Biology subjects

Guo, D.

Publications and source records attributed to Guo, D..

10 recordsLinked to original sources

bioRxiv2018

Heart Rate n-Variability (HRnV): A Novel Representation of Beat-to-Beat Variation in Electrocardiography

Heart rate variability (HRV) is a widely adopted tool for evaluating changes in cardiac autonomic regulation. The majority of efforts have focused on developing methods to assess HRV by deriving sophisticated parameters with linear and nonlinear techniques and adopting advanced signal processing tools for efficient noise removal and accurate QRS detection. In this paper, we propose a novel representation of beat-to-beat variation in an electrocardiogram (ECG), called heart rate n-variability (HRnV), as an alternative to conventional HRV measures. We derived two novel HRnV measures based on non-overlapped and overlapped RR intervals. We also conducted a simulation study by using an ECG record from the MIT-BIH Normal Sinus Rhythm Database to demonstrate the feasibility of calculating HRnV parameters. Among the time domain parameters, we observed that the values were generally incremental with the increase in n. We observed the same trend of changes for the frequency domain parameters. In the nonlinear analysis, the differences between HRV and HRnV from Poincare plot measures were obvious, while those from entropy and detrended fluctuation analysis metrics were not. HRnV measures enable us to augment conventional HRV measures with additional parameters. Although issues remain to be addressed regarding HRnV, we hope to stimulate a new stream of research on this new representation of HRV. HRnV is an important addition to HRV and will contribute to extending the landscape of current studies on HRV.

bioengineering↗

bioRxiv2018

A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses

The identification of homologous genes with functional overlap in forward genetic screens is severely limited. Here we report the generation of over 14,000 amiRNA-expressing plants that enable screens of the functionally redundant gene space in Arabidopsis. A protocol is developed here for isolating robust and reproducible amiRNA-mutants. Examples of validation approaches and essential controls are presented for two new amiRNA mutants that exhibit genetically redundant phenotypes and circumvent double mutant lethality. In a forward genetic screen for abscisic acid (ABA)-mediated inhibition of seed germination, amiRNAs that target combinations of known redundant ABA receptor and SnRK2 kinase genes were rapidly isolated, providing a strong proof of principle for this approach. A new ABA insensitive amiRNA line is isolated, which targets three genes encoding avirulence-induced gene2-like (AIG2) genes. A thermal imaging screen for plants with impaired stomatal opening in response to low CO2 exposure led here to isolation of a new amiRNA targeting two essential proteasomal subunits, PAB1 and PAB2. The seed library of 14,000 T2 amiRNA lines generated here provides a new platform for forward genetic screens and is being made available to the Arabidopsis Biological Resource Center (ABRC) and optimized procedures for amiRNA screening and controls are described.\n\nHighlightThe generation of over 14,000 amiRNA-expressing plants is reported that are being made publicly available enabling screens of redundant genes in Arabidopsis. Identification of known and new genes is reported.

plant biology↗

bioRxiv2018

The reduced prevalence of macrolide resistance in Mycoplasma pneumoniae clinical isolates from pediatric patients in Beijing in 2016

Older children especially from seven to thirteen years old are more prone to develop Mycoplasma pneumoniae (MP) infection; in winter children are more susceptible to infect with MP. In Beijing, China in 2016 the rates of macrolide resistance of MP were 69.48% (in total children), 61.59% (in outpatients) and 79.28% (in hospitalized patients), respectively. All the macrolide resistant isolates harbored A2063G or A2064G mutation in the 23S rRNA gene. Seven isolates showed a mixed infection. Susceptibility results showed that 73 isolates with the A2063G mutation demonstrated different levels resistance to erythromycin (MIC=8 to>256g/ml), azithromycin (MIC=8 to>64g/ml) and josamycin (MIC=2 to 8g/ml). No cross-resistance was observed in the in the antibiotics of levofloxacin and tetracycline against MP.

microbiology↗

bioRxiv2018

Overexpressed microRNA-141-3p enhance proliferation via targeting PLAG1 in non-diabetic macrosomia

Several studies have shown microRNAs (miRNAs) could regulate the placental development, yet the role and mechanism of miRNAs in the development of non-diabetic macrosomia (NDFMS) remains unclear. The key miRNA that abnormal expressed in NDFMS placentas was screened out by miRNA microarray and verified using qRT-PCR in 91 subjects. The effects of the key miRNA were verified by proliferation assay and invasion assay in HTR-8/SVneo cell, and also in pregnant C57BL/6J mice. miR-141-3p was determined as the key miRNA with the most significant difference, which could promote the proliferation and invasion by regulating the expression of target gene PLAG1. Overexpression of PLAG1 could reverse the effect of cell proliferation and invasion ability caused by miR-141-3p overexpression. Significant difference in fetal birth weight was observed between the control group and treated group with miR-141-3p agomir in late pregnancy, but not in early pregnancy. This study revealed miR-141-3p could increase the proliferation of placenta to participate in the occurrence and development of NDFMS through regulating PLAG1 expression.

developmental biology↗

bioRxiv2018

Local Polyploidy Phenomenon in Escherichia coli and its significance in genetic engineering

Classic Helmstetter & Cooper model asserted that the multifork phenomenon in the process of replication. However, the impacts of the multifork on the evolution and genetic engineering are still vague. Here, we employed CRISPR/Cas9 technology to knock-out eighteen Escherichia coli chromosomal fragments (over 50 kb) that represent all areas of the chromosome. We demonstrated that a single cell could have wild-type, color-reporter, and antibiotic-resistant genes simultaneously in the same locus of the different branches of the duplication forks after multiple rounds of deletions and replacements. This phenomenon that a single cell had different genotypes in its local polyploid chromosomes, which was similar to eukaryotic heterozygote, was named as local polyploidy. Under a defined selective pressure condition, offspring cells containing at least a copy of conditionally beneficial mutation could be enriched, and other alleles could be kept silently and peacefully in the duplication fork(s) of the same cell. The significance of this phenomenon in the genetic engineering was discussed.

microbiology↗

bioRxiv2018

Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells

Estrogen regulates diverse physiological effects and drives breast tumor progression by directly activating estrogen receptor (ER). However, due to the stochastic nature of gene transcription and the resulting heterogeneous cellular response, it is important to investigate estrogen-stimulated gene expression profiles at the single-cell level in order to fully understand how ER regulates transcription in breast cancer cells. In this study, we performed single-cell transcriptome analysis on ER-positive breast cancer cell lines following 17{beta}-estradiol stimulation. Overall, we observed robust gene expression diversity between individual cells. Moreover, we found over two thirds of the genes in breast cancer cells displayed a bimodal expression pattern, which caused averaging artifacts and masked the identification of potential estrogen-regulated genes. We overcame this issue by reconstructing a dynamic estrogen-responsive transcriptional network from discrete time points into a pseudotemporal continuum. Pathway analysis of the differentially expressed genes derived from the pseudotemporal analysis showed an estrogen-stimulated metabolic switch that favored biosynthesis and cell proliferation but reduced estrogen degradation. In addition, we identified folate-mediated one-carbon metabolism as a novel estrogen-regulated pathway in breast cancer cells. Notably, estrogen stimulation reprogramed this pathway through the mitochondrial folate pathway to coordinately fuel polyamine and de novo purine synthesis. Finally, we showed AZIN1 and PPAT, key regulators in the above pathways, are direct ER target genes and essential for breast cancer cell survival and growth. In summary, our single-cell study illustrated a dynamic transcriptional heterogeneity in ER-positive breast cancer cells in response to estrogen stimulation and uncovered a novel mechanism of an estrogen-mediated metabolic switch.

genomics↗

bioRxiv2017

Genome-wide analysis yields new loci associating with aortic valve stenosis

Aortic valve stenosis (AS) is the most common valvular heart disease, characterized by a thickened and calcified valve causing left ventricular outflow obstruction. Severe AS is a significant cause of morbidity and mortality, affecting approximately 5% of those over 70 years of age1,2,3. Little is known about the genetics of AS, although recently a variant at the LPA locus4 and a rare MYH6 missense variant were found to associate with AS5. We report a large genome-wide association study (GWAS) with a follow-up in up to 7,307 AS cases and 801,073 controls. We identified two new AS loci, on chromosome 1p21 near PALMD (rs7543130; OR=1.20, P=1.2x10-22) and on chromosome 2q22 in TEX41 (rs1830321; OR=1.15, P=1.8x10-13). Rs7543130 also associates with bicuspid aortic valve (BAV) (OR=1.28, P=6.6x10-10) and aortic root diameter (P=1.30x10-8) and rs1830321 associates with BAV (OR=1.12, P=5.3x10-3 and coronary artery disease (CAD) (OR=1.05, P=9.3x10-5). These results indicate that AS is partly rooted in the same processes as cardiac development and atherosclerosis.

genetics↗

bioRxiv2017

Strong positive biodiversity-productivity relationships in a subtropical forest experiment

Forest ecosystems contribute substantially to global terrestrial primary productivity and climate regulation, but, in contrast to grasslands, experimental evidence for a positive biodiversity-productivity relationship in highly diverse forests is still lacking1. Here, we provide such evidence from a large forest biodiversity experiment with a novel design2 in subtropical China. Productivity (stand-level tree basal area, aboveground volume and carbon and their annual increment) increased linearly with the logarithm of tree species richness. Additive partitioning3 showed that increasing positive complementarity effects combined with weakening negative selection effects caused a strengthening of the relationship over time. In 2-species mixed stands, complementary effects increased with functional distance and selection effects with vertical crown dissimilarity between species. Understorey shrubs reduced stand-level tree productivity, but this effect of competition was attenuated by shrub species richness, indicating that a diverse understorey may facilitate overall ecosystem functioning. Identical biodiversity-productivity relationships were found in plots of different size, suggesting that extrapolation to larger scales is possible. Our results highlight the potential of multi-species afforestation strategies to simultaneously contribute to mitigation of climate change and biodiversity restoration.

ecology↗

bioRxiv2017

Integrated transcriptome and epigenome analyses identify alternative splicing as a novel candidate linking histone modifications to embryonic stem cell fate decision

BackgroundUnderstanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-mRNA splicing, and cell-cycle progression. However, their intricate interrelations and joint contributions to ESC fate decision remain unclear.\n\nResultsWe analyze the transcriptomes and epigenomes of human ESC and five types of differentiated cells. We identify thousands of alternatively spliced exons and reveal their development and lineage-dependent characterizations. Several histone modifications show dynamic changes in alternatively spliced exons and three are strongly associated with 52.8% of alternative splicing events upon hESC differentiation. The histone modification-associated alternatively spliced genes predominantly function in G2/M phases and ATM/ATR-mediated DNA damage response pathway for cell differentiation, whereas other alternatively spliced genes are enriched in the G1 phase and pathways for self-renewal. These results imply a potential epigenetic mechanism by which some histone modifications contribute to ESC fate decision through the regulation of alternative splicing in specific pathways and cell-cycle genes. Supported by experimental validations and extended dataset from Roadmap/ENCODE projects, we exemplify this mechanism by a cell cycle-related transcription factor, PBX1, which regulates the pluripotency regulatory network by binding to NANOG. We suggest that the isoform switch from PBX1a to PBX1b links H3K36me3 to hESC fate determination through the PSIP1/SRSF1 adaptor, which results in the exon skipping of PBX1.\n\nConclusionWe reveal the mechanism by which alternative splicing links histone modifications to stem cell fate decision.

bioinformatics↗

bioRxiv2017

A mutation in the LMOD1 actin-binding domain segregating with disease in a large British family with thoracic aortic aneurysms and dissections

We describe a mutation in LMOD1, which predisposes individuals to thoracic aortic aneurysms and dissections in a large multi-generation British family. Exome variant profiles for the proband and two distantly related affected relatives were generated and a rare protein-altering, heterozygous variant was identified, present in all the exome-sequenced affected individuals. The allele c.1784T>C, p.(V595A) in LMOD1 is located in a known actin-binding WH2 domain and is carried by all living affected individuals in the family. LMOD1 was further assessed in a consecutive series of 98 UK TAAD patients and one further mutation was found, yielding an incidence of [~]2% in our study group. Assessment of LMOD1 in international TAAD cohorts discovered nine other missense variants of which three were classed as likely pathogenic.\n\nValidation of LMOD1 was undertaken using a zebrafish animal model. Knock-down of both lmod1a and lmod1b paralogs using morpholino oligonucleotides showed a reproducible abnormal phenotype involving the aortic arches under off-target controls. Injection of the human LMOD1 c.1784T>C, p.(V595A) mutation demonstrated a likely dominant negative effect and illustrated a loss of function cause.\n\nMutations found in the WH2 actin-binding domain of LMOD1 may delay actin polymerization and therefore compromise actin length, dynamics and interaction with myosin in the smooth muscle contraction pathway.

genetics↗