Gene Categories Research Articles

Construction and characteristic analysis of the cultural genes map of Grand Canal bridge facilities: a case study in Hangzhou section, China

ABSTRACT Taking the representative bridge facilities of the Hangzhou section of the Grand Canal as an example, uses the reverse transcription extraction method to refine cultural elements information, and classifies and analyzes to obtain the cultural gene identification framework of the Grand Canal bridge facilities. Based on this, various types of cultural genes are encoded according to the principle of cultural gene classification, in order to clarify the four major types of cultural genes: main genes, accessory genes, hybrid genes, and variant genes, forming a cultural gene encoding sequence map and analyzing their basic characteristics. The results show: 1) a cultural gene identification framework for the cultural genes of the Grand Canal bridge facilities composed of 6 gene categories, 8 identification factors, and 17 identification indicators has been established. 2) Accessory genes account for the largest proportion in the four major categories of cultural genes, followed by main genes, and the proportions of mixed genes and variant genes are the same. 3) The genetic features, functional positioning, and value inheritance paths contained in each type of cultural gene are different. The research results provide new ideas for the scientific protection and inheritance of the cultural heritage of the Grand Canal.

From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives.

The yellow fever mosquito (Aedes aegypti) is an organism of high medical importance because it is the primary vector for diseases such as yellow fever, Zika, dengue, and chikungunya. Its medical importance has made it a subject of numerous efforts to understand their biology. One such effort, was the development of a high-quality reference genome (AaegL5). However, this reference genome was sourced from a highly inbred laboratory strain with unknown geographic origin. Thus, the reference is not representative of a wild mosquito, let alone one from its native range in sub-Saharan Africa. To better understand the genetic architecture of Ae. aegypti and their sister species, we developed two de novo chromosome-scale genomes with sequences sourced from single individuals: one of Ae. aegypti formosus (Aaf) from Burkina Faso and one of Ae. mascarensis (Am) from Mauritius. Both genomes exhibit high contiguity and gene completeness, comparable to AaegL5. While Aaf exhibits high degree of synteny to AaegL5, it also exhibits several large inversions. We further conducted comparative genomic analyses using our genomes and other publicly available culicid reference genomes to find extensive chromosomal rearrangements between major lineages. Overrepresentation analysis of expanded genes in Aaf, AaegL5, and Am revealed that while the overarching category of genes that have expanded are similar, the specific genes that have expanded differ. Our findings elucidate novel insights into chromosome evolution at both microevolutionary and macroevolutionary scales. The genomic resources we present are additions to the arsenal of biologists in understanding mosquito biology and genome evolution.

Comparative insights into genomic variability and adaptation in the chloroplast genomes of Salvia japonica and Salvia rosmarinus

Chloroplast genomes provide important information about phylogenetics, plant evolution, and adaptive processes. This study examines the chloroplast genomes of Salvia japonica and Salvia rosmarinus. We conducted structural and functional annotations to identify significant variations in gene content and organization. We found that S. rosmarinus has fewer photosystem II (psb) genes and a greater abundance of hypothetical genes (ycf). This may help maintain genomic stability while facilitating species evolution. There are big differences in insertion-deletion events (indels) and single nucleotide polymorphisms (SNPs) in important gene families, like NADH dehydrogenase and ribosomal proteins. We determined this organizational difference by applying Principal Component Analysis (PCA) to the genomes of the two species, which belong to different and distinct gene categories. Sequence alignment revealed gaps and inconsistencies in genes related to RNA polymerase and photosynthesis. The fact that S. japonica and S. rosmarinus have a lot of different genes and may have adapted to live in different environments suggests that they have had different evolutionary paths. These results give us important information about how Salvia species have evolved and give us a way to think about how chloroplast genomes change in different ecological settings. This study provides a basis for understanding the evolution of the chloroplast genome in the genus Salvia. This study has been significant in clarifying the role of photosynthetic and hypothetical genes in controlling environmental responses. Future study must use transcriptome and ecological data to enhance our understanding of the impact of genetic variants on functionality.

Research Progress on Gene Regulation of Plant Floral Organogenesis.

Flowers, serving as the reproductive structures of angiosperms, perform an integral role in plant biology and are fundamental to understanding plant evolution and taxonomy. The growth and organogenesis of flowers are driven by numerous factors, such as external environmental conditions and internal physiological processes, resulting in diverse traits across species or even within the same species. Among these factors, genes play a central role, governing the entire developmental process. The regulation of floral genesis by these genes has become a significant focus of research. In the AE model of floral development, the five structural whorls (calyx, corolla, stamens, pistils, and ovules) are controlled by five groups of genes: A, B, C, D, and E. These genes interact to give rise to a complex control system that governs the floral organsgenesis. The activation or suppression of specific gene categories results in structural modifications to floral organs, with variations observed across different species. The present article examines the regulatory roles of key genes, including genes within the MADS-box and AP2/ERF gene clusters, such as AP1, AP2, AP3, AG, STK, SHP, SEP, PI, and AGL6, as well as other genes, like NAP, SPL, TGA, PAN, and WOX, in shaping floral organ genesis. In addition, it analyzes the molecular-level effects of these genes on floral organ formation. The findings offer a deeper understanding of the genetic governance of floral organ genesis across plant species.

The brain, rapid eye movement sleep, and major depressive disorder: A multimodal neuroimaging study

BackgroundEvidence has established the prominent involvement of rapid eye movement (REM) sleep disturbance in major depressive disorder (MDD). However, the neural correlates of REM sleep in MDD and their clinical significance are less clear. MethodsCross-sectional and longitudinal polysomnography and resting-state functional MRI data were collected from 131 MDD patients and 71 healthy controls to measure REM sleep and voxel-mirrored homotopic connectivity (VMHC). Correlation and mediation analyses were performed to examine the associations between REM sleep, VMHC, and clinical variables. Moreover, we conducted spatial correlations between the neural correlates of REM sleep and a multimodal collection of reference brain maps to facilitate genetic, structural and functional annotations. ResultsMDD patients exhibited REM sleep abnormalities manifesting as higher REM sleep latency and lower REM sleep duration, which were correlated with decreased VMHC of the precentral gyrus and inferior parietal lobe and mediated their associations with more severe anxiety symptoms. Longitudinal data showed that VMHC increase of the inferior parietal lobe was related to improvement of depression symptoms in MDD patients. Spatial correlation analyses revealed that the neural correlates of REM sleep in MDD were linked to gene categories primarily involving cellular metabolic process, signal pathway, and ion channel activity as well as linked to cortical microstructure, metabolism, electrophysiology, and cannabinoid receptor. ConclusionThese findings may add important context to the growing literature on the complex interplay between sleep and MDD, and more broadly may inform future treatment for depression via regulating sleep.

Expression profile of cellular microRNAs and their potential role in cervical cancer

Background. Cervical cancer (CC) is the fourth leading cause of cancer-related morbidity and mortality among women. Despite the established etiologic factor of cervical cancer, especially high-risk human papillomavirus (HPV, human papillomavirus) and available vaccine prophylaxis, the issue persists both in understanding the mechanism of HPV-associated carcinogenesis and in developing new approaches for diagnosis and treatment of cervical cancer. Epigenetic regulation of gene expression by means of microRNAs plays an important role in the pathogenesis of cervical cancer. Therefore, the search for new differentially expressed microRNAs in order to reveal new mechanisms of HPV-associated transformation of tumor cells is of high priority. AIM: To explore microRNAs with differentiated expression in the cervical cancer tissue and to assess the functional potential of their detection in silico. MATERIALS AND METHODS: The spectrum of microRNAs characterizing by modified expression in the tumor tissue of HPV16-positive squamous cell carcinomas of the cervix was determined using NGS sequencing (Next Generation Sequencing) of tumor tissue and of apparently unchanged adjacent epithelium obtained with the use of microdissection. Potential target genes of the investigated microRNAs were identified using MirTargetLink, Tarbase v9.0, and LinkedOmics services. Gene Set Enrichment Analysis was performed using Metascape. The relations between the level of microRNA expression and clinical SCC features (according to TCGA data, CESC sample) were searched using USCS Xena service. RESULTS: NGS-sequencing of paired HPV16-positive specimens of tumor tissue and normal cervical tissue resulted in the identification of 42 differentially expressed microRNAs. Specifically, the levels of 22 microRNAs in the tumor tissue were higher than in the apparently normal adjacent epithelium, while 20 microRNAs demonstrated lower levels in the tumor specimens. Analysis of the potential targets of significant microRNAs revealed multiple functional gene categories, potentially involved in carcinogenesis as well as an association with clinical features. We showed that increased expression levels of microRNA-20b in the tumor tissue correlated with the risk of distant metastases, whereas the lower levels of microRNA-218-1 and microRNA -218-2 were associated with unfavorable prognosis of disease. With regard to microRNA-363, -615, and -769, their increase in cervical cancer was described for the first time, and the potential targets and signaling pathways associated with THEIR EXPRESSION LEVELS WERE IDENTIFIED. CONCLUSION: The search for differentially expressed microRNAs in cervical cancer has revealed a spectrum of microRNAs with potentially important role in the process of malignant transformation and persistence of tumor phenotype. In addition to microRNAs demonstrating functional characteristics described in the world literature, we found microRNAs that play an unknown role in cervical cancer. In this relation, the potentially relevant targets were identified that could be helpful in understanding the mechanisms of carcinogenesis. The data obtained may form the basis for the development of new approaches to the diagnosis and therapy of SCC.

Coordinated repression of totipotency-associated gene loci by histone methyltransferase EHMT2 through binding to LINE-1 regulatory elements.

Mouse embryonic stem cells (mESCs) and other naïve pluripotent stem cells can reverse typical developmental trajectories and, at low frequency, de-differentiate into 2-cell-like cells (2CLCs) that resemble the mammalian embryo during zygotic genome activation (ZGA). This affords the opportunity to reveal molecular principles that govern the pre-implantation stages of mammalian development. We leveraged a multipurpose allele for acute protein depletion and efficient immunoprecipitation to dissect the molecular functions of the chromatin repressor EHMT2, a candidate antagonist of the mESC-to-2CLC transition. This allowed us to define categories of EHMT2 target genes characterized by distinct modes of EHMT2 chromatin engagement and repression. Most notably, EHMT2 directly represses large clusters of co-regulated gene loci that comprise a significant fraction of the 2CLC-specific transcriptome by initiating H3K9me2 spreading from distal LINE-1 elements. EHMT2 counteracts the recruitment of the activator DPPA2/4 to promoter-proximal endogenous retroviral elements (ERVs) at 2CLC genes. EHMT2 depletion elevates the expression of ZGA-associated transcripts in 2CLCs and synergizes with spliceosome inhibition and retinoic acid signaling in facilitating the mESC-to-2CLC transition. In contrast to ZGA-associated genes, repression of germ layer-associated transcripts by EHMT2 occurs outside of gene clusters in collaboration with ZFP462 and entails binding to non-repeat enhancers. Our observations show that EHMT2 attenuates the bidirectional differentiation potential of mouse pluripotent stem cells and define molecular modes for locus-specific transcriptional repression by this essential histone methyltransferase.

Rates of evolution differ between cell types identified by single-cell RNAseq in threespine stickleback.

Rates of evolutionary change vary by gene. While some broad gene categories are highly conserved with little divergence over time, others undergo continuous selection pressure and are highly divergent. Here, we combine single-cell RNA sequencing (scRNAseq) with evolutionary genomics to understand whether certain cell types exhibit faster evolutionary divergence (using their characteristic genes), than other types of cells. Merging scRNAseq with population genomic data, we show that cell types differ in the rate at which their characteristic genes evolve, as measured by allele frequency divergence among many populations (F ST ) and between species (dN/dS ratios). Neutrophils, B cells, and fibroblasts exhibit elevated F ST at characteristic genes, while eosinophils in the intestine and thrombocytes in the head kidney exhibit lower F ST than the average for 1000 random genes. Gene network centrality also differed between immune- and non-immune-associated genes, and closeness centrality was positively related to gene F ST . These results highlight the value of merging single cell RNA sequencing technology with evolutionary population genomic data, and reveal that genes which define immune cell types exhibit especially rapid evolution.

Transcriptomic Analysis of the CAM Species Kalanchoë fedtschenkoi Under Low- and High-Temperature Regimes.

Temperature stress is one of the major limiting environmental factors that negatively impact global crop yields. Kalanchoë fedtschenkoi is an obligate crassulacean acid metabolism (CAM) plant species, exhibiting much higher water-use efficiency and tolerance to drought and heat stresses than C3 or C4 plant species. Previous studies on gene expression responses to low- or high-temperature stress have been focused on C3 and C4 plants. There is a lack of information about the regulation of gene expression by low and high temperatures in CAM plants. To address this knowledge gap, we performed transcriptome sequencing (RNA-Seq) of leaf and root tissues of K. fedtschenkoi under cold (8 °C), normal (25 °C), and heat (37 °C) conditions at dawn (i.e., 2 h before the light period) and dusk (i.e., 2 h before the dark period). Our analysis revealed differentially expressed genes (DEGs) under cold or heat treatment in comparison to normal conditions in leaf or root tissue at each of the two time points. In particular, DEGs exhibiting either the same or opposite direction of expression change (either up-regulated or down-regulated) under cold and heat treatments were identified. In addition, we analyzed gene co-expression modules regulated by cold or heat treatment, and we performed in-depth analyses of expression regulation by temperature stresses for selected gene categories, including CAM-related genes, genes encoding heat shock factors and heat shock proteins, circadian rhythm genes, and stomatal movement genes. Our study highlights both the common and distinct molecular strategies employed by CAM and C3/C4 plants in adapting to extreme temperatures, providing new insights into the molecular mechanisms underlying temperature stress responses in CAM species.

Metagenomic inference of microbial community composition and function in the weathering crust aquifer of a temperate glacier

Bacterial, fungal, and algal communities that colonize aquatic systems on glacial ice surfaces mediate biogeochemical reactions that alter meltwater composition and affect meltwater production and storage. In this study, we sought to improve understanding of microbial communities inhabiting the shallow aquifer that forms seasonally within the ice surface of a glacier’s ablation zone (i.e., the weathering crust aquifer). Using a metagenomic approach, we compared gene contents of microbial assemblages in the weathering crust aquifer (WCA) of the Matanuska Glacier (Alaska, USA) to those recovered from supraglacial features and englacial ice. High abundances of Pseudomonadota, Cyanobacteriota, Actinomycetota, and Bacteroidota were observed across all samples, while taxa in class Gammaproteobacteria were found at significantly higher abundances in the weathering crust aquifer. The weathering crust aquifer samples also contained higher abundances of Dothideomycetes and Microbotryomyetes; fungal classes commonly observed in snow and other icy ecosystems. Phylogenetic analysis of 18S rRNA and rbcL gene sequences indicated high abundances of algae in the WCA that are closely related (> 98% and > 93% identity, respectively) to taxa of Ancylonema (Streptophyta) and Ochromonas (Ochrophyta) reported from glacial ice surfaces in Svalbard and Antarctic sea ice. Many functional gene categories (e.g., homeostasis, cellular regulation, and stress responses) were enriched in samples from the weathering crust aquifer compared to those from proximal englacial and supraglacial habitats, providing evidence for ecological specialization in the communities. The identification of phagotrophic phytoflagellate taxa and genes involved in mixotrophy implies that combined phototrophic and heterotrophic production may assist with persistence in the low light, low energy, and ephemeral conditions of the weathering crust environment. The compositional and functional differences we have documented indicate distinct microbial distributions and functional processes occur in the weathering crust aquifer environment, and we discuss how deciphering these nuances is essential for developing a more complete understanding of ecosystem biogeochemistry in supraglacial hydrological systems.

Multitask-Based Anti-Collision Trajectory Planning of Redundant Manipulators.

During performing multiple tasks of a redundant manipulator, the obstacles affect the sequential order of task areas and the joint trajectories. The end-effector is constrained to visit multiple task areas with an optimal anti-collision path, while the joints are required to move smoothly and avoid predefined obstacles. A special encoding genetic algorithm (SEGA) is proposed for multitask-based anti-collision trajectory planning. Firstly, the spatial occupancy relationship between obstacles and manipulator is developed utilizing the theory of spherical enclosing box and spatial superposition. The obstacles are detected according to the relative position relationship between linear segments and spheres. Secondly, each joint trajectory between adjacent task areas is depicted with a sixth-degree polynomial. Additionally, each joint trajectory is improved via optimizing the unknown six-order coefficient. By searching for optimal sequential order of task areas, optimal collision detection results, and optimal joint trajectories, the multitask-based anti-collision trajectory planning problem is transformed into a parameter optimization problem. In SEGA, the cost function consists of two parts, including the end-effector path length and the variation of joint angles. Moreover, each chromosome consists of three categories of genes, including the sequential order of task areas, the sequential order of joint configurations corresponding to task areas, and the unknown coefficients for anti-collision joint trajectories. Finally, numerical simulations are carried out to verify the proposed method.

Genome-wide identification of a MADS-box transcription factor family and their expression during floral development in Coptis teeta wall

BackgroundMADS-box transcription factors have been shown to be involved in multiple developmental processes, including the regulation of floral organ formation and pollen maturation. However, the role of the MADS-box gene family in floral development of the alpine plant species Coptis teeta Wall, which is widely used in Traditional Chinese Medicine (TCM), is unknown.ResultsSixty-six MADS-box genes were identified in the C. teeta genome. These genes were shown to be unevenly distributed throughout the genome of C. teeta. The majority of which (49) were classified as type I MADS-box genes and were further subdivided into four groups (Mα, Mβ, Mγ and Mδ). The remainder were identified as belonging to the type II MADS-box gene category. It was observed that four pairs of segmental and tandem duplication had occurred in the C. teeta MADS-box gene family, and that the ratios of Ka/Ks were less than 1, suggesting that these genes may have experienced purifying selection during evolution. Gene expression profiling analysis revealed that 38 MADS-box genes displayed differential expression patterns between the M and F floral phenotypes. Sixteen of these MADS-box genes were further verified by RT-qPCR. The 3D structure of each subfamily gene was predicted, further indicating that MADS-box genes of the same type possess structural similarities to the known template.ConclusionsThese data provide new insights into the molecular mechanism of dichogamy and herkogamy formation in C. teeta and establish a solid foundation for future studies of the MADS-box genes family in this medicinal plant species.

Unraveling the genetic mechanisms of maize ear diameter heterosis

Hybridization has long been a crucial strategy for breeders aiming to develop high-yield crops vital for global food security. However, the exact molecular mechanisms driving heterosis (hybrid vigor) remain a topic of debate. Maize (Zea mays), which demonstrates pronounced heterosis, serves as an ideal model for studying this phenomenon. In our study, we carefully measured phenotypic changes in ear diameter, tracing its development from the inflorescence meristem (IM) to the floral meristem (FM) stages. Our findings revealed a complex progression: the hybrid's ear diameter followed an additive pattern during the IM and spikelet pair meristem (SPM) stages, shifted to incomplete dominance at the spikelet meristem (SM) stage, and ultimately displayed over-dominance at the FM stage. Notably, significant phenotypic changes occurred during the SM stage with gene expression primarily showing non-additive patterns. Gene Ontology (GO) enrichment analysis highlighted the role of cell redox homeostasis genes, which exhibited over-dominant expression in hybrids, as key contributors to heterosis. Furthermore, we identified a distinct gene expression category—dominant maternal or paternal gene expression in F1 hybrids (DMP)—characterized by exclusive expression in the hybrid and one parent, while remaining inactive in the other. This category of DMP genes plays a pivotal role in shaping the diverse gene expression patterns observed in hybrids, distinguishing them from their parental lines. In conclusion, the widespread occurrence of non-additive expression seems to enhance the efficiency of biological processes and energy distribution in hybrids, ultimately driving the manifestation of heterosis.

Feedstock-dependent antibiotic resistance gene patterns and expression profiles in industrial scale biogas plants revealed by meta-omics technology

This study investigated antimicrobial resistance in the anaerobic digesters of two industrial-scale biogas plants processing agricultural biomass and municipal wastewater sludge. A combination of deep sequencing and genome-centric workflow was implemented for metagenomic and metatranscriptomics data analysis to comprehensively examine potential antimicrobial resistance in microbial communities. Anaerobic microbes were found to harbour numerous antibiotic resistance genes (ARGs), with 58.85% of the metagenome-assembled genomes (MAGs) harbouring antibiotic resistance. A moderately positive correlation was observed between the abundance and expression of ARGs. ARGs were located primarily on bacterial chromosomes. A higher expression of resistance genes was observed on plasmids than on chromosomes. Risk index assessment suggests that most ARGs identified posed a significant risk to human health. However, potentially pathogenic bacteria showed lower ARG expression than non-pathogenic ones, indicating that anaerobic treatment is effective against pathogenic microbes. Resistomes at the gene category level were associated with various antibiotic resistance categories, including multidrug resistance, beta-lactams, glycopeptides, peptides, and macrolide-lincosamide-streptogramin (MLS). Differential expression analysis revealed specific genes associated with potential pathogenicity, emphasizing the importance of active gene expression in assessing the risks associated with ARGs.

Whole‑exome sequencing insights into synchronous bilateral breast cancer with discordant molecular subtypes.

The incidence of synchronous bilateral breast cancer (SBBC) is very low, and SBBC with discordant molecular subtypes is even more uncommon. As such, little is known about the pathogenesis of SBBC with discordant molecular subtypes, and reports about this entity are scarce. In the present study, the case of a 72-year-old female patient who presented with SBBC with discordant molecular subtypes is reported, with a stage IA hormone receptor negative {human epidermal growth factor receptor-2 [HER2(+)]} tumor in the left breast and a stage IIIA hormone sensitive tumor [HER2(-)] in the right breast. Whole-exome sequencing was performed to identify the differential genetic variations in the BBC tissues. A total of 8 key mutated cancer susceptibility genes (ALK, BRCA1, FAT1, HNF1A, KDR, PTCH1, SDHA and SETBP1) were screened, and mutations were found in 10 vital cancer driver genes, including BRCA1, EBF1, MET, NF2, NUMA1 RALGAPA1, ROBO2, SMYD4, UBR5 and ZNF844. The high-frequency mutated genes mainly contained missense mutations, among which single nucleotide variants were the most common mutations, with C > T and C > A as the main forms. The pathways associated with the high frequency mutated genes were further elucidated by functional category and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. Heterogeneity in the hormone receptor and HER2 status of SBBC poses unique therapeutic challenges. Future studies should aim to identify the optimal management strategy for this disease.

Identification of a seven-gene prognostic model for renal cell carcinoma associated with CD8+T lymphocyte cell.

CD8+ T lymphocytes are important elements of the tumor microenvironment, hence their involvement in the development and progression of tumors is complex. Data on the precise tumor-infiltrating lymphocytes gene signature in renal cell carcinoma (RCC) remain limited. Therefore, this study created a tumor-infiltrating lymphocytes-related predictive model for patients with RCC using data from The Cancer Genome Atlas. The most important genes associated with CD8 + T lymphocytes were identified using weighted gene co-expression network analysis. Functional categories of important genes were revealed using gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes signaling pathway analyses. A CD8 + T lymphocyte-related prognostic model with 7 important genes was simultaneously created using the least absolute shrinkage and selection operator, univariate and multivariate Cox regressions, and the 7 genes were expressed particularly in CD8 + T lymphocytes according to single-cell sequencing data obtained from the Gene Expression Omnibus. This study identified a seven-gene prognostic model associated with CD8 + T lymphocytes that may significantly influence risk stratification in patients with RCC. The genes included in the model are apolipoprotein B mRNA editing catalytic polypeptide 3G, CD3 gamma, eomesodermin, protein tyrosine phosphatase, non-receptor type 7, signal regulatory protein gamma, Fas ligand, and T-cell immunoreceptor with Ig and ITIM domains.

Molecular mechanisms and behavioral relevance underlying neural correlates of childhood neglect

BackgroundChildhood neglect is associated with brain changes, yet the molecular mechanisms and behavioral relevance underlying such associations remain elusive. MethodsWe calculated fractional amplitude of low-frequency fluctuations (fALFF) using resting-state functional MRI and tested their correlation with childhood neglect across a large sample of 510 healthy young adults. Then, we investigated the spatial relationships of the identified neural correlates of childhood neglect with gene expression, neurotransmitter, and behavioral domain atlases. ResultsWe found that more severe childhood neglect was correlated with higher fALFF in the bilateral anterior cingulate cortex. Remarkably, the identified neural correlates of childhood neglect were spatially correlated with expression of gene categories primarily involving neuron, synapse, ion channel, cognitive and perceptual processes, and physiological response and regulation. Concurrently, there were significant associations between the neural correlates and specific neurotransmitter systems including serotonin and GABA. Finally, neural correlates of childhood neglect were associated with diverse behavioral domains implicating mental disorders, emotion, cognition, and sensory perception. LimitationsThe cross-sectional study design cannot unequivocally establish causality. ConclusionsOur findings may not only add to the current knowledge regarding the relationship between childhood neglect and mental health, but also have clinical implications for developing preventive strategies for individuals exposed to childhood neglect who are at risk for mental disorders.

Generation and analysis of mouse embryonic stem cells with knockout of the Mcph1 (microcephalin) gene.

Chromatin is not randomly distributed within the nucleus, but organized in a three-dimensional structure that plays a critical role in genome functions. Сohesin and condensins are conserved multi-subunit protein complexes that participate in mammalian genome organization by extruding chromatin loops. The fine temporal regulation of these complexes is facilitated by a number of other proteins, one of which is microcephalin (Mcph1). Mcph1 prevents condensin II from associating with chromatin through interphase. Loss of Mcph1 induces chromosome hypercondensation; it is not clear to what extent this reorganization affects gene expression. In this study, we generated several mouse embryonic stem cell (mESC) lines with knockout of the Mcph1 gene and analyzed their gene expression profile. Gene Ontology analyses of differentially expressed genes (DEGs) after Mcph1 knockout revealed gene categories related to general metabolism and olfactory receptor function but not to cell cycle control previously described for Mcph1. We did not find a correlation between the DEGs and their frequency of lamina association. Thus, this evidence questions the hypothesis that Mcph1 knockout-mediated chromatin reorganization governs gene expression in mESCs. Among the negative effects of Mcph1 knockout, we observed numerous chromosomal aberrations, including micronucleus formation and chromosome fusion. This confirms the role of Mcph1 in maintaining genome integrity described previously. In our opinion, dysfunction of Mcph1 may be a kind of "Rosetta stone" for deciphering the function of condensin II in the interphase nucleus. Thus, the cell lines with knocked-out Mcph1 can be used to further study the influence of chromatin structural proteins on gene expression.

A Perspective of Tailoring Dielectric Genes for 2D Materials Toward Advanced Electromagnetic Functions

Abstract2D materials and their composites with electromagnetic properties are becoming increasingly popular. Obtaining insight into the nature of electromagnetic (EM) response manipulation is imperative to guide scientific research and technological exploitation at such a critical time. From this perspective, the dielectric genes of 2D material hybrids have been highlighted based on the recent literature. This endows an unlimited possibility of manipulating the EM response, even at elevated temperatures. The definitions and criteria of dielectric genes toward 2D material hybrids and composites are systematically clarified and summarized. The dielectric gene categories are successfully discriminated, including the conduction networks, intrinsic defects, impurity defects, and interfaces in the composite, and their temperature evolution is revealed in detail. More importantly, tuning strategies for microwave absorption, electromagnetic shielding effectiveness, and expanded electromagnetic functions are thoroughly discussed. Finally, significant predictions are provided for multispectral electromagnetic functions, and future applications of multifunctional exploration are anticipated. Dielectric genes will open an unexpected horizon for advanced functional materials in the coming 5G/6G age, providing a significant boost to promoting environmental electromagnetic protection, electromagnetic devices, and next‐generation smart devices.

Transcriptome analysis of Sesuvium portulacastrum L. uncovers key genes and pathways involved in root formation in response to low-temperature stress.

Sesuvium portulacastrum L., a perennial facultative halophyte, is extensively distributed across tropical and subtropical coastal regions. Its limited cold tolerance significantly impacts both the productivity and the geographical distribution of this species in higher-latitude areas. In this study, we employed RNA-Seq technology to delineate the transcriptomic alterations in Sesuvium plants exposed to low temperatures, thus advancing our comprehension of the molecular underpinnings of this physiological adaptation and root formation. Our findings demonstrated differential expression of 10,805, 16,389, and 10,503 genes in the low versus moderate temperature (LT vs. MT), moderate versus high temperature (MT vs. HT), and low versus high temperature (LT vs. HT) comparative analyses, respectively. Notably, the gene categories "structural molecule activity", "ribosome biogenesis", and "ribosome" were particularly enriched among the LT vs. HT-specific differentially expressed genes (DEGs). When synthesizing the insights from these three comparative studies, the principal pathways associated with the cold response mechanism were identified as "carbon fixation in photosynthetic organisms", "starch and sucrose metabolism", "plant hormone signal transduction", "glycolysis/gluconeogenesis", and "photosynthesis". In addition, we elucidated the involvement of auxin signaling pathways, adventitious root formation (ARF), lateral root formation (LRF), and novel genes associated with shoot system development in root formation. Subsequently, we constructed a network diagram to investigate the interplay between hormone levels and pivotal genes, thereby clarifying the regulatory pathways of plant root formation under low-temperature stress and isolating key genes instrumental in root development. This study has provided critical insights into the molecular mechanisms that facilitate the adaptation to cold stress and root formation in S. portulacastrum.