Biology subjects

Qin, M.

Publications and source records attributed to Qin, M..

30 records · Page 2Linked to original sources

bioRxiv2022

Right atrial mechanism contributes to atrial fibrillation in a canine model of pulmonary arterial hypertension

ObjectivesThe aim of this study was to investigate proarrhythmic substrates of atrial fibrillation (AF) in a canine model of dehydromonophylline (DMCT)-induced pulmonary arterial hypertension (PAH). MethodsAll cannines (n=12) underwent baseline echocardiographic and hemodynamic examinations, 7 of which were injected with DMCT (3.0mg/kg) to induce PAH via jugular vein cannulation. The control beagles (n=5) were given the same dose of normal saline. Then, both groups were monitored by insertable cardiac monitors. Hemodynamic, echocardiographic, electrophysiological and histological examinations were performed 8 weeks later. ResultsIn PAH group, 2 died after the injection (mortality 28.6%). Thus, 10 beagles (PAH group: 5, control group: 5) underwent all the examinations. The pulmonary artery pressure increased significantly while the right atrium (RA) and right ventricle expanded slightly. Spontaneous AF episodes were recorded in all PAH canines 1 week after the injection. The AF burden increased rapidly from 1 week (7.6{+/-}1.8%) and remained high after 2-3 weeks (32.0{+/-}4.9% at 8 weeks). Compared with the control group, the PAH group had abbreviated effective refractory periods (ERPs), increased atrial ERP dispersion, and slower conduction velocities. Notably, AF susceptibility and atrial remodeling in RA was more significant those in LA, such as increased WOV(39.0{+/-}6.5ms vs. 28.0{+/-}5.7ms, P=0.022), enlarged low voltage regions (7.66{+/-}0.46% vs. 4.40{+/-}0.55%, P<0.0001) and fibrosis (8.22{+/-}0.61% vs. 4.93{+/-}0.60%, P <0.0001). ConclusionsDMCT-induced canine PAH model increased the incidence of spontaneous and induced AF. The electrophysiological and structural remodeling of the RA facilitated the AF genesis.

physiology↗

bioRxiv2021

Highly sensitive genetically-encoded sensors for population and subcellular imaging of cAMP in vivo

Cyclic adenosine monophosphate (cAMP) integrates information from diverse G protein-coupled receptors, such as neuromodulator receptors, to regulate pivotal biological processes in a cellular- and subcellular-specific manner. However, in vivo cellular-resolution imaging of cAMP dynamics in neurons has not been demonstrated. Here, we screen existing genetically-encoded cAMP sensors, and further develop the best performer to derive three improved variants, called cAMPFIREs. These sensors exhibit up to ten-fold increased sensitivity to cAMP and a corrected, cytosolic distribution. cAMPFIREs are compatible with both ratiometric and fluorescence lifetime imaging, and can detect cAMP dynamics elicited by norepinephrine at physiologically-relevant, nanomolar concentrations. Imaging of cAMPFIREs in awake mice reveals tonic levels of cAMP in cortical neurons that are associated with wakefulness, and are differentially regulated in different subcellular compartments. Furthermore, enforced locomotion elicits neuron-specific, bidirectional cAMP dynamics, in part, mediated by norepinephrine. Finally, cAMPFIREs also function in Drosophila, suggesting that they have broad applicability for studying intracellular signaling in vivo.

neuroscience↗

bioRxiv2021

Temperature and Guanidine Hydrochloride effects on the folding thermodynamics of WW domain and variants

We used simulations based on an all atom Go model to calculate the folding temperatures (Tfs) and free energies ({Delta}Gs) of two variants of the WW domain, which is a small all {beta}-sheet protein. The results, without adjusting any parameter, are in good agreement with experiments, thus validating the simulations. We then used the Molecular Transfer Model to predict the changes in the {Delta}G and Tfs as guanidine hydrochloride concentration is varied. The predictions can be readily tested in experiments.

biophysics↗

bioRxiv2021

CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity

Safe, economical and effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to achieve adequate herd immunity and halt the pandemic. We have constructed a novel SARS-CoV-2 vaccine, CoVac501, which is a self-adjuvanting peptide vaccine conjugated with Toll-like receptor 7 (TLR7) agonists. The vaccine contains two immunodominant peptides screened from receptor-binding domain (RBD) and is fully chemically synthesized. And the vaccine has optimized nanoemulsion formulation, outstanding stability and safety. In non-human primates (NHPs), CoVac501 elicited high and persistent titers of RBD-specific and protective neutralizing antibodies (NAbs), which were also effective to RBD mutations. CoVac501 was found to elicit the increase of memory T cells, antigen-specific CD8+ T cell responses and Th1-biased CD4+ T cell immune responses in NHPs. More importantly, the sera from the immunized NHPs can prevent infection of live SARS-CoV-2 in vitro. One-Sentence SummaryA novel SARS-CoV-2 vaccine we developed, CoVac501, which is a fully chemically synthesized and self-adjuvanting peptides conjugated with TLR7 agonists, can induce high-efficient humoral and cellular immune responses against SARS-CoV-2.

immunology↗

bioRxiv2021

Distinct in vivo dynamics of excitatory synapses onto cortical pyramidal neurons and inhibitory interneurons

Cortical function relies on the balanced activation of excitatory and inhibitory neurons. However, little is known about the organization and dynamics of shaft excitatory synapses onto cortical inhibitory interneurons, which cannot be easily identified morphologically. Here, we fluorescently visualize the excitatory postsynaptic marker PSD-95 at endogenous levels as a proxy for excitatory synapses onto layer 2/3 pyramidal neurons and parvalbumin-positive (PV+) inhibitory interneurons in the mouse barrel cortex. Longitudinal in vivo imaging reveals that, while synaptic weights in both neuronal types are log-normally distributed, synapses onto PV+ neurons are less heterogeneous and more stable. Markov-model analyses suggest that the synaptic weight distribution is set intrinsically by ongoing cell type-specific dynamics, and substantial changes are due to accumulated gradual changes. Synaptic weight dynamics are multiplicative, i.e., changes scale with weights, though PV+ synapses also exhibit an additive component. These results reveal that cell type-specific processes govern cortical synaptic strengths and dynamics.

neuroscience↗

bioRxiv2021

Emergence of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Co-harbouring a blaNDM-1-carrying Virulent Plasmid and a blaKPC-2-carrying Plasmid in an Egyptian Hospital

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Egyptian hospitals has been reported. However, the genetic basis and the analysis of the plasmids associated with CR-hypervirulent-KP (CR-HvKP) in Egypt are not presented. Therefore, we attempt to decipher the plasmids sequences, which are responsible for transferring the determinants of carbapenem-resistance, particularly the blaNDM-1 and blaKPC-2. Out of 34 K. pneumoniae isolates collected from two tertiary hospitals in Egypt, 31 were CRKP. Whole-genome sequencing revealed that our isolates were related to 13 different sequence types (STs). The most prevalent ST was ST101, followed by ST383, and ST11. Among the CRKP isolates, one isolate named EBSI036 has been reassessed using Nanopore sequencing. Genetic environment analysis showed that EBSI036 carried 20 antibiotic resistance genes and was identified as CR-HvKP strain, it harboured four plasmids, namely; pEBSI036-1-NDM-VIR, pEBSI036-2-KPC, pEBSI036-3, and pEBSI036-4. The two carbapenemase genes, blaNDM-1 and blaKPC-2, were located on plasmids pEBSI036-1-NDM-VIR and pEBSI036-2-KPC, respectively. The IncFIB:IncHI1B hybrid plasmid pEBSI036-1-NDM-VIR also carried some virulence factors, including regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD, iutA). Thus, we set out this study to analyse in-depth the genetic basis of pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. We reported for the first time a high-risk clone ST11 KL47 serotype of CR-HvKP strain isolated from the blood of a 60-year-old hospitalised female patient from the ICU in a tertiary-care hospital in Egypt, which showed the cohabitation of a novel hybrid plasmid coharbouring the blaNDM-1 and virulence genes, besides a blaKPC-2-carrying plasmid. IMPORTANCECRKP had been registered in the critical priority tier by the World Health Organization and became a significant menace to public health. Therefore, we set out this study to analyse in-depth the genetic basis of pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. Herein, we reported for the first time (to the best of our knowledge) a high-risk clone ST11 KL47 serotype of CR-HvKP strain isolated from the blood of a 60-year-old hospitalised female patient in a tertiary-care hospital from the ICU in Egypt, which showed the cohabitation of a novel hybrid plasmid co-harbouring the blaNDM-1 and virulence genes, besides a blaKPC-2-carrying plasmid. Herein, the high rate of CRKP might be due to the continuous usage of carbapenems as empirical therapy, besides the failure to implement an antibiotic stewardship program in Egyptian hospitals. Thus, this study serves to alert the contagious disease clinicians to the presence of hypervirulence in CRKP isolates in Egyptian hospitals.

microbiology↗

bioRxiv2020

High-fidelity, efficient, and reversible labeling of endogenous proteins using CRISPR-based designer exon insertion

Precise and efficient insertion of large DNA fragments into somatic cells using gene editing technologies to label or modify endogenous proteins remains challenging. Non-specific insertions/deletions (INDELs) resulting from the non-homologous end joining pathway make the process error-prone. Further, the insert is not readily removable. Here, we describe a method called CRISPR-mediated insertion of exon (CRISPIE) that can precisely and reversibly label endogenous proteins using CRISPR/Cas9-based editing. CRISPIE inserts a designer donor module, which consists of an exon encoding the protein sequence flanked by intron sequences, into an intronic location in the target gene. INDELs at the insertion junction will be spliced out, leaving mRNAs nearly error-free. We used CRISPIE to fluorescently label endogenous proteins in neurons in vivo with previously unachieved efficiency. We demonstrate that this method is broadly applicable, and that the insert can be readily removed later. CRISPIE permits protein sequence insertion with high fidelity, efficiency, and flexibility.

cell biology↗

bioRxiv2020

Evaluation of Fecal Immunoassays for Canine Echinococcus Infection in China

Human echinococcosis is present worldwide but it is in China that prevalence is the highest. Western China and in particular the Tibetan plateau is the region where the burden of echinococcosis is the most important. Dogs are a major carrier of echinococcosis and monitoring the presence of Echinococcus worms in dogs is therefore essential for efficiently controlling the disease. Detection kits based on three different technologies, i.e. sandwich ELISA, ELISA and gold immunodiffusion are currently marketed and used in China. The objective of this work was to assess the efficacy of these kits, in particular with respect to sensitivity and specificity. Four fecal antigen detection kits for canine echinococcosis covering the three technologies were obtained from companies and tested in parallel on 220 fecal samples. The results indicate that the performance is lower than expected, in particular in terms of sensitivity. The best results were obtained with the sandwich ELISA technology. The gold immunofiltration yielded the poorest results. In all cases, further development is needed to improve the performance of these kits, which represent a key element for the control of echinococcosis. Author summaryAlthough present worldwide, human echinococcosis is at its highest prevalence in Western China and particularly on the Tibetan plateau. Controlling echinococcosis is a national priority and routine monitoring must be established. Dogs are the main carriers of echinococcosis and surveying Echinococcus worms in dogs is therefore a key issue. Commercial detection kits are currently in use in China for monitoring the presence of Echinococcosis in dogs. These kits are based on three different technologies, i.e. sandwich ELISA with two monoclonal antibodies, ELISA, and gold immunodiffusion. National survey programs are essential for the control of echinococcosis and it is thus very important to assess the efficacy of these kits, planned to be used for the national survey programs. The work was thus undertaken to assess this efficacy, in particular with respect to sensitivity and specificity. Four fecal antigen detection kits for canine echinococcosis covering the three technologies were obtained from companies and tested in parallel on 220 fecal samples. The performance was lower than expected, in particular for their sensitivity, which ranged from 51.5% to 83.9% with only two samples displaying a worm burden lower than 100. Three out of four kits showed non-specific cross-reactions with other parasites. The best results were obtained with the sandwich ELISA technology, whereas gold immunofiltration yielded the poorest results. However, in all cases, further development is strongly needed to improve the performance of these kits, which represent a key element for the control of echinococcosis.

zoology↗

bioRxiv2020

An Antioxidant Enzyme Therapeutic for COVID-19

The COVID-19 pandemic has taken a significant toll on people worldwide, and there are currently no specific antivirus drugs or vaccines. We report herein a therapeutic based on catalase, an antioxidant enzyme that can effectively breakdown hydrogen peroxide and minimize the downstream reactive oxygen species, which are excessively produced resulting from the infection and inflammatory process. Catalase assists to regulate production of cytokines, protect oxidative injury, and repress replication of SARS-CoV-2, as demonstrated in human leukocytes and alveolar epithelial cells, and rhesus macaques, without noticeable toxicity. Such a therapeutic can be readily manufactured at low cost as a potential treatment for COVID-19.

biochemistry↗

bioRxiv2020

Myristoylation alone is sufficient for PKA catalytic subunits to fractionally associate with the plasma membrane to regulate neuronal functions

Myristoylation is a post-translational modification that plays diverse functional roles in many protein species. The myristate moiety is considered insufficient for protein-membrane associations unless additional membrane-affinity motifs, such as a stretch of positively charged residues, are present. Here, we report that the electrically neutral N-terminal fragment of the protein kinase A catalytic subunit (PKA-C), in which myristoylation is the only functional motif, is sufficient for membrane association. This myristoylation can associate a fraction of PKA-C molecules or fluorescent proteins (FPs) to the plasma membrane in neuronal dendrites. The net neutral charge of PKA-C is evolutionally conserved, even though its membrane affinity can be readily tuned by changing charges near the myristoylation site. The observed membrane association, while moderate, is sufficient to concentrate PKA activity at the membrane by nearly 20-fold, and is required for PKA regulation of AMPA receptors at neuronal synapses. Our results indicate that myristoylation alone may be sufficient to drive functionally significant membrane association in the absence of assisting motifs. This provides a revised foundation for the understanding of how myristoylation regulates protein functions.

cell biology↗

bioRxiv2019

Transcriptome Analysis of xa5-mediated Resistance to Bacterial Leaf Streak in Rice (Oryza sativa L.)

Bacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation with water as control. The results showed that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways, suggesting that xa5 displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.

plant biology↗

bioRxiv2018

LRScaf: Improving Draft Genomes Using Long Noisy Reads

BackgroundThe advent of Third Generation Sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promised to enhance the quality of fragmental draft assemblies constructed from Next Generation Sequencing (NGS) technologies. To date, a few of algorithms, i.e., SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS, have been released that are capable of improving draft assemblies. However, hybrid assembly on large genomes is still challenging.\n\nResultsWe develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf), that is capable of boosting assembly contiguity to a large extent using long reads. In our experiment, our method significantly improves the contiguity of human draft assemblies, increasing the NG50 value of CHM1 from 127.5 Kb to 10.4 Mb using 20-fold coverage PacBio dataset and the NG50 value of NA12878 from 115.7 Kb to 17.4 Mb using 35-fold coverage Nanopore dataset. The run time for the scaffolding procedure using LRScaf is the shortest in all cases of our experiment. Compared with the run time of SSPACE-LongRead, LRScaf is faster 300 times for S. cerevisiae and 2,300 times for D. melanogaster. The peak RAM of LRScaf, by contrast, is more efficient than LINKS in our test. For the rice case, the peak RAM of LINKS (877.72 Gb) is about 196 times higher than LRScaf. For the experiment of human assembly, the peak RAM of LINKS is beyond the capacity of system memory (1 Tb) whereas LRScaf takes 20.28 and 41.20 Gb on CHM1 and NA12878 datasets.\n\nConclusionsThe new method, LRScaf, yields the best or at least moderate contiguity and accuracy of scaffolds in the shortest run time compared with the state-of-the-art methods. Furthermore, it offers a new opportunity for the hybrid assembly of large genomes.

bioinformatics↗