Biology subjects

Jian, L.

Publications and source records attributed to Jian, L..

7 recordsLinked to original sources

bioRxiv2025

Cognitive Mode Detectable with Task-Based fMRI: Default Mode B (DMB)

In the context of task-based functional magnetic resonance imaging (fMRI), cognitive modes can be defined as task-general cognitive/sensory/motor processes which reliably elicit specific blood-oxygen-level-dependent (BOLD) signal pattern configurations. A number of cognitive modes are detectable with task-based fMRI, and here we focus on Default Mode B (DMB), a task-negative and late-trial peaking cognitive mode. The BOLD signal configurations associated with DMB are modulated by a range of tasks, and here we present eight. For each task, we report: (1) specific pattern-based (as opposed to coordinate-based) anatomical details essential for distinguishing DMB from other BOLD-based cognitive modes, and (2) task-induced BOLD signal changes associated with DMB over a range of task conditions. In order to facilitate recognition, we nick-named the anatomical patterns specific to DMB as follows: (1) In Flight, (2) Medial Temporal Dots, (3) Snowman Nose, (4) Angel Wings, and (5) Tripod. Evidence for DMB was derived from the timing and magnitude of task-induced BOLD signal changes induced by the following tasks: working memory, spatial capacity, semantic association, evidence integration, Ravens matrices, autobiographical event simulation, meditation and social perception. It was observed that deactivations in DMB were sensitive to cognitive load during attention to specific features of the external environment, based on evidence from working memory, spatial capacity, semantic association, evidence integration, and Ravens matrices. It was also observed that activations in DMB involved a cognitive process for engaging in mental projection into self-relevant social narratives, based on evidence from autobiographical event simulation, meditation, and social perception. Future research may explore DMB activation over a wider range of tasks in larger samples.

neuroscience↗

bioRxiv2025

Malignant ascites enhance γδ T cell cytotoxicity towards ovarian cancer via modulating chemokines secretion from the cancer cells that recruits γδ T cells

Ovarian cancer patients usually develops peritoneal metastasis and malignant ascites in the advanced stages, which form immuno-suppressive tumor microenvironments that limit the efficacy of immuno-therapies. However, during our previous research trying to develop a {gamma}{delta} T cell-based cell therapy, we noticed that the malignant ascites may enhance the cytotoxicity of {gamma}{delta} T cells towards ovarian cancer cells. Herein, in this work we showed that the phenomenon is real and the low molecular weight components in the ascites act on the cancer to promote the killing by {gamma}{delta} T cells. Transcriptome analysis and in vitro experiments revealed that the malignant ascites induce the secretion of chemokines CXCL2 and CXCL8 by ovarian cancer cells, which recruits {gamma}{delta} T cells through the chemokine receptors CXCR1 and CXCR2, to enhance the cytotoxicity of {gamma}{delta} T cells. Metabolomics analysis discovered compounds that are responsible for the enhancement of {gamma}{delta} T cell cytotoxicity, one of which follows the aforementioned mechanism, while other compounds reflect undiscovered mechanisms. Overall, we presented the positive side of the malignant ascites in anti-tumor immunity, revealed the underlining mechanisms and at least partially interpreted the molecular basis. Our work thus provides new insights into the development of cell therapies for ovarian cancer.

immunology↗

bioRxiv2025

Investigation of the Mechanism of Action of JinHuangJieDu against SARS-CoV-2 Infection and Inflammation Based on Network Pharmacology and Experimental Validation

Withdrawal StatementThe authors have withdrawn this manuscript because additional experiments are required to enhance the completeness and clarity of the study. Therefore, the authors do not wish this work to be cited as a reference for any project. If you have any questions, please contact the corresponding author at lcchenlong@163.com.

cell biology↗

bioRxiv2022

An immune-lncRNA risk model to predict prognosis for patients with head and neck squamous cell carcinoma

Backgroundlong noncoding RNA (lncRNA) are closely correlated with the occurrence and development of tumors. The purpose of this research is to construct a risk model of immune-related lncRNAs that can be used for predicting the survival and prognosis of head and neck squamous cell carcinoma (HNSCC) patients and further exploring the immune function of immune-lncRNAs. Methodsobtained detailed transcriptional data and clinical information for 545 cases of HNSCC from The Cancer Genome Atlas (TCGA). Combined lncRNAs and the immune gene sets from the Molecular Signatures Database (MSigDB) were employed to construct co{square}expression networks, the significant correlation of immune-lncRNAs obtained from the results of Cox regression analysis were used to build the model. Survival analysis and QRT-PCR were used to confirm the expression of immune-lncRNAs and optimize the risk model. Then single-cell RNA Sequencing (scRNA-seq) dataset analysis of laryngeal squamous cell carcinoma (LSCC), co-expression analysis, correlation analysis and immunohistochemistry were used to explore the immune function of immune-lncRNAs. ResultsA total of 13 immune-lncRNAs including AC104083.1AC004148.2AL357033.4AC116914.2AC024075.1AC008115.3PCED1B-AS1RAB11B-AS1AC004687.1 AL450992.2EP300-AS1AC024075.2AC136475.2 were identified to construct the risk model. In this model, low-risk patients had higher overall survival (OS, P=1.923e-12, hazard ratio=2.104, 95% CI: 1.622-2.730). AC004687.1 and PCED1B-AS1 were overexpressed in T cells and were closely related to the genes encoding major histocompatibility complex II (MHC II) molecules. And the results of QRT-PCR and immunohistochemistry showed the expression significant positively correlated with HLA-DR which is one of the MHC II classical molecules. Conclusionthe immune-associated risk model constructed by 13 lncRNAs has good prognostic value for HNSCC. AC004687.1 and PCED1B-AS1 are significant correlating to clinical characteristics and MHC II, we provide a new insight into the immune function of lncRNAs.

bioinformatics↗

bioRxiv2021

Portrait of a genus: the genetic diversity of Zea

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 65 million single nucleotide polymorphisms (SNPs), 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. The variation map reveals evidence of selection within taxa displaying novel adaptations such as perenniality and regrowth. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in the genes underlying adaptations to both environments. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

evolutionary biology↗

bioRxiv2020

Binding Ability Prediction between Spike Protein and Human ACE2 Reveals the Adaptive Strategy of SARS-CoV-2 in Humans

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus causing an outbreak of COVID-19 globally in the past six months. A relatively higher divergence on the spike protein of SASR-CoV-2 enables it to transmit across species efficiently. We particularly believe that the adaptive mutations of the receptor-binding domain (RBD) of spike protein in SARS-CoV-2 might be essential to its high transmissibility among humans. Thus here we collected 2,142 high-quality genome sequences of SARS-CoV-2 from 160 regions in over 50 countries and reconstructed their phylogeny, and also analyzed the interaction between the polymorphisms of spike protein and human ACE2 (hACE2). Phylogenetic analysis of SARS-CoV-2 and coronavirus in other hosts show SARS-CoV-2 is highly possible originated from Bat-CoV (RaTG13) found in horseshoe bat and a recombination event may occur on the spike protein of Pangolin-CoV to imbue it the ability to infect humans. Moreover, compared to the S gene of SARS-CoV-2, it is more conserved in the direct-binding sites of RBD and we noticed that spike protein of SARS-CoV-2 may under a consensus evolution to adapt to human hosts better. 3,860 amino acid mutations in spike protein RBD (T333-C525) of SARS-CoV-2 were simulated and their stability and affinity binding to hACE2 (S19-D615) were calculated. Our analysis indicates SARS-CoV-2 could infect humans from different populations with no preference, and a higher divergence in the spike protein of SARS-CoV-2 at the early stage of this pandemic may be a good indicator that could show the pathway of SARS-CoV-2 transmitting from the natural reservoir to human beings.

microbiology↗

bioRxiv2019

qKW9 encodes a pentatricopeptide repeat protein affecting photosynthesis and grain filling in maize

Kernel weight is an important yield component in maize that was selected during domestication. Many kernel weight genes have been identified through mutant analysis, and are mostly involved in the biogenesis and functional maintenance of organelles or other fundamental cellular activities. However, only a limited number of loci underlying quantitative variation in kernel weight have been cloned. Here we characterize a maize kernel weight QTL, qKW9 and find that it encodes a DYW motif pentatricopeptide repeat protein involved in C-to-U editing of NdhB, a subunit of the chloroplast NADH dehydrogenase-like complex. In a null qKW9 background, C-to-U editing of NdhB was abolished, and photosynthesis was reduced, suggesting that qKW9 regulates kernel weight by controling the maternal source of photosynthate for grain filling. Characterization of qKW9 highlights the importance of optimizing photosynthesis on maize grain yield production.

plant biology↗