Biology subjects

Fang, K.

Publications and source records attributed to Fang, K..

23 records · Page 2Linked to original sources

bioRxiv2020

Virulence evolution of multiple infections with vertically and horizontally transmitted fungal species in a natural plant system

The virulence evolution of multiple infections of parasites from the same species has been modelled widely in evolution theory, and the trajectories of evolution are relevant to parasite transmission mode, as well as to parasite and host population dynamics. However, experimental studies on this topic remain scarce, particularly regarding multiple infections by different parasite species. In this study, we employed the invasive plant Ageratina adenophora to verify the predictions made by the model. We observed that A. adenophora was a highly susceptible host to phylogenetically diverse foliar pathogens with mixed vertical and horizontal transmission within leaf spots. The pathogen community structure at the leaf spot level was determined by transmission mode. Over time, the pathogen community decreased in diversity; meanwhile, the vertically transmitted pathogens exhibited decreased virulence to the host A. adenophora, but the horizontally transmitted pathogens exhibited increased virulence to the host. Our results demonstrate that the predictions of classical models are still valid in a complex environment. Moreover, we propose that it is very important to determine whether the primary foliar pathogen of a given plant host is relevant to seedborne fungi, as this characteristic is an important factor in understanding pathogen-host interactions.

ecology↗

bioRxiv2020

Convergent molecular, cellular, and neural signatures of major depressive disorder

Major depressive disorder emerges from the complex interactions of biological systems that span across genes and molecules through cells, circuits, networks, and behavior. Establishing how neurobiological processes coalesce to contribute to the onset and maintenance of depression requires a multi-scale approach, encompassing measures of brain structure and function as well as genetic and cell-specific genomic data. Here, we examined anatomical (cortical thickness) and functional (functional variability, global brain connectivity) correlates of depression and negative affect across three population-imaging datasets: UK Biobank, Genome Superstruct Project, and ENIGMA (combined N[≥]23,723). Integrative analyses incorporated measures of cortical gene expression, post-mortem patient transcriptional data, depression GWAS, and single-cell transcription. Neuroimaging correlates of depression and negative affect were consistent across the three independent datasets. Linking ex-vivo gene downregulation with in-vivo neuroimaging, we found that genomic correlates of depression-linked neuroimaging phenotypes tracked gene downregulation in post-mortem cortical tissue samples of patients with depression. Integrated analysis of single-cell and Allen Human Brain Atlas expression data implicated somatostatin interneurons and astrocytes as consistent cell associates of depression, through both in-vivo imaging and ex-vivo cortical gene dysregulation. Providing converging evidence for these observations, GWAS derived polygenic risk for depression was enriched for genes expressed in interneurons, but not glia. Underscoring the translational potential of multi-scale approaches, the genomic correlates of depression-linked brain function and structure were enriched for known and novel disorder relevant molecular pathways. These findings bridge across levels to connect specific genes, cell classes, and biological pathways to in-vivo imaging correlates of depression. Key FindingsO_LIMajor depressive disorder and negative affect are associated with replicable profiles of cortical anatomy and function across independent population-level neuroimaging datasets (combined N[≥]23,723). C_LIO_LISomatostatin interneurons are consistent spatial transcriptional associates of in-vivo depression-linked imaging phenotypes. C_LIO_LIIntegrative single-cell gene expression analysis associate somatostatin interneurons and astrocytes with both in-vivo depression-linked imaging and ex-vivo gene downregulation in independent MDD cortical tissue samples. C_LIO_LITranscriptional correlates of in-vivo depression imaging phenotypes selectively capture gene downregulation in post-mortem tissue samples from patients with depression, but not other psychiatric disorders. C_LIO_LIIndicating that some cell classes are preferentially sensitive to inherited disease liability, genome-wide risk for depression is enriched among interneurons, but not glia. C_LIO_LIGene associates of depression-linked anatomy and function identify specific neurotransmitter systems, molecular signaling pathways, and receptors, suggesting possible targets for pharmaceutical intervention. C_LI

neuroscience↗

bioRxiv2020

Prediction of meiosis-essential genes based upon the dynamic proteomes responsive to spermatogenesis

Mammalian meiosis is a specific cell division process during sexual reproduction, whereas a comprehensive proteome of the different meiotic stages has not been systematically investigated. Here, we isolated different types of spermatocytes from the testes of spermatogenesis-synchronized mice and quantified the corresponding proteomes with high-resolution mass spectrometry. A total of 8,002 proteins were identified in nine types of germ cells, and the protein signatures of spermatogenesis were characterized using the dynamic proteomes. A supervised machine learning package, FuncProFinder, was developed to predict meiosis-essential candidate genes based on changes in their protein abundance. Of the candidates without functional annotation, four of the ten genes with the highest prediction scores, Zcwpw1, Tesmin, 1700102P08Rik, and Kctd19, were validated as meiosis-essential genes using knockout mouse models. The proteomic analysis of spermatogenic cells provides a solid foundation for studying the mechanism of mammalian meiosis.

developmental biology↗

bioRxiv2019

Reticulocyte Infection Leads to Altered Behaviour, Drug Sensitivity and Host Cell Remodelling by Plasmodium falciparum.

Plasmodia are host-specific, both at the organism and cellular levels. During asexual development, Plasmodium spp. infect cells of erythroid lineage, with an overall propensity towards reticulocytes. This applies to even Plasmodium (P.) falciparum, the most common causative agent of human malaria, implications of which remain unexplored. Herein, for the first time, we characterize the developmental stages and features of P. falciparum cultured in vitro in young reticulocytes (CD71+) in comparison to standard normocyte (CD71-) cultures. We demonstrate that there are notable differences in the patterns of invasion, development and sensitivity to potent antimalarials (such as artemisinin and dihydroartemisinin) for parasites residing in CD71+ reticulocytes. Through a transcriptomic approach, we report that P. falciparum parasites are able to sense the host cell environment, and calibrate their metabolic and host cell remodelling pathways through differential gene expression. These results form an exciting avenue on which hitherto unexplored interactions between Plasmodium spp and different stages of host red blood cells could be investigated in the broader contexts of drug resistance, host tropism and zoonosis. Author SummaryParasites causing malaria infect red blood cells for development and proliferation during asexual development. This asexual erythrocytic stage determines higher parasite densities and eventual disease manifestation. Although the most virulent species of Plasmodium infecting humans known as Plasmodium falciparum is able to infect red blood cells of all ages, these parasites show a preference for younger blood cells. Of note, the biochemical and biophysical properties of young and adult red blood cells vary significantly. Herein, we undertook a comparative profiling of invasion process, parasite development and drug response of Plasmoddium falciparum in two host cells: young red blood cells (reticulocytes) and mature red blood cells (normocytes). We demonstrate that P. falciparum infects human reticulocytes with higher affinity and demonstrate differential sensitivity to drugs such as artemisinin while they reside within reticulocytes. Furthermore, we show that P. falciparum is able to detect differences in host environment and adapt to it by changing the expression of genes required for host cell remodelling.

microbiology↗

bioRxiv2018

Nuclear export of chimeric mRNAs depends on an lncRNA-triggered autoregulatory loop

Aberrant chromosomal translocations leading to tumorigenesis have been ascribed to the heterogeneously oncogenic functions. However, how fusion transcripts exporting remains to be declared. Here, we showed that the nuclear speckle-specific long non coding RNA MALAT1 controls chimeric mRNA export processes and regulates myeloid progenitor cell differentiation in malignant hematopoiesis. We demonstrated that MALAT1 regulates chimeric mRNAs export in an m6A-dependent manner and thus controls hematopoietic cell differentiation. Specifically, reducing MALAT1 or m6A methyltransferases and the reader YTHDC1 result in the universal retention of distinct oncogenic gene mRNAs in nucleus. Mechanically, MALAT1 hijacks both the chimeric mRNAs and fusion proteins in nuclear speckles during chromosomal translocations and mediates the colocalization of oncogenic fusion proteins with METTL14. MALAT1 and fusion protein complexes serve as a functional loading bridge for the interaction of chimeric mRNA and METTL14. This study demonstrated a universal mechanism of chimeric mRNA transport that involves lncRNA-fusion protein-m6A autoregulatory loop for controlling myeloid cell differentiation. Targeting the lncRNA-triggered autoregulatory loop to disrupt chimeric mRNA transport might represent a new common paradigm for treating blood malignancies.

cancer biology↗