From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements.

Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.

Comparing Gene Expression Between Planktonic and Biofilm Cells of Foodborne Bacterial Pathogens Through RT-qPCR.

Like most microorganisms, important foodborne pathogenic bacteria, such as Salmonella enterica, Listeria monocytogenes, and several others as well, can attach to surfaces, of either abiotic or biotic nature, and create biofilms on them, provided the existence of supportive environmental conditions (e.g., permissive growth temperature, adequate humidity, and nutrient presence). Inside those sessile communities, the enclosed bacteria typically present a gene expression profile that differs from the one that would be displayed by the same cells growing planktonically in liquid media (free-swimming cells). This altered gene expression has important consequences on cellular physiology and behavior, including stress tolerance and induction of virulence. In this chapter, the methodology to use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to monitor and comparatively quantify expression changes in preselected genes of bacteria between planktonic and biofilm growth modes is presented.

Biosimilars Versus Originators in Children With Juvenile Idiopathic Arthritis: A Real-World Experience.

INTRODUCTION: We aimed to evaluate the efficacy, safety, and immunogenicity profile of Etanercept (ETA) and Adalimumab (ADA) biosimilars (BIOs) compared to their originators in children with juvenile idiopathic arthritis (JIA). METHOD: Eighty-one JIA children treated with ETA or ADA originators or BIOs were examined at baseline (T0) and after 3- (T1), 6- (T2), 12- (T3), and 24-(T4) months after starting treatment. RESULTS: Lower Juvenile Arthritis Disease Activity Score 10 (JADAS-10) scores were reported at T1, T2, T3, and T4 in JIA children treated with BIOs than originators (all p < 0.05). At T1 and T3, anti-drugs antibodies levels were lower in children receiving BIOs than originators (p = 0.04 and p = 0.0007, respectively), even after adjustments (both p < 0.05). Relapses were lower for BIOs compared to originators (p < 0.001). Safety profile was comparable between the groups (p > 0.05). DISCUSSION: A better overall profile of BIOs than originators was demonstrated in JIA children, but larger confirmatory studies are needed.

Protocol for in vitro transcribing mRNAs with defined poly(A)-tail lengths and visualizing sequential PABP binding.

Quantifying the number of proteins that interact with mRNAs, in particular with poly(A) tails of mRNAs, is crucial for understanding gene regulation. Biochemical assays offer significant advantages for this purpose. Here, we present a protocol for synthesizing mRNAs with accurate, length-specific poly(A) tails through a PCR-based approach. We also describe steps for an in vitro (i.e., cell-free) approach for visualizing the sequential binding of Cytoplasmic Poly(A)-Binding Proteins (PABPCs) to these poly(A) tails. We detail quality control steps throughout the procedure. For complete details on the use and execution of this protocol, please refer to Grandi et al.1.

Exposure of Arabidopsis thaliana Mutants to Genotoxic Stress Provides New Insights for the Involvement of TDP1α and TDP1ß genes in DNA-Damage Response.

Genotoxic stress activates the DNA-damage response (DDR) signalling cascades responsible for maintaining genome integrity. Downstream DNA repair pathways include the tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme that hydrolyses the phosphodiester bond between the tyrosine of topoisomerase I (TopI) and 3'-phosphate of DNA. The plant TDP1 subfamily contains the canonical TDP1α gene and the TDP1ß gene whose functions are not fully elucidated. The current study proposes to investigate the involvement of TDP1 genes in DDR-related processes by using Arabidopsis thaliana mutants treated with genotoxic agents. The phenotypic and molecular characterization of tdp1α, tdp1ß and tdp1α/ß mutants treated with cisplatin (CIS), curcumin (CUR), NSC120686 (NSC), zeocin (ZEO), and camptothecin (CPT), evidenced that while tdp1ß was highly sensitive to CIS and CPT, tdp1α was more sensitive to NSC. Gene expression analyses showing upregulation of the TDP2 gene in the double mutant indicate the presence of compensatory mechanisms. The downregulation of POL2A gene in the tdp1ß mutant along with the upregulation of the TDP1ß gene in pol2a mutants, together with its sensitivity to replication inhibitors (CIS, CTP), point towards a function of this gene in the response to replication stress. Therefore, this study brings novel information relative to the activity of TDP1 genes in plants.

Integrating Deep Learning and Synthetic Biology: A Co-Design Approach for Enhancing Gene Expression via N-Terminal Coding Sequences.

N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering. However, current methods for NCS optimization such as rational design and statistics-guided approaches are labor-intensive yield only relatively small improvements. This paper introduces a deep learning/synthetic biology codesigned few-shot training workflow for NCS optimization. Our method utilizes k-nearest encoding followed by word2vec to encode the NCS, then performs feature extraction using attention mechanisms, before constructing a time-series network for predicting gene expression intensity, and finally a direct search algorithm identifies the optimal NCS with limited training data. We took green fluorescent protein (GFP) expressed by Bacillus subtilis as a reporting protein of NCSs, and employed the fluorescence enhancement factor as the metric of NCS optimization. Within just six iterative experiments, our model generated an NCS (MLD62) that increased average GFP expression by 5.41-fold, outperforming the state-of-the-art NCS designs. Extending our findings beyond GFP, we showed that our engineered NCS (MLD62) can effectively boost the production of N-acetylneuraminic acid by enhancing the expression of the crucial rate-limiting GNA1 gene, demonstrating its practical utility. We have open-sourced our NCS expression database and experimental procedures for public use.

Brucea javanica Seed Oil Emulsion and Shengmai Injections Improve Peripheral Microcirculation in Treatment of Gastric Cancer.

OBJECTIVE: To explore and verify the effect and potential mechanism of Brucea javanica Seed Oil Emulsion Injection (YDZI) and Shengmai Injection (SMI) on peripheral microcirculation dysfunction in treatment of gastric cancer (GC). METHODS: The potential mechanisms of YDZI and SMI were explored through network pharmacology and verified by cellular and clinical experiments. Human microvascular endothelial cells (HMECs) were cultured for quantitative real-time polymerase chain reaction, Western blot analysis, and human umbilical vein endothelial cells (HUVECs) were cultured for tube formation assay. Twenty healthy volunteers and 97 patients with GC were enrolled. Patients were divided into surgical resection, surgical resection with chemotherapy, and surgical resection with chemotherapy combining YDZI and SMI groups. Forearm skin blood perfusion was measured and recorded by laser speckle contrast imaging coupled with post-occlusive reactive hyperemia. Cutaneous vascular conductance and microvascular reactivity parameters were calculated and compared across the groups. RESULTS: After network pharmacology analysis, 4 ingredients, 82 active compounds, and 92 related genes in YDZI and SMI were screened out. ß-Sitosterol, an active ingredient and intersection compound of YDZI and SMI, upregulated the expression of vascular endothelial growth factor A (VEGFA) and prostaglandin-endoperoxide synthase 2 (PTGS2, P<0.01), downregulated the expression of caspase 9 (CASP9) and estrogen receptor 1 (ESR1, P<0.01) in HMECs under oxaliplatin stimulation, and promoted tube formation through VEGFA. Chemotherapy significantly impaired the microvascular reactivity in GC patients, whereas YDZI and SMI ameliorated this injury (P<0.05 or P<0.01). CONCLUSIONS: YDZI and SMI ameliorated peripheral microvascular reactivity in GC patients. ß-Sitosterol may improve peripheral microcirculation by regulating VEGFA, PTGS2, ESR1, and CASP9.

Immune response for acute Aeromonas hydrophila infection in two distinct color morphs of northern snakehead, Channa argus.

To compare and analyze the differences in immunological response between the two color morphs of Channa argus, a fish cohort was divided into four groups: black C argus + PBS (B-PBS), black C argus + Aeromonas hydrophila (B-Ah), white C. argus + PBS (W-PBS), and white C. argus + A hydrophila (W-Ah). The B-PBS and W-PBS groups received 100 µL PBS, while the B-Ah and W-Ah groups received 3.6 × 105 CFU/mL A. hydrophila in the same volume. The death rate in each group was noted, changes in plasma biochemical indicators and the expression of liver immune-related genes were examined, and transcriptome techniques were used to compare the differences between the two colors of C. argus following stress. No mortality occurred in the B-PBS and W-PBS groups. Mortality in the W-Ah and B-Ah groups showed an upward and then downward trend after A. hydrophila injection. The highest mortality occurred within 24 h and was higher in the W-Ah group than in the B-Ah group. MDA levels in the B-Ah and W-Ah groups increased and then decreased, while SOD and T-AOC showed the reverse tendency. The W-Ah and W-PBS groups differed significantly in MDA at 3, 12, and 24 h, SOD from 6 to 96 h, and T-AOC between 6 and 48 h. Plasma MDA and T-AOC levels at 12 h and SOD levels at 24 and 48 h differed significantly between the B-PBS and B-Ah groups. In both the W-Ah and B-Ah groups, the expression levels of IL-1ß and IL-8 in the liver showed a temporal pattern with an initial increase followed by a decrease, reaching peak levels after 24 h, while IL-10 showed the reverse pattern. Transcriptome analysis of the liver revealed significant differences between the two C. argus colors. Differential genes in black C. argus were mainly enriched in steroid biosynthesis, glycolysis/gluconeogenesis, and glutathione and propanoate metabolism pathways 24 h after infection. In contrast, differential genes in white C. argus were mainly enriched in pathways such as oxidative phosphorylation, pancreatic secretion, and protein digestion and absorption 24 h after infection. After A. hydrophila infection, white C. argus had higher mortality, more severe oxidative stress and inflammatory responses, and lower antioxidant capacity than black C. argus.

Links between fecal microplastics and parameters related to metabolic dysfunction-associated steatotic liver disease (MASLD) in humans: An exploratory study.

Microplastics (MPs) can persist in the environment and human body. Murine studies showed that exposure to MPs could cause metabolic dysregulation, contributing metabolic dysfunction-associated steatotic liver disease (MASLD) or steatohepatitis (MASH). However, research on the role of MPs in humans is limited. Thus, we aimed to assess links between human fecal MPs and liver histology, gene expression, immune cells and intestinal microbiota (IM). We included 6 lean healthy liver donors and 6 normal liver (obese) and 11 MASH patients. Overall, pre-BSx, we observed no significant differences in fecal MPs between groups. However, fecal MP fibers and total MPs positively correlated with portal and total macrophages and total killer T cells while total fecal MPs were positively correlated with natural killer cells. Additionally, 19 genes related to immune system and apoptosis correlated with fecal MPs at baseline. Fecal MP fibers correlated positively with fecal Bifidobacterium and negatively with Lachnospiraceae. Patients with MASH (n = 11) were re-assessed 12-months post-bariatric surgery (BSx) and we found that those with persistent disease (n = 4) had higher fecal MP fragments than those with normalized liver histology (n = 7). At 12-month post-BSx, MP fragments positively correlated with helper T cells and total MPs positively correlated with natural killer T cells and B cells. Our study is the first to look at 1) the role of MPs in MASH and its association with IM, immune cells and hepatic gene expression and 2) look at the role of MPs longitudinally in MASH persistence following BSx. Future research should further explore this relationship.

Predictive model of gene expression regulating invasion and migration of M2 macrophages in breast cancer: clinical prognosis and therapeutic implications.

Background: Breast cancer (BRCA) has surpassed lung cancer to become the malignant tumor with the highest incidence in female population. It occurs in malignant cells in breast tissue and is common worldwide. An increasing body of research indicates that M2 macrophages are critical to the occurrence and progression of BRCA. The aim of this work is to build a predictive model of genes related to invasion and migration of M2 macrophages, forecast the prognosis of patients with BRCA, and then evaluate the efficacy of some targeted treatments. Methods: The Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database supplied the GSE20685 dataset, whereas the expression profile a clinical details of BRCA patients were obtained from The Cancer Genome Atlas (TCGA; https://portal.gdc.cancer.gov/) database. The genes linked to M2 macrophages and the differentially elevated genes of invasion and migration were found in GSE20685. To explore the prognosis-related invasion and migration M2 macrophage genes, the TCGA-BRCA dataset was merged with Cox regression and least absolute shrinkage and selection operator (LASSO) regression. GSE58812 was utilized for external validation. After calculating each patient's risk score, the prognostic model was examined by analyses of immune infiltration, medication sensitivity, mutation, and enrichment of the risk score. Results: The risk score had a strong correlation with both several immune cells and popular anti-tumor medications. Additionally, it was discovered that the risk score was a separate prognostic factor for BRCA. Conclusions: Based on invasion and migration-related M2 macrophage genes, we investigated and validated predictive characteristics in our study that may offer helpful insights into the progression and prognosis of BRCA.

Endophytic Bacteria Induce Thiamine (Vitamin B1) Production in Oil Palm (Elaeis guineensis).

Thiamine or vitamin B1 is a micronutrient that has a crucial function in all living organisms and involved in several biochemical reactions. Concerning the capability of thiamine in inducing plant health, a study was carried out by applying bacterial endophytes (Pseudomonas aeruginosa and Burkholderia cepacia cultures) in four-month-old oil palm seedlings (Elaeis guineensis) via soil drenching technique to evaluate the effect towards thiamine. Spear leaves were sampled day 0 to 14 to analyse the expression of gene coding for the first two enzymes thiamine biosynthesis pathway, THI4 and THIC via qPCR analysis. The gene expression by qPCR showed a significant increase of up to 3-fold while high-performance liquid chromatography (HPLC) analysis for quantification of thiamine and its derivatives accumulated ~ 20-fold in total thiamine when compared to control seedlings. However, concentration of thiamine metabolites was negatively correlated with the expression of THIC and THI4 gene transcripts suggesting post-transcriptional regulation mediated by an RNA regulatory element, a thiamine pyrophosphate (TPP) riboswitch. Our findings demonstrated that the application of bacterial endophytes affected thiamine biosynthesis and enhanced overall thiamine content. This might increase the plant's resistance towards stress and would be useful in oil palm maintenance for maximum yield production.

NJGCG: A node-based joint Gaussian copula graphical model for gene networks inference across multiple states.

Inferring the interactions between genes is essential for understanding the mechanisms underlying biological processes. Gene networks will change along with the change of environment and state. The accumulation of gene expression data from multiple states makes it possible to estimate the gene networks in various states based on computational methods. However, most existing gene network inference methods focus on estimating a gene network from a single state, ignoring the similarities between networks in different but related states. Moreover, in addition to individual edges, similarities and differences between different networks may also be driven by hub genes. But existing network inference methods rarely consider hub genes, which affects the accuracy of network estimation. In this paper, we propose a novel node-based joint Gaussian copula graphical (NJGCG) model to infer multiple gene networks from gene expression data containing heterogeneous samples jointly. Our model can handle various gene expression data with missing values. Furthermore, a tree-structured group lasso penalty is designed to identify the common and specific hub genes in different gene networks. Simulation studies show that our proposed method outperforms other compared methods in all cases. We also apply NJGCG to infer the gene networks for different stages of differentiation in mouse embryonic stem cells and different subtypes of breast cancer, and explore changes in gene networks across different stages of differentiation or different subtypes of breast cancer. The common and specific hub genes in the estimated gene networks are closely related to stem cell differentiation processes and heterogeneity within breast cancers.

Repeated release of cerium oxide nanoparticles altered algal responses: Growth, photosynthesis, and photosynthetic gene expression.

The expanding production of engineered nanomaterials (ENMs) can eventually cause their increased release into and presence in aquatic ecosystems, potentially threatening the health of aquatic organisms and the stability of the ecological environment. Generally, ENMs are repeatedly released into real-world aquatic environments in relatively low concentrations, potentially affecting photosynthesis in primary producers such as algae. However, knowledge regarding the effects of repeated exposure to ENMs on algal photosynthesis is still lacking. Herein, the physiological responses of the freshwater algae Chlorella vulgaris following single and repeated exposures to cerium oxide nanoparticles (CeO2 NPs) were investigated at 10 mg/L, with a focus on photosynthesis. The results showed that repeated exposures triggered increased photosynthetic pigment contents, oxidative stress levels, decreased photosynthetic performance, and lower biomass in C. vulgaris compared to a single exposure. Photosynthesis-related genes (i.e., petA, petB, psaA, atpB, and rbcL) were found to be upregulated following repeated exposures. Particularly for petB, repeated rather than single exposure treatment significantly upregulated its expression levels by 2.92-10.24-fold compared to unexposed controls. Furthermore, increased exposure times could aggravate the interaction between CeO2 NPs and algae, elevating 8.13%, 12.13%, and 20.51% Ce distribution on the algal cell surface or intracellularly, compared to a single exposure. This study is the first to investigate the effects of ENM exposure times on algal photosynthesis, providing new insights into the assessment of the risks these materials pose to real-world aquatic environments.

In vitro analysis of VEGF-mediated endothelial permeability and the potential therapeutic role of Anti-VEGF in severe dengue.

Background: Vascular endothelial growth factor (VEGF) is one of the proteins involved in dengue immunopathogenesis. It is overexpressed in severe dengue and contributes to vascular permeability and plasma leakage. In this study, we investigated the effects of VEGF and anti-VEGF treatments on endothelial cells in vitro, to assess the potential use of anti-VEGF antibodies in managing severe dengue. Methods: Human pulmonary microvascular endothelial cells were treated with VEGF and a VEGF/anti-VEGF combination. The effects of the treatments were studied using an endothelial permeability assay and microarray gene expression profiling. In the permeability assay, the fluorescein isothiocyanate (FITC)-dextran fluorescence signal across the endothelial monolayer was recorded, and the cells were stained with PECAM-1 to detect gap formation. RNA was extracted from treated cells for microarray gene profiling and analysis. The results were analyzed for differentially expressed genes (DEGs) and gene enrichment analysis. The DEGs were subjected to STRING to construct the protein-protein interaction network and then Cytoscape to identify the hub genes. Results: VEGF-treated endothelial cells showed greater movement of FITC-dextran across the monolayer than VEGF/anti-VEGF-treated cells. There were 111 DEGs for VEGF-treated cells and 118 DEGs for VEGF/anti-VEGF-treated cells. The genes upregulated in VEGF-treated cells were enriched in inflammatory responses and regulation of the endothelial barrier, nitric oxide synthesis, angiogenesis, and the nucleotide-binding oligomerization domain-like receptor signaling pathway. Top 10 hub genes were identified from the DEGs. Conclusions: VEGF treatment increased permeability across endothelial cells, while anti-VEGF reduced this leakage. Analysis of VEGF-treated endothelial cells identified hub genes implicated in severe dengue. The top 10 hub genes were TNF, IL1B, IL6, CCL2, PTGS2, ICAM1, CXCL2, CXCL1, CSF2, and TLR2. The results of this study show that using anti-VEGF antibodies to neutralize VEGF may be a promising therapy to prevent the progression of dengue to severe dengue.

The mRNA dynamics underpinning translational control mechanisms of Drosophila melanogaster oogenesis.

Advances in the study of mRNAs have yielded major new insights into post-transcriptional control of gene expression. Focus on the spatial regulation of mRNAs in highly polarized cells has demonstrated that mRNAs translocate through cells as mRNA:protein granules (mRNPs). These complex self-assemblies containing nuclear and cytoplasmic proteins are fundamental to the coordinated translation throughout cellular development. Initial studies on translational control necessitated fixed tissue, but the last 30 years have sparked innovative live-cell studies in several cell types to deliver a far more nuanced picture of how mRNA-protein dynamics exert translational control. In this review, we weave together the events that underpin mRNA processes and showcase the pivotal studies that revealed how a multitude of protein factors engage with a transcript. We highlight a mRNA's ability to act as a 'super scaffold' to facilitate molecular condensate formation and further moderate translational control. We focus on the Drosophila melanogaster germline due to the extensive post-transcriptional regulation occurring during early oogenesis. The complexity of the spatio-temporal expression of maternal transcripts in egg chambers allows for the exploration of a wide range of mechanisms that are crucial to the life cycle of mRNAs.

Evaluating the Contribution of Model Complexity in Predicting Robustness in Synthetic Genetic Circuits.

The design-build-test-learn workflow is pivotal in synthetic biology as it seeks to broaden access to diverse levels of expertise and enhance circuit complexity through recent advancements in automation. The design of complex circuits depends on developing precise models and parameter values for predicting the circuit performance and noise resilience. However, obtaining characterized parameters under diverse experimental conditions is a significant challenge, often requiring substantial time, funding, and expertise. This work compares five computational models of three different genetic circuit implementations of the same logic function to evaluate their relative predictive capabilities. The primary focus is on determining whether simpler models can yield conclusions similar to those of more complex ones and whether certain models offer greater analytical benefits. These models explore the influence of noise, parametrization, and model complexity on predictions of synthetic circuit performance through simulation. The findings suggest that when developing a new circuit without characterized parts or an existing design, any model can effectively predict the optimal implementation by facilitating qualitative comparison of designs' failure probabilities (e.g., higher or lower). However, when characterized parts are available and accurate quantitative differences in failure probabilities are desired, employing a more precise model with characterized parts becomes necessary, albeit requiring additional effort.

A scoring model for the expression of genes related to programmed cell death predicts immunotherapy response and prognosis in lung adenocarcinoma.

BACKGROUND: Lung adenocarcinoma (LUAD) continues to be the leading cause of cancer death worldwide, driven by environmental factors like smoking and genetic predispositions. LUAD has a high mortality rate, and new biomarkers are urgently needed to improve treatment strategies and patient management. Programmed cell death (PCD) is involved in tumor progression and response to treatment. Therefore, there is a need for an extensive study of the role and functions of PCD-related genes (PCDRGs) in lung adenocarcinoma so as to understand the pathophysiologic features of lung adenocarcinoma. METHODS: Based on TCGA and GEO databases, this research is aimed at screening differentially expressed PCD-related genes in lung adenocarcinoma. We conducted GO, and KEGG analysis to establish the link between these genes and biological processes. By applying various machine learning algorithms such as CoxBoost analysis, we developed PCD-related indices (PCDI) that were used to verify their ability to predict prognosis with the use of other datasets. This was done in addition to exploring the biological functions of PCD genes associated with lung adenocarcinoma by assessing the relationship between immune cell components of tumor microenvironment and PCD genes together with examining how they affect drug sensitivity. RESULTS: The research presented in this article offers significant insights into LUAD. The authors identified 113 PCDRGs that were differentially expressed in LUAD. These genes are implicated in various biological functions, including High risk ing apoptosis, ferroptosis, and pathways specific to non-small cell lung cancer. Notably, the PCDI proved effective in distinguishing between High risk and Low risk LUAD patients, demonstrating a higher accuracy in prognosis prediction compared to traditional clinical indicators such as age and gender. This high prediction accuracy was validated in both test and validation cohorts. Additionally, these genes showed significant correlations with immune cell infiltration and drug sensitivity in LUAD patients. CONCLUSION: We analysed the expression and function of PCDRGs in LUAD and revealed their correlation with patient survival, the immune microenvironment and drug sensitivity. The constructed PCDI model provides a scientific basis for the personalised treatment of lung adenocarcinoma, and future optimisation of treatment strategies based on these genes may improve patient clinical outcomes.

Analyzing the expression of the transcriptome in adipose tissue of fat- and thin-tailed sheep.

Significant efforts have been made to understand how fat deposition in sheep tail is regulated in genetic, transcriptomic, physiologic, biochemical, and metabolic levels in order to elucidate the complex mechanisms underlying the energy storage, lipid metabolism in adipose tissue, adaptability to harsh environments, and evolutionary domestication. Through RNA-seq data analysis, we are able to compare the gene expression of fat-tailed sheep versus thin-tailed sheep breeds in an acceptable resolution at transcriptome level. The purpose of this study was to compare the transcriptomes of Ghezel (fat-tailed) and Zel (thin-tailed) sheep. Total RNA from subcutaneous and tail tissue samples from healthy lambs was sequenced (150b PE) to identify differentially expressed genes (DEGs) between the two mentioned tissues and between the Ghezel and Zel sheep breeds. Further downstream pathway and network analyses were conducted afterwards. The results uncovered the association of the most important DEGs such as CAV1, ALB, and SOCS3 with cellular signaling pathways of lipids metabolism. It seems that the SOCS3 gene plays an important role in the differential deposition of lipid in the tails of two phenotypically different sheep breeds. Although the detail of gene expression in the tail and subcutaneous tissues of two morphologically different breeds was decoded here, to fully understand how differential expression of the SOCS3 gene affects the fat synthesis, further studies are needed.

Clinical and molecular response to alpha1-oleate treatment in patients with bladder cancer.

BACKGROUND: The tumoricidal complex alpha1-oleate targets bladder cancer cells, triggering rapid, apoptosis-like tumor cell death. Clinical effects of alpha1-oleate were recently observed in patients with non-muscle invasive bladder cancer (NMIBC), using a randomized, placebo-controlled study protocol. AIMS: To investigate if there are dose-dependent effects of alpha1-oleate. MATERIALS AND METHODS: Here, patients with NMIBC were treated by intravesical instillation of increasing concentrations of alpha1-oleate (1.7, 8.5, or 17 mM) and the treatment response was defined relative to a placebo group. RESULTS: Strong, dose-dependent anti-tumor effects were detected in alpha1-oleate treated patients for a combination of molecular and clinical indicators; a complete or partial response was detected in 88% of tumors treated with 8.5 mM compared to 47% of tumors treated with 1.7 mM of alpha1-oleate. Uptake of alpha1-oleate by the tumor triggered rapid shedding of tumor cells into the urine and cell death by an apoptosis-like mechanism. RNA sequencing of tissue biopsies confirmed the activation of apoptotic cell death and strong inhibition of cancer gene networks, including bladder cancer related genes. Drug-related side effects were not recorded, except for local irritation at the site of instillation. DISCUSSION AND CONCLUSIONS: These dose-dependent anti-tumor effects of alpha1-oleate are promising and support the potential of alpha1-oleate treatment in patients with NMIBC.

Transcriptome analysis provides new insight into the mechanism of Bombyx mori under zinc exposure.

Zinc is a significant source of heavy metal pollution that poses risks to both human health and biodiversity. Excessive concentrations of zinc can hinder the growth and development of insects and trigger cell death through oxidative damage. The midgut is the main organ affected by exposure to heavy metals. The silkworm, a prominent insect species belonging to the Lepidoptera class and widely used in China, serves as a model for studying the genetic response to heavy metal stress. In this study, high-throughput sequencing technology was employed to investigate detoxification-related genes in the midgut that are induced by zinc exposure. A total of 11,320 unigenes and 14,723 transcripts were identified, with 553 differentially expressed genes (DEGs) detected, among which 394 were up-regulated and 159 were down-regulated. The Gene Ontology (GO) analysis revealed that 452 DEGs were involved in 18 biological process subclasses, 14 cellular component subclasses and 8 molecular functional subclasses. Furthermore, the KEGG analysis demonstrated enrichment in pathways such as Protein digestion, absorption and Lysosome. Validation of the expression levels of 9 detoxification-related DEGs through qRT-PCR confirmed the accuracy of the RNA-seq results. This study not only contributes new insights into the detoxification mechanisms mechanism of silkworms against zinc contamination, but also serves as a foundation basis for understanding the molecular detoxification processes in lepidopteran insects.