Acquisition and transcriptomic analysis of tissue micro-regions using a capillary-based method.

Profiling the site-specific transcriptomes of microregions of interest (mROIs) contributes to a complete understanding of multicellular organisms. However, the simple and efficient isolation of mROIs for spatially detecting gene expression remains challenging. Here, we develop an efficient capillary-based microdissection system (CMS) for precisely isolating targeted samples from tissue sections.

Rapid and high accuracy identification of culture medium by CNN of Raman spectra.

Culture media are widely used for biological research and production. It is essential for the growth of microorganisms, cells, or tissues. It includes complex components like carbohydrates, proteins, vitamins, and minerals.

Digital SERS immunoassay of Interleukin-6 based on Au@Ag-Au nanotags.

Interleukin-6 (IL-6) is a crucial cytokine involved in inflammation and immune regulation. However, the detection of IL-6 with ultrasensitivity and high specificity remains a significant challenge due to the inherent complexity of biofluids. Herein, we present a digital surface enhanced Raman scattering (SERS) immunoassay using core-shell Au@Ag-Au nanotags for IL-6 detection with ultrasensitivity and high reliability.

Spatial transcriptomic profiling of isolated microregions in tissue sections utilizing laser-induced forward transfer.

Profiling gene expression while preserving cell locations aids in the comprehensive understanding of cell fates in multicellular organisms. However, simple and flexible isolation of microregions of interest (mROIs) for spatial transcriptomics is still challenging. We present a laser-induced forward transfer (LIFT)-based method combined with a full-length mRNA-sequencing protocol (LIFT-seq) for profiling region-specific tissues.

Organic matter composition and stability in estuarine wetlands depending on soil salinity.

Coastal wetlands are key players in mitigating global climate change by sequestering soil organic matter. Soil organic matter consists of less stable particulate organic matter (POM) and more stable mineral-associated organic matter (MAOM). The distribution and drivers of MAOM and POM in coastal wetlands have received little attention, despite the processes and mechanisms differ from that in the upland soils.

Transcriptomic profiling of nuclei from paraformaldehyde-fixed and formalin-fixed paraffin-embedded brain tissues.

Background: Paraformaldehyde (PFA) fixation is necessary for histochemical staining, and formalin-fixed and paraffin-embedded (FFPE) tissue archives are the largest repository of clinically annotated specimens. Single-cell gene expression workflows have recently been developed for PFA-fixed and FFPE tissue specimens. However, for tissues where intact cells are hard to recover, including tissues containing highly interconnected neurons, single-nuclear transcriptomics is beneficial.

Effect of Different Staining Methods on Brain Cryosections.

Staining frozen sections is often required to distinguish cell types for spatial transcriptomic studies of the brain. The impact of the staining methods on the RNA integrity of the cells becomes one of the limitations of spatial transcriptome technology with microdissection. However, there is a lack of systematic comparisons of different staining modalities for the pretreatment of frozen sections of brain tissue as well as their effects on transcriptome sequencing results.

Ratiometric SERS quantification of SO vapor based on Au@Ag-Au with Raman reporter as internal standard.

Practical gas sensing application requires sensors to quantify target analytes with high sensitivity and reproducibility. However, conventional surface enhanced Raman scattering (SERS) sensor lacks reproducibility and quantification arising from variations of "hot spot" distribution and measurement conditions. Here, a ratio-dependent SERS sensor was developed for quantitative label-free gas sensing.

Silicon fractionations in coastal wetland sediments: Implications for biogeochemical silicon cycling.

Coastal wetland sediment is important reservoir for silicon (Si), and plays an essential role in controlling its biogeochemical cycling. However, little is known about Si fractionations and the associated factors driving their transformations in coastal wetland sediments. In this study, we applied an optimized sequential Si extraction method to separate six sub-fractions of non-crystalline Si (Si) in sediments from two coastal wetlands, including Si in dissolved silicate (Si), Si in the adsorbed silicate (Si), Si bound to organic matter (Si), Si occluded in pedogenic oxides and hydroxides (Si), Si in biogenic amorphous silica (Si), and Si in pedogenic amorphous silica (Si).

A computer vision and residual neural network (ResNet) combined method for automated and accurate yeast replicative aging analysis of high-throughput microfluidic single-cell images.

With the rapid development of microfluidic platforms in high-throughput single-cell culturing, laborious operation to manipulate massive budding yeast cells (Saccharomyces cerevisiae) in replicative aging studies has been greatly simplified and automated. As a result, large datasets of microscopy images bring challenges to fast and accurately determine yeast replicative lifespan (RLS), which is the most important parameter to study cell aging. Based on our microfluidic diploid yeast long-term culturing (DYLC) chip that features 1100 traps to immobilize single cells and record their proliferation and aging via time-lapse imaging, herein, a dedicated algorithm combined with computer vision and residual neural network (ResNet) was presented to efficiently process tremendous micrographs in a high-throughput and automated manner.

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.

Construction of multiplexed transcriptome NGS libraries of microdissected tissue samples based on combinational DNA barcode microbeads.

The combination of single-cell RNA sequencing and microdissection techniques that preserves positional information has become a major tool for spatial transcriptome analyses. However, high costs and time requirements, especially for experiments at the single cell scale, make it challenging for this approach to meet the demand for increased throughput. Therefore, we proposed combinational DNA barcode (CDB)-seq as a medium-throughput, multiplexed approach combining Smart-3SEQ and CDB magnetic microbeads for transcriptome analyses of microdissected tissue samples.

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.

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.

[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.

Spatial transcriptomics: recent developments and insights in respiratory research.

The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies.

The weathering process of carbonatite: weathering time.

Soil formation by rock weathering is driven by a combination of parent material, climate, organisms, topography, and time. Among these soil-forming factors, time plays a pivotal role in the weathering of carbonatite but it is a challenging factor to study quantitatively. A method for determining the weathering duration of carbonatite based on its weathering characteristics over a century-scale time period has not been clearly established.

Nutrient availability and acid erosion determine the early colonization of limestone by lithobiontic microorganisms.

Introduction: Microorganisms, including the pioneer microorganisms that play a role in the early colonization of rock, are extremely important biological factors in rock deterioration. The interaction of microorganisms with limestone leads to biodeterioration, accelerates soil formation, and plays an important role in the restoration of degraded ecosystems that cannot be ignored. However, the process of microbial colonization of sterile limestone in the early stages of ecological succession is unclear, as are the factors that affect the colonization.

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.

Low-frequency transcranial magnetic stimulation protects cognition in mice with chronic unpredictable mild stress through autophagy regulation.

Although transcranial magnetic stimulation (TMS) has been approved for the treatment of major depression, few studies have analyzed the ability of low-frequency TMS (LF-TMS) to treat depressive symptoms. Our study confirmed that LF-TMS protects the cognitive function,which can play a certain reference role in the future clinical treatment. The effectiveness of high-frequency TMS therapy has been well documented.