Differential Patterns Research Articles

Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression.

Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps. We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells. EAD workflow is available at https://isarnassiri.github.io/scDIV/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).

Digital health literacy among primary and secondary school teachers-a quantitative study.

Digital health literacy (DHL) is a key competency for individuals' daily decisions toward their health behavior and wellbeing. While there is much focus on health literacy (HL) among the general population, teachers have been rarely addressed. Given the shortages in the teaching workforce in Europe and the impact of demanding working conditions on their health, it is important to address DHL in teachers. This paper examines the DHL of primary and secondary teachers and its associations with sociodemographic and school-related factors. An online cross-sectional study was conducted with 1,600 German primary and secondary school teachers between October and December 2022. To assess DHL, the Digital Health Literacy Instrument (DHLI) including seven subscales was used. Statistical analyses were conducted on item and subscale level and an overall DHL score was calculated. Next to descriptive analyses, bivariate and regression analyses were conducted to explore potential associations with sociodemographic and school-related factors. The frequency of difficulty in using digital health information varied across DHL dimensions and was greatest for protecting privacy (70.9%) and evaluating reliability (40.0%). In multivariate analysis, females more often reported a sufficient ability of adding content (OR = 1.61, CI = 1.05-2.48), while males more often reported a sufficient ability to protect their privacy (OR = 0.45, CI = 0.27-0.75). Teachers with leadership positions more often reported a sufficient ability in adding content (OR = 1.78, CI = 1.07-2.98). Regarding the ability to determine the relevance of online health-related information, no associations with a predictor variable were found. The results suggest that it is important to examine the individual dimensions of DHL and their distinct associations with sociodemographic and school-level factors, rather than just to rely on the overall level of DHL. The differential patterns identified in this study suggest a greater intervention need for teachers from higher age groups, primary and secondary general schools, and those without leadership roles. However, based on the limited predictive power of the variables included, further individual and school-level factors and their potential association with DHL should be investigated in the future. The promotion of DHL should be integrated into both teacher education and in-service training.

The Gap Junction Inhibitor Octanol Decreases Proliferation and Increases Glial Differentiation of Postnatal Neural Progenitor Cells.

Neural precursor cells (NPCs) that persist in the postnatal/adult subventricular zone (SVZ) express connexins that form hemichannels and gap junctions. Gap junctional communication plays a role in NPC proliferation and differentiation during development, but its relevance on postnatal age remains to be elucidated. In this work we aimed to evaluate the effect of the blockade of gap junctional communication on proliferation and cell fate of NPCs obtained from the SVZ of postnatal rats. NPCs were isolated and expanded in culture as neurospheres. Electron microscopy revealed the existence of gap junctions among neurosphere cells. Treatment of cultures with octanol, a broad-spectrum gap junction blocker, or with Gap27, a specific blocker for gap junctions formed by connexin43, produced a significant decrease in bromodeoxyuridine incorporation. Octanol treatment also exerted a dose-dependent antiproliferative effect on glioblastoma cells. To analyze possible actions on NPC fate, cells were seeded in the absence of mitogens. Treatment with octanol led to an increase in the percentage of astrocytes and oligodendrocyte precursors, whereas the percentage of neurons remained unchanged. Gap27 treatment, in contrast, did not modify the differentiation pattern of SVZ NPCs. Our results indicate that general blockade of gap junctions with octanol induces significant effects on the behavior of postnatal SVZ NPCs, by reducing proliferation and promoting glial differentiation.

Differential expression analyses and detection of SNP loci associated with environmental variables: Are salinity and temperature factors involved in population differentiation and speciation in Odontesthes?

Environmental factors play a key role in individual adaptation to different local conditions. Because of this, studies about the physiological and genetic responses of individuals exposed to different natural environments offer clues about mechanisms involved in population differentiation, and as a subsequent result, speciation. Marine environments are especially suited to survey this kind of phenomena because they commonly harbor species adapted to different local conditions along a geographic continuum. Silversides belonging to Odontesthes are commonly distributed in tropical and temperate regions of South America and exhibit noticeable phenotypic plasticity, which allows them to adapt to contrasting environments. In this study, the genetic expression of O. argentinensis sampled along the Uruguayan Atlantic coast and estuarine adjacent areas was investigated. In addition, the correlation between individual genotypes and environmental variables was also analysed in O. argentinensis and O. bonariensis. Results obtained suggest a differential expression pattern of low magnitude among individuals from the different areas sampled and a correlation between several SNP loci and environmental variables. The analyses carried out did not show a clear differentiation among individuals sampled along different salinity regimens, but enriched GOTerms seem to be driven by water oxygen content. On the other hand, a total of 46 SNPs analysed in O. argentinensis and O. bonariensis showed a correlation with salinity and temperature. Although none of the correlated SNPs and corresponding genes from our both analyses were directly associated with hypoxia, genes related to the cardiovascular system and muscle cell differentiation were found. All these genes are interesting candidates for future studies since they are closely related to the differentially expressed genes. Although salinity was also mentioned as an important parameter limiting introgression between O. argentinensis and O. bonariensis, it was found that salinity does not drive differential expression in O. argentinensis, but rather oxygen levels. Moreover, salinity does not directly affect the structure and genetic divergence of the populations, they appear to be structured based on their degree of isolation and geographical distance between them. Further studies, like genome-wide analyses, could help to elucidate additional genes adapted to the different environments in these silverside species.

Long-term evolution of Streptococcus mitis and Streptococcus pneumoniae leads to higher genetic diversity within rather than between human populations.

Evaluation of the apportionment of genetic diversity of human bacterial commensals within and between human populations is an important step in the characterization of their evolutionary potential. Recent studies showed a correlation between the genomic diversity of human commensal strains and that of their host, but the strength of this correlation and of the geographic structure among human populations is a matter of debate. Here, we studied the genomic diversity and evolution of the phylogenetically related oro-nasopharyngeal healthy-carriage Streptococcus mitis and Streptococcus pneumoniae, whose lifestyles range from stricter commensalism to high pathogenic potential. A total of 119 S. mitis genomes showed higher within- and among-host variation than 810 S. pneumoniae genomes in European, East Asian and African populations. Summary statistics of the site-frequency spectrum for synonymous and non-synonymous variation and ABC modelling showed this difference to be due to higher ancestral bacterial population effective size (Ne) in S. mitis, whose genomic variation has been maintained close to mutation-drift equilibrium across (at least many) generations, whereas S. pneumoniae has been expanding from a smaller ancestral bacterial population. Strikingly, both species show limited differentiation among human populations. As genetic differentiation is inversely proportional to the product of effective population size and migration rate (Nem), we argue that large Ne have led to similar differentiation patterns, even if m is very low for S. mitis. We conclude that more diversity within than among human populations and limited population differentiation must be common features of the human microbiome due to large Ne.

Environmental variation predicts patterns of genomic variation in an African tropical forest frog

Central African rainforests are predicted to be disproportionately affected by future climate change. How species will cope with these changes is unclear, but rapid environmental changes will likely impose strong selection pressures. Here we examined environmental drivers of genomic variation in the central African puddle frog (Phrynobatrachus auritus) to identify areas of elevated environmentally-associated turnover. We also compared current and future climate models to pinpoint areas of high genomic vulnerability where allele frequencies will have to shift the most in order to keep pace with future climate change. Neither physical landscape barriers nor the effects of past Pleistocene refugia influenced genomic differentiation. Alternatively, geographic distance and seasonal aspects of precipitation are the most important drivers of SNP allele frequency variation. Patterns of genomic differentiation coincided with key ecological gradients across the forest-savanna ecotone, montane areas, and a coastal to interior rainfall gradient. Areas of greatest vulnerability were found in the lower Sanaga basin, the southeastern region of Cameroon, and southwest Gabon. In contrast with past conservation efforts that have focused on hotspots of species richness or endemism, our findings highlight the importance of maintaining environmentally heterogeneous landscapes to preserve genomic variation and ongoing evolutionary processes in the face of climate change.

Single-cell and bulk RNA-seq unveils the immune infiltration landscape associated with cuproptosis in cerebral cavernous malformations

BackgroundCerebral cavernous malformations (CCMs) are vascular abnormalities associated with deregulated angiogenesis. Their pathogenesis and optimal treatment remain unclear. This study aims to investigate the molecular signatures of cuproptosis, a newly identified type of cell death, associated with CCMs development.MethodsBulk RNA sequencing (RNA-seq) from 15 CCM and 6 control samples were performed with consensus clustering and clustered to two subtypes based on expression levels of cuproptosis-related genes (CRGs). Differentially expressed genes and immune infiltration between subtypes were then identified. Machine learning algorithms including the least absolute shrinkage and selection operator and random forest were employed to screen for hub genes for CCMs associated with cuproptosis. Furthermore, Pathway enrichment and correlation analysis were used to explore the functions of hub genes and their association with immune phenotypes in CCMs. An external dataset was then employed for validation. Finally, employing the Cellchat algorithm on a single-cell RNA-seq dataset, we explored potential mechanisms underlying the participation of these hub genes in cell-cell communication in CCMs.ResultsOur study revealed two distinct CCM subtypes with differential pattern of CRG expression and immune infiltration. Three hub genes (BTBD10, PFDN4, and CEMIP) were identified and validated, which may significantly associate with CCM pathogenesis. These genes were found to be significantly upregulated in CCM endothelial cells (ECs) and were validated through immunofluorescence and western blot analysis. Single-cell RNA-seq analysis revealed the cellular co-expression patterns of these hub genes, particularly highlighting the high expression of BTBD10 and PFDN4 in ECs. Additionally, a significant co-localization was also observed between BTBD10 and the pivotal cuproptosis gene FDX1 in Mki67+ tip cells, indicating the crucial role of cuproptosis for angiogenesis in CCMs. The study also explored the cell-cell communication between subcluster of ECs expressing these hub genes and immune cells, particularly M2 macrophages, suggesting a role for these interactions in CCM pathogenesis.ConclusionThis study identifies molecular signatures linking cuproptosis to CCMs pathogenesis. Three hub genes—PFDN4, CEMIP, and BTBD10—may influence disease progression by modulating immunity. Further research is needed to understand their precise disease mechanisms and evaluate their potential as biomarkers or therapeutic targets for CCMs.

Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

The sandfish Holothuria (Metriatyla) scabra, is a high-value tropical sea cucumber harvested from wild stocks for over four centuries in multi-species fisheries across its Indo-Pacific distribution, for the global bêche-de-mer (BDM) trade. Within Southeast Asia, the Philippines is an important centre of the BDM trade, however overharvesting and largely open fishery management have resulted in declining catch volumes. Sandfish mariculture has been developed to supplement BDM supply and assist restocking efforts; however, it is heavily reliant on wild populations for broodstock supply. Consequently, to inform fishery, mariculture, germplasm and translocation management policies for both wild and captive resources, a high-resolution genomic audit of 16 wild sandfish populations was conducted, employing a proven genotyping-by-sequencing approach for this species (DArTseq). Genomic data (8,266 selectively-neutral and 117 putatively-adaptive SNPs) were used to assess fine-scale genetic structure, diversity, relatedness, population connectivity and local adaptation at both broad (biogeographic region) and local (within-biogeographic region) scales. An independent hydrodynamic particle dispersal model was also used to assess population connectivity. The overall pattern of population differentiation at the country level for H. scabra in the Philippines is complex, with nine genetic stocks and respective management units delineated across 5 biogeographic regions: (1) Celebes Sea, (2) North and (3) South Philippine Seas, (4) South China and Internal Seas and (5) Sulu Sea. Genetic connectivity is highest within proximate marine biogeographic regions (mean Fst=0.016), with greater separation evident between geographically distant sites (Fst range=0.041–0.045). Signatures of local adaptation were detected among six biogeographic regions, with genetic bottlenecks at 5 sites, particularly within historically heavily-exploited locations in the western and central Philippines. Genetic structure is influenced by geographic distance, larval dispersal capacity, species-specific larval development and settlement attributes, variable ocean current-mediated gene flow, source and sink location geography and habitat heterogeneity across the archipelago. Data reported here will inform accurate and sustainable fishery regulation, conservation of genetic diversity, direct broodstock sourcing for mariculture and guide restocking interventions across the Philippines.

Identification of disulfidptosis-associated genes and characterization of immune cell infiltration in thyroid carcinoma.

The primary objective of this study is to conduct a comprehensive screening and analysis of differentially expressed genes related to disulfidoptosis (DEDRGs) in thyroid carcinoma (THCA). This entails delving into the intricate characterization of immune cell infiltration within the THCA context and subsequently formulating and validating a novel prognostic model. To achieve our objectives, we first delineated two distinct subtypes of disulfidoptosis-related genes (DRGs) via consensus clustering methodology. Subsequently, employing the limma R package, we identified the DEDRGs critical for our investigation. These DEDRGs underwent meticulous validation across various databases, alongside an in-depth analysis of gene regulation. Employing functional enrichment techniques, we explored the potential molecular mechanisms underlying disulfidoptosis in THCA. Furthermore, we scrutinized the immune landscape within the two identified subtypes utilizing CIBERSORT and ESTIMATE algorithms. The construction of the prognostic model for THCA entailed intricate methodologies including univariate, multivariate Cox regression, and LASSO regression algorithms. The validity and efficacy of our prognostic model were corroborated through Kaplan-Meier survival curves and ROC curves. Additionally, a nomogram was meticulously formulated to facilitate the prediction of patient prognosis. To fortify our findings, we conducted a comprehensive Bayesian co-localization analysis coupled with rigorous in vitro experimentation, aimed at unequivocally establishing the validity of the identified DEDRGs. Our analyses unveiled Cluster C1, characterized by elevated expression levels of DEDRGs, as harboring a favorable prognosis accompanied by abundant immune cell infiltration. Correlation analyses underscored predominantly positive associations among the DEDRGs, further affirming their significance in THCA. Differential expression patterns of DEDRGs between tumor samples and normal tissues were evident across the GEPIA and HPA databases. Insights from the TIMER database underscored a robust correlation between DEDRGs and immune cell infiltration. KEGG analysis elucidated the enrichment of DEDRGs primarily in pivotal pathways including MAPK, PPAR signaling pathway, and Proteoglycans in cancer. Furthermore, analyses using CIBERSORT and ESTIMATE algorithms shed light on the crucial role played by DEDRGs in shaping the immune microenvironment. The prognostic model, anchored by five genes intricately associated with THCA prognosis, exhibited commendable predictive accuracy and was intricately linked to the tumor immune microenvironment. Notably, patients categorized with low-risk scores stood to potentially benefit more from immunotherapy. The validation of DEDRGs unequivocally underscores the protective role of INF2 in THCA. In summary, our study delineates two discernible subtypes intricately associated with DRGs, revealing profound disparities in immune infiltration and survival prognosis within the THCA milieu. The implications of our findings extend to potential treatment strategies for THCA patients, which could entail targeted interventions directed towards DEDRGs and prognostic genes, thereby influencing disulfidptosis and the immune microenvironment. Moreover, the robust predictive capability demonstrated by our prognostic model, based on the five genes (ANGPTL7, FIRRE, ODAPH, PROKR1, SFRP5), underscores its potential clinical utility in guiding personalized therapeutic approaches for THCA patients.

The comparative toxicity of biobased, modified biobased, biodegradable, and petrochemical-based microplastics on the brackish water flea Diaphanosoma celebensis

The escalating production and improper disposal of petrochemical-based plastics have led to a global pollution issue with microplastics (MPs), which pose a significant ecological threat. Biobased and biodegradable plastics are believed to mitigate plastic pollution. However, their environmental fate and toxicity remain poorly understood. This study compares the in vivo effects of different types of MPs, poly(butylene adipate-co-terephthalate) as a biodegradable plastic, polylactic acid (PLA) as a biobased plastic, β-cyclodextrin-grafted PLA as a modified biobased plastic, and low density polyethylene as the reference petrochemical-based plastic, on the key aquatic primary consumer Diaphanosoma celebensis. Exposure to MPs resulted in significant reproductive decline, with comparable effects observed irrespective of MP type or concentration. Exposure to MPs induced distinct responses in redox stress, with transcriptional profiling revealing differential gene expression patterns that indicate varied cellular responses to different types of MPs. ATP-binding cassette transporter activity assays demonstrated altered efflux activity, mainly in response to modified biobased and biodegradable MPs. Overall, this study highlights the comparable in vivo and in vitro effects of biobased, biodegradable, and petrochemical-based MPs on aquatic primary consumers, highlighting their potential ecological implications.

Circulating kidney injury molecule-1 (KIM-1) biomarker analysis in IMmotion010: A randomized phase 3 study of adjuvant (adj) atezolizumab (atezo) vs placebo (pbo) in patients (pts) with renal cell carcinoma (RCC) at increased risk of recurrence after resection.

4506 Background: In IMmotion010, adj atezo did not prolong investigator-assessed disease-free survival (DFS; primary endpoint) vs pbo after resection in pts with RCC (HR: 0.93, 95% CI: 0.75, 1.15; P=0.50; Pal Lancet 2023). This exploratory analysis of circulating protein biomarkers was performed to identify high-risk pts with minimal residual disease (MRD) who may show differential benefit from treatment (tx) with atezo. Methods: Pts with RCC with clear-cell or sarcomatoid component and increased recurrence risk post nephrectomy were randomized 1:1 to atezo 1200 mg or pbo IV q3w for 16 cycles or 1 year. A retrospective proteomics analysis was done with an affinity-based proximity extension assay (PEA) panel of ≈3000 analytes to identify circulating proteins with differential abundance patterns in matched serum samples (baseline vs at recurrence). A high sensitivity electrochemiluminescence (ECL) assay was then used to evaluate levels of KIM-1, a membrane glycoprotein overexpressed in clear-cell and papillary RCC, in all available baseline and post-tx serum samples. Outcomes in pts with KIM-1 high (≥86 pg/mL) vs low status at baseline were analyzed. Results: In pts with matched PEA samples (n=73), circulating KIM-1 was identified as the most significantly enriched protein at recurrence vs baseline. Of 778 pts enrolled in IMmotion010, 752 (97%) had baseline KIM-1 data (high: 300 [40%]; low: 452 [60%]). KIM-1–high status was associated with reduced DFS, and pts with KIM-1 high had better DFS with atezo vs pbo (Table). Longitudinal analysis of matched samples showed that in KIM-1–high pts, 9% (12/138) and 26% (36/141) of pts had a ≥30% increase from baseline in KIM-1 levels at Cycle 4 Day 1 with atezo vs pbo, compared with 16% (34/213) and 12% (25/207) in KIM-1-low pts, respectively. A ≥30% KIM-1 increase was associated with worse DFS in both KIM-1–high (atezo HR: 1.68, 95% CI: 0.77, 3.69; pbo HR: 3.53, 95% CI: 2.24, 5.58) and KIM-1–low (atezo HR: 3.56, 95% CI 2.21, 5.75; pbo HR: 3.22, 95% CI: 1.81, 5.70) subgroups. In pts with matched ECL samples (n=103), median KIM-1 levels were higher ( P<0.001) at recurrence (172 pg/mL) than at baseline (79 pg/mL). Conclusions: In IMmotion010, high baseline serum KIM-1 levels were associated with poorer prognosis but improved clinical outcomes with atezo vs pbo. Increased post-tx KIM-1 was associated with worse DFS. These data suggest that circulating KIM-1 may be a non-invasive marker of MRD and disease recurrence and be associated with benefit from atezo in adj RCC. Further investigation of KIM-1 in adj RCC is warranted. Clinical trial information: NCT03024996 . [Table: see text]

Investigation of a potential protein biomarker signature that may predict clinical benefit of NT-I7 and pembrolizumab in patients with cold gastrointestinal tumors.

2563 Background: Microsatellite stable colorectal (MSS-CRC) and pancreatic cancer (PDAC) are immunologically cold tumors due to low immunogenicity and lack of genomic diversity. NT-I7, a long-acting IL-7, and pembrolizumab (pembro) show efficacy in these hard-to-treat indications. While a limited set of patients (pts) achieve objective response, frequency and duration of the disease control rate point to a larger subset obtaining clinical benefit. To identify novel predictive biomarkers, we analyzed baseline peripheral and biopsy samples from pts based on treatment duration. Methods: Open-label Phase 2a study in pts with relapsed/refractory checkpoint inhibitor-naïve MSS-CRC and PDAC; NT-I7 1200 µg/kg IM every 6 weeks (Q6W), pembro 200 mg IV Q3W. Subjects were grouped by treatment duration, measured in NT-I7 doses administered before treatment discontinuation for any cause: 1 dose was short (ST), 2-3 doses medium (MT) and ≥4 doses long (LT). Correlative studies included peripheral (proteomics, T cell receptor sequencing [TCRseq], single cell RNA sequencing [scRNAseq]), and biopsy (genomics, transcriptomics, TCRseq). Results: As of 02OCT2023, 53 evaluable pts completed or discontinued treatment; 5 are still on follow up. ST group included 21 pts, MT 22 and LT 10 (including all 5 partial responders). Tumor biopsies were confirmed MSS with low tumor mutational burden (TMB). LT pts had similar age (59.0 [53.0-71.5] vs 66.0 [47.3-73.5]; ST vs LT) and lower baseline tumor burden (81.0 mm vs 58.0 mm; ST vs LT, p = 0.022). Biopsy analysis showed LT pts had, at baseline, upregulated pathways related to immune activity despite confirmed cold tumor status. Baseline scRNAseq in peripheral blood showed that stem-like CD8 T cells (precursors of exhausted [TPEX] and stem-cell memory [TSCM]) had a differential activation pattern in LT pts; those pathways were enriched in memory effector subsets in ST pts. Preserved antigen-specific stemness may be needed for NT-I7 + pembro efficacy. Baseline concentrations of 3 proteins that can be produced by growing tumors were significantly increased in ST pts. Pts were classified based on elevated levels of these potential biomarkers: POSITIVE (≥2 biomarkers; 20 pts) and NEGATIVE (≤1 biomarker; 33 pts). Pts with NEGATIVE signature at baseline had significantly higher overall survival, regardless of ST, MT or LT status (13.2 vs 8.9 months, p = 0.030). Conclusions: Preserved tumor-specific TPEX activity may be required for NT-I7 + pembro activity based on its presence in LT pts, who remained on treatment the longest. According to this analysis, there are 3 potentially predictive protein biomarkers that may help identify a pt subset more likely to experience clinical benefits from the combination treatment of NT-I7 + pembro. Further verification of the predictive nature of this signature in independent cohorts is ongoing. Clinical trial information: NCT04332653 .

Non-invasive diagnosis of nature of pulmonary nodules using the whole genome methylation sequencing of circulating cell-free DNA.

e20038 Background: The frequent false-positive results of lung cancer screening of low-dose computed tomography (LDCT) remains a challenge. In this study, we aimed to establish a novel panel of cancer-specific methylated regions detected from circulating cell-free DNA (cfDNA) for differentiating malignant pulmonary nodules (PNs) from benign lesions in high-risk patients. Methods: We performed DNA methylation profiling by high throughput DNA bisulfite sequencing in tissue samples (nodule size < 3 cm in diameter) to learn methylation patterns that differentiate cancerous tumors from benign lesions. Then we filtered out differential methylation patterns in circulating cfDNA that are consistent with tissue expression patterns and built an assay for plasma sample classification. Area under the curve was computed for each receiving operation curve, and 95% confidence intervals were also estimated by bootstrapping with 1,000 iterations. Results: We first performed the whole genome methylation sequencing of 100 tissue samples from PNs to learn cancer-specific methylation patterns, and obtained 2,406 differential hypermethylated regions and 16,028 differential hypomethylated regions. These tissue-derived DNA methylation markers were further filtered using a training set of 42 plasma samples and 11 markers were ultimately identified to build a diagnostic prediction model. This methylation panel provided promising results in an independent validation set of additional 17 plasma samples, with a sensitivity of 66.67% (95% CI: 0.25–1.00) and a specificity of 79.17% for differentiating patients with malignant tumor (N = 12) from patients with benign lesions (n = 5). A further validation study of this methylation panel in the cancer genome atlas data set demonstrated significant discriminatory performance in distinguishing patients with lung cancer from subjects without malignancy (area under the curve = 0.88). Conclusions: Our model based on the measurement of circulating cfDNA methylation provide a minimally invasive procedure for differentiation of early-stage lung cancer and nonmalignant pulmonary nodules, and may guide management of positive LDCT screening results. Additional clinical studies with larger sample size are needed to establish the robustness of this model.

Acute ethanol disrupts conditioned inhibition in the male rat.

Alcohol can disrupt conditioned sexual inhibition (CSI) established by first-order conditioning in male rats. CSI can also be induced using second-order conditioning, during which male rats are trained to associate a neutral odor with a nonreceptive female. As a result, when given access to two receptive females (one scented and one unscented) during a copulatory preference test, they display CSI toward the scented female. The present study examined the effect of low-to-moderate doses of alcohol on CSI and brain activation following exposure to alcohol and the olfactory cue alone. Sexually-naïve Long-Evans rats received alternate conditioning sessions with unscented receptive or scented (almond extract) non-receptive females. Following the conditioning phase, males were injected with saline, alcohol 0.5g/kg or 1g/kg, 45min before a copulatory test with two receptive females, with one bearing the olfactory cue. Fos activation was later assessed, following exposure to alcohol and the olfactory cue alone, in several brain regions involved in the expression and regulation of male sexual behavior. While males in the saline group displayed sexual avoidance towards the scented female, those injected with alcohol before the copulatory test, regardless of the dose, copulated indiscriminately with both females. Subsequent exposure to alcohol and the olfactory cue alone induced different Fos expression between groups in several brain regions. Low to moderate doses of alcohol disrupt conditioned sexual inhibition in male rats and induce a differential pattern of neural activation, particularly in regions involved in the expression and regulation of sexual behavior.

The Efficacy of Imiquimod-Induced Psoriasis Model on Murine Cells.

Keratinocytes are an essential component of the epidermis that undergoes constant proliferation and differentiation. However, the dysregulation of keratinocyte differentiation has been implicated in various skin disorders such as psoriasis. Imiquimod, otherwise known as IMQ, is a topical immunomodulator often used to induce psoriasis-like lesions in murine models for research purposes. This study focuses on the efficacy of using IMQ to induce a psoriasis-like model on murine skin cells by analyzing single-cell RNA sequencing and trajectory analysis. The results indicate a few differences between IMQ-induced and control murine cells, primarily the increased keratinocyte and immune cell populations, which reflects the cell identity found on psoriatic skin. However, trajectory analysis reveals that IMQ-induced cells have quite a linear differentiation pattern compared to the branched pattern found in control cells. As a result, further research must be conducted to explore differing factors between psoriatic cells and IMQ-induced cells to determine its usefulness in mimicking psoriasis-like conditions for research.

Transcriptomic analysis reveals differential gene expression patterns of Lacticaseibacillus casei ATCC 393 in response to ultrasound stress

In recent years, there has been a growing interest in modulating the performance of probiotic, mainly Lactic Acid Bacteria (LAB), in the field of probiotic food. Attenuation, induced by sub-lethal stresses, delays the probiotic metabolism, and induces a metabolic shift as survival strategy. In this paper, RNA sequencing was used to uncover the transcriptional regulation in Lacticaseibacillus casei ATCC 393 after ultrasound-induced attenuation. Six (T) and 8 (ST) min of sonication induced a significant differential expression of 742 and 409 genes, respectively. We identified 198 up-regulated and 321 down-regulated genes in T, and similarly 321 up-regulated and 249 down-regulated in ST. These results revealed a strong defensive response at 6 min, followed by adaptation at 8 min. Ultrasound attenuation modified the expression of genes related to a series of crucial biomolecular processes including membrane transport, carbohydrate and purine metabolism, phage-related genes, and translation. Specifically, genes encoding PTS transporters and genes involved in the glycolytic pathway and pyruvate metabolism were up-regulated, indicating an increased need for energy supply, as also suggested by an increase in the transcription of purine biosynthetic genes. Instead, protein translation, a high-energy process, was inhibited with the down-regulation of ribosomal protein biosynthetic genes. Moreover, phage-related genes were down-regulated suggesting a tight transcriptional control on DNA structure. The observed phenomena highlight the cell need of ATP to cope with the multiple ultrasound stresses and the activation of processes to stabilize and preserve the DNA structure. Our work demonstrates that ultrasound has remarkable effects on the tested strain and elucidates the involvement of different pathways in its defensive stress-response and in the modification of its phenotype.

Spatial and Temporal Heterogeneity of Eco-Environmental Quality in Yanhe Watershed (China) Using the Remote-Sensing-Based Ecological Index (RSEI)

The long-term impacts of climate change and human activities have resulted in the Yanhe watershed, a typical watershed in the Loess Plateau region, exhibiting a high degree of vulnerability and significant heterogeneity in ecological environmental quality. This has led to environmental degradation and complex socio-ecological challenges. Consequently, there is an urgent need to carry out research on the spatial and temporal differentiation patterns of ecological environment quality. By utilizing remote sensing data spanning 21 years, this study evaluated the evolutionary trends and consistency of ecological environment quality (EEQ) within the Yanhe watershed based on the remote-sensing-based ecological index (RSEI). Furthermore, it examined global and local spatial autocorrelation of the RSEI by constructing a hexagonal grid, thereby revealing the spatiotemporal characteristics of EEQ at different scales within the Yanhe watershed. The results were as follows: (1) The EEQ has exhibited an overall upward trend in the past two decades, while it has displayed significant fluctuations; (2) the Global Moran’s I values for the years 2000, 2010, and 2020 were 0.18, 0.32, and 0.21, respectively, indicating a presence of spatial autocorrelation within the RSEI; (3) the overall EEQ of the Yanhe watershed will continue to improve, although the ecological quality in certain areas remains unstable due to local natural conditions and human activities. This research not only contributes to the technical framework for analyzing the spatiotemporal heterogeneity of EEQ but also provides actionable insights for ecosystem restoration and sustainability within the Loess Plateau watershed. Our work advances the understanding of ecological dynamics in semi-arid regions and offers a model for assessing ecological quality in similar environmental contexts.

C57BL/6J offspring mice reared by a single-mother exhibit, compared to mice reared in a biparental parenting structure, distinct neural activation patterns and heightened ethanol-induced anxiolysis.

Parenting experiences with caregivers play a key role in neurodevelopment. We recently reported that adolescents reared by a single-mother (SM) display an anxiety-prone phenotype and drink more alcohol, compared to peers derived from a biparental (BP) rearing condition. To investigate if SM and BP offspring infant mice exhibit differential sensitivity to ethanol-induced locomotor activity and differential activity patterns in brain areas related to anxiety response. We also analyzed anxiety response and ethanol-induced anxiolysis in SM and BP adolescents. Mice reared in SM or BP conditions were assessed for (a) ethanol-induced locomotor activity at infancy, (b) central expression of Fos-like proteins (likely represented mostly by FosB, a transcription factor that accumulates after chronic stimuli exposure and serves as a molecular marker of neural plasticity) and cathecolaminergic activity, and (c) anxiety-like behavior and ethanol-induced anxiolysis in adolescence. Infant mice were sensitive to the stimulating effects of 2.0g/kg alcohol, regardless parenting structure. SM mice exhibited, relative to BP mice, a significantly greater number of Fos-like positive cells in the central amygdala and basolateral amygdala nuclei. Ethanol treatment, but not parenting condition, induced greater activation of dopaminergic neurons in ventral tegmental area. SM, but not BP, adolescent mice were sensitive to ethanol-induced anxiolysis. These results highlight the complex relationship between parenting experiences and neurodevelopment. The SM parenting may result in greater neural activation patterns in brain areas associated with anxiety response, potentially contributing to increased basal anxiety and alcohol sensitivity.

ABDS: a bioinformatics tool suite for analyzing biologically diverse samples.

Bioinformatics software tools are essential to identify informative molecular features that define different phenotypic sample groups. Among the most fundamental and interrelated tasks are missing value imputation, signature gene detection, and differential pattern visualization. However, many commonly used analytics tools can be problematic when handling biologically diverse samples if either informative missingness possess high missing rates with mixed missing mechanisms, or multiple sample groups are compared and visualized in parallel. We developed the ABDS tool suite specifically for analyzing biologically diverse samples. Collectively, a mechanism-integrated group-wise pre-imputation scheme is proposed to retain informative missingness associated with signature genes, a cosine-based one-sample test is extended to detect group-silenced signature genes, and a unified heatmap is designed to display multiple sample groups. We describe the methodological principles and demonstrate the effectiveness of three analytics tools under targeted scenarios, supported by comparative evaluations and biomedical showcases. As an open-source R package, ABDS tool suite complements rather than replaces existing tools and will allow biologists to more accurately detect interpretable molecular signals among phenotypically diverse sample groups.

Hand movement trajectories illustrate the mechanism underlying Kurt Lewin's distinction between approach-approach and avoidance-avoidance motivational conflicts.

Classic motivational conflicts theory (Lewin, 1931) distinguishes between approach-approach, and avoidance-avoidance conflicts. Previous research has focused solely on testing the theory's prediction that avoidance-avoidance conflicts are more difficult to resolve than approach-approach ones, using outcome measures (decision time and self-reports). The theory, however, specifies a force-fields mechanism to account for this difference in conflict resolution difficulty, whereby avoidance-avoidance conflicts (compared to approach-approach ones) elicit more (a) oscillations and (b) return to the middle point between options. However, this force-fields mechanism has never been empirically tested, arguably due to a lack of the tools to do so. In five studies (N = 534 U.K. residents), we use mouse-tracking measures to provide insight into the force-fields mechanism. We show that the force-fields' mechanistic properties-oscillations and returns to the middle point-distinguish the two types of conflict and uniquely account for conflict resolution difficulty beyond standard conflict-strength measures. Moreover, we test a novel, theory-driven prediction and robustly show a differential pattern of increased oscillations as a function of the decision-maker's proximity to the decision options. Finally, we test a boundary condition moderating the influence of conflict type on both the force-fields' mechanistic properties and conflict resolution difficulty. (PsycInfo Database Record (c) 2024 APA, all rights reserved).