Cap Analysis Research Articles

Carbon Storage Dynamics in Lower Shimentan Formation of the Qiantang Sag, East China Sea Shelf Basin: Stratigraphy, Reservoir – Cap Analysis, and Source – Sink Compatibility

Carbon Storage Dynamics in Lower Shimentan Formation of the Qiantang Sag, East China Sea Shelf Basin: Stratigraphy, Reservoir – Cap Analysis, and Source – Sink Compatibility

Enhancers regulate genes linked to severe and mild childhood asthma

BackgroundChildren with severe asthma suffer from recurrent symptoms and impaired quality of life despite advanced treatment. Underlying causes of severe asthma are not completely understood, although genetic mechanisms are known to be important. ObjectiveThe aim of this study was to identify gene regulatory enhancers in leukocytes, to describe the role of these enhancers in regulating genes related to severe and mild asthma in children, and to identify known asthma-related SNPs situated in proximity to enhancers. MethodsGene enhancers were identified and expression of enhancers and genes were measured by Cap Analysis Gene Expression (CAGE) data from peripheral blood leukocytes from children with severe asthma (n = 13), mild asthma (n = 15), and age-matched controls (n = 9). ResultsFrom a comprehensive set of 8,289 identified enhancers, we further defined a robust sub-set of the high-confidence and most highly expressed 4,738 enhancers. Known single nucleotide polymorphisms, SNPs, related to asthma coincided with enhancers in general as well as with specific enhancer-gene interactions. Blocks of enhancer clusters were associated with genes including TGF-beta, PPAR and IL-11 signaling as well as genes related to vitamin A and D metabolism. A signature of 91 enhancers distinguished between children with severe and mild asthma as well as controls. ConclusionsGene regulatory enhancers were identified in leukocytes with potential roles related to severe and mild asthma in children. Enhancers hosting known SNPs give the opportunity to formulate mechanistic hypotheses about the functions of these SNPs.

A comparative analysis of capping and reducing agents of microbial cell Aspergillus niger and Bacillus subtilis for biosynthesis of Ag doped ZnO nanoparticles

In this study, green synthesis of Ag doped ZnO (AZNPR) has been carried out using the sol-gel method at pH 8.0, using two types of microbial cells, namely Aspergillus niger and Bacillus subtilis as capping and reducing agents. This work centred on the phytomediated biosynthesis and characterisation of AZNPR and its biological utility. Based on infrared analysis, phytochemicals present in microbial cells are extracellular enzymes namely proteolytic, amylolytic, lipolytic, cellulolytic, and pectinase, which can be extracted from A. niger and B. subtilis and are responsible for controlling the growth of AZNPR. The formation of AZNPR was characterised using different analyses. The FTIR shows absorption band located at ∼864 cm−1 that shows the interaction between Ag and ZnO. The XRD results showed the presence of crystalline AZNPR in the forms of hexagonal wurtzite ZnO and Ag. Microstructural and size examination showed that AZNPR was in the form of nanorods with homogeneous distribution with a size of rods in A. niger media 137.0 nm, while in B. subtilis media 197.4 nm. The Ag–ZnO nanorods revealed the ability to inhibit Candida albicans species, a fungus causing infectious disease, with an inhibition zone measuring 2.1–3.2 mm at 24 h.

Transcriptome analysis of long non-coding RNAs in Mycobacterium avium complex-infected macrophages.

Mycobacterium avium complex (MAC) is a non-tuberculous mycobacterium widely distributed in the environment. Even though MAC infection is increasing in older women and immunocompromised patients, to our knowledge there has been no comprehensive analysis of the MAC-infected host-cell transcriptome-and particularly of long non-coding RNAs (lncRNAs). By using in vitro-cultured primary mouse bone-marrow-derived macrophages (BMDMs) and Cap analysis of gene expression, we analyzed the transcriptional and kinetic landscape of macrophage genes, with a focus on lncRNAs, during MAC infection. MAC infection of macrophages induced the expression of immune/inflammatory response genes and other genes similar to those involved in M1 macrophage activation, consistent with previous reports, although Nos2 (M1 activation) and Arg1 (M2 activation) had distinct expression profiles. We identified 31 upregulated and 30 downregulated lncRNA promoters corresponding respectively to 18 and 26 lncRNAs. Upregulated lncRNAs were clustered into two groups-early and late upregulated-predicted to be associated with immune activation and the immune response to infection, respectively. Furthermore, an Ingenuity Pathway Analysis revealed canonical pathways and upstream transcription regulators associated with differentially expressed lncRNAs. Several differentially expressed lncRNAs reported elsewhere underwent expressional changes upon M1 or M2 preactivation and subsequent MAC infection. Finally, we showed that expressional change of lncRNAs in MAC-infected BMDMs was mediated by toll-like receptor 2, although there may be other mechanisms that sense MAC infection. We identified differentially expressed lncRNAs in MAC-infected BMDMs, revealing diverse features that imply the distinct roles of these lncRNAs in MAC infection and macrophage polarization.

Abstract LB274: Nuclear transporter HIKESHI is a novel independent poor overall survival for pancreatic cancer; targeting can inhibit pancreatic cancer growth via HSP70 suppression

Abstract HIKESHI, under heat stress conditions, has been reported to transport molecular chaperone HSP70 into the nucleus to prevent cancer cell death from heat stress. The tumor-supporting roles of molecular chaperones in various solid tumors are explored extensively. Yet, the sole targeting of the molecular chaperones could not significantly impact anticancer treatment. Thus, we hypothesized that the specific transporter protein HIKESHI might improve this outcome. However, understanding of the clinical relevance of HIKESHI in pancreatic cancer remained unclear, and few studies addressed the HIKESHI role in cancer and whether targeting can inhibit pancreatic cancer cell viability and the other HSPs. Here, we first investigated the expression pattern of the HIKESHI protein in surgically resected pancreatic cancer samples (n=142) and analyzed the clinical relevance of the HIKESHI. We found that the HIKESHI protein was overexpressed in cancer compared to the adjacent normal tissue, and positive expression of cancer HIKESHI was related to poor overall survival. In addition, HIKESHI-positive expression in cancer was identified as an independent prognostic marker for overall survival. Next, using shRNA, we established the stable HIKESHI-suppressed pancreatic cancer cell line (PANC-1). HIKESHI suppression inhibited cell growth and colony formation ability in vitro. The expression and nuclear translocation of HSP70 and HSP110/105 were suppressed in HIKESHI-suppressed cells compared to the control shRNA cells despite no heat stress conditions. Furthermore, we found that the tumor growth, HIKESHI, and Ki67 expression in HIKESHI-suppressed tumors were inhibited compared to the control shRNA tumors. Next, we performed Cap Analysis of Gene Expression and IP-MS analysis to discover the potential downstream and novel interactive partner of the HIKESHI protein. The extensive mechanism of these analyses is under investigation. Our findings suggest that targeting HIKESHI may be a promising therapeutic strategy against refractory pancreatic cancer. Citation Format: Bilguun Erkhem-Ochir, Takehiko Yokobori, Gendensuren Dorjkhorloo, Haruka Okami, Takaomi Seki, Norifumi Harimoto, Ryo Muranushi, Kouki Hoshino, Kei Hagiwara, Norihiro Ishii, Mariko Tsukagoshi, Kenichiro Araki, Hiroshi Saeki, Ken Shirabe. Nuclear transporter HIKESHI is a novel independent poor overall survival for pancreatic cancer; targeting can inhibit pancreatic cancer growth via HSP70 suppression [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 LB274.

Abstract 774: Genetic architecture, evolutionary genomics, and genomic risk of prostate cancer in sub-Saharan Africa

Abstract Men of African descent have the highest prostate cancer (CaP) incidence and mortality rates, yet the genetic basis of CaP in African men has been understudied. We performed the first large-scale genomic analysis of CaP across sub-Saharan Africa (SSA). We evaluated the evolutionary history of CaP-associated loci, generated a novel genomic risk score, inferred ancestry-specific genetic architectures, and fine-mapped disease associations using in 3,963 CaP cases and 3,509 controls recruited in Ghana, Nigeria, Senegal, South Africa, and Uganda through the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network. Fifteen independent associations at 8q24.21, 6q22.1, and 11q13.3 reached genome-wide significance, including four novel associations. Multiple lead SNPs were private alleles in SSA, a pattern arising from recent mutations and the out-of-Africa bottleneck. These SSA-specific alleles contribute to haplotypes with odds ratios for CaP above 2.4. The genetic architecture of CaP differs across SSA, with effect size differences contributing more to this heterogeneity than allele frequency differences. Population genetic analyses reveal that SSA CaP associations are largely governed by neutral evolution, as opposed to natural selection. This finding is consistent with the late onset of this disease. Focusing on 2,502 age-matched cases and 2,222 non-cancer controls, we generated a novel genomic predictor of CaP. We then assessed the extent to which this polygenic risk score was correlated with age of onset, PSA levels, genetic ancestry, and family history of study participants. The performance of this novel polygenic risk score was tested on other populations of African descent, as well as populations with non-African ancestry. Our findings emphasize the utility of conducting genetic studies in diverse populations. Citation Format: Timothy R. Rebbeck, Rohini Janivara, Wenlong C. Chen, Ujani Hazra, MADCaP Network, Joseph Lachance. Genetic architecture, evolutionary genomics, and genomic risk of prostate cancer in sub-Saharan Africa [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 774.

Identification of XTH Family Genes and Expression Analysis of Endosperm Weakening in Lettuce (Lactuca sativa L.)

Seed germination requires the relaxation of endosperm cap and radicle cell walls, with cell wall hydrolases playing a significant role in this process. Our study revealed that a type of cell wall hydrolase, xyloglucan endotransglucosylase, may significantly contribute to endosperm weakening during lettuce seed germination. Through bioinformatics analysis, the XTH gene family in lettuce was divided into five subfamilies localized on nine chromosomes. Notably, there were significant differences in gene structure among the members of the LsXTHs family containing 1–4 exons and 20 conserved motifs. Among these motifs, motif1, motif2, and motif3 encoded the XTH structural domain. The promoter regions of LsXTHs contained a large number of cis-acting elements responsive to various abiotic stresses, such as drought, anaerobiosis, low temperature, high temperature, and salt stress. Germination experiments showed that seeds imbibed in water and 5 μmol/L abscisic acid (ABA) were able to achieve typical germination with radicle protrusion from the endosperm cap, achieving germination of 100% and 36%, respectively. Conversely, in 0.3% sodium dichloroisocyanurate (SDIC), the swollen seeds were unable to germinate or complete atypical germination, resulting in a germination rate of 30%. Compared to the control, the mechanical strength of the endosperm cap of seeds imbibed in 0.3% SDIC for 8 h increased by 14%, indicating that SDIC may inhibit seed germination by enhancing the mechanical strength of the endosperm cap. Enzyme activity analysis revealed that during lettuce seed germination, XTH enzyme activity in the endosperm cap was significantly higher than in other tissues and increased gradually with imbibition. Transcriptome analysis of the endosperm cap detected the expression of 10 LsXTH genes. Among these, LsXTH43 exhibited the highest expression during germination and was significantly upregulated two-fold by high temperatures, suggesting a potential role in the high-temperature germination of lettuce seeds. Additionally, SDIC downregulated the expression of LsXTHs to varying degrees, with the expression of LsXTH15 reduced to only 6% of its original level. Low temperature, high temperature, drought, and salt stress all reduced the expression of most LsXTHs to different degrees; when seeds germinated under waterlogging and cadmium stress, LsXTH6, LsXTH7, LsXTH8, LsXTH32, and LsXTH33 were all upregulated to some extent.

NTRK2 expression in gastrointestinal stromal tumors with a special emphasis on the clinicopathological and prognostic impacts

Gastrointestinal stromal tumors (GISTs) are typically characterized by activating mutations of the KIT proto-oncogene receptor tyrosine kinase (KIT) or platelet-derived growth factor receptor alpha (PDGFRA). Recently, the neurotrophic tyrosine receptor kinase (NTRK) fusion was reported in a small subset of wild-type GIST. We examined trk IHC and NTRK gene expressions in GIST. Pan-trk immunohistochemistry (IHC) was positive in 25 (all 16 duodenal and 9 out of 16 small intestinal GISTs) of 139 cases, and all pan-trk positive cases showed diffuse and strong expression of c-kit. Interestingly, all of these cases showed only trkB but not trkA/trkC expression. Cap analysis of gene expression (CAGE) analysis identified increased number of genes whose promoters were activated in pan-trk/trkB positive GISTs. Imbalanced expression of NTRK2, which suggests the presence of NTRK2 fusion, was not observed in any of trkB positive GISTs, despite higher mRNA expression. TrkB expression was found in duodenal GISTs and more than half of small intestinal GISTs, and this subset of cases showed poor prognosis. However, there was not clear difference in clinical outcomes according to the trkB expression status in small intestinal GISTs. These findings may provide a possible hypothesis for trkB overexpression contributing to the tumorigenesis and aggressive clinical outcome in GISTs of duodenal origin.

Improved-FSDT-based solid-shell element for buckling analysis of plate, spherical cap, and cylindrical shell of FG porous materials

This study's objective is to propose a full three-dimensional finite element modeling for examining the buckling behaviors of functionally graded (FG) porous materials with plates, spherical cap, and cylindrical shapes. An improved first-order shear deformation theory (IFSDT) is utilized in order to develop the three-dimensional solid-shell element. The governing equations are developed in a way that offers a parabolic distribution of the transverse shear strains through the FG porous shell thickness and a zero condition of the transverse shear stresses on the top and bottom surfaces. The given IFSDT solid-shell element has the ability to model any kind of shell structures and incorporates a three-dimensional material law. In this study, two types of porosity distribution functions are considered. The performance of the current IFSDT solid-shell element has been demonstrated by examining the buckling behavior of Functionally Graded Porous plates, spherical caps, and cylindrical shells. The effect of the porosity distribution, porosity coefficient, power-law index, geometrical design parameters and boundary conditions on the buckling behaviors of FG porous shells structures is evaluated.

Evolution of Investment Banking: Analysis of Sbi Caps in Financial Statements

Evolution of Investment Banking: Analysis of Sbi Caps in Financial Statements

A budding yeast CAGE dataset comprising two cell types.

The budding yeast Saccharomyces cerevisiae is an excellent model organism for studying chromatin regulation with high-resolution genome-wide analyses. Since newly generated genome-wide data are often compared with publicly available datasets, expanding our dataset repertoire will be beneficial for the field. Information on transcription start sites (TSSs) determined at base pair resolution is essential for elucidating mechanisms of transcription and related chromatin regulation, yet no datasets that cover two different cell types are available. Here, we present a CAGE (cap analysis of gene expression) dataset for a-cells and α-cells grown in defined and rich media. Cell type-specific genes were differentially expressed as expected, ensuring the reliability of the data. Some of the differentially expressed TSSs were medium-specific or detected due to unrecognized chromosome rearrangement. By comparing the CAGE data with a high-resolution nucleosome map, major TSSs were primarily found in +1 nucleosomes, with a peak approximately 30 bp from the promoter-proximal end of the nucleosome. The dataset is available at DDBJ/GEA.

Human RFX6 regulates endoderm patterning at the primitive gut tube stage.

Transcriptional factor RFX6 is known to be a causal gene of Mitchell-Riley syndrome (MRS), an autosomal recessive neonatal diabetes associated with pancreatic hypoplasia and intestinal atresia/malformation. The morphological defects are limited to posterior foregut and mid-hindgut endodermal lineages and do not occur in the anterior foregut lineage; the mechanism remains to be fully elucidated. In this study, we generated RFX6+/eGFP heterozygous knockin and RFX6eGFP/eGFP homozygous knockin/knockout human-induced pluripotent stem cell (hiPSC) lines and performed in vitro endoderm differentiation to clarify the role of RFX6 in early endoderm development. RFX6 expression was found to surge at the primitive gut tube (PGT) stage in comparison with that in the undifferentiated or definitive endoderm stage. At the PGT stage, the expression of PDX1 and CDX2, posterior foregut and mid-hindgut master regulators, respectively, was decreased by the RFX6 deficit. PDX1+ and CDX2+ cells were mostly green fluorescent protein (GFP)+ in RFX6+/eGFP hiPSCs, but their cell number was markedly decreased in RFX6eGFP/eGFP hiPSCs. The expression of SOX2, an anterior foregut marker, was not affected by the RFX6 deficit. In addition, we found a putative RFX6-binding X-box motif using cap analysis of gene expression-seq and the motif-containing sequences in the enhancer regions of PDX1 and CDX2 bound to RFX6 in vitro. Thus, RFX6 regulates the ParaHox genes PDX1 and CDX2 but does not affect SOX2 in early endodermal differentiation, suggesting that defects in early stage endoderm patterning account for the morphological pathology of MRS.

Exploring the surface epitope and nuclear localization analysis of porcine circovirus type 3 capsid protein

Porcine circovirus 3 (PCV3) is a newly emerging virus associated with porcine dermatitis and nephropathy syndrome (PDNS) and reproductive disorders, impacting global pig populations. Porcine circoviruses contain two major open reading frames (ORFs), and the ORF2 encodes the viral capsid protein (Cap). Cap is the most antigenic structural protein and an ideal candidate for the development of vaccines and diagnostic reagents. This study generated a monoclonal antibody (MAb) specific to PCV3 Cap, MAb CCC160, for diagnosis and pathogenesis studies of this novel virus. The MAb specifically recognized PCV3-infected swine lymph node tissue in an immunohistochemical analysis confirming its clinical diagnostic potential. In addition, a novel linear B-cell epitope recognized by MAb CCC160 was identified at the amino acid region 120–134 of Cap. Nuclear localization analysis of PCV3 Cap revealed a potential nuclear localization signal (NLS) in the middle region (aa 131–143) in addition to the dominant N-terminal NLS that is already known. A cell viability assay further demonstrated that the cytotoxicity of PCV3 Cap is correlated with its nuclear localization, indicating a crucial role of Cap in the pathogenic mechanism of PCV3. A full-length construct of PCV3 Cap was successfully expressed using a baculovirus expression system and purified recombinant proteins self-assembled into virus-like particles (VLPs). The protein constitution of the VLPs was confirmed by MAb CCC160 recognition, indicating the correct conformation and specificity of VLP and exhibiting the linear epitope aa 120–134 on the VLP surface. These results provide insights for developing diagnostic tools and potential VLP vaccines for PCV3, revealing its pathogenesis and antigenic properties.

Core promoterome of barley embryo

Precise localization and dissection of gene promoters are key to understanding transcriptional gene regulation and to successful bioengineering applications. The core RNA polymerase II initiation machinery is highly conserved among eukaryotes, leading to a general expectation of equivalent underlying mechanisms. Still, less is known about promoters in the plant kingdom. In this study, we employed cap analysis of gene expression (CAGE) at three embryonic developmental stages in barley to accurately map, annotate, and quantify transcription initiation events. Unsupervised discovery of de novo sequence clusters grouped promoters based on characteristic initiator and position-specific core-promoter motifs. This grouping was complemented by the annotation of transcription factor binding site (TFBS) motifs. Integration with genome-wide epigenomic data sets and gene ontology (GO) enrichment analysis further delineated the chromatin environments and functional roles of genes associated with distinct promoter categories. The TATA-box presence governs all features explored, supporting the general model of two separate genomic regulatory environments. We describe the extent and implications of alternative transcription initiation events, including those that are specific to developmental stages, which can affect the protein sequence or the presence of regions that regulate translation. The generated promoterome dataset provides a valuable genomic resource for enhancing the functional annotation of the barley genome. It also offers insights into the transcriptional regulation of individual genes and presents opportunities for the informed manipulation of promoter architecture, with the aim of enhancing traits of agronomic importance.

Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat

Transposable elements (TEs) comprise ~85% of the common wheat genome, which are highly diverse among subgenomes, possibly contribute to polyploid plasticity, but the causality is only assumed. Here, by integrating data from gene expression cap analysis and epigenome profiling via hidden Markov model in common wheat, we detect a large proportion of enhancer-like elements (ELEs) derived from TEs producing nascent noncoding transcripts, namely ELE-RNAs, which are well indicative of the regulatory activity of ELEs. Quantifying ELE-RNA transcriptome across typical developmental stages reveals that TE-initiated ELE-RNAs are mainly from RLG_famc7.3 specifically expanded in subgenome A. Acquisition of spike-specific transcription factor binding likely confers spike-specific expression of RLG_famc7.3-initiated ELE-RNAs. Knockdown of RLG_famc7.3-initiated ELE-RNAs resulted in global downregulation of spike-specific genes and abnormal spike development. These findings link TE expansion to regulatory specificity and polyploid developmental plasticity, highlighting the functional impact of TE-driven regulatory innovation on polyploid evolution.

Copy number loss of KDM5D may be a predictive biomarker for ATR inhibitor treatment in male patients with pulmonary squamous cell carcinoma.

A limited number of patients with lung squamous cell carcinoma (SCC) benefit clinically from molecular targeted drugs because of a lack of targetable driver alterations. We aimed to understand the prevalence and clinical significance of lysine-specific demethylase 5D (KDM5D) copy number loss in SCC and explore its potential as a predictive biomarker for ataxia-telangiectasia and Rad3-related (ATR) inhibitor treatment. We evaluated KDM5D copy number loss in 173 surgically resected SCCs from male patients using fluorescence in situ hybridization. KDM5D copy number loss was detected in 75 of the 173 patients (43%). Genome-wide expression profiles of the transcription start sites (TSSs) were obtained from 17 SCCs, for which the cap analysis of gene expression assay was performed, revealing that upregulated genes in tumors with the KDM5D copy number loss are associated with 'cell cycle', whereas downregulated genes in tumors with KDM5D copy number loss were associated with 'immune response'. Clinicopathologically, SCCs with KDM5D copy number loss were associated with late pathological stage (p = 0.0085) and high stromal content (p = 0.0254). Multiplexed fluorescent immunohistochemistry showed that the number of tumor-infiltrating CD8+ /T-bet+ T cells was lower in SCCs with KDM5D copy number loss than in wild-type tumors. In conclusion, approximately 40% of the male patients with SCC exhibited KDM5D copy number loss. Tumors in patients who show this distinct phenotype can be 'cold tumors', which are characterized by the paucity of tumor T-cell infiltration and usually do not respond to immunotherapy. Thus, they may be candidates for trials with ATR inhibitors.

Uydu görüntüleri kullanılarak kıyı şeridi değişimi analizi ve gelecekteki konumunun belirlenmesi için etkili bir yaklaşım: Burdur Gölü örneği

Lake shoreline changes can have a significant impact on the biodiversity and ecosystems of wetland. This study was aimed to calculate the coastal change of Lake Burdur in Turkey during the elapsed period from 2013 to 2023. Within this framework both remote sensing based aproach and Digital Shoreline Analysis System (DSAS) was performed using Landsat-7 (TM) and Landsat-8 (OLI) images. To estimate shoreline change rates along the coastal zone, statistical parameters such as End Point Rate (EPR), Linear Regression Rate (LRR), and Net Shoreline Movement (NSM) were calculated. A hybrid algorithm, Normalized Difference Vegetation Index (NDVI) and Tasseled Cap Analysis, is utilized to emphasize the distinction between the lake bodies and coastal zone. The maximum shoreline change in the northeast part of the lake was observed, and it resulted in a change of 543.12 m/yr for EPR and 610.07 m/yr for LRR statistics in the 2013-2023 time period. The lake to land position has only been observed in a small amount which are resulted in for EPR -4.91 m/yr. and -3.17 m/yr for LRR statistics. The lake area decreased from 139 km2 to 118 km2 between 2013 and 2023. The results indicate that if the decision-maker does not measure, the area of the lake will be lost by 14% until 2033 and 27% until 2043.

OVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults.

While some old adults stay healthy and non-frail up to late in life, others experience multimorbidity and frailty often accompanied by a pro-inflammatory state. The underlying molecular mechanisms for those differences are still obscure. Here, we used gene expression analysis to understand the molecular underpinning between non-frail and frail individuals in old age. Twenty-four adults (50% non-frail and 50% frail) from InCHIANTI study were included. Total RNA extracted from whole blood was analyzed by Cap Analysis of Gene Expression (CAGE). CAGE identified transcription start site (TSS) and active enhancer regions. We identified a set of differentially expressed (DE) TSS and enhancer between non-frail and frail and male and female participants. Several DE TSSs were annotated as lncRNA (XIST and TTTY14) and antisense RNAs (ZFX-AS1 and OVCH1 Antisense RNA 1). The promoter region chr6:366,786,54-366,787,97;+ was DE and overlapping the longevity CDKN1A gene. GWAS-LD enrichment analysis identifies overlapping LD-blocks with the DE regions with reported traits in GWAS catalog (isovolumetric relaxation time and urinary tract infection frequency). Furthermore, we used weighted gene co-expression network analysis (WGCNA) to identify changes of gene expression associated with clinical traits and identify key gene modules. We performed functional enrichment analysis of the gene modules with significant trait/module correlation. One gene module is showing a very distinct pattern in hub genes. Glycogen Phosphorylase L (PYGL) was the top ranked hub gene between non-frail and frail. We predicted transcription factor binding sites (TFBS) and motif activity. TF involved in age-related pathways (e.g., FOXO3 and MYC) shows different expression patterns between non-frail and frail participants. Expanding the study of OVCH1 Antisense RNA 1 and PYGL may help understand the mechanisms leading to loss of homeostasis that ultimately causes frailty.

Age-Related Gene and Protein Expression in Mouse Mandibular Condyle Analyzed by Cap Analysis of Gene Expression and Immunohistochemistry

Introduction: Aging, an inevitable physiological process, leads to morphological and histological degenerative changes in the mandibular condylar cartilage (MCC); however, the molecular mechanism has not yet been elucidated, and little information is available on age-related factors. Therefore, this study was designed to identify age-related factors by investigating the age-related differentially expressed genes (DEGs) and localization of their translated protein expression in the mandibular condyle. Methods: Mandibular condyles were collected from 10- and 50-week-old mice. Total RNA was extracted from the samples and then analyzed using cap analysis of gene expression (CAGE) to identify age-related DEGs. Gene ontology (GO) enrichment analysis was performed to determine which biological processes were most affected by aging in terms of gene expression using Metascape. The mandibular condyle samples were processed for histology to investigate morphological changes caused by aging and for immunohistochemistry to localize the protein expression encoded by age-related genes identified with CAGE. Semi-quantitative immunohistochemistry was performed to assess age-related extracellular matrix (ECM) protein levels in the MCC. The histological sections were also used for Alcian blue histochemistry to detect glycosaminoglycans (GAGs). Results: GO enrichment analysis revealed that the genes related to “extracellular matrix organization,” including Acan, Col1a1, Col1a2, Col2a1, Mmp3, Mmp9, and Mmp13, were most differentially expressed in the aged mandibular condyle. Among these seven genes, Mmp3 was upregulated, and the others were downregulated with aging. Histological examination showed the age-related morphological and histological changes in the MCC. Immunohistochemical investigation showed the localization of matrix metalloproteinases (MMPs)-3, -9, and -13 and their substrate proteins, aggrecan, type I collagen, and type II collagen, in the mandibular condyle at 10 and 50 weeks, indicating different localizations between the young and the aged. In the aged MCC, semi-quantitative immunohistochemistry showed a significant decrease in the aggrecan protein level, and Alcian blue histochemistry showed a decrease in GAGs. Conclusion: MMP-3, MMP-9, and MMP-13 contribute to the remodeling of the ECM of the MCC and subchondral bone during aging by degrading ECM proteins at specific times and sites under the regulation of their production and secretion.

Regional geomagnetic core field and secular variation model over the Iberian Peninsula from 2014 to 2020 based on the R-SCHA technique

The Earth’s magnetic field originated in the fluid core, the so-called core field, is the dominant contribution to the geomagnetic field. Since ancient times, the core geomagnetic field has been used primarily for geographical orientation and navigation by means of compasses. Nowadays, thanks to the large amount of geomagnetic data available, core field models can be developed on a global or regional scale. Global models resolve large-scale geomagnetic field features, while regional models can resolve greater detail over a particular region. The spherical harmonic cap analysis is a widely used technique for regional-scale modelling of the geomagnetic field. In this work we have developed a regional model of the core field and its secular variation between 2014.5 and 2020.5 over the Iberian Peninsula, based on data from Swarm satellites, geomagnetic observatories and repeat stations. Its performance has been validated by comparing the fit to the available geomagnetic data using the regional model and the global models IGRF and CHAOS over the whole spatio-temporal range studied. In order to optimise the model, a detailed study of its input parameters has been carried out, showing that not all parameters have an equal influence on the modelling. This new model reproduces the input data with a root mean square error of 2.9 nT, improving the outcome of global models on this region. The results of this work will allow the Spanish Instituto Geográfico Nacional to produce the magnetic cartography of Iberia and the Balearic Islands in 2020.0, which for the first time will be based on a regional core field model, replacing the polynomial variation method used in the past.Graphical abstract