Search Results (489)

The need for unpredictable sequences of bits is common in many important security applications. These sequences can only be generated by true random number generators (TRNGs). Apart from the natural analog domain for TRNGs, this type of generator is also required as a digital-based solution, particularly leveraging field-programmable gate array (FPGA) platforms. Despite the number of existing FPGA-based implementations, new solutions that use different types of entropy sources, utilize fewer FPGA resources, or ensure higher throughput are still being sought. This paper presents an architecture of a simple TRNG targeted for implementation in FPGAs. As a source of entropy, the TRNG exploits jitter in capacitive oscillators and metastability in flip-flops. The capacitive oscillators, in turn, use the input–output cells of an FPGA chip and unconnected external pins and cyclically charge and discharge the parasitic capacitance associated with these pins. The TRNG needs a small number of FPGA resources, namely 13 look-up tables (LUTs), 12 flip-flops, and 3 unused pins. Its throughput is approximately 12.5 Mbit/s for AMD/Xilinx Artix-7 FPGA family chips. The presented TRNG passes all the NIST statistical tests for a wide range of operating conditions. Full article

As synthetic biology advances toward precise design, the construction of high-quality mutant libraries has become essential for large-scale functional screening. Traditional approaches, such as random and saturation mutagenesis, often suffer from low accuracy, high bias, and limited coverage. An ideal method should offer controlled mutagenesis, comprehensive coverage, high throughput, operational simplicity, and controllable outcomes, enabling effective large-scale screening. Here, we developed a high-throughput, precisely controlled method for constructing a mutagenesis library based on chip-based oligonucleotide synthesis. Using PSMD10 as a model, we constructed a full-length amber codon scanning mutagenesis library with 93.75% mutation coverage. Among the five polymerases evaluated, KAPA HiFi HotStart, Platinum SuperFi II and Hot-Start Pfu DNA Polymerase demonstrated higher amplification efficiency and lower chimera formation rates, making them preferred enzymes for optimized library construction. Analysis of unmapped reads highlighted key technical factors, such as oligonucleotide synthesis errors and chimeric sequence formation caused by incomplete extension of DNA polymerase or synthesis across discontinuous templates during PCR. To improve efficiency and fidelity, we recommend refining PCR conditions and strengthening oligo synthesis quality control. We establish an efficient, scalable, precisely controlled mutagenesis library construction strategy tailored for high-throughput functional research and recommend using a high-fidelity, low-bias polymerase to ensure quality. Full article

Olanzapine and clozapine, two of the most efficacious second-generation antipsychotic drugs (SGAs), are known to cause serious metabolic side effects. Despite their clinical utility, the epigenetic basis of these metabolic side-effects remains poorly understood. This exploratory study investigated whether histone methylation is associated with metabolic disorders following chronic SGA treatment. Rats were treated with olanzapine or clozapine for 9 weeks and then sacrificed 2 h after the final treatment. After evaluating the metabolic parameters, Chromatin immunoprecipitation (ChIP)-deep sequencing was conducted on liver tissue pooled from twelve samples per group to quantify histone H3K4me2 methylation and transcriptional changes. Gene ontology term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to explore shared functional pathways of genes with differential histone methylation. Key findings revealed that both olanzapine and clozapine induced widespread changes in hepatic histone methylation, particularly hypermethylation at H3K4me2 across genes involved in lipid and glucose metabolism, insulin signalling, and adipogenesis. Olanzapine- and clozapine-treated rats displayed increased H3K4me2 levels at numerous gene loci and at distinct genomic regions. These findings suggest the importance of monitoring metabolic parameters in psychiatric patients and potential novel strategies to mitigate SGA-induced metabolic side effects. Full article

Background: Inbreeding is a major genetic problem that reduces fertility and causes genetic disorders. Some breeders of dromedary camels use the same bull for many years due to its excellent characteristics, leading to mating with offspring and subsequent generations, resulting in increased homozygosity and genetic disorders. We hypothesize that inbreeding is associated with infertility in dromedary camels with normal and uninfected reproductive tracts. Methods: We genotyped 96 samples from seven camel breeds using the Illumina 55K SNP BeadChip, including five confirmed infertile individuals. Inbreeding coefficients (F) were calculated using PLINK based on heterozygosity and runs of homozygosity. Genome-wide association analysis using logistic regression was performed to identify potential genomic regions associated with infertility. Results: All five infertile camels showed significantly higher F values (>0.15) compared to 91 fertile individuals (<0.10, p < 0.001). The genome-wide association analysis failed to identify specific genomic regions linked to infertility, likely due to limited statistical power (n = 5 cases) and the polygenic nature of fertility traits. Population structure analysis revealed genetic differentiation related to coat color, with two significant SNPs on chromosome 3 near SLC30A5 (p < ${10}^{-7}$). Conclusions: Our results demonstrate that elevated inbreeding is strongly associated with infertility in dromedary camels. Future studies should employ larger sample sizes (≥50 infertile individuals) or whole-genome sequencing (35× coverage) to identify specific genomic regions. Implementation of breeding strategies avoiding related matings (F < 0.10) is recommended to maintain reproductive performance in camel herds. Full article

Genome sequencing has possibly been the greatest step in the development of advanced tools for animal genetic improvement: knowledge of gene sequences and use of haplotype markers for productivity traits can provide important improvements in yield production and optimisation of reproductive program. Next-generation and, more recently, third-generation sequencing techniques enormously increased the ability to produce sequences from single individuals and increased the interest in exome or whole-genome sequencing as an alternative to SNP chips in breeding programs as these techniques allowed for the capture of a wider range of variations, including characterisation of rare variants, structural variations, and copy number changes. Here, we present a procedure, based on fast de novo assembly and a scaffolding step, to quickly build an almost complete genome starting from long reads obtained in a single sequencing run. The procedure, applied to sequences from five water buffaloes, was able to independently build, for each individual, an almost complete high-quality genome with highly continuous chromosome sequences; in most cases, over 90% of the length of the reference chromosome was covered by less than ten long contigs. Unlike other pipelines based on slower assemblers or which require many sequencing data, in 1–2 days, the proposed procedure can go from a single run to continuous genome assembly, supporting fast analysis of large chromosome structures, potentially useful for improving animal breeding and productivity. Full article

An emerging challenge in prostate cancer (PCa) treatment is the development of drug cross-resistance, wherein resistance to enzalutamide (ENZ), an androgen receptor signaling inhibitor (ARSI), also confers resistance to subsequent ARSI and docetaxel (DTX) treatments. The mechanisms underlying this drug cross-resistance remain unclear. Through RNA sequencing, we identified 93 overlapping differentially expressed genes (DEGs) in ENZ- and DTX-resistant PCa cells. Among the DEGs, HSPB1, which encodes heat shock protein 27 (HSP27), emerged as a key gene of interest. HSP27 is a known target of lens epithelium-derived growth factor p75 (LEDGF/p75), a transcription coactivator regulated by glucocorticoid receptor (GR). Both GR and LEDGF/p75 are overexpressed in advanced PCa and promote drug resistance. HSP27 was overexpressed in ENZ and DTX cross-resistant PCa cell lines and its expression was decreased upon GR or LEDGF/p75 silencing. ChIP sequencing confirmed GR binding at the HSPB1 promoter. Pharmacological targeting of HSP27 in drug-resistant cells reduced proliferation, clonogenicity, and tumorsphere formation, and restored sensitivity to ENZ and DTX. Notably, high transcript expression of a GR-LEDGF/p75-HSP27 gene panel correlated with worse overall survival in PCa patients (n = 4259). These findings identified this axis as a driver of PCa drug cross-resistance and promising therapeutic target for overcoming treatment failure. Full article

The submandibular glands (SMGs), along with the parotid and sublingual glands, generate the majority of saliva and play critical roles in maintaining oral and systemic health. Despite their physiological importance, long-term therapeutic options for salivary gland dysfunction remain limited, highlighting the need for a deeper molecular understanding of SMG biology, particularly in humans. To address this knowledge gap, we have performed transcriptomic- and epigenomic-based analyses and molecular characterization of the human SMG. Our integrated analysis of multiorgan RNA-sequencing datasets has identified an SMG-enriched gene expression signature comprising 289 protein-coding and 75 long non-coding RNA (lncRNA) genes that include both known regulators of salivary gland function and several novel candidates ripe for future exploration. To complement these transcriptomic studies, we have generated chromatin immunoprecipitation sequencing (ChIP-seq) datasets of key histone modifications on human SMGs. Our epigenomic analyses have allowed us to identify genome-wide enhancers and super-enhancers that are likely to drive genes and regulatory pathways that are important in human SMG biology. Finally, comparative analysis with mouse and human SMG and other tissue datasets reveals evolutionary conserved gene and regulatory networks, underscoring fundamental mechanisms of salivary gland biology. Collectively, this study offers a valuable knowledge-based resource that can facilitate targeted research on salivary gland dysfunction in human patients. Full article

G-quadruplex (G4) ChIP-Seq data are critical for studying the roles of G4 structures in various biological processes, yet their reproducibility remains systematically uncharacterized. In this study, we evaluated the consistency of in vivo G4 peaks across multiple replicates in three publicly available datasets. We observed considerable heterogeneity in peak calls, with only a minority of peaks shared across all replicates. To address this challenge, we compared three computational methods—IDR, MSPC, and ChIP-R—for assessing reproducibility and found that MSPC is the optimal solution in reconciling inconsistent signals in G4 ChIP-Seq data. We further demonstrated that employing at least three replicates significantly improved detection accuracy compared to conventional two-replicate designs, while four replicates proved sufficient to achieve reproducible outcomes, with diminishing returns beyond this number. Moreover, we showed that the reproducibility-aware analytical strategies can partially mitigate the adverse effects of low sequencing depth, though they do not fully substitute for high-quality data. Based on our findings, we recommend 10 million mapped reads as a minimum standard for G4 ChIP-Seq experiments, with 15 million or more reads being preferable for optimal results. Our study provides practical guidelines for experimental design and data analysis in G4 studies, emphasizing the importance of replication and robust bioinformatic strategies to enhance the reliability of genome-wide G4 mapping. Full article

Plants have evolved a complex, multilayered immune system that integrates molecular recognition, signaling pathways, epigenetic regulation, and small RNA-mediated control. Recent studies have shown that DNA-level regulatory mechanisms, such as RNA-directed DNA methylation (RdDM), histone modifications, and chromatin remodeling, are critical for modulating immune gene expression, allowing for rapid and accurate pathogen-defense responses. The epigenetic landscape not only maintains immunological homeostasis but also promotes stress-responsive transcription via stable chromatin modifications. These changes contribute to immunological priming, a process in which earlier exposure to pathogens or abiotic stress causes a heightened state of preparedness for future encounters. Small RNAs, including siRNAs, miRNAs, and phasiRNAs, are essential for gene silencing before and after transcription, fine-tuning immune responses, and inhibiting negative regulators. These RNA molecules interact closely with chromatin features, influencing histone acetylation/methylation (e.g., H3K4me3, H3K27me3) and guiding DNA methylation patterns. Epigenetically encoded immune memory can be stable across multiple generations, resulting in the transgenerational inheritance of stress resilience. Such memory effects have been observed in rice, tomato, maize, and Arabidopsis. This review summarizes new findings on short RNA biology, chromatin-level immunological control, and epigenetic memory in plant defense. Emerging technologies, such as ATAC-seq (Assay for Transposase-Accessible Chromatin using Sequencing), ChIP-seq (Chromatin Immunoprecipitation followed by Sequencing), bisulfite sequencing, and CRISPR/dCas9-based epigenome editing, are helping researchers comprehend these pathways. These developments hold an opportunity for establishing epigenetic breeding strategies that target the production of non-GMO, stress-resistant crops for sustainable agriculture. Full article

Stomata on the leaves of wheat serve as important gateways for gas exchange with the external environment. Their morphological characteristics, such as size and density, are closely related to physiological processes like photosynthesis and transpiration. However, due to the limitations of existing analysis methods, the efficiency of analyzing and mining stomatal phenotypes and their associated genes still requires improvement. To enhance the accuracy and efficiency of stomatal phenotype traits analysis and to uncover the related key genes, this study selected 210 wheat varieties. A novel semantic segmentation model based on transformer for wheat stomata, called Wheat Stoma Former (WSF), was proposed. This model enables fully automated and highly efficient stomatal mask extraction and accurately analyzes phenotypic traits such as the length, width, area, and number of stomata on both the adaxial (Ad) and abaxial (Ab) surfaces of wheat leaves based on the mask images. The model evaluation results indicate that coefficients of determination (R²) between the predicted values and the actual measurements for stomatal length, width, area, and number were 0.88, 0.86, 0.81, and 0.93, respectively, demonstrating the model’s high precision and effectiveness in stomatal phenotypic trait analysis. The phenotypic data were combined with sequencing data from the wheat 660 K SNP chip and subjected to a genome-wide association study (GWAS) to analyze the genetic basis of stomatal traits, including length, width, and number, on both adaxial and abaxial surfaces. A total of 36 SNP peak loci significantly associated with stomatal traits were identified. Through candidate gene identification and functional analysis, two genes—TraesCS2B02G178000 (on chromosome 2B, related to stomatal number on the abaxial surface) and TraesCS6A02G290600 (on chromosome 6A, related to stomatal length on the adaxial surface)—were found to be associated with stomatal traits involved in regulating stomatal movement and closure, respectively. In conclusion, our WSF model demonstrates valuable advances in accurate and efficient stomatal phenotyping for locating genes related to stomatal traits in wheat and provides breeders with accurate phenotypic data for the selection and breeding of water-efficient wheat varieties. Full article

Acute respiratory distress syndrome (ARDS) is a life-threatening condition with high mortality. A central driver in its pathogenesis is alveolar epithelial cell (AEC) dysfunction, which leads to disruption of the epithelial barrier, impaired fluid clearance, and dysregulated inflammatory responses. This review summarizes the key mechanisms underlying AEC injury, including programmed cell death (apoptosis, pyroptosis, necroptosis, ferroptosis), oxidative stress, mitochondrial dysfunction, epigenetic reprogramming (DNA methylation, histone modifications), metabolic rewiring (succinate accumulation), and spatiotemporal heterogeneity revealed by single-cell sequencing and spatial transcriptomics. Multicellular crosstalk involving epithelial–immune–endothelial networks and the gut-lung axis further shapes disease progression. Building on these mechanistic foundations, we evaluate emerging AEC-targeted interventions such as pharmacologic agents (antioxidants, anti-inflammatories), biologics (mesenchymal stem cells and engineered exosomes), and gene-based approaches (adeno-associated virus and CRISPR-Cas9 systems delivered via smart nanocarriers). Complementary strategies include microbiome modulation through probiotics, short-chain fatty acids, or fecal microbiota transplantation, and biomarker-guided precision medicine (e.g., sRAGE, exosomal miRNAs) to enable promise individualized regimens. We also discuss translational hurdles, including nanotoxicity, mesenchymal stem cell (MSC) heterogeneity, and gene-editing safety, and highlight future opportunities involving AI-driven multi-omics, lung-on-chip platforms, and epithelium-centered regenerative therapies. By integrating mechanistic insights with innovative therapeutic strategies, this review aims to outline a roadmap toward epithelium-targeted, precision-guided therapies for ARDS. Full article

Random number generators play a critical role in ensuring information security, supporting encrypted communications, and preventing data leakage. However, the random number generators widely used in hardware are faced with potential threats such as environmental disturbances and fault injection attacks. Especially in automotive-grade environments, chips encounter threat scenarios involving multidimensional fault injection, which may lead to functional failures or malicious exploitation, endangering the security of the entire system. This paper focuses on a Counter Mode Deterministic Random Bit Generator (CTR-DRBG) based on the AES-128 algorithm and implements a hardware prototype system compliant with the NIST SP 800-22 standard on an FPGA platform. Centering on typical fault modes such as temperature disturbances, voltage glitches, electromagnetic interference, and bit flips, single-dimensional and multidimensional fault injection and simulated fault injection experiments were designed and conducted. The impact characteristics and sensitivities of electromagnetic faults, voltage faults, and temperature faults regarding the output sequences of random numbers were systematically evaluated. The experimental results show that this type of random number generator exhibits modular-level differential vulnerability under physical disturbances, especially in the data transmission processes of encryption paths and critical registers, which demonstrate higher sensitivity to flip-type faults. This research provides a feasible analysis framework and practical basis for the security assessment and fault-tolerant design of random number generators, possessing certain engineering applicability and theoretical reference value. Full article

This paper presents an innovative and low-cost approach to the dispensing of multiple liquids on a microfluidic chip with the aim of dispensing liquids in a controlled sequence. The project focused on the design and development of a microfluidic liquid dispensing system that is an integral part of the Lab-on-Chip (LOC). Liquids are often dispensed into LOCs through blisters, syringes, or electric microfluidic pumps, but these can be impractical for Point-of-Care (POC) settings, especially in remote areas. Additionally, incorrect volumes of biochemical reagents and the introduction of reagents outside the sequence can distort the results of the diagnosis. The process undertaken involved designing and 3D printing prototypes of the dispensing system, along with laser cutting and manufacturing the Polymethyl Methacrylate (PMMA) LOC devices intended for receiving the liquids. The proposed novel low-cost dispensing system uses manually operated actuators and cams to disperse metered fluids sequentially to minimise end-user errors at POC settings. Full article

The Xinglong buffalo is a local swamp buffalo breed adapted to tropical regions in China. To facilitate the protection and utilization of valuable genetic resources, we first developed the breed-specific single nucleotide polymorphism (SNP) liquid-phase chip based on genotyping-by-target-sequencing (GBTS) technology. Whole-genome resequencing data from 143 buffaloes, resulting in 34,757,694 SNPs, were used to identify 1208 breed-specific and 2889 background sites. This chip also incorporates 965 functional SNP sites derived from literature, including SNPs significantly associated with immunity, reproduction, growth, and production. A total of 5062 SNP sites were successfully identified for the development of a 5K liquid-phase genome-wide breeding chip for the Xinglong buffalo. The validation of the chip using 93 samples showed a high detection rate with good repeatability and consistency. In addition, the chip exhibits strong capabilities in clustering and kinship analysis. Results of kinship analysis underscored the importance of a breed-specific chip for the Xinglong buffalo. These results highlight the advantages of a low-density, cost-effective, and breed-specific SNP chip for accurate genotyping. This chip will support future endeavors in molecular breeding, conservation, and genetic evaluation of Xinglong buffalo, thereby facilitating the sustainable utilization of this valuable indigenous germplasm resource. Full article

FOXL2 (forkhead box protein L2) is a transcription factor, its function and regulatory mechanism have been mainly studied in mammals; related research on marine invertebrates is still insufficient. It was found that oogenesis was affected, and even a small number of cells resembling spermatogonial morphology appeared in C. farreri ovaries after the FOXL2 was knocked down through RNA interference (RNAi) technology in our laboratory previously. Based on previous research, this paper conducted transcriptome sequencing and differential expression analysis on the ovarian tissues between the experimental group (post-RNAi) and the control group (pre-RNAi) of C. farreri, and used recombinant C. farreri FOXL2 protein for antibody production in Chromatin Immunoprecipitation Sequencing (ChIP seq) experiments to comprehensively analyze the pathways and key genes regulated by FOXL2 during oogenesis. The results showed that in the RNAi experimental group, 389 genes were upregulated, and 1615 genes were downregulated. Among the differentially expressed genes (DEGs), the differential genes related to gender or gonadal development are relatively concentrated in physiological processes such as steroid hormone synthesis, spermatogenesis, gonadal development, and ovarian function maintenance, as well as the FoxO and estrogen signaling pathways. Combining transcriptome and ChIP-seq data, it was found that there were some genes related to sex gonadal development among genes which were directly regulated by FOXL2, such as Wnt4, SIRT1, HSD17B8, GABABR1, KRAS, NOTCH1, HSD11B1, cPLA2, ADCY9, IP3R1, PLCB4, and Wnt1. This study lays the foundation for a deeper understanding of the FOXL2′s specific regulatory mechanism during oogenesis in scallops as a transcription factor. Full article