Biology subjects

Wang, G.

Publications and source records attributed to Wang, G..

At least 487 records · Page 27Linked to original sources

bioRxiv2019

Transcriptome-wide map of m6A circRNAs identified in hypoxic pulmonary hypertension rat model

Hypoxic pulmonary hypertension (HPH) is a lethal disease. CircRNAs and m6A circRNAs have been reported to be associated with cancer progression, but the expression profiling of m6A circRNAs has not been identified in HPH. This study was to investigate the transcriptome-wide map of m6A circRNAs in HPH. In this study, hypoxia-induced PH rat model was established. Total RNA was extracted and purified from lungs of rats, then circRNAs were detected and annotated by RNA-seq analysis. m6A RNA Immunoprecipitation (MeRIP) was performed following rRNA depletion, and RNA-seq library was constructed. CircRNA-miRNA-mRNA co-expression network was also constructed. In vitro, total m6A was measured. m6A circXpo6 and m6A circTmtc3 were detected in pulmonary artery smooth muscle cells (PASMCs) and pulmonary artery endothelial cells (PAECs) exposed to 21% O2 and 1% O2 for 48 h, respectively. m6A abundance in 166 circRNAs was significantly upregulated and m6A abundance in 191 circRNAs was significantly downregulated in lungs of HPH rats. m6A abundance in circRNAs was significantly reduced in hypoxia in vitro. m6A circRNAs were mainly derived from single exons of protein-coding genes. m6A influenced the circRNA-miRNA-mRNA co-expression network in hypoxia. m6A circXpo6 and m6A circTmtc3 were downregulated in hypoxia. In general, our study firstly identified the transcriptome-wide map of m6A circRNAs in HPH. m6A level in circRNAs was decreased in lungs of HPH rats and in PASMCs and PAECs exposed to hypoxia. Downregulated or upregulated m6A level influenced circRNA-miRNA-mRNA co-expression network in HPH. Moreover, we firstly identified two downregulated m6A circRNAs in HPH: circXpo6 and circTmtc3. We suggested that m6A circRNAs may be used as a potential diagnostic marker or therapy target in the future.\n\nAuthor summaryHPH is a disease with great morbidity and mortality. It is often caused by chronic hypoxic lung diseases, such as chronic obstructive pulmonary disease and interstitial lung diseases. It lacks effective therapy methods so far. CircRNAs are a type of non-coding RNAs and can be used as biomarkers because they are differentially enriched in specific cell types or tissues and not easily degraded. m6A is identified as the most universal modification on non-coding RNAs in eukaryotes. CircRNAs can be modified by m6A. m6A circRNAs in HPH is not well understood yet. Here we identify the transcriptome-wide map of m6A circRNAs in HPH. We elucidate that m6A level in circRNAs is decreased in lungs of HPH rats and in PASMCs and PAECs exposed to hypoxia. We find that downregulated or upregulated m6A level influences circRNA- miRNA-mRNA co-expression network in HPH. Moreover, we are the first to identify two downregulated m6A circRNAs in HPH: circXpo6 and circTmtc3. We suggest that m6A circRNAs may be used as a potential diagnostic marker or therapy target in the future.

genetics↗

bioRxiv2019

Host sex and genotype modify the gut microbiome response to helminth infection

The microbial community can be altered by direct/indirect interactions with parasites infecting host. Direct interactions can arise from physical/chemical contact with the parasite. Indirect interactions can involve parasite-induced changes in host immunity. If so, this would represent a case of genetic polymorphism in one species controlling an ecological interaction between other species. Here, we report a test of this expectation: we experimentally exposed Gasterosteus aculeatus to their naturally co-evolved parasite, Schistocephalus solidus. The host microbiome differed in response to parasite exposure, and between infected and uninfected fish. The microbial response to infection differed between host sexes, and also varied between variants at autosomal quantitative trait loci (QTL). These results indicate that host genotype regulates the indirect effect of infection on a vertebrate gut microbiome. Our results also raise the possibility that this sex-bias may be related to sex-specific microbial responses to the presence (or, absence) of helminthes. Therefore, helminth-based therapeutics as possible treatments for inflammatory bowel diseases might need to take account of these interactions, potentially requiring therapies tailored to host sex or genotype.

microbiology↗

bioRxiv2019

Hematological and Neurological Expressed 1 (HN1): a predictive and pharmacodynamic biomarker of metformin response in endometrial cancers.

Preoperative use of metformin in obese women with endometrioid endometrial cancer (EEC) reduces tumor proliferation and inhibits the mammalian target of rapamycin (mTOR) pathway, though is only effective in select cases. This study sought to identify a predictive and/or pharmacodynamic proteomic signature of metformin response to tailor its pharmacologic use. Matched pre- and post-metformin treated tumor tissues from a recently completed phase 0 window trial of metformin in EEC patients (ClinicalTrials.gov: NCT01911247), were analyzed by mass spectrometry (MS)-based proteomic and immunohistochemical analyses. Hematological and neurological expressed 1 (HN1) was significantly elevated in metformin responders (n=13) versus non-responders (n=7), which was also found to decrease in abundance in metformin responders following treatment; observations that were verified by immunohistochemical staining for HN1. Metformin response and loss of HN1 was assessed in RL95-2 and ACI-181 endometrial cancer cell lines. We further identified that silencing of HN1 abundance does not alter cellular response to metformin or basal cell proliferation, but that HN1 abundance does decrease in response to metformin treatment in RL95-2 and ACI-181 endometrial cancer cell lines. These data suggest that HN1 represents a predictive and pharmacodynamic biomarker of metformin response that, if validated in larger patient populations, may enable pre-operative EEC patient stratification to metformin treatment and the ability to monitor patient response.\n\nNovelty and ImpactHematological and Neurological Expressed 1 (HN1) is elevated in endometrioid endometrial cancer (EEC) patients that respond to metformin vs non-responders and decreases after treatment. HN1 decreases after metformin treatment of EEC cells in vitro, but is not necessary for metformin response or proliferation. We report HN1 as a novel predictive and pharmacodynamic biomarker of metformin response in EEC that may enable pre-operative EEC patient stratification to metformin treatment and the ability to monitor patient response.

cancer biology↗

bioRxiv2019

Discovery Of UFO Proteins: Human-Virus Chimeric Proteins Generated During Influenza Virus Infection

Influenza A virus (IAV) is a threat to mankind because it generates yearly epidemics and poorly predictable sporadic pandemics with catastrophic potential. IAV has a small RNA genome composed of 8 mini-chromosomes (segments) that constitute a 5UTR followed by a coding region and a 3UTR. Transcription of IAV RNA into mRNA depends on host mRNA, as the viral polymerase cleaves 5m7G-capped nascent transcripts to use as primers to initiate viral mRNA synthesis. We hypothesized that captured host transcripts bearing AUG could drive the expression of upstream ORFs in the viral segments, a phenomenon that would depend on the translatability of the viral 5UTRs. Here we report the existence of this mechanism, which generates host-virus chimeric proteins. We label these proteins as Upstream Flu ORFs (UFO). Depending on the frame, two types of host-virus UFO proteins are made: canonical viral proteins with human-derived N term extensions or novel uncharacterized proteins. Here we show that both types are made during IAV infection. Sequences that enable chimeric protein synthesis are conserved across IAV strains, indicating that selection allowed the expansion of the proteome diversity of IAV in infected cells to include multiple human-virus proteins.

microbiology↗

bioRxiv2019

Projected changes of alpine grassland carbon dynamics in response to climate change and elevated CO2 concentrations under Representative Concentration Pathways (RCP) scenarios

The Tibetan Plateau is an important component of the global carbon cycle due to the large permafrost carbon pool and its vulnerability to climate warming. The Tibetan Plateau has experienced a noticeable warming over the past few decades and is projected to continue warming in the future. However, the direction and magnitude of carbon fluxes responses to climate change and elevated CO2 concentration under Representative Concentration Pathways (RCP) scenarios in the Tibetan Plateau grassland are poorly known. Here, we used a calibrated and validated biogeochemistry model, CENTURY, to quantify the contributions of climate change and elevated CO2 on the future carbon budget in the alpine grassland under three RCP scenarios. Though the Tibetan Plateau grassland was projected a net carbon sink of 16 ~ 25 Tg C yr-1 in the 21st century, the capacity of carbon sequestration was predicted to decrease gradually because climate-driven increases in heterotrophic respiration (Rh) (with linear slopes 0.49 ~ 1.62 g C m-2 yr-1) was greater than the net primary production (NPP) (0.35 ~ 1.52 g C m-2 yr-1). However, the elevated CO2 contributed more to plant growth (1.9% ~ 7.3%) than decomposition (1.7% ~ 6.1%), which could offset the warming-induced carbon loss. The interannual and decadal-scale dynamics of the carbon fluxes in the alpine grassland were primarily controlled by temperature, while the role of precipitation became increasingly important in modulating carbon cycle. The strengthened correlation between precipitation and carbon budget suggested that further research should consider the performance of precipitation in evaluating carbon dynamics in a warmer climate scenario.

ecology↗

bioRxiv2019

Integrating Genome-Wide Association and eQTLs Studies Identifies the Genes Associated with Age at Menarche and Age at Natural Menopause

ObjectiveAn early onset of menarche and, later, menopause are well-established risk factors for the development of breast cancer and endometrial cancer. Although the largest GWASs have identified 389 independent signals for age at menarche (AAM) and 44 regions for age at menopause (ANM), GWAS can only identify the associations between variants and traits. The aim of this study was to identify genes whose expression levels were associated with AAM or ANM due to pleiotropy or causality by integrating GWAS data with genome-wide expression quantitative trait loci (eQTLs) data. We also aimed to identify the pleiotropic genes that influenced two phenotypes.\n\nMethodWe employed GWAS data of AAM and ANM and Genome-wide eQTL data from whole blood. The summary data-based Mendelian randomization (SMR) method was used to prioritize the associated genes for further study. The colocalization analysis was used to identify the pleiotropic genes.\n\nResultsWe identified 31 genes whose expression was associated with AAM and 24 genes whose expression was associated with ANM due to pleiotropy or causality. Two pleiotropic genes were identified to be associated with two phenotypes.\n\nConclusionThe results point out the most possible genes which were responsible for the association. Our study prioritizes the associated genes for further functional mechanistic study of AAM and ANM and illustrates the benefit of integrating different omics of data into the study of complex traits.

genetics↗

bioRxiv2019

Parasite histones mediate leak and coagulopathy in cerebral malaria

Coagulopathy and leak, specific to the brain vasculature, are central pathogenetic components of cerebral malaria (CM). It is unclear how the parasite, Plasmodium falciparum, triggers these processes. Extracellular histones, released from damaged host cells, bind to cell membranes and cause coagulation activation, platelet aggregation and vascular leak in diverse critical illnesses. In CM patients with P. falciparum, serum histones correlate with fibrin formation, thrombocytopenia, and endothelial activation and predict brain swelling on magnetic resonance imaging and fatal outcome. Post-mortem, histones bind to the luminal vascular surface, co-localizing with P. falciparum-infected erythrocytes (IE), and with thrombosis and leak. Purified P. falciparum histones cause toxicity and barrier disruption in cultured human brain microvascular endothelial cells, as does serum from CM patients, reversed by anti-histone antibodies and non-anticoagulant heparin. These data implicate parasite histones as a key trigger of fatal brain swelling in CM. Neutralizing histones with agents such as non-anticoagulant heparin warrant exploration to prevent brain swelling and improve outcome.

microbiology↗

bioRxiv2019

Quantitative proteomic profiling of tumor-associated vascular endothelial cells in colorectal cancer

SummeryTo investigate the global proteomic profiles of vascular endothelial cells (VECs) in the tumor microenvironment and antiangiogenic therapy for colorectal cancer (CRC), matched pairs of normal (NVECs) and tumor-associated VECs (TVECs) were purified from CRC tissues by laser capture microdissection and subjected to iTRAQ based quantitative proteomics analysis. Here, 216 differentially expressed proteins (DEPs) were identified and performed bioinformatics analysis. Interestingly, these proteins were implicated in epithelial mesenchymal transition (EMT), ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway, angiogenesis and HIF-1 signaling pathway, which may play important roles in CRC angiogenesis. Among these DEPs, Tenascin-C (TNC) was found to upregulated in the TVECs of CRC and be correlate with CRC multistage carcinogenesis and metastasis. Furthermore, the reduction of tumor-derived TNC could attenuate human umbilical vein endothelial cell (HUVEC) proliferation, migration and tube formation through ITGB3/FAK/Akt signaling pathway. Based on the present work, we provided a large-scale proteomic profiling of VECs in CRC with quantitative information, a certain number of potential antiangiogenic targets and a novel vision in the angiogenesis bio-mechanism of CRC. Summery statementWe provided large-scale proteomic profiling of vascular endothelial cells in colorectal cancer with quantitative information, a number of potential antiangiogenic targets and a novel vision in the angiogenesis bio-mechanism of CRC.

cancer biology↗

bioRxiv2019

RPW8/HR Repeats Predict NLR-dependent Hybrid Performance

Hybrid offspring can look very different from their parents, including having greatly increased or decreased fitness. In many plant species, conflicts between divergent elements of the immune system can cause hybrids to express autoimmunity, a generally deleterious syndrome known as hybrid necrosis. We are investigating multiple hybrid necrosis cases in Arabidopsis thaliana that are caused by allele-specific interactions between different variants at two unlinked resistance (R) gene clusters. One is the RESISTANCE TO PERONOSPORA PARASITICA 7 (RPP7) cluster, which encodes an intracellular nucleotide binding site-leucine rich repeat (NLR) immune receptors that confer strain-specific resistance to oomycetes. The other is the RESISTANCE TO POWDERY MILDEW 8 (RPW8)/HOMOLOG OF RPW8 (HR) locus, which encodes atypical resistance proteins that can confer broad-spectrum resistance to filamentous pathogens. There is extensive structural variation in the RPW8/HR cluster, both at the level of gene copy number and at the level of C-terminal protein repeats of unknown function. We demonstrate that the number of RPW8/HR repeats correlate, albeit in a complex manner, with the severity of hybrid necrosis when these alleles are combined with specific RPP7 variants. This observation suggests that gross structural differences, rather than individual amino acid polymorphisms, guide the genetic interaction between RPW8/HR and RPP7 alleles. We discuss these findings in light of the similarity of RPW8/HR proteins with pore-forming toxins, MLKL and HET-S, from mammals and fungi.

genetics↗

bioRxiv2019

The regulatory factor ELF1 triggers a critical wave of transcription in the antiviral response to type I interferon

The transcription of interferon-stimulated genes (ISGs) is classically triggered via activation of the JAK-STAT pathway, and together, ISGs raise a multifaceted antiviral barrier. An increasing body of evidence reports the existence of additional, non-canonical pathways and transcription factors that coordinate ISG expression. Detailed knowledge of how heterogenous mechanisms regulate ISG expression is crucial for the rational design of drugs targeting the type I interferon response. Here, we characterize the first ETS transcription factor family member as a regulator of non-canonical ISG expression: E74-like ETS transcription factor 1 (ELF1). Using high-content microscopy to quantify viral infection over time, we found that ELF1, itself an ISG, inhibits eight diverse RNA and DNA viruses uniquely at multi-cycle replication. ELF1 did not regulate expression of type I or II interferons, and ELF1s antiviral effect was not abolished by the absence of STAT1 or by inhibition of JAK phosphorylation. Accordingly, comparative expression analyses by RNAseq revealed that the ELF1 transcriptional program is distinct from, and delayed with respect to, the immediate interferon response. Finally, knockdown experiments demonstrated that ELF1 is a critical component of the antiviral interferon response in vitro and in vivo. Our findings reveal a previously overlooked mechanism of non-canonical ISG regulation that both amplifies and prolongs the initial interferon response by expressing broadly antiviral restriction factors. AUTHOR SUMMARYOver 60 years after their discovery, we still struggle to understand exactly how interferons inhibit viruses. Our gap in knowledge stems, on one hand, from the sheer number of interferon-stimulated effector genes, of which only few have been characterized in mechanistic detail. On the other hand, our knowledge of interferon-regulated gene transcription is constantly evolving. We know that different regulatory mechanisms greatly influence the quality, magnitude, and timing of interferon-stimulated gene expression, all of which may contribute to the antiviral mechanism of interferons. Deciphering these regulatory mechanisms is indispensable for understanding this critical first line of host defense, and for harnessing the power of interferons in novel antiviral therapies. Here, we report a novel mechanism of interferon-induced gene regulation by an interferon-stimulated gene, which, paradoxically, inhibits viruses in the absence of additional interferon signaling: E74-like ETS transcription factor 1 (ELF1) raises an unusually delayed antiviral program that potently restricts propagation of all viruses tested in our study. Reduced levels of ELF1 significantly diminished interferon-mediated host defenses against influenza A virus in vitro and in vivo, suggesting a critical but previously overlooked role in the type I interferon response. The transcriptional program raised by ELF1 is vast and comprises over 400 potentially antiviral genes, which are almost entirely distinct from those known to be induced by interferon. Taken together, our data provide evidence for a critical secondary wave of antiviral protection that adds both "quality" and "time" to the type I interferon response.

immunology↗

bioRxiv2019

The properties of 5-methyltetrahydrofolate dehydrogenase (MthfD) and its role in the tetrahydrofolate (THF)-dependent dicamba demethylation system in Rhizorhabdus dicambivorans Ndbn-20

The herbicide dicamba is initially degrade via demethylation in Rhizorhabdus dicambivorans Ndbn-20. A gene cluster scaffold 66 containing a THF-dependent dicamba methyltransferase dmt and three THF metabolic-related genes, namely, mthfD, dhc and purU, is responsible for dicamba demethylation in this strain. However, the characteristics and functions of MthfD, Dhc and PurU have not been elucidated. In this study, MthfD was synthesized in Escherichia coli BL21(DE3) and purified as a His6-tagged protein. Purified MthfD was found to be a monomer, and exhibited 5-CH3-THF dehydrogenase activity in vitro. The Kcat and Km for 5-CH3-THF were 0.23 s-1 and 16.48 M, respectively. However, 5,10-CH2-THF reductase activity was not detected for MthfD yet. Gene disruption results showed that mthfD is essential for dicamba degradation, whereas dhc is dispensable. Our studies revealed that MthfD physiologically is a 5-CH3-THF dehydrogenase that catalyzes the irreversible dehydrogenation of 5-CH3-THF to 5,10-CH2-THF in the THF regeneration pathway during dicamba demethylation in R. dicambivorans Ndbn-20.

microbiology↗

bioRxiv2019

Bacterial and Archaeal Communities in Recycling Effluents from a Bauxite Flotation Plant

Recycling effluent has become a bottleneck and an environmental risk associated with the regular production of bauxite via flotation and the sustainable development of the aluminum industry in China. To find a practical direction for biotreatment, the bacterial and archaeal communities in recycling effluents containing concentrate and tailings from bauxite flotation plants were investigated by a metagenomic sequencing method in association with the evaluated geochemical properties. The results showed that Paracoccus, Desulfomicrobium, Exiguobacterium, Tindallia, Ercella and Anoxynatronum were the primary bacterial genera and Methanothrix, Methanobacterium, Nitrososphaera and Methanosarcina were the dominant archaeal genera. Upon combining the microbial diversity and the geochemical properties of the two sample types, the microbial community containing Desulfomicrobium, Paracoccus, Tindallia, Methanobacterium, Methanothrix and Nitrososphaera was better adapted to the biodegradation of flotation collectors, and the microbial community consisting of Paracoccus, Exiguobacterium, Methanothrix and Methanobacterium was more efficient at hydrolyzed polyacrylamide (HPAM) biodegradation. In addition, a large proportion of unclassified OTUs has indicated that recycling effluent is a worthy resource for isolating new strains from the Firmicutes phylum.

microbiology↗

bioRxiv2019

One-time Nitrogen Fertilization Shifts Switchgrass Soil Microbiomes within a Context of Larger Spatial and Temporal Variation

Soil microbiome responses to short-term nitrogen (N) inputs within the context of existing spatio-temporal variability remain uncertain. Here, we examined soil bacterial and fungal communities pre/post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha-1 as NH4NO3) for the first time since planting. Soils were collected at two depths, 0-5 and 5-15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions, and soil metagenomic analysis. Baseline assessment prior to fertilization revealed no pre-existing differences in either bacterial or fungal communities across plots. The one-time N fertilization increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12-22 % of the variation in bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. Thus, variability within the field might override the changes induced by N addition. Continued analyses of these trends over time with fertilization and management are needed to understand whether these transient effects change over time.

ecology↗

bioRxiv2018

A simple new approach to variable selection in regression, with application to genetic fine-mapping

We introduce a simple new approach to variable selection in linear regression, with a particular focus on quantifying uncertainty in which variables should be selected. The approach is based on a new model -- the "Sum of Single Effects" (SuSiE) model -- which comes from writing the sparse vector of regression coefficients as a sum of "single-effect" vectors, each with one non-zero element. We also introduce a corresponding new fitting procedure -- Iterative Bayesian Stepwise Selection (IBSS) -- which is a Bayesian analogue of stepwise selection methods. IBSS shares the computational simplicity and speed of traditional stepwise methods, but instead of selecting a single variable at each step, IBSS computes a distribution on variables that captures uncertainty in which variable to select. We provide a formal justification of this intuitive algorithm by showing that it optimizes a variational approximation to the posterior distribution under the SuSiE model. Further, this approximate posterior distribution naturally yields convenient novel summaries of uncertainty in variable selection, providing a Credible Set of variables for each selection. Our methods are particularly well-suited to settings where variables are highly correlated and detectable effects are sparse, both of which are characteristics of genetic fine-mapping applications. We demonstrate through numerical experiments that our methods outper-form existing methods for this task, and illustrate their application to fine-mapping genetic variants influencing alternative splicing in human cell-lines. We also discuss the potential and challenges for applying these methods to generic variable selection problems.

bioinformatics↗

bioRxiv2018

Osmoregulation in freshwaters: Gene expression in the gills of a Neotropical cichlid in contrasting pH and ionic environments

Freshwater habitats of the Neotropics exhibit a gradient from relatively neutral, ion-rich whitewater to acidic, ion-poor blackwater. Closely related species often show complementary distributions among ionic habitats, suggesting that adaptation to divergent osmoregulatory environments may be an important driver of Neotropical fish diversity. However, little is known about the evolutionary tradeoffs involved in ionoregulation across distinct freshwater environments. Here, we surveyed gill mRNA expression of Cichla ocellaris var. monoculus, a Neotropical cichlid, to examine cellular and physiological responses to experimental conditions mimicking whitewater and blackwater.\n\nGene ontology enrichment of expressed genes indicated that the gills were remodeled during both forms of environmental challenge, with changes biased towards the cellular membrane. We observed expression of signaling pathways from both the acute and extended response phases, including evidence that growth hormone (GH) may mediate osmoregulation in whitewater through paracrine expression of insulin-like growth factor I (IGF-I), but not through the GH receptor, which instead showed correlated up-regulation with the prolactin receptor and insulin-like growth factor II in blackwater.\n\nDifferential expression of genes related to paracellular tight junctions and transcellular ion transport showed responses similar to euryhaline fishes in fresh versus seawater, with some exceptions, suggesting that relaxed ion retention via the gills, possibly mediated by the GH/IGF-I axis, is a strong candidate for evolutionary modification in whitewater and blackwater endemic populations. In each osmoregulatory domain, we saw examples of contrasting differential expression of paralogs of genes that are single copy in most terrestrial vertebrates, indicating that adaption by fishes to diverse physicochemcial environments has capitalized on diversification of osmoregulatory gene families.

ecology↗

bioRxiv2018

A study on the protective effects of CpG ODN-induced mucosal immunity against lung injury in a mouse ARDS model

This study aims to determine the feasibility of using oligodeoxynucleotides with unmethylated cytosine-guanine dinucleotide sequences (CpG ODN) as an immunity protection strategy for a mouse model of acute respiratory distress syndrome (ARDS). This is a prospective laboratory animal investigation. 20-week old BALB/c mice in Animal research laboratory were randomized into groups. An ARDS model was induced in mice using lipopolysaccharides. CpG ODN was intranasally and transrectally immunized before or after the 3rd and 7th day of establishing the ARDS model. Mice were euthanized on day seven after the 2nd immunization. Then, retroorbital bleeding was carried, out and the chest was rapidly opened to collect the trachea and tissues from both lungs for testing. CpG ODN significantly improved the pathologic impairment in mice lung, especially after the intranasal administration of 50 ug. This resulted in the least severe lung tissue injury. Furthermore, IL-6 and IL-8 concentrations were lower, which was second to mice treated with the rectal administration of 20 g CpG ODN. In contrast, the nasal and rectal administration of CpG ODN in BALB/c mice before LPS immunization did not appear to exhibit any significant protective effects. In conclusion, the intranasal administration of CpG ODN may be is a potential treatment approach to ARDS. More studies are needed to further determine the protective mechanism of CpG ODN.

immunology↗

bioRxiv2018

Multiplexed pooled library screening with Cpf1

RNA interference and CRISPR/Cas9-based pooled library screens have revolutionized the field of functional genomics. However, currently available pooled library screens face a trade-off between library effectiveness and library complexity. We developed a multiplexed, high-throughput screening strategy based on an optimized AsCpf1 nuclease that minimizes library size without sacrificing gene targeting efficiency. Our AsCpf1-based multiplexed library performed similarly well compared to currently available CRISPR/Cas9 libraries, but with a single polycistronic crRNA clone targeting each gene. With this strategy, we constructed the smallest whole-genome knock-out library available, \"Mini-human\" for the human genome, which is one-fourth the size of the smallest CRISPR library currently available.

systems biology↗

bioRxiv2018

Structural and Practical Identifiability of Dual-input Kinetic Modeling in Dynamic PET of Liver Inflammation

Dynamic 18F-FDG PET with tracer kinetic modeling has the potential to noninvasively evaluate human liver inflammation using the FDG blood-to-tissue transport rate K1. Accurate kinetic modeling of dynamic liver PET data and K1 quantification requires the knowledge of dual-blood input function from the hepatic artery and portal vein. While the arterial input function can be derived from the aortic region on dynamic PET images, it is difficult to extract the portal vein input function accurately from PET. The optimization-derived dual-input kinetic modeling approach has been proposed to overcome this problem by jointly estimating the portal vein input function and FDG tracer kinetics from time activity curve fitting. In this paper, we further characterize the model properties by analyzing the structural identifiability of the model parameters using the Laplace transform and practical identifiability using Monte Carlo simulation based on fourteen patient datasets. The theoretical analysis has indicated that all the kinetic parameters of the dual-input kinetic model are structurally identifiable, though subject to local solutions. The Monte Carlo simulation results have shown that FDG K1 can be estimated reliably in the whole-liver region of interest with reasonable bias, standard deviation, and high correlation between estimated and original values, indicating of practical identifiability of K1. The result has also demonstrated the correlation between K1 and histological liver inflammation scores is reliable. FDG K1 quantification by the optimization-derived dual-input kinetic model is promising for assessing liver inflammation.

bioengineering↗