Deep-Cloud: A Deep Neural Network-Based Approach for Analyzing Differentially Expressed Genes of RNA-seq Data.

Presently, the field of analyzing differentially expressed genes (DEGs) of RNA-seq data is still in its infancy, with new approaches constantly being proposed. Taking advantage of deep neural networks to explore gene expression information on RNA-seq data can provide a novel possibility in the biomedical field. In this study, a novel approach based on a deep learning algorithm and cloud model was developed, named Deep-Cloud. Its main advantage is not only using a convolutional neural network and long short-term memory to extract original data features and estimate gene expression of RNA-seq data but also combining the statistical method of the cloud model to quantify the uncertainty and carry out in-depth analysis of the DEGs between the disease groups and the control groups. Compared with traditional analysis software of DEGs, the Deep-cloud model further improves the sensitivity and accuracy of obtaining DEGs from RNA-seq data. Overall, the proposed new approach Deep-cloud paves a new pathway for mining RNA-seq data in the biomedical field.

A comprehensive characterization of cell-free RNA in spent blastocyst medium and quality prediction for blastocyst.

The rate of pregnancy can be affected by many factors in assisted reproductive technology (ART), and one of which is the quality of embryos. Therefore, selecting the embryos with high potential is crucial for the outcome. Fifteen spent blastocyst medium (SBM) samples were collected from 14 patients who received in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI), seven from high-grade embryos and eight from low-grade embryos. Cell-free RNA (cf-RNA) profile of SBM samples were analyzed by RNA sequencing in the present study. It was found that a large amount of cf-RNA were released into SBM, including protein-coding genes (68.9%) and long noncoding RNAs (lncRNAs) (17.26%). Furthermore, a high correlation was observed between blastocyst genes and SBM genes. And the cf-mRNAs of SBM were highly fragmented, and coding sequence (CDS) and untranslated (UTR) regions were released equally. Two hundred and thirty-two differentially expressed genes were identified in high-grade SBM (hSBM) and low-grade SBM (lSBM), which could be potential biomarker in distinguishing the embryos with different quality as an alternative or supplementary approach for subjective morphology criteria. Hence, cf-RNAs sequencing revealed the characterization of circulating transcriptomes of embryos with different quality. Based on the results, the genes related to blastocyst quality were screened, including the genes closely related to translation, immune-signaling pathway, and amino acid metabolism. Overall, the present study showed the types of SBM cf-RNAs, and the integrated analysis of cf-RNAs profiling with morphology grading displayed its potential in predicting blastocyst quality. The present study provided valuable scientific basis for noninvasive embryo selection in ART by RNA-profiling analysis.

Spatial Transcriptomic Analysis Reveals Regional Transcript Changes in Early and Late Stages of rd1 Model Mice with Retinitis Pigmentosa.

Retinitis pigmentosa (RP) is the leading cause of inherited blindness with a genetically heterogeneous disorder. Currently, there is no effective treatment that can protect vision for those with RP. In recent decades, the rd1 mouse has been used to study the pathological mechanisms of RP. Molecular biological studies using rd1 mice have clarified the mechanism of the apoptosis of photoreceptor cells in the early stage of RP. However, the pathological changes in RP over time remain unclear. The unknown pathology mechanism of RP over time and the difficulty of clinical treatment make it urgent to perform more refined and spatially informed molecular biology studies of RP. In this study, spatial transcriptomic analysis is used to study the changes in different retinal layers of rd1 mice at different ages. The results demonstrate the pattern of photoreceptor apoptosis between rd1 mice and the control group. Not only was oxidative stress enhanced in the late stage of RP, but it was accompanied by an up-regulation of the VEGF pathway. Analysis of temporal kinetic trends has further identified patterns of changes in the key pathways of the early and late stages, to help understand the important pathogenesis of RP. Overall, the application of spatial transcriptomics to rd1 mice can help to elucidate the important pathogenesis of RP involving photoreceptor apoptosis and retinal remodeling.

Single-Nucleus RNA-Seq: Open the Era of Great Navigation for FFPE Tissue.

Single-cell sequencing (scRNA-seq) has revolutionized our ability to explore heterogeneity and genetic variations at the single-cell level, opening up new avenues for understanding disease mechanisms and cell-cell interactions. Single-nucleus RNA-sequencing (snRNA-seq) is emerging as a promising solution to scRNA-seq due to its reduced ionized transcription bias and compatibility with richer samples. This approach will provide an exciting opportunity for in-depth exploration of billions of formalin-fixed paraffin-embedded (FFPE) tissues. Recent advancements in single-cell/nucleus gene expression workflows tailored for FFPE tissues have demonstrated their feasibility and provided crucial guidance for future studies utilizing FFPE specimens. In this review, we provide a broad overview of the nuclear preparation strategies, the latest technologies of snRNA-seq applicable to FFPE samples. Finally, the limitations and potential technical developments of snRNA-seq in FFPE samples are summarized. The development of snRNA-seq technologies for FFPE samples will lay a foundation for transcriptomic studies of valuable samples in clinical medicine and human sample banks.

Spatial Transcriptome Profiling of Mouse Hippocampal Single Cell Microzone in Parkinson's Disease.

The hippocampus is an important part of the limbic system in the human brain that has essential roles in spatial navigation and cognitive functions. It is still unknown how gene expression changes in single-cell in different spatial locations of the hippocampus of Parkinson's disease. The purpose of this study was to analyze the gene expression features of single cells in different spatial locations of mouse hippocampus, and to explore the effects of gene expression regulation on learning and memory mechanisms. Here, we obtained 74 single-cell samples from different spatial locations in a mouse hippocampus through microdissection technology, and used single-cell RNA-sequencing and spatial transcriptome sequencing to visualize and quantify the single-cell transcriptome features of tissue sections. The results of differential expression analysis showed that the expression of Sv2b, Neurod6, Grp and Stk32b genes in a hippocampus single cell at different locations was significantly different, and the marker genes of CA1, CA3 and DG subregions were identified. The results of gene function enrichment analysis showed that the up-regulated differentially expressed genes Tubb2a, Eno1, Atp2b1, Plk2, Map4, Pex5l, Fibcd1 and Pdzd2 were mainly involved in neuron to neuron synapse, vesicle-mediated transport in synapse, calcium signaling pathway and neurodegenerative disease pathways, thus affecting learning and memory function. It revealed the transcriptome profile and heterogeneity of spatially located cells in the hippocampus of PD for the first time, and demonstrated that the impaired learning and memory ability of PD was affected by the synergistic effect of CA1 and CA3 subregions neuron genes. These results are crucial for understanding the pathological mechanism of the Parkinson's disease and making precise treatment plans.

Occurrence, consumption level, fate and ecotoxicology risk of beta-agonist pharmaceuticals in a wastewater treatment plant in Eastern China.

Beta-agonist pharmaceuticals are widely used in humans and livestock for disease treatment, legal or illegal growth promotion in food animals, bodybuilding, weight loss, and sports doping. The occurrence of beta-agonists in wastewater treatment plants and their subsequent environmental impacts require greater attention. This study determined the levels of 12 beta-agonists in a wastewater treatment plant and evaluated their ecotoxicological risks as well as consumption levels and risks to human health. Among the 12 selected beta-agonists, all were detected in wastewater and 11 in sludge. In most cases, the concentrations of beta-agonists were higher in spring than in summer. Their total average daily mass loads per capita in the influent and effluent were 1.35 µg/d/p and 2.11 µg/d/p, respectively. The overall removal efficiencies of individual beta-agonists ranged from -295.3 to 71.2%. Ecotoxicological risk assessment revealed a low risk to daphnid and green algae from the levels of fenoterol and the mixture of 12 selected beta-agonists in the effluent. The daily consumption levels of individual beta-agonists per capita were 0.028-1.200 µg/d/p. Regular monitoring of beta-agonists in municipal sewage systems and their risk assessment based on toxicological data are urgently required in the future.

[Imputation method for dropout in single-cell transcriptome data].

Single-cell transcriptome sequencing (scRNA-seq) can resolve the expression characteristics of cells in tissues with single-cell precision, enabling researchers to quantify cellular heterogeneity within populations with higher resolution, revealing potentially heterogeneous cell populations and the dynamics of complex tissues. However, the presence of a large number of technical zeros in scRNA-seq data will have an impact on downstream analysis of cell clustering, differential genes, cell annotation, and pseudotime, hindering the discovery of meaningful biological signals. The main idea to solve this problem is to make use of the potential correlation between cells and genes, and to impute the technical zeros through the observed data. Based on this, this paper reviewed the basic methods of imputing technical zeros in the scRNA-seq data and discussed the advantages and disadvantages of the existing methods. Finally, recommendations and perspectives on the use and development of the method were provided.

Ultrasensitive detection of multiple Alzheimer's disease biomarkers by SERS-LFA.

Alzheimer's disease (AD) is one of the top public health crises in the 21st century, especially in an aging society. Early diagnosis, prevention, and intervention can significantly reduce the risk of AD. Detection of multiple AD biomarkers in blood is an effective strategy and has drawn more and more attention in recent years. However, the concentration of AD biomarkers is very low, therefore, point-of-care testing (POCT) techniques are needed for sensitive detection. Herein, a lateral flow assay, based on Surface-enhanced Raman scattering nanotags (SERS-LFA), is proposed for the simultaneous quantification of multiple AD biomarkers including Amyloid-beta 42, Amyloid-beta 40, tau proteins, and neurofilament light chain. The limit of detection for four AD biomarkers is 138.1, 191.2, 257.1, and 309.1 fg mL-1, respectively, which are two orders of magnitude lower than their concentrations in blood. Compared with the existing detection technology, SERS-LFA has the advantages of high specificity, high sensitivity, low cost, multiple detection, and rapid detection. Therefore, SERS-LFA has a broad application prospect in the early diagnosis and monitoring of AD in the future.

Comparative analysis of circular RNA enrichment methods.

The circRNAs sequencing results vary due to the different enrichment methods and their performance is needed to systematic comparison. This study investigated the effects of different circRNA enrichment methods on sequencing results, including abundance and species of circRNAs, as well as the sensitivity and precision. This experiment was carried out by following four common circRNA enrichment methods: including ribosomal RNA depletion (rRNA-), polyadenylation and poly (A+) RNA depletion followed by RNase R treatment (polyA+RNase R), rRNA-+polyA+RNase R and polyA+RNase R+ rRNA-. The results showed that polyA+RNase R+ rRNA - enrichment method obtained more circRNA number, higher sensitivity and abundance among them; polyA+RNase R method obtained higher precision. The linear RNAs can be thoroughly removed in all enrichment methods except rRNA depletion method. Overall, our results helps researchers to quickly selection a circRNA enrichment of suitable for own study among many enrichment methods, and it provides a benchmark framework for future improvements circRNA enrichment methods.[Figure: see text].

A high-throughput microfluidic diploid yeast long-term culturing (DYLC) chip capable of bud reorientation and concerted daughter dissection for replicative lifespan determination.

BACKGROUND: Budding yeast, Saccharomyces cerevisiae, has been extensively favored as a model organism in aging and age-related studies, thanks to versatile microfluidic chips for cell dynamics assay and replicative lifespan (RLS) determination at single-cell resolution. However, previous microfluidic structures aiming to immobilize haploid yeast may impose excessive spatial constraint and mechanical stress on cells, especially for larger diploid cells that sprout in a bipolar pattern. RESULTS: We developed a high-throughput microfluidic chip for diploid yeast long-term culturing (DYLC), optical inspection and cell-aging analysis. The DYLC chip features 1100 "leaky bowl"-shaped traps formatted in an array to dock single cells under laminar-perfused medium and effectively remove daughter cells by hydraulic shear forces. The delicate microstructures of cell traps enable hydrodynamic rotation of newborn buds, so as to ensure bud reorientation towards downstream and concerted daughter dissection thereafter. The traps provide sufficient space for cell-volume enlargement during aging, and thus properly alleviate structural compression and external stress on budding yeast. Trapping efficiency and long-term maintenance of single cells were optimized according to computational fluid dynamics simulations and experimental characterization in terms of critical parameters of the trap and array geometries. Owing to the self-filling of daughter cells dissected from traps upstream, an initial trapping efficiency of about 70% can rapidly reach a high value of over 92% after 4-hour cell culturing. During yeast proliferation and aging, cellular processes of growth, budding and daughter dissection were continuously tracked for over 60 h by time-lapse imaging. Yeast RLS and budding time interval (BTI) were directly calculated by the sequential two-digit codes indicating the budding status in images. With the employed diploid yeast strain, we obtained an RLS of 24.29 ± 3.65 generations, and verified the extension of BTI in the first couple of generations after birth and the last several generations approaching death, as well as cell de-synchronization along diploid yeast aging. CONCLUSIONS: The DYLC chip offers a promising platform for reliable capture and culturing of diploid yeast cells and for life-long tracking of cell dynamics and replicative aging processes so that grasping comprehensive insights of aging mechanism in complex eukaryotic cells.

Defining Specific Cell States of MPTP-Induced Parkinson's Disease by Single-Nucleus RNA Sequencing.

Parkinson's disease (PD) is a neurodegenerative disease with an impairment of movement execution that is related to age and genetic and environmental factors. 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a neurotoxin widely used to induce PD models, but the effect of MPTP on the cells and genes of PD has not been fully elucidated. By single-nucleus RNA sequencing, we uncovered the PD-specific cells and revealed the changes in their cellular states, including astrocytosis and endothelial cells' absence, as well as a cluster of medium spiny neuron cells unique to PD. Furthermore, trajectory analysis of astrocyte and endothelial cell populations predicted candidate target gene sets that might be associated with PD. Notably, the detailed regulatory roles of astrocyte-specific transcription factors Dbx2 and Sox13 in PD were revealed in our work. Finally, we characterized the cell-cell communications of PD-specific cells and found that the overall communication strength was enhanced in PD compared with a matched control, especially the signaling pathways of NRXN and NEGR. Our work provides an overview of the changes in cellular states of the MPTP-induced mouse brain.

Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues.

BACKGROUND: Single-cell RNA sequencing (scRNA-seq) provides new insights to address biological and medical questions, and it will benefit more from the ultralow input RNA or subcellular sequencing. RESULTS: Here, we present a highly sensitive library construction protocol for ultralow input RNA sequencing (ulRNA-seq). We systematically evaluate experimental conditions of this protocol, such as reverse transcriptase, template-switching oligos (TSO), and template RNA structure. It was found that Maxima H Minus reverse transcriptase and rN modified TSO, as well as all RNA templates capped with m7G improved the sequencing sensitivity and low abundance gene detection ability. RNA-seq libraries were successfully prepared from total RNA samples as low as 0.5 pg, and more than 2000 genes have been identified. CONCLUSIONS: The ability of low abundance gene detection and sensitivity were largely enhanced with this optimized protocol. It was also confirmed in single-cell sequencing, that more genes and cell markers were identified compared to conventional sequencing method. We expect that ulRNA-seq will sequence and transcriptome characterization for the subcellular of disease tissue, to find the corresponding treatment plan.

Design and 3D modeling investigation of a microfluidic electrode array for electrical impedance measurement of single yeast cells.

High-resolution microscopic imaging may cause intensive image processing and potential impact of light irradiation on yeast replicative lifespan (RLS). Electrical impedance spectroscopy (EIS) could be alternatively used to perform high-throughput and label-free yeast RLS assays. Prior to fabricating EIS-integrated microfluidic devices for yeast RLS determination, systematic modeling and theoretical investigation are crucial for device design and optimization. Here, we report three-dimensional (3D) finite-element modeling and simulations of EIS measurement in a microfluidic single yeast in situ impedance array (SYIIA), which is designed by patterning an electrode matrix underneath a cell-trapping array. SYIIA was instantiated and modeled as a 5 × 5 sensing array comprising 25 units for cell immobilization, culturing, and time-lapse EIS recording. Simulations of yeast growing and budding in a sensing unit demonstrated that EIS signals enable the characterization of cell growth and daughter-cell dissections. In the 5 × 5 sensing array, simulation results indicated that when monitoring a target cell, daughter dissections in its surrounding traps may induce variations of the recorded EIS signals, which could cause mistakes in identifying target daughter-cell dissections. To eliminate the mis-identifications, electrode array pitch was optimized. Therefore, the results could conduct the design and optimization of microfluidic electrode-array-integrated devices for high-throughput and accurate yeast RLS assays.

Low bias multiple displacement amplification with confinement effect based on agarose gel.

Multiple displacement amplification (MDA) is a popular single-cell whole-genome amplification (WGA) technique that can greatly improve the amplification efficiency of single-cell genomes. However, there is an inherent problem that cannot be completely solved, that is, the amplification bias. We here propose an improved MDA method based on low melting agarose gel, named gelMDA. Firstly, the agarose gel and solution were characterized with SEM and fluorescent reagent. Then, we used gelMDA for cDNA amplification in library preparation of RNA-seq, and conventional MDA was used as a comparison. The sensitivity, efficiency of gelMDA, and amplification bias were evaluated with fluorescence curve, product yield, and the sequencing results. Finally, gelMDA was used for single-cell transcriptome sequencing. The results showed that the sensitivity and product yield of gelMDA were significantly higher than those of conventional MDA. A lower coefficient of variation (CV) and a higher reproducibility were obtained from gelMDA sequencing results. A region of 30 µm in diameter was amplified from the tissue sections and successfully sequenced. In conclusion, gelMDA obtained higher amplification efficiency and lower amplification bias in the present study. It suggested the great potential in single-cell RNA amplification and sequencing.

Single symbiotic cell transcriptome sequencing of coral.

Zooxanthellae and coral can form an intracellular symbiotic system. Yet, little is known about the molecular mechanism underlying this symbiosis. In this study, we characterized the symbiosis based on analyses of gene expression at the single-cell level. Among 9110 single coral cells, we identified 4871 symbiotic cells based on the detection of both coral and zooxanthellae gene transcripts within a single cell. Using the bioinformatics tool Seurat, symbiotic cells were further clustered into five groups, 52 genes exhibited differential expression between groups. We proposed an index called the "symbiosis index", to indicate the degree of gene expression of both species in a single symbiotic cell. Interestingly, the index differed distinctly among the five groups. The symbiosis index was highly correlated with the expression of the coral gene gfas1.m1.6761 (ANKRD40), which encodes ankyrin repeat domain-containing protein 40 and is involved in DNA replication (r = 0.76). Two metabolism-related genes, DAGLA and betaGlu, were highly expressed in cells with a high symbiosis index. Four zooxanthellae genes, PRPF19, ATRN, aAA-ATPases and AK812-SmicGene44833, exhibited substantial changes in expression levels when zooxanthellae lived within coral. A trajectory analysis suggested that cells with a higher symbiosis index may be derived from those with a lower index during coral colony development. Taken together, our results provide evidence for zooxanthellae residing within coral, forming a symbiotic system. The symbiosis index is an effective indicator of different cell groups, with lineage relationships among groups. Additionally, we identified specific genes that exhibit expression changes in the symbiotic system.

Vertical Flow Assay for Inflammatory Biomarkers Based on Nanofluidic Channel Array and SERS Nanotags.

There is a great demand for the development of detection assays for inflammation infection diagnosis with high throughput and ultrasensitivity. Herein, a vertical flow assay system with functionalized nanoporous anodic aluminum oxide (AAO) as sensing membrane, and encoded core-shell surface enhanced Raman scattering (SERS) nanotags as labels for multiple inflammatory biomarkers detection is presented. A 2 × 2 test array on the porous AAO is developed and modified with multiple capture antibodies to capture inflammatory biomarkers from samples. Due to the high surface area to volume ratio of the AAO membrane, and its influence on plasmonic coupling, the electromagnetic field of the encoded core-shell SERS nanotags is enhanced. Detection limits of 53.4, 4.72, 48.3, and 7.53 fg mL-1 are realized for C reactive protein, interleukin-6, serum amyloid A, and procalcitonin, respectively, with a linear dynamic range spanning at least five orders of magnitude. In addition, the proposed method also shows acceptable accuracy and repeatability for the detection of clinical samples. Therefore, this approach is expected to be a powerful point of care testing tool for disease diagnosis in facility limited areas.

Plasmon-coupled microcavity aptasensors for visual and ultra-sensitive simultaneous detection of Staphylococcus aureus and Escherichia coli.

Septicemia and bacteremia are serious infections in the bloodstream. Thus, time-saving and ultra-sensitive pathogenic bacteria detection is highly required. Herein, we constructed gold nanoparticle-modified polystyrene microspheres (Au/PS) as plasmon-coupled microcavities to realize simultaneous detection of Staphylococcus aureus and Escherichia coli based on a fluorescence and surface-enhanced Raman spectroscopy (SERS) dual-mode method. Fluorescence imaging, serving as a means for assistant validation and rapid screening, was carried out to achieve qualitative and semi-quantitative determination, which gave us visual information of the existence and distribution of the target bacteria. Meanwhile, SERS test was conducted to realize ultra-sensitive quantitative detection. The evanescent wave aroused from total internal reflection in PS microcavities coupled with the localized electromagnetic field from surface plasmons of gold nanoparticles to improve light-matter interaction synergistically, leading to an enhancement factor of 2.25 × 1011 for SERS sensing. The whole measurement was carried out in a typical sandwich assay of "capture probe-target bacteria-signal probe." As a result, calibrated concentration response curves demonstrated the sensitive quantitative detection with the limit of detection (LOD) of 3 cfu/mL for S. aureus and 2 cfu/mL for E. coli. This rapid, ultra-sensitive, and visual sensing method was further developed for dual-bacteria detection in the whole blood samples.

Photothermal Effect in Plasmonic Nanotip for LSPR Sensing.

The influence of heat generation on the conventional process of LSPR based sensing has not been explored thus far. Therefore, a need exists to draw attention toward the heat generation issue during LSPR sensing as it may affect the refractive index of the analyte, leading to incorrect sensory conclusions. This manuscript addresses the connection between the photo-thermal effect and LSPR. We numerically analyzed the heat performance of a gold cladded nanotip. The numerical results predict a change in the micro-scale temperature in the microenvironment near the nanotip. These numerical results predict a temperature increase of more than 20 K near the apex of the nanotip, which depends on numerous factors including the input optical power and the diameter of the fiber. We analytically show that this change in the temperature influences a change in the refractive index of the microenvironment in the vicinity of the nanotip. In accordance with our numerical and analytical findings, we experimentally show an LSPR shift induced by a change in the input power of the source. We believe that our work will bring the importance of temperature dependence in nanotip based LSPR sensing to the fore.

Vertical flow assays based on core-shell SERS nanotags for multiplex prostate cancer biomarker detection.

Rapid, simultaneous, and sensitive quantification of multiplex prostate biomarkers plays an important role in early diagnosis, especially for obese men and patients. Herein, a surface-enhanced Raman scattering (SERS)-based vertical flow assay (VFA) is presented for simultaneous detection of multiplex prostate cancer biomarkers, such as prostate-specific antigen (PSA), carcinoembryonic antigen (CEA), and alpha-fetoprotein (AFP) on a single test spot. In practice, Raman dyes (RDs) encoded core-shell SERS nanotags instead of conventional gold colloids used in the colorimetric assay are employed in the sensing membrane of SERS based VFAs for multiplex protein detection. Because of the enhanced Raman signal of the core-shell nanostructure and the high surface area to volume ratio (SVR) of the porous sensing membrane, this proposed biosensor shows a wide linear dynamic range (LDR) with detection limits of 0.37, 0.43, and 0.26 pg mL-1 for PSA, CEA, and AFP, respectively, suggesting that this approach can be a good candidate in point of care testing (POCT) for rapid and sensitive biomarker detection and has a huge potential in multiplex analysis and cancer diagnosis.