukaryotic vector pVbcr-abl expression cDNA fragment of bcr-abl fusion gene was constructed and used to immunize BALB/c mice. Serum level of bcr-abl specific antibody was detected by enzyme-linked immunosorbent assay (ELISA). Twenty days later the immunized mice were subcutaneously inoculated SP2/0/bcr-abl cells. The survival time, tumor growth time and lymphocytic infiltration were observed. T cells infiltration into tumor tissue was analyzed by immunohistochemistry. Changes of T cell subset in the spleen of mice was analyzed by fluorescent-activated cell sorting (FACS) and the cytotoxicity T lymphocyte (CTL) activity in spleen by lactate dehydrogenase (LDH)-release assay. RESULTS: The eukaryotic expression vector pVbcr-abl was constructed successfully, and highly expressed the cDNA fragment of bcr-abl fusion gene. The BALB/c mice immunized with the vector could generate the specific antibody and CTL, resulting in a specific immunoprotection. There were dramatic differences in the tumor-forming time, tumor ulcer appearing time and tumor-growing speed between the immunized and the control groups. The mice had longer survival time in the immunized group than in the control group. There were a large amount of CD3(+) T cells infiltration in tumor tissue of the immunized mice. The spleen cells from the immunized mice had higher CTL activity with a alteration of T cell subset, the CD4(+)/CD8(+) ratio being 1.54 +/- 0.29, higher than that of control group (1.18 +/- 0.30). CONCLUSION: The recombinant eukaryotic expression plasmid pVbcr-abl can induce in vivo not only the generation of specific antibody, but also high level of specific CTL activity, resulting in killing the SP2/0/bcr-abl tumor cells directly and inhibiting the tumor growth.

Animals↗

PubMed2006

[Influences of bcr-abl gene vaccine on inoculated SP2/0/bcr-abl tumor cells in mice].

To study the influence of vaccine of bcr-abl fusion gene fragment on inoculated SP2/0/bcr-abl tumor cells in mice, BALB/c mice were immunized with pVbcr-abl, pVbcr-abl/mIL7 plasmids, respectively, then SP2/0/bcr-abl cells expressing the fragment of bcr-abl fusion gene were inoculated subcutaneously into the groin of BALB/c mice in order to observe the effect of vaccine on growth of inoculated SP2/0/bcr-abl tumor cells. The results showed that there were distinct differences on the time of tumor growth, the time of tumor ulceration, tumor volume and survival time of mice bearing tumor between two immunized groups and two control groups (blank and vacant plasmid groups). The mice immunized with pVbcr-abl/mIL7 lived longer as compared to mice immunized with pVbcr-abl. The tissue of inoculated tumor was more compact, tumor organ was larger, tumor form was irregular in 2 control groups, while the tissue of inoculated tumor was looser, tumor volume was smaller, and with mass inflammatory infiltration in two immunized groups. Moreover, the metastatic tumor cells were found in the livers of control groups, but not observed in two immunized groups. It is concluded that the protection occurred in immunized mice which inhibited the growth of SP2/0/bcr-abl tumor cell in vivo.

Animals↗

PubMed2005

Slit and Robo control cardiac cell polarity and morphogenesis.

Basic aspects of heart morphogenesis involving migration, cell polarization, tissue alignment, and lumen formation may be conserved between Drosophila and humans, but little is known about the mechanisms that orchestrate the assembly of the heart tube in either organism. The extracellular-matrix molecule Slit and its Robo-family receptors are conserved regulators of axonal guidance. Here, we report a novel role of the Drosophila slit, robo, and robo2 genes in heart morphogenesis. Slit and Robo proteins specifically accumulate at the dorsal midline between the bilateral myocardial progenitors forming a linear tube. Manipulation of Slit localization or its overexpression causes disruption in heart tube alignment and assembly, and slit-deficient hearts show disruptions in cell-polarity marker localization within the myocardium. Similar phenotypes are observed when Robo and Robo2 are manipulated. Rescue experiments suggest that Slit is secreted from the myocardial progenitors and that Robo and Robo2 act in myocardial and pericardial cells, respectively. Genetic interactions suggest a cardiac morphogenesis network involving Slit/Robo, cell-polarity proteins, and other membrane-associated proteins. We conclude that Slit and Robo proteins contribute significantly to Drosophila heart morphogenesis by guiding heart cell alignment and adhesion and/or by inhibiting cell mixing between the bilateral compartments of heart cell progenitors and ensuring proper polarity of the myocardial epithelium.

Animals↗

PubMed2005

High-resolution, large dynamic range fiber length measurement based on a frequency-shifted asymmetric Sagnac interferometer.

We propose and experimentally demonstrate a single-mode fiber length and dispersion measurement system based on what we believe to be a novel frequency-shifted asymmetric Sagnac interferometer incorporating an acousto-optic modulator (AOM). By sweeping the driving frequency of the AOM, which is asymmetrically placed in the Sagnac loop, the optical length of the fiber can be determined by measuring the corresponding variation in the phase delay between the two counterpropagating light beams. Combined with a high-resolution data processing algorithm, this system yields a dynamic range from a few centimeters to 60 km (limited by our availability of long fibers) with a resolution of approximately 1 part per million for long fibers.

Journal Article↗

PubMed2005

Neuromancer Tbx20-related genes (H15/midline) promote cell fate specification and morphogenesis of the Drosophila heart.

The Tbx family of transcription factors are prominently expressed in the early cardiac primordium throughout the animal kingdom. Mutations in Tbx genes result invariably in defective formation and function of the heart, including congenital heart disease in humans. Similar to their vertebrate counterpart, the Drosophila Tbx20 gene pair, neuromancer1 (nmr1, FlyBase:H15) and neuromancer2 (nmr2, Flybase:mid), exhibits a dynamic expression pattern, including in all contractile myocardial cells. Deletion mutants of nmr1 combined with mesoderm-specific knock-down of nmr2 exhibit phenotypes that suggest nmr is critical for correct specification of the cardiac progenitor populations as well as for morphogenesis and assembly of the contractile heart tube. Loss-of-nmr-function causes a switch in cell fates in the cardiogenic region, in that the progenitors expressing the homeobox gene even skipped (eve) are expanded accompanied by a corresponding reduction of the progenitors expressing the homeobox gene ladybird (lbe). As a result, the number of differentiating myocardial cells is severely reduced whereas pericardial cell populations are expanded. Conversely, pan-mesodermal expression of nmr represses eve, while causing an expansion of cardiac lbe expression, as well as ectopic mesodermal expression of the homeobox gene tinman. In addition, nmr mutants with less severe penetrance exhibit cell alignment defects of the myocardium at the dorsal midline, suggesting nmr is also required for cell polarity acquisition of the heart tube. In exploring the regulation of nmr, we find that the GATA factor Pannier is essential for cardiac expression, and acts synergistically with Tinman in promoting nmr expression. Moreover, reducing nmr function in the absence of pannier further aggravates the deficit in cardiac mesoderm specification. Taken together, the data suggest that nmr acts both in concert with and subsequent to pannier and tinman in cardiac specification and differentiation. We propose that nmr is another determinant of cardiogenesis, along with tinman and pannier.

Animals↗

PubMed2005

[Microvessel counts and the expressions of chemotactic factors in the pathological scar tissues].

OBJECTIVE: To explore the microvessel counts and the expressions of interleukin-8 (IL-8), monocyte chemoattractant protein-1 (MCP-1), and macrophage inflammatory protein-1 ( MIP-1) alpha mRNA in the pathological scar tissues. METHODS: Immunohistochemical method of avidin-biotin complex was used for microvessel counts on the routinely formalin-fixed and paraffin-embedded sections of specimens of hypertrophic scars, keloids, normal skin, and surgical scar, and in situ hybridization for the expressions of IL-8, MCP-1, MIP-1alpha mRNA. RESULTS: The microvessel counts as well as the positive rates and the scorings of IL-8, MCP-1, and MIP-1alpha mRNA were significantly higher in pathological scars than those in the normal skin and surgical scar (all P < 0.05). The microvessel counts were significantly higher in the positive cases of IL-8, MCP-1 and MIP-1alpha mRNA than those in the negative ones (P < 0.05). The close positive correlations were found among the microvessel counts and the expressive scorings of 3 factors (P < 0.05). The close positive correlations were also found among the expressive scorings of IL-8, MCP-1, and MIP-1alpha mRNA in pathological scars. Microvessel counts were significantly higher in hypertrophic scars with the course less than 1 year than those with the course more than 1 year. CONCLUSION: IL-8, MCP-1 and MIP-1alpha play important roles in promoting the neovascularization of pathological scars.

Adolescent↗

PubMed2005

[Establishment of mouse SP2/0 cell line stably expressing bcr-abl fusion gene fragment].

To establish SP2/0 cell line H-2(d) stably expressing bcr-abl fusion gene fragment, the bcr-abl fusion gene was subcloned into retroviral vector pLXSN from pGEMbcr-abl. The recombinant retroviral vector pLXSNbcr-abl was transfected into PT67 packaging cells with the help of lipofectamine. The positive clones were selected out and cultured after G418 selection. Then viral supernatant was collected to determine viral titer, the viral titer was 2 x 10(7) CFU/ml. The SP2/0 cells were infected with the collected viral supernatant. The results showed that after G418 selection, the bcr-abl fusion gene was integrated into the chromosome of SP2/0 cells infected stably, with recombinant retrovirus and expressed in SP2/0 cells confirmed by PCR and RT-PCR respectively. In conclusion, the mouse tumor cell lines expressing the bcr-abl fusion protein were successfully established and would be used as a experimental cell model for anti-CML immunotherapy.

Animals↗