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Biology subjects

Yi, L.

Publications and source records attributed to Yi, L..

50 records · Page 3Linked to original sources

After migration into blood circulation, hematopoietic stem cells can stably self-renew and maintain bone marrow while being skewed toward myeloid lineage when submitted to serial transplantation.

Hematopoietic stem cells (HSCs) mainly reside in bone marrow (BM) within niches providing an appropriate environment for their survival and self-renewal. Although, small numbers of HSCs can quit their residing environment to migrate into blood circulation and re-engraft elsewhere in BM. Mobilizing agents such as granulocyte colony stimulating factor (G-CSF) can amplify this process by inducing massive HSC mobilization into blood circulation. This method is widely used in clinics to treat hematological disorders. However, in physiological conditions, the properties of HSCs after migration (called migratory HSCs) remain incompletely characterized. In this study, we investigated the capacity of migratory HSCs to self-renew, reconstitute and maintain BM. We show that after migration, HSCs can stably self-renew and maintain BM in homeostasis. However, while stably repopulating BM of irradiated recipients, migratory HSCs show a defect in lymphoid lineage reconstitution when subjected to serial transplantations. Our findings provide interesting knowledge on HSC properties after migration, which may benefits therapeutic research on HSC-based therapies to treat hematological disorders.

cell biology↗

The parathyroid hormone-dependent activation of osteoblasts enhances hematopoietic stem cell migration and reduces their engraftment abilities

Hematopoietic stem cells (HSCs) in the bone marrow (BM) reside in HSC niches ensuring their maintenance. The HSC niche is made up of perivascular and trabecular cells including osteoblasts whose role on HSCs remains to be clearly defined. Increased numbers of osteoblasts have been observed in the CL2 transgenic mouse expressing a constitutively activated form of the parathyroid hormone (PTH)/PTH-related peptide receptor. This mouse model mimicking PTH anabolic effect has also been described to exhibit increased numbers of the BM stem/progenitor population. Furthermore, PTH is known to induce BM stem/progenitor cell migration into blood circulation. However PTH role on long-term repopulating HSCs (LT-HSCs) is incompletely known. Here we show that CL2 BM contains a regular proportion of LT-HSCs, suggesting that osteoblasts may not be a determinant of LT-HSC numbers but act mainly on more mature progenitors. We further show increased LT-HSC migration in CL2 mice correlated with higher granulocyte colony-stimulating factor (G-CSF) serum levels, supporting the idea that PTH can enhance the migration of LT-HSCs. Finally, we found a defect in the ability of CL2 BM HSCs to reconstitute irradiated BM suggesting that PTH activation of osteoblasts negatively influences abilities of HSC population to engraft and reconstitute irradiated BM. In summary, our study highlights new insights into the role of the PTH-dependent activation of osteoblasts on LT-HSC migration and their BM repopulation abilities. Our findings will be useful to improve treatments on hematological disorders, especially therapies involving HSC harvest and transplantation.

cell biology↗

A valid protective immune response elicited in rhesus macaques by an inactivated vaccine is capable of defending against SARS-CoV-2 infection

With the relatively serious global epidemic outbreak of SARS-CoV-2 infection, public concerns focus on not only clinical therapeutic measures and public quarantine for this disease but also the development of vaccines. The technical design of our SARS-CoV-2 inactivated vaccine provides a viral antigen that enables the exposure of more than one structural protein based upon the antibody composition of COVID-19 patients convalescent serum. This design led to valid immunity with increasing neutralizing antibody titers and a CTL response detected post-immunization of this vaccine by two injections in rhesus macaques. Further, this elicited immunoprotection in macaques enables not only to restrain completely viral replication in tissues of immunized animals, compared to the adjuvant control and those immunized by an RBD peptide vaccine, but also to significantly alleviate inflammatory lesion in lung tissues in histo-pathologic detection, compared to the adjuvant control with developed interstitial pneumonia. The data obtained from these macaques immunized with the inactivated vaccine or RBD peptide vaccine suggest that immunity with a clinically protective effect against SARS-CoV-2 infection should include not only specific neutralizing antibodies but also specific CTL responses against at least the S and N antigens.

immunology↗

Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803

Synechocystis sp. PCC 6803 (hereafter: Synechocystis) is a model organism for studying photosynthesis, energy metabolism, and environmental stress. Though known as the first fully sequenced phototrophic organism, Synechocystis still has almost half of its proteome without functional annotations. In this study, we obtained 291 protein complexes, including 24,092 protein-protein interactions (PPIs) among 2062 proteins by using co-fractionation and LC/MS/MS. The additional level of PPIs information not only revealed the roles of photosynthesis in metabolism, cell motility, DNA repair, cell division, and other physiological processes, but also showed how protein functions vary from bacteria to higher plants due to the changed interaction partner. It also allows us to uncover functions of hypothetical proteins, such as Sll0445, Sll0446, S110447 participating in photosynthesis and cell motility, and Sll1334 regulating the expression of fatty acid. Here we presented the most extensive protein interaction data in Synechocystis so far, which might provide critical insights into the fundamental molecular mechanism in Cyanobacterium.

biochemistry↗

Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells

Anti-cancer drugs commonly target signal transduction proteins activated by mutation. In patients with BRAFV600E melanoma, small molecule RAF and MEK kinase inhibitors cause dramatic but often transient tumor regression. Emerging evidence suggests that cancer cells adapting by non-genetic mechanisms constitute a reservoir for the development of drug-resistant tumors. Here, we show that few hours after exposure to RAF/MEK inhibitors, BRAFV600E melanomas undergo adaptive changes involving disruption of negative feedback and sporadic pulsatile reactivation of the MAPK pathway, so that MAPK activity is transiently high enough in some cells to drive proliferation. Quantitative proteomics and computational modeling show that pulsatile MAPK reactivation is possible due to the co-existence in cells of two MAPK cascades: one driven by BRAFV600E that is drug-sensitive and a second driven by receptors that is drug-resistant. Paradoxically, this may account both for the frequent emergence of drug resistance and for the tolerability of RAF/MEK therapy in patients.

cancer biology↗

Whole-genome sequencing of 128 camels across Asia provides insights into origin and migration of domestic Bactrian camels

The domestic Bactrian camels were treated as the principal means of locomotion between the eastern and western cultures in history. To address the question of their origin, we performed whole-genome sequencing of 128 camels across Asia, including representative populations of domestic Bactrian camels from the Mongolian Plateau to the Caspian Sea, as well as the extant wild Bactrian camels and dromedaries. The domestic and wild Bactrian camels showed remarkable genetic divergence since they were split from dromedaries, confirming they were separated species. The wild Bactrian camels made also little contribution to the ancestry of domestic ones. Among the domestic Bactrian camels, those from Iran exhibited the largest genetic distance from others, and were the first population to separate in the phylogeny. Although evident admixture was observed between domestic Bactrian camels and dromedaries living around the Caspian Sea, the large genetic distance and basal position of Iranian Bactrian camels could not be explained by introgression alone. Taken together, our study favored the Iranian origin of domestic Bactrian camels, which were then immigrated eastward to Mongolia where the native wild Bactrian camels inhabited. This study illustrated the complex genomic landscape of migration underlying domestication in Bactrian camels.

genomics↗

CoolBox: a interactive genomic data explorer for Jupyter Notebook

SummaryCoolBox is a Python package for interactive genomic data exploration based on Jupyter notebook. It provides a ggplot2-like Application Programming Interface (API) for genomic data visualization, and a Jupyter/ipywidgets based Graphical User Interface (GUI) for interactive data exploration. CoolBox is a versatile multi-omics explorer supporting most types of data formats generated by various sequencing technologies like RNA-Seq, ChIP-Seq, ChIA-PET and Hi-C.\n\nAvailability and implementationCoolBox is purely implemented with Python, and the GUI widget in Jupyter notebook is based on the ipywidgets package. It is open-source and available under GPLv3 license at https://github.com/GangCaoLab/CoolBox.

bioinformatics↗

Autistic traits lower the flexibility of information sampling: insights from a two-stage decision model

Information sampling can reduce uncertainty in future decisions but is often costly. To maximize reward, people need to balance sampling cost and information gain. Here we aimed to understand how autistic traits influence the optimality of information sampling and to identify the particularly affected cognitive processes. Healthy human adults with different levels of autistic traits performed a probabilistic inference task, where they could sequentially sample information to increase their likelihood of correct inference and may choose to stop at any moment. We manipulated the cost and evidence associated with each sample and compared participants performance to strategies that maximize expected gain. We found that participants were overall close to optimal but also showed autistic-trait-related differences. Participants with higher autistic traits had a higher efficiency of winning rewards when the sampling cost was zero but a lower efficiency when the cost was high and the evidence was more ambiguous.\n\nComputational modeling of participants sampling choices and decision times revealed a two-stage decision process, with the second stage being an optional second thought. Participants may consider cost in the first stage and evidence in the second stage, or in the reverse order. The probability of choosing stopping at a specific stage increases with increasing cost or increasing evidence. Surprisingly, autistic traits did not influence the decision in either stage. However, participants with higher autistic traits inclined to consider cost first, while those with lower autistic traits considered cost or evidence first in a more balanced way. This would lead to the observed autistic-trait-related advantages or disadvantages in sampling optimality, depending on whether the optimal sampling strategy is determined only by cost or jointly by cost and evidence.\n\nAuthor SummaryChildren with autism can spend hours practicing lining up toys or learning all about cars or lighthouses. This kind of behaviors, we think, may reflect suboptimal information sampling strategies, that is, a failure to balance the gain of information with the cost (time, energy, or money) of information sampling. We hypothesized that suboptimal information sampling is a general characteristic of people with autism or high level of autistic traits. In our experiment, we tested how participants may adjust their sampling strategies with the change of sampling cost and information gain in the environment. Though all participants were healthy young adults who had similar IQs, higher autistic traits were associated with higher or lower efficiency of winning rewards under different conditions. Counterintuitively, participants with different levels of autistic traits did not differ in the general tendency of oversampling or undersampling, or in the decision they would reach when a specific set of sampling cost or information gain was considered. Instead, participants with higher autistic traits consistently considered sampling cost first and only weighed information gain during a second thought, while those with lower autistic traits had more diverse sampling strategies that consequently better balanced sampling cost and information gain.

neuroscience↗

Characterization and repurposing of the endogenous Type I-F CRISPR-Cas system of Zymomonas mobilis for genome engineering

Establishment of production platform organisms through prokaryotic engineering represents an efficient means to generate alternatives for yielding renewable biochemicals and biofuels from sustainable resources. Zymomonas mobilis, a natural facultative anaerobic ethanologen, possesses many attractive physiological attributes, making it an important industrial microorganism. To facilitate the broad applications of this strain for biorefinery, an efficient genome engineering toolkit for Z. mobilis was established in this study by repurposing the endogenous Type I-F CRISPR-Cas system upon its functional characterization, and further updated. This toolkit includes a series of genome engineering plasmids, each carrying an artificial self-targeting CRISPR and a donor DNA for the recovery of recombinants. Using the updated toolkit, genome engineering purposes were achieved with efficiencies of up to 100%, including knockout of cas3 gene, replacement of cas3 with the mCherry-encoding rfp gene, nucleotide substitutions in cas3, and deletion of two large genomic fragments up to 10 kb. This study established thus far the most efficient, straightforward and convenient genome engineering toolkit for Z. mobilis, and laid a foundation for further native CRISPRi studies in Z. mobilis, which extended the application scope of CRISPR-based technologies, and could also be applied to other industrial microorganisms with unexploited endogenous CRISPR-Cas systems.

bioengineering↗

A direct comparison of genome alignment and transcriptome pseudoalignment

MotivationGenome alignment of reads is the first step of most genome analysis workflows. In the case of RNA-Seq, transcriptome pseudoalignment of reads is a fast alternative to genome alignment, but the different \"coordinate systems\" of the genome and transcriptome have made it difficult to perform direct comparisons between the approaches.\n\nResultsWe have developed tools for converting genome alignments to transcriptome pseudoalignments, and conversely, for projecting transcriptome pseudoalignments to genome alignments. Using these tools, we performed a direct comparison of genome alignment with transcriptome pseudoalignment. We find that both approaches produce similar quantifications. This means that for many applications genome alignment and transcriptome pseudoalignment are interchangeable.\n\nAvailability and Implementationbam2tcc is a C++14 software for converting alignments in SAM/BAM format to transcript compatibility counts (TCCs) and is available at https://github.com/pachterlab/bam2tcc. kallisto genomebam is a user option of kallisto that outputs a sorted BAM file in genome coordinates as part of transcriptome pseudoalignment. The feature has been released with kallisto v0.44.0, and is available at https://pachterlab.github.io/kallisto/.\n\nSupplementary MaterialN/A\n\nContactLior Pachter (lpachter@caltech.edu)

bioinformatics↗

Identification of transcriptional signatures for cell types from single-cell RNA-Seq

Single-cell RNA-Seq makes it possible to characterize the transcriptomes of cell types and identify their transcriptional signatures via differential analysis. We present a fast and accurate method for discriminating cell types that takes advantage of the large numbers of cells that are assayed. When applied to transcript compatibility counts obtained via pseudoalignment, our approach provides a quantification-free analysis of 3 single-cell RNA-Seq that can identify previously undetectable marker genes.

bioinformatics↗

Gene-level differential analysis at transcript-level resolution

Gene-level differential expression analysis based on RNA-Seq is more robust, powerful and biologically actionable than transcript-level differential analysis. However aggregation of transcript counts prior to analysis results can mask transcript-level dynamics. We demonstrate that aggregating the results of transcript-level analysis allow for gene-level analysis with transcript-level resolution. We also show that p-value aggregation methods, typically used for meta-analyses, greatly increase the sensitivity of gene-level differential analyses. Furthermore, such aggregation can be applied directly to transcript compatibility counts obtained during pseudoalignment, thereby allowing for rapid and accurate model-free differential testing. The methods are general, allowing for testing not only of genes but also of any groups of transcripts, and we showcase an example where we apply them to perturbation analysis of gene ontologies.

bioinformatics↗

Molecular evolution, diversity and adaptation of H7N9 influenza A viruses in China

A novel H7N9 avian influenza virus has caused five human epidemics in China since 2013. The substantial increase in prevalence and the emergence of antigenically divergent or highly pathogenic (HP) H7N9 strains during the current outbreak raises concerns about the epizootic-potential of these viruses. Here, we investigate the evolution and adaptation of H7N9 by combining publicly available data with newly generated virus sequences isolated in Guangdong between 2015-2017. Phylogenetic analyses show that currently-circulating H7N9 viruses belong to distinct lineages with differing spatial distributions. Using ancestral sequence reconstruction and structural modelling we have identified parallel amino-acid changes on multiple separate lineages. Furthermore, we infer mutations in HA primarily occur at sites involved in receptor-recognition and/or antigenicity. We also identify seven new HP strains, which likely emerged from viruses circulating in eastern Guangdong around March 2016 and is further associated with a high rate of adaptive molecular evolution.

evolutionary biology↗

H+- and Na+- elicited swift changes of the microtubule system in the biflagellated green alga Chlamydomonas

The microtubule cytoskeletal system is integral to diverse cellular processes. Although microtubules are known for dynamic instability, the system is tightly controlled in typical interphase animal cells. In contrast, diverse evidence suggests that the system is mercurial in the unicellular fresh water green alga, Chlamydomonas, but intense autofluorescence from photosynthesis pigments has hindered the investigation. By expressing a bright fluorescent reporter protein at the endogenous level, we demonstrate in real time discreet sweeping changes in algal microtubules elicited by fluctuation of intracellular H+ and Na+. These results suggest disparate sensitivity of this vital yet delicate system in diverse organisms; and illuminate how pH may drive crucial cellular processes; how plants respond to, and perhaps sense stresses; and how many species could be susceptible to accelerated changes in global environments.

cell biology↗