Molecular Biological Approaches Research Articles

Umbilical cord mesenchymal stem cell exosomes alleviate necrotizing enterocolitis in neonatal mice by regulating intestinal epithelial cells autophagy

BACKGROUND Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease that affects premature infants. Although mounting evidence supports the therapeutic effect of exosomes on NEC, the underlying mechanisms remain unclear. AIM To investigate the mechanisms underlying the regulation of inflammatory response and intestinal barrier function by umbilical cord mesenchymal stem cell (UCMSCs) exosomes, as well as their potential in alleviating NEC in neonatal mice. METHODS NEC was induced in 5-d-old C57BL/6 pups through hypoxia and gavage feeding of formula containing lipopolysaccharide (LPS), after which the mice received human UCMSC exosomes (hUCMSC-exos). The control mice were allowed to breastfeed with their dams. Ileal tissues were collected from the mice and analyzed by histopathology and immunoblotting. Colon tissues were collected from NEC neonates and analyzed by immunofluorescence. Molecular biology and cell culture approaches were employed to study the related mechanisms in intestinal epithelial cells. RESULTS We found that autophagy is overactivated in intestinal epithelial cells during NEC, resulting in reduced expression of tight junction proteins and an increased inflammatory response. The ability of hUCMSC-exos to ameliorate NEC in a mouse model was dependent on decreased intestinal autophagy. We also showed that hUCMSC-exos alleviate the inflammatory response and increase migration ability in intestinal epithelial cells induced by LPS. CONCLUSION These results contribute to a better understanding of the protective mechanisms of hUCMSC-exos against NEC and provide a new theoretical and experimental foundation for NEC treatment. These findings also enhance our understanding of the role of the autophagy mechanism in NEC, offering potential avenues for identifying new therapeutic targets.

Association between Reactive Oxygen Species, Transcription Factors, and Candidate Genes in Drought-Resistant Sorghum.

Drought stress is one of the most severe natural disasters in terms of its frequency, length, impact intensity, and associated losses, making it a significant threat to agricultural productivity. Sorghum (Sorghum bicolor), a C4 plant, shows a wide range of morphological, physiological, and biochemical adaptations in response to drought stress, paving the way for it to endure harsh environments. In arid environments, sorghum exhibits enhanced water uptake and reduced dissipation through its morphological activity, allowing it to withstand drought stress. Sorghum exhibits physiological and biochemical resistance to drought, primarily by adjusting its osmotic potential, scavenging reactive oxygen species, and changing the activities of its antioxidant enzymes. In addition, certain sorghum genes exhibit downregulation capabilities in response to drought stress. Therefore, in the current review, we explore drought tolerance in sorghum, encompassing its morphological characteristics and physiological mechanisms and the identification and selection of its functional genes. The use of modern biotechnological and molecular biological approaches to improving sorghum resistance is critical for selecting and breeding drought-tolerant sorghum varieties.

Peroxidase in plant defense: Novel insights for cadmium accumulation in rice (Oryza sativa L.)

Phenylpropanoid biosynthesis plays crucial roles in the adaptation to cadmium (Cd) stress. Nevertheless, few reports have dabbled in physiological mechanisms of such super pathway regulating Cd accumulation in plants. Herein, by integrating transcriptomic, histological and molecular biology approaches, the present study dedicated to clarify molecular mechanism on how rice adapt to Cd stress via phenylpropanoid biosynthesis. Our analysis identified that the enhancement of phenylpropanoid biosynthesis was as a key response to Cd stress. Intriguingly, POD occupied a significant part in this process, with the number of POD related genes accounted for 26/29 of all upregulated genes in phenylpropanoid biosynthesis. We further used SHAM (salicylhydroxamic acid, the POD inhibitor) to validate that POD exhibited a negative correlation with the Cd accumulation in rice tissues, and proposed two intrinsic molecular mechanisms on POD in contributing to Cd detoxification. One strategy was that POD promoted the formation of lignin and CSs both in endodermis and exodermis for intercepting Cd influx. In detail, inhibited POD induced by external addition of SHAM decreased the content of lignin by 50.98–66.65 % and delayed percentage of the DTIP-CS to root length by 39.17–104.51 %. The other strategy was expression of transporter genes involved in Cd uptake, including OsIRT1, OsIRT2, OsZIP1 and OsZIP, negatively regulated by POD. In a word, our findings firstly draws a direct link between POD activity and the Cd accumulation, which is imperative for the breeding of rice with low-Cd-accumulating capacity in the future.

Pyroptosis and mitochondrial function participated in miR-654-3p-protected against myocardial infarction

Myocardial infarction (MI) is one of the leading causes of heart failure with highly complicated pathogeneses. miR-654-3p has been recognized as a pivotal regulator of controlling cell survival. However, the function of miR-654-3p in cardiomyocytes and MI has yet to be reported. This study aimed to identify the role of miR-654-3p in the regulation of myocardial infarction. To understand the contribution of miR-654-3p on heart function, we generated cardiac-specific knockdown and overexpression mice using AAV9 technology in MI injury. Mechanically, we combined cellular and molecular techniques, pharmaceutical treatment, RNA sequencing, and functional testing to elucidate the potential pathological mechanisms. We identified that mice subjected to MI decreased the expression of miR-654-3p in the border and infarcted area. Mice lacking miR-654-3p in the heart showed some inflammation infiltration and myocardial fibrosis, resulting in a mild cardiac injury. Furthermore, we found a deficiency of miR-654-3p in cardiomyocytes resulted in pyroptotic cell death but not other programmed cell death. Intriguingly, miR-654-3p deficiency aggravated MI-induced cardiac dysfunction, accompanied by higher myocardial fibrosis and cardiac enzymes and augmented pyroptosis activation. Cardiac elevating miR-654-3p prevented myocardial fibrosis and inflammation infiltration and decreased pyroptosis profile, thereby attenuating MI-induced cardiac damage. Using RNA sequence and molecular biological approaches, we found overexpression of miR-654-3p in the heart promoted the metabolic ability of the cardiomyocytes by promoting mitochondrial metabolism and mitochondrial respiration function. Our finding identified the character of miR-654-3p in protecting against MI damage by mediating pyroptosis and mitochondrial metabolism. These findings provide a new mechanism for miR-654-3p involvement in the pathogenesis of MI and reveal novel therapeutic targets.miR-654-3p expression was decreased after MI. Mice lacking miR-654-3p in the heart showed some inflammation infiltration and myocardial fibrosis, resulting in a mild cardiac injury. The deficiency of miR-654-3p in cardiomyocytes resulted in pyroptotic cell death. miR-654-3p deficiency aggravated MI-induced cardiac dysfunction, accompanied by higher myocardial fibrosis and cardiac enzymes and augmented pyroptosis activation. Overexpression of miR-654-3p prevented myocardial fibrosis and inflammation infiltration and decreased pyroptosis profile, thereby attenuating MI-induced cardiac damage. Overexpression of miR-654-3p in the heart promoted the metabolic ability of the cardiomyocytes by promoting mitochondrial metabolism and mitochondrial respiration function.

Fagopyrum Dibotrys Rhizoma regulates pulmonary lipid metabolic homeostasis and the ERK-cPLA2 pathway to alleviate asthma in mice

BackgroundAsthma is a complex disease with mechanisms involving multiple factors, and there is still a lack of highly effective and low-side-effect drugs. Traditional Chinese medicine Fagopyrum Dibotrys Rhizoma (FDR) has been applied for the treatment of acute and chronic bronchitis as well as bronchial asthma due to its favorable pharmacological activity. However, the exact mechanism of FDR remains unclear. ObjectiveA mouse model of asthma was created using OVA and HDM. To investigate the mechanism of FDR in asthma treatment, a combination of network pharmacology, lipidomics, and molecular biology approaches was employed. MethodsTo evaluate the therapeutic effects of FDR on asthma, we established two distinct models of asthma in C57BL/6 J mice using OVA and HDM, respectively. We then employed LC-MS to analyze the major chemical constituents in FDR. Next, the network pharmacology approach was used to predict the potential targets and mechanisms of FDR in asthma treatment. Additionally, lipidomics analysis of mouse serum was conducted using LC-MS. Finally, the impact of FDR on the ERK -cPLA2 signaling pathway was investigated through Western Blotting assay. ResultsFDR treatment has been shown to improve histomorphological changes, lung function and inflammation in models of OVA and HDM-induced asthma. Using UPLC/LTQ-Orbitrap-MS, we were able to identify 12 potential active components. Network pharmacology analysis revealed that FDR shares 75 targets with asthma. Further analysis using GO and KEGG pathways demonstrated the involvement of key pathways such as PI3K-Akt, TNF, and MAPK. Additionally, lipidomics analysis of the serum from OVA and HDM induced asthma mice showed disturbances in lipid metabolism, which were effectively ameliorated by FDR treatment. Mechanistically, FDR inhibits ERK1/2-cPLA2, leading to a reduction in lysophospholipids and restoration of lipid balance, thereby aiding in the treatment of asthma. ConclusionFDR has been shown to improve lipid metabolism disorder in the serum of asthmatic mice, thereby potentially serving as a treatment for asthma. This can be achieved by regulating the activation levels of ERK1/2 and p38MAPK. Consequently, the production of lysophosphatide is reduced, thereby alleviating the disorder of lipid metabolism and achieving the desired therapeutic effect in asthma treatment.

#2881 Glucose free-based solutions reduce oxidative stress in peritoneal dialysis: support for a new promising approach

Abstract Background and Aims Oxidative stress (OxSt) and inflammation are common in CKD which are known CV and mortality risk factors. In peritoneal dialysis (PD) OxSt and Inflammation even increase due to the use of glucose-based solutions. This study evaluated in PD patients the effect of 3 and 6 months treatment with icodextrin-based glucose-free solutions on OxSt and inflammation. Method In 15 PD patients using a molecular biology approach, p22phox protein expression (Western blot), subunit of NADPH oxidase, essential for OxSt activation, MYPT-1 phosphorylation state, marker of RhoA/Rho kinase pathway activity, deeply involved in OxSt generation (Western blot) and Malondialdehyde (MDA) production (fluorimetric assay), marker of lipid peroxidation, have been evaluated. High-sensitive C Reactive Protein (hsCRP) (immunoturbidimetric assay) and interleukin (IL)-6 (chemiluminescence assay), have been used as marker of inflammation. Results p22phox protein expression, MYPT-1 phosphorylation, and MDA level were reduced after 3 months from the start of icodextrin based solutions (1.28 ± 0.18 d.u. vs 1.50 ± 0.19, p = 0.049; 0.89 ± 0.03 vs 0.98 ± 0.03, p = 0.004; 4.20 ± 0.18 nmol/mL vs 4.84 ± 0.32 nmol/mL, p = 0.045, respectively). In a subgroup of 9 patients who continued the treatment up to 6 months MYPT-1 phosphorylation was further reduced at 6 months compared to baseline (0.84 ± 0.06 vs 0.99 ± 0.04, p = 0.043), while p22phox protein expression was reduced only at 6 months from baseline (1.03 ± 0.05 vs 1.68 ± 0.22, p = 0.021). In this subgroup MDA blood level was reduced at 6 months from baseline (4.03 ± 0.24 nmol/mL vs 4.68 ± 0.32, p = 0.024) and was also significantly reduced vs 3 months (4.03 ± 0.24 vs 4.35 ± 0.21, p = 0.008). IL-6 level, although reduced compared to baseline, did not reach statistical significance both at 3 and 6 months, while hsPCR was unchanged. Conclusion The icodextrin-based PD solutions mediated reduction of OxSt related proteins and inflammation we have provided, although obtained in a small cohort of patients and for a limited time duration, strongly support the rationale of using in PD osmo-metabolic agents-based solutions replacing the currently used glucose-based fluids. The results of ongoing studies with these agents in PD patients will provide definitive proofs to better preserve peritoneal membrane integrity and residual renal function but also to reduce CV risk factors such as OxSt and inflammation.

Employment of diverse in vitro systems for analyzing multiple aspects of disease, hereditary hemorrhagic telangiectasia (HHT)

BackgroundIn vitro disease modeling enables translational research by providing insight into disease pathophysiology and molecular mechanisms, leading to the development of novel therapeutics. Nevertheless, in vitro systems have limitations for recapitulating the complexity of tissues, and a single model system is insufficient to gain a comprehensive understanding of a disease.ResultsHere we explored the potential of using several models in combination to provide mechanistic insight into hereditary hemorrhagic telangiectasia (HHT), a genetic vascular disorder. Genome editing was performed to establish hPSCs (H9) with ENG haploinsufficiency and several in vitro models were used to recapitulate the functional aspects of the cells that constitute blood vessels. In a 2D culture system, endothelial cells showed early senescence, reduced viability, and heightened susceptibility to apoptotic insults, and smooth muscle cells (SMCs) exhibited similar behavior to their wild-type counterparts. Features of HHT were evident in 3D blood-vessel organoid systems, including thickening of capillary structures, decreased interaction between ECs and surrounding SMCs, and reduced cell viability. Features of ENG haploinsufficiency were observed in arterial and venous EC subtypes, with arterial ECs showing significant impairments. Molecular biological approaches confirmed the significant downregulation of Notch signaling in HHT-ECs.ConclusionsOverall, we demonstrated refined research strategies to enhance our comprehension of HHT, providing valuable insights for pathogenic analysis and the exploration of innovative therapeutic interventions. Additionally, these results underscore the importance of employing diverse in vitro systems to assess multiple aspects of disease, which is challenging using a single in vitro system.

Dickkopf-related protein 1 as a biomarker of local immune status and worse prognosis of Oral squamous cell carcinoma.

Oral squamous cell carcinoma (OSCC) is an infiltrative malignancy characterized by a significantly elevated recurrence rate. Dickkopf-related protein 1 (DKK1), which plays an oncogene role in many cancers, acts as an inhibitor of the Wingless protein (Wnt) signaling pathway. Currently, there is a lack of consensus regarding the role of DKK1 in OSCC or its clinical significance. To examine the role and effect of DKK1 in OSCC. The identification of differentially expressed genes (DEGs) in OSCC was conducted by utilizing databases such as The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A comprehensive analysis of gene expression profile interactions (GEPIA) and Kaplan-Meier curve were conducted to investigate the associations among DEGs, patient survival and prognosis in individuals with OSCC. The biological function of DKK1 in OSCC was investigated by using molecular biology approaches. The expression of DKK1 was found to be upregulated in OSCC tissues at various stages. High levels of DKK1 expression exhibited a positive correlation with the overall survival (OS) and progression-free survival (PFS) rates among OSCC patients. DKK1 knockdown suppressed the proliferation and induced apoptotic response in OSCC cells. Moreover, DKK1 exerted a positive regulatory effect on HMGA2 expression, thereby modulating cell growth and apoptosis in OSCC. The expression of DKK1 was found to be positively correlated with the infiltration of immune cells in patients with OSCC. Additionally, higher levels of CD4 + T cells were associated with improved 5-year survival rates. DKK1 is a prognostic biomarker for patients with OSCC.

Intelligent detection method of microparticle virus in silkworm based on YOLOv8 improved algorithm

The presence of microparticle viruses significantly impacts the quality of silkworm seeds for domestic sericulture, making their exclusion from detection in silkworm seed production crucial. Traditional methods for detecting microparticle viruses in silkworms, such as manual microscopic observation, molecular biology, and immunological approaches, are cumbersome and unable to achieve intelligent, batch real-time detection. To address this challenge, we employ the YOLOv8 algorithm in this paper. Firstly, NAM attention is introduced in the original algorithm’s Backbone component, allowing the model to extract more generic feature information. Secondly, ODConv replaces Conv in the Head component of the original algorithm, enhancing the model’s ability to identify microparticle viruses. Finally, NWD-LOSS modifies the CIoU loss of the original algorithm to obtain a more accurate prediction box. Experimental results demonstrate that the NN-YOLOv8 model outperforms mainstream detection algorithms in detecting silkworm microparticle diseases. With an average detection time of 22.6 milliseconds per image, the model shows promising prospects for future applications. This model improvement enhances detection efficiency and reduces human resource costs, effectively realizing detection intelligence.

Abstract PO1-25-07: Obesity, breast cancer, and adipose-derived mesenchymal stem/stromal cells: The complex cross-signaling in the tumor microenvironment

Abstract Objective: Breast cancer is the most frequently diagnosed cancer and a common cause of cancer related death in women. The breast cancer microenvironment (TME) is mainly composed of adipose tissue, consisting of adipocytes, adipose-derived mesenchymal stem/stromal cells (bASCs) and immune cells. Interestingly, it is well recognized that obesity, as indicated by increased body mass index (BMI≥30), is associated with an enhanced risk of more aggressive breast cancer (BC) as well as reduced patient survival. Therefore, we asked how BC affects the biological functionality of bASC, how obesity fuels this process, and on the other hand how these cells influence BC cells. Methods: Multiple molecular biological approaches as transcriptomic profiling and diverse functional assays were conducted to characterize at least 5 lean and obese patients derived bASCs samples near the TME (lean/obese-aT) or distant (lean/obese-dT). Afterwards, these cells were used to investigate the interaction with BC cells in 2-dimensional and 3-dimensional cell culture experiments. Moreover, immunohistological analyses were conducted in 16 lean and 16 obese breast cancer patients (grade 3-4). Results: The TME shifts bASCs towards cancer supporting phenotypes into an inflammatory cancer-associated phenotype, whereas ob-aT bASCs are prone to be cancer-educated into a myofibroblastic phenotype with a significant deregulated gene expression, cytokine/chemokine secretion, and reduced differentiation capacity. In corroberation, these BMI dependent de-differentiation processes could be confirmed in breast cancer tissue. Moreover, the cell-cell interaction of BC cells with aT-bASCs increased their proliferation, motility, and chemoresistance. Conclusions: The study found multiple pathways deregulated in bASCs associated with tumor promoting effects. Additionally, it revealed the role of aT-bASCs in promoting breast cancer progression on a functional and molecular level. Citation Format: Andreas Ritter, Christine Solbach, Juping Yuan. Obesity, breast cancer, and adipose-derived mesenchymal stem/stromal cells: The complex cross-signaling in the tumor microenvironment [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-25-07.

월동 배추의 추위 스트레스 반응성 ERF 유전자 발굴과 활용

To mitigate plant freeze damage caused by extreme weather events, we need to elucidate the freeze resistance mechanism of freeze-tolerant plants through molecular biological approaches. Our research focuses on identifying the cold stress responsive, ERF(Ethylene-Responsive transcription Factor) genes that confer freeze tolerance in overwintering Chinese cabbage. Additionally, we aim to explore the molecular basis for conferring freezing tolerance to other organisms through genetic transformation. Expression of the ERF, cold stress responsive gene in overwintering Chinese cabbage, leads to the synthesis of AFP(Antifreeze Protein), which results in cellular freezing tolerance. We identified and sequenced functionally important ERF domain regions within the ERF genes, which we named BrERF1 and BrERF2. Their responsiveness to cold stress was confirmed through RT-PCR and qRT-PCR. Furthermore, we propose strategies to introduce BrERF1 and BrERF2 insertion plasmids into other organisms for transformation. Significant improvements in the freezing tolerance of transgenic organisms are expected to improve the productivity of these target organisms. In particular, the development of permanently transgenic plants using the BrERFs gene offers the possibility of increasing plant production under cold stress.

Non-Pigmented Antarctic Yeasts and Their Resistance to Toxic Metals

Despite the key role in biogeochemical processes and in the functioning of terrestrial ecosystems, yeasts of Antarctic regions still remain insufficiently studied. The study and analysis of the composition of Antarctic microbial communities remains relevant and is carried out using molecular biological approaches. The investigation of their resistance to toxic metal ions is essential to select industrially promising strains that can contribute to the development of new methods of metals detoxification via microorganisms. Aim. To determine the taxonomic position of non-pigmented Antarctic yeasts and investigate their resistance to toxic metal ions. Methods. The objects of the research are yeasts isolated from Antarctic phytocenoses. They were grown on malt wort (pH 5.0–5.5, temperature 18–20 °C). Isolation of genomic DNA was performed via the commercial DNA-sorb kit. Amplification of DNA was carried out using primers NL1 and NL4. Phylogenetic analysis was conducted by construction of trees (dendrograms) showing the position of the studied strains among closely related and typical species. The resistance of yeasts to toxic metal ions was established by cultivation in the concentration gradient of Ni2+, Co2+, CrO42-, and Сu2+. The ecophysiological traits of the isolated yeast strains including psychro- and halotolerance were determined. Results. Phylogenetic analysis showed a high percentage of similarity (99.5–99.6 %) of sequences of 18S rRNA genes of Antarctic yeast strains with the yeast sequences from the GenBank database. Psychrotolerant and halotolerant Antarctic yeast strains S11 and S12 were identified as Leucosporidium scottii and Debaryomyces hansenii, respectively. The studied yeast strains were found to be the most resistant to metal ions Ni2+ and Co2+. Strain of L. scottii S11 grew at 800 mg/L of Co2+, and D. hansenii S12 – at 750 mg/L of Ni2+. The yeasts were the least resistant to CrO42-: the L. scottii S11 and D. hansenii S12 strains grew at concentrations of 25 mg/L and 150 mg/L, respectively. In the presence of Cu2+, they grew at the same concentration – 600 mg/L. The combined action of toxic metal ions resulted in the increased toxic effects on the studied yeasts. Conclusions. The nucleotide sequences of 18S rRNA gene fragment of yeast strains S11 and S12 were included in the GenBank database under the numbers LT220858 and LT220859. Metal-resistant psychrotolerant yeast strains can be used to evaluate the metals content in polar regions as well as to bioremediate metal-contaminated ecosystems. However, further research is needed to develop and optimize bioremediation processes.

Characterization of sequences, expression profiling, and natural allelic variation analysis of the MYC gene family in sorghum (Sorghum bicolor)

Sorghum aphid (Melanaphis sacchari) and head smut fungi (Sporisorium reilianum) infesting sorghum cause delayed growth and development, and reduce yield and quality. This study use bioinformatics and molecular biological approaches to profile the gene expression pattern during sorghum development and under pest infestation, and analyzed the natural allelic DNA variation of sorghum MYC gene family. The findings provide insights for potential application in breeding the stress resistant and high productivity sorghum varieties. The results indicated that there are 28 MYC genes identified in sorghum genome, distributed on 10 chromosomes. The bHLH_MYC_N and HLH domains are the conserved domains of the MYC gene in sorghum. Gene expression analysis showed that SbbHLH35.7g exhibited high expression levels in leaves, SbAbaIn showed strong expression in early grains, and SbMYC2.1g showed high expression levels in mature pollen. In anti-aphid strains at the 5-leaf stage, SbAbaIn, SbLHW.4g and SbLHW.2g were significantly induced in leaves, while SbbHLH35.7g displayed the highest expression level in panicle tissue, which was significantly induced by the infection of head smut. Promoter cis-element analysis identified methyl jasmonate (MJ), abscisic acid (ABA), salicylic acid (SA) and MYB-binding sites related to drought-stress inducibility. Furthermore, genomic resequencing data analysis revealed natural allelic DNA variations such as single nucleotide polymorphism (SNP) and insertion-deletion (INDEL) for the key SbMYCs. Protein interaction network analysis using STRING indicated that SbAbaIn interacts with TIFYdomain protein, and SbbHLH35.7g interacts with MDR and imporin. SbMYCs exhibited temporal and spatial expression patterns and played vital roles during the sorghum development. Infestation by sugarcane aphids and head smut fungi induced the expression of SbAbaIn and SbbHLH35.7g, respectively. SbAbaIn modulated the jasmonic acid (JA) pathway to regulate the expression of defensive genes, conferring resistance to insects. On the other hand, SbbHLH35.7g participated in detoxification reactions to defend against pathogens.

Efficiency of moderately hypofractionated radiotherapy in NSCLC cell model.

The current standard of radiotherapy for inoperable locally advanced NSCLCs with single fraction doses of 2.0 Gy, results in poor outcomes. Several fractionation schedules have been explored that developed over the past decades to increasingly more hypofractionated treatments. Moderate hypofractionated radiotherapy, as an alternative treatment, has gained clinical importance due to shorter duration and higher patient convenience. However, clinical trials show controversial results, adding to the need for pre-clinical radiobiological studies of this schedule. We examined in comparative analysis the efficiency of moderate hypofractionation and normofractionation in four different NSCLC cell lines and fibroblasts using several molecular-biological approaches. Cells were daily irradiated with 24x2.75 Gy (moderate hypofractionation) or with 30x2 Gy (normofractionation), imitating the clinical situation. Proliferation and growth rate via direct counting of cell numbers, MTT assay and measurements of DNA-synthesizing cells (EdU assay), DNA repair efficiency via immunocytochemical staining of residual γH2AX/53BP1 foci and cell surviving via clonogenic assay (CSA) were experimentally evaluated. Overall, the four tumor cell lines and fibroblasts showed different sensitivity to both radiation regimes, indicating cell specificity of the effect. The absolute cell numbers and the CSA revealed significant differences between schedules (P < 0.0001 for all employed cell lines and both assays) with a stronger effect of moderate hypofractionation. Our results provide evidence for the similar effectiveness and toxicity of both regimes, with some favorable evidence towards a moderate hypofractionation. This indicates that increasing the dose per fraction may improve patient survival and therapy outcomes.

Structural determinants for activation of the Tau kinase CDK5 by the serotonin receptor 5-HT7R

BackgroundMultiple neurodegenerative diseases are induced by the formation and deposition of protein aggregates. In particular, the microtubule-associated protein Tau leads to the development of so-called tauopathies characterized by the aggregation of hyperphosphorylated Tau within neurons. We recently showed that the constitutive activity of the serotonin receptor 7 (5-HT7R) is required for Tau hyperphosphorylation and aggregation through activation of the cyclin-dependent kinase 5 (CDK5). We also demonstrated physical interaction between 5-HT7R and CDK5 at the plasma membrane suggesting that the 5-HT7R/CDK5 complex is an integral part of the signaling network involved in Tau-mediated pathology.MethodsUsing biochemical, microscopic, molecular biological, computational and AI-based approaches, we investigated structural requirements for the formation of 5-HT7R/CDK5 complex.ResultsWe demonstrated that 5-HT7R domains responsible for coupling to Gs proteins are not involved in receptor interaction with CDK5. We also created a structural model of the 5-HT7R/CDK5 complex and refined the interaction interface. The model predicted two conserved phenylalanine residues, F278 and F281, within the third intracellular loop of 5-HT7R to be potentially important for complex formation. While site-directed mutagenesis of these residues did not influence Gs protein-mediated receptor signaling, replacement of both phenylalanines by alanine residues significantly reduced 5-HT7R/CDK5 interaction and receptor-mediated CDK5 activation, leading to reduced Tau hyperphosphorylation and aggregation. Molecular dynamics simulations of 5-HT7R/CDK5 complex for wild-type and receptor mutants confirmed binding interface stability of the initial model.ConclusionsOur results provide a structural basis for the development of novel drugs targeting the 5-HT7R/CDK5 interaction interface for the selective treatment of Tau-related disorders, including frontotemporal dementia and Alzheimer’s disease.

Adopting Mechanistic Molecular Biology Approaches in Exposome Research for Causal Understanding.

Through investigating the combined impact of the environmental exposures experienced by an individual throughout their lifetime, exposome research provides opportunities to understand and mitigate negative health outcomes. While current exposome research is driven by epidemiological studies that identify associations between exposures and effects, new frameworks integrating more substantial population-level metadata, including electronic health and administrative records, will shed further light on characterizing environmental exposure risks. Molecular biology offers methods and concepts to study the biological and health impacts of exposomes in experimental and computational systems. Of particular importance is the growing use of omics readouts in epidemiological and clinical studies. This paper calls for the adoption of mechanistic molecular biology approaches in exposome research as an essential step in understanding the genotype and exposure interactions underlying human phenotypes. A series of recommendations are presented to make the necessary and appropriate steps to move from exposure association to causation, with a huge potential to inform precision medicine and population health. This includes establishing hypothesis-driven laboratory testing within the exposome field, supported by appropriate methods to read across from model systems research to human.

A molecular biology approach to identify Francisella tularensis proteins that interact with Band 3 of human erythrocytes.

Francisella tularensis is a pathogenic gram-negative bacterium that causes the zoonotic disease Tularemia. In addition, F. tularensis is classified as a Class A Bioterrorism agent by the CDC due to the ease of aerosolization and the ability of this bacterium to cause fatal infection in low doses. Previous studies suggest that invasion of mammalian erythrocytes by F. tularensis helps to increase colonization of ticks, an arthropod vector of this pathogen. Our laboratory previously found that the erythrocyte membrane glycoprotein, Band 3 is required by F. tularensis for invasion of red blood cells. Therefore, we predict that bacterial proteins interact with Band 3 to facilitate invasion. To identify these proteins, we will express codon-optimized Band 3 linked to a Glutathione-S transferase tag in F. tularensis LVS. Subsequent pull-down assays may reveal F. tularensis protein binding partners to Band 3 responsible for facilitating erythrocyte invasion.

Novel milestones for early esophageal carcinoma: From bench to bed.

Esophageal cancer (EC) is the seventh most common cancer worldwide, and esophageal squamous cell carcinoma (ESCC) accounts for the majority of cases of EC. To effectively diagnose and treat ESCC and improve patient prognosis, timely diagnosis in the initial phase of the illness is necessary. This article offers a detailed summary of the latest advancements and emerging technologies in the timely identification of ECs. Molecular biology and epigenetics approaches involve the use of molecular mechanisms combined with fluorescence quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology (next-generation sequencing), and digital PCR technology to study endogenous or exogenous biomolecular changes in the human body and provide a decision-making basis for the diagnosis, treatment, and prognosis of diseases. The investigation of the microbiome is a swiftly progressing area in human cancer research, and microorganisms with complex functions are potential components of the tumor microenvironment. The intratumoral microbiota was also found to be connected to tumor progression. The application of endoscopy as a crucial technique for the early identification of ESCC has been essential, and with ongoing advancements in technology, endoscopy has continuously improved. With the advancement of artificial intelligence (AI) technology, the utilization of AI in the detection of gastrointestinal tumors has become increasingly prevalent. The implementation of AI can effectively resolve the discrepancies among observers, improve the detection rate, assist in predicting the depth of invasion and differentiation status, guide the pericancerous margins, and aid in a more accurate diagnosis of ESCC.

Geometric morphometrics casts light on phylogenetic relevance of cephalopod beak morphological.

The feeding organ of cephalopod species, the beak, can be used to reveal important ecological information. In this study, geometric morphometric approaches were employed to investigate the phylogenetic relevance and classification effect of beak lateral profile shape. The two-dimensional beak morphologies of 1164 pairs of 24 species from 13 genera and five families were constructed, and their evolutionary relationships and taxonomic status were confirmed using geometric morphometrics and molecular biology approaches. We also assessed the phylogenetic signals of beak shape. The analysis results show shape variation in the beak mainly in the rostrum, hood, and lateral wall. The overall shape parameters (all PCs) of the upper and lower beak are more useful for species identification. The shapes of the upper and lower beak show a strong phylogenetic signal, and the phenogram based on the beak shape basically reflected the families' taxonomic positions. We also hypothesized that the shape variation in the beaks of cephalopods may be ascribed to genetic and environmental differences. In summary, beaks are a reliable material for the classification of cephalopod species. Geometric morphometric approaches are a powerful tool to reveal the identification, phylogenetic relevance and phenotypic diversity of beak shape in cephalopods.

Establishment and application of a rapid diagnostic method for BVDV and IBRV using recombinase polymerase amplification-lateral flow device.

Bovine Viral Diarrhea Virus (BVDV) and Infectious Bovine Rhinotracheitis Virus (IBRV) are the two most prevalent infectious diseases in cattle. They both can cause persistent infection and immunosuppression, resulting in significant economic losses in the livestock industry. Therefore, rapid detection of early BVDV and IBRV infections is crucial. In this study, a method for the rapid detection of BVDV and IBRV was established by using recombinase polymerase amplification (RPA) combined with lateral flow device (LFD). By optimizing the temperature and time conditions of the RPA reaction, the sensitivity, specificity, and clinical performance were evaluated. The results indicated that the RPA reaction could be completed at 40°C within 25 min. The LOD for BVDV and IBRV by RPA-LFD were 5.1 × 101 copies/μL and 6.65 × 101 copies/μL, respectively, with no cross-reactivity observed with other viruses such as CSFV, BRSV, BPIV3, BRV, and BCoV. Testing of 32 clinical samples showed consistent results between RPA-LFD and qPCR. The RPA-LFD method established in this study can be used for the rapid clinical detection of BVDV and IBRV, which providing a rapid and convenient molecular biology approach for on-site rapid detection and epidemiological investigations. Simultaneously, it offers technical support for the prevention and control of these viruses.