Biology subjects

Lu, L.

Publications and source records attributed to Lu, L..

At least 127 records · Page 7Linked to original sources

bioRxiv2023

The novel roles of bovine milk-derived exosomes on skin anti-aging

Exosomes are small vesicles released from cells and present in various mammal biological fluids, such as bovine milk, which worked for skin care for many years besides dairy. In addition, Exosomes were regarded as a vehicle for intercellular communication. Therefore, we aimed to investigate the novel roles of bovine milk-derived exosomes (MK-Exo) on human skin anti-aging. Purified MK-Exo can be directly uptake by the keratinocytes and fibroblast in vitro and upregulate the expression of the natural factors related to skin moisturizing, including Filaggrin (FLG), Aquaporin 3 (AQP3), CD44 in the keratinocytes and hyaluronidase (HAS2) in the fibroblast, and MK-Exo promoted the cell migration of the fibroblast, while rescue its expression of type I collagen (Col I), type III collagen (Col III) after ultraviolet radiation. Furthermore, the phototoxicity test, photoallergy test, repeated skin irritation test, skin allergy test, and patch test confirm the safety of MK-Exo on the skin. Finally, the roles of MK-Exo in preserving moisture and anti-wrinkle were also identified in humans. Then, MK-Exo was smeared on the facial skin of 31 female volunteers twice a day for 28 days, and the functions were evaluated following the safety assessment in vivo. These studies reveal the novel roles of bovine milk-derived exosomes in human skin aging, which opens a new way of skin care.

cell biology↗

bioRxiv2023

Scalable Solar-Driven Chemical Production by Semiconductor Biohybrids Synthesized from Wastewater Pollutants

Semiconductors biohybrids integrate the best of biological catalysts and semiconductor nanomaterials for solar-to-chemical conversion. To realize the potential of hybrid systems at the commercial level, it remains an urgent need for cost-competitive and environmentally friendly approaches to scaling up. Here, we successfully tackle this challenge through developing biohybrid route that co-utilize multi-pollutants in wastewater to produce semiconductor biohybrids in-situ for solar-to-chemical production. To achieve cost-effective biohybrid production, we introduced an aerobic sulfate reduction pathway into Vibrio natriegens to enable the direct utilization of the heavy metal ions (i.e., Cd2+), sulfate, and organics in the wastewater to biosynthesize functional semiconductor nanoparticles in living V. natriegens. Furthermore, 2,3-butanediol biosynthetic pathway was introduced into the V. natriegens hybrid to couple the solar energy for enhanced bioproduction. We demonstrated the scalability of this system in a 5-L illuminated fermenter using wastewater as the feedstock, which resulted in production of 13 g/L of 2,3-butanediol. Life cycle analysis showed this specific biohybrid route had a significantly lower cost and reduced CO2 emission compared to both pure sugars fermentation and fossil-based routes. In addition to providing a promising step toward sustainable commercializing semiconductor biohybrids for biomanufacturing, our work may lead to hybrid living matter toward future waste to wealth conversion.

synthetic biology↗

bioRxiv2023

A novel purity analysis method of bovine milk-derived exosomes by two-dimensional ultra-performance liquid chromatography

Exosomes have been implicated in many biological processes as intercellular communication carriers. Because exosomes are increasingly explored as natural vehicles for cell and gene therapies, and drug delivery applications, it is critical to have high-quality samples. Protein:particle ratio, ELISA, western blotting, polymerase chain reaction, and size-exclusion high-performance liquid chromatography are the main methods that have been extensively applied to analyze exosomes purity in recent years. However, there is currently no well-established method that is convenient for routine quality analysis of small-size impurities in exosomes samples. Here, a size-exclusion high-performance liquid chromatography (SE-HPLC), an ion-exchange high-performance liquid chromatography (IEX-HPLC), and a novel two-dimensional high-performance liquid chromatography (2D-HPLC) method were used to detect the purity of bovine milk-derived exosomes with different processes of exosome isolation in detail. The results showed that the 2D-HPLC method could enhance the accuracy of detecting exosomal purity with higher precision and accuracy of instrumental, reduced personal error and experimental cost, shortened analysis time greatly, and more automation. The 2D-HPLC method is rapid, exhibits high selectivity, and has good sensitivity, thus making it well-suited for application in the pharmaceutical and toxicological analysis of exosomes.

biochemistry↗

bioRxiv2023

Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution

Structural variations (SVs) are a major source of domestication and improvement traits, however SV profiles of duck and their phenotypic impacts largely hidden. We present the first duck pan-genome constructed using five genome assemblies capturing [~]40.98 Mb new sequences. This pan-genome together with high-depth sequencing data ([~]46.5X) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to ducks domestication and improvement. By combining quantitative genetics with molecular experiments, we dissect how TE-derived SVs change gene expression of IGF2BP1 and generate a novel transcript of MITF, shaping bodyweight and white plumage. In the IGF2BP1 locus, the TE-derived SV explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). Our findings highlight the importance of using a pan-genome as a reference in genomics studies and explore the roles of TE-derived SVs in trait formation and in livestock breeding.

genetics↗

bioRxiv2023

Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomes

Single-cell nanopore sequencing of full-length mRNAs (scNanoRNAseq) is transforming singlecell multi-omics studies. However, challenges include computational complexity and dependence on short-read curation. To address this, we developed a comprehensive toolkit, scNanoGPS to calculate same-cell genotypes-phenotypes without short-read guidance. We applied scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell lines. Standalone, scNanoGPS accurately deconvoluted error-prone long-reads into single-cells and single-molecules. Further, scNanoGPS simultaneously accessed both phenotypes (expressions/isoforms) and genotypes (mutations) of individual cells. Our analyses revealed that tumor and stroma/immune cells often expressed significantly distinct combinations of isoforms (DCIs). In a kidney tumor, we identified 924 genes with DCIs involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Moreover, transcriptome-wide mutation analyses identified many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting critical roles of different populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing.

bioinformatics↗

bioRxiv2023

The landscape of m1A modification and its posttranscriptional regulatory functions in primary neurons

Cerebral ischaemia-reperfusion injury, during which neurons undergo oxygen-glucose deprivation/reoxygenation (OGD/R), is a notable pathological process in many neurological diseases. N1-methyladenosine (m1A) is an RNA modification that can affect gene expression and RNA stability. The m1A landscape and potential functions of m1A modification in neurons remain poorly understood. We explored RNA (mRNA, lncRNA, and circRNA) m1A modification in normal and OGD/R-treated neurons and the effect of m1A on diverse RNAs. We investigated the m1A landscape in primary neurons, identified m1A-modified RNAs, and found that OGD/R increased the number of m1A RNAs. m1A modification might also affect the regulatory mechanisms of noncoding RNAs, e.g., lncRNA-RBP interactions and circRNA translation. We showed that m1A modification mediates the circRNA/lncRNA-miRNA-mRNA ceRNA mechanism and that 3UTR methylation of mRNAs can hinder miRNA-mRNA binding. Three methylation patterns were identified, and genes with different patterns had intrinsic mechanisms with potential m1A-regulatory specificity. Systematic analysis of the m1A landscape in normal and OGD/R neurons lays a critical foundation for understanding RNA methylation and provides new perspectives and a theoretical basis for treating and developing drugs for OGD/R pathology-related diseases.

neuroscience↗

bioRxiv2023

Molecular Imaging with Fibroblast Activation Protein Tracers depicts Inflammatory Joint Damage and its Transition to Resolution of Inflammation

Joint fibroblasts play an important role in the transition from joint inflammation to irreversible joint damage. There is no established clinical method to measure fibroblast activation during inflammation and their phenotypic dynamics upon therapy to date. Here we show that upon treatment with IL-17A/TNF-blocking antibodies fibroblasts change their phenotype from a destructive IL-6+/MMP3+THY1+ to a CD200+DKK3+ subtype, actively inducing resolution of inflammation. This phenotypic switch can be visualized due to so far unexplored different capacities of fibroblast subtypes with regard to receptor internalization of small molecular tracers with high affinity to FAP. Although FAP expression levels are comparable between fibroblast subtypes in the joint, FAP internalisation rate correlates with the destructive potential of fibroblasts and resolving fibroblasts have a lower FAP internalisation rate, providing a valuable imaging tool to visualize the transition from joint damage to resolution of inflammation.

immunology↗

bioRxiv2022

Polarity-driven three-dimensional spontaneous rotation of a cell doublet

Cell mechanical interactions play a fundamental role in the self-organisation of organisms. How these interactions drive coordinated cell movement in three-dimensions remains unclear. Here we report that cell doublets embedded in a 3D extracellular matrix undergo spontaneous rotations and we investigate the rotation mechanism using live cell imaging, quantitative measurements, mechanical perturbations, and theory. We find that rotation is driven by a polarized distribution of myosin within cell cortices. The mismatched orientation of this polarized distribution breaks the doublet mirror symmetry. In addition, cells adhere at their interface through adherens junctions and with the extracellular matrix through focal contacts near myosin clusters. Using a physical theory describing the doublet as two interacting active surfaces, we find that rotation is driven by myosin-generated gradients of active tension, whose profiles are dictated by interacting cell polarity axes. We show that interface three-dimensional shapes can be understood from the Curie principle: shapes symmetries are related to broken symmetries of myosin distribution in cortices. To test for the rotation mechanism, we suppress myosin clusters using laser ablation and we generate new myosin clusters by optogenetics. Our work clarifies how polarity-oriented active mechanical forces drive collective cell motion in three dimensions.

biophysics↗

bioRxiv2022

Soft multimodal opto-electric biointerfaces for co-localized optical and electrical recording of cell function

Optical fluorescence and electrical monitoring of cell activity are two powerful approaches to study organ functions. Simultaneous recording of optical and electrical data types will provide complementary information from and take advantage of each approach. However, devices that can concurrently record optical signals from the same cell population underneath the microelectrodes have not been widely explored and remain a grand technical challenge. This work presents an innovative flexible opto-electric device that monolithically integrates transparent gold nanogrid microelectrodes directly above microscale light-emitting diodes, photodetectors, and optical filters to achieve co-localized crosstalk-free optical fluorescence and electrical recording. The optimized gold nanogrid microelectrodes show excellent optical transparency (>81%) and low normalized 1 kHz electrochemical impedance (6.3 {Omega} cm2). The optical recording subsystem offers high wavelength selectivity (>1,300) and linearity (R2 >0.99) for exciting and capturing green fluorescence from various fluorescent reporters in measurement ranges relevant to in vivo applications with minimal thermal effects. The opto-electric device exhibits remarkable durability under soaking for 40 days and repetitive mechanical bending for 5,000 cycles. The work may provide a versatile approach for constructing mechanically compliant biointerfaces containing crosstalk-free optical and electrical modalities with widespread application potentials in basic and clinical research.

bioengineering↗

bioRxiv2022

An oral vaccine for SARS-CoV-2 RBD mRNA-bovine milk-derived exosomes induces a neutralizing antibody response in vivo

The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) that causes the coronavirus disease 2019 (COVID-19) has presented numerous challenges to global health. The vaccines, including lipid-based nanoparticle mRNA, inactivated virus and recombined protein, have been used to prevent SARS-CoV-2 infections in clinics and are immensely helpful against the epidemic. Here, we first present an oral mRNA vaccine based on bovine milk-derived exosomes (milk-exos), which encodes the SARS-CoV-2 receptor binding domain (RBD) as an immunogen. The results indicated that RBD mRNA delivered by milk-derived exosomes can produce secreted RBD peptide in 293 cells in vitro and stimulated neutralizing antibodies against RBD in mice. These results indicated that bovine milk-derived exosome-based mRNA vaccine could serve as a new strategy for preventing SARS-CoV-2 infection. Meanwhile, it also can work as a new oral delivery system for mRNA. One Sentence SummaryOral SARS-CoV-2 mRNA vaccine based on bovine milk-derived exosomes can stimulate neutralizing antibodies in mice.

immunology↗

bioRxiv2022

West Nile Virus spread in Europe - phylogeographic pattern analysis and key drivers

Spread and emergence of West Nile virus (WNV) in Europe have been very different from those observed in North America. Here, we describe key drivers by combining viral genome sequences with epidemiological data and possible factors of spread into phylodynamic models. WNV in Europe has greater lineage diversity than other regions of the world, suggesting repeated introductions and local amplification. Among the six lineages found in Europe, WNV-2a is predominant, has spread to at least 14 countries and evolved into two major co-circulating clusters (A and B). Both of these seem to originate from regions of Central Europe. Viruses of Cluster A emerged earlier and have spread towards the west of Europe with higher genetic diversity. Amongst multiple drivers, high agriculture activities were associated with both spread direction and velocity. Our study suggests future surveillance activities should be strengthened in Central Europe and Southeast European countries, and enhanced monitoring should be targeted to areas with high agriculture activities.

evolutionary biology↗

bioRxiv2022

Transparent and stretchable metal nanowire composite recording microelectrode arrays

Transparent microelectrodes have received much attention from the biomedical community due to their unique advantages in concurrent crosstalk-free electrical and optical interrogation of cell/tissue activity. Despite recent progress in constructing transparent microelectrodes, a major challenge is to simultaneously achieve desirable mechanical stretchability, optical transparency, electrochemical performance, and chemical stability for high-fidelity, conformal, and stable interfacing with soft tissue/organ systems. To address this challenge, we have designed microelectrode arrays (MEAs) with gold coated silver nanowires (Au-Ag NWs) by combining technical advances in materials, fabrication, and mechanics. The Au coating improves both the chemical stability and electrochemical impedance of the Au-Ag NWs microelectrodes with only slight changes in optical properties. The MEAs exhibit a high optical transparency >80% at 550 nm, a low normalized 1 kHz electrochemical impedance of 1.2-7.5 {Omega} cm2, stable chemical and electromechanical performance after exposure to oxygen plasma for 5 minutes and cyclic stretching for 600 cycles at 20% strain, superior to other transparent microelectrode alternatives. The MEAs easily conform to curvilinear heart surfaces for co-localized electrophysiological and optical mapping of cardiac function. This work demonstrates that stretchable transparent metal nanowire MEAs are promising candidates for diverse biomedical science and engineering applications, particularly under mechanically dynamic conditions.

bioengineering↗

bioRxiv2022

Analysis of sex differential genes at whole genome level reveals their organ- and chromosome-dependent expressions, regulations, and interactions

Males and females possess genomes that are almost identical but differ in morbidity, prevalence, severity, response to therapies and mortality of many diseases. We comprehensively analyzed gene expression data in seven tissues from BXD recombinant inbred (RI) mouse strains. We found that there were considerable differences in the numbers and functions among different tissues and between autosomal and sex chromosomes. Among sex differential genes, those on autosomal chromosomes mainly function to regulate metabolic pathways related to their host organs, while those on sex chromosomes mainly regulate nuclear proteins required for DNA replication or transcription during early development. Kidney possessed the fewest sex differential genes on sex chromosomes. The sexually dimorphic genes expressed on X chromosomes were all related to perception, while genes on the autosomal chromosomes were related to metabolism. These patterns of gene expression do not translate into similarity of protein structures, rather they are grouping with function.

cell biology↗

bioRxiv2022

Distinguish characters of luminal and glandular epithelium from mouse uterus using a novel enzyme-based separation method

The uterine luminal epithelium, glandular epithelium, and stromal cells are vital for the establishment of pregnancy. Previously studies have shown various methods to isolate mouse uterine epithelium and stromal cells, including Laser Capture Microdissection (LCM), enzyme digestion, and Immunomagnetic beads. Despite the importance of the endometrial epithelium as the site of implantation and nutritional support for the conceptus, there is no isolated method to separate the luminal epithelium and glandular epithelium. Here, we establish a novel enzyme-based way to separate two types of epithelium and keep their viability. In this article, we analyzed their purity by mRNA level, immunostaining, and transcriptome analysis. Our isolation method revealed several unstudied luminal and glandular epithelial markers in transcriptome analysis. We further demonstrated the viability of the isolated epithelium by 2D and 3D cultures. The results showed that we successfully separated the endometrial luminal epithelium and glandular epithelium. We also provided an experimental model for the following study of the physiological function of the different parts of the uterus and related diseases.

cell biology↗

bioRxiv2022

Type 17 Follicular Helper T (Tfh17) Cells are Superior for Memory Maintenance

A defining feature of successful vaccination is the ability to induce long-lived antigen- specific memory cells. Follicular helper T (Tfh) cells specialize in providing help to B cells in mounting protective humoral immunity in infection and after vaccination. Memory Tfh cells that retain the CXCR5 expression can confer protection through enhancing humoral response upon antigen re-exposure but how they are maintained is poorly understood. CXCR5+ memory Tfh cells in human blood are divided into Tfh1, Tfh2 and Tfh17 cells by the expression of chemokine receptors CXCR3 and CCR6 associated with Th1 and Th17 respectively. Here, we developed a new method to induce Tfh1, Tfh2 and Tfh17-like (iTfh1, iTfh2 and iTfh17) cells in vitro. Although all three iTfh subsets efficiently support antibody responses in recipient mice with immediate immunization, iTfh17 cells are superior to iTfh1 and iTfh2 cells in supporting antibody response to a later immunization after extended resting in vivo to mimic memory maintenance. Notably, the counterpart human Tfh17 cells are selectively enriched in CCR7+ central memory Tfh (TfhCM) with survival and proliferative advantages. Furthermore, the analysis of multiple human cohorts that received different vaccines for HBV, influenza virus, tetanus toxin or measles revealed that vaccine-specific Tfh17 cells outcompete Tfh1 or Tfh2 cells for the persistence in memory phase. Therefore, the complementary mouse and human results showing the advantage of Tfh17 cells in maintenance and memory function supports the notion that Tfh17-induced immunization might be preferable in vaccine development to confer long-term protection.

immunology↗

bioRxiv2022

Multifunctional flexible electro-optical arrays for simultaneous spatiotemporal cardiac mapping and modulation

Bioelectronic devices that allow simultaneous accurate monitoring and control of the spatiotemporal patterns of cardiac activity provide an effective means to understand the mechanisms and optimize therapeutic strategies for heart disease. Optogenetics is a promising technology for cardiac research due to its advantages such as cell-type selectivity and high space-time resolution, but its efficacy is limited by the insufficient number of modulation channels and lack of simultaneous spatiotemporal mapping capabilities in current cardiac optogenetics tools. Here we present soft implantable electro-optical cardiac devices integrating multilayered highly uniform arrays of transparent microelectrodes and multicolor micro-light-emitting-diodes in thin, flexible platforms for mechanically compliant high-content electrical mapping and single-/multi-site optogenetics and electrical stimulation without light-induced artifacts. Systematic benchtop characterizations, together with ex vivo and in vivo evaluations on healthy and diseased small animal and human hearts demonstrate their functionalities in real-time spatiotemporal mapping and control of cardiac rhythm and function, with broad applications in basic and ultimately clinical cardiology.

bioengineering↗

bioRxiv2022

Microfluidic chemostatic bioreactor for high-throughput screening and sustainable co-harvesting of biomass and biodiesel in microalgae

As a renewable and sustainable source for energy, environment, and biomedical applications, microalgae and microalgal biodiesel have attracted great attention. However, their applications are confined due to the cost-efficiency of microalgal mass production. One-step strategy and continuous culturing systems could be solutions. However, current studies for optimization throughout microalgae-based biofuel production pipelines are generally derived from the batch culture process. Better tools are needed to study algal growth kinetics in continuous systems. A microfluidics chemostatic bioreactor array was presented, providing low-adhesion cultivation for algae in the gas, nutrition, and temperature (GNT) well-controlled environment with high throughput. The chip wasused to mimic the continuous culture environment of bioreactors. It allowed simultaneously studying of 8x8 different chemostatic conditions on algal growth and oil production in parallel on a 7x7 cm2 footprint. On-chip experiments of batch and continuous cultures of Chlorella. sp. were performed to study growth and lipid accumulation under different nitrogen concentrations. The results demonstrated that microalgal cultures can be regulated to grow and accumulate lipids concurrently, thus enhancing lipid productivity in one step. The developed on-chip culturing condition screening, which was more suitable for continuous bioreactor, was achieved at a half shorter time, 64-times higher throughput, and less reagent consumption. It could be used to establish chemostat cultures in continuous bioreactors which can dramatically accelerate the development of renewable and sustainable algal for CO2 fixation and biosynthesis and related systems for advanced sustainable energy, food, pharmacy, and agriculture with enormous social and ecological benefits. TEASERSustainable microfluidic bioreactor for 64 times higher-throughput screening CO2 fixation and biomass and biodiesel production in microalgae.

bioengineering↗

bioRxiv2022

A microfluidic droplet array demonstrating high-throughput screening in individual lipid-producing microalgae

Microalgae are a group of photoautotrophic microorganisms which could use carbon dioxide for autosynthesis. They have been envisioned as one of the most prospective feedstock for renewable oil. However, great endeavors will still be needed to increase their economic feasibility; the screening of competitive species and suitable culture conditions are such issues. To greatly accelerate these rather laborious steps and also improve their experimental lump-sum-manner, we developed a microfluidic droplet-based 2x103 resolution "identification card", which allowed high throughput real-time monitoring of individual algae among population. A novel fluid-blocking-based droplet generating and trapping performance were integrated in the platform which made it excellent in operational simplicity, rapidity and stability and full of the potentials in single-cell-isolation/screening. The developed platform was successfully used to screen three unicellular algae, namely, Isochrysis zhanjiangensis, Platymonas subcordiformis and Platymonas helgolandica var. tsingtaoensis. In situ bioassays of the lipid accumulation and cell proliferation at single cell level for interspecies comparison were possible. Nitrogen stress condition can be indentified that induce positive-skewed frequency distribution of lipid content.

bioengineering↗