Search Results (491)

In the context of advancing sustainable energy solutions, this paper provides a detailed modelling study of the process integration of biomass gasification to produce syngas and subsequent methanation for methane production. The process is assumed to take place in a circulating fluidised bed and three adiabatic fixed-bed reactors. To address the low H₂/CO ratio of syngas produced from biomass gasification using air, three pre-methanation scenarios were evaluated: water gas shift reaction (scenario 1), H₂ addition through Power-to-Gas (scenario 2), and splitting syngas into pure H₂ and CO and then recombining them in a 3:1 ratio (scenario 3). The findings reveal that each scenario presents a unique balance of efficiency, decarbonisation potential, and technological integration. Scenario 2 achieves the highest overall efficiency at 62%, highlighting the importance of integrating renewable electricity into the methane industry. Scenario 1, which incorporates WGS and CO₂ capture, offers an environmentally friendly solution with an overall efficiency of 59%. In contrast, Scenario 3, involving H₂/CO separation and recombination, achieves only 44.4% efficiency due to energy losses during separation, despite its operational simplicity. Methane yields were highest in Scenario 1, while Scenario 2 offers the most significant potential for integration with decarbonised power systems. The model was validated using published data and feedstock characteristics from experimental work and industrial projects. The results showed good agreement and supported the accuracy of the simulation in reflecting realistic biomass processing for methane production. Full article

In this study, we performed whole-genome resequencing (WGS) to investigate genomic variation and functional divergence among four wild Cymbidium species—C. ensifolium, C. sinense, C. kanran, and C. floribundum—collected from Fujian Province, China. A total of 350.58 Gbp of high-quality sequencing data was obtained from 13 samples, enabling comprehensive identification of SNPs and InDels. Genomic variants were unevenly distributed, with lower variation in gene-rich regions and higher levels in non-coding areas. Circos plots and variant density heatmaps revealed significant regional differences across chromosomes, with longer chromosomes exhibiting greater variant enrichment in 1 Mb windows. C. floribundum harbored the highest number of nonsynonymous SNPs and InDel-associated genes, whereas C. sinense and C. kanran had fewer mutations. KEGG pathway enrichment analysis revealed species-specific functional divergence, particularly in metabolism, stress response, and secondary metabolite biosynthesis. Population structure analysis and principal component analysis (PCA) indicated genetic differentiation among these species Notably, C. kanran exhibited high within-population genetic diversity. These findings provide essential genomic resources for the conservation and functional studies of wild Cymbidium species in subtropical China. Full article

Background: Structural variants (SVs) play a significant role in gene function and are implicated in numerous human diseases. With advances in sequencing technologies, identifying SVs through whole-genome sequencing (WGS) has become a key area of research. However, variability in SV detection persists due to the wide range of available tools and the absence of standardized methodologies. Methods: We assessed the accuracy of SV detection across various short-read (srWGS) and long-read (lrWGS) sequencing technologies—including Illumina short reads, PacBio long reads, and Oxford Nanopore Technologies (ONT) long reads—using deletion calls from the HG002 benchmark dataset. We examined how variables such as variant calling algorithms, reference genome choice, alignment strategies, and sequencing coverage influence SV detection performance. Results: DRAGEN v4.2 delivered the highest accuracy among ten srWGS callers tested. Notably, leveraging a graph-based multigenome reference improved SV calling in complex genomic regions. Moreover, we proved that combining minimap2 with Manta achieved performance comparable to DRAGEN for srWGS. For PacBio lrWGS data, Sniffles2 outperformed the other two tested tools. For ONT lrWGS, alignment with minimap2—among four aligners tested—consistently led to the best results. At up to 10× coverage, Duet achieved the highest accuracy, while at higher coverages, Dysgu yielded the best results. Conclusions: These results show for the first time that alignment software choice significantly impacts SV calling from srWGS, with results comparable to commercial solutions. For lrWGS, the performance depends on the technology and coverage. Full article

Background/Objectives: Male infertility is a major health concern with a complex etiopathology, yet a substantial proportion of cases remain idiopathic. Mitochondrial dysfunction and non-coding RNA (ncRNA) deregulation have both been implicated in impaired spermatogenesis, but their interplay remains poorly understood. This study aimed to identify infertility-specific variants in ncRNAs that affect mitochondrial dynamics and homeostasis and to explore their roles. Methods: Whole-genome sequencing (WGS) was performed on genomic DNA samples from teratozoospermic, asthenozoospermic, oligozoospermic, and normozoospermic men. Variants uniquely present in infertile individuals and mapped to ncRNAs that affect mitochondrial dynamics were selected and prioritized using bioinformatics tools. An independent transcriptomic validation was conducted using RNA-sequencing data from testicular biopsies of men with non-obstructive azoospermia (NOA) to determine whether the ncRNAs harboring WGS-derived variants were transcriptionally altered. Results: We identified several infertility-specific variants located in lncRNAs known to interact with mitochondrial regulators, including GAS5, HOTAIR, PVT1, MEG3, and CDKN2B-AS1. Transcriptomic analysis confirmed significant deregulation of these lncRNAs in azoospermic testicular samples. Bioinformatic analysis also implicated the disruption of lncRNA–miRNA–mitochondria networks, potentially contributing to mitochondrial membrane potential loss, elevated reactive oxygen species (ROS) production, impaired mitophagy, and germ cell apoptosis. Conclusions: Our integrative genomic and transcriptomic analysis highlights lncRNA–mitochondrial gene interactions as a novel regulatory layer in male infertility, while the identified lncRNAs hold promise as biomarkers and therapeutic targets. However, future functional studies are warranted to elucidate their mechanistic roles and potential for clinical translation in reproductive medicine. Full article

Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple antibiotics. Methods: We conducted a point prevalence survey (PPS) to assess the prevalence of VRE and VVE colonization in hospitalized patients. Rectal swabs were collected from 160 patients and analyzed using molecular assays (MAs) and culture. Whole-genome sequencing (WGS) and core-genome multilocus sequence typing (cgMLST) were performed to identify the genetic diversity. Results: Of the 160 rectal swabs collected, 54 (33.7%) tested positive for the vanA and/or vanB genes. Culture-based methods identified 47 positive samples (29.3%); of these, 44 isolates were identified as E. faecium and 3 as E. faecalis. Based on the resistance profiles, 35 isolates (74.5%) were classified as VRE, while 12 (25.5%) were classified as VVE. WGS and cgMLST analyses identified seven clusters of E. faecium, with sequence type (ST) 80 being the most prevalent. Various resistance genes and virulence factors were identified, and this study also highlighted intra- and inter-ward transmission of VRE strains. Conclusions: Our findings underscore the potential for virulence and resistance of both the VRE and VVE strains, and they highlight the importance of effective infection control measures to prevent their spread. VVE in particular should be carefully monitored as they often escape detection. Integrating molecular data with clinical information will hopefully enhance our ability to predict and prevent future VRE infections. Full article

Background: Salmonella is a bacterium that causes foodborne infections. This study characterized two strains isolated from cheese and beef in Brazil using whole-genome sequencing (WGS). Objectives: We evaluated their antimicrobial resistance profiles, virulence factors, plasmid content, serotypes and phylogenetic relationships. Methods: DNA was extracted and sequenced on the NovaSeq 6000 platform; the pangenome was assembled using the Roary tool; and the phylogenetic tree was constructed via IQ-TREE. Results and Discussion: For contextualization and comparison, 3493 Salmonella genomes of Brazilian origin from NCBI were analyzed. In our isolates, both strains carried the aac(6′)-Iaa_1 gene, while only Schwarzengrund harbored the qnrB19_1 gene and the Col440I_1 plasmid. Cerro presented the islands SPI-1, SPI-2, SPI-3, SPI-4, SPI-5 and SPI-9, while Schwarzengrund also possessed SPI-13 and SPI-14. Upon comparison with other Brazilian genomes, we observed that Cerro and Schwarzengrund represented only 0.40% and 2.03% of the national database, respectively. Furthermore, they revealed that Schwarzengrund presented higher levels of antimicrobial resistance, a finding supported by the higher frequency of plasmids in this serovar. Furthermore, national data corroborated our findings that SPI-13 and SPI-14 were absent in Cerro. A virulence analysis revealed distinct profiles: the cdtB and pltABC genes were present in the Schwarzengrund isolates, while the sseK and tldE1 family genes were exclusive to Cerro. The results indicated that the sequenced strains have pathogenic potential but exhibit low levels of antimicrobial resistance compared to national data. The greater diversity of SPIs in Schwarzengrund explains their prevalence and higher virulence potential. Conclusions: Finally, the serovars exhibit distinct virulence profiles, which results in different clinical outcomes. Full article

Genomic prediction has emerged as a powerful tool in aquaculture breeding, but its effectiveness depends on the careful selection of informative single nucleotide polymorphisms (SNPs) and the application of appropriate prediction models. This study aimed to enhance genomic prediction accuracy in Russian sturgeon (Acipenser gueldenstaedtii) by optimizing SNP selection strategies and exploring the performance of linear and machine learning models. Three economically important traits—caviar yield, caviar color, and body weight—were selected due to their direct relevance to breeding goals and market value. Whole-genome sequencing (WGS) data were obtained from 971 individuals with an average sequencing depth of 13.52×. To reduce marker density and eliminate redundancy, three SNP selection strategies were applied: (1) genome-wide association study (GWAS)-based prioritization to select trait-associated SNPs; (2) linkage disequilibrium (LD) pruning to retain independent markers; and (3) random sampling as a control. Genomic prediction was conducted using both linear (e.g., GBLUP) and machine learning models (e.g., random forest) across varying SNP densities (1 K to 50 K). Results showed that GWAS-based SNP selection consistently outperformed other strategies, especially at moderate densities (≥10 K), improving prediction accuracy by up to 3.4% compared to the full WGS dataset. LD-based selection at higher densities (30 K and 50 K) achieved comparable performance to full WGS. Notably, machine learning models, particularly random forest, exceeded the performance of linear models, yielding an additional 2.0% increase in accuracy when combined with GWAS-selected SNPs. In conclusion, integrating WGS data with GWAS-informed SNP selection and advanced machine learning models offers a promising framework for improving genomic prediction in sturgeon and holds promise for broader applications in aquaculture breeding programs. Full article

A metasurface capable of flexibly manipulating electromagnetic waves to realize holograms presents significant potential in millimeter-wave imaging systems and data storage domains. In this study, full-space three-dimensional holograms are realized from a reflection–transmission integrated reconfigurable metasurface, which can achieve nearly 360° phase coverage in reflection space and 180° phase coverage in transmission space. By adjusting the voltage applied to the constituting electronically tunable meta-atoms of the metasurface, an octahedron hologram constituted by three hologram images in different focal planes is generated in the reflection space at 6.25 GHz. Moreover, a diamond hologram, also composed of three hologram images in different focal planes, is achieved in the transmission space at 6.75 GHz. Both the numerical simulation and experimental measurement are performed to validate the full-space holograms implemented by the modified weighted Gerchberg–Saxton (WGS) algorithm with specific phase distribution in different imaging planes. The obtained results pave the way for a wide range of new applications, such as next-generation three-dimensional displays for immersive viewing experiences, high-capacity optical communication systems with enhanced data encoding capabilities, and ultra-secure anti-counterfeiting solutions that are extremely difficult to replicate. Full article

This study evaluates the performance of nine satellite and model-based daily surface soil moisture products, encompassing sixteen algorithm versions across mainland China to support sustainable land and water management. The assessment utilizes 2018 in situ measurements from over 2400 stations in China’s Automatic Soil Moisture Monitoring Network. All products were standardized to a 0.25° × 0.25° grid in the WGS-84 coordinate system through reprojection and resampling for consistent comparison. Daily averaged station observations were matched to product pixels using a 10 km radius buffer, with the mean station value as the reference for each time series after rigorous quality control. Results reveal distinct performance rankings, with SMAP-based products, particularly the SMAP_IB descending orbit variant, achieving the lowest unbiased root mean square deviation (ubRMSD) and highest correlation with in situ data. Blended products like ESA CCI and NOAA SMOPS, alongside reanalysis datasets such as ERA5 and MERRA2, outperformed SMOS and China’s FY3 products. The SoMo.ml product showed the broadest spatial coverage and strong temporal consistency, while FY3-based products showed limitations in spatial reliability and seasonal dynamics capture. These findings provide critical insights for selecting appropriate soil moisture datasets to enhance sustainable agricultural practices, optimize water resource allocation, monitor ecosystem resilience, and support climate adaptation strategies, therefore advancing sustainable development across diverse geographical regions in China. Full article

This case report describes a novel intronic mutation, CYP21A2:c.738+75C>T (rs1463196531), identified in a 4-year-old male with congenital adrenal insufficiency, and expands the known mutation spectrum associated with this condition. The patient, born full-term to unrelated parents, presented with adrenal failure within the first month of life, characterized by acute adrenal crisis symptoms such as vomiting, dehydration, weight loss, hypotension, and electrolyte imbalances. Hormonal evaluations confirmed primary adrenocortical insufficiency, necessitating ongoing hydrocortisone and fludrocortisone therapy. Using family trio-based amplicon sequencing of the CYP21A2 gene, we identified compound heterozygosity consisting of a full gene deletion and a novel pathogenic intronic mutation. Additionally, analysis of WGS data was performed to rule out pathogenic variants in genes that might lead to a similar phenotype, thereby eliminating the possibility of other genes contributing to the proband’s disease. This case demonstrates the potential of using amplicon sequencing in molecular genetic diagnostic testing to detect rare intronic variants in the CYP21A2 gene in cases of early-onset adrenal failure. It also contributes to a better understanding of the genetic basis of congenital adrenal hyperplasia (CAH), which remains a significant autosomal recessive disorder affecting cortisol and aldosterone production, with an incidence of 1 in 10,000 to 1 in 15,000 globally. Full article

Background and Objectives: Infections caused by non-tuberculous mycobacteria (NTM), including Mycobacterium abscessus complex (MABc), are increasing globally and are notoriously difficult to treat due to the intrinsic resistance of these bacteria to many common antibiotics. The aims of this study were to demonstrate the in vitro activity of imipenem/relebactam against MABc clinical isolates and to determine any in vitro synergism between imipenem/relebactam and other antimicrobials. Methods: A nationwide collection of 175 MABc clinical respiratory isolates obtained from 24 hospitals in Spain (August 2022–April 2023) was studied. Fifteen different antimicrobial agents were comprised, including imipenem/relebactam. MICs were determined according to CLSI criteria, and the synergism studies were performed with the selected clinical isolates. Results: Of the 175 isolates obtained, 110 were identified as M. abscessus subsp. abscessus (62.9%), 51 as M. abscessus subsp. massiliense (29.1%), and 14 as M. abscessus subsp. bolleti (8%). The antibiotics yielding the highest susceptibility rates were tigecycline, eravacycline, and omadacycline (100%); followed by imipenem/relebactam and clofazimine (97.6%); and finally amikacin (94.6%). Only four isolates were resistant to imipenem/relebactam, three of which were further characterized by WGS, revealing MABc mutations in Bla_Mab as well as D,D- and L,D-transpeptidades and mspA porin, which may play an important role in reduced susceptibility to imipenem/relebactam, even though none were previously described or associated with resistance to β-lactams. Conclusions: Our data demonstrate that relebactam improved the anti-MABc activity of imipenem, representing a β-lactam for the treatment of MABc infections. Furthermore, imipenem/relebactam demonstrated in vitro synergism with other anti-MABc treatments, thus supporting its use as part of dual regimens. Full article

Background: Enterobacterales are among the most frequent causes of healthcare-associated infections and are increasingly affected by antimicrobial resistance. Antibiotic use disrupts the gut microbiota, facilitating colonization by multidrug-resistant organisms, including carbapenemase-producing Enterobacterales (CPE). While animal studies have suggested that certain antibiotic classes may increase the risk of CPE acquisition, clinical data identifying which classes are most implicated remain limited. Methods: We conducted a single-center, retrospective case-control study (2021–2024) comparing antibiotic prescriptions in patients who acquired CPE with those in controls hospitalized in the same unit and during the same risk period but who did not acquire CPE. The objective of this study was to identify which antibiotic classes or pharmacological properties are associated with the acquisition of carbapenemase-producing Enterobacterales (CPE) in hospitalized patients. Results: During the study period, 35 cases and 70 controls were included. Most cases acquired NDM-type metalloenzymes. Before the risk period, 55 patients had received antibiotic therapy. Univariate analysis identified an association between CPE acquisition and the prescription of fluoroquinolones and antibiotics excreted in bile. During the risk period, only metronidazole prescription was significantly associated with CPE acquisition. Our study has several limitations, including the small sample size, the single-center retrospective design, and the lack of molecular typing (e.g., WGS) to confirm potential clonal transmission. Conclusions: In this preliminary study, metronidazole use was associated with an increased risk of CPE acquisition during risk periods. However, these results should be interpreted cautiously and need to be confirmed in larger, multicenter studies. The high exposure of patients to multiple antibiotic classes highlights the importance of strict antibiotic stewardship policies in the current era of global CPE dissemination. Full article

The purpose of this study was to investigate the taxonomic and phylogenomic placement of the proposed genus ‘Solwaraspora’ within the context of other marine genera using a dual-omics approach. Initially, we isolated bacteria from marine tunicates, squirts, and sponges, which were morphologically similar to an emerging genus (identified as ‘Micromonospora_E’ by the GTDB-tk2 database using whole genome sequence data) by colony shape, size, and clustering pattern, but only found five strains in our dataset belonging to this distinction. Due to the minimally explored nature of this genus, we sought to identify more bacterial strains with similar morphology to Micromonospora‘Micromonospora_E’ by whole genome sequencing (WGS). Within our collection, we noted 35 strains that met this criterion and extracted genomic information to perform WGS on these strains. With this information, we studied taxonomic and phylogenomic relationships among these organisms. Using the data gathered from WGS, we were able to identify an additional five strains labeled by the GTDB-tk2 database as Micromonospora‘Micromonospora_E’, as well as construct phylogenomic trees to examine the evolutionary relationships between these strains. ANI values were calculated between strains from our dataset and type strains of Micromonospora and Plantactinospora as well as against an outgroup Streptomyces strain. No type strains are available for ‘Solwaraspora’. Using MALDI-TOF MS, we positively identified ‘Solwaraspora’, which was supported by the phylogenomic tree showing Micromonospora’Micromonospora_E’ (‘Solwaraspora’) in a distinct clade from Plantactinospora and Micromonospora. Additionally, we discovered gene cluster families (GCFs) in alignment with genera, as well as a large representation of biosynthetic gene clusters (BGCs) coming from the ‘Solwaraspora’ strains. These findings suggest significant potential to discover novel chemistry from ‘Solwaraspora’, adding to the importance of investigating this new genus of bacteria. Full article

The aim of this study was to examine the genetic characteristics that could be associated with the virulence characteristics of Escherichia coli collected from clinical samples. A collection of 100 non-repetitive E. coli isolates was analyzed. All isolates were typed by MLST. String production, biofilm formation and serum resistance were examined for all isolates. Twenty E. coli isolates were completely sequenced Illumina platform. The results showed that the majority of E. coli isolates (87%) produced significant levels of biofilm, while none of the isolates were positive for string test and resistance to serum. Additionally, the presence of CRISPR/Cas systems (type I-E or I-F) was found in 18% of the isolates. Analysis of WGS data found that all sequenced isolates harbored a variety of virulence genes that could be implicated in adherence, invasion, iron uptake. Also, WGS data confirmed the presence of a wide variety of resistance genes, including ESBL- and carbapenemase-encoding genes. In conclusion, an important percentage (87%) of the E. coli isolates had a significant ability to form biofilm. Biofilms, due to their heterogeneous nature and ability to make microorganisms tolerant to multiple antimicrobials, complicate treatment strategies. Thus, in combination with the presence of multidrug resistance, expression of virulence factors could challenge antimicrobial therapy of infections caused by such bacteria. Full article

For PEM fuel cell operation, high-purity hydrogen gas containing only trace amounts of carbon monoxide is a prerequisite. The water–gas shift reaction (WGSR) is an industrially applied mature operation mode to convert CO with H₂O into CO₂ (making it easy to separate, if necessary) and H₂. Since the WGS reaction is an exothermic equilibrium reaction, low temperatures (below 200 °C) lead to full CO conversion. Thus, highly active ultra-low-temperature WGSR catalysts have to be applied. A homogeneous Ru SILP (supported ionic liquid phase) catalyst based on the precursor complex [Ru(CO)₃Cl₂]₂ has been identified to operate at such low temperature levels. However, in a hydrogen rich atmosphere, transition metal complexes are prone to form nanoparticles (NPs) when dissolved in ionic liquids (ILs). In this article, the behavior of an anionic SILP WGSR catalyst, i.e., [Ru(CO)₃Cl₃]⁻ dissolved in [BMMIM]Cl, in an H₂-rich CO environment is described. The data reveal that during the WGSR, Ru nanoparticles form in the catalyst when very low CO concentrations are reached. The Ru NPs formation has been confirmed by transmission electron microscopy imaging and X-ray diffraction (XRD). Full article