Biology subjects

Wu, X.

Publications and source records attributed to Wu, X..

At least 505 records · Page 28Linked to original sources

bioRxiv2021

Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7

Three prevalent SARS-CoV-2 Variants of Concern (VOCs) were emerged and caused epidemic waves. It is essential to uncover the key genetic changes that cause the high transmissibility of VOCs. However, different viral mutations are generally tightly linked so traditional population genetic methods may not reliably detect beneficial mutation. In this study, we proposed a new pandemic-scale phylogenomic approach to detect mutations crucial to transmissibility. We analyzed 3,646,973 high-quality SARS-CoV-2 genomic sequences and the epidemiology metadata. Based on the sequential occurrence order of mutations and the instantaneously accelerated furcation rate, the analysis revealed that two non-coding mutations at the position of 28271 (g.a28271-/t) might be crucial for the high transmissibility of Alpha, Delta and Omicron VOCs. Both two mutations cause an A-to-T change at the core Kozak site of the N gene. The analysis also revealed that the non-coding mutations (g.a28271-/t) alone are unlikely to cause high viral transmissibility, indicating epistasis or multilocus interaction in viral transmissibility. A convergent evolutionary analysis revealed that g.a28271-/t, S:P681H/R and N:R203K/M occur independently in the three-VOC lineages, suggesting a potential interaction among these mutations. Therefore, this study unveils that non-synonymous and non-coding mutations could affect the transmissibility synergistically.

evolutionary biology↗

bioRxiv2021

The cortical hubs related to recovery of consciousness

Background and ObjectivesThe neural mechanism that enables the recovery of consciousness in patients with unresponsive wakefulness syndrome (UWS) remains unclear. The aim of the current study is to characterize the cortical hub regions related to the recovery of consciousness in patients with UWS. MethodsVoxel-wise degree centrality analysis was adopted to identify the cortical hubs related to the recovery of consciousness, for which a total of 27 UWS patients were used, including 13 patients who emerged from UWS (UWS-E), and 14 patients who remained in UWS (UWS-R) at least three months after the experiment performance. Furthermore, other recoverable unconscious states including three independent deep sleep datasets (n = 12, 9, 9 respectively) and three independent anesthesia datasets (n = 27, 14, 6 respectively) were adopted as validation groups. Spatial similarity of the hub characteristic with the validation groups between the UWS-E and UWS-R was compared using the dice coefficient. Finally, with the cortical regions persistently shown as hubs across UWS-E and validation states, functional connectivity analysis was further performed to explore the connectivity patterns underlying the recovery of consciousness. ResultsFour cortical hubs were identified with significantly higher degree centrality for UWS-E than UWS-R, including the anterior precuneus, left inferior parietal lobule, left inferior frontal gyrus, and left middle frontal gyrus, of which the degree centrality value also positively correlated with the patients Glasgow Outcome Scale (GOS) score. Furthermore, the anterior precuneus was found to show significantly higher similarity of hub characteristics as well as functional connectivity pattern between UWS-E and validation groups, compared with UWS-R. DiscussionThe results suggest that the recovery of consciousness may be relevant to the integrity of cortical hubs, especially the anterior precuneus. The identified cortical hub regions could serve as potential targets for noninvasive stimulation aimed at promoting the patients consciousness recovery.

neuroscience↗

bioRxiv2021

Caerin 1.1 and 1.9 peptides from Australian tree frog inhibit antibiotic-resistant bacteria growth in a murine skin infection model

Host-defence caerin 1.9 peptide was originally isolated from skin secretion of Australian tree frog, and inhibits the growth of a wide range of bacteria in vitro. In this study, we demonstrated that caerin 1.9 shows high bioactivity against several bacteria strains, such as Staphylococcus aureus, Acinetobacter Baumannii, methicillin-resistant Staphylococcus aureus (MRSA), and Streptococcus hemolyiicus in vitro. Importantly, unlike antibiotic Tazocin, caerin 1.9 does not induce bacterial resistance after 30 rounds of in vitro culture. Moreover, caerin 1.1, another peptide of caerin family, has additive antibacterial effect when used together with caerin 1.9. Furthermore, caerin 1.1 and 1.9 prepared in the form of a temperature sensitive gel inhibit MRSA growth in skin bacterial infection model of two murine strains. These results indicate that caerin 1.1 and 1.9 may have the advantage than conventional antibiotics against bacterial infection of skin.

microbiology↗

bioRxiv2021

Post-encoding reactivation promotes one-shot learning of episodes in humans

Prior animal and human work have shown that post-encoding reinstatement plays an important role in organizing the temporal sequence of unfolding episodes in memory. Here, we investigated whether post-encoding reinstatement serves to promote the encoding of one-shot episodic learning beyond the temporal structure in humans. In experiment 1, participants encoded sequences of pictures depicting unique and meaningful episodic-like events. We used representational similarity analysis on scalp electroencephalography recordings during encoding and found evidence of rapid picture elicited EEG patterns reinstatement at episodic offset (around 500ms post-episode). Memory reinstatement was not observed between successive elements within an episode and the degree of memory reinstatement at episodic offset predicted later recall for that episode. In experiment 2, participants encoded a shuffled version of the picture sequences from experiment 1, rendering each episode meaningless to the participant but temporally structured as in experiment 1, and we found no evidence of memory reinstatement at episodic offset. These results suggest that post-encoding memory reinstatement is akin to the rapid formation of unique and meaningful episodes that unfold over time.

neuroscience↗

bioRxiv2021

Twelve-month specific IgG response to SARS-CoV-2 receptor-binding domain among COVID-19 convalescent plasma donors in Wuhan

To investigate the duration of humoral immune response in convalescent coronavirus disease 2019 (COVID-19) patients, we conduct a 12-month longitudinal study through collecting a total of 1,782 plasma samples from 869 convalescent plasma donors in Wuhan, China and test specific antibody responses. The results show that positive rate of IgG antibody against receptor-binding domain of spike protein (RBD-IgG) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the COVID-19 convalescent plasma donors exceeded 70% for 12 months post diagnosis. The level of RBD-IgG decreases with time, with the titer stabilizing at 64.3% of the initial level by the 9th month. Moreover, male plasma donors produce more RBD-IgG than female, and age of the patients positively correlates with the RBD-IgG titer. A strong positive correlation between RBD-IgG and neutralizing antibody titers is also identified. These results facilitate our understanding of SARS-CoV-2-induced immune memory to promote vaccine and therapy development.

immunology↗

bioRxiv2021

Integrin α6 upregulation in nucleus pulposus cell under high oxygen tension attenuates intervertebral disc degeneration

The destruction of low oxygen microenvironment played critical roles in the pathogenesis of intervertebral disk degeneration (IVDD). In this study, high oxygen tension (HOT) treatment upregulated integrin 6(ITG 6) expression, which could be alleviated by blocking PI3K/AKT signaling pathway. And the levels of ITG 6 expression were increased in the NP tissue from IVDD patients and IVDD rat model with mild degeneration, which were reduced as degeneration degree increases. Further studies found that ITG 6 could protect NP cells against HOT-induced apoptosis and oxidative stress, and protect NP cells from HOT-inhibited ECM proteins synthesis. ITG 6 upregulation by HOT contributed to maintain a NP tissue homeostasis through the interaction with hypoxia inducible factor-1 (HIF-1). Furthermore, silencing of ITG 6 in vivo could obviously accelerate puncture-induced IVDD. Taken together, ITG 6 upregulation by HOT in NP cells might be a protective factor in IVDD as well as restore NP cell function.

cell biology↗

bioRxiv2021

A multiepitope fusion protein-based p-ELISA method for diagnosing bovine and goat brucellosis

In recent years, the incidence of brucellosis has increased annually, which has caused tremendous economic losses in agriculture and husbandry in various countries. Therefore, developing rapid, sensitive and specific diagnostic techniques for brucellosis has become critical brucellosis research. Bioinformatics technology was used to predict the B cell epitopes of the main antigen proteins of Brucella, and the validity of each epitope was verified by indirect enzyme-linked immunosorbent assay (iELISA). The verified epitopes were connected in series to construct a multiepitope fusion protein, goat, bovine brucellosis sera, and rabbit sera were collected to verify the antigenicity and specificity of this protein. Then, the fusion protein was used as a diagnostic antigen to construct paper-based ELISA (p-ELISA) technology. A total of 22 effective epitopes were predicted, and a fusion protein was successfully constructed, which showed good antigenicity and specificity. The constructed p-ELISA method was used for the simultaneous detection of bovine and goat brucellosis. ROC curve analysis showed that the sensitivity and specificity of protein detection in goat serum were 98.85% and 98.51%, respectively. The positive and the negative predictive value was 99.29% and 98.15%, respectively. When assessing bovine serum, the sensitivity and specificity were 97.85% and 96.61%, respectively. The positive and the negative predictive value was 98.28% and 97.33%, respectively. This study combined bioinformatics, fusion protein development and p-ELISA technologies to establish a sensitive and specific rapid diagnosis technology for brucellosis that can be used to assess the serum of bovine, goats and other livestock. IMPORTANCEBrucellosis has caused tremendous economic losses in agriculture and husbandry in various countries. Therefore, developing rapid, sensitive and specific diagnostic techniques for brucellosis has become critical brucellosis research. In this study, we used immunoinformatic technology to predict the B cell epitopes in the major outer membrane proteins of Brucella, synthesized polypeptides and coupled them with KLH, screened these polypeptides by iELISA methods, selected effective polypeptides as diagnostic antigens, and established a p-ELISA for brucellosis diagnosis based on a multiepitope fusion protein that can be used to assess the serum of bovine, goats and other livestock.

microbiology↗

bioRxiv2021

State-Transition Analysis of Time-Sequential microRNA Expression Predicts Development of Acute Myeloid Leukemia

MicroRNAs (miRNAs) are small non-coding RNA molecules involved in post-transcriptional regulation of gene expression and have been shown to hold prognostic value in a variety of settings, including acute myeloid leukemia (AML). However, the temporal dynamics of miRNA expression profiles as it relates to AML initiation and progression is poorly understood. Using serial samples from a mouse model of AML, we show that the miRNA transcriptome undergoes state-transition during AML initiation and progression. The AML state-transition was visualized and modeled by constructing an AML state-space from singular value decomposition of the time-series miRNA sequencing data. Within the AML state-space, we identified critical points of AML development characterized by unique differentially expressed miRNAs compared to healthy controls at critical points of leukemogenesis (early, transition, and late). Interestingly, we observed that changes in miRNA expression during leukemogenesis followed two patterns: 1) a monotonic pattern with continuously increasing or decreasing expression; and 2) a non-monotonic pattern with a local maximum or minimum at the transition critical point which was the "point of no-return" from health to AML. We validated the AML state-space and dynamics in an independent cohort of mice and demonstrated the state-transition model accurately predicted time to AML. Of note, we show that the miRNA-derived state-transition model produced a state-space and critical points that were strikingly similar, but not identical to that produced by the coding (i.e., messenger [m]RNA-based) transcriptome. This indicates that while both miRNA and mRNA expression may provide similar information, they also capture independent features of AML state-transition. SignificanceWe show that the microRNA transcriptome undergoes a global state transition during the initiation and progression of acute myeloid leukemia, and accurately predicts time to disease development.

cancer biology↗

bioRxiv2021

Extracellular vesicles mediate the intercellular exchange of nanoparticles

In order to exert their therapeutic effects, nanoparticles (NPs) often need to travel into the tissues composed of multilayered cells. Accumulative evidence has revealed the crucial role of transcellular transport route (entry into one cell, exocytosis, and re-entry into another) in this process. While NP endocytosis and subcellular transport have been intensively characterized, the exocytosis and re-entry steps are poorly understood, which becomes a barrier to improve NP delivery into complex tissues. Here, we termed the exocytosis and re-entry steps together as intercellular exchange. We developed a collagen-based 3D assay to specifically monitor and quantify the intercellular exchange events of NPs, and distinguish the contributions of several potential mechanisms. Our results showed that NPs can be exocytosed freely or enclosed inside extracellular vesicles (EVs) for re-entry, while direct cell-cell contact is hardly involved. EVs account for a significant fraction of NP intercellular exchange, and its importance in NP transport was demonstrated in vitro and in vivo. Intriguingly, while freely released NPs engage with the same cellular receptors for re-entry, EV-enclosed ones bypass this dependence. These studies provide an easy and precise system to investigate the intercellular exchange stage of NP delivery, and shed the first light in the importance of EVs in NP transport between cells and across complex tissues.

pharmacology and toxicology↗

bioRxiv2021

Increased complement activation is a distinctive feature of severe SARS-CoV-2 infection.

Complement activation has been implicated in the pathogenesis of severe SARS-CoV-2 infection. However, it remains to be determined whether increased complement activation is a broad indicator of critical illness (and thus, no different in COVID-19). It is also unclear which pathways are contributing to complement activation in COVID-19, and, if complement activation is associated with certain features of severe SARS-CoV-2 infection, such as endothelial injury and hypercoagulability. To address these questions, we investigated complement activation in the plasma from patients with COVID-19 prospectively enrolled at two tertiary care centers. We compared our patients to two non-COVID cohorts: (a) patients hospitalized with influenza, and (b) patients admitted to the intensive care unit (ICU) with acute respiratory failure requiring invasive mechanical ventilation (IMV). We demonstrate that circulating markers of complement activation (i.e., sC5b-9) are elevated in patients with COVID-19 compared to those with influenza and to patients with non-COVID-19 respiratory failure. Further, the results facilitate distinguishing those who are at higher risk of worse outcomes such as requiring ICU admission, or IMV. Moreover, the results indicate enhanced activation of the alternative complement pathway is most prevalent in patients with severe COVID-19 and is associated with markers of endothelial injury (i.e., Ang2) as well as hypercoagulability (i.e., thrombomodulin and von Willebrand factor). Our findings identify complement activation to be a distinctive feature of COVID-19, and provide specific targets that may be utilized for risk prognostication, drug discovery and personalized clinical trials. SUMMMARYComplement has been implicated in COVID-19. However, whether this is distinctive of COVID-19 remains unanswered. Ma et al report increased complement activation in COVID-19 compared to influenza and non-COVID respiratory failure, and demonstrate alternative pathway activation as a key marker of multiorgan failure and death.

immunology↗

bioRxiv2021

Single Unit Analysis and Wide-Field Imaging Reveal Alterations in Excitatory andInhibitory Neurons in Glioma

Several studies have attributed the development of tumor-associated seizures to an excitatory-inhibitory imbalance, highlighting the importance of resolving the spatiotemporal interplay of different neuronal populations within the peritumoral microenvironment. We combined methods for microelectrode array recordings and single unit analysis during ictal events with wide-field optical mapping of pyramidal neurons in an ex vivo acute slice model of diffusely infiltrating glioma in Thy1-GCaMP6f mice. This approach allowed for characterization of excitatory and inhibitory populations across an extended peritumoral cortical region. As expected, measures of excitability were increased in tumor-bearing slices compared to control. This was accompanied by marked functional alterations in single units classified as fast-spiking interneurons, including reduced firing, altered timing with respect to excitatory firing, and deficits in surround inhibition. Inhibiting mTOR with AZD8055 reversed these glioma-induced changes to excitatory and inhibitory neuronal populations, suggesting a prominent role for functional mechanisms linked to mTOR activation.

cancer biology↗

bioRxiv2021

Competitive coordination of the dual roles of the Hedgehog co-receptor in homophilic adhesion and signal reception

Hedgehog (Hh) signaling patterns embryonic tissues and contributes to homeostasis in adults. In Drosophila, Hh transport and signaling are thought to occur along a specialized class of actin-rich filopodia, termed cytonemes. Here, we report that Interference hedgehog (Ihog) not only forms a Hh receptor complex with Patched to mediate intracellular signaling, but Ihog also engages in trans-homophilic binding leading to cytoneme stabilization in a manner independent of its role as the Hh receptor. Both functions of Ihog (trans-homophilic binding for cytoneme stabilization and Hh binding for ligand sensing) involve a region of the first fibronectin repeat of the extracellular domain. Thus, the Ihog-Ihog interaction and the Hh-Ihog interaction cannot occur simultaneously for a single Ihog molecule. By combining experimental data and mathematical modeling, we determined that Hh-Ihog heterophilic interaction dominates and Hh can disrupt and displace Ihog molecules involved in trans-homophilic binding. Consequently, we proposed that the weaker Ihog-Ihog trans interaction promotes and stabilizes direct membrane contacts along cytonemes and that, as the cytoneme encounters secreted Hh ligands, the ligands trigger release of Ihog from trans Ihog-Ihog complex enabling transport or internalization of the Hh ligand-Ihog-Patched -receptor complex. Thus, the seemingly incompatible functions of Ihog in homophilic adhesion and ligand binding cooperate to assist Hh transport and reception along the cytonemes. One-sentence summaryApparently incompatible functions of Ihog in homophilic adhesion and ligand binding cooperate in Hh transport and reception.

bioinformatics↗

bioRxiv2021

Molecular epidemiology of human respiratory syncytial virus with severe acute respiratory infection in Huzhou from 2016 to 2019

BackgroundHuman respiratory syncytial virus (HRSV) is one of the major cause of acute lower respiratory infection in infants, the elderly and people with low immunity worldwide. Based on antigenic and genetic variations, Human respiratory syncytial virus is divided into two subgroups (A and B). Each of the subgroups is further categorized into genotypes based on the phylogenetic analyses of the sequences of the second hypervariable region. MethodsNasopharyngeal swabs (NPSs) were collected from patients of the First Peoples Hospital in Huzhou from January 2016 to December 2019. Real-time RT-PCR (qPCR) was performed using double nucleic acid detection kit for respiratory syncytial virus (A\B) (Shenzhen shengkeyuan) with the ABI Q7 (Applied Biosystems). For genotyping, the primer set A-F/A-R was used to amplify the G protein of HRSV-A. Primer set B-F/B-R was used to amplify the G protein of HRSV-B. The phylogenetic analysis was constructed using the neighbor-joining algorithm with the Kimura two-parameter model and supported statistically by bootstrapping with 1000 replicates with MEGA software (version 7.0) with 1000 bootstrap replicates. ResultsA total of 973 nasopharyngeal swab samples were collected from January 2016 to December 2019, and 63 samples were positive for RSV nucleic acid, with the detection rate of 6.47%. Of the positive specimens, 28 were belonged to HRSV-A, and 35 were belonged to HRSV-B. Infection with RSV was found in all age groups tested, with the 0-1 year age group having the highest detection rate 15.2%. The detection rate was high from November to next March. Phylogenetic analysis clustered HRSV-A strains identified in Huzhou into ON1genotype. All 17 of the HRSV-B strains belonged to BA9 genotype. ConclusionsWe analyzed the HRSV strains circulation in Huzhou from January 2016 to December 2019 in Huzhou, China. This is the first molecular analysis on HRSV in Huzhou. We found Subgroup A and B of RSV were co-circulating and the 0-1 year age group having the highest infection rate.

molecular biology↗

bioRxiv2021

A potent bispecific nanobody protects hACE2 mice against SARS-CoV-2 infection via intranasal administration

The dramatically expanding COVID-19 needs multiple effective countermeasures. Neutralizing antibodies are a potential therapeutic strategy for treating COVID-19. A number of neutralizing nanobodies (Nbs) were reported for their in vitro activities. However, in vivo protection of these nanobodies was not reported in animal models. In the current report, we characterized several RBD-specific Nbs isolated from a screen of an Nb library derived from an alpaca immunized with SARS-CoV-2 spike glycoprotein (S); among them, three Nbs exhibited picomolar potency against SARS-CoV-2 live virus, pseudotyped viruses, and 15 circulating SARS-CoV-2 variants. To improve the efficacy, various configurations of Nbs were engineered. Nb15-NbH-Nb15, a novel trimer constituted of three Nbs, was constructed to be bispecific for human serum albumin (HSA) and RBD of SARS-CoV-2. Nb15-NbH-Nb15 exhibited sub-ng/ml neutralization potency against the wild-type and currently circulating variants of SARS-CoV-2 with a long half-life in vivo. In addition, we showed that intranasal administration of Nb15-NbH-Nb15 provided 100% protection for both prophylactic and therapeutic purposes against SARS-CoV-2 infection in transgenic hACE2 mice. Nb15-NbH-Nb15 is a potential candidate for both prevention and treatment of SARS-CoV-2 through respiratory administration. One sentence summaryNb15-NbH-Nb15, with a novel heterotrimeric bispecific configuration, exhibited potent and broad neutralization potency against SARS-CoV-2 in vitro and provided in vivo protection against SARS-CoV-2 infection in hACE2 transgenic mice via intranasal delivery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/429275v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@a30bc8org.highwire.dtl.DTLVardef@5a872eorg.highwire.dtl.DTLVardef@1610f74org.highwire.dtl.DTLVardef@13d9bd8_HPS_FORMAT_FIGEXP M_FIG Graphical abstract: C_FIG HighlightsO_LIWe described a novel heterotrimeric configuration of Nb-NbH-Nb (Nb15-NbH-Nb15) that exhibited improved viral inhibition and stability. C_LIO_LINb15-NbH-Nb15 provides ultrahigh neutralization potency against SARS-CoV-2 wild type and 18 mutant variants, including the current circulating variants of D614G and N501Y predominantly in the UK and South Africa. C_LIO_LIIt is the first to demonstrate the Nbs efficacy in preventing and treating SARS-CoV-2 infection in hACE2 transgenic mice via intranasal delivery. C_LI

microbiology↗

bioRxiv2021

Synergistic Therapy of Doxorubicin with Cationic Anticancer Peptide L-K6 Reverses Multidrug Resistance in Cancer Cells in vitro via P-glycoprotein Inhibition

Multidrug resistance (MDR) is one of the major obstacles to efficient chemotherapy against cancers, resulting from the overexpression of drug efflux transporters such as P-glycoprotein (P-gP). In the present study, we aimed to evaluate the MDR reversal activity and synergistic therapeutic potential of cationic anticancer peptide L-K6 with doxorubicin (DOX) on P-gP-overexpressing and DOX-resistant MCF-7/Adr human breast cancer cells. Flow cytometry and confocal laser scanning microscopy were used to determine the intracellular accumulation of DOX and another P-gP substrate, Rho123. P-gP-Glo assay, Western blot and Biacore analysis were further performed to evaluate the P-gP function and expression. The cytotoxicity in MCF-7 or MCF-7/Adr cells was measured by MTT assay. Flow cytometry assay and confocal laser scanning microscopy observation clearly revealed an increased intracellular accumulation of DOX and Rho123 in MCF-7/Adr cells treated with L-K6, suggesting a P-gP inhibiting potential. Biacore analysis, P-gP-Glo assay and Western blot further confirmed that L-K6 could directly interact with P-gP, inhibit P-gP function and decrease P-gP expression in MCF-7/Adr cells. In addition, as expected, the data from MTT assay indicated that L-K6 restored the sensitivity of MCF-7/Adr cells to DOX, indicating a MDR reversal potential and a promising synergistic anticancer activity. All these findings may provide experimental evidence to support the promising applications and synergistic therapeutic potential of peptidic P-gP inhibitors against MDR cancer.

pharmacology and toxicology↗

bioRxiv2021

Knockdown of Dnmt1 links Gene body DNA methylation to regulation of gene expression and maternal-zygotic transition in the wasp Nasonia

Gene body methylation (GBM) is an ancestral aspect of DNA methylation (Sarda, Zeng, Hunt, & Yi, 2012; Yi, 2012; Zemach, McDaniel, Silva, & Zilberman, 2010) whose role in development has been obscured by the more prominent roles of promoter and CpG island methylation. The wasp Nasonia has little promoter and CpG island methylation, yet retains strong GBM (Park et al., 2011; Wang et al., 2013; Werren et al., 2010), making it an excellent model for elucidating the role of GBM. Here we show that Nasonia DNA methyl transferase 1a (Nv-Dnmt1a) knockdown leads to failures in cellularization and gastrulation of the embryo. Both of these disrupted events are hallmarks of the maternal-zygotic transition (MZT) in insects. Analysis of the embryonic transcriptome and methylome revealed strong reduction of GBM and widespread disruption of gene expression during embryogenesis after Nv-Dnmt1a knockdown. There was a strong correlation between loss of GBM and reduced gene expression in thousands of methylated loci, while affected unmethylated genes tended to be upregulated. We propose that reduced GBM and subsequent lower expression levels of methylated genes was the direct effect of Nv-Dnmt1 knockdown, and that this disruption led to widespread downstream dysregulation of MZT, and manifesting in developmental failure at gastrulation. Significance StatementThe importance of gene-body methylation (GBM) in development is unclear, due to the difficulty in teasing apart the effects of cis-regulatory methylation from those of GBM in vertebrate model systems. Unlike vertebrate models, the methylation machinery in the jewel wasp Nasonia vitripennis appears to exclusively mediate GBM, thus simplifying interpretation of the role of GBM in development. Knockdown of DNMT1 (Nv-Dnmt1a) in Nasonia leads to embryonic lethality, which we show is caused by a failure of cellularization and gastrulation. Nv-Dnmt1a knockdown resulted in a global loss of GBM in the embryo, which was strongly correlated with a down-regulation of gene expression. We propose that GBM facilitated by Nv-Dnmt1a is required for proper zygotic genome activation in the wasp.

genomics↗

bioRxiv2021

Differential regulation of progranulin derived granulin peptides

Haploinsufficiency of progranulin (PGRN) is a leading cause of frontotemporal lobar degeneration (FTLD). PGRN is comprised of 7.5 granulin repeats and is processed into individual granulin peptides in the lysosome. However, very little is known about the levels and regulations of individual granulin peptides due to the lack of specific antibodies. Here we report the generation and characterization of antibodies specific to each granulin peptide. We found that the levels of granulins C, E and F are differentially regulated compared to granulins A and B. Furthermore, we demonstrated that granulin B, C and E are heavily glycosylated and the glycosylation pattern of granulin C varies in different physiological and pathological conditions. Deficiency of lysosomal proteases leads to alterations in the levels of a specific subset of granulins. These data support that the levels of individual granulin peptides are differentially regulated under physiological and pathological conditions and provide novel insights into how granulin peptides function in the lysosome.

neuroscience↗

bioRxiv2021

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy.

We probed a transcriptomic dataset of pilocarpine-induced TLE using various ontological, machine-learning, and systems-biology approaches. We showed that, underneath the complex and penetrant changes, moderate-to-subtle upregulated homeostatic and downregulated synaptic changes associated with the dentate gyrus and hippocampal subfields could not only predict TLE but various other forms of epilepsy. At the cellular level, pyramidal neurons and interneurons showed disparate changes, whereas the proportion of non-neuronal cells increased steadily. A probabilistic Bayesian network demonstrated an aberrant and oscillating physiological interaction between oligodendrocytes and interneurons in driving seizures. Validating the Bayesian inference, we showed that the cell types driving the seizures were associated with known antiepileptic and epileptic drugs. These findings provide predictive biomarkers of epilepsy, insights into the cellular connections and causal changes associated with TLE and a drug discovery method focusing on these events.

systems biology↗