Comparative Gene Expression Analysis Research Articles

Comparative analysis of intestinal structure, enzyme activity, intestinal microbiota and gene expression in different segments of pufferfish (Takifugu Obscurus)

The structure of fish intestines does not have a clear regional division, while the function of the intestines may be related to their structure. Therefore, in this study, the delimitation of intestinal segments in pufferfish (Takifugu obscurus) was achieved by morphological analysis. Subsequently, enzyme activity, intestinal microbiota, and gene expression were examined to compare the differences among the pufferfish various segments. According to four morphological parameters: height of mucosa folds (HF), width of mucosa folds (WF), thickness of muscularis (TM), and cross-sectional area (CSA), the pufferfish's intestine was divided into anterior intestine (AI), middle intestine (MI), and posterior intestine (PI). The activity levels of amylase, lipase, and trypsin in the AI and MI were significantly higher than these in the PI. According to the analysis of 16S rDNA, the dominant microbiota at the phylum level in the different segments were Epsilonbacteraeota, Spirochaetes, and Proteobacteria. At the genus level, there were variations observed in the relative abundance of Brevinema, Mycobacterium, Bradyrhizobium, and Microvirga. α diversity analysis revealed that the richness indexes (Ace and Chao1) were the lowest in the MI, while β diversity analysis revealed significant difference in intestinal microbial community composition among the three intestinal segments. Furthermore, RNA-Seq was used to identify differential expression genes (DEGs) and biological pathways among the different intestinal segments. The DEGs between the AI and MI were enriched in pancreatic secretion and protein digestion and absorption, those between AI and PI were involved in ascorbate and aldarate metabolism and glutathione metabolism, and those between MI and PI were involved in steroid biosynthesis, fat digestion and absorption, vitamin digestion and absorption, and glycine, serine and threonine metabolism. In conclusion, the presented results compare and analyze the differences in various intestinal segments of pufferfish, which will be conductive to future exploration of the functions of these different segments.

Comparative Analysis of ITGΒ6 Gene Expression in Oral Cancer

The goal of this study was to determine the quality and quantity of ITGβ6 gene expression in oral squamous cell carcinoma (OSCC). Two Cell lines (H357) and (Vβ6) were used to analyses β6protein and gene expression by using BAC assay, SDS-PAGE gel, and western blotting, agarose gel as well as real- time PCR techniques. The western blotting and real-time PCR studies demonstrated high level of protein expressions in the transected Vβ6 cells line which shown as clear thick band. On the other hand, a protein expression of H357 cells line was less and gives weak band. Therefore, Squamous cell lines from the oral mucosa that express β6 are linked to increased invasion and progression. This highlights the significance of understanding cancer progression mechanisms and the impact of varying expression levels in different tumors.

Competition-driven phenotypic plasticity in Iron acquisition and aromatic utilization confers a fitness advantage to Pseudomonas putida in an Iron-limited rhizospheric environment

Iron scarcity poses a critical challenge for rhizospheric bacteria like Pseudomonas putida in the competitive rhizosphere. Despite its dependence on iron for essential functions such as root colonization, motility, and aromatic compound utilization, P. putida exhibits limited capability for heterologous siderophore utilization and primarily relies on the secretion of a single siderophore, pyoverdine. This study investigates the mechanisms by which P. putida acquires iron in an iron-limited, aromatic-rich, rhizosphere-like environment. Our findings demonstrate that P. putida exhibits significant phenotypic plasticity, dynamically modulating pyoverdine secretion in response to competitive pressures and substrate availability. This adaptive strategy optimizes energy expenditure and iron acquisition, providing a competitive advantage. Comparative gene expression analysis supports these observations, revealing the molecular underpinnings of this plasticity. Enhanced pyoverdine production driven by competition compensates for the bacterium's limited siderophore repertoire and facilitates rapid aromatic compound utilization, conferring a distinct fitness advantage in iron-deprived conditions. This study elucidates the complex interplay between competition, iron uptake, and aromatic compound utilization that underpins the rhizospheric success of P. putida.

Single-cell transcriptomic profiling of lung fibroblasts in a bleomycin-induced systemic sclerosis mouse model

Systemic sclerosis (SSc) is a complex autoimmune disease characterized by fibrosis, vascular abnormalities, and immune dysfunction, with no definitive cure. Patients with progressive pulmonary fibrosis face a high mortality risk, underscoring the urgent need for effective treatments. Although fibroblasts are recognized as key drivers of fibrosis, the precise molecular mechanisms remain poorly understood. In this study, we employ single-cell RNA sequencing to explore the role of fibroblasts in pulmonary fibrosis. Using a mouse model induced by subcutaneous bleomycin administration, we identify two distinct fibroblast subpopulations: nephronectin-positive (NPNT) and peptidase inhibitor 16-positive cells(PI16). NPNT-positive fibroblasts, located around the alveoli, exhibit increased extracellular matrix expression following bleomycin treatment. To further understand pulmonary fibrosis, subcutaneous and intratracheal bleomycin-induced mouse models are compared. A comparative gene expression analysis reveals shared and unique features between the models, highlighting the complexity of the fibrotic process. These findings offer valuable insights into the molecular mechanisms of SSc-associated pulmonary fibrosis and may inform the development of therapies targeting specific fibroblast subpopulations or pathways.

Comparative Analysis of Phytochemicals and Gene Expression in Soybean (Glycine max) Under Acute Moderated and Severe Elevated Ozone: Unravelling the Role of Antioxidant Defence

ABSTRACTThe increasing concentrations of ground‐level ozone (O3) resulting from industrialisation and anthropogenic activities present a substantial environmental threat to agricultural productivity, particularly affecting O3‐sensitive crops such as soybeans. The effects of acute O3 exposure on soybean yield attributes and seed quality and whether soybean showed different detoxification mechanisms in response to moderate and severe O3 stress are not extensively explored. In this study, soybean seedlings were exposed to moderate (80 nmol mol−1) and acute severe (200 nmol mol−1) O3 stress, and then growth parameters, yield attributes, reactive oxygen species (ROS) levels, enzymatic and non‐enzymatic antioxidant properties and associated gene expression in the leaves were assessed. The results revealed that moderate O3 exposure enhanced growth parameters but reduced the 100‐grain weight, while acute severe exposure sharply depressed growth parameters, yield attributes and the 100‐grain weight. Moderate O3 fumigation significantly increased hydrogen peroxide (H2O2) levels and catalase (CAT) activity from 4 to 32 h. Acute severe O3 stress induced the overproduction of superoxide anions (O2.−) and H2O2 during nearly the whole experiment period, but only enhanced superoxide dismutase (SOD) activity at 32 h, and showed no stimulatory effects on CAT activity. Additionally, the relative expression levels of the SOD and CAT gene family in soybean leaves exposed to elevated O3 were upregulated, peaking at 8 h. Moderate O3 treatment enhanced reduced glutathione (GSH) and ascorbate (AsA) levels and increased the activities of AsA–GSH cycle‐related enzymes. In contrast, acute severe O3 exposure inhibited GSH and AsA contents and markedly suppressed AsA–GSH cycle‐related enzymes, particularly from 8 to 32 h. Redundancy analysis indicated that CAT and AsA play crucial roles in scavenging O3‐induced ROS under moderate stress, while ascorbate peroxidase (APX) and GSH were more effective under acute severe stress conditions. These findings provide insights into the differential impacts of acute O3 stress on soybeans, emphasising the importance of considering both crop yield and grain quality in assessing O3 risks to crops.

Comparative Analysis of Gene Expression at Sea Level and High Altitude: A Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) Approach.

This research studies the gene expression in response to different oxygen environments and looks at high vs low oxygen environments. Tracking down the activity of some of these genes, namely VHLEL, VEGF and HIF-1α, quantitative real-time polymerase chain reaction (PCR) analysis was done for the study group at sea level in Jeddah and at high altitude in Taif city. It has been found that these genes are much more active in higher altitudes which indicates that there is a biological mechanism that makes those specific sites more oversized for the issue of low oxygen. This knowledge is beneficial as it helps in understanding how people grow to live in high-altitude regions. This is positive, especially in justifying the use of the methods in treatment of altitude sickness and other related diseases. Although these findings bring some hope, it would be equally important to include more participants in future studies in order to consolidate our findings and gain deeper understanding of physiological adaptation in low oxygen. This research work has potential significant contribution to the medical profession under conditions of similar environment.

Comparative Study of Photobiomodulation Effects on Alveolar Socket Hard Tissue Healing in Rats: Application of 980 nm Versus 810 nm Lasers.

Background: This study aimed to explore the differential effects of photobiomodulation (PBM) via 980 nm and 810 nm lasers on the hard tissue healing of rat alveolar sockets, with a focus on a comparative analysis of hard tissue regeneration and osteogenic gene expression. Objective: This study aimed to explore the effects of PBM using 980 nm and 810 nm lasers on hard tissue healing of rat alveolar sockets, focusing on hard tissue regeneration and osteogenic gene expression. Materials and Methods: Thirty-six male Wistar rats (5 weeks old) had both right and left maxillary first molars extracted. Post extraction, the right alveolar sockets received PBM treatment with either 980 nm (0.3 W, 18 J/cm2) or 810 nm (0.1 W, 6 J/cm2) lasers for seven days, whereas the left sockets served as controls. Rats were euthanized on days 3, 7, 14, and 28 for histopathological, immunohistochemical, micro computed tomography (micro-CT), and quantitative polymerase chain reactionanalyses. Results: On day 3, early granulation tissue, neovascularization, and inflammatory cell aggregates were observed in all groups. By day 7, active osteoclasts and osteoblasts were noted, with a significant increase in CD31-positive cells in the 980 nm group (p < 0.05). Day 14 showed new bone formation, and by day 28, increased cancellous bone and collagen content were present in all groups, with no significant differences between them (p > 0.05). Gene expression analysis revealed higher BMP-2 and Runx-2 levels in laser-treated groups on day 14 (p < 0.05), with the 980 nm group having higher BMP-2 levels than the 810 nm group (p < 0.05). Bone sialoprotein expression was higher in laser-treated groups on days 14 and 28 (p < 0.05), and osteocalcin expression was highest in the 980 nm group on both days (p < 0.05). Micro-CT analysis showed no significant differences among groups in bone mineral density, bone surface (BS)/bone volume (BV), or bone volume (BV)/TV (total volume) indices. Conclusion: PBM with 980 nm and 810 nm lasers promotes early-stage hard tissue healing in extraction sockets, with the 980 nm laser more effectively enhancing osteogenic gene expression, suggesting its potential as an adjunctive therapy in dental and oral surgery.

Comparative Analysis of Intestinal TLR4 Gene Expression and Functional Verification in Lepus yarkandensis and Oryctolagus cuniculus.

Lepus yarkandensis live year-round in harsh desert environments and are less susceptible to enteritis. The living conditions of Oryctolagus cuniculus in captivity were suitable, but they were highly susceptible to death by Gram-negative bacteria infected with inflammatory bowel disease complex.TLR4 is closely related to the occurrence of enteritis, and the neighbor-joining topology based on the 12S rDNA sequences showed that the relationship between O. cuniculus and L. yarkandensis is as high as 98%.Therefore, we chose O. cuniculus and L. yarkandensis for comparative study.The purpose of this study was to investigate the role of Toll-like receptor 4 (TLR4) in the regulation of immunity and inflammation in the intestinal tract of L. yarkandensis. In this study, the TLR4 gene was cloned for the first time in the colon of L. yarkandensis. The expression of TLR4 in the intestinal tissues of L. yarkandensis and O. cuniculus was detected by histological observation, real-time fluorescence quantification PCR(qRT-PCR), and protein blotting (Western blot).An LPS-induced cell inflammation model was constructed in vitro, and ELISA was used to examine the effect of pEGFP-N1-TLR4 and siRNA knockout on the anti-inflammatory ability of the TLR4 gene. The results showed that the open reading frame of the L. yarkandensis TLR4 gene was 2520bp in length. Compared with the sequence of O. cuniculus, there were 15 differences in the TLR4 amino acid sequence of L. yarkandensis, 12 of which occurred in the LRR domain and 2 in the TIR domain, and the sequence changed from G to D at position 298. Immunohistochemistry showed that TLR4 was mainly expressed in the epithelial cells of the colon L. yarkandensis, and the expression level of TLR4 in the cecum and colon was significantly lower compared with that of O. cuniculus. qRT-PCR and Western blot results showed that the expression level of TLR4 in the colon of L. yarkandensis was significantly lower than that of O. cuniculus. At the cellular level, ELISA showed that overexpression of the TLR4 protein in L. yarkandensis could reduce the LPS-induced inflammatory response. Therefore, according to the above results, the protein structure and function of L. yarkandensis TLR4 may be different due to the change of nucleotide, which affects its binding with LPS and the activation of downstream molecules, so that L. yarkandensis is not prone to enteritis and can adapt to the harsh desert environment for a long time. This study also laid the foundation for improving the disease resistance of O. cuniculus and promoting the development and utilization of genes in L. yarkandensis.

Cross-Species Studies Reveal That Dysregulated Mitochondrial Gene Expression and Electron Transport Complex I Activity Are Crucial for Sarcopenia

The significance of complex I of the electron transport chain (ETC) in the aging process is widely acknowledged; however, its specific impact on the development of sarcopenia in muscle remains poorly understood. This study elucidated the correlation between complex I inhibition and sarcopenia by conducting a comparative analysis of skeletal muscle gene expression in sarcopenia phenotypes from rats, mice, and humans. Our findings reveal a common mechanistic link across species, particularly highlighting the correlation between the suppression of complex I of ETC activity and dysregulated mitochondrial transcription and translation in sarcopenia phenotypes. Additionally, we observed macrophage dysfunction alongside abnormal metabolic processes within skeletal muscle tissues across all species, implicating their pathogenic role in the onset of sarcopenia. These discoveries underscore the importance of understanding the shared mechanisms associated with complex I of ETC in sarcopenia development. The identified correlations provide valuable insights into potential targets for therapeutic interventions aimed at mitigating the impact of sarcopenia, a condition with substantial implications for aging populations.

Abstract C106: Enhanced characterization of molecular attributes through multi-omics analysis and comprehensive evaluation of global and local genomic ancestry in colorectal cancer among Hispanic-Latinos

Abstract Introduction: Colorectal cancer (CRC) remains a significant public health challenge, representing the second leading cause of cancer-related mortality in the United States. Although mortality rates have generally decreased, the Hispanic/Latino (H/L) population in the Los Angeles area still experiences mortality rates up to 20% higher than those of their Caucasian American counterparts. Additionally, they are often diagnosed at a younger age and with more advanced disease stages, highlighting significant disparities in CRC outcomes. Currently, there are limited studies integrating clinical and multi-omics data from H/L populations, which are crucial for understanding the implications of colorectal tumorigenesis and addressing these disparities effectively. Methods: Clinical and genomic sequencing data were obtained from 60 primary CRC Tumor/Normal (T/N) samples within the Hispanic/Latino (H/L) population in the Los Angeles area through the PE-CGS network. For comparison, we analyzed 3,578 samples from non-Hispanic Whites (NHW) obtained from public databases. Additionally, we retrieved three CRC samples with spatial transcriptomic (ST) data from the 10xGenomics database. Using Whole Exome and RNA sequencing data, we performed somatic mutations, somatic copy number alterations (SCNAs), differential gene expression, cellular pathways, gene fusions, and global &amp; local genomic ancestry analyses. The ST data underwent analysis utilizing newly released bioinformatics tools. Clinical and genomic data were integrated. Results: In these studies, distinct Amerindian (AMR) genomic ancestry proportion, age at diagnosis, and tumor localization patterns were observed, alongside significant mutations in key genes such as APC, TP53, and KRAS. The studies revealed evident cancer heterogeneity, influenced by factors such as mutation type, microsatellite instability, tumor subsite, and ethnicity. Additionally, several previously well-defined SCNAs were detected in the majority of tumors. Comparative analysis of gene expression and cellular pathways between H/L and NHW samples revealed distinct patterns. Furthermore, we identified gene fusions that potentially contribute to oncogenic activity in CRC. Ancestry analysis pointed to a predominant AMR ancestry. Notably, distinct associations of genetic ancestry with CRC tumor clinicopathological characteristics were identified. ST analysis delineated separate cancer, immune, and stroma components within the tumors. Conclusion: Our research has explored the molecular profiling of CRC tumors in H/L patients, providing crucial insights into the characterization of CRC tumors at the DNA and RNA levels, as well as the complex clinical and genomic diversity within our target population. Additionally, it offers valuable insights into the heterogeneity of CRC tumors and the tumor microenvironment. These findings establish the groundwork for subsequent projects, potentially leading to precision medicine approaches. Citation Format: Enrique I. Velazquez-Villarreal, Brigette Waldrup, Yonatan Amzaleg, Yuxin Jin, Mackenzie Postel, Donna Loza, Serina Ovalle, Elizabeth Quino, Carmen Chavez, Julie Culver, Mariana C. Stern, Heinz-Josef Lenz, David W. Craig, John D. Carpten. Enhanced characterization of molecular attributes through multi-omics analysis and comprehensive evaluation of global and local genomic ancestry in colorectal cancer among Hispanic-Latinos [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C106.

Comparative Physiological and Gene Expression Analyses Provide Insights into Ion Transports and Osmotic Adjustment of Sweet Sorghum under Salt Stress

Comparative Physiological and Gene Expression Analyses Provide Insights into Ion Transports and Osmotic Adjustment of Sweet Sorghum under Salt Stress

Denoiseit: denoising gene expression data using rank based isolation trees

BackgroundSelecting informative genes or eliminating uninformative ones before any downstream gene expression analysis is a standard task with great impact on the results. A carefully curated gene set significantly enhances the likelihood of identifying meaningful biomarkers.MethodIn contrast to the conventional forward gene search methods that focus on selecting highly informative genes, we propose a backward search method, DenoiseIt, that aims to remove potential outlier genes yielding a robust gene set with reduced noise. The gene set constructed by DenoiseIt is expected to capture biologically significant genes while pruning irrelevant ones to the greatest extent possible. Therefore, it also enhances the quality of downstream comparative gene expression analysis. DenoiseIt utilizes non-negative matrix factorization in conjunction with isolation forests to identify outlier rank features and remove their associated genes.ResultsDenoiseIt was applied to both bulk and single-cell RNA-seq data collected from TCGA and a COVID-19 cohort to show that it proficiently identified and removed genes exhibiting expression anomalies confined to specific samples rather than a known group. DenoiseIt also showed to reduce the level of technical noise while preserving a higher proportion of biologically relevant genes compared to existing methods. The DenoiseIt Software is publicly available on GitHub at https://github.com/cobi-git/DenoiseIt

Comparative Physiological and Gene Expression Analyses Reveal Mechanisms Involved in Maintaining Photosynthesis Capacity, Alleviating Ion Toxicity and Oxidative Stress of Kentucky Bluegrass under NaCl Treatment.

Kentucky bluegrass (Poa pratensis L.), a widely used cool-season turfgrass, shows a high sensitivity to soil salinity. Clarifying the adaptative mechanisms of Kentucky bluegrass that serve to improve its salt tolerance in saline environments is urgent for the application of this turfgrass in salt-affected regions. In this study, physiological responses of the Kentucky bluegrass cultivars "Explorer" and "Blue Best" to NaCl treatment, as well as gene expressions related to photosynthesis, ion transport, and ROS degradation, were analyzed. The results showed that the growth of "Explorer" was obviously better compared to "Blue Best" under 400 mM NaCl treatment. "Explorer" exhibited a much stronger photosynthetic capacity than "Blue Best" under NaCl treatment, and the expression of key genes involved in chlorophyll biosynthesis, photosystem II, and the Calvin cycle in "Explorer" was greatly induced by salt treatment. Compared with "Blue Best", "Explorer" could effectively maintain Na+/K+ homeostasis in its leaves under NaCl treatment, which can be attributed to upregulated expression of genes, such as HKT1;5, HAK5, and SKOR. The relative membrane permeability and contents of O2- and H2O2 in "Explorer" were significantly lower than those in "Blue Best" under NaCl treatment, and, correspondingly, the activities of SOD and POD in the former were significantly higher than in the latter. Moreover, the expression of genes involved in the biosynthesis of enzymes in the ROS-scavenging system of "Explorer" was immediately upregulated after NaCl treatment. Additionally, free proline and betaine are important organic osmolytes for maintaining hydration status in Kentucky bluegrass under NaCl treatment, as the contents of these metabolites in "Explorer" were significantly higher than in "Blue Best". This work lays a theoretical basis for the improvement of salt tolerance in Kentucky bluegrass.

Transcriptomic Analysis Reveals Sex-Based Differences in The Prefrontal Cortex of Autism Spectrum Disorder Patients.

The prevalence of neurological disorders often varies by sex, with conditions such as Alzheimer's disease and autism spectrum disorder (ASD) demonstrating notable differences in incidence. The aim of this study is to understand the molecular basis for these divergences in order to facilitate the creation of sex-specific therapeutic strategies. This study is a bioinformatic analysis of publicly available RNA sequencing datasets involving autism patients. The study utilized RNA sequencing data from postmortem human brains' prefrontal cortex, including 38 neurotypical controls and 34 individuals with ASD. The sequencing data was obtained from previously published papers, and we downloaded the raw data from SRA. We investigated the molecular basis of sex-biased presentation in ASD through comprehensive transcriptomic analysis. Comparative analysis of gene expression between male and female subjects, both autistic and unaffected, was conducted, using a significance level of ≤0.01. In autistic individuals, 136 genes demonstrated differential expression between sexes, predominantly upregulated in males, indicating a bias in male gene expression. Among these, 12 genes were identified as risk factors in the SFARI dataset. While most sex-biased genes were autosomal, expression differences on sex chromosomes were also observed in neurotypical subjects. Notable genes included TCF7L2, collagen family genes, and solute carrier family genes. In ASD males, extracellular matrix (ECM) organization emerged as a significant pathway, while immune-related processes were prominent in unaffected individuals. Our study highlights the impact of the ECM pathway in ASD, with notable differences between sexes, particularly in males. MIR424 shows promise as a potential biomarker for ASD in males. Recognizing the importance of sex differences in ASD transcriptomic research is crucial, as these variances provide insights into the disorder's pathophysiology and may guide the development of more personalized treatments for both sexes.

Engineered uterine primary myometrial cells with high-mobility group AT-hook 2 overexpression display a leiomyoma-like transcriptional and epigenomic phenotype

To determine if engineered HMGA2 overexpressing uterine primary myometrial cells recapitulate the transcriptional and epigenomic features of HMGA2-subtype leiomyomas. Isolated primary, "normal" myometrial cells from 3 patients were engineered to overexpress HMGA2 to determine how HMGA2 establishes transcriptomic and epigenomic features of HMGA2-overexpressing leiomyoma. Academic research laboratory PATIENTS: Primary myometrial cells were isolated from normal myometrium obtained from three patients undergoing hysterectomy. Not applicable MAIN OUTCOME MEASURES: Determined genome-wide transcriptomic and epigenomic features of engineered HMGA2-overexpressing uterine primary myometrial cells. Engineered HMGA2-V5-overexpressing primary myometrial cells approximated the HMGA2 expression level observed in HMGA2-overexpression subtype leiomyoma. HMGA2-V5 expression resulted in differential expression of 1612 genes (FDR < 0.05) which were found to be enriched in pathways associated with leiomyoma formation, including extracellular matrix organization. Comparative gene expression analysis between HMGA2-V5 engineered primary cells and HMGA2-overexpression subtype leiomyoma revealed significant overlap of differentially expressed genes. Mechanistically, HMGA2-V5 overexpression resulted in 41,323 regions with differential H3K27ac deposition (FDR < 0.05) and 205,605 regions of altered chromatin accessibility (FDR < 0.05). Transcription factor binding site analysis implicated the AP-1 family of transcription factors. • What clinical problem is addressed by these studies? About 10-15% of the uterine leiomyoma cases exhibit increased expression of HMGA2; our study addresses the primary role of HMGA2 overexpression in the pathogenesis of leiomyoma. • What are the key findings? Ectopic expression of HMGA2 in primary myometrial cells transforms transcriptional and epigenomic machinery in these cells which to some extent resemble features of leiomyoma. • How do these findings apply to human fertility or the reproductive process? Our study provides a comprehensive analysis into the changes occurring in epigenome of myometrial cells when HMGA2 is overexpressed. Because epigenome can be targeted with drugs, therefore understanding alterations in epigenome provides new avenues for treating leiomyoma which affects reproductive age women.

Comparative Cytological and Gene Expression Analysis Reveals That a Common Wild Rice Inbred Line Showed Stronger Drought Tolerance Compared with the Cultivar Rice.

Common wild rice (Oryza rufipogon Griff.) is an important germplasm resource containing valuable genes. Our previous analysis reported a stable wild rice inbred line, Huaye3, which derives from the common wild rice of Guangdong Province. However, there was no information about its drought tolerance ability. Here, we assessed the germination characteristics and seedling growth between the Dawennuo and Huaye3 under five concentrations of PEG6000 treatment (0, 5%, 10%, 15%, and 20%). Huaye3 showed a stronger drought tolerance ability, and its seed germination rate still reached more than 52.50% compared with Dawennuo, which was only 25.83% under the 20% PEG6000 treatment. Cytological observations between the Dawennuo and Huaye3 indicated the root tip elongation zone and buds of Huaye3 were less affected by the PEG6000 treatment, resulting in a lower percentage of abnormalities of cortical cells, stele, and shrinkage of epidermal cells. Using the re-sequencing analysis, we detected 13,909 genes that existed in the genetic variation compared with Dawennuo. Of these genes, 39 were annotated as drought stress-related genes and their variance existed in the CDS region. Our study proved the strong drought stress tolerance ability of Huaye3, which provides the theoretical basis for the drought resistance germplasm selection in rice.

MitoPADdb: A database of mitochondrial proteins associated with diseases

Mitochondrial protein/gene mutations and expression variations contribute to the pathogenesis of various diseases, such as neurodegenerative and metabolic diseases. Detailed studies on mitochondrial protein-encoding (MPE) genes across diseases can provide clues for novel therapeutic strategies. Here, we collected, compiled, and manually curated the MPE gene mutation and expression variations data and their association with diseases in a single platform named mitoPADdb. The database contains 810 genes with 18,356 mutations and 1284 qualitative expression variations associated with 1793 diseases, grouped into 15 categories. It allows users to perform a comparative quantitative gene expression analysis for 317 transcriptomic studies across disease categories. Further, it provides information on MPE genes-associated molecular pathways. The mitoPADdb is a valuable resource for investigating mitochondrial dysfunction-related diseases. It can be accessed via http://bicresources.jcbose.ac.in/ssaha4/mitopaddb/index.html.

Single-neuron analysis of aging-associated changes in learning reveals impairments in transcriptional plasticity.

The molecular mechanisms underlying age-related declines in learning and long-term memory are still not fully understood. To address this gap, our study focused on investigating the transcriptional landscape of a singularly identified motor neuron L7 in Aplysia, which is pivotal in a specific type of nonassociative learning known as sensitization of the siphon-withdraw reflex. Employing total RNAseq analysis on a single isolated L7 motor neuron after short-term or long-term sensitization (LTS) training of Aplysia at 8, 10, and 12 months (representing mature, late mature, and senescent stages), we uncovered aberrant changes in transcriptional plasticity during the aging process. Our findings specifically highlight changes in the expression of messenger RNAs (mRNAs) that encode transcription factors, translation regulators, RNA methylation participants, and contributors to cytoskeletal rearrangements during learning and long noncoding RNAs (lncRNAs). Furthermore, our comparative gene expression analysis identified distinct transcriptional alterations in two other neurons, namely the motor neuron L11 and the giant cholinergic neuron R2, whose roles in LTS are not yet fully elucidated. Taken together, our analyses underscore cell type-specific impairments in the expression of key components related to learning and memory within the transcriptome as organisms age, shedding light on the complex molecular mechanisms driving cognitive decline during aging.

Risk assessment, fitness cost and transcriptome analysis of cyantraniliprole resistance in Spodoptera frugiperda

Spodoptera frugiperda is a notorious invasive pest causing substantial yield losses of crops and has developed resistance to various types of insecticides. In this study, a cyantraniliprole-resistant strain, SfCYAN-R, was obtained from a susceptible strain, SfCYAN-S, after 13 generations of selection with cyantraniliprole. The fitness cost in SfCYAN-R strain was evaluated, and the putative resistance-related genes were explored by RNA-seq analysis. The results showed that SfCYAN-R strain developed 23.97-fold resistance to cyantraniliprole with the realistic heritability of 0.127. The development time of eggs, larvae, prepupae and pupae in SfCYAN-R strain was significantly prolonged than that in SfCYAN-S strain, but no difference in pupation rate, emergence rate and female fecundity was observed between SfCYAN-R and SfCYAN-S strains. Comparative gene expression analysis between SfCYAN-R and SfCYAN-S strains identified 776 significant differentially expressed genes (DEGs), among which several DEGs associated with xenobiotic metabolism were upregulated in SfCYAN-R strain. These results provide insights into the resistance mechanisms of cyantraniliprole and would be helpful for resistance management of S. frugiperda.

Integration of Image Pattern Recognition and Photon Sensor for Analyzing Cytokine Gene Expression Using πCode MicroDisc.

Current quantitative gene expression detection in genomic and transcriptomic research heavily relies on quantitative real-time PCR (qPCR). While existing multiplex gene detection techniques offer simultaneous analysis of multiple targets, we present an alternative assay capable of detecting gene expression simultaneously within a single well. This highly sensitive method utilizes πCode MicroDiscs, featuring unique identification patterns and fluorescent detection. Our study compared this multiplex πCode platform with a qPCR platform for profiling cytokine gene expression. The πCode MicroDisc assay successfully demonstrated the expression of polymerization markers for M1- and M2-like macrophages generated from THP-1-derived macrophages in a qualitative assay. Additionally, our findings suggest a pattern agreement between the πCode assay and the qPCR assay, indicating the potential of the πCode technology for comparative gene expression analysis. Regarding the inherent sensitivity and linearity, the developed πCode assay primarily provides qualitative gene expression to discriminate the polarization of macrophages. This remarkable capability presents substantial advantages for researchers, rendering the technology highly suitable for high-throughput applications in clinical diagnosis and disease monitoring.