Biology subjects

Niu, C.

Publications and source records attributed to Niu, C..

32 records · Page 2Linked to original sources

bioRxiv2023

Standardisation of cell-free DNA measurements: An International Study on Comparability of Low Concentration DNA Measurements using cancer variants

For the impact of genomic testing from liquid biopsies to be maximized, mechanisms to ensure reproducible and comparable test performance will be required. This can be established and maintained through reference measurement procedures and materials with property values that are internationally comparable through traceability to a common standard. To achieve this objective, an interlaboratory study was organised to explore digital PCR (dPCR) for standardisation of cell-free DNA (cfDNA) quantification. Blinded samples of wild-type/variant mixtures of two DNA sequences (BRAF p.V600E single nucleotide variant or EGFR exon 19 deletion) were provided to 12 laboratories. Laboratories independently designed and applied dPCR assays to determine absolute and relative quantities, with no guidance provided to harmonise the approach. The mean and coefficient of variation (CV) of copy number concentrations for variant sequences were 18 copies/L (CV 7.2%) (BRAF variant sample) and 9 copies/L (CV 25%) (EGFR variant sample) while the mean variant allele frequencies (vAF) were 8.0% (CV 5.3%) and 0.080% (CV 29%) respectively. This study demonstrated that dPCR was capable of exceptional technical accuracy for variant copy number concentration and vAF, even when different assays and platforms were used. This implies that dPCR offers a unique analytical methodology that can be deployed globally in supporting comparability for cfDNA testing based on the existing framework of the International System of units of measurement.

genetics↗

bioRxiv2023

Genetic dissection of BDNF and TrkB expression in glial cells

The brain-derived neurotrophic factor (BDNF) and its high-affinity receptor tropomyosin-related kinase receptor B (TrkB) are widely expressed in the central nervous system. It is well documented that neurons express BDNF and full-length TrkB (TrkB.FL), and a lower level of truncated TrkB (TrkB.T). With conflicting results, glial cells also have been reported to express BDNF and TrkB. In the current study, we employed a more sensitive and reliable genetic method to characterize the expression of BDNF and TrkB in glial cells in the mouse brain. We utilized three Cre mouse strains in which Cre recombinase is expressed in the same cells as BDNF, TrkB.FL, or all TrkB isoforms, and crossed them to Cre-dependent EGFP reporter mice to label BDNF- or TrkB-expressing cells. We performed immunohistochemistry with glial cell markers to examine the expression of BDNF and TrkB in microglia, astrocytes, and oligodendrocytes. Surprisingly, we found no BDNF- or TrkB-expressing microglia in the brain and spinal cord. Consistent with previous studies, most astrocytes only express TrkB.T in the adult brain. Moreover, there are a small number of astrocytes and oligodendrocytes that express BDNF, the function of which is to be determined. We also found that oligodendrocyte precursor cells, but not mature oligodendrocytes, express both TrkB.FL and TrkB.T in the adult brain. These results not only clarify the expression of BDNF and TrkB in glial cells, but also open opportunities to investigate previously unidentified roles of BDNF and TrkB in glial cells.

neuroscience↗

bioRxiv2023

Design of multi-epitope vaccine candidate against Brucella type IV secretion system (T4SS)

Objective the dominant epitopes of T and B cells of VirB8 and VirB10 of Brucella type IV. Secretory systems were predicted and analyzed by bioinformatics, and then multi-epitope vaccines were constructed by reverse vaccination. Methods The amino acid sequences of VirB8 and VirB10 were obtained from the UniProt database, T and B cell dominant epitopes were selected and supplemented with adjuvants to construct a multi-epitope vaccine, SOPMA and RoseTTAFold were applied to predict secondary and tertiary structures respectively for immune simulations. Finally, molecular dynamics simulations of iMEV-TLR4 were then performed. Results one cytotoxic T lymphocyte (CTL) epitope, five helper T lymphocyte (HTL) epitopes, two linear B cell epitopes and three conformational B cell epitopes were obtained in VirB8. 1 cytotoxic T lymphocyte (CTL) epitope, 4 helper T lymphocyte (HTL) epitopes, 4 linear B cell epitopes, and 3 conformational B cell epitopes were obtained in VirB10. The resulting multiepitope vaccine is a protein with good antigenicity, hydrophilicity, and stability. Conclusion a novel brucella multiepitope vaccine was designed by reverse vaccination, and this study provides a theoretical basis for further research.

bioinformatics↗

bioRxiv2023

The cation channel mechanisms of subthreshold inward depolarizing currents in the VTA dopaminergic neurons and their roles in the depression-like behavior

The slow-intrinsic-pacemaker dopaminergic (DA) neurons originating in the ventral tegmental area (VTA) are implicated in various mood- and emotion-related disorders, such as anxiety, fear, stress and depression. Abnormal activity of projection-specific VTA DA neurons is the key factor in the development of these disorders. Here, we describe the crucial role for the NALCN and TRPC6, non-selective cation channels in mediating the subthreshold inward depolarizing current and driving the firing of action potentials of VTA DA neurons in physiological condition. Furthermore, we demonstrate that down-regulation of TRPC6 protein expression in the VTA DA neurons likely contributes to the reduced activity of projection-specific VTA DA neuron in chronic mild unpredictable stress (CMUS) depressive mice. In consistent with these, selective knockdown of TRPC6 channels in the VTA DA neurons conferred mice with depression-like behavior. This current study suggests down-regulation of TRPC6 expression/function is involved in reduced VTA DA neuron firing and chronic stress-induced depression-like behavior of mice.

neuroscience↗

bioRxiv2023

CT Multi-Task Learning with a Large Image-Text (LIT) Model

Large language models (LLM) not only empower multiple language tasks but also serve as a general interface across different spaces. Up to now, it has not been demonstrated yet how to effectively translate the successes of LLMs in the computer vision field to the medical imaging field which involves high-dimensional and multi-modal medical images. In this paper, we report a feasibility study of building a multi-task CT large image-text (LIT) model for lung cancer diagnosis by combining an LLM and a large image model (LIM). Specifically, the LLM and LIM are used as encoders to perceive multi-modal information under task-specific text prompts, which synergizes multi-source information and task-specific and patient-specific priors for optimized diagnostic performance. The key components of our LIT model and associated techniques are evaluated with an emphasis on 3D lung CT analysis. Our initial results show that the LIT model performs multiple medical tasks well, including lung segmentation, lung nodule detection, and lung cancer classification. Active efforts are in progress to develop large image-language models for superior medical imaging in diverse applications and optimal patient outcomes.

bioinformatics↗

bioRxiv2023

Inhibition mechanism and antiviral activity of an α-ketoamide based SARS-CoV-2 main protease inhibitor

SARS-CoV-2 has demonstrated extraordinary ability to evade antibody immunity by antigenic drift. Small molecule drugs may provide effective therapy while being part of a solution to circumvent SARS-CoV-2 immune escape. In this study we report an -ketoamide based peptidomimetic inhibitor of SARS-CoV-2 main protease (Mpro), RAY1216. Enzyme inhibition kinetic analysis established that RAY1216 is a slow-tight inhibitor with a Ki of 8.6 nM; RAY1216 has a drug-target residence time of 104 min compared to 9 min of PF-07321332 (nirmatrelvir), the antiviral component in Paxlovid, suggesting that RAY1216 is approximately 12 times slower to dissociate from the protease-inhibitor complex compared to PF-07321332. Crystal structure of SARS-CoV-2 Mpro:RAY1216 complex demonstrates that RAY1216 is covalently attached to the catalytic Cys145 through the -ketoamide warhead; more extensive interactions are identified between bound RAY1216 and Mpro active site compared to PF-07321332, consistent with a more stable acyl-enzyme inhibition complex for RAY1216. In cell culture and human ACE2 transgenic mouse models, RAY1216 demonstrates comparable antiviral activities towards different SARS-CoV-2 virus variants compared to PF-07321332. Improvement in pharmacokinetics has been observed for RAY1216 over PF-07321332 in various animal models, which may allow RAY1216 to be used without ritonavir. RAY1216 is currently undergoing phase III clinical trials (https://clinicaltrials.gov/ct2/show/NCT05620160) to test real-world therapeutic efficacy against COVID-19.

biochemistry↗

bioRxiv2022

Genome Mining and Biochemical Characterization of a Bifunctional Type I Diterpene Synthase from a Marine-Derived Fungus

We report the identification of the tnd biosynthetic cluster from the marine-derived fungal strain Aspergillus flavipes CNL-338 and in vivo characterization of a cryptic type I diterpene synthase. Heterologous expression of the bifunctional terpene synthase TndC in Saccharomyces cerevisiae led to the discovery of a new diterpene backbone, talarodiene, harboring a benzo[a]cyclopenta[d]cyclooctane tricyclic fused ring system. The cyclization mechanism that converts geranylgeranyl diphosphate to the tricyclic hydrocarbon skeleton was investigated using 13C-labeling studies and stable isotope tracer experiments showed the biotransformation of talarodiene into talaronoid C.

bioengineering↗

bioRxiv2021

TET1 controls Cxcl1 induction by DNA demethylation and promotes neutrophil recruitment during acute lung injury

Neutrophils are rapidly recruited from the peripheral blood to the inflammatory site to initiate inflammatory response against pathogenic infections. The process to recruit neutrophils must be properly regulated since the abnormal accumulation of neutrophils can cause organ damage and dysfunction. The acute respiratory distress syndrome (ARDS)/acute lung injury (ALI) is a common cause of respiratory failure that is characterized by the infiltration of neutrophils and epithelial integrity disruption. Indeed, recent studies suggest a pathogenic role of neutrophils in the clinic severity of the coronavirus disease 2019 (COVID-19) ARDS. The chemokine CXCL1, which is rapidly induced by inflammatory stimuli, plays a key role in neutrophil influx during lung inflammation. The molecular basis of Cxcl1 induction is not fully understood. Here we report that TET1, a member of the ten eleven translocation (TET) methylcytosine dioxygenase protein family, displays a striking specificity in the regulation of gene expression in macrophages. RNA sequencing (RNA-seq) analysis showed that Tet1 disruption significantly altered the expression of only 48 genes that include Cxcl1 and several other genes known to be important for cell migration and trafficking in bone marrow derived macrophages (BMDMs) in response to LPS stimulation. TET1 regulates the induction of Cxcl1 by facilitating the DNA demethylation of the Cxcl1 promoter. In Tet1-/- mice, the induction of Cxcl1 was suppressed, resulting in defective neutrophil recruitment to the lung during LPS-induced acute lung injury. Our results identify a novel epigenetic mechanism that selectively controls Cxcl1 induction and neutrophil recruitment during acute lung injury. Key PointsO_LITET1 has a striking specificity in macrophage gene regulation and controls Cxcl1 induction by inflammatory stimuli via DNA demethylation C_LIO_LINeutrophil recruitment is defective in Tet1 deficient mice during acute lung injury C_LI

immunology↗

bioRxiv2021

Defining the Sensitivity Landscape of 74,389 EGFR Variants to Tyrosine Kinase Inhibitors

BackgroundTyrosine kinase inhibitors (TKIs) therapy is a standard treatment for patients with advanced non-small-cell lung carcinoma (NSCLC) when activating epidermal growth factor receptor (EGFR) mutations are detected. However, except for the well-studied EGFR mutations, most EGFR mutations lack treatment regimens. MethodsWe constructed two EGFR variant libraries containing substitutions, deletions, or insertions using the saturation mutagenesis method. All the variants were located in the EGFR mutation hotspot (exons 18-21). The sensitivity of these variants to afatinib, erlotinib, gefitinib, icotinib, and osimertinib was systematically studied by determining their enrichment in massively parallel cytotoxicity assays using an endogenous EGFR-depleted cell line, PC9. ResultsA total of 3,914 and 70,475 variants were detected in the constructed EGFR Substitution-Deletion (Sub-Del) and exon 20 Insertion (Ins) libraries, accounting for 99.3% and 55.8% of the designed variants, respectively. Of the 3,914 Sub-Del variants, 813 were highly enriched in the reversible TKI (erlotinib, gefitinib, icotinib) cytotoxicity assays and 51 were enriched in the irreversible TKI (afatinib, osimertinib) cytotoxicity assays. For the 70,475 Ins variants, insertions at amino acid positions 770-774 were highly enriched in all the five TKI cytotoxicity assays. Moreover, the top 5% of the enriched insertion variants included a glycine or serine insertion at high frequency. ConclusionsWe present a comprehensive reference for the sensitivity of EGFR variants to five commonly used TKIs. The approach used here should be applicable to other genes and targeted drugs.

genetics↗

bioRxiv2021

Dynamics of glioma-associated microglia and macrophages reveals their divergent roles in the immune response of brain

Glioma microenvironment contains numerous myeloid cells, including brain-resident microglia and recruited monocytes and macrophages (Mo/M{varphi}). When studied collectively, these cells presented pro-tumor effects. Yet, little is known about the differences among these myeloid populations. Using single-cell sequencing analysis, we studied the phenotypic characteristics, spatial variances, and dynamic changes of these relatively heterogeneous cell populations. Microglia populations with distinct spatial distribution presented different functional states, including tumor-associated subsets with phagocytic and lipid metabolism signature. Notably, this subset of glioma-associated microglia shared similar trait in a diverse spectrum of neuropathogenesis. In contrast, Mo/M{varphi} highly expressed genes related to angiogenesis, tumor invasion, and immune evasion. Moreover, identifying the Mo/M{varphi} subsets had prognostic and classificatory value in clinical application. These results thus eliminate the long-existing ambiguity about the role of microglia and Mo/M{varphi} in glioma pathogenesis, and reveal their prognostic and therapeutic value for glioma patients.

immunology↗

bioRxiv2021

Catching a liar through facial expression of fear

The leakage theory in the field of deception detection predicted that liars could not repress the leaked felt emotions (e.g., the fear or delight); and people who were lying would feel fear (to be discovered), especially under the high-stake situations. Therefore, we assumed that the aim of revealing deceits could be reached via analyzing the facial expression of fear. Detecting and analyzing the subtle leaked fear facial expressions is a challenging task for laypeople. It is, however, a relatively easy job for computer vision and machine learning. To test the hypothesis, we analyzed video clips from a game show "The moment of truth" by using OpenFace (for outputting the Action Units of fear and face landmarks) and WEKA (for classifying the video clips in which the players was lying or telling the truth). The results showed that some algorithms could achieve an accuracy of greater than 80% merely using AUs of fear. Besides, the total durations of AU 20 of fear were found to be shorter under the lying condition than under the truth-telling condition. Further analysis found the cause why durations of fear were shorter was that the duration from peak to offset of AU20 under the lying condition was less than that under the truth-telling condition. The results also showed that the facial movements around the eyes were more asymmetrical while people telling lies. All the results suggested that there do exist facial clues to deception, and fear could be a cue for distinguishing liars from truth-tellers.

neuroscience↗

bioRxiv2019

Host fruit as a suitable bacteria growth substrate that promotes larval development of Bactrocera dorsalis (Diptera: Tephritidae)

The ability of a host plant to act as a substrate or media for larval development may depend on how good it is at offering suitable nutrients for bacterial growth. In this study, we hypothesized that the suitability of a fruit type for fruit fly larval development is positively correlated with the ability of that fruit to act as a substrate/media for fruit fly symbiotic bacterial growth. We allowed a single female fruit fly to lay eggs on five different host fruits, then we monitored the larval development parameters across five generations and analyzed the bacterial community structure of larvae developing in 2 of these hosts (apple and banana) at the first and fifth generations. Results indicate that the larval length and dry weight did not vary significantly across experimental generations, but were greatly affected by fruit types and larval stages. The larval development time was extended considerably in apple and tomato but shortened in banana and mango. There was a significant shift in bacterial community structure and composition across fruits and generations. The bacterial community of larvae within the same fruit (apple and banana) clustered and was similar to the parental female (with the predominance of Proteobacteria), but there was a shift at the fifth generation (dominance of Firmicutes). Banana offered a suitable better development and growth to larvae and bacteria, respectively, compared to apple in which reduced larval development and bacterial growth were recorded. Although additional experiments are needed to adequately show that the differences in microbiome seen in fruit fly larval guts are the actual driver of different developmental outcomes of larvae on the different fruits, at the very least, our study has provided intriguing data suggesting interaction between the diets and gut microbial communities on insect development.\n\nImportance and Significance of the studyTephritid fruit flies entertain complex interactions with gut bacteria. These bacteria are known to provide nutritional benefits to their hosts, by supplementing missing nutrients from the host diets and regulating energy balance. Foraging for food is a risky exercise for the insect which is exposed to ecological adversities, including predators. Therefore, making beneficial choice among available food substrates is a question of survival for the flies and bacteria as well. Our study demonstrates interactions between the host fly and its intestinal bacteria in sustaining the larval development while foraging optimally on different fruit types. These findings add a novel step into our understanding of the interactions between the gut microbial communities and B. dorsalis and provide avenues for developing control strategies to limit the devastative incidence of the fly.

microbiology↗

bioRxiv2018

Temporal modulation of host aerobic glycolysis determines the outcome of M. marinum infection

Macrophages are the first-line host defense where the invading Mycobacterium tuberculosis (Mtb) encounters. It has been recently reported that host aerobic glycolysis was elevated post the infection by a couple of virulent mycobacterial species. However, whether this metabolic transition is required for host defense against intracellular pathogens and the underlying mechanisms remain to be further investigated. By analyzing carbon metabolism, we found that macrophages infected by M. marinum, a surrogate mycobacterial specie to Mtb, showed a strong elevation of glycolysis. Next, three glycolysis inhibitors were examined for their ability to inhibit mycobacterial proliferation inside RAW264.7, a murine macrophage-like cell line. Among them, a glucose analog, 2-deoxyglucose (2-DG) displayed a protective effect on assisting host to resist mycobacterial infection, which was further validated in zebrafish-infection model. The phagocytosis of M. marinum was significantly decreased in macrophages pre-treated with 2-DG at concentrations of 0.5 and 1 mM, at which no inhibitory effect was posed on M. marinum growth in vitro. Moreover, 2-DG pre-treatment exerted a significant protective effect on zebrafish larvae to limit the proliferation of M. marinum, and such effect was correlated to tumor necrosis factor alpha (TNF-). On the contrary, the 2-DG treatment post infection did not restrain proliferation of M. marinum in WT zebrafish, and even accelerated bacterial replication in TNF--/- zebrafish. Together, modulation of glycolysis prior to infection boosts host immunity against M. marinum infection, indicating a potential intervention strategy to control mycobacterial infection.\n\nAuthor SummaryAs an intracellular pathogen, Mtb exploits multiple strategies to invade and hijack macrophages for its own advantages. Accordingly, recent investigations have shown that Mtb infection is accompanied with an alteration of host glucose metabolism. Macrophage and zebrafish infection models of M. marinum, facilitating our understanding towards mycobacterial pathogenesis, were applied in this study. We found that the pre-treatment of macrophages with a glucose analog, 2-DG, inhibited aerobic glycolysis and made host cells more inert to phagocytose the bud. In infected zebrafish larvae, bacterial load inside host pretreated with 2-DG remains at a significantly lower level compared to the untreated group. These findings imply that the modulation of host glycolysis regulates the fate of M. marinum infection, and indicate a promising metabolic target in TB intervention.

microbiology↗

bioRxiv2018

Intestinal bacteria modulate the foraging behavior of the Oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae)

The gut microbiome of insects directly or indirectly affects the metabolism, immune status, sensory perception and feeding behavior of its host. Here, we examine the hypothesis that in the Oriental fruit fly (Bactrocera dorsalis, Diptera: Tephritidae), the presence or absence of gut symbionts affects foraging behavior and nutrient ingestion. We offered protein starved flies, symbiotic or aposymbiotic, a choice between diets containing all amino acids or only the non-essential ones. The different diets were presented in a foraging arena as drops that varied in their size and density, creating an imbalanced foraging environment. Suppressing the microbiome resulted in significant changes of the foraging behavior of both male and female flies. Aposymbiotic flies responded faster to the diets offered in experimental arenas, spent more time feeding, ingested more drops of food, and were constrained to feed on time consuming patches (containing small drops of food), when these offered the full complement of amino acids. We discuss these results in the context of previous studies on the effect of the gut microbiome on host behavior, and suggest that these be extended to the life history dimension.\n\nImportance and significance of the studyThe gut bacteria of tephritid fruit flies provide nutritional benefits to their hosts, by making essential amino-acids readily available. Foraging for food is risky, as active flies are exposed to predators and incur a considerable investment of time and energy. Therefore, making beneficial compromises between the feeding time and nutrient ingestion is a question of survival for the flies. Our study demonstrates how gut bacteria drive this behavior by allowing symbiotic flies to forage optimally while acquiring essential nutrients. This finding adds a novel step to the nexus connecting the insect gut, its microbiome, the nervous system, chemoreception to individual patterns of foraging.

animal behavior and cognition↗