Quantification Of Genes Research Articles

Effect of estrogen and progesterone on intracellular free zinc and zinc transporter expression in bovine oviduct epithelial cells

Zinc (Zn) plays essential roles in numerous cellular processes. However, there is limited understanding of Zn homeostasis within the bovine reproductive system. This study investigated the influence of estradiol (E2) and progesterone (P4) on Zn transporter expression and intracellular free Zn levels in bovine oviduct epithelial cells (BOEC). For this purpose, cells were harvested from slaughtered cows and cultured in vitro. Intracellular Zn concentrations were measured using FluoZin-3AM staining, while real-time polymerase chain reaction assessed Zn transporter gene expression and quantification. Overall, our results confirmed the gene expression of all the evaluated Zn transporters (ZIP6, ZIP8, ZIP14, ZnT3, ZnT7 and ZnT9), denoted and the active role of E2 and P4 in intracellular Zn regulation. Our findings suggest an interaction between Zn, E2 and P4.

A novel bioprospecting strategy via 13C-based high-throughput probing of active methylotrophs inhabiting oil reservoir surface soil

Methane-oxidizing bacteria (MOB) have long been considered as a microbial indicator for oil and gas prospecting. However, due to the phylogenetically narrow breath of ecophysiologically distinct MOB, classic culture-dependent approaches could not discriminate MOB population at fine resolution, and accurately reflect the abundance of active MOB in the soil above oil and gas reservoirs. Here, we presented a novel microbial anomaly detection (MAD) strategy to quantitatively identify specific indicator methylotrophs in the surface soils for bioprospecting oil and gas reservoirs by using a combination of 13C-DNA stable isotope probing (SIP), high-throughput sequencing (HTS), quantitative PCR (qPCR) and geostatistical analysis. The Chunguang oilfield of the Junggar Basin was selected as a model system in western China, and type I methanotrophic Methylobacter was most active in the topsoil above the productive oil wells, while type II methanotrophic Methylosinus predominated in the dry well soils, exhibiting clear differences between non- and oil reservoir soils. Similar results were observed by quantification of Methylobacter pmoA genes as a specific bioindicator for the prediction of unknown reservoirs by grid sampling. A microbial anomaly distribution map based on geostatistical analysis further showed that the anomalous zones were highly consistent with petroleum, geological and seismic data, and validated by subsequent drilling. Over seven years, a total of 24 wells have been designed and drilled into the targeted anomaly, and the success rate via the MAD prospecting strategy was 83 %. Our results suggested that molecular techniques are powerful tools for oil and gas prospecting. This study indicates that the exploration efficiency could be significantly improved by integrating multi-disciplinary information in geophysics and geomicrobiology while reducing the drilling risk to a greater extent.

The Role of Soil Abundance of TxtAB in Potato Common Scab Disease Severity.

Common scab is an economically costly soilborne disease of potato endemic in many potato-growing regions. The disease is caused by species of Streptomyces bacteria that produce the phytotoxin thaxtomin A. The primary disease management tool available to growers is planting resistant cultivars, but no cultivar is fully resistant to common scab, and partially resistant cultivars are often not the preferred choice of growers because of agronomic or market considerations. Therefore, growers would benefit from knowledge of the presence and severity of common scab infestations in field soils to make informed planting decisions. We implemented a quantitative PCR diagnostic assay to enable field detection and quantification of all strains of Streptomyces that cause common scab in the United States through amplification of thaxtomin A biosynthetic genes. Greenhouse trials confirmed that pathogen abundance was highly correlated with disease severity for five distinct phytopathogenic Streptomyces species, although the degree of disease severity was dependent on the pathogen species. Correlations between the abundance of the thaxtomin biosynthetic genes from field soil with disease on tubers at field sites across four U.S. states and across 2 years were not as strong as correlations observed in greenhouse assays. We also developed an effective droplet digital PCR diagnostic assay that also has potential for field quantification of thaxtomin biosynthetic genes. Further improvement of the PCR assays and added modeling of other environmental factors that impact disease outcome, such as soil composition, can aid growers in making informed planting decisions.

Iontolysis using an electrically excited solid source of aqueous copper ions compatible with bacterial gene quantification

Iontolysis was demonstrated as a feasible low-voltage and low-frequency technique for bacterial DNA extraction. This was achieved through mild electrical excitation (3 Vpp with a 0.5 VDC offset at 5 Hz sinusoidal signal) of submerged copper thin films serving as a solid source for releasing aqueous copper ions into the bacterial sample upon electrical stimulation. The technique achieved approximately 40 % of the lysing efficiency of bead beating after 5 min. The electrical power consumption per Escherichia coli K12 bacterial sample was approximately 25 mW, making it suitable for use with existing portable analyzers. Its compatibility with the existing intercalating fluorescent dye gene quantification technique was demonstrated with high linearity (R2 = 0.97). Notably, it suggested the minimal presence of interfering species that may have been generated from the iontolysis byproducts. This compatibility is essential for existing bacterial gene quantification techniques to leverage the low electrical power consumption, simplicity of design and manufacturing, and ease of storage and shipping of the proposed iontolysis.

Recombinant Production of Pseudomonas aeruginosa Rhamnolipids in P. putida KT2440 on Acetobacterium woodii Cultures Grown Chemo-Autotrophically with Carbon Dioxide and Hydrogen.

The establishment of sustainable processes for the production of commodity chemicals is one of today's central challenges for biotechnological industries. The chemo-autotrophic fixation of CO2 and the subsequent production of acetate by acetogenic bacteria via anaerobic gas fermentation represents a promising platform for the ecologically sustainable production of high-value biocommodities via sequential fermentation processes. In this study, the applicability of acetate-containing cell-free spent medium of the gas-fermenting acetogenic bacterium A. woodii WP1 as the feeder strain for growth and the recombinant production of P. aeruginosa PAO1 mono-rhamnolipids in the well-established nonpathogenic producer strain P. putida KT2440 were investigated. Additionally, the potential possibility of a simplified production process without the necessary separation of feeder strain cells was elucidated via the cultivation of P. putida in cell-containing A. woodii culture broth. For these cultures, the content of both strains was investigated by examining the relative quantification of strain-exclusive genes via qPCR. The recombinant production of mono-rhamnolipids was successfully achieved with maximum titers of approximately 360-400 mg/L for both cell-free and cell-containing A. woodii spent medium. The reported processes therefore represent a successful proof of principle for gas fermentation-derived acetate as a potential sustainable carbon source for future recombinant rhamnolipid production processes by P. putida KT2440.

Microbial Assemblages and Metabolic Activity in Organic‐Rich Subterranean Estuaries: Impact of Climate and Land Use Changes

AbstractMicrobial communities in subterranean estuaries mediate biogeochemical reactions of coastal groundwater discharging into the oceans; however, studies on their response to abrupt environmental changes caused by climate and land use alterations are still limited. In this study, we conducted a controlled laboratory study using combined geochemical and metagenomic approaches to investigate microbial structures and their metabolic pathways under a wide range of nitrate () inputs, saline solutions, and incubation times. These factors served as proxies for land use, salinization of the shallow aquifer, and climate changes. We found a highly reducing habitat and an amplification of genes related to denitrification, sulfate reduction, and methanogenesis processes. Core communities consisting of Clostridia, Bacilli, Alphaproteobacteria, Gammaproteobacteria, and Desulfobaccia were observed across all treatments. The metabolic prediction of plant‐derived organic matter (i.e., tannin and lignin) degradation was not affected by inputs or salinity because of it being implemented by core communities and the abundance of electron donors and acceptors. Quantification of denitrification genes shows that they are susceptible to inputs and seawater ions. Long‐term incubation allowed sufficient time for microbes to degrade less labile DOM, promoting the re‐release of buried solid phase organic matter into the active carbon cycle and increasing the relative abundance of biofilm or spore‐forming taxa while decreasing that of rare taxa. Our results illustrate the sensitivity of microbial assemblages to environmental changes and their capacity to altering the C and N cycles in coastal areas, further affecting coastal water quality and ecosystem‐scale biogeochemistry.

Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC)

High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from 13C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from 13C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.

Shifts in C-degradation genes and microbial metabolic activity with vegetation types affected the surface soil organic carbon pool

The incorporation of plant-derived biomass by microorganisms into deceased microbial biomass, i.e., a “microbial carbon pump”, is essential for forming a soil carbon (C) pool. Therefore, microbial communities and associated functions could shape the formation of soil organic C (SOC) composition and persistence. However, the mechanism by which microorganisms mediate the degradation of various types of biomass (such as plant or microbial) and its impact on SOC formation under different vegetation types remains unclear. Herein, we analyzed microbial communities, carbohydrate-activated enzymes (CAZymes), absolute quantification of C-degradation genes, and extracellular enzyme activities to track microbial-mediated SOC formation under three vegetation types on the Loess Plateau. Changes in vegetation type influenced microbial community structure and distributions of certain bacterial groups. Specifically, dominant bacterial taxa shifted from oligotrophic Actinobacteria to eutrophic Proteobacteria from grass to forest soil. The proportion of microbial CAZymes responsible for decomposing plant-derived components (86–89%) exceeded that of microbial-derived components (11–14%), suggesting a greater capacity for the degradation of deceased plant biomass by microorganisms. There was a reduction of 14%–17% in the absolute abundance of specific C-degradation genes for hemicellulose and cellulose in forest soil compared to grass, while an increase of 20%–32% was observed in lignin and chitin degradation. This indicated a higher decomposition potential of lignin and chitin by microorganisms in forest soil. The number of CAZymes genes involved in the degradation of bacteria-derived biomass (peptidoglycan) was higher than fungi-derived biomass (chitin and glucans) and had a close correlation with the qCO2, microbial biomass C (MBC), and particulate organic C (POC). The abundance of C-degrading genes increased with the increase in the corresponding enzyme activity, indicating that enzyme activity is regulated by functional genes. In conclusion, shifts in CAZymes genes encoding for the degradation of diverse carbon sources could impact microbial metabolic activity through a microbial “carbon pump” regulation process. This mechanism could facilitate the formation of soil organic carbon and its fractions across different vegetation types.

Comprehensive RNA-sequencing analysis of colorectal cancer in a Korean cohort

Considering the recent increase in the number of colorectal cancer (CRC) cases in South Korea, we aimed to clarify the molecular characteristics of CRC unique to the Korean population. To gain insights into the complexities of CRC and promote the exchange of critical data, RNA-sequencing (RNA-Seq) analysis was performed to reveal the molecular mechanisms that drive the development and progression of CRC; this analysis is critical for developing effective treatment strategies. We performed RNA-Seq analysis of CRC and adjacent normal tissue samples from 214 Korean participants (comprising a total of 381 including 169 normal and 212 tumor samples) to investigate differential gene expression between the groups. We identified 19,575 genes expressed in CRC and normal tissues, with 3,830 differentially expressed genes (DEGs) between the groups. Functional annotation analysis revealed that the upregulated DEGs were significantly enriched in pathways related to the cell cycle, DNA replication, and IL-17, whereas the downregulated DEGs were enriched in metabolic pathways. We also analyzed the relationship between clinical information and subtypes using the Consensus Molecular Subtype (CMS) classification. Furthermore, we compared groups clustered within our dataset to CMS groups and performed additional analysis of the methylation data between DEGs and CMS groups to provide comprehensive biological insights from various perspectives. Our study provides valuable insights into the molecular mechanisms underlying CRC in Korean patients and serves as a platform for identifying potential target genes for this disease. The raw data and processed results have been deposited in a public repository for further analysis and exploration. Data availability statementThe RNA-Seq data have been deposited in the Korean Nucleotide Archive under the accession number KAP230608 (https://www.kobic.re.kr/kona/search_bioproject?bioproject_id=KAP230608#none). Clinical data, preprocessed gene quantification (RSEM), normalized gene expression data (log2CPM), and downstream analysis results have been deposited in Zenodo (https://doi.org/10.5281/zenodo.8333650). Further information and requests for experimental resources should be directed to and will be fulfilled by the corresponding authors, Kil-yong Lee (cyboryee@hanmail.net), Jin Ok Yang (joy@kribb.re.kr), and Young-Joon Kim (yjkim@yonsei.ac.kr).

Preliminary monosodium glutamate-induced changes in mammary gland receptors and gene expression, water channel, oxidative stress, and some lactogenic biomarkers in lactating rats

BackgroundChanges induced by monosodium glutamate (MSG) can negatively impact milk production and secretion, among other adverse effects. This study aimed to investigate the effects of MSG consumption on receptor gene expression and quantification of hormones and receptors, as well as oxidative stress biomarkers and other lactogenic parameters in lactating animals. Twenty-four female Wistar rats, nine weeks of age, were randomly assigned to four groups, each containing six rats, at parturition. The rats in groups II, III, and IV were given varying doses of monosodium glutamate (MSG); while, group I was given distilled water and served as the control. The experimental period lasted two (2) weeks.ResultsThe groups administered with MSG showed a significant decrease in mammary PRLR gene expression (p < 0.05), as well as a marked reduction (p < 0.05) in mammary PRLR, OXT receptor, AQP-3, brain antioxidant enzymes (SOD, GPx, and CAT), and pituitary SOD compared to the control group (p < 0.05). Furthermore, there was a significant increase (p < 0.05) in reactive oxygen species levels in the serum and mammary gland homogenates, erythrocyte osmotic fragility, and elevated (p < 0.05) brain and pituitary MDA levels in the MSG-administered groups compared to the control group. Daily milk yields were significantly decreased (p < 0.05) in the MSG-administered groups between days 10 and 14 of lactation.ConclusionThe findings of this study suggest that prolonged consumption of MSG could interfere with lactation-associated functions via increased ROS production, reduced antioxidants, decreased AQP-3, mammary prolactin and oxytocin receptors, and prolactin receptor mRNA in lactating Wistar rats.Graphical

Metagenomic absolute quantification of antibiotic resistance genes and virulence factor genes-carrying bacterial genomes in anaerobic digesters

Sewage treatment works have been considered as hotspots for the dissemination of antibiotic resistance genes (ARGs). Anaerobic digestion (AD) has emerged as a promising approach for controlling the spread of ARGs while destroying biomass in sludge. Evaluating the impact of AD on ARG removal relies on the absolute quantification of ARGs. In this study, we quantified the ARG concentrations in both full-scale and lab-scale AD systems using a cellular spike-ins based absolute quantification approach. Results demonstrated that AD effectively removed 68 ± 18 %, 55 ± 12 %, and 57 ± 19 % of total ARGs in semi-continuous AD digesters, with solid retention times of 15, 20, and 25 days, respectively. The removal efficiency of total ARGs increased as the AD process progressed in the batch digesters over 40 days. A significant negative correlation was observed between digestion time and the concentrations of certain ARG types, such as beta-lactam, sulfonamide, and tetracycline. However, certain potential pathogenic antibiotic resistant bacteria (PARB) and multi-resistant high-risk ARGs-carrying populations robustly persisted throughout the AD process, regardless of the operating conditions. This study highlighted the influence of the AD process and its operating parameters on ARG removal, and revealed the broad spectrum and persistence of PARB in AD systems. These findings provided critical insights for the management of microbial hazards.

The beneficial endophytic microbes enhanced tobacco defense system to resist bacterial wilt disease

BackgroundThe vital role of rhizosphere microbiome in protecting plants against pathogen infection has been well characterized. By contrast, beneficial effects of the plant endophytic microbiome and interactions with plants remain poorly understood. Here, we integrated microbial community analysis, culture-based methods and plant defense gene quantification to systematically investigate the responses of endophytic root and stem microbiomes and the defense system of the tobacco plant to Ralstonia solanacearum, a bacterial pathogen causing bacterial wilt disease worldwide.ResultsAn obvious reduction of community diversity and changes of microbial composition were observed in tobacco root and stem compartments upon R. solanacearum infection. Beneficial endophytic microbes were enriched in both diseased root and stem compartments, and beneficial microbes enriched in roots were more diverse than those in stems. Several beneficial bacteria enriched in diseased roots showed positive correlations with the pathogen abundance and exhibited great antagonistic activities against R. solanacearum. At the same time, the expression of key genes participating in plant defense signaling pathways and activities of plant defense enzymes were activated with R. solanacearum infection. Inoculation of beneficial endophyte Burkholderia ASV_550 in soils could greatly enhance the tobacco defense system in the presence of pathogen and decrease the disease incidence.ConclusionsThe recruited beneficial microbes exhibited an enhancement of the defense system of host plants. This work provides endophyte evidence for the “cry for help” strategy in plants and advances the current understanding of plant–microbe interactions in resisting plant disease.Graphical

Relative quantification of the recA gene for antimicrobial susceptibility testing in response to ciprofloxacin for pathogens of concern

Antimicrobial resistance (AR) is one of the greatest threats to global health and is associated with higher treatment costs, longer hospital stays, and increased mortality. Current gold standard antimicrobial susceptibility tests (AST) rely on organism growth rates that result in prolonged time-to-answer for slow growing organisms. Changes in the cellular transcriptome can be rapid in the presence of stressors such as antibiotic pressure, providing the opportunity to develop AST towards transcriptomic signatures. Here, we show that relative quantification of the recA gene is an indicator of pathogen susceptibly when select species are challenged with relevant concentrations of ciprofloxacin. We demonstrate that ciprofloxacin susceptible strains of Y. pestis and B. anthracis have significant increases in relative recA gene expression after 15 min of exposure while resistant strains show no significant differences. Building upon this data, we designed and optimized seven duplex RT-qPCR assays targeting the recA and 16S rRNA gene, response and housekeeping genes, respectively, for multiple biothreat and ESKAPE pathogens. Final evaluation of all seven duplex assays tested against 124 ciprofloxacin susceptible and resistant strains, including Tier 1 pathogens, demonstrated an overall categorical agreement compared to microbroth dilution of 97% using a defined cutoff. Testing pathogen strains commonly associated with urinary tract infections in contrived mock sample sets demonstrated an overall categorical agreement of 96%. These data indicate relative quantification of a single highly conserved gene accurately determines susceptibility for multiple bacterial species in response to ciprofloxacin.

Regulation of the P53 tumor suppressor gene and the Mcl-2 oncogene expression by an active herbal component delivered through a smart thermo-pH-sensitive PLGA carrier to improve Osteosarcoma treatment.

Osteosarcoma (OS), a lethal malignancy, has witnessed an escalating incidence rate. Contemporary therapeutic strategies for this cancer have proven to be inadequate, primarily due to their extensive side effects and the lack of specificity in targeting the molecular pathways implicated in this disease. Consequently, this project is aimed to manufacture and characterize Poly (Lactic-co-glycolic acid) embodying curcumin, a phytocompound devoid of adverse effects which not only exerts an anti-neoplastic influence but also significantly modulates the genetic pathways associated with this malignancy. In this investigation, multiple formulations of PLGA-Cur were synthesized, and the choice of optimal formula was made considering the efficiency of nanoparticle encapsulation and the drug dispersion rate from synthesized PLGA. The selected formulation's physical and chemical attributes, such as its dimension, polydispersity index of the formulation, surface electrical charge, physical-spatial structure, and stability, were examined using methods, including Dynamic light scattering (DLS), Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), and spectrophotometry. Subsequently, the absence of interaction between the drug and the system was assessed using Fourier Transform Infrared Spectroscopy (FT-IR), and cellular uptake was evaluated using fluorescence microscopy. The smart system's responsiveness to environmental stimuli was determined using the dialysis bag method and its anti-tumor properties were investigated on the SAOS-2 cell line. Finally, to evaluate the system's genetic impact on bone cancer, the molecular quantification of the P53 tumor suppressor gene and the oncogene MCL-2 was analyzed using real-time PCR and their protein expression levels were also examined. The PLGAs synthesized in this study exhibited an encapsulation rate of 91.5 ± 1.16% and a maximum release rate of 71 ± 1%, which were responsive to various stimuli. The size of the PLGAs was 12.5 ± 321.2nm, with an electric charge of -38.9 ± 2.6mV and a PDI of 0.107, indicating suitable morphology and stability. Furthermore, both the system and the drug retained their natural properties after inoculation. The system was readily absorbed by cancer cells and effectively exerted its anti-cancer properties. Notably, the system had a significant impact on the mentioned genes' expression. The produced nanosystem, possessing optimal physicochemical properties, has the potential to enhance the anti-cancer efficacy of curcumin. This is achieved by altering molecular and genetic pathways within cancer cells, thereby positioning it as a viable adjunctive treatment modality and also synthesizing of this herbal base drug system consider as a completely novel method for cancer therapy that can efficiently modulate genetical pathways involved.

DDK-Linker: a network-based strategy identifies disease signals by linking high-throughput omics datasets to disease knowledge.

The high-throughput genomic and proteomic scanning approaches allow investigators to measure the quantification of genome-wide genes (or gene products) for certain disease conditions, which plays an essential role in promoting the discovery of disease mechanisms. The high-throughput approaches often generate a large gene list of interest (GOIs), such as differentially expressed genes/proteins. However, researchers have to perform manual triage and validation to explore the most promising, biologically plausible linkages between the known disease genes and GOIs (disease signals) for further study. Here, to address this challenge, we proposed a network-based strategy DDK-Linker to facilitate the exploration of disease signals hidden in omics data by linking GOIs to disease knowns genes. Specifically, it reconstructed gene distances in the protein-protein interaction (PPI) network through six network methods (random walk with restart, Deepwalk, Node2Vec, LINE, HOPE, Laplacian) to discover disease signals in omics data that have shorter distances to disease genes. Furthermore, benefiting from the establishment of knowledge base we established, the abundant bioinformatics annotations were provided for each candidate disease signal. To assist in omics data interpretation and facilitate the usage, we have developed this strategy into an application that users can access through a website or download the R package. We believe DDK-Linker will accelerate the exploring of disease genes and drug targets in a variety of omics data, such as genomics, transcriptomics and proteomics data, and provide clues for complex disease mechanism and pharmacological research. DDK-Linker is freely accessible at http://ddklinker.ncpsb.org.cn/.

Biological Signaling Network in Myocardial Infarction in Young Adults. A Study of Transcriptome Analysis

Background: Myocardial infarction (MI) is the common manifestation of coronary heart disease that develops from occlusion of coronary arteries. Several risk factors of MI were identified, but data pertaining to genetics and molecular mechanisms involved in the development of MI is limited. Therefore, the present study attempts to analyze the peripheral blood transcriptome information of MI patients and unveil the key genes involved in the pathogenesis of MI. Methods: Total RNA was extracted from the blood sample for illumine sequencing, and raw data obtained were subjected to quality control (QC) using the FastQC tool, followed by trimming of raw data by the fastp tool. Further processed high-quality data were aligned onto the human reference genome using HISAT2 aligner. Gene quantification was done using the feature Counts plugin in the subread package. The raw read counts were given as input to the differential expression analysis (DESeq2) R package for the computation of differentially expressed genes. Gene set enrichment analysis for gene ontology was done using the clusterProfiler R package. Results: A total of 609 genes were significantly expressed in the present study, of which 561 genes were upregulated and 48 genes were downregulated. This study presents overall changes in genes involved in different categories such as biological processes, molecular functions, and cellular components in responses to MI. Conclusions: The significantly deregulated genes identified in the present study not only indicate the molecular and cellular changes but also suggest the scope for the detection of specific gene markers for MI.

Comparative Methods for Demystifying Spatial Transcriptomics.

Spatial Transcriptomics (ST), coined as the term for parallel RNA-Seq on cell populations ordered spatially on a histological tissue section, has recently become increasingly popular, especially in experiments where microfluidics-based single-cell sequencing fails, such as assays on neurons. ST platforms, like the 10x Visium technology investigated herein, therefore produce in a single experiment simultaneously thousands of RNA readouts, captured by an array of micrometer scale spots under the histological section. Therefore, a central challenge of analyzing ST experiments consists of analyzing the gene expression morphology of all spots to delineate clusters of similar cell mixtures, which are then compared to each other to identify up- or down-regulated marker genes. Moreover, another level of complexity in ST experiments, compared to traditional RNA-Seq, is imposed by staining the tissue section with protein markers of cells or cell components to identify spots providing relevant information afterward. The corresponding microscopy images need to be analyzed in addition to the RNA-Seq read mappings on the reference genome and transcriptome sequences. Focusing on the software suite provided by the Visium platform manufacturer, we break down the ST analysis pipeline into its four essential steps-the image analysis, the read alignment, the gene quantification, and the spot clustering-and compare results obtained when using reads from different subsets of spots and/or when employing alternative genome or transcriptome references. Our comparative analyses demonstrate the impact of spot selection and the choice of genome/transcriptome references on the analysis results when employing the manufacturer's pipeline.

Artificial infection pathway of largemouth bass LMBV and identification of resistant and susceptible individuals

Identifying disease-resistant and disease-susceptible materials in largemouth bass can provide fundamental analytical information for disease-resistant breeding research on this species. To date, no stable and effective artificial infection pathway has been established against largemouth bass virus (LMBV) in largemouth bass. In this study, using the pathogen at a concentration of 1.60 × 105 TCID50/mL, largemouth bass juveniles were infected using three different methods: muscle injection, feeding, and immersion. A comprehensive comparative study was conducted on parameters such as disease progression, viral load, pathological changes, and electron microscopy. The results revealed that the injection group experienced rapid mortality, with all individuals dying within 6 days after the infection. The feeding group showed minimal mortality, with an overall mortality rate of 28.57%. The immersion group reached its peak mortality on the 9th day after infection, with an accumulated mortality rate of 63.24%. Viral gene quantification results showed that while in the injection group muscles had the highest viral load followed by the liver and spleen, the other infection methods led to the highest viral loads in the liver and spleen. Tissue pathology and electron microscopy observations revealed that the liver and spleen exhibited the most significant pathological changes and were the easiest organs to detect viral particles, indicating that the liver and spleen are the primary target organs of LMBV in largemouth bass. In conclusion, this study suggests that immersing largemouth bass in LMBV at a concentration of 1.99 × 103 c/mL (diluted 80 times) closely mimics the natural infection rate, allowing for a clear differentiation between causes of death and survival, making it an almost non-invasive artificial infection method that closely resembles natural infection conditions. These findings can provide crucial support for the accurate identification of disease-resistant and disease-susceptible materials in largemouth bass and the breeding of disease-resistant varieties.

Differential expression of alpha-synuclein in the hippocampus of SHR and SLA16 isogenic rat strains

Two inbred strains, Lewis (LEW) and Spontaneously Hypertensive Rats (SHR), are well-known for their contrasting behavior related to anxiety/emotionality. Studies with these two strains led to the discovery of the Quantitative Trait Loci (QTL) on chromosome 4 (Anxrr16). To better understand the influences of this genomic region, the congenic rat strain SLA16 (SHR.LEW-Anxrr16) was developed. SLA16 rats present higher hyperactivity/impulsivity, deficits in learning and memory, and lower basal blood pressure than the SHR strain, even though genetic differences between them are only in chromosome 4. Thus, the present study proposed the alpha-synuclein and the dopaminergic system as candidates to explain the differential behavior of SHR and SLA16 strains. To accomplish this, beyond the behavioral analysis, we performed (I) the Snca gene expression and (II) quantification of the alpha-synuclein protein in the hippocampus (HPC), prefrontal cortex (PFC), and striatum (STR) of SHR and SLA16 strains; (III) sequencing of the 3′UTR of the Snca gene; and (IV) evaluation of miRNA binding in the 3′UTR site. A Single Nucleotide Polymorphism (SNP) was identified in the 3′UTR of the Snca gene, which exhibited upregulation in the HPC of SHR compared to SLA16 females. Alpha-synuclein protein was higher in the HPC of SHR males compared to SLA16 males. The results of this work suggested that differences in alpha-synuclein HPC content could be influenced by miRNA regulation and associated with behavioral differences between SHR and SLA16 animals.

Multiplex Microarrays in 96-Well Plates Photoactivated with 4-Azidotetrafluorobenzaldehyde for the Identification and Quantification of β-Lactamase Genes and Their RNA Transcripts.

Antibiotic-resistant bacteria represent a global issue that calls for novel approaches to diagnosis and treatment. Given the variety of genetic factors that determine resistance, multiplex methods hold promise in this area. We developed a novel method to covalently attach oligonucleotide probes to the wells of polystyrene plates using photoactivation with 4-azidotetrafluorobenzaldehyde. Then, it was used to develop the technique of microarrays in the wells. It consists of the following steps: activating polystyrene, hybridizing the probes with biotinylated target DNA, and developing the result using a streptavidin-peroxidase conjugate with colorimetric detection. The first microarray was designed to identify 11 different gene types and 16 single-nucleotide polymorphisms (SNPs) of clinically relevant ESBLs and carbapenemases, which confer Gram-negative bacteria resistance to β-lactam antibiotics. The detection of bla genes in 65 clinical isolates of Enterobacteriaceae demonstrated the high sensitivity and reproducibility of the technique. The highly reproducible spot staining of colorimetric microarrays allowed us to design a second microarray that was intended to quantify four different types of bla mRNAs in order to ascertain their expressions. The combination of reliable performance, high throughput in standard 96-well plates, and inexpensive colorimetric detection makes the microarrays suitable for routine clinical application and for the study of multi-drug resistant bacteria.