Twofold Change Research Articles

Ethylene modulates wheat response to phosphate deficiency.

Ethylene involves in the response to P deficiency in some model plants, but its relevance to wheat remains limited. Following our recent study demonstrating the role of differentially expressed genes (DEGs) encoding ethylene response factors (ERFs) in response to P starvation in wheat, this study aims to investigate the remodelling of ethylene pathway and the physiological roles of ethylene in wheat under P deficiency using transcriptome analysis and the addition of exogenous ethylene analogue ethephon or ethylene inhibitors. ERFs with at least a two-fold change upon P deficiency were biasedly enriched on chromosome 4 B. A group of genes encoding ACC synthase and ACC oxidase were upregulated under P starvation, indicating an increase in ACC and ethylene content, which was verified by biochemical measurements and gas chromatography-mass spectrometry analysis. Under P deficiency, both root and shoot biomass decreased with the application of exogenous ethephon or ethylene inhibitors, while root fork numbers and root surface area decreased upon ethephon treatment. The phosphate (Pi) concentrations in roots and old leaves increased with ethephon treatment, and it's redistribution in roots and younger leaves was altered under Pi starvation. Our findings could serve as a guideline for breeding germplasm with high Pi efficiency.

High-throughput root phenotyping and association analysis identified potential genomic regions for phosphorus use efficiency in wheat (Triticum aestivum L.).

Association analysis identified 77 marker-trait associations (MTAs) for PUE traits, of which 10 were high-confidence MTAs. Candidate-gene mining and in-silico expression analysis identified 13 putative candidate genes for PUE traits. Bread wheat (Triticum aestivum L.) is a major cereal crop affected by phosphorus (P) deficiency, which affects root characteristics, plant biomass, and other attributes related to P-use efficiency (PUE). Understanding the genetic mechanisms of PUE traits helps in developing bread wheat cultivars that perform well in low-P environments. With this objective, we evaluated a bread wheat panel comprising 304 accessions for 14 PUE traits with high-throughput phenotyping under low-P and optimum-P treatments and observed a significant genetic variation among germplasm lines for studied traits. Genome-wide association study (GWAS) using 14,025 high-quality single-nucleotide polymorphisms identified 77 marker-trait associations (MTAs), of which 10 were chosen as high-confidence MTAs as they had > 10% phenotypic variation with logarithm of odds (LOD) scores of more than five. Candidate-gene (CG) mining from high-confidence MTAs identified 180 unique gene models, of which 78 were differentially expressed (DEGs) with at least twofold change in expression under low-P over optimum-P. Of the 78-DEGs, 13 were thought to be putative CGs as they exhibited functional relevance to PUE traits. These CGs mainly encode for important proteins and their products involved in regulating root system architecture, P uptake, transport, and utilization. Promoter analysis from 1500bp upstream of gene start site for 13 putative CGs revealed the presence of light responsive, salicylic-acid responsive, gibberellic-acid (GA)-responsive, auxin-responsive, and cold responsive cis-regulatory elements. High-confidence MTAs and putative CGs identified in this study can be employed in breeding programs to improve PUE traits in bread wheat.

Dynamics of Changes in the Surface Area of Water Bodies in Subsidence Basins in Mining Areas

The Silesian Upland in southern Poland is known as a place where subsidence processes induced by mining activities occur in an area of nearly 1500 square kilometres, with many water bodies that formed in subsidence basins. This study concerned the dynamics of changes in the occurrence, boundaries and area of water bodies in subsidence basins (using orthoimagery from 1996 to 2023), as well as the assessment of the factors underlying the morphogenetic and hydrogenetic transformations of these basins. Within the subsidence basins covered by the study, water bodies occupied a total area that changed from 9.22 hectares in 1996 to 48.43 hectares in 2003, with a maximum of 52.30 hectares in 2009. The obtained figures testify to the extremely dynamic changes taking place in subsidence basins, which are unprecedented within such short time intervals in the case of other morphogenetic types of lakes and anthropogenic water bodies (for instance, from 1996 to 2003, the basin of the Brantka water body in Bytom underwent a more than two-fold change in its area, with RA values in the range of 54.4% to 131.9). A reflection of the dynamics of short-term changes in the water bodies in question in the period from 1996 to 2023 is the increase in the water area of the three studied water bodies, which was projected by linear regression to range from 0.09 hectares/year to 0.56 hectares/year. The area change trends, as determined by polynomial regression, suggest a slight decrease in the water table within the last few years, as well as within the next few years, for each of the studied basins.

Metabolic-driven analytics of traumatic brain injury and neuroprotection by ethyl pyruvate

BackgroundResearch on traumatic brain injury (TBI) highlights the significance of counteracting its metabolic impact via exogenous fuels to support metabolism and diminish cellular damage. While ethyl pyruvate (EP) treatment shows promise in normalizing cellular metabolism and providing neuroprotection, there is a gap in understanding the precise metabolic pathways involved. Metabolomic analysis of the acute post-injury metabolic effects, with and without EP treatment, aims to deepen our knowledge by identifying and comparing the metabolite profiles, thereby illuminating the injury's effects and EP's therapeutic potential.MethodsIn the current study, an untargeted metabolomics approach was used to reveal brain metabolism changes in rats 24 h after a controlled cortical impact (CCI) injury, with or without EP treatment. Using principal component analysis (PCA), volcano plots, Random Forest and pathway analysis we differentiated the brain metabolomes of CCI and sham injured animals treated with saline (Veh) or EP, identifying key metabolites and pathways affected by injury. Additionally, the effect of EP on the non-injured brain was also explored.ResultsPCA showed a clear separation of the four study groups (sham-Veh, CCI-Veh, sham-EP, CCI-EP) based on injury. Following CCI injury (CCI-Veh), 109 metabolites belonging to the amino acid, carbohydrate, lipid, nucleotide, and xenobiotic families exhibited a twofold change at 24 h compared to the sham-Veh group, with 93 of these significantly increasing and 16 significantly decreasing (p < 0.05). CCI animals were treated with EP (CCI-EP) showed only 5 metabolites in the carbohydrate, amino acids, peptides, nucleotides, lipids, and xenobiotics super families that exhibited a twofold change, compared to the CCI-Veh group (p < 0.05). In the non-injured brain, EP treatment (sham-EP) resulted in a twofold change in 6 metabolites within the amino acid, peptide, nucleotide, and lipid super families compared to saline treated sham animals (sham-Veh, p < 0.05).ConclusionsThis study delineates the unique metabolic signatures resulting from a CCI injury and those related to EP treatment in both the injured and non-injured brain, underscoring the metabolic adaptations to brain injury and the effects of EP. Our analysis uncovers significant shifts in metabolites associated with inflammation, energy metabolism, and neuroprotection after injury, and demonstrates how EP intervention after injury alters metabolites associated with mitigating inflammation and oxidative damage.

Growth of a Tessellation: Geometric rules for the Development of Stingray Skeletal Patterns.

The skeletons of sharks and rays, fashioned from cartilage, and armored by a veneer of mineralized tiles (tesserae) present a mathematical challenge: How can the continuous covering be maintained as the skeleton expands? This study, using microCT and custom visual data analyses of growing stingray skeletons, systematically examines tessellation patterns and morphologies of the many thousand interacting tesserae covering the hyomandibula (a skeletal element critical to feeding), over a two-fold developmental change in hyomandibula length. The number of tesserae remains surprisingly constant, even as the hyomandibula expands isometrically, with all hyomandibulae displaying self-similar distributions of tesserae shapes/sizes. Although the distribution of tesserae geometries largely agrees with the rules for polyhedra tiling of complex surfaces-dominated by hexagons and a minor fraction of pentagons and heptagons, but very few other polygons-the agreement with Euler's classic mathematical laws is not perfect. Contrary to the assumed uniform growth rate (which is shown would create geometric incompatibilities), larger tesserae grow faster to accommodate skeletal expansion. It is hypothesized that this local regulation of global system complexity is driven by tension (from cartilaginous core expansion) in the fibers connecting tesserae, with strain-responsive cells orchestrating local mineral apposition.

MicroRNA Signature in an In Vitro Keratinocyte Model of Diabetic Wound Healing.

Treating diabetic wounds effectively remains a significant clinical challenge. Emerging studies suggest that microRNAs (miRNAs) play crucial roles in various physiological and pathological processes and hold promise as therapeutic tools. This study investigates the miRNA expression profile in keratinocytes using a cell model of diabetic wounds. Microarray analysis revealed that 43 miRNAs from wounded keratinocytes incubated under diabetic conditions (high glucose/hypoxia) exhibited a two-fold change in expression compared to those incubated under normal conditions (low glucose/normoxia). Quantitative RT-PCR confirmed significant differences in the expression of eight miRNAs, with miR-3138 and miR-3679-5p being further analyzed for their roles in keratinocyte migration. Transfection with a miR-3138 mimic and a miR-3679-5p inhibitor indicated that upregulation of miR-3138 and downregulation of miR-3679-5p enhance keratinocyte migration in both normal and diabetic wounds. Pathway and gene ontology (GO) analyses identified potential pathways and functional annotations associated with miR-3138 and miR-3679-5p in diabetic wound healing. Potential human gene targets of miR-3138 and miR-3679-5p were predicted using a three-way comparison of the TargetScan, miRDB, and DIANA databases. This study elucidates the miRNA expression signature of human keratinocytes in a diabetes-like environment, providing deeper insights into the pathogenesis of diabetic wounds.

Designing a Low-Cost Force Plate for Postural Assessment

The purpose of this study was to develop a pair of single-pedestal types with a low-cost and user-friendly force plate for assessing ground reaction force (GRF), center of pressure (COP), and plantar pressure distribution (PPD). These parameters are crucial for assessing human movement and maintaining body balance. The load cells were tested with standard weights of 5, 10, 15, and 20 kg. Using linear regression, the analysis showed a strong linear relationship between the load cell output and the standard weight, with an R-squared value of 0.99. Furthermore, the error margin was determined to be less than +/- 5%. In the initial equipment assessment, a healthy female was evaluated the posture under both eye-open and eye-closed conditions through three sets of measurements. The results showed about a two-fold change in the COP parameter, possibly due to swaying when the eyes were closed. Additionally, the PPD parameter revealed varying foot weight distribution levels, even though the GRF values were almost the same. The equipment's graphic user interface (GUI) provides real-time graphical representations for GRF, COP, and PPD, aiding in training effectiveness for enhancing postural assessment under professional guidance. In future studies, we plan to use the developed equipment to observe its effectiveness by measuring a larger and more diverse population.

Engineering a Microfluidic Platform to Cryopreserve Stem Cells: A DMSO-Free Sustainable Approach.

Human adipose-derived stem cells (hASCs) are cryopreserved traditionally using dimethyl sulfoxide (DMSO) as the cryoprotectant agent. DMSO penetrates cell membranes and prevents cellular damage during cryopreservation. However, DMSO is not inert to cells, inducing cytotoxic effects by causing mitochondrial dysfunction, reduced cell proliferation, and impaired hASCs transplantation. Additionally, large-scale production of DMSO and contamination can adversely impact the environment. A sustainable, green alternative to DMSO is trehalose, a natural disaccharide cryoprotectant agent that does not pose any risk of cytotoxicity. However, the cellular permeability of trehalose is less compared to DMSO. Here, a microfluidic chip is developed for the intracellular delivery of trehalose in hASCs. The chip is designed for mechanoporation, which creates transient pores in cell membranes by mechanical deformation. Mechanoporation allows the sparingly permeable trehalose to be internalized within the cell cytosol. The amount of trehalose delivered intracellularly is quantified and optimized based on cellular compatibility and functionality. Furthermore, whole-transcriptome sequencing confirms that less than 1% of all target genes display at least a twofold change in expression when cells are passed through the chip compared to untreated cells. Overall, the results confirm the feasibility and effectiveness of using this microfluidic chip for DMSO-free cryopreservation of hASCs.

Effects of standard heat treatment on micro-to nanostructure heterogeneities in a Rene 65 Ni-based superalloy billet

Advancements in the manufacturing of aeroengine components with superior mechanical properties rely on the microstructure homogeneity of industrially forged Ni-based superalloys. Billets often contain microstructural heterogeneities that can persist throughout the process, potentially compromising the integrity of the final product. Rene 65 is a relatively new superalloy with high-temperature mechanical properties superior to those of Alloy 718. However, systematic studies on its microstructure-property relationships are scarce. Here, we correlate the microstructural evolution with the hardness of a Rene 65 billet subjected to industrial processing and standard heat treatments. Multiscale microstructural heterogeneities, including grain size, geometrically necessary dislocations, twin boundary density, and the multimodal distribution of γʹ precipitates, are characterised. Grain growth occurs near the billet centre. Precipitation varies with radial position, showing up to a two-fold change in primary and secondary γʹ fractions. Tertiary γʹ precipitates exhibit variations in morphology and chemical composition, with Cr and Co enrichment near the billet surface. These heterogeneities arise from varying strain distributions and cooling rates during radial forging. Sub-solvus annealing and ageing are shown to mitigate these heterogeneities by promoting recrystallisation, recovery, and homogeneous precipitation of tertiary γʹ. A strengthening model elucidates the active mechanisms in as-received and heat-tread conditions, predicting hardness with a deviation of <8 %. Analyses of grain boundaries and γ/γʹ interfaces reveal strong segregation of Mo, W, Nb, C and B before and after heat treatment, with Mo and B showing the highest interfacial excess values. Insights into the microstructural evolution and its impact on properties could guide the development of next-generation aerospace parts.

Analysis of serum proteomic profiles of endangered Siamese and Burmese Eld's deer infected with subclinical Babesia bovis in Thailand

The endangered Eld's deer is a conserved species in Thailand, where tropical parasitic infections are endemic. Although Eld's deer with babesiosis are generally asymptomatic, they can still harbor the parasite and serve as reservoirs for ticks, spreading the infection to healthy animals within the herd. The present study aimed to investigate potential serum proteome biomarkers of Eld's deer with subclinical Babesia bovis infection. A total of 67 blood samples were collected from captive Siamese and Burmese Eld's deer showing no signs of parasitic infection. The nested polymerase chain reaction (nPCR) of a conserved spherical body protein 2 (sbp-2) gene of B. bovis was utilized to classify Eld's deer groups, with 25.37 % (17/67) testing positive for B. bovis. Additionally, the application of proteomic studies showed that six B. bovis proteins, such as Obg-like ATPase 1 (OLA1) and heat shock protein 90 (HSP90), were significantly upregulated by more than a two-fold change compared with the PCR-negative samples. Of the 55 overexpressed serum proteins in the PCR-positives, alpha 2-HS glycoprotein (AHSG) and immunoglobulin lambda variable 2–8 (IGLV2–8) were notably among the top 10 proteins with the highest area under curve (AUC) values. Hence, they were proposed as potential biomarkers for subclinical B. bovis infection in Eld's deer. Analysis of the protein interaction network revealed interactions between Eld's deer AHSG and B. bovis OLA1 and HSP90, alongside associations with other proteins such as erb-b2 receptor tyrosine kinase 2 (ERBB2) and epidermal growth factor receptor (EGFR). These interactions were involved in the immune system pathway and inflammatory responses. Our findings shed light on subclinical infection of B. bovis in Eld's deer and identify potential biomarkers, contributing to the further effective detection and monitoring of B. bovis infection in this endangered species.

The soybean plasma membrane GmDR1 protein conferring broad-spectrum disease and pest resistance regulates several receptor kinases and NLR proteins

Overexpression of Glycine max disease resistant 1 (GmDR1) exhibits broad-spectrum resistance against Fusarium virguliforme, Heterodera glycines (soybean cyst nematode), Tetranychus urticae (Koch) (spider mites), and Aphis glycines Matsumura (soybean aphids) in soybean. To understand the mechanisms of broad-spectrum immunity mediated by GmDR1, the transcriptomes of a strong and a weak GmDR1-overexpressor following treatment with chitin, a pathogen- and pest-associated molecular pattern (PAMP) common to these organisms, were investigated. The strong and weak GmDR1-overexpressors exhibited altered expression of 6098 and 992 genes, respectively, as compared to the nontransgenic control following chitin treatment. However, only 192 chitin- and 115 buffer-responsive genes exhibited over two-fold changes in expression levels in both strong and weak GmDR1-overexpressors as compared to the control. MapMan analysis of the 192 chitin-responsive genes revealed 64 biotic stress-related genes, of which 53 were induced and 11 repressed as compared to the control. The 53 chitin-induced genes include nine genes that encode receptor kinases, 13 encode nucleotide-binding leucine-rich repeat (NLR) receptor proteins, seven encode WRKY transcription factors, four ethylene response factors, and three MYB-like transcription factors. Investigation of a subset of these genes revealed three receptor protein kinases, seven NLR proteins, and one WRKY transcription factor genes that are induced following F. virguliforme and H. glycines infection. The integral plasma membrane GmDR1 protein most likely recognizes PAMPs including chitin and activates transcription of genes encoding receptor kinases, NLR proteins and defense-related genes. GmDR1 could be a pattern recognition receptor that regulates the expression of several NLRs for expression of PAMP-triggered immunity and/or priming the effector triggered immunity.

Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle.

Animal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change's impact on livestock is more intense in tropical countries like India where dairy cattle crossbreeds are more sensitive to heat stress. The main reason for this study was to find the missing relative changes in transcript levels in thermo-neutral and heat stress conditions in crossbred cattle through whole-transcriptome analysis of RNA-Seq data. Differentially expressed genes (DEGs) identified based on the minimum log twofold change value and false discovery rate 0.05 revealed 468 up-regulated genes and 2273 down-regulated significant genes. Functional annotation and pathway analysis of these significant DEGs were compared based on Gene Ontology (Biological process), Kyoto Encyclopedia of Genes and Genome (KEGG), and Reactome pathways using g: Profiler, ShinyGO v0.76, and iDEP.951 web tools. On finding network visualization, the most over-represented and correlated pathways were neuronal and sensory organ development, calcium signalling pathway, Mitogen-activated protein kinase (MAPK) and Smad signalling pathway, Ras-proximate-1, or Ras-related protein 1 (Rap 1) signalling pathway, apoptosis, and oxidative stress. Similarly, down-regulated genes were most expressed in mRNA processing, immune system, B-cell receptor signalling pathway, Nucleotide oligomerization domain(NOD)-like receptors (NLRs) signalling pathway and nonsense-mediated decay (NMD) pathway. The heat stress-responsive genes identified in this study will facilitate our understanding of the molecular basis for climate resilience and heat tolerance in Indian dairy crossbreeds.

Direct and indirect responses of the Arabidopsis transcriptome to an induced increase in trehalose 6-phosphate.

Trehalose 6-phosphate (Tre6P) is an essential signal metabolite that regulates the level of sucrose, linking growth and development to the metabolic status. We hypothesized that Tre6P plays a role in mediating the regulation of gene expression by sucrose. To test this, we performed transcriptomic profiling on Arabidopsis (Arabidopsis thaliana) plants that expressed a bacterial TREHALOSE 6-PHOSPHATE SYNTHASE (TPS) under the control of an ethanol-inducible promoter. Induction led to a 4-fold rise in Tre6P levels, a concomitant decrease in sucrose, significant changes (FDR ≤ 0.05) of over 13,000 transcripts, and 2-fold or larger changes of over 5,000 transcripts. Comparison with nine published responses to sugar availability allowed some of these changes to be linked to the rise in Tre6P, while others were probably due to lower sucrose or other indirect effects. Changes linked to Tre6P included repression of photosynthesis-related gene expression and induction of many growth-related processes including ribosome biogenesis. About 500 starvation-related genes are known to be induced by SUCROSE-NON-FERMENTING-1-RELATED KINASE 1 (SnRK1). They were largely repressed by Tre6P in a manner consistent with SnRK1 inhibition by Tre6P. SnRK1 also represses many genes that are involved in biosynthesis and growth. These responded to Tre6P in a more complex manner, pointing toward Tre6P interacting with other C-signaling pathways. Additionally, elevated Tre6P modified the expression of genes encoding regulatory subunits of the SnRK1 complex and TPS class II and FCS-LIKE ZINC FINGER proteins that are thought to modulate SnRK1 function and genes involved in circadian, TARGET OF RAPAMYCIN, light, abscisic acid, and other hormone signaling.

Abstract LB329: Interleukin6 as a Potential Prognostic Marker and Therapeutic Target in Oral Squamous Cell Carcinoma

Abstract This study investigates the role of interleukin (IL)-6 in oral squamous cell carcinoma (OSCC), evaluating its potential as a prognostic marker and therapeutic target. This study involved 95 untreated OSCC patients, with pre-surgical serum IL-6 levels measured by Electro chemiluminescence immunoassay (ECLIA). Patients were categorized into high (78 patients) and low (17 patients) IL-6 groups based on a cutoff value of 8 pg/mL.A strong correlation was observed between higher IL-6 levels and lower overall survival (P&amp;lt;0.0001) and disease-free survival (P=0.0283). Serum IL-6 levels also showed a strong positive correlation with certain blood test markers such as neutrophil and lymphocyte fractions and C-reactive protein (CRP), and a negative correlation with albumin levels. These findings suggest a link between systemic inflammation, malnutrition, and the Inflammation-based prognostic score (IBPS).Further analysis through microarray assessed the gene expression in primary tumor tissues, revealing 513 genes with more than a two-fold change in the high IL-6 group compared to controls. Gene Ontology analysis indicated increased metabolic activity in the high IL-6 group and suppressed inflammation and immune-related molecules in the low IL-6 group.Immunohistochemical staining for IL-6 in tumor tissues showed its presence mainly in the stroma, particularly in cancer-associated fibroblasts (CAFs) identified by vimentin and α-SMA positivity. Both OSCC cell lines and CAFs established from OSCC tissues demonstrated high IL-6 secretion, especially in cell lines derived from lymph node metastases. Furthermore, cell lines from primary, lymph node, and lung metastases exhibited high IL-6 secretion, with HRAS mutations also identified. Knockdown of HRAS using siRNA reduced IL-6 secretion.Finally, in vivo experiments using an anti-IL-6 receptor antibody showed that blocking IL-6 signaling reduced the proliferation of OSCC cell lines.The study concludes that IL-6 is a useful prognostic and therapeutic target in OSCC. The wide applicability of IL-6 testing and the clinical use of anti-human IL-6R antibody drugs, combined with aggressive nutritional intervention, suggest a potential paradigm shift in OSCC treatment. Citation Format: Hiroyuki Goda, Tomoko Adachi, Koh-ichi Nakashiro, Nobuyuki Kuribayashi, Daisuke Uchida. Interleukin6 as a Potential Prognostic Marker and Therapeutic Target in Oral Squamous Cell Carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB329.

Conjugated linoleic acid (CLA) reduces HFD-induced obesity by enhancing BAT thermogenesis and iWAT browning via the CD36-AMPK pathway.

The antiobesity effect of conjugated linoleic acid (CLA) has been reported. However, the underlying mechanisms have not been fully clarified. Thus, this study aimed to investigate the effects of CLA on thermogenesis of interscapular brown adipose tissue (iBAT) and browning of inguinal subcutaneous white adipose tissue (iWAT) and explore the possible signaling pathway. The in vivo results showed that CLA enhanced the O2 consumption and heat production in HFD (high-fat diet)-fed female mice by roughly 38%. Meanwhile, CLA increased the average iBAT temperature by 2°C at the room temperature and cold exposure, respectively. Correspondingly, CLA caused 1.6-and 2.4-fold increases in the expression of UCP1 (uncoupling protein 1) of BAT and iWAT, respectively, suggesting the activated iBAT thermogenesis and iWAT browning in HFD-fed female mice. Meanwhile, CLA could promote the formation of brown and beige adipocytes in differentiated stromal vascular cells (SVCs) isolated from iBAT and iWAT (the expressions of UCP1 were promoted by about twofold changes). In possible mechanisms, CLA stimulated the expression of CD36 and the activation of theAMPK pathway in mice iBAT and iWAT as well as the differentiated SVCs. However, inhibition of CD36 and AMPK (adenosine 5'-monophosphate-activated protein kinase) abolished the promotive effects of CLA on brown and beige adipocytes formation. Hence, we showed that CLA reduced HFD-induced obesity through enhancing iBAT thermogenesis and iWAT browning via theCD36-AMPK pathway.

Comparative proteomics reveals different protein expression in platelets in patients with alcoholic liver cirrhosis

BackgroundThe role of platelets in disease progression as well as the function of platelets as part of the haemostatic and immunological system in patients with liver cirrhosis is only incompletely understood. This is partly due to difficulties in assessing platelet function. Proteome analyses of platelets have been used to further investigate the role of platelets in other diseases.AimTo assess possible changes in the platelet proteome during different stages of alcohol induced liver cirrhosis compared to healthy donors.Patients and methodsA 45 ml blood sample was drawn from 18 participants aged 18–80 years evenly divided into three groups of healthy donors, patients with less advanced alcohol induced liver cirrhosis (Child-Pugh < 7) and patients with advanced liver cirrhosis (Child-Pugh > 10). The blood was processed to isolate platelets and perform subsequent two-dimensional gel-electrophoresis using a SYPRO™ Ruby dye. After computational analysation significantly in- or decreased protein spots (defined as a two-fold abundance change between different study cohorts and ANOVA < 0.05) were identified via liquid chromatography–mass spectrometry (LCMS) and searching against human protein databases.ResultsThe comparative analysis identified four platelet proteins with progressively decreased protein expression in patients with liver cirrhosis. More specifically Ras-related protein Rab-7a (Rab-7a), Ran-specific binding protein 1 (RANBP1), Rho GDP-dissociation inhibitor 1 (RhoGDI1), and 14–3-3 gamma.ConclusionThere is significant change in protein expression in the platelet proteome throughout the disease progression of alcohol induced liver cirrhosis. The identified proteins are possibly involved in haemostatic and immunoregulatory function of platelets.

Exploring the link between particulate matter pollution and acute respiratory infection risk in children using generalized estimating equations analysis: a robust statistical approach

BackgroundIndia is facing a burdensome public health challenge due to air pollution, with a particularly high burden of acute respiratory infections (ARI) among children. To address this issue, our study aims to evaluate the association between exposure to fine particulate matter (PM2.5) and ARI incidence in young children in India.Materials and methodsOur study used PM2.5 data provided by the Atmospheric Composition Analysis Group at Washington University to assess the association between PM2.5 exposure and ARI incidence in 223,375 children sampled from the 2019–2021 Demographic Health Survey in India. We employed the generalized estimating equation and reported odds ratios and 95% confidence intervals for a 10 µg/m3 increase in PM2.5 and quartiles of PM2.5 exposure.ResultsEach 10 µg/m3 increase in PM2.5 levels was associated with an increased odds of ARI (OR: 1.23, 95% CI: 1.19–1.27). A change from the first quartile of PM2.5 (2.5–34.4 µg/m3) to the second quartile (34.5–51.5 µg/m3) of PM2.5 was associated with a two-fold change (OR: 2.06, 95% CI: 1.60–2.66) in the odds of developing ARI. Similarly, comparing the first quartile to the fourth quartile of PM2.5 exposure (78.3–128.9 µg/m3) resulted in an over four-fold increase in the odds of ARI (OR: 4.45, 95% CI: 3.37–5.87).ConclusionMitigation efforts must be continued implementing higher restrictions in India and to bring new interventions to ensure safe levels of air for reducing the burden of disease and mortality associated with air pollution in India.

Informational Updates and the Derivative Pricing Kernel

It is common in financial markets for market makers to offer prices on derivative instruments even though they are uncertain about the underlying asset’s value. This paper studies the mathematical problem that arises as a result. Derivatives are priced in the risk-neutral framework, so as the market maker acquires more information about the underlying asset, the change of measure for transition to the risk-neutral framework (the pricing kernel) evolves. This evolution takes a precise form when the market maker is Bayesian. It is shown that Bayesian updates can be characterized as additional informational drift in the underlying asset’s stochastic process. With Bayesian updates, the change of measure needed for pricing derivatives is two-fold: the first change is from the prior probability measure to the posterior probability measure, and the second change is from the posterior probability measure to the risk-neutral measure. The relation between the regular pricing kernel and the pricing kernel under this two-fold change of measure is characterized.

Leukocyte differential gene expression prognostic value for high versus low seizure frequency in temporal lobe epilepsy

BackgroundThis study was performed to test the hypothesis that systemic leukocyte gene expression has prognostic value differentiating low from high seizure frequency refractory temporal lobe epilepsy (TLE).MethodsA consecutive series of patients with refractory temporal lobe epilepsy was studied. Based on a median baseline seizure frequency of 2.0 seizures per month, low versus high seizure frequency was defined as ≤ 2 seizures/month and > 2 seizures/month, respectively. Systemic leukocyte gene expression was analyzed for prognostic value for TLE seizure frequency. All differentially expressed genes were analyzed, with Ingenuity® Pathway Analysis (IPA®) and Reactome, to identify leukocyte gene expression and biological pathways with prognostic value for seizure frequency.ResultsThere were ten males and six females with a mean age of 39.4 years (range: 16 to 62 years, standard error of mean: 3.6 years). There were five patients in the high and eleven patients in the low seizure frequency cohorts, respectively. Based on a threshold of twofold change (p < 0.001, FC > 2.0, FDR < 0.05) and expression within at least two pathways from both Reactome and Ingenuity® Pathway Analysis (IPA®), 13 differentially expressed leukocyte genes were identified which were all over-expressed in the low when compared to the high seizure frequency groups, including NCF2, HMOX1, RHOB, FCGR2A, PRKCD, RAC2, TLR1, CHP1, TNFRSF1A, IFNGR1, LYN, MYD88, and CASP1. Similar analysis identified four differentially expressed genes which were all over-expressed in the high when compared to the low seizure frequency groups, including AK1, F2R, GNB5, and TYMS.ConclusionsLow and high seizure frequency TLE are predicted by the respective upregulation and downregulation of specific leukocyte genes involved in canonical pathways of neuroinflammation, oxidative stress and lipid peroxidation, GABA (γ-aminobutyric acid) inhibition, and AMPA and NMDA receptor signaling. Furthermore, high seizure frequency-TLE is distinguished prognostically from low seizure frequency-TLE by differentially increased specific leukocyte gene expression involved in GABA inhibition and NMDA receptor signaling. High and low seizure frequency patients appear to represent two mechanistically different forms of temporal lobe epilepsy based on leukocyte gene expression.

Tracking the effects of PLGA-based nanoparticles on protein expression in living cells through quantitative proteomics.

Mass spectrometry (MS)-based proteomics can identify and quantify the differential abundance of expressed proteins in parallel, and bottom-up proteomic approaches are even approaching comprehensive coverage of the complex eukaryotic proteome. Protein-nanoparticle (NP) interactions have been extensively studied owing to their importance in biological applications and nanotoxicology. However, the proteome-level effects of NPs on cells have received little attention, although changes in protein abundance can reflect the direct effects of nanocarriers on protein expression. Herein, we investigated the effect of PLGA-based NPs on protein expression in HepG2 cells using a label-free quantitative proteomics approach with data independent acquisition (DIA). The percentage of two-fold change in the protein expression of cells treated with PLGA-based NPs was less than 10.15% during a 6 hour observation period. Among the changed proteins, we found that dynamic proteins involved in cell division, localization, and transport are more likely to be more susceptible to PLGA-based NPs.