Biology subjects

Lu, H.

Publications and source records attributed to Lu, H..

At least 271 records · Page 15Linked to original sources

bioRxiv2020

Novel Functional metabolites that affect biofilm formation are regulated by bioavailable iron with siderophore-dependent pathway

Biofilms are broadly formed by diverse microorganisms under stressful environments and are basically surrounded by an EPS matrix, enabling bacterial cells to confer more resistance to biocides, antibiotics and other invasions than their planktonic counterparts. However, biofilm formation causes problems in various fields, including clinical infections, environmental pollution, agricultural production and industrial contamination. Unfortunately, the mechanism of biofilm formation has not been completely elucidated, and currently, we lack an efficient strategy to tackle these tough problems and destroy biofilms. In the present study, we sought to decipher the mechanism of biofilm formation through the regulation of functional metabolites regulated by iron. By exposing bacterial cells to various concentrations of iron, we found that iron can regulate biofilm formation, and phenotypic changes were obviously dependent on iron concentration. A functional metabolome assay was further implemented to investigate the regulatory mechanism of iron on biofilm formation; we verified that siderophores (linear enterobactin, yersiniabactin, di-glucosylated-salmochelin and HPTT-COOH) mostly account for the transportation of iron into bacterial cells. Then, bioavailable iron was recruited by bacterial cells to direct the biosynthesis and expression of five functional metabolites (L-tryptophan, 5-MTA, spermidine, CMP and L-leucine), which were identified as new effectors that directly regulate biofilm formation. Taken together, this study is the first to identify five new metabolic effectors to efficiently regulate biofilm formation, the biosynthesis and expression of these functional metabolites can be targeted to tackle the challenging problems associated with biofilm formation in different fields.

microbiology↗

bioRxiv2020

Artificial Pinnae for Imitating Spatial Target Localization by the Brown Long-Eared Bat (Plecotus auritus)

Echolocating bats locate a target by echolocation and their performance is related to the shape of the binaural conformation in bats. In this study, we developed an artificial sonar system based on the vertical sound localization characteristics of the brown long-eared bat (Plecotus auritus). First, using the finite element method, we found that the beam of the first side lobe formed by a pinna constructed according to that in the brown long-eared bat shifted in an almost linear manner in the vertical direction as the frequency changed from 30 kHz to 60 kHz. We established a model of the relationship between the time-frequency features of the echo emitted by brown long-eared bats and the spatial direction by using the pre-trained neural network. We also developed a majority vote-based method called sliding window cumulative peak estimation (SWCPE) to optimize the outputs from the neural network. In addition, an L-shaped pinna structure was designed to simultaneously estimate the azimuth and elevation. Our field experiments indicated that the binaural conformation and relative binaural orientation both played vital roles in spatial target localization by these bats. Accurate echolocation can be achieved using a simple binaural sonar device even without binaural time difference information.

animal behavior and cognition↗

bioRxiv2020

SR-B1 uptake of HDL promotes prostate cancer proliferation and tumor progression

High density lipoprotein (HDL) metabolism, in part, is facilitated by scavenger receptor class B, type 1 (SR-B1) that mediates its uptake into cells. SR-B1 is upregulated in prostate cancer tissue. Here, we report that knockout (KO) of SR-B1 via CRISPR/Cas9 editing led to reduced HDL uptake into prostate cancer cells, and reduced their proliferation in response to HDL. In vivo studies using syngeneic SR-B1 wildtype (SR-B1+/+) and SR-B1 KO (SR-B1-/-) prostate cancer cells in WT and apolipoprotein-AI KO (apoA1-KO) C57BL/6J mice showed that WT hosts, containing higher levels of total and HDL-cholesterol, grew larger tumors than apoA1-KO hosts with lower levels of total and HDL-cholesterol. Furthermore, SR-B1-/- prostate cancer cells formed smaller tumors in WT hosts, than SR-B1+/+ cells in same host model. Tumor volume data was overall similar to survival data. We conclude that tumoral SR-B1 KO reduced HDL-mediated increases in prostate cancer cell proliferation and disease progression.

cancer biology↗

bioRxiv2020

Improving multi-site autism classification based on site-dependence minimisation and second-order functional connectivity

Autism spectrum disorder (ASD) has no objective diagnosis method despite having a high prevalence. Machine learning has been widely used to develop classification models for ASD using neuroimaging data. Recently, studies have shifted towards using large multi-site neuroimaging datasets to boost the clinical applicability and statistical power of results. However, the classification performance is hindered by the heterogeneous nature of agglomerative datasets. In this paper, we propose new methods for multi-site autism classification using the Autism Brain Imaging Data Exchange (ABIDE) dataset. We firstly propose a new second-order measure of functional connectivity (FC) named as Tangent Pearson embedding to extract better features for classification. Then we assess the statistical dependence between acquisition sites and FC features, and apply a domain adaptation approach to minimise the site dependence of FC features to improve classification. Our analysis shows that 1) statistical dependence between site and FC features is statistically significant at the 5% level, and 2) extracting second-order features from neuroimaging data and minimising their site dependence can improve over state-of-the-art classification results on the ABIDE dataset, achieving a classification accuracy of 73%.

neuroscience↗

bioRxiv2020

Alterations of human lung and gut microbiome in non-small cell lung carcinomas and distant metastasis

BackgroundNon-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide. Although dysbiosis of lung and gut microbiota have been associated with NSCLC, their relative contributions are unclear; in addition, their roles in distant metastasis (DM) are still illusive. ResultsWe surveyed the fecal and sputum (as a proxy for lung) microbiota in healthy controls and NSCLC patients of various stages, and found significant perturbations of gut- and sputum-microbiota in patients with NSCLC and DM. Machine-learning models combining both microbiota (mixed models) performed better than either dataset in patient stratification, with the highest area under the curve (AUC) value of 0.842. Sputum-microbiota contributed more than the gut in the mixed models; in addition, sputum-only models performed similarly to the mixed models in most cases. Several microbial-biomarkers were shared by both microbiota, indicating their similar roles at distinct body sites. Microbial-biomarkers of distinct disease stages were mostly shared, suggesting biomarkers for distant metastasis could be acquired early. Furthermore, Pseudomonas aeruginosa, a species previously associated with wound infections, was significantly more abundant in brain metastasis, indicating distinct types of DMs could have different microbial-biomarkers. ConclusionOur results indicate that alterations of sputum-microbiota have stronger relationships with NSCLC and distant metastasis than the gut, and strongly support the feasibility of metagenome-based non-invasive disease diagnosis and risk evaluation.

microbiology↗

bioRxiv2019

A portable, low-cost device for precise control of specimen temperature under stereomicroscopes

To facilitate precise and convenient control of biological sample temperature, we developed a low-cost device that can be used independently or with any stereomicroscope. The purpose of the device is to control the thermal environment during experimental intervals in which a specimen must be manipulated outside of an incubator, e.g. for dissection or slide-mounting in preparation for imaging. Sample temperatures can be both cooled to below and heated to above room temperatures, and stably maintained at a precision of +/- 0.1{degrees}C. To demonstrate the utility of this device, we report improved characterization of the penetrance of a short-acting temperature-sensitive allele in C. elegans embryos, and identification of the upper temperature threshold for embryonic viability for six Caenorhabditis species. By controlling the temperature environment even as a specimen is manipulated, this device offers consistency and flexibility, reduces environmental noise, and enables precision timing in experiments requiring temperature shifts.

developmental biology↗

bioRxiv2019

Deficiency of Norepinephrine Transmission In Brain Contributed To Seizure-Induced Respiratory Arrest In the DBA/1 Mouse SUDEP Model

ObjectiveSudden unexpected death in epilepsy (SUDEP) is the leading cause of mortality in patients in patients with intractable epilepsy. However, the pathogenesis of SUDEP seems to be poorly understood. Our previous findings showed that the incidence of seizure-induced respiratory arrest (S-IRA) was markedly reduced by atomoxetine in a murine SUDEP model. Because the central NE -1 receptor (NE-1R) plays a vital role in regulating respiratory function, we hypothesized that the suppression of S-IRA by atomoxetine was mediated by NE/NE-1R interactions that can be reversed by NE-1R antagonism. MethodsWe examined whether atomoxetine-mediated suppression of S-IRA evoked by either acoustic stimulation or pentylenetetrazole (PTZ) in DBA/1 mice can be reversed by intraperitoneal (IP) and intracerebroventricular (ICV) administration of prazosin, a selective antagonist of NE-1R. The content and activity of tyrosine hydroxylase (TH), a rate-limiting enzyme for NE synthesis, in the lower brainstem was measured by ELISA. Electroencephalograms (EEG) were obtained by using the PTZ-evoked SUDEP model. ResultsAtomoxetine-mediated suppression of S-IRA evoked by either acoustic stimulation or PTZ was significantly reversed by low doses of IP and ICV prazosin. Neither repetitive acoustic stimulation nor S-IRA reduced TH levels in lower brainstem. However, the enzyme activity of TH levels in lower brainstem was significantly increased by mechanical ventilation with DBA/1 mice ,which makes dead DBA/1 mice suffered from S-IRA and SUDEP recover. EEG data showed that although the protective effect of atomoxetine was reversed by prazosin, neither drug affected EEG activity. SignificanceThese data suggest that deficient synthesis of NE and norepinephrinergic neurotransmission contributes to S-IRA and that the NE-1R is a potential therapeutic target for the prevention of SUDEP.

neuroscience↗

bioRxiv2019

HeALTH: An Automated Platform for Long-term Longitudinal Studies of Whole Organisms under Precise Environmental Control

Health and longevity in all organisms are strongly influenced by the environment. To fully understand how environmental factors interact with genetic and stochastic factors to modulate the aging process, it is crucial to precisely control environmental conditions for long-term studies. In the commonly used model organism Caenorhabditis elegans, existing assays for healthspan and lifespan have inherent limitations, making it difficult to perform large-scale, longitudinal aging studies under precise environmental control. To address this constraint, we developed the Health and Lifespan Testing Hub (HeALTH), an automated, microfluidic-based system for robust, long-term, longitudinal behavioral monitoring. Our system provides spatiotemporal environmental control. We demonstrate health and lifespan studies under a variety of genetic and environmental perturbations while observing how individuality plays a role in the aging process. This system is generalizable beyond aging research for C. elegans, particularly for short- or long-term behavioral assays, and is also possible to be adapted for other model systems.

animal behavior and cognition↗

bioRxiv2019

Deletion of mouse Setd4 promotes the recovery of hematopoietic failure.

Acquired hematopoietic failure is commonly caused by therapeutic and accidental exposure to toxic agents to the bone marrow (BM). Efficient recovery from the BM failure is not only dictated by the intrinsic sensitivity and proliferation capacity of the hematopoietic stem and progenitor cells, but also nourished by the BM environment niche. Identification of genetic factors that improve the recovery from hematopoietic failure is essential. Vertebrate SETD4 is a poorly characterized, putative non-histone methyl-transferase whose physiological substrates have not yet been fully identified. By inducing Setd4 deletion in adult mice, we found that loss of Setd4 improved the survival of whole body irradiation induced BM failure. This was associated with improved recoveries of long-term and short-term hematopoietic stem cells (HSC), and early progenitor cells. BM transplantation analyses surprisingly showed that the improved recovery was not due to a radiation resistance of the Setd4 deficient HSC, but that Setd4 deficient HSC were actually more sensitive to radiation. However, the Setd4 deficient mice were better recipients for allogeneic HSC transplantation. Furthermore, there was an enhanced splenic erythropoiesis in Setd4 deficient mice. These findings not only revealed a previously unrecognized role of the Setd4 as a unique modulator of hematopoiesis, but also underscored the critical role of the BM niche in the recovery of hematopoietic failure. These studies also implicated Setd4 as a potential target for therapeutic inhibition to improve the conditioning of the BM niche prior to allogeneic transplantation. Key pointsO_LIDeletion of Setd4 in adult mice improved the survival from hematopoietic failure. C_LIO_LISetd4 deficiency sensitized HSCs to radiation, but improved bone marrow environment niche. C_LIO_LIThe study suggests that SETD4 as a potential inhibitory target to improve bone marrow niche function for recovery of bone marrow failure. C_LI

developmental biology↗

bioRxiv2019

microRNA seedless sites attenuate strong-seed-site-mediated target repression

MicroRNAs (miRNAs) regulate protein-coding gene expression primarily through cognitive binding sites in the 3 untranslated regions (3' UTRs). Seed sites are sequences in messenger RNAs (mRNAs) that form perfect Watson-Crick base-paring with a miRNAs seed region, which can effectively reduce mRNA abundance and/or repress protein translation. Some seedless sites, which do no form perfect seed-pairing with a miRNA, can also lead to target repression, often with lower efficacy. Here we report the surprising finding that when seedless sites and seed sites are co-present in the same 3UTR, seedless sites attenuate strong-seed-site-mediated target suppression, independent of 3' UTR length. This attenuation effect is detectable in >70% of transcriptomic datasets examined, in which specific miRNAs are experimentally increased or decreased. The attenuation effect is confirmed by 3UTR reporter assays and mediated through base-pairing between miRNA and seedless sites. Furthermore, this seedless-site-based attenuation effect could affect seed sites of the same miRNA or another miRNA, thus partially explaining the variability in target suppression and miRNA-mediated gene upregulation. Our findings reveal an unexpected principle of miRNA-mediated gene regulation, and could impact the understanding of many miRNA-regulated biological processes.

bioinformatics↗

bioRxiv2019

Use of a glycan library reveals a new model for enteric virus oligosaccharide binding and virion stabilization

Enteric viruses infect the gastrointestinal tract and bacteria can promote replication and transmission of several enteric viruses. Viruses can be inactivated by exposure to heat or bleach, but poliovirus, coxsackievirus B3, and reovirus can be stabilized by bacteria or bacterial polysaccharides, limiting inactivation and aiding transmission. We previously demonstrated that certain N-acetylglucosamine (GlcNAc)-containing polysaccharides can stabilize poliovirus. However, the detailed virus-glycan binding specificity and glycan chain length requirements, and thus the mechanism of virion stabilization, has been unclear. A previous limitation was our lack of defined-length glycans to probe mechanisms and consequences of virus-glycan interactions. Here, we generated a panel of polysaccharides and oligosaccharides to determine the properties required for binding and stabilization of poliovirus. Poliovirus virions are non-enveloped icosahedral 30 nm particles with 60 copies of each of four capsid proteins, VP1-4. VP1 surrounds the fivefold axis and our past work indicates that this region likely contains the glycan binding site. We found that relatively short GlcNAc oligosaccharides, such as a six unit GlcNAc oligomer, can bind poliovirus but fail to enhance virion stability. Virion stabilization required binding of long GlcNAc polymers of greater than 20 units. Our data suggest a model where GlcNAc polymers greater than 20 units bind and bridge adjacent fivefold axes, thus aiding capsid rigidity and stability. This study provides a deeper understanding of enteric virus-bacterial glycan interactions, which is important for virion environmental stability and transmission.\n\nImportanceEnteric viruses are transmitted through the fecal-oral route, but how enteric viruses survive in the environment is unclear. Previously, we found that bacterial polysaccharides enhance poliovirus stability against heat or bleach inactivation, but the specific molecular requirements have been unknown. Here we showed that certain short chain oligosaccharides can bind to poliovirus but do not increase virion stability. Long chain polysaccharides bind and may bridge adjacent sites on the viral surface, thus increasing capsid rigidity and stability. This work defines the unique interactions of poliovirus and glycans, which provides insight into virion environmental stability and transmission.

microbiology↗

bioRxiv2019

Function of ex vivo stimulated Natural killer T cells from patients with chronic HIV-1 infection

Natural killer T (NKT) cells are innate immune cells that are responsible for the first line of antiviral defense, through crosstalk with downstream antigen-presenting cells, natural killer cells, and adaptive immune cells. Previous studies have indicated that NKT cell function is severely impaired in patients with chronic HIV-1 infection. It was reported that alpha-galactosylceramide, a potent agonist antigen for NKT cells, failed to trigger the expansion of NKT cells, or the production of anti-viral cytokines by NKT cells from HIV-1 infected patients in an in vitro assay, in which peripheral blood mononuclear cells (PBMCs) were cultured in the presence of alpha-galactosylceramide. In this study, we stimulated banked peripheral blood mononuclear cells from HIV-1-infected patients with dendritic cells (DC) generated ex vivo and loaded with alpha-galactosylceramide. The results showed that NKT cells were expanded in HIV infected subjects except in patients with advanced AIDS. Expanded NKT cells were capable of producing antiviral cytokines. Our results indicate that NKT cells in HIV infected individuals are potential targets for therapeutic intervention.

immunology↗

bioRxiv2019

A Multicellular Network Mechanism for Temperature-Robust Food Sensing

Responsiveness to external cues is a hallmark of biological systems. In complex environments, organisms must remain responsive to specific inputs even as other internal or external factors fluctuate. Here we show how Caenorhabditis elegans can discriminate between food levels to modulate lifespan despite temperature perturbations. While robustness of fixed outputs has been described, our findings uncover a more complex robustness process that maintains food-responsiveness. This end-to-end robustness from environment to physiology is mediated by food-sensing neurons that communicate via TGF-{beta} and serotonin signals to form a multicellular gene network. Mechanistically, specific regulations in this network change with temperature to maintain similar food-responsiveness in the lifespan output. Together, our findings provide a basis for gene-environment interactions and unveil computations that integrate environmental cues to govern physiology.

systems biology↗

bioRxiv2019

The role of swnR gene on the biosynthesis pathway of the swainsonine in Metarhizium anisopliae

Swainsonine (SW) is the principal toxic ingredient of locoweeds, and is produced by fungi including Metarhizium anisopliae, Slafractonia leguminicola, and Alternaria oxytropis. Studies of the SW biosynthesis pathway in these fungi have demonstrated the requirement for a swnK gene and the presence of a variety of other SWN cluster genes, but have not determined a precise role for the swnR gene, which encodes a NADB Rossmann-fold reductase, nor if it is necessary for the biosynthesis of SW. In this study, we used homologous recombination (HR) to knock out the swnR gene of M. anisopliae to determine its effect on the SW biosynthesis pathway. The concentration of SW was measured in the fermentation broth of M. anisopliae at 1 d, 3 d, 5 d and 7 d using a Q Exactive Mass Spectrometer. The gene for swnR was detected by RT-qPCR. To determine the role of the swnR gene in the SW biosynthesis pathway of M. anisopliae, we used PEG-mediated homologous recombination (HR) to transform a wild-type strain (WT) with a Benomyl (ben)-resistant fragment to knock out the swnR gene producing a mutant-type strain (MT). A complemented-type (CT) strain was produced by adding a complementation vector that contains the glufosinate (herbicide) resistance (bar) gene as a marker. The content of SW decreased, but was not eliminated in the fermentation broth of the MT strain, and returned to the original level in the CT strain. These results indicate that the swnR gene plays a crucial role in the SW biosynthesis pathway of M. anisopliae, but suggests that another gene in the fungus may share the function of swnR.

molecular biology↗

bioRxiv2019

Upon microbial challenge human neutrophils undergo rapid changes in nuclear architecture to orchestrate an immediate inflammatory gene program

Differentiating neutrophils undergo large-scale changes in nuclear morphology. How such alterations in structure are established and modulated upon exposure to microbial agents is largely unknown. Here, we found that prior to encounter with bacteria, an armamentarium of inflammatory genes was positioned in a transcriptionally passive environment suppressing premature transcriptional activation. Upon microbial exposure, however, human neutrophils rapidly (<3 hours) repositioned the ensemble of pro-inflammatory genes towards the transcriptionally permissive compartment. We show that the repositioning of genes was closely associated with the swift recruitment of cohesin across the inflammatory enhancer landscape permitting an immediate transcriptional response upon bacterial exposure. These data reveal at the mechanistic level how upon microbial challenge human neutrophils undergo rapid changes in nuclear architecture to orchestrate an immediate inflammatory gene program.

genomics↗

bioRxiv2019

Single cell map of the human ovarian cortex.

The human ovary orchestrates sex hormone production and undergoes monthly structural changes to release mature oocytes. The outer lining of the ovary (cortex) has a key role in defining fertility in women as it harbors the ovarian reserve. It has been postulated that putative oogonial stem cells exist in the ovarian cortex and that these can be captured by DDX4 antibody isolation. We analysed on a single cell level the transcriptome and cell surface antigen profiles of over 24,000 cells from high quality ovarian cortex samples from 21 patients. Our single cell mapping reveals transcriptional profiles of six main cell types; oocytes, granulosa cells, immune cells, endothelial cells, perivascular cells, and stromal cells. Cells captured by DDX4 antibody are perivascular cells, not oogonial stem cells. Our data does not support the existence of germline stem cells in adult human ovaries thereby reinforcing the dogma of a limited ovarian reserve.

cell biology↗

bioRxiv2019

MeCP2 deletion impaired layer 2/3-dominant dynamic reorganization of cortical circuit during motor skill learning

Rett Syndrome (RTT) is a severe neurodevelopmental disorder caused by loss of function of the X-linked Methyl-CpG-binding protein 2 (MECP2). Several case studies report that gross motor function can be improved in children with RTT through treadmill walking, but whether the MeCP2-deficient motor circuit can support actual motor learning remains unclear. We used two-photon calcium imaging to simultaneously observe layer (L) 2/3 and L5a excitatory neuronal activity in the motor cortex (M1) while mice adapted to changing speeds on a computerized running wheel. Despite circuit hypoactivity and weakened functional connectivity across L2/3 and L5a, the Mecp2-null circuits firing pattern evolved with improved performance over two weeks. Moreover, trained mice became less anxious and lived 20% longer than untrained mice. Since motor deficits and anxiety are core symptoms of Rett, which is not diagnosed until well after symptom onset, these results underscore the benefit of motor learning.

neuroscience↗

bioRxiv2019

Angle-tuned Coil: A Focal Spot-size Adjustable Transcranial Magnetic Stimulator

BackgroundConventional transcranial magnetic stimulation (TMS) coils are limited by the depth-focality tradeoff rule and the emission field intensity from coils with either small or large apertures will diverge quickly at less than one aperture diameter distance away from the coil. To utilize a better depth-focality tradeoff rule and accomplish deep and focused stimulation, a new approach needs to be employed.\n\nObjectivesWe report a new TMS coil design that can deliver deep and spot size adjustable stimulation to deep brain regions.\n\nMethodsIn our design, we introduce a magnetic core at the center of a coil to help confine the magnetic field and prevent leakage. We further tilted the wire wrapping angle of the coil to break its ring symmetry and accomplish tunable focusing by adjusting the tilting angle.\n\nResultsBy comparing the electric field decay curves of five types of coils, our results concluded the proposed novel method to improve the coils depth-focality profile. Both theoretical calculations and experimental data collectively demonstrated that by using a larger tilting angle, we were able to accomplish a more tightly focused stimulation at any distance away from the coil.\n\nConclusionEnlarging the tilting angle of the coil wire wrapping and applying magnetic core significantly improved the spatial resolution of the field without inducing considerable effect on field decay speed. Our novel TMS coil design plots a new curve in the depth-focality profile with better performance than the existing conventional coil designs in the tradeoff rule.

bioengineering↗