Search Results (6,647)

(1) Background: A safe and effective nucleic acid sample transportation method was developed that is suitable for underdeveloped areas which lack advanced sequencing capabilities, specifically for virus genomic sequencing and infectious disease monitoring. (2) Methods: This study evaluated the use of Flinders Technology Associates (FTA) cards for transporting amplified whole-genome DNA from 120 SARS-CoV-2-positive nasopharyngeal swab samples in Sierra Leone. Nucleic acid extraction and whole-genome amplification were conducted at a local laboratory. Amplified products were applied to FTA Elute cards for room temperature shipment to China CDC for elution and sequencing. (3) Results: The FTA card method achieved a 9.6% recovery rate for amplicons, sufficient for viral genome sequencing. In total, 86 (71.7%) high-quality SRAS-CoV-2 genomic sequences were obtained, with the majority reaching depths exceeding 100X. Sequence analysis revealed co-circulation of Delta, Omicron, and B.1 lineages. Higher Ct values in the original sample significantly reduced coverage and depth, with Ct ≤ 27; 73.6% of samples yielded effective sequences. (4) Conclusions: Transportation of amplified nucleic acid samples using FTA cards enables virus genomic sequencing in resource-limited areas. This approach can potentially improve local virus surveillance and outbreak response capabilities. Further optimizations could improve sequence recovery rate. Implementing this method could significantly enhance sequencing accessibility in underdeveloped regions. Full article

Alterations in aggressive-variant prostate cancer-associated tumor suppressor genes (AVPC-TSG: TP53, RB1, PTEN) are related with androgen insensitivity and aggressive disease. However, their prognostic and predictive role in metastatic hormone-sensitive prostate cancer (mHSPC) is unclear. This single-center retrospective study assesses the value of AVPC-TSG alterations in refining prognosis and predicting the response to androgen receptor pathway inhibitors (ARPIs) in mHSPC. We included 158 patients with genomic tumor sequencing undergoing treatment for mHSPC between 2013 and 2023. We compared patients with AVPC-TSGalt tumors (≥1 alteration in TP53, RB1, or PTEN/PI3K/AKT pathway genes) to those with AVPC-TSGwt tumors (i.e., without alterations in AVPC-TSG). Cox analyses were performed for progression-free survival (PFS) and overall survival (OS). AVPC-TSGwt status was associated with improved PFS and OS in both univariate and multivariate (MV) analyses (MV PFS: HR 0.58, 95%CI: 0.38–0.89, p = 0.012; MV OS: HR 0.48, 95%CI: 0.26–0.91, p = 0.025). AVPC-TSGalt mHSPC patients seemed to derive no PFS benefit from ARPI addition (PFS: HR 1.13, 95%CI: 0.58–2.19, p = 0.721), while AVPC-TSGwt mHSPC patients did (PFS: HR 0.51, 95%CI: 0.28–0.93 p = 0.029). Integrating AVPC-TSG status with CHAARTED volume criteria, we identified three distinct subgroups: “good risk” (AVPC-TSGwt low volume), “intermediate risk” (either AVPC-TSGalt low volume or AVPC-TSGwt high volume), and “poor risk” (AVPC-TSGalt high volume) with median PFS of 46.8, 28.2, and 15.7 months, respectively. Only the “intermediate risk” subgroup seemed to derive PFS benefit from ARPI addition (HR 0.36, 95%CI: 0.19–0.70, p = 0.002). AVPC-TSG status assessment refines prognosis and may predict PFS benefits of ARPIs in mHSPC. AVPC-TSGalt mHSPC patients should be considered for clinical trials as they may not benefit from current standard approaches. Full article

Beef cattle breed improvement holds strategic significance in the livestock industry. Pinan cattle, developed through years of selective breeding in Xinye County, Henan Province, exhibit superior traits including thin skin, fine bone structure, rapid growth, high dressing percentage, excellent meat yield, and superior feed efficiency. However, research on the genetic characteristics of Pinan cattle remains in its infancy. In this study, we investigated population genetic diversity and positive selection signals in Pinang cattle based on whole-genome resequencing data. Using a selective sweep approach, we identified 98 candidate genes associated with growth, reproduction, and immunity, along with 13 high-confidence missense mutations, which may underlie key traits in this population. Based on the critical roles of the NDN and PARVA genes in reproduction and muscle development, the predominant T allele at the NDN c.581T > A and PARVA c.893T > A loci in the Pinan cattle population may partially explain their advantages in sexual precocity and rapid growth compared to other breeds or populations. This study provides an important theoretical basis for the genetic improvement of native beef cattle and lays a scientific foundation for further investigation into the growth and development mechanisms of Pinan cattle. Full article

Edible fungi, a group of globally significant macrofungi, are highly valued for their unique flavors and substantial nutritional and medicinal properties. Understanding the molecular mechanisms governing their growth, development, gene function, biosynthesis of valuable compounds, and environmental adaptation is crucial for enhancing yield and quality, providing essential scientific support for industrial progress. Genomics, transcriptomics, and proteomics, as cornerstone life science technologies, offer powerful, integrated approaches to decipher genetic codes, reveal gene expression patterns, and elucidate complex metabolic networks in edible fungi. These advancements are transitioning research from traditional cultivation methods towards deeper molecular biology exploration. This review synthesizes key progress in applying genomics, transcriptomics, and proteomics to edible fungi, with a particular focus on metabolism-related research and the fundamentals of metabolic network construction. It discusses how these technologies, independently and in preliminary integration, uncover critical steps and regulatory mechanisms within endogenous metabolic pathways. While acknowledging the importance of metabolomics and epigenomics as cutting-edge areas, this review focuses on the “classical triad” of genomics, transcriptomics, and proteomics due to their technological maturity, data accessibility, and established application base in elucidating core metabolic mechanisms in edible fungi. The goal is to deepen the understanding of edible fungi metabolic mechanisms, providing a vital theoretical basis and practical insights for optimizing cultivation, enabling genetic improvement, harnessing bioactive substances, and promoting industrial upgrading, thereby boosting the overall efficiency and competitiveness of the edible fungi industry. Full article

Wastewater-based epidemiology (WBE) offers valuable insight into viral circulation at the community level. In this study, we combined digital PCR (dPCR) with molecular typing to investigate the prevalence and diversity of human adenoviruses (HAdVs) in untreated wastewater samples collected throughout Italy. HAdV genomes were detected in over 93% of the 168 samples analyzed, with concentrations up to 4.5 × 10⁶ genome copies per liter. For genotypic characterization, we used nested PCR followed by Sanger and Oxford Nanopore Technologies (ONTs) long-read sequencing. While Sanger sequencing identified three dominant genotypes (HAdV-A12, HAdV-B3, and HAdV-F41), ONT sequencing provided enhanced resolution, confirming all previously identified types and revealing seven additional genotypes: HAdV-B21, HAdV-C5, HAdV-D45, HAdV-D46, HAdV-D49, HAdV-D83, and HAdV-F40. This comprehensive approach highlights the added value of ONT long-read sequencing in uncovering the genetic complexity of adenoviruses in wastewater, particularly in detecting rare or low abundance types that conventional methods may miss. Our findings highlight the value of integrating quantitative and high-resolution molecular tools in WBE to improve surveillance and better understand the epidemiology of viral pathogens circulating in the human population. Full article

Agraz (Vaccinium meridionale Swartz) is a shrub native to the Neotropical region of South America, including Colombia, Ecuador, Venezuela, and Peru. Known for its edible fruits valued for their nutritional, nutraceutical, and medicinal properties, the species remains underexplored despite its potential. This research aimed to investigate the genetic diversity and population structure of agraz in Colombia, focusing on native individuals from Santander and commercial individuals from Boyacá and Cundinamarca, providing insights that can support conservation and genetic improvement efforts. Methods: In this study, genotyping by sequencing (GBS) was used to analyze genetic variation and population structure in V. meridionale. The sequencing data were aligned to the V. corymbosum cv. Draper v1.0 reference genome. The obtained single-nucleotide polymorphisms (SNPs) were employed to evaluate genetic diversity, population differentiation, and inbreeding coefficients, with measures such as expected heterozygosity and F-statistics providing insights into population structure and genetic composition across regions. Results: A total of 12,910 SNPs were obtained, and the results revealed moderate genetic diversity within the agraz populations, characterized by an expected heterozygosity (He) of 0.3586. A negative Fis value indicated an excess of heterozygosity and low genetic differentiation among the sampled regions. Population structure analysis identified three distinct subpopulations, with Subpopulation 3 exhibiting the most unique genetic composition. Conclusions: This study provides the first genetic diversity analysis of V. meridionale in Colombia using the GBS approach. The findings contribute to the understanding of the species’ genetic variability and offer valuable information for conservation strategies, genetic improvement and breeding programs to enhance its agricultural potential and ensure the sustainable utilization of agraz resources. Full article

For centuries, plant-derived natural products (NPs) have been fundamental to traditional medicine, providing essential therapeutic compounds. Ethnobotanical knowledge has historically guided NP discovery, leading to the identification of key pharmaceuticals such as aspirin, morphine, and artemisinin. However, conventional bioactivity-guided fractionation methods for NP isolation are labour-intensive and can result in the loss of bioactive properties due to the focus on a single compound. Advances in omics sciences—genomics, transcriptomics, proteomics, metabolomics, and phenomics—coupled with computational tools have altogether revolutionised NP research by enabling high-throughput screening and more precise compound identification. This review explores how integrating traditional medicinal knowledge with multi-omics strategies enhances NP discovery. We highlight emerging bioinformatics tools, mass spectrometry techniques, and metabologenomics approaches that accelerate the identification, annotation, and functional characterisation of plant-derived metabolites. Additionally, we discuss challenges in omics data integration and propose strategies to harness ethnobotanical knowledge for targeted NP discovery and drug development. By combining traditional wisdom with modern scientific advancements, this integrated approach paves the way for novel therapeutic discoveries and the sustainable utilisation of medicinal plants. Full article

Genomic selection plays a crucial role in breeding programs designed to improve quantitative traits, particularly considering the limitations of traditional methods in terms of accuracy and efficiency. Through the integration of genomic data, breeders are able to obtain more accurate predictions of breeding values. In this study, we proposed and evaluated four deep learning architectures—CNN-LSTM, CNN-ResNet, LSTM-ResNet, and CNN-ResNet-LSTM—that are specifically designed for genomic prediction in crops. After conducting a comprehensive evaluation across multiple datasets, including those for wheat, corn, and rice, the LSTM-ResNet model exhibited superior performance by achieving the highest prediction accuracy in 10 out of 18 traits across four datasets. Additionally, the CNN-ResNet-LSTM model demonstrated notable results, showcasing the best predictive performance for four traits. These findings underscore the efficacy of hybrid models in identifying complex patterns, as they integrate skip connections to mitigate the vanishing gradient problem and enable the extraction of hierarchical features while elucidating intricate relationships among genetic markers. Our analysis of SNP sampling indicated that maintaining SNP counts within the range of 1000 to the full set significantly influences prediction efficiency. Furthermore, we conducted a comprehensive comparative analysis of predictive performance among random selection, marker-assisted selection, and genomic selection utilizing wheat datasets. Collectively, these results provide significant insights into crop genetics, enhancing breeding predictions and advancing global food security and sustainability. Full article

Hemp (Cannabis sativa L.) is a versatile crop that can be processed to obtain different products with multiple applications. Its seeds are a well-documented ancient source of proteins, fibers and fats, all of which possess high nutritional value. Additionally, metabolites such as flavones and phenols are present in the seeds, contributing to their antioxidant properties. Due to hemp seeds’ distinctive nutritional profile, the interest in exploring the potential use in food and nutraceuticals is growing, and they can be considered an interesting and promising alternative resource for human and animal feeding. Omics studies on hemp seeds and their by-products are also being developed, and they contribute to improving our knowledge about the genome, transcriptome, proteome, metabolome/lipidome, and ionome of these sustainable food resources. This review illustrates the main nutrients and bioactive compounds of hemp seeds and explores the most relevant omics techniques and investigations related to them. It also addresses the various products derived from processing the whole seed, such as oil, dehulled seeds, hulls, flour, cakes, meals, and proteins. Moreover, this work discusses research aimed at elucidating the molecular mechanisms underlying their protein, lipid, fiber, and metabolic profile. The advantages of using omics and multi-omics approaches to highlight the nutritional values of hemp seed by-products are also discussed. In our opinion, this work represents an excellent starting point for researchers interested in studying hemp seeds as source of nutrients and bioactive compounds from a multi-level molecular perspective. Full article

Cyanobacteria-derived peptides represent a promising class of anticancer agents due to their structural diversity and potent bioactivity. They exert cytotoxic effects through mechanisms including microtubule disruption, histone deacetylase inhibition, and apoptosis induction. Several peptides—most notably the dolastatin-derived auristatins—have achieved clinical success as cytotoxic payloads in antibody–drug conjugates (ADCs). However, challenges such as limited tumor selectivity, systemic toxicity, and production scalability remain barriers to broader application. Recent advances in targeted delivery technologies, combination therapy strategies, synthetic biology, and genome mining offer promising solutions. Emerging data from preclinical and clinical studies highlight their therapeutic potential, particularly in treatment-resistant cancers. In this review, we (i) summarize key cyanobacterial peptides and their molecular mechanisms of action, (ii) examine progress toward clinical translation, and (iii) explore biotechnological approaches enabling sustainable production and structural diversification. We also discuss future directions for enhancing specificity and the therapeutic index to fully exploit the potential of these marine-derived peptides in oncology. Full article

To play a role effectively, biocontrol fungi must fight against plant immune response and establish a symbiotic interaction with their host. After successfully colonizing the host plant, the biocontrol fungi may deliver beneficial effects related to plant health and resistance against phytopathogens. These fungi use a variety of tactics to bypass the host immune response, including the production of effector proteins, miRNA interference, manipulation of host defense mechanisms, and others. In this review article, we discussed these strategies of biocontrol fungi based on recent findings. These methods enable the fungi to escape the plant’s intrinsic immunity and finely adjust the plant’s defense signaling cascades. Additionally, we discussed the importance of the physical barrier in the form of host cell walls and elucidated how biocontrol fungi use a combination of mechanical and enzymatic tactics to overcome this obstacle. Given the evolving comprehensions from molecular biology, genomics, and ecology, this review article highlights the prospective for a holistic, interdisciplinary approach to improve our understanding of the biocontrol mechanism. Full article

A histological evaluation remains the cornerstone of diagnosing highly malignant osteosarcoma, having demonstrated its efficacy and reliability over several decades. However, despite these advancements, misdiagnoses with severe consequences, including inadequate surgical procedures, continue to occur. Consequently, there is a pressing need to further enhance diagnostic security. Adjunct immunohistochemical approaches have demonstrated significant effectiveness in regard to cancer diagnostics, generally. However, their utility for identifying highly malignant osteosarcoma is limited. Molecular genetic findings have significantly improved the diagnosis of Ewing’s sarcoma by identifying specific translocations and have been used to detect specific IDH gene mutations in chondrosarcoma. Nevertheless, molecular genetic alterations in highly malignant osteosarcoma exhibit a high degree of complexity, thereby limiting their diagnostic utility. Given that only 1–2% of the human genome comprises protein-coding sequences, the growing number of non-coding regulatory RNAs, which are increasingly being elucidated, has garnered substantial attention in the field of clinical cancer diagnostics. Over the past several years, patterns of altered non-coding RNA expression have been identified that facilitate the distinction between benign and malignant tumors in various organs. In the field of bone tumors, the experience of this approach has been limited thus far. The divergent expression of microRNAs has demonstrated utility for differentiating osteosarcoma from osteoblastoma and discriminating between osteosarcoma and giant-cell tumors of bone and fibrous dysplasia. However, the application of non-coding RNA expression patterns for the differential diagnosis of osteosarcoma is still in its preliminary stages. This review provides an overview of the current status of non-coding RNAs in osteosarcoma diagnostics, in conjunction with a histological evaluation. The potential of this approach is discussed comprehensively. Full article

Background: Geranylgeranyl pyrophosphate synthase (GGPS) is a pivotal enzyme in terpene biosynthesis, influencing the production of carotenoids, chlorophylls, and diverse phytohormones. This study aimed to identify and characterize the StGGPS gene family in potato (Solanum tuberosum) to elucidate its involvement in carotenoid synthesis and responses to abiotic stresses. Methods: Employing bioinformatics approaches, including HMMER, SMART, and Pfam, we conducted a genome-wide identification of StGGPS genes. Subsequent phylogenetic analysis, gene structure characterization, conserved motif detection, and synteny analysis were performed to investigate evolutionary relationships within the family. The expression patterns of StGGPS genes were then analyzed using RNA-seq data and quantitative real-time PCR (qRT-PCR) in potato tubers exhibiting different pigmentation and under drought and salt stress conditions. Results: Eleven StGGPS genes were identified, unevenly distributed across seven chromosomes, and classified into three subfamilies based on phylogenetic and structural analyses. Synteny analysis revealed one intra-genomic duplicate pair (StGGPS1/StGGPS4) and conserved orthologs with other Solanaceae species. Promoter analysis identified cis-elements related to light response and abiotic stress (e.g., ABRE and CGTCA-motif). Expression data showed differential regulation of StGGPS genes in colored tubers, with yellow and red tubers exhibiting higher expression of carotenoid-related genes. Under drought stress, StGGPS10 was significantly upregulated (5.2-fold, p < 0.001), while StGGPS6 showed salt-responsive induction (3.8-fold, p < 0.001), linking them to ABA signaling and cytoskeletal dynamics, respectively. Conclusions: This study provides a comprehensive overview of the StGGPS gene family, highlighting their roles in carotenoid biosynthesis and abiotic stress responses. The stress-specific expression patterns of StGGPS10 and StGGPS6 offer potential targets for genetic improvement of potato stress resilience. Full article

Next-generation sequencing (NGS) has been well applied to assess genetic abnormalities in various biological samples to investigate disease mechanisms. With the advent of high-throughput and automatic testing platforms, NGS can identify radiation-sensitive and dose-responsive biomarkers, contributing to triage patients and determining risk groups for treatment in a nuclear emergency. While bulk NGS provides a snapshot of the average gene expression or genomic changes within a group of cells after the radiation, it cannot provide information on individual cells within the population. On the other hand, single-cell sequencing involves isolating individual cells and sequencing the genetic material from each cell separately. This approach allows for the identification of gene expression and genomic changes in individual cells, providing a high-resolution view of cellular diversity and heterogeneity within a sample. Single-cell sequencing is particularly useful to identify cell-specific features of dose-response and organ-response genes. While single-cell RNA sequencing (scRNA-seq) technology is still emerging in radiation research, it holds significant promise for identifying biomarkers related to radiation exposure and tailoring post-radiation medical care. This review aims to focus on current methods of radiation dosimetry and recently identified biomarkers associated with radiation exposure. Additionally, it addresses the development of NGS techniques in the context of radiation situations, such as cancer treatment and emergency events, with a particular emphasis on single-cell sequencing technology. Full article

Polyamines play a pivotal role in regulating the growth and metabolic adaptation of microalgae, yet their integrative regulatory roles remain underexplored. This review advances a comprehensive perspective of microalgae growth, integrating polyamine dynamics, amino acid metabolism, and redox balance. Polyamines (putrescine, spermidine, and spermine) biology in microalgae, particularly Chlamydomonas reinhardtii, is reviewed, exploring their critical function in modulating cell cycle progression, enzymatic activity, and stress responses through nucleic acid stabilization, protein synthesis regulation, and post-translational modifications. This review explores how the exogenous supplementation of polyamines modifies their intracellular dynamics, affecting growth phases and metabolic transitions, highlighting the complex regulation of internal pools of these molecules. Comparative analyses with Chlorella ohadii and Scenedesmus obliquus indicated species-specific responses to polyamine fluctuations, linking putrescine and spermine levels to important tunable metabolic shifts and fast growth phenotypes in phototrophic conditions. The integration of multi-omic approaches and computational modeling has already provided novel insights into polyamine-mediated growth regulation, highlighting their potential in optimizing microalgae biomass production for biotechnological applications. In addition, genomic-based modeling approaches have revealed target genes and cellular compartments as bottlenecks for the enhancement of microalgae growth, including mitochondria and transporters. System-based analyses have evidenced the overlap of the polyamines biosynthetic pathway with amino acids (especially arginine) metabolism and Nitric Oxide (NO) generation. Further association of the H₂O₂ production with polyamines metabolism reveals novel insights into microalgae growth, combining the role of the H₂O₂/NO rate regulation with the appropriate balance of the mitochondria and chloroplast functionality. System-level analysis of cell growth metabolism would, therefore, be beneficial to the understanding of the regulatory networks governing this phenotype, fostering metabolic engineering strategies to enhance growth, stress resilience, and lipid accumulation in microalgae. This review consolidates current knowledge and proposes future research directions to unravel the complex interplay of polyamines in microalgal physiology, opening new paths for the optimization of biomass production and biotechnological applications. Full article