Pathway Mapping Research Articles

Mapping chemical reaction pathways in discharge plasmas: An approach based on force-directed layout

In the exploration of humid air discharges at atmospheric pressure using chemical kinetics, the mapping of chemical reaction pathways emerges as a crucial instrument for deciphering the underlying mechanisms of the reaction system. In this study, we employed a force-directed layout method to create diagrams of chemical reaction pathways based on simulation results from a global model of humid air discharges at atmospheric pressure. This innovative approach aids in addressing the challenges traditionally associated with mapping these pathways, notably the difficulty in balancing intuitiveness with the precise representation of physical data. In our method, the mass of each node in the diagram is determined by the species density, and the natural length between nodes is defined according to reaction rates, with the forces acting upon the nodes dictated by the variance between the actual distance and this natural length. The final arrangement of the nodes is established upon reaching a stable equilibrium after undergoing damped motion in response to these forces. This methodology not only provides a tangible and intuitive visualization of the complex interactions within discharge plasmas but also enables a detailed sensitivity analysis to assess the significance of various reactions.

A Comprehensive Review on Potential Molecular Drug Targets for the Management of Alzheimer's Disease.

Alzheimer's disease (AD) is an onset and incurable neurodegenerative disorder that has been linked to various genetic, environmental, and lifestyle factors. Recent research has revealed several potential targets for drug development, such as the prevention of Aβ production and removal, prevention of tau hyperphosphorylation, and keeping neurons alive. Drugs that target numerous ADrelated variables have been developed, and early results are encouraging. This review provides a concise map of the different receptor signaling pathways associated with Alzheimer's Disease, as well as insight into drug design based on these pathways. It discusses the molecular mechanisms of AD pathogenesis, such as oxidative stress, aging, Aβ turnover, thiol groups, and mitochondrial activities, and their role in the disease. It also reviews the potential drug targets, in vivo active agents, and docking studies done in AD and provides prospects for future drug development. This review intends to provide more clarity on the molecular processes that occur in Alzheimer's patient's brains, which can be of use in diagnosing and preventing the condition.

Abstract 1841: Investigating mechanisms of tumor eradication by blocking SIAH E3 ligase, a major tumor vulnerability, in EGFR/RAS-driven human cancer

Abstract Introduction: Hyperactivation of the EGFR/RAS pathway is a major driver of tumorigenesis and metastasis. It has been difficult to design effective therapies contravening the compensatory EGFR/RAS downstream effector pathways to achieve curative antitumor efficacy. Seven in absentia homologues (SIAH1 and SIAH2) are RING-domain E3 ubiquitin ligases that function as the most downstream signaling gatekeeper of the EGFR/RAS pathway. Our prior studies demonstrated that SIAH inhibition led to tumor eradication of multiple malignant human cancers cell lines in xenograft models. We propose that SIAH is a major tumor vulnerability/actionable drug target for inhibiting persistent EGFR/RAS pathway activation; we aim to elucidate the molecular mechanisms underpinning antitumor efficacy of our SIAH inhibitor. Methods: Reverse phase protein arrays (RPPAs) in conjunction with Principal Component Analysis (PCA) were used to quantify fold-changes of 300 proteins/phospho-proteins that were significantly up- or down-regulated in response to SIAH inhibition (p < 0.001). Independent RPPA assays were performed in triplicate on doxycycline (DOX)-inducible MiaPaCa, MDA-MB-231, MDA-MB-468, HeLa, and A459 cell lines in which our SIAH inhibitor, SIAH2 PD, expression was induced by a Tet-ON/OFF system. Four experimental conditions were used: Tet-ON control cells without DOX (group A) and with DOX induction (group B), Tet-ON-SIAH2 PD cancer cells without DOX (no SIAH2 PD inhibitor expression in group C) and with DOX induction (SIAH2 PD inhibitor expression in group D). The ratios of D/C/B/A, D/C, D/B, C/A, and B/A were calculated in a pairwise comparison after normalization to GAPDH as an internal control. To validate identified targets of interest, immunoblotting of biological quadruplicate cell lysates for each respective cell line were performed for group C and D at 3-, 5-, and 7-days post DOX induction; target proteins’ expression normalized to β-actin, α-Tubulin, or GAPDH respectively, and the pathway alterations induced by SIAH2 inhibition were standardized, quantified, and analyzed. Results: RPPA analyses identified 6 proteins (NFκB, Caspase-7, PARP, Cofilin, PD-L1, and Collagens) exhibiting differential expression in response to SIAH2 blockade. Western blot analyses independently confirmed their altered expression patterns, further supporting their roles as the biological readout of SIAH2 loss-of-function in human cancer cells. Conclusion: The RPPA-based cancer pathway mapping provides valuable molecular insight into the antitumor efficacy and reveals a major tumor vulnerability in human cancer pathway/network rewiring when SIAH2 is blocked in late-stage malignant cells. The kinomic data support our innovative strategy to design anti-SIAH-based anti-EGFR/RAS target therapies to control and eradicate undruggable and incurable human cancers in the future. Citation Format: Jonathan M. Baker, Andrew Howell, Ashleigh Hannah, Julia Wulfkuhle, Natalie Stahr, Rosa Gallagher, Emanuel Petricoin, Amy Tang. Investigating mechanisms of tumor eradication by blocking SIAH E3 ligase, a major tumor vulnerability, in EGFR/RAS-driven human cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1841.

Abstract 5978: Therapeutic targeting of MELK using a drug repurposing approach to combat TNBC cells

Abstract Background: Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer linked to high chemo-resistant metastatic cases and limited therapeutic options due to the absence of conventional bioreceptors. Therefore, to treat TNBC, it is imperative to identify promising druggable biological targets. Experimental Procedures: An integrated bioinformatic analysis of microarray datasets was performed to identify significantly differentially expressed genes (DEGs) in TNBC. For selecting a potent therapeutic target, the function and significance of the upregulated DEGs in TNBC was investigated by an in silico study employing the UALCAN portal, String database, KM plotter, and Enrichr tools. This analysis included gene expression validation, insights into protein-protein interactions, survival analysis, and pathway mapping of the genes. To obtain potent drugs binding to the selected target MELK (maternal embryonic leucine zipper kinase), a drug repurposing approach was employed starting with virtual screening followed by molecular dynamic simulation (MDS) using GROMACS. Further, the anti-cancer activity of the top two drugs was validated by live-dead imaging, gene expression analyses, MTT-based cell viability and ROS detection assays. Results: Based on a stringent criterion for significant DEG identification (log2|FC|>1 & adjust P-value < 0.05), 25 overlapping upregulated genes were obtained from three selected datasets. Further, in silico analysis revealed that MELK is significantly upregulated across the four stages and subtypes of breast cancer, including TNBC. Higher MELK expression and its oncogenic interactions correlated with poor overall survival of TNBC patients. Evidence suggests that the existing inhibitor for MELK (OTSSP167) has shown poor specificity. Therefore, to block its activity, a library of 1293 FDA-approved drugs was screened against the kinase domain of MELK. MDS study and analysis using parameters like RMSD, RMSF and pair distance revealed that the top 10 drugs were strongly stabilized by H-bonds in the binding pocket of MELK, with minimal deviation and reduced fluctuations of MELK upon drug binding. Binding free energy calculation of drug-MELK interaction using the MM-PBSA method revealed that nine drugs possessed higher binding energy than the inhibitor. The top two drugs obtained from the study (originally kinase and reductase inhibitors respectively) were further validated for their in vitro anti-cancer efficacy in MDA-MB-231 and MDA-MB-468 cells. Treatment with these drugs exhibited (a) a dose-dependent decrease in proliferation, (b) significant cell death, (c) a marked increase in the cellular ROS levels, and (d) a decrease in the expression of MELK and its downstream targets in TNBC cell lines. Conclusion: The present study opens the avenue for using repurposed drugs as potential therapeutic molecules against MELK activity to combat TNBC progression. Citation Format: Arisha Arora, Shilpi Sarkar, Siddhartha S. Ghosh. Therapeutic targeting of MELK using a drug repurposing approach to combat TNBC cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5978.

Vertebral Subluxation and Systems Biology: An Integrative Review Exploring the Salutogenic Influence of Chiropractic Care on the Neuroendocrine-Immune System.

In this paperwe synthesize an expansive body of literature examining the multifaceted influence of chiropractic care on processes withinand modulators of the neuroendocrine-immune (NEI) system, for the purpose of generating an inductive hypothesis regarding the potential impacts of chiropractic care on integrated physiology. Taking a broad, interdisciplinary, and integrative view of two decades of research-documented outcomes of chiropractic care, inclusive of reports ranging from systematic and meta-analysis and randomized and observational trialsto case and cohort studies, this review encapsulates a rigorous analysis of research and suggests the appropriateness of a more integrative perspective on the impact of chiropractic care on systemic physiology. A novel perspective on the salutogenic, health-promotingeffects of chiropractic adjustment is presented, focused on the improvement of physical indicators of well-being and adaptability such as blood pressure, heart rate variability, and sleep, potential benefits that may be facilitated through multiple neurologically mediated pathways. Our findings support the biological plausibility of complex benefits from chiropractic intervention that is not limited to simple neuromusculoskeletal outcomes and opennew avenues for future research, specifically the exploration and mapping of the precise neural pathways and networks influenced by chiropractic adjustment.

Deciphering the Receptor-Mediated Signaling Pathways of Interleukin-19 and Interleukin-20.

Interleukin-19 (IL-19) and Interleukin-20 (IL-20) are inflammatory cytokines belonging to the IL-10 family with immunoregulatory properties. Emerging evidence highlights the importance of association of these cytokines with both immunological and inflammatory disorders, including chronic inflammation, cardiac dysfunction, and cancer. IL-19 and IL-20 bind to the heterodimeric receptor complex and induce multiple downstream signaling cascades by activating the signal transducer and activator of transcription 3 (STAT3), Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK), AKT serine/threonine kinase 1 (AKT1), and NFKB inhibitor alpha (NFKBIA), leading to proinflammatory and anti-inflammatory reactions in cancer, inflammation, tumor microenvironment, and infectious diseases. Considering the significant role of these cytokines, we integrated its cellular signaling network by combining multiomics molecular events associated with 56 molecules of induced by IL-19 and 156 molecules of by IL-20. The reactions of these signaling events are classified into enzyme catalysis/post-translational modifications, activation/inhibition events, molecular associations, gene regulations at the mRNA and protein level, and the protein translocation events. We believe that this signaling pathway map would serve as a knowledge base, that aid researchers and clinicians to understand and explore the intricate mechanisms and identify novel signaling components and therapeutic targets for diseases associated with dysregulated IL-19 and IL-20 signaling.

Characterization of the signal transduction cascade for inflammatory gene expression in fibroblasts with ATM-ATR deficiencies after Ionizing radiation

Background and purposeIonizing radiation (IR) induces DNA double-strand breaks (DSBs), leading to micronuclei formation, which has emerged as a key mediator of inflammatory responses after IR. This study aimed to investigate the signaling cascade in inflammatory gene expression using fibroblasts harboring DNA damage response deficiency after exposure to IR. Materials and methodsMicronuclei formation was examined in human dermal fibroblasts derived from patients with deficiencies in ATM, ATR, MRE11, XLF, Artemis, or BRCA2 after IR. RNA-sequencing analysis was performed to assess gene expression, pathway mapping, and the balance of transcriptional activity using the transcription factor–based downstream gene expression mapping (TDEM) method developed in this study. ResultsDeficiencies in ATM, ATR, or MRE11 led to increased micronuclei formation after IR compared to normal cells. RNA-seq analysis revealed significant upregulation of inflammatory expression in cells deficient in ATM, ATR, or MRE11 following IR. Pathway mapping analysis identified the upregulation of RIG-I, MDA-5, IRF7, IL6, and interferon stimulated gene expression after IR. These changes were pronounced in cells deficient in ATM, ATR, or MRE11. TDEM analysis suggested the differential activation of STAT1/3–pathway between ATM and ATR deficiency. ConclusionEnhanced micronuclei formation upon ATM, ATR, or MRE11 deficiency activated the cGAS/STING, RIG-I-MDA-5-IRF7-IL6 pathway, resulting in its downstream interferon stimulated gene expression following exposure to IR. Our study provides comprehensive information regarding the status of inflammation-related gene expression under DSB repair deficiency after IR. The generated dataset may be useful in developing functional biomarkers to accurately identify patients sensitive to radiotherapy.

Double outlet right ventricle - the 50% rule has always been about the conus.

There has been much variability in the definition of double outlet right ventricle (DORV) spanning the last century. Historically, emphasis has been placed on the assignment of the great arteries to the right ventricle as a definition of DORV. In this review, we aim to underscore the importance of conal muscle, rather than rules surrounding assignment of great arteries to ventricles. We will be outlining the variability in patient anatomy that results from variations in conal muscle development in DORV, which may not fit perfectly into predefined constructs. This anatomic variability directly determines physiology and surgical repair options. There is a growing appreciation of the utility of cross-sectional imaging in complex DORV, and the generation of patient-specific 3D models with virtual reality simulations for surgical planning. These models improve the prediction of candidacy for biventricular repair and allow the mapping of complex baffle pathways preoperatively. DORV is not a disease entity in itself, but rather a vast spectrum of disorders associated with maldevelopment of conal muscle and often abnormal expansion of one the great vessels. Patient-specific 3D models will be crucial for improved surgical planning and patient outcomes.

Is the Comparator in Your Diagnostic Cost-Effectiveness Model “Standard of Care”? Recommendations from Literature Reviews and Expert Interviews on How to Identify and Operationalize It

ObjectivesThis research aimed to develop best-practice recommendations for identifying the “standard of care” (SoC) and integrate it when it is the comparator in diagnostic economic models (SoC comparator). MethodsA multi-methods approach comprising 2 pragmatic literature reviews and 9 expert interviews was used. Experts rated their agreement with draft recommendations based on the authors’ analysis of the reviews. These were refined iteratively to produce final recommendations. ResultsFourteen best-practice recommendations are provided. Care pathway mapping (using quantitative, qualitative, or mixed-methods approaches) should be used for identifying the SoC comparator. Guidelines analysis can be integrated with expert opinion to identify pathway variability and discrepancies from clinical practice. For integrating the SoC comparator into the model, recommendations around structure, input sourcing, data aggregation and reporting, input uncertainty, and model variability are presented. For example, modelers should consider that the reference standard is not synonymous with the SoC, and the SoC may not be the only comparator. The comparator limitations should be discussed with clinical experts, but elicitation of its diagnostic accuracy is not recommended. Probabilistic sensitivity analysis is recommended when evaluating the overall input uncertainty, and deterministic sensitivity analysis is useful when there is high model uncertainty or SoC variability. Consensus could not be reached for some topics (eg, the role of real-world data, model averaging, and alternative model structures), but the reported discussions provide points for consideration. ConclusionsTo our knowledge, this is the first guidance to support modelers when identifying and operationalizing the SoC comparator in diagnostic cost-effectiveness models.

Identification of a transcription factor AoMsn2 of the Hog1 signaling pathway contributes to fungal growth, development and pathogenicity in Arthrobotrys oligospora

IntroductionArthrobotrys oligospora has been utilized as a model strain to study the interaction between fungi and nematodes owing to its ability to capture nematodes by developing specialized traps. A previous study showed that high-osmolarity glycerol (Hog1) signaling regulates the osmoregulation and nematocidal activity of A. oligospora. However, the function of downstream transcription factors of the Hog1 signaling in the nematode-trapping (NT) fungi remains unclear. ObjectiveThis study aimed to investigate the functions and potential regulatory network of AoMsn2, a downstream transcription factor of the Hog1 signaling pathway in A. oligospora. MethodsThe function of AoMsn2 was characterized using targeted gene deletion, phenotypic experiments, real-time quantitative PCR, RNA sequencing, untargeted metabolomics, and yeast two-hybrid analysis. ResultsLoss of Aomsn2 significantly enlarged and swollen the hyphae, with an increase in septa and a significant decrease in nuclei. In particular, spore yield, spore germination rate, traps, and nematode predation efficiency were remarkably decreased in the mutants. Phenotypic and transcriptomic analyses revealed that AoMsn2 is essential for fatty acid metabolism and autophagic pathways. Additionally, untargeted metabolomic analysis identified an important function of AoMsn2 in the modulation of secondary metabolites. Furtherly, we analyzed the protein interaction network of AoMsn2 based on the Kyoto Encyclopedia of Genes and Genomes pathway map and the online website STRING. Finally, Hog1 and six putative targeted proteins of AoMsn2 were identified by Y2H analysis. ConclusionOur study reveals that AoMsn2 plays crucial roles in the growth, conidiation, trap development, fatty acid metabolism, and secondary metabolism, as well as establishes a broad basis for understanding the regulatory mechanisms of trap morphogenesis and environmental adaptation in NT fungi.

Mechanically Robust, Flexible, Fast Responding Temperature Sensor and High‐Resolution Array with Ionically Conductive Double Cross‐Linked Hydrogel

AbstractHydrogel‐based sensing devices show potential in wearable electronics. However, most hydrogels are mechanically weak, bringing functional stability problems in real usage environment that may interact with occasionally external forces. There are demands to develop robust hydrogel‐based devices with good performances. Here, a highly sensitive temperature sensor with robust, ionic conductive, and double cross‐linked polyacrylamide‐sodium alginate hydrogel is developed. It is found that ions with larger radius show higher sensitivity to temperature changes (e.g., Ba2+) in the hydrogel, because ion movement is dependent with ion sizes. The sensor shows advantages of fast response (2.02 s of 40 °C temperature difference), wide sensing range (22–100 °C), and high robustness (withstanding 2000 cyclic compression and 175 N m−1 for 180° anti‐peeling test). The wearable sensor can effectively distinguish the temperatures of various body parts (0.9 °C temperature difference) and monitor respiration (0.5 °C temperature difference) in real‐time. A wearable 5×5 sensing array is developed for direct human‐body temperature mapping, achieving an optimum resolution of ≈0.15 mm−1 and enabling a clear mapping of superficial vascular pathways at the wrist. This study provides a practical and optimized approach for the implementation of wearable conductive hydrogel‐based devices in the field of human health.

Preparing for and Not Waiting for Surgery.

Cancer surgery is an essential treatment strategy but can disrupt patients' physical and psychological health. With worldwide demand for surgery expected to increase, this review aims to raise awareness of this global public health concern, present a stepwise framework for preoperative risk evaluation, and propose the adoption of personalised prehabilitation to mitigate risk. Perioperative medicine is a growing speciality that aims to improve clinical outcome by preparing patients for the stress associated with surgery. Preparation should begin at contemplation of surgery, with universal screening for established risk factors, physical fitness, nutritional status, psychological health, and, where applicable, frailty and cognitive function. Patients at risk should undergo a formal assessment with a qualified healthcare professional which informs meaningful shared decision-making discussion and personalised prehabilitation prescription incorporating, where indicated, exercise, nutrition, psychological support, 'surgery schools', and referral to existing local services. The foundational principles of prehabilitation can be adapted to local context, culture, and population. Clinical services should be co-designed with all stakeholders, including patient representatives, and require careful mapping of patient pathways and use of multi-disciplinary professional input. Future research should optimise prehabilitation interventions, adopting standardised outcome measures and robust health economic evaluation.

Transcriptome analysis of effects of Tecrl deficiency on cardiometabolic and calcium regulation in cardiac tissue.

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a hereditary heart disease characterized by bidirectional or polymorphic ventricular tachycardia and an increased risk of sudden cardiac death. Although trans-2,3-enoyl-CoA reductase like (TECRL) is a newly reported pathogenic gene leading to CPVT that can influence intracellular calcium regulation, the unidentified mechanism underlying the pathogenesis of TECRL deficiency-mediated CPVT remains mainly elusive. In the present study, Tecrl knockout (KO) mice were established and the differentially expressed genes (DEGs) were investigated by RNA-sequencing from the heart tissues. In addition, 857 DEGs were identified in Tecrl KO mice. Subsequently, a weighted gene co-expression network analysis was conducted to discern the pivotal pathways implicated in the Tecrl-mediated regulatory network. Moreover, pathway mapping analyses demonstrated that essential metabolism-related pathways were significantly enriched, notably the fatty acid metabolic process and calcium regulation. Collectively, the data suggested a synergistic relationship between Tecrl deficiency and cardiometabolic and calcium regulation during the development of CPVT. Therefore, further studies on the potential function of TECRL in cardiac tissues would be beneficial to elucidate the pathogenesis of CPVT.

GC/MS and LC/MS serum metabolomic analysis of Chinese LN patients

China, being a densely populated nation, faces a substantial economic burden due to a high incidence of lupus nephritis (LN) cases. The concealed onset of LN has resulted in many individuals have missed the optimal timing for treatment. The aim of the research is to study the serum metabolomics of Chinese LN patients using gas chromatography (GC)/mass spectrometry (MS) and liquid chromatography (LC)/MS to identify potential diagnostic markers. Fifty LN patients and fifty normal controls, matched for Body Mass Index (BMI) and age, were selected. Serum analysis was conducted using GC/MS and LC/MS, followed by multivariate statistical analysis. Various multidimensional analyses, including principal component analysis, partial least squares discrimination analysis, and orthogonal partial least squares discrimination analysis, along with one-dimensional analyses such as t-tests, were performed. Metabolites with variable importance in projection value > 1 and a p-value < 0.05 were considered critical biomarkers for LN. Furthermore, identified biomarkers delineated relevant metabolic pathways, and a metabolic pathway map was obtained from the database. Forty-one metabolites were identified as potential LN biomarkers, primarily associated with immune regulation, energy metabolism, intestinal microbial metabolism, renal damage, and oxidative stress. The potential for diagnosing LN and other diseases through metabolomics is demonstrated. Future research should explore larger sample sizes, metabolomic comparisons across different diseases and health states, and integration of metabolomics with clinical diagnostics. Such studies will enhance the understanding of metabolomics in medical diagnosis and provide robust support for its practical application.

Transcriptional responses of Crassostrea hongkongensis under high and low salinity stress

Salinity, a key limiting factor, affects the distribution and survival of marine species. The Hong Kong oyster (Crassostrea hongkongensis), a euryhaline species found along the coast of the South China Sea, has become a major aquaculture bivalve species. To determine the molecular mechanism by which oysters respond to coastal waters with varying salinity levels, we used RNA-seq to sequence the gill samples of oysters exposed to normal (25 ‰, S25), low (5 ‰, S5) and high (35 ‰, S35) salinity conditions for one month. The results revealed different expression transcriptome levels among oysters living under low and high salinity conditions. Using high-throughput sequencing, we identified 811 up-regulated genes and 769 down-regulated genes. As determined by KEGG pathway mapping, the differentially expressed genes (DEGs) were significantly enriched in the prion diseases, histidine metabolism, arginine and proline metabolism, and beta-alanine metabolism pathways in both the S5 vs. S25 and S35 vs. S25 group comparison. Several DEGs including heat shock 70 kDa protein 12B-like, poly (ADP-ribose) polymerase (PARP), and tripartite motif-containing protein 2 (TRIM2), and low-density lipoprotein receptor-like, as well as KEGG pathways, including arginine and proline metabolism, apoptosis, PPAR signaling pathway, the thyroid hormone signaling pathway, were concerning response to salinity stress. Additionally, eight DEGs involved in salinity adaptation were selected for RT-qPCR validation, and the results confirmed the credibility of the transcriptome sequencing data. Overall, we designed a one-month, medium-term experiment to examine the responses of C. hongkongensis exposed to different levels of salinity stress and performed transcriptome analysis using high-throughput sequencing. Our results enhance current understanding of the molecular mechanisms of salinity stress responses in C. hongkongensis and provided insights into the osmotic biology of oysters.

Colocalising proteins and polysaccharides in plants for cell wall and trafficking studies.

Plant cell walls (PCWs) are intricate structures with complex polysaccharides delivered by distinct trafficking routes. Unravelling the intricate trafficking pathways of polysaccharides and proteins involved in PCW biosynthesis is a crucial first step towards understanding the complexities of plant growth and development. This study investigated the feasibility of employing a multi-modal approach that combines transmission electron microscopy (TEM) with molecular-genetic tagging and antibody labelling techniques to differentiate these pathways at the nanoscale. The genetically encoded electron microscopy (EM) tag APEX2 was fused to Arabidopsis thaliana cellulose synthase 6 (AtCESA6) and Nicotiana alata ARABINAN DEFICIENT LIKE 1 (NaARADL1), and these were transiently expressed in Nicotiana benthamiana leaves. APEX2 localization was then combined with immunolabeling using pectin-specific antibodies (JIM5 and JIM7). Our results demonstrate distinct trafficking patterns for AtCESA6 and NaARADL, with AtCESA6 localized primarily to the plasma membrane and vesicles, while NaARADL1 was found in the trans-Golgi network and cytoplasmic vesicles. Pectin epitopes were observed near the plasma membrane, in Golgi-associated vesicles, and in secretory vesicle clusters (SVCs) with both APEX2 constructs. Notably, JIM7 labelling was found in vesicles adjacent to APEX2-AtCESA6 vesicles, suggesting potential co-trafficking. This integrative approach offers a powerful tool for elucidating the dynamic interactions between PCW components at the nanoscale level. The methodology presented here facilitates the precise mapping of protein and polysaccharide trafficking pathways, advancing our understanding of PCW biosynthesis and providing avenues for future research aimed at engineering plant cell walls for various applications.

Transfer to community and prison mental health care from Ireland's main remand prison over three years: 2015-2017.

The post-release period is associated with an increased risk of morbidity and mortality. Previous studies have identified deficits in pre-release planning for mentally ill people in prison, particularly in remand settings. We aimed to determine the proportion of mentally ill people in Ireland's main remand prison who were referred for mental health follow up in community and prison settings, who achieved face to face contact with the receiving service. This retrospective observational cohort study was based in Ireland's main male remand prison, Cloverhill. Participants included all those individuals on the caseload of the prison inreach mental health team who were referred for mental health follow up in community and prison settings at the time of discharge, prison transfer or release from custody over a three-year period, 2015 - 2017. Successful transfer of care (TOC) was defined as face-to-face contact with the receiving service, confirmed by written correspondence or by follow up telephone call. Clinical, demographic and offence related variables were recorded for all participants. There were 911 discharges from the prison inreach mental health team within the three-year study period. Of these, 121 were admitted to hospital, 166 were transferred to other prison inreach mental health services and 237 were discharged to community based mental health follow up in psychiatric outpatient or primary care settings. One third (304/911) had an ICD-10 diagnosis of schizophreniform or bipolar disorder (F20-31) and 37.5% (161/911) were homeless. Over 90% (152/166) of those referred to mental health teams in other prisons achieved successful TOC, with a median of six days to first face-to face assessment. Overall, 59% (140/237) of those referred to community psychiatric outpatient or primary care services achieved TOC following referral on release from custody, with a median of nine days from release to assessment. Clinical and demographic variables did not differ between those achieving and not achieving successful TOC, other than having had input from the PICLS Housing Support Service. Successful transfer of care can be achieved in remand settings using a systematic approach with an emphasis on early and sustained interagency liaison and clear mapping of patient pathways. For incarcerated individuals experiencing homelessness and mental health disorders, provision of a housing support service was associated with increased likelihood of successful transfer of care to community mental health supports.

Unraveling the Role of TREM2 and CD33 in Alzheimer’s Disease

Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized by the accumulation of amyloid plaques and neurofibrillary tangles. This study investigates the role of two key genes, TREM2 and CD33, in AD pathogenesis. Gene expression profiles from human brain samples and transgenic mouse models were analyzed using data from the Gene Expression Omnibus. Differential gene expression analysis revealed significant upregulation of TREM2 and CD33 in AD samples compared to controls. Analysis of KEGG pathway, a database composed of biological pathway maps, showed TREM2 involvement in osteoclast differentiation and CD33 in hematopoietic cell lineage. String database analysis highlighted both genes' roles in regulating tumor necrosis factor production and cytokine production. Furthermore, TREM2 variants in AD patients were examined, identifying six variants (H157Y, R98W, D87N, T66M, Y38C, and Q33X) exclusive to AD samples. The R47H variant showed the strongest correlation with AD (p&lt;0.001). The following SNPs of CD33 were identified as contributors to AD development: rs3826656, rs3865444, and rs12459419. These findings suggest that TREM2 and CD33 play crucial roles in AD progression, potentially through modulation of microglial function and inflammatory responses. These genes may serve as promising targets for developing novel AD therapeutics and biomarkers.

OsCBL1 mediates rice response to local nitrate signaling: insights into regulatory networks and gene expression.

Nitrate is a significant source of nitrogen in soils and also serves as a critical signal for root development. Previous studies have demonstrated that the local nitrate supply promotes lateral root elongation primarily through local nitrate signals, rather than nutritional effects. In this study, we report that Calcineurin B-like protein 1 (OsCBL1) positively regulates local nitrate signaling, thereby triggering lateral root colonization, as revealed by a comparative analysis of the phenotype and whole transcriptome of the knockdown mutant (OsCBL1-KD) and the wild-type (WT). In the split-root system, the knockdown of OsCBL1 was found to inhibit local nitrate-induced lateral root growth. Transcriptome analyses identified 398 differentially expressed genes (DEGs) that were under the control of OsCBL1 and associated with the phenotype of nitrate-induced lateral root colonization. Further analysis revealed that the nitrate transporter/sensor gene OsNRT1.1B was up-regulated under Sp-NaNO3 conditions compared to Sp-NaCl in WT but not in OsCBL1-KD plants. Pathway mapping of DEGs (i.e., genes exhibiting a significant change in expression in the Sp-NaNO3 condition compared to the Sp-NaCl condition) revealed a preferential upregulation of genes involved in lignin biosynthesis and a downregulation of genes involved in auxin and salicylic acid signaling. This suggests that OsCBL1 might function as a transmitter within the auxin, salicylic acid signaling, lignin biosynthesis, and nitrate sensor (OsNRT1.1B)-mediated pathways in response to local nitrate signaling. We also identified a transcriptional regulatory network downstream of OsCBL1 in nitrate-rich patches that is centered on several core transcription factors. Our study provides new insights into how plants adapt to an inhomogeneous distribution of nitrogen in the soil.

Gut microbiota functional profiling in autism spectrum disorders: bacterial VOCs and related metabolic pathways acting as disease biomarkers and predictors.

Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental disorder. Major interplays between the gastrointestinal (GI) tract and the central nervous system (CNS) seem to be driven by gut microbiota (GM). Herein, we provide a GM functional characterization, based on GM metabolomics, mapping of bacterial biochemical pathways, and anamnestic, clinical, and nutritional patient metadata. Fecal samples collected from children with ASD and neurotypical children were analyzed by gas-chromatography mass spectrometry coupled with solid phase microextraction (GC-MS/SPME) to determine volatile organic compounds (VOCs) associated with the metataxonomic approach by 16S rRNA gene sequencing. Multivariate and univariate statistical analyses assessed differential VOC profiles and relationships with ASD anamnestic and clinical features for biomarker discovery. Multiple web-based and machine learning (ML) models identified metabolic predictors of disease and network analyses correlated GM ecological and metabolic patterns. The GM core volatilome for all ASD patients was characterized by a high concentration of 1-pentanol, 1-butanol, phenyl ethyl alcohol; benzeneacetaldehyde, octadecanal, tetradecanal; methyl isobutyl ketone, 2-hexanone, acetone; acetic, propanoic, 3-methyl-butanoic and 2-methyl-propanoic acids; indole and skatole; and o-cymene. Patients were stratified based on age, GI symptoms, and ASD severity symptoms. Disease risk prediction allowed us to associate butanoic acid with subjects older than 5 years, indole with the absence of GI symptoms and low disease severity, propanoic acid with the ASD risk group, and p-cymene with ASD symptoms, all based on the predictive CBCL-EXT scale. The HistGradientBoostingClassifier model classified ASD patients vs. CTRLs by an accuracy of 89%, based on methyl isobutyl ketone, benzeneacetaldehyde, phenyl ethyl alcohol, ethanol, butanoic acid, octadecane, acetic acid, skatole, and tetradecanal features. LogisticRegression models corroborated methyl isobutyl ketone, benzeneacetaldehyde, phenyl ethyl alcohol, skatole, and acetic acid as ASD predictors. Our results will aid the development of advanced clinical decision support systems (CDSSs), assisted by ML models, for advanced ASD-personalized medicine, based on omics data integrated into electronic health/medical records. Furthermore, new ASD screening strategies based on GM-related predictors could be used to improve ASD risk assessment by uncovering novel ASD onset and risk predictors.