Tibial cortex transverse transport surgery improves wound healing in patients with severe type 2 DFUs by activating a systemic immune response: a cross-sectional study.

BACKGROUND: Tibial cortex transverse transport (TTT) surgery has become an ideal treatment for patients with type 2 severe diabetic foot ulcerations (DFUs) while conventional treatments are ineffective. Based on our clinical practice experience, the protective immune response from TTT surgery may play a role against infections to promote wound healing in patients with DFUs. Therefore, this research aimed to systematically study the specific clinical efficacy and the mechanism of TTT surgery. MATERIALS AND METHODS: Between June 2022 and September 2023, 68 patients with type 2 severe DFUs were enrolled and therapized by TTT surgery in this cross-sectional and experimental study. Major clinical outcomes including limb salvage rate and antibiotics usage rate were investigated. Ten clinical characteristics and laboratory features of glucose metabolism and kidney function were statistically analyzed. Blood samples from 6 key time points of TTT surgery were collected for label-free proteomics and clinical immune biomarker analysis. Besides, tissue samples from 3 key time points were for spatially resolved metabolomics and transcriptomics analysis, as well as applied to validate the key TTT-regulated molecules by RT-qPCR. RESULTS: Notably, 64.7% of patients did not use antibiotics during the entire TTT surgery. TTT surgery can achieve a high limb salvage rate of 92.6% in patients with unilateral or bilateral DFUs. Pathway analysis of a total of 252 differentially expressed proteins (DEPs) from the proteomic revealed that the immune response induced by TTT surgery at different stages was first comprehensively verified through multi-omics combined with immune biomarker analysis. The function of upward transport was activating the systemic immune response, and wound healing occurs with downward transport. The spatial metabolic characteristics of skin tissue from patients with DFUs indicated downregulated levels of stearoylcarnitine and the glycerophospholipid metabolism pathway in skin tissue from patients with severe DFUs. Finally, the expressions of PRNP (prion protein) to activate the immune response, PLCB3 (PLCB3, phospholipase C beta 3) and VE-cadherin to play roles in neovascularization, and PPDPF (pancreatic progenitor cell differentiation and proliferation factor), LAMC2 (laminin subunit gamma 2) and SPRR2G (small proline rich protein 2G) to facilitate the developmental process mainly keratinocyte differentiation were statistically significant in skin tissues through transcriptomic and RT-qPCR analysis. CONCLUSION: Tibial cortex transverse transport (TTT) surgery demonstrates favorable outcomes for patients with severe type 2 DFUs by activating a systemic immune response, contributing to anti-infection, ulcer recurrence, and the limb salvage rate for unilateral or bilateral DFUs. The specific clinical immune responses, candidate proteins, genes, and metabolic characteristics provide directions for in-depth mechanistic research on TTT surgery. Further research and public awareness are needed to optimize TTT surgery in patients with severe type 2 DFUs.

High positive predictive value of CNVs detected by clinical exome sequencing in suspected genetic diseases.

BACKGROUND: Genetic disorders often manifest as abnormal fetal or childhood development. Copy number variations (CNVs) represent a significant genetic mechanism underlying such disorders. Despite their importance, the effectiveness of clinical exome sequencing (CES) in detecting CNVs, particularly small ones, remains incompletely understood. We aimed to evaluate the detection of both large and small CNVs using CES in a substantial clinical cohort, including parent-offspring trios and proband only analysis. METHODS: We conducted a retrospective analysis of CES data from 2428 families, collected from 2018 to 2021. Detected CNV were categorized as large or small, and various validation techniques including chromosome microarray (CMA), Multiplex ligation-dependent probe amplification assay (MLPA), and/or PCR-based methods, were employed for cross-validation. RESULTS: Our CNV discovery pipeline identified 171 CNV events in 154 cases, resulting in an overall detection rate of 6.3%. Validation was performed on 113 CNVs from 103 cases to assess CES reliability. The overall concordance rate between CES and other validation methods was 88.49% (100/113). Specifically, CES demonstrated complete consistency in detecting large CNV. However, for small CNVs, consistency rates were 81.08% (30/37) for deletions and 73.91% (17/23) for duplications. CONCLUSION: CES demonstrated high sensitivity and reliability in CNV detection. It emerges as an economical and dependable option for the clinical CNV detection in cases of developmental abnormalities, especially fetal structural abnormalities.

Characterization of second primary malignancies post CAR T-cell therapy: real-world insights from the two global pharmacovigilance databases of FAERS and VigiBase.

Background: The FDA's alerts regarding the T-cell lymphoma risk post CAR-T therapy has garnered global attention, yet a comprehensive profile of second primary malignancies (SPMs) following CAR-T treatment is lacking. Methods: We extracted adverse event reports of hematological malignancies (HMs) patients with clearly definable SPMs from the FAERS and VigiBase databases (2017-2023). Disproportionality analysis using reporting odds ratio (ROR) and adjusted ROR was performed to assess associations between SPMs and CAR-T therapy. Time-to-onset analysis explored factors affecting SPM manifestation. Findings: SPMs post CAR T-cell therapy include HMs and solid tumors. T-cell lymphoma and myelodysplastic syndromes were consistently identified as positive signals across the overall and subgroup analyses. Hematological SPMs showed earlier onset with increasing annual incidence post CAR-T therapy, whereas solid tumors exhibit delayed manifestation. SPMs in CAR-T recipients had significantly earlier onset than non-recipients. Furthermore, age-specific characteristics reveal earlier SPM manifestations in pediatric, adolescent, and young adult populations compared to older populations post CAR-T therapy. Interpretation: The current SPM profile highlights the necessity of long-term safety monitoring for all CAR-T recipients given the observed yearly increase of SPMs. Customizing long-term SPM screening across different age groups may enhance early detection and intervention strategies, ultimately improving patient outcomes in the follow-up of CAR-T recipients. Funding: This work was supported by grants from the Natural Science Foundation of Guangdong Province (2018A030313846 and 2021A1515012593), the Science and Technology Planning Project of Guangdong Province (2019A030317020), the National Natural Science Foundation of China (81802257, 81871859, 81772457, 82172750, 82172811, and 82260546), the Guangdong Basic and Applied Basic Research Foundation (Guangdong-Guangzhou Joint Funds) (2022A1515111212), and the Science and Technology Program of Guangzhou (2023A04J1257).

Choline consumption reduces CVD risk via body composition modification.

Despite extensive research on the relationship between choline and cardiovascular disease (CVD), conflicting findings have been reported. We aim to investigate the relationship between choline and CVD. Our analysis screened a retrospective cohort study of 14,663 participants from the National Health and Nutrition Examination Survey conducted between 2013 and 2018. Propensity score matching and restricted cubic splines was used to access the association between choline intake and the risk of CVD. A two-sample Mendelian randomization (MR) analysis was conducted to examine the potential causality. Additionally, sets of single cell RNA-sequencing data were extracted and analyzed, in order to explore the role of choline metabolism pathway in the progression and severity of the CVD and the underlying potential mechanisms involved. The adjusted odds ratios and 95% confidence intervals for stroke were 0.72 (0.53-0.98; p = 0.035) for quartile 3 and 0.54 (0.39-0.75; p < 0.001) for quartile 4. A stratified analysis revealed that the relationship between choline intake and stroke varied among different body mass index and waist circumference groups. The results of MR analysis showed that choline and phosphatidylcholine had a predominantly negative causal effect on fat percentage, fat mass, and fat-free mass, while glycine had opposite effects. Results from bioinformatics analysis revealed that alterations in the choline metabolism pathway following stroke may be associated with the prognosis. Our study indicated that the consumption of an appropriate quantity of choline in the diet may help to protect against CVD and the effect may be choline-mediated, resulting in a healthier body composition. Furthermore, the regulation of the choline metabolism pathway following stroke may be a promising therapeutic target.

REDD1 knockdown ameliorates endothelial cell senescence through repressing TXNIP-mediated oxidative stress.

Endothelial cell senescence characterized by reactive oxygen species (ROS) accumulation and chronic inflammation is widely recognized as a key contributor to atherosclerosis (AS). Regulated in development and DNA damage response 1 (REDD1), a conserved stress-response protein that regulates ROS production, is involved in the pathogenesis of various age-related diseases. However, the role of REDD1 in endothelial cell senescence is still unclear. Here, we screened REDD1 as a differentially expressed senescence-related gene in the AS progression using bioinformatics methods, and validated the upregulation of REDD1 expression in AS plaques, senescent endothelial cells, and aging aorta by constructing AS mice, D-galactose (DG)-induced senescent endothelial cells and DG-induced accelerated aging mice, respectively. siRNA against REDD1 could improve DG-induced premature senescence of endothelial cells and inhibit ROS accumulation, similar to antioxidant N-Acetylcysteine (NAC) treatment. Meanwhile, NAC reduced the upregulation of REDD1 induced by DG, supporting the positive feedback loop between REDD1 and ROS contributes to endothelial cell senescence. Mechanistically, the regulatory effect of REDD1 on ROS might be related to the TXNIP-REDD1 interaction in DG-induced endothelial cell senescence. Collectively, experiments above provide evidence that REDD1 participates in endothelial cell senescence through repressing TXNIP-mediated oxidative stress, which may be involved in the progression of atherosclerosis.

Impact of age-related gut microbiota dysbiosis and reduced short-chain fatty acids on the autonomic nervous system and atrial fibrillation in rats.

Objective: Aging is the most significant contributor to the increasing prevalence of atrial fibrillation (AF). Dysbiosis of gut microbiota has been implicated in age-related diseases, but its role in AF development remains unclear. This study aimed to investigate the correlations between changes in the autonomic nervous system, short-chain fatty acids (SCFAs), and alterations in gut microbiota in aged rats with AF. Methods: Electrophysiological experiments were conducted to assess AF induction rates and heart rate variability in rats. 16S rRNA gene sequences extracted from fecal samples were used to assess the gut microbial composition. Gas and liquid chromatography-mass spectroscopy was used to identify SCFAs in fecal samples. Results: The study found that aged rats exhibited a higher incidence of AF and reduced heart rate variability compared to young rats. Omics research revealed disrupted gut microbiota in aged rats, specifically a decreased Firmicutes to Bacteroidetes ratio. Additionally, fecal SCFA levels were significantly lower in aged rats. Importantly, correlation analysis indicated a significant association between decreased SCFAs and declining heart rate variability in aged rats. Conclusions: These findings suggest that SCFAs, as metabolites of gut microbiota, may play a regulatory role in autonomic nervous function and potentially influence the onset and progression of AF in aged rats. These results provide novel insights into the involvement of SCFAs and autonomic nervous system function in the pathogenesis of AF. These results provide novel insights into the involvement of SCFAs and autonomic nervous system function in the pathogenesis of AF.

Intercellular adhesion molecule-1 suppresses TMZ chemosensitivity in acquired TMZ-resistant gliomas by increasing assembly of ABCB1 on the membrane.

AIMS: Despite aggressive treatment, the recurrence of glioma is an inevitable occurrence, leading to unsatisfactory clinical outcomes. A plausible explanation for this phenomenon is the phenotypic alterations that glioma cells undergo aggressive therapies, such as TMZ-therapy. However, the underlying mechanisms behind these changes are not well understood. METHODS: The TMZ chemotherapy resistance model was employed to assess the expression of intercellular adhesion molecule-1 (ICAM1) in both in vitro and in vivo settings. The potential role of ICAM1 in regulating TMZ chemotherapy resistance was investigated through knockout and overexpression techniques. Furthermore, the mechanism underlying ICAM1-mediated TMZ chemotherapy resistance was examined using diverse molecular biological methods, and the lipid raft protein was subsequently isolated to investigate the cellular subcomponents where ICAM1 operates. RESULTS: Acquired TMZ resistant (TMZ-R) glioma models heightened production of intercellular adhesion molecule-1 (ICAM1) in TMZ-R glioma cells. Additionally, we observed a significant suppression of TMZ-R glioma proliferation upon inhibition of ICAM1, which was attributed to the enhanced intracellular accumulation of TMZ. Our findings provide evidence supporting the role of ICAM1, a proinflammatory marker, in promoting the expression of ABCB1 on the cell membrane of TMZ-resistant cells. We have elucidated the mechanistic pathway by which ICAM1 modulates phosphorylated moesin, leading to an increase in ABCB1 expression on the membrane. Furthermore, our research has revealed that the regulation of moesin by ICAM1 was instrumental in facilitating the assembly of ABCB1 exclusively on the lipid raft of the membrane. CONCLUSIONS: Our findings suggest that ICAM1 is an important mediator in TMZ-resistant gliomas and targeting ICAM1 may provide a new strategy for enhancing the efficacy of TMZ therapy against glioma.

Clinical Characteristics and Prognosis of Herpes Zoster Laryngitis With Vocal Fold Immobility.

OBJECTIVE: To investigate the clinical characteristics and prognosis of herpes zoster laryngitis with vocal fold immobility. STUDY DESIGN: Retrospective study. METHODS: Clinical characteristics, laryngeal signs on strobolaryngoscopy, imaging examination findings, and outcomes of patients were analyzed retrospectively. RESULTS: This study included 17 patients (11 males [64.7%] and six females [35.3%]), with a mean age of 63.3 ± 6.7 years. The primary symptoms were hoarseness (94.1%), dysphagia (76.5%), pharyngalgia on one side (76.5%), and aspiration (70.6%). No patient had skin herpes of the head and neck. The duration of symptoms was 5-30 days (median: 10 days). Twelve patients (70.6%) were in an immunocompromised state before the disease. Strobolaryngoscopy showed congestion and swelling of the mucosa on one side of the larynx, with whitish eruptions on the supraglottic mucosa and ipsilateral vocal fold immobility. Five patients (29.4%) exhibited signs of ipsilateral accessory nerve injury. The imaging examination showed supraglottic inflammatory changes in 12 patients (70.6%). Among the 14 patients whose treatment could be clearly described, only one patient received antiviral treatment, whereas others received neurotrophic and symptomatic treatment. Notably, all patients demonstrated good outcomes because their symptoms eventually returned to normal. CONCLUSION: Herpes zoster laryngitis is caused by varicella-zoster virus infection of the vagus nerve. It is characterized by laryngeal herpetic changes on one side and unilateral vocal fold immobility. The inducement of the disease tends to be associated with the abnormal immune state of patients. It can be easily misdiagnosed because of the absence of skin herpetic changes. Regardless of antiviral therapy, patients generally exhibit a favorable outcome.

Management of resilient urban integrated energy system: State-of-the-art and future directions.

The urban integrated energy system (UIES) is the fundamental infrastructure supporting the operation of resilient cities. The resilience of UIES plays a critical role in effectively responding to extreme events. We provide a comprehensive review on the management of resilient UIES. Firstly, we examine the existing studies on the resilience of UIES through quantitative and qualitative methodologies. Secondly, it points out that the coupling characteristics of UIES have a dual impact on resilience. The definition of UIES resilience can be understood from three perspectives, namely partial resilience versus total resilience, physical resilience versus digital resilience, and current resilience versus future resilience. Thirdly, this review summarizes the strategies for improving the resilience of UIES across three distinct stages, namely before, during, and after extreme events. The resilience of UIES can be enhanced by effective measures to prediction, adaptation, and assessment. Finally, the challenges faced by management of resilient UIES are presented and discussed, in terms of mitigating compound risks, modeling complex systems, addressing data collection and quality issue, and collaborating within multi stakeholders.

[Effects of Straw Addition on N2O and CO2 Emissions from Red Soil Subjected to Different Long-Term Fertilization].

Straw return, as an important measure for soil fertility improvement in farmland, significantly affects the emissions of greenhouse gases N2O and CO2. Thus, the collected soil samples from five long-term (30-year) fertilization treatments (no fertilization, CK; recommended chemical fertilizer, F; 200 % of recommended chemical fertilizer, 2F; pig manure, M; and chemical fertilizer combined with pig manure, FM) were amended with and without straw and incubated under constant temperature and humidity conditions (25 ℃ and 65 % maximum field water holding capacity) for 20 days so as to investigate the key factors influencing N2O and CO2 emissions in response to straw addition in long-term fertilization treatments. The results showed that fertilization significantly increased N2O emissions. Compared to those under the unfertilized treatment[(22.05 ±2.09) µg·kg-1, calculated as nitrogen, the same as below], cumulative N2O emissions from the chemical fertilizer treatments significantly increased by 119 %-195 %[(48.38 ±20.81) µg·kg-1 and (65.13 ±12.55) µg·kg-1 from the F and 2F treatments, respectively], and those from the manure treatments increased by 275 %-399 %[(82.72 ±12.73) µg·kg-1 and (1 101.99 ±425.71) µg·kg-1 from the M and FM treatments, respectively]. Soil NO3--N, DOC, and DTN were the main factors influencing N2O emissions from fertilized treatments in the absence of straw addition. Straw addition significantly increased cumulative N2O emissions by 345 % and 247 % in the 2F and M treatments, respectively, compared to those in the corresponding fertilized treatments without straw addition, with no significant effect on N2O emissions in the CK, F, and FM treatments. Straw addition increased DOC content and microbial activity and decreased soil NO3--N and DTN contents, thereby increasing N2O emissions. Fertilization also significantly increased CO2 emissions. Compared to those from the unfertilized treatment, cumulative CO2 emissions from the manure treatments significantly increased by 120 %-130 %[(122.11 ±4.3) mg·kg-1 (calculated as carbon, the same as below) and (116.47 ±4.55) mg·kg-1 from the M and FM treatments, respectively], and those in the 2F treatment increased by 28 %[(65.13 ±12.55) mg·kg-1]. In the absence of straw addition, soil MBC, DOC, and DTN were the main factors influencing CO2 emissions. Compared to those in the treatments without straw addition, straw addition significantly increased cumulative CO2 emissions by 660 %-1132 % among fertilization treatments, due to increased DOC and MBC contents and enhanced microbial activity. In conclusion, straw addition significantly increased N2O and CO2 emissions through increased soil DTN consumption and DOC content among fertilization treatments. In soils treated with manure amendment, straw return should be rationally considered for the purpose of balancing the comprehensive trade-offs between fertility improvement and greenhouse gas emissions.

Tuber transcriptome analysis reveals a novel WRKY transcription factor StWRKY70 potentially involved in potato pigmentation.

Tuber flesh pigmentation, conferred by the presence of secondary metabolite anthocyanins, is one of many key agronomic traits for potato tubers. Although several genes of potato anthocyanin biosynthesis have been reported, transcription factors (TFs) contributing to tuber flesh pigmentation are still not fully understood. In this study, transcriptomic profiling of diploid potato accessions with or without tuber flesh pigmentation was conducted and genes of the anthocyanin biosynthesis pathway were found significantly enriched within the 1435 differentially expressed genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) and connectivity analysis pinpointed a subset of 173 genes closely related to the key biosynthetic gene StDFR. Of the eight transcription factors in the subset, group III WRKY StWRKY70, was chosen for showing high connectivity to StDFR and ten other anthocyanin biosynthetic genes and homology to known WRKYs of anthocyanin pathway. The transient activation assay showed StWRKY70 predominantly stimulated the expression of StDFR and StANS as well as the accumulation of anthocyanins by enhancing the function of the MYB transcription factor StAN1. Furthermore, the interaction between StWRKY70 and StAN1 was verified by Y2H and BiFC. Our analysis discovered a new transcriptional activator StWRKY70 which potentially involved in tuber flesh pigmentation, thus may lay the foundation for deciphering how the WRKY-MYB-bHLH-WD40 (WRKY-MBW) complex regulate the accumulation of anthocyanins and provide new strategies to breed for more nutritious potato varieties with enhanced tuber flesh anthocyanins.

Immunoregulation of Glia after spinal cord injury: a bibliometric analysis.

Objective: Immunoregulation is a complex and critical process in the pathological process of spinal cord injury (SCI), which is regulated by various factors and plays an important role in the functional repair of SCI. This study aimed to explore the research hotspots and trends of glial cell immunoregulation after SCI from a bibliometric perspective. Methods: Data on publications related to glial cell immunoregulation after SCI, published from 2004 to 2023, were obtained from the Web of Science Core Collection. Countries, institutions, authors, journals, and keywords in the topic were quantitatively analyzed using the R package "bibliometrix", VOSviewer, Citespace, and the Bibliometrics Online Analysis Platform. Results: A total of 613 papers were included, with an average annual growth rate of 9.39%. The papers came from 36 countries, with the United States having the highest output, initiating collaborations with 27 countries. Nantong University was the most influential institution. We identified 3,177 authors, of whom Schwartz, m, of the Weizmann Institute of Science, was ranked first regarding both field-specific H-index (18) and average number of citations per document (151.44). Glia ranked first among journals with 2,574 total citations. The keywords "microglia," "activation," "macrophages," "astrocytes," and "neuroinflammation" represented recent hot topics and are expected to remain a focus of future research. Conclusion: These findings strongly suggest that the immunomodulatory effects of microglia, astrocytes, and glial cell interactions may be critical in promoting nerve regeneration and repair after SCI. Research on the immunoregulation of glial cells after SCI is emerging, and there should be greater cooperation and communication between countries and institutions to promote the development of this field and benefit more SCI patients.

Dynamic Changes of Fundus and Predictors of Visual Prognosis in New-Onset Vogt-Koyanagi-Harada Disease.

PURPOSE: To characterize the dynamic changes of fundus in Vogt-Koyanagi-Harada (VKH) disease through enhanced spectral-domain optical coherence tomography (EDI-OCT) and explore the predictors of visual prognosis. METHODS: In this retrospective cohort study, a total of 2152 VKH patients referred to our uveitis center from January 2013 to April 2022 were screened; 151 new-onset VKH patients (299 eyes) and 82 healthy controls (164 eyes) were included. The manifestations of fundus at baseline, 1 month, 3 months, and 12 months after treatment were analysed and their relevance to visual prognosis were evaluated. RESULTS: After retinal detachment (RD) (97.3%) and optic disc swelling (100%) presented at baseline, retinal reattachment (81.6%) and the granular hyperreflective depositions at the retinal pigment epithelium (RPE) (61.5%) were observed at month 1. The RPE and ellipsoid zone rearrangement accompanying interdigitation zone attenuation (57.9%) was noted finally. Choroidal thickness of patients was higher than that in the controls at baseline and month 1 (both P < 0.001). Best-corrected visual acuity (BCVA) (logarithm of the minimum angle of resolution [logMAR]) (P < 0.001; OR, 4.01), subretinal fibrinoid exudate (P < 0.001; OR, 3.9) and RPE folds (p = 0.001; OR, 2.39) at baseline, and the RD at month 1 (P < 0.001; OR, 3.42) were associated with visual prognosis. CONCLUSIONS: New-onset VKH patients after treatment exhibited dynamic changes in the fundus especially the outer retina during a 12-month period. The BCVA, subretinal fibrinoid exudate, and RPE folds at baseline, and RD at month May 1, serve as predictors of visual prognosis.

Neuroendoscopic Parafascicular Evacuation of Spontaneous Intracerebral Hemorrhage (NESICH Technique): A Multicenter Technical Experience with Preliminary Findings.

INTRODUCTION: Intracerebral hemorrhage (ICH) is a severe manifestation of stroke, demonstrating notably elevated global mortality and morbidity. Thus far, effective therapeutic strategies for ICH have proven elusive. Currently, minimally invasive techniques are widely employed for ICH management, particularly using endoscopic hematoma evacuation in cases of deep ICH. Exploration of strategies to achieve meticulous surgery and diminish iatrogenic harm, especially to the corticospinal tract, with the objective of enhancing the neurological prognosis of patients, needs further efforts. METHODS: We comprehensively collected detailed demographic, clinical, radiographic, surgical, and postoperative treatment and recovery data for patients who underwent endoscopic hematoma removal. This thorough inclusion of data intends to offer a comprehensive overview of our technical experience in this study. RESULTS: One hundred fifty-four eligible patients with deep supratentorial intracerebral hemorrhage who underwent endoscopic hematoma removal were included in this study. The mean hematoma volume was 42 ml, with 74 instances of left-sided hematoma and 80 cases of right-sided hematoma. The median Glasgow Coma Scale (GCS) score at admission was 10 (range from 4 to 15), and the median time from symptom onset to surgery was 18 (range 2 to 96) h. The mean hematoma clearance rate was 89%. The rebleeding and mortality rates within 1 month after surgery were 3.2% and 7.8%, respectively. At the 6-month mark, the proportion of patients with modified Rankin Scale (mRS) scores of 0-3 was 58.4%. CONCLUSION: Both the reduction of surgery-related injury and the protection of the residual corticospinal tract through endoscopic hematoma removal may potentially enhance neurological functional outcomes in patients with deep ICH, warranting validation in a forthcoming multicenter clinical study.

Short-Read RNA-Seq.

RNA sequencing (RNA-Seq) has emerged as a powerful and versatile tool for the comprehensive analysis of transcriptomes and has been widely used to investigate gene expression, copy number variation, alternative splicing, and novel transcript discovery. This chapter outlines the methodology for conducting short-read RNA-Seq, starting from RNA enrichment to library preparation and sequencing. Throughout the chapter, practical tips and best practices are provided to guide researchers in order to optimize each step of the RNA-Seq workflow. Multiple quality control steps throughout the workflow that are critical to obtain high-quality RNA-Seq data are also discussed.

Long non-coding RNA MALAT 1 and PHOX2B expression in olfactory neuroblastomas and sympathetic neuroblastomas.

Long noncoding RNAs (lncRNAs) participate in transcriptional, epigenetic, and post-transcriptional regulation of gene expression and may influence carcinogenesis. MALAT1 is a lncRNA that is expressed in endocrine and many other neoplasms and it has been shown to have oncogenic and/or tumor suppressor effects in tumor development. Olfactory neuroblastomas arise in the nasal cavity while sympathetic neuroblastomas are present mainly in the adrenal and periadrenal regions. These neoplasms have overlapping histopathological features. Rare cases of sympathetic neuroblastomas metastatic to the nasal cavity have been reported. PHOX2B has been shown to be relatively specific for sympathetic neuroblastomas, but only a limited number of cases of olfactory neuroblastomas have been examined for PHOX2B expression. This study aimed to explore the potential utilization of MALAT1 and PHOX2B in distinguishing these two entities. Tissue microarrays (TMA) were created for olfactory neuroblastomas (n = 26) and sympathetic neuroblastomas (n = 52). MALAT1 lncRNA expression was assessed by in situ hybridization using RNAScope technology. TMA slides were scanned by Vectra multispectral imaging system and image analysis and quantification were performed with inForm software. PHOX2B expression was analyzed by immunohistochemistry. MALAT1 showed predominantly nuclear expression in both tumor types and MALAT1 expression was 2-fold higher in olfactory neuroblastomas compared to sympathetic neuroblastomas (p < 0.0001). PHOX2B showed nuclear staining in most sympathetic neuroblastomas (51/52, 98 %) while only 1 olfactory neuroblastoma (3.8 %) was focally positive for this marker. These findings suggest immunostaining of PHOX2B could be an excellent marker in distinguishing between these two tumor types.

Kiwi-Inspired Rational Nanoarchitecture with Intensified and Discrete Magneto-Fluorescent Functionalities for Ultrasensitive Point-of-Care Immunoassay.

Fluorescent lateral flow immunoassays (FLFIA) is a well-established rapid detection technique for quantitative analysis. However, achieving accurate analysis of biomarkers at the pg mL-1 level using FLFIA still poses challenges. Herein, an ultrasensitive FLFIA platform is reported utilizing a kiwi-type magneto-fluorescent silica nanohybrid (designated as MFS) that serves as both a target-enrichment substrate and an optical signal enhancement label. The spatially-layered architecture comprises a Fe3O4 core, an endocarp-fibers like dendritic mesoporous silica, seed-like quantum dots, and a kiwi-flesh like silica matrix. The MFS demonstrates heightened fluorescence brightness, swift magnetic response, excellent size uniformity, and dispersibility in water. Through liquid-phase capturing and fluorescence-enhanced signal amplification, as well as magnetic-enrichment sample amplification and magnetic-separation noise reduction, the MFS-based FLFIA is successfully applied to the detection of cardiac troponin I that achieved a limit of detection at 8.4 pg mL-1, tens of times lower than those of previously published fluorescent and colorimetric lateral flow immunoassays. This work offers insights into the strategic design of magneto-fluorescent synergetic signal amplification on LFIA platform and underscores their prospects in high-sensitive rapid and on-site diagnosis of biomarkers.

An approach based on a combination of toxicological experiments and in silico predictions to investigate the adverse outcome pathway (AOP) of paraquat neuro-immunotoxicity.

Paraquat (PQ) exposure is strongly associated with neurotoxicity. However, research on the neurotoxicity mechanisms of PQ varies in terms of endpoints of toxic assessment, resulting in a great challenge to understand the early neurotoxic effects of PQ. In this study, we developed an adverse outcome pathway (AOP) to investigate PQ-induced neuro-immunotoxicity from an immunological perspective, combining of traditional toxicology methods and computer simulations. In vivo, PQ can microstructurally lead to an early synaptic loss in the brain mice, which is a large degree regarded as a main reason for cognitive impairment to mice behavior. Both in vitro and in vivo demonstrated synapse loss is caused by excessive activation of the complement C1q/C3-CD11b pathway, which mediates microglial phagocytosis dysfunction. Additionally, the interaction between PQ and C1q was validated by molecular simulation docking. Our findings extend the AOP framework related to PQ neurotoxicity from a neuro-immunotoxic perspective, highlighting C1q activation as the initiating event for PQ-induced neuro-immunotoxicity. In addition, downstream complement cascades induce abnormal microglial phagocytosis, resulting in reduced synaptic density and subsequent non-motor dysfunction. These findings deepen our understanding of neurotoxicity and provide a theoretical basis for ecological risk assessment of PQ.