Analysis of crucial molecules involved in herniated discs and degenerative disc disease

OBJECTIVES: Herniated discs and degenerative disc disease are major health problems worldwide. However, their pathogenesis remains obscure. This study aimed to explore the molecular mechanisms of these ailments and to identify underlying therapeutic targets. MATERIAL AND METHODS: Using the GSE23130 microarray datasets downloaded from the Gene Expression Omnibus database, differentially co-expressed genes and links were identified using the differentially co-expressed gene and link method with a false discovery rate ,0.25 as a significant threshold. Subsequently, the underlying molecular mechanisms of the differential co-expression of these genes were investigated using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, the transcriptional regulatory relationship was also investigated. RESULTS: Through the analysis of the gene expression profiles of different specimens from patients with these diseases, 539 differentially co-expressed genes were identified for these ailments. The ten most significant signaling pathways involving the differentially co-expressed genes were identified by enrichment analysis. Among these pathways, apoptosis and extracellular matrix-receptor interaction pathways have been reported to be related to these diseases. A total of 62 pairs of regulatory relationships between transcription factors and their target genes were identified as critical for the pathogenesis of these diseases. CONCLUSION: The results of our study will help to identify the mechanisms responsible for herniated discs and degenerative disc disease and provides a theoretical basis for further therapeutic study

Xenon Iron Oxides Predicted as Potential Xe Hosts in Earth’s Lower Mantle

An enduring geological mystery concerns the missing xenon problem, referring to the abnormally low concentration of xenon compared to other noble gases in Earth’s atmosphere. Identifying mantle minerals that can capture and stabilize xenon has been a great challenge in materials physics and xenon chemistry. Here, using an advanced crystal structure search algorithm in conjunction with first-principles calculations we find reactions of xenon with recently discovered iron peroxide FeO2, forming robust xenon-iron oxides Xe2FeO2 and XeFe3O6 with significant Xe-O bonding in a wide range of pressure-temperature conditions corresponding to vast regions in Earth’s lower mantle. Calculated mass density and sound velocities validate Xe-Fe oxides as viable lower-mantle constituents. Meanwhile, Fe oxides do not react with Kr, Ar and Ne. It means that if Xe exists in the lower mantle at the same pressures as FeO2, xenon-iron oxides are predicted as potential Xe hosts in Earth’s lower mantle and could provide the repository for the atmosphere’s missing Xe. These findings establish robust materials basis, formation mechanism, and geological viability of these Xe-Fe oxides, which advance fundamental knowledge for understanding xenon chemistry and physics mechanisms for the possible deep-Earth Xe reservoir

New Family of Robust 2D Topological Insulators in van der Waals Heterostructures

We predict a new family of robust two-dimensional (2D) topological insulators in van der Waals heterostructures comprising graphene and chalcogenides BiTeX (X=Cl, Br and I). The layered structures of both constituent materials produce a naturally smooth interface that is conducive to proximity induced new topological states. First principles calculations reveal intrinsic topologically nontrivial bulk energy gaps as large as 70-80 meV, which can be further enhanced up to 120 meV by compression. The strong spin-orbit coupling in BiTeX has a significant influence on the graphene Dirac states, resulting in the topologically nontrivial band structure, which is confirmed by calculated nontrivial Z2 index and an explicit demonstration of metallic edge states. Such heterostructures offer an unique Dirac transport system that combines the 2D Dirac states from graphene and 1D Dirac edge states from the topological insulator, and it offers new ideas for innovative device designs

GPX8 regulates pan-apoptosis in gliomas to promote microglial migration and mediate immunotherapy responses

IntroductionGliomas have emerged as the predominant brain tumor type in recent decades, yet the exploration of non-apoptotic cell death regulated by the pan-optosome complex, known as pan-apoptosis, remains largely unexplored in this context. This study aims to illuminate the molecular properties of pan-apoptosis-related genes in glioma patients, classifying them and developing a signature using machine learning techniques.MethodsThe prognostic significance, mutation features, immunological characteristics, and pharmaceutical prediction performance of this signature were comprehensively investigated. Furthermore, GPX8, a gene of interest, was extensively examined for its prognostic value, immunological characteristics, medication prediction performance, and immunotherapy prediction potential. ResultsExperimental techniques such as CCK-8, Transwell, and EdU investigations revealed that GPX8 acts as a tumor accelerator in gliomas. At the single-cell RNA sequencing level, GPX8 appeared to facilitate cell contact between tumor cells and macrophages, potentially enhancing microglial migration. ConclusionsThe incorporation of pan-apoptosis-related features shows promising potential for clinical applications in predicting tumor progression and advancing immunotherapeutic strategies. However, further in vitro and in vivo investigations are necessary to validate the tumorigenic and immunogenic processes associated with GPX8 in gliomas

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The complete chloroplast genome of Ishige okamurae

Ishige okamurae plays an important role in marine ecosystem and biological resource utilization. The total length of chloroplast genome was 129,988 bp, containing a large single-copy region (LSC, 77,531 bp), a small single-copy region (SSC, 41,795 bp) and a pair of inverted repeat regions (IRs, 10,662 bp). The circular genome consisted of 101 protein-coding genes, 29 tRNA genes, and six rRNA genes, with a total of 136. Phylogenetic analysis confirmed the position of I. okamurae within the Phaeophyta

Preparation of CPD Photolyase Nanoliposomes Derived from Antarctic Microalgae and Their Effect on UVB-Induced Skin Damage in Mice

UVB radiation is known to trigger the block of DNA replication and transcription by forming cyclobutane pyrimidine dimer (CPD), which results in severe skin damage. CPD photolyase, a kind of DNA repair enzyme, can efficiently repair CPDs that are absent in humans and mice. Although exogenous CPD photolyases have beneficial effects on skin diseases, the mechanisms of CPD photolyases on the skin remain unknown. Here, this study prepared CPD photolyase nanoliposomes (CPDNL) from Antarctic Chlamydomonas sp. ICE-L, which thrives in harsh, high-UVB conditions, and evaluated their protective mechanisms against UVB-induced damage in mice. CPDNL were optimized using response surface methodology, characterized by a mean particle size of 105.5 nm, with an encapsulation efficiency of 63.3%. Topical application of CPDNL prevented UVB-induced erythema, epidermal thickness, and wrinkles in mice. CPDNL mitigated UVB-induced DNA damage by significantly decreasing the CPD concentration. CPDNL exhibited antioxidant properties as they reduced the production of reactive oxygen species (ROS) and malondialdehyde. Through activation of the NF-κB pathway, CPDNL reduced the expression of pro-inflammatory cytokines including IL-6, TNF-α, and COX-2. Furthermore, CPDNL suppressed the MAPK signaling activation by downregulating the mRNA and protein expression of ERK, JNK, and p38 as well as AP-1. The MMP-1 and MMP-2 expressions were also remarkably decreased, which inhibited the collagen degradation. Therefore, we concluded that CPDNL exerted DNA repair, antioxidant, anti-inflammation, and anti-wrinkle properties as well as collagen protection via regulation of the NF-κB/MAPK/MMP signaling pathways in UVB-induced mice, demonstrating that Antarctic CPD photolyases have the potential for skincare products against UVB and photoaging

Characterization of the complete chloroplast genome of the Pohlia nutans M211 from Antarctica

The Antarctic Pohlia nutans M211 complete chloroplast (cp) genome, sequenced using Illumina NovaSeq PE150, was 125,199 bp in length. It contained 19,836 bp of inverted repeat (IR) regions that separated a large single-copy region (LSC) of 86,738 bp and a small single-copy region (SSC) of 18,580 bp. The whole-genome encodes 132 genes (80 protein-coding genes, 36 tRNA genes, and 8 rRNA genes) and had 29.5% GC content. The M211 was congruent with Sanionia uncinata (KM111545.1) according to the Phylogenetic tree analyses

The complete chloroplast genome of Spartina alterniflora

Spartina alterniflora (also named as Sporobolus alterniflorus) grows in coastal salt marshes area, which has important economic value in coastal natural wetlands. In the process of this research, the whole chloroplast genome sequence of Spartina alterniflora was recovered by Illumina sequencing. The complete genome was 135,560 bp in length with 38.45% GC content which was a circular genome containing a large single-copy region (LSC, 80,828 bp), a small single-copy region (SSC, 12,714 bp) and a pair of inverted repeat regions (IRs, 42,018 bp). Totally, it encodes 130 genes, including 84 protein-coding genes, 38 tRNAs, and 8 rRNAs. Phylogenetic analysis indicated that Spartina alterniflora was closely related to Sporobolus maritimus

The complete chloroplast genome of Phaeodactylum tricornutum ICE-H isolated from the Antarctic sea ice

Phaeodactylum tricornutum ICE-H is a single-cell eukaryotic alga that can grow in the extreme Antarctic environment. The complete chloroplast genome of Phaeodactylum tricornutum ICE-H was assembled with the Illumina sequencing. The chloroplast genome was 117,363 bp in size, containing a large single-copy region (LSC, 63,668 bp), a small single-copy region (SSC, 39,871 bp), and a pair of inverted repeat regions (IRs, 13,824 bp each). The overall GC content was 32.15%. A total of 168 genes were predicted including 132 protein-coding genes, 30 tRNAs, and 6 rRNAs. Phylogenetic analysis indicated that Phaeodactylum tricornutum ICE-H was closely related to Didymosphenia geminata