Trimmomatic: a flexible trimmer for Illumina sequence data

Identification of FLYWCH1 as a regulator of platinum-resistance in epithelial ovarian cancer

Platinum-based combination chemotherapy remains the backbone of first-line treatment for patients with advanced epithelial ovarian cancer (EOC). While most patients initially respond well to the treatment, patients with relapse ultimately develop platinum resistance. This study identified FLYWCH-type zinc finger-containing protein 1 (FLYWCH1) as an important regulator in the resistance development process. We showed that the loss of FLYWCH1 promotes platinum resistance in EOC cells, and the low FLYWCH1 expression is correlated with poor prognosis of EOC patients. In platinum-sensitive cells, FLYWCH1 colocalizes with H3K9me3, but this association is significantly reduced when cells acquire resistance. The suppression of FLYWCH1 induces gene expression changes resulting in the deregulation of pathways associated with resistance. In line with its connection to H3K9me3, FLYWCH1 induces gene silencing in a synthetic reporter assay and the suppression of FLYWCH1 alters H3K9me3 at promoter regions and repeat elements. The loss of FLYWCH1 leads to the derepression of LTR and Alu repeats, thereby increasing transcriptional plasticity and driving the resistance development process. Our data highlight the importance of FLYWCH1 in chromatin biology and acquisition of platinum resistance through transcriptional plasticity and propose FLYWCH1 as a potential biomarker for predicting treatment responses in EOC patients.

Novel island species elucidate a species complex of Neotropical crocodiles

The evolutionary history of Neotropical crocodiles has remained elusive. They inhabit a broad geographic range with populations spanning from coastal, inland, and insular locations. Using a selection of natural insular, coastal, and one inland population of C. acutus, coastal C. moreletii, and the single surviving population of C. rhombifer, we discovered a remarkable genetic diversity for the group. Moreover, geometric morphometric results of skull shapes shows that these crocodylus species span a morphological cline. We recovered a high genetic differentiation between C. moreletii, C. rhombifer, and five clusters of C. acutus. The genetic and geographic differences among the C. acutus clusters were used to suggest these may be a species complex. Several ecological, morphological and genetics traits are identified in the well-studied populations from Banco Chinchorro and Cozumel islands off the Mexican Yucatan Peninsula to support discrete species designations for these populations. This work suggests the presence of rapid, recent evolution of several cryptic Crocodylus species throughout the Neotropics.

Nanoscale piezoelectric patches preserve electrical integrity of infarcted hearts

Ischemic heart disease is the leading cause of death worldwide. Several approaches have been explored to restore cardiac function, however few investigated new strategies to improve electrical functional recovery. Herein, we have investigated the impact of piezoelectric patches (Piezo patches), capable of generating electric charges upon mechanical deformation, on rat cardiac slices, healthy and ischemic hearts (ex vivo), on infarcted mice (in vivo) and on healthy and infarcted pigs (in vivo). Piezo patches did not preclude cardiac slice contractility, while compared with electrically inert control patches. In addition, Piezo patches showed an adequate safety profile in a working heart model as no electrophysiologic alterations were detected in healthy hearts. Epicardial implantation of Piezo patches in acutely infarcted mice hearts significantly improved myocardial electrical integrity without disturbing systolic function. Moreover, Piezo patches partially prevented ischemia-related adverse cardiac remodeling, reducing left ventricular chamber dilatation and compensatory hypertrophy. Coherently, Piezo patch-implanted hearts revealed downregulation of genes associated with extracellular matrix remodeling. Importantly, in vivo implantation of Piezo patches in porcine hearts revealed to be electrically safe as no major effects in its electrophysiology were detected. Overall, the results presented here endorse Piezo patches as a promising therapeutic strategy to improve post-myocardial infarction structural and electrical remodeling.

Diverse effects of Bacillus sp. NYG5-emitted volatile organic compounds on plant growth, rhizosphere microbiome, and soil chemistry

Bacterial strains in the rhizosphere secrete volatile organic compounds (VOCs) that play critical roles in inter- and intra-kingdom signaling, influencing both microbe-microbe and microbe-plant interactions. In this study we evaluated the plant growth-promoting effects of VOCs emitted by Bacillus sp. NYG5 on Arabidopsis thaliana, Nicotiana tabacum, and Cucumis sativus, focusing on VOC-induced alterations in plant metabolic pathways, rhizosphere microbial communities, and soil chemical properties. NYG5 VOCs enhanced plant biomass across all tested species and induced significant shifts in rhizosphere microbial community composition, specifically increasing relative abundance of Gammaproteobacteria and reducing Deltaproteobacteria (Linear discriminant analysis Effect Size, p < 0.05). Soil analysis revealed a considerable reduction in humic substance concentrations following VOCs exposure, as detected by fluorescent spectral analysis. Using SPME-GC-MS, several novel VOCs were identified, some of which directly promoted plant growth. Transcriptomic analysis of N. tabacum exposed to NYG5 VOCs demonstrated activation of pathways related to phenylpropanoid biosynthesis, sugar metabolism, and hormone signal transduction. Within the phenylpropanoid biosynthesis pathway, a significant upregulation (p adj = 1.16e-14) of caffeic acid 3-O-methyltransferase was observed, a key enzyme leading to lignin and suberin monomer biosynthesis. These results highlight the complex mechanisms through which bacterial VOCs influence plant growth, including metabolic modulation, rhizosphere microbiome restructuring, and soil chemical changes. Collectively, this study highlights the pivotal role of bacterial VOCs in shaping plant-microbe-soil interactions.

Exploring viral diversity in fermented vegetables through viral metagenomics

Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.

Characterization of a new lytic bacteriophage (vB_KpnM_KP1) targeting Klebsiella pneumoniae strains associated with nosocomial infections

A new bacteriophage, vB_KpnM_KP1, was identified and characterized, exhibiting a strong lytic effect on Klebsiella pneumoniae. Host range analysis revealed its effectiveness against 77.4% of clinical strains, achieving complete lysis of those associated with urinary tract infections (UTIs). Phage stability tests demonstrated that vB_KpnM_KP1 remained stable at neutral pH and across all tested temperatures. However, inactivation was observed at high ethanol concentrations and extreme pH levels. Transmission electron microscopy (TEM) analysis identified vB_KpnM_KP1 as a Myo-type phage with an icosahedral head and a contractile tail. Moreover, genome annotation of vB_KpnM_KP1 revealed a linear DNA genome of 174,802 bp, containing 307 open reading frames. Functional predictions suggest the presence of genes involved in DNA replication, transcription, morphogenesis, and cell lysis. Phylogenetic analysis classified vB_KpnM_KP1 within the Slopekvirus genus of the Straboviridae family, showing high sequence identity with phages that infect Enterobacter, Escherichia and Klebsiella species. These findings highlight the potential of phage vB_KpnM_KP1 as an alternative treatment for multidrug-resistant K. pneumoniae infections, particularly in UTIs, while offering valuable insights into its stability and genetic composition.

Krüppel-like factor 5 remodels lipid metabolism in exercised skeletal muscle

Regular physical activity induces a variety of health benefits, preventing and counteracting diseases caused by a sedentary lifestyle. However, the molecular underpinnings of skeletal muscle plasticity in exercise remain poorly understood. We identified a role of the Krüppel-Like Factor 5 (Klf5) in this process, in particular in the regulation of lipid homeostasis. Surprisingly, gain- and loss-of-function studies in muscle in vivo revealed seemingly opposite functions of Klf5 in the response to an acute exercise bout and chronic training, modulating lipid oxidation and synthesis, respectively. Thus, even though only transiently induced, the function of Klf5 is complex and fundamental for a normal long-term training response. These findings highlight the importance of this mediator of external stress response to adaptive remodeling of skeletal muscle tissue.

Phylogenetic Diversity and Geographic Distribution of Atlantic Salmon Calicivirus in Major Salmon Farming Regions

Salovirus is a genus within the family Caliciviridae, which contains a single member species, Salovirus nordlandense, also known as Atlantic salmon calicivirus (ASCV). While previous work has shown that ASCV can replicate in fish cell lines and establish systemic infection in vivo, its exact role in disease remains unclear and very little is known about its geographic distribution and evolution among Atlantic salmon. To expand the phylogenetic range of ASCV and better understand its potential role in disease, we screened publicly available transcriptomes for ASCV-like sequences. Notably, we detected ASCV in sequencing projects of Atlantic salmon (Salmo salar) (n = 40) and wild common whitefish (Coregonus lavaretus) (n = 1), across Chile, Scotland and Norway. Our phylogenetic analysis identified two viral species, which we provisionally name Salovirus nordlandense 1 and 2, each containing distinct genotypes. Both viral species were found in all three countries, with no clear geographic pattern, indicating that saloviruses have spread through the Atlantic salmon trade. It was notable that 88% of these transcriptomes were generated for the study of other pathogens, including infectious salmon anaemia virus, piscine myocarditis virus and Piscirickettsia salmonis, suggesting that saloviruses might be frequently associated with co-infections. Overall, this study indicates that viruses, like ASCV, can silently spread through aquacultural practices, potentially contributing to a variety of fish diseases.

Variant filters using segregation information improve mapping of nectar-production genes in sunflower (Helianthus annuus L.)

Accurate variant calling is critical for identifying the genetic basis of complex traits, yet filters used in variant detection may inadvertently exclude valuable genetic information. In this study, we compare common sequencing depth filters, used to eliminate error-prone variants associated with repetitive regions and technical issues, with a biologically relevant filtering approach that targets expected Mendelian segregation. The resulting variant sets were evaluated in the context of nectar volume quantitative trait loci (QTL) mapping in sunflower (Helianthus annuus L.). Our previous research failed to detect an interval containing a strong candidate gene for nectar production (HaCWINV2). We removed hard filters and implemented a chi-square goodness-of-fit test to retain variants that segregate according to expected genetic ratios. We demonstrate that biologically relevant filtering retains more significant QTL and candidate genes, including HaCWINV2, while removing variants due to technical errors more effectively, and accounted for 48.55% of nectar production phenotypic variation. In finding nine putative homologs of Arabidopsis genes with nectary function within QTL regions, we demonstrate that this filtering strategy has a higher power of true variant detection in QTL mapping than the commonly used variant depth filtering strategy. Future research will adapt the technique to multiple population contexts, such as genomic selection.

miRNA and piRNA differential expression profiles in Alzheimer's disease: A potential source of pathology and tool for diagnosis

Alzheimer's Disease (AD) is the most prevalent form of dementia and one of the leading causes of death in the United States, and despite our best efforts and recent advancements, a treatment that stops or substantially slows its progression has remained elusive. Small extracellular vesicles (sEVs), hold the potential to alleviate some of the common issues in the field by serving to better differentiate AD and non-AD individuals. These vesicles could provide insights into therapeutic targets, and potentially an avenue towards early detection. We compared the sEV cargo profiles of AD and non-AD brains (n = 6) and identified significant differences in both the micro RNA (miRNA) and Piwi-interacting RNA (piRNA) cargo through sEV isolation from temporal cortex tissue, followed by small RNA sequencing, and differential expression analysis. Differentially expressed miRNAs targeting systems relevant to AD included miR-206, miR-4516, miR-219a-5p, and miR-486-5p. Significant piRNAs included piR-6,565,525, piR-2,947,194, piR-7,181,973, and piR-7,326,987. These targets warrant further study for their potential role in the progression of AD pathology by dysregulating cellular activity; additionally, future large-scale studies of neuronal sEV miRNA profiles may facilitate the development of diagnostic tools which can aid in clinical trial design and recruitment. Longitudinal analysis of sEV data, perhaps accessible through plasma surveyance, will help determine at what point these miRNA and/or piRNA profiles begin to diverge between AD and non-AD individuals.

Molecular and genomic investigation unveils Pseudomonas putida as an emerging multidrug-resistant pathogen linked to bovine clinical mastitis

Pseudomonas putida is one of the emerging pathogens responsible causing mastitis in lactating animals. This study investigated the prevalence, antimicrobial resistance (AMR), genetic diversity and virulence factor genes (VFGs) to highlight the pathogenic potentials of P. putida strains isolated from milk, feces and farm soil of dairy cows diagnosed with clinical mastitis (CM). A total of 110 samples were collected and analyzed, revealing an overall prevalence of P. putida in dairy farms at 40.90 %, with specific prevalence rates of 42.22 % in milk, 26.67 % in feces, and 31.11 % in farm soil. In vitro antimicrobial assays demonstrated that 76.0 % P. putida isolates exhibited multidrug resistance (MDR, resistance to ≥ 3 antibiotics), particularly showing high resistance to oxacillin, ampicillin, nalidixic acid, and aztreonam. Conversely, P. putida isolates showed the highest susceptibility against imipenem. The genome analysis of three MDR P. putida strains 11CM-M1 (milk), 11CM-F1 (feces) and 11CM-S1 (farm soil), showed a close evolutionary relationship with different strains of Pseudomonas spp. isolated from bovine mastitis milk and feces samples, human stool, and samples sourced from hospital environment. The assembled genomes of three P. putida strains encoded nine antibiotic resistance genes (ARGs), 36 VFGs, and 367 metabolic subsystems, highlighting a complex functional profile and potential for pathogenicity. The detailed analysis of these ARGs and VFGs demonstrated that P. putida strains employ distinct mechanisms of resistance (e.g., efflux pumps), biofilm formation, and virulence factors, including adhesins, secreted toxins, and lipopolysaccharides, which contribute to their pathogenic potential. Given the lack of reports linking P. putida strains to bovine mastitis in Bangladesh, the increasing trend of AMR, along with the presence of significant ARGs and VFGs in the studied strains, underscores the need for more intensive research, including animal model experiment, to better elucidate the pathogenesis and inform treatment decisions for mastitis in dairy animals.

Elicitor Specific Mechanisms of Defence Priming in Oak Seedlings Against Powdery Mildew

Defence priming sensitises plant defences to enable a faster and/or stronger response to subsequent stress. Various chemicals can trigger priming; however, the response remains unexplored in oak. Here, we characterise salicylic acid (SA)-, jasmonic acid (JA)-, and β-aminobutyric acid (BABA)-induced priming of oak seedlings against the causal agent of powdery mildew (Erysiphe alphitoides, PM). Whilst JA had no effects, BABA and SA enhanced resistance by priming callose deposition and SA-dependent gene expression, respectively. Untargeted transcriptome and metabolome analyses revealed genes and metabolites uniquely primed by BABA, SA, and JA. Enrichment analyses demonstrated a limited number of pathways differentiating the three treatments or the resistance-inducing elicitors BABA and SA. However, a similar mode of action between BABA and JA was identified. Moreover, our analyses revealed a lack of crosstalk between SA and JA. Interestingly, priming by BABA was linked to alkaloid, lignan, phenylpropanoid, and indolitic compounds biosynthesis. Moreover, integration of the omics analyses revealed the role of ubiquitination and protein degradation in priming by BABA. Our results confirm the existence of chemical-induced priming in oak and has identified specific molecular markers associated with well-characterised elicitors.

Plourde M, Joly DL, Germain H. Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity

The different steps of alternative splicing (AS) in plants and its regulatory mechanisms have already been studied extensively. Its broader impact on cell identity, plant immunity-related genes, and their study as a whole remains to be investigated. Using transgenic plants, we sorted 11 different Arabidopsis thaliana cell types ranging from root to aerial organs using fluorescence-activated cell sorting. RNA-seq data were analyzed with vast-tools and enabled us to generate a high-resolution AS landscape across multiple cell types, all collected through the same experimental procedure. The analysis of cell type-specific gene expression and alternative splicing events highlights the importance of AS on transcription and AS regulation itself. AS is also shown to be tightly linked to cell identity. By using closely related cell types, we captured alternative splicing events involved in specific stages of plant development. The columella cells, among others, show intensified AS regulation and an interesting splicing profile, especially regarding immunity-related genes. Overall, our analysis brings a valuable tool in the study of cell type identity, plant immunity, and AS.

Incorporation of microgastropoda species provides novel insights into phylogeny of Trochoidea (Gastropoda: Vetigastropoda)

Trochoidea is the richest and most diverse group within Vetigastropoda, serving as one of the main focuses on studies of marine ecology and systematics. Both morphological and molecular studies have sought to resolve the phylogenetic framework of Trochoidea; however, the phylogenetic relationships among some lineages remain controversial. In order to explore the phylogenetic relationships within Trochoidea, we sequenced the mitochondrial genomes of 9 trochoids and analyzed them with data from 38 previously published mitochondrial genomes and 27 transcriptomic data representing 11 families within this group. The mitochondrial genomes of all Trochidae exhibited a consistent gene arrangement and showed conserved genome size and nucleotide composition; however, Colloniidae and Phasianellidae showed higher levels of gene order rearrangement. Furthermore, three-nucleotide insertions were observed in the cox1 gene of Colloniidae and nad4L gene of Phasianellidae, while three-nucleotide deletions were detected in nad4 gene of Trochidae. Both maximum likelihood and Bayesian inference analyses supported the monophyly of all families within the Trochoidea, except Tegulidae, and placed Liotiidae as sister to the rest of Trochoidea with poor to moderate support. Areneidae was recovered as the sister group to a clade including Phasianellidae and Colloniidae. These findings challenge the traditional classification of this family based on both morphological and molecular data. Our study provides new insights into the phylogeny of Trochoidea, especially with the incorporation of micromolluscs taxa, and highlight the significance of incorporating microgastropoda taxa into molecular phylogenetic reconstructions of gastropod subgroups.

Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from companion animals and human infections in Europe

In high-income countries, dogs and cats are often considered members of the family. Because of this proximity, it has been suggested that pets and humans might exchange bacterial species from their gut microbiota, with multidrug resistant bacteria being of particular concern. The aim of this study was to compare the genomes of third-generation cephalosporin-resistant (3GC-R) Escherichia coli responsible for human and pet infections in Europe. Whole-genome sequencing data from 3GC-R E. coli isolated from clinical samples of humans, dogs and cats, and published in eight European studies were re-analyzed using bioinformatics tools. The acquired genes responsible for 3GC-R were identified. The sequence type (ST) of all genomes were assessed by multilocus sequence typing. Alpha and beta diversities were measured within and between the two populations. We included genomes of 1327 3GC-R E. coli isolated from humans and animals with 109 (8.2 %) being responsible for infections in dogs and cat, and 1218 (91.8 %) responsible for human infections. Alpha diversity analysis suggested greater diversity within ST and 3GC-R genes in the animal population. Beta diversity analysis by principal coordinate analysis separated animal and human strains. ST131 was more abundant in human strains (43.4 %) than in animal strains (14.7 %) (p < 0.001). Six STs, including ST372, were identified almost exclusively in 3GC-R E. coli from animal origin. The bla CTX-M-15 gene was more frequent in humans (49.24 %) than in companion animals (17.9 %) (p < 0.001). The resistance genes bla CMY-2 (30.8 %) and bla CTX-M-1 (15.4 %) were more frequent in E. coli isolated from pets (p < 0.001). We found that populations of 3GC-R E. coli responsible for human and pet infections in Europe do not overlap. Although it cannot rule out occasional transmission of bacteria between pets and humans within a household, it suggests that dogs and cats are not a major source of human infection with this antibiotic-resistant pathogen.

Highly Pathogenic Avian Influenza Virus in Mammals: Lack of Detection in Cattle With Respiratory Tract Infections and Genetic Analysis of Sporadic Spillover Infections in Wild Mammals in Bavaria, Southern Germany, 2022-2023

BACKGROUND

In 2021, the H5N1 clade 2.3.4.4b Avian Influenza Viruses (AIVs) emerged on the American continent. At the same time, a further global spread took place. Infections have been reported in avian species as well as in over 50 mammalian species in 26 countries, and often result in severe disease with notable neurological pathology. Outbreaks in dairy cattle in the United States in 2024 illustrate viral transmission at a non-traditional interface and cross-species transmission. This development raises significant global concern regarding the virus's potential for wider spread. Given that H5N1 infections in birds reached record-high levels in Germany by late 2022, it is important to investigate whether Influenza A Virus (IAV) infections were also occurring in mammals sharing habitats with wild birds.

METHODS AND RESULTS

Selected wild and domestic mammal populations were monitored over a two-year period (from January 2022 to December 2023), which coincided with a major infection period in wild birds in Bavaria. Genomes of Highly Pathogenic Avian IAV H5N1 (clade 2.3.4.4b) were detected in red foxes but not in samples from ruminants such as red deer or domestic cattle. Analyses of viral whole genome sequences revealed several mutations associated with mammalian adaptation.

CONCLUSION

Our results indicate a high frequency of spillover events to red foxes at a time when there was a peak of H5N1 infections in wild birds in Bavaria. Phylogenetic analyses show no specifically close genetic relationship between viruses detected in mammalian predators within a geographic area. While direct fox-to-fox transmission has not yet been reported, the H5N1 clade 2.3.4.4b AIVs' ability to spread through non-traditional interfaces and to cross species barriers underlines the importance of continuous IAV surveillance in mammals and possibly including previously unknown host species.

A bioinspired microbial taste chip with artificial intelligence-enabled high selectivity and ultra-short response time

Real-time water pollution monitoring is crucial as global water pollution has become an urgent issue endangering the health of humanity. Microbial taste chips are promising for water pollution monitoring due to the advantages of short response time and real-time monitoring capability. However, although more than 200 journal research articles on microbial taste chips have been reported to date, sensor selectivity, which is the foremost critical parameter, remains an unsolved challenge even after utilizing gene-editing techniques. In addition, the response time is long and takes at least 3 min. Herein, we report a breakthrough to solve the selectivity challenge by a bioinspired wireless microfluidic microbial taste chip with artificial-intelligence(AI)-enabled high selectivity. Utilizing gated recurrent unit(GRU)-based deep learning algorithms, we demonstrate a classification accuracy of 98.9% for Cu2+, Pb2+, and Cr6+ by harnessing the different temporal output current patterns of the chips to different pollutants. A shortest 48-s response time is achieved, 3.75 times shorter than the fastest previously reported counterpart. The chip enables real-time sensing of Cu2+, Pb2+, and Cr6+ with high accuracy and linearity. Combined with a small footprint and wireless connectivity, the chip may find applications in real-time quantitative heavy metal ions in water monitoring and contribute to global efforts in fighting water pollution.

Tracking Antimicrobial Resistant Organisms Timely: a workflow validation study for successive core-genome SNP-based nosocomial transmission analysis

Background and Objectives

Effective infection prevention and control (IPC) interventions in hospitals require timely information to determine the potential transmission of antimicrobial-resistant (AMR) organisms. We proposed and developed a successive core-genome SNP (cgSNP)-based phylogenetic analysis workflow, 'Tracking Antimicrobial Resistant Organisms Timely' (TAROT), using the Oxford Nanopore Technologies (ONT) sequencer for MRSA, and compared the results with those obtained using the Illumina sequencer.

Methods

We have developed a TAROT workflow for successive phylogenetic analysis using ONT data. We sequenced 34 MRSA strains isolated from Toho University Omori Medical Center using MinION (ONT) and MiSeq (Illumina). Each strain's ONT data were inputted into TAROT (TAROT-ONT), and successive cgSNP-based phylogenetic analyses were conducted. Illumina data were processed with a batched cgSNP-based phylogenetic analysis. Assembly-based analysis identified AMR genes, AMR mutations and virulence genes.

Results

MinION generated an average sequence depth of 262× for the ST8 reference genome within 3 h. TAROT-ONT successively generated 11 phylogenetic trees for 14 ST8 strains, 7 trees for 10 ST1 strains and 2 trees for 5 ST5 strains. Highly suspected transmission pairs (pairwise cgSNP< 5) were detected in trees #6 through #11 for ST8, trees #3, #5 and #7 for ST1, and tree #2 for ST5. Differences in pairwise cgSNP value between TAROT-ONT and Illumina ranged from zero to two within pairs with fewer than 20 cgSNPs using Illumina. TAROT-ONT bioinformatic analysis for each strain required 5-42 min. The identification of AMR genes, mutations and virulence genes showed high concordance between ONT and Illumina.

Conclusions

TAROT-ONT can facilitate effective IPC intervention for MRSA nosocomial transmissions by providing timely feedback through successive phylogenetic analyses based on cgSNPs.

Molecular characterization of emerging multi-drug resistant Clostridium perfringens isolated from pork production chains in Korea

Clostridium perfringens is a common cause of foodborne illnesses and is involved in human and animal gastrointestinal diseases. Surveillance of C. perfringens in the pork production chain is crucial to manage the risk of pathogen transmission. This study aimed to investigate the prevalence, antimicrobial resistance profile, and genomic characteristics of C. perfringens in pork production chains in Korea. The overall prevalence of C. perfringens was 23.6% (330/1397), with 48.8 (178/365), 16.6 (138/832), and 7.0% (14/200) in pig farms, slaughterhouses, and retail markets, respectively. Toxinotyping revealed 98.9% type A and 1.1% type C isolates. Among them, 29.1% carried the beta-2 toxin gene. Antimicrobial susceptibility tests identified 20 multi-drug resistant isolates, with the highest resistance against tetracycline (65.1%). Whole-genome sequencing further revealed 17 antimicrobial resistance and 12 virulence genes. Subsequent phylogenetic analysis identified three clonal clusters, two of which revealed a clonal relationship with human clinical isolates reported in China. The ST408 isolate from the retail pork meat, IJCP45, harboured the optrA gene in a plasmid and was identical to known optrA-carrying plasmids in C. perfringens from livestock in China, suggesting the introduction and dissemination of optrA by the transmission of a specific plasmid in east Asian countries. To our knowledge, this is the first comprehensive study of C. perfringens in the pork meat production system as an "One Health" approach. The study findings provide baseline data for the distribution and genetic characteristics of pig-associated C. perfringens in Korea and indicate the zoonotic transmission potential of C. perfringens from pigs to humans.

Green light suppresses cell growth but enhances photosynthetic rate and MIB biosynthesis in PE-containing Pseudanabaena

2-Methylisoborneol (MIB) is a notorious musty odorant in drinking water systems, produced by cyanobacteria during the biosynthesis of photosynthetic pigments. This study investigated the physiological adaptation of Pseudanabaena cinerea, a phycoerythrin (PE)-containing and MIB-producing cyanobacterium, by inducing chromatic acclimation under different light color. Our findings revealed that red light enhanced growth rates by stimulating the tricarboxylic acid (TCA) cycle and associated metabolic processes, while green light significantly increased photosynthetic pigment content and electron transport efficiency. MIB yield correlated nonlinearly with chlorophyll a (Chl a) content, modeled by a logarithmic-linear equation (R2 = 0.74, p < 0.01). This was supported by the strong correlation between mic and chlG gene expression at the RNA level (R2 = 0.85, p < 0.01). The model showed that < 2 % of carbon flux is allocated to MIB biosynthesis compared to Chl a production, indicating that MIB biosynthesis is synergistic, not competitive, with photosynthetic pigment production. The red-shift in light spectra due to increased water turbidity observed in the field led to changes in photosynthetic pigments, which decreased MIB levels. This study improves our understanding of MIB-producing cyanobacteria under variable light conditions and offers insights for mitigating MIB occurrences in surface waters.

Draft genome sequence data on Bacillus safensis FB03 isolated from the rhizosphere soil of leguminous plant in Bangladesh

With the aim of investigating the biotechnological potential of Bacillus safensis' FB03, isolated from the rhizosphere soil of Bahrind region of Bangladesh, the current work focused on its complete genomic analysis and phenotypic description. The size of the genome of the isolate was 3.6 Mb with 41.59 % GC content. Genome annotation revealed the presence of many genes related to siderophore production, enzyme degradation, UV and stress tolerance. Six biosynthesis gene clusters for bacillibacin, bacilysin, bottromycin, Schizokinen, fengycin, and lychensin were identified through genome mining. Significantly, FB03 was found to contain only two acquired antimicrobial resistance genes and was anticipated to be non-pathogenic to humans. The openness of the Bacillus safensis pan-genome was demonstrated by the pan-genome analysis. According to this research, Bacillus safensis FB03 may be a good fit for a variety of biotechnological applications.

A biofilm-targeting lipo-peptoid to treat Pseudomonas aeruginosa and Staphylococcus aureus co-infections

Antibiotic-resistant bacterial infections are a significant clinical challenge, especially when involving multiple species. Antimicrobial peptides and their synthetic analogues, peptoids, which target bacterial cell membranes as well as intracellular components, offer potential solutions. We evaluated the biological activities of novel peptoids TM11-TM20, which include an additional charged NLys residue, against multidrug-resistant Pseudomonas aeruginosa and Staphylococcus aureus, both in vitro and in vivo. Building on insights from previously reported compounds TM1-TM10, the lipo-peptoid TM18, which forms self-assembled ellipsoidal micelles, demonstrated potent antimicrobial, anti-biofilm, and anti-abscess activity. Transcriptome sequencing (RNA-seq) revealed that TM18 disrupted gene expression pathways linked to antibiotic resistance and tolerance, and biofilm formation in both pathogens. Under dual-species conditions, TM18 induced overlapping but attenuated transcriptional changes, suggesting a priming effect that enhances bacterial tolerance. In a murine skin infection model, TM18 significantly reduced dermonecrosis and bacterial burden in mono-species infections. When combined with the antibiotic meropenem, they synergistically nearly cleared co-infections. Our findings highlight that TM18 has potential as a novel therapeutic for combating antibiotic-resistant pathogens and associated biofilm-driven tolerance.

Transcriptomic analysis of intracellular RNA granules and small extracellular vesicles: Unmasking their overlap in a cell model of Huntington's disease

Huntington's disease (HD) arises from the abnormal expansion of a CAG repeat in the HTT gene. The mutant CAG repeat triggers aberrant RNA-protein interactions and translates into toxic aggregate-prone polyglutamine protein. These aberrant RNA-protein ineractions also seed the formation of cytoplasmic liquid-like granules, such as stress granules. Emerging evidence demonstrates that granules formed via liquid-liquid phase separation can mature into gel-like inclusions that persist within the cell and may act as precursor to aggregates that occur in patients' tissue. Thus, deregulation of RNA granules is an important component of neurodegeneration. Interestingly, both the formation of intracellular membrane-less organelles like stress granules and the secretion of small extracellular vesicles (sEVs) increase upon stress and under disease conditions. sEVs are lipid membrane-bound particles that are secreted from all cell types and may participate in the spreading of misfolded proteins and aberrant RNA-protein complexes across the central nervous system in neurodegenerative diseases like HD. In this study, we performed a comparative transcriptomic analysis of sEVs and RNA granules in an HD model. RNA granules and sEVs were isolated from an inducible HD cell model. Both sEVs and RNA granules were isolated from induced (HD) and non-induced (control) cells and analyzed by RNA sequencing. Our comparative analysis between the transcriptomics data of HD RNA granules and sEVs showed that: (I) intracellular RNA granules and extracellular RNA vesicles share content, (II) several non-coding RNAs translocate to RNA granules, and (III) the composition of RNA granules and sEVs is affected in HD cells. Our data showing common transcripts in intracellular RNA granules and extracellular sEVs suggest that formation of RNA granules and sEV loading may be related. Moreover, we found a high abundance of lncRNAs in both control and HD samples, with several transcripts under REST regulation, highlighting their potential role in HD pathogenesis and selective incorporation into sEVs. The transcriptome cargo of RNA granules or sEVs may serve as a source for diagnostic strategies. For example, disease-specific RNA-signatures of sEVs can serve as biomarker of central nervous system diseases. Therefore, we compared our dataset to transcriptomic data from HD patient sEVs in blood. However, our data suggest that the cell-type specific signature of sEV-secreted RNAs as well as their high variability may make it difficult to detect these biomarkers in blood.

Exploratory analysis of differences at the transcriptional interface between the maternal and fetal compartments of the sheep placenta and potential influence of fetal sex

An understanding of the inner workings of the placenta is imperative to elucidate how the maternal and fetal compartments coordinate to mediate fetal development. The two compartments can be separated and studied before term in sheep, a feat not possible in humans, thus providing a valuable translational model. This study investigated differential expression of gene signaling networks in the maternal and fetal compartments of the placenta and explored the potential influence of fetal sex. On approximately gestational day 120 (term: 147 days), ewes were euthanized and fetuses removed and sexed. Placentomes [n = 5 male, n = 3 female] were collected, and caruncles (maternal) and cotyledons (fetal) were separated and sequenced to assess RNA expression. Analysis revealed 2627 differentially expressed genes (FDR<0.01, abslog2FC ≥ 2) contributing to key transcriptional differences between maternal and fetal compartments, which suggested that the maternal compartment drives extracellular signaling at the interface whereas the fetal compartment controls internal mechanisms crucial for fetal-placental development. X-chromosome inactivation equalized expression of a vast majority of X-linked genes in the fetal compartment. Additionally, the female placenta had more fine-tuned regulation of key pathways for fetal-placental development, such as DNA replication, mRNA surveillance, and RNA transport, compared to males, which had enrichment of metabolic pathways including TCA cycle and galactose metabolism. These findings, in addition to supporting differences in expression in the maternal and fetal placental compartments and the possible influence of fetal sex, offer a transcriptional platform to compare placental perturbations that occur at the maternal-fetal interface that contribute to adverse pregnancy outcomes.

Multipronged impact of environmental temperature on Staphylococcus aureus infection by phage Kayvirus rodi: Implications for biofilm control

Environmental cues sometimes have a direct impact on phage particle stability, as well as bacterial physiology and metabolism, having a profound effect on phage infection outcome. Here, we explore the impact of temperature on the interplay between phage Kayvirus rodi (phiIPLA-RODI) and its host, Staphylococcus aureus. Our results show that phiIPLA-RODI is a more effective predator at room (25 °C) compared to body temperature (37 °C) against planktonic cultures of several strains with varying degrees of phage susceptibility. This result differs from most known examples of temperature-dependent phage infection, in which optimum infection is correlated with the host growth rate. Further characterization of this phenomenon was carried out with strains IPLA15 and IPLA16, whose respective MICs were 7 log units and a 1-log unit higher at 37 °C than at 25 °C. Our results demonstrated that the phage also had a greater impact at room temperature during biofilm development and for the treatment of preformed biofilms. There was no difference in phage adsorption between the two temperatures for strain IPLA16. Conversely, adsorption of phiIPLA-RODI to IPLA15 was reduced at 37 °C compared to 25 °C. Moreover, confocal microscopy analysis indicated that the biofilm matrix of both strains has a greater content of PIA/PNAG at 37 °C than at 25 °C. Regarding infection parameters, we observed longer duration of the lytic cycle at 25 °C for both strains, and infection of IPLA15 by phiIPLA-RODI resulted in a smaller burst size at 37 °C than at 25 °C. Finally, we also found that the rate of phage resistant mutant selection was higher at 37 °C for both strains. Altogether, this information highlights the impact that bacterial responses to environmental factors have on phage-host interactions. Moreover, phage phiIPLA-RODI appears to be a highly effective candidate for biofilm disinfection at room temperature, while its efficacy in biofilm-related infections will require combination with other antimicrobials.

Investigation of the female genital tract microbiome and its association with hydrosalpinx in women undergoing salpingectomy

OBJECTIVE

To describe the microbiome of the vagina and fallopian tubes (FT) and its relation with hydrosalpinx.

METHODS

Case-control study was conducted in women who underwent salpingectomy for hydrosalpinx (case) or other indications (controls). Samples were obtained during surgery and subjected to 16S rRNA amplicon sequencing, and analyses of alpha diversity and beta diversity measures were compared between sites and groups. Differential abundance of bacteria associated with vaginal dysbiosis was compared between cases and controls.

RESULTS

Nine women with hydrosalpinx and 23 women without hydrosalpinx were included in the study. The mean age of studied women was 41 (range: 29-54) and most (89%) were premenopausal. After in silico decontamination, only 30% of control FT samples and 10% of case FT samples had evidence of bacterial presence. The vaginal microbiome of control patients showed greater abundance of lactobacilli, whereas the vaginal microbiome of case patients contained relatively more bacterial vaginosis-associated bacteria, such as Prevotella and Atopobium. A significant difference was found in alpha and beta diversity between vaginal and FT microbiomes in control patients as FT samples were more diverse. We found that women with hydrosalpinx had a more "dysbiotic" vaginal microbiome and in women without hydrosalpinx, microbial composition within the vagina and FT differed, possibly representing two distinct ecological environments.

CONCLUSION

Women undergoing salpingectomy for various reasons harbored bacteria within their FT, while women with hydrosalpinx generally did not. This suggests that even though infection may be an underlying cause of hydrosalpinx, bacteria may not be present by the time patients require surgery.

Study of Hsp90α and Hsp90β role in virus replication using cell lines with Hsp90 gene knockouts

Replication of the human Enterovirus 71 (EV71) and herpes simplex virus 1 (HSV-1) requires Hsp90 chaperone activity. Vertebrate cells express two cytosolic Hsp90 proteins, Hsp90α and Hsp90β. Earlier reports suggested that EV71 replication might depend solely on the Hsp90β, whereas HSV-1 replication depended on Hsp90α. Here, we describe construction of the cell line knockouts missing Hsp90α or Hsp90β protein. Using these cells, we found that HSV-1 and, another enterovirus, Coxsackievirus B5 (CVB5) replicate in both Hsp90α and Hsp90β knockout cells with equal efficiency. The presented results demonstrate that cell lines with a mutation inactivating the specific HSP90 gene might be an easy-to-use and robust system to study specific cellular functions of Hsp90α and Hsp90β.

Microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary responding to tidal fluctuation

Tidal fluctuation disturbances and amplified anthropogenic activities are defining characteristics of the intertidal zones of mountainous river estuaries. The accumulation and degradation of organic matter and nutrients in the sediments result in a complex element migration and transformation dynamics. Nonetheless, microbial transformation of dissolved organic sulfur (DOS) in the intertidal sediments upon tidal fluctuation remains poorly understood. Here, by taking a representative small mountainous river estuary in southeast China as an example, we synthesize evidence describing the composition of dissolved organic matter (DOM), microbial community structure and metabolic functions in sediments of variable depths (0-80 cm) at both high and low tide via FT-ICR-MS and metagenomic approach. Labile DOM, e.g., aliphatic and proteins were more inclined to be enriched in shallow sediments (0-30 cm). Upon tidal inundation, Thaumarchaeota was verified to facilitate the accumulation of recalcitrant organic matter through the mevalonate pathway, elevating the proportion of carboxyl-rich alicyclic molecules (CRAMs) and lignins in sediments. Whereas during ebb period, the microbial production of DOS through assimilated sulfate reduction (ASR) was signally intensified, contributing to the accumulation of sulfur-containing organic matter in deeper sediments. Based on the associations between Kyoto encyclopedia of Genes and Genomes modules and DOM formulas, cobalamin biosynthesis, ASR, and cysteine biosynthesis were observed positively correlated with the accumulation of sulfur-containing organic matter. Microbial community exhibited obvious taxonomic and functional variations between flood and ebb states. Nitrososphaerta in shallow sediments (0∼30 cm) was beneficial for the production of nitrogen-containing organic matter, while Bathyarchaeota and Chloroflexota in deep sediments (70-80 cm) predominantly governed the mineralization of organic matter. We firstly provided metagenomic evidence for the microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary, which will be key to predicting coastal carbon storage and offer an important scientific basis for formulating intertidal ecosystem management and restoration strategies.

Research on the histopathology of Larimichthys crocea affected by white gill disease and analysis of its bacterial and viral community characteristics

White gill disease (WGD) is one of the major diseases affecting Larimichthys crocea, although its etiology remains unclear. To investigate the causes of WGD, this study selected WGD-affected Larimichthys crocea (WG) and healthy Larimichthys crocea (NH) from multiple aquaculture regions for pathological analysis and analysis of bacterial and viral community characteristics. The results indicated severe tissue damage and significant inflammatory responses, as evidenced by clinical manifestations and electron microscopy. Two bacterial species, Photobacterium damselae and Vibrio campbellii, were isolated from all lesion tissues. Additionally, 16S full-length sequencing results showed that Photobacterium damselae and Vibrio campbellii dominated in the tissues of Larimichthys crocea, with a combined relative abundance of approximately 90 %. There were no significant differences in α-diversity and β-diversity between the NH group and WG group from the three aquaculture regions, and no significant biomarkers were identified. The diversity of DNA and RNA viruses did not show significant differences between the NH and WG groups, although both types of viruses exhibited notable synergistic and antagonistic relationships. Analyses from 16S full-length sequencing, metagenomics, and metatranscriptomics revealed that the related functional genes were primarily enriched in various metabolic pathways, including glycine biosynthesis, membrane transport, and energy metabolism. The metatranscriptomic analysis indicated that the expression levels of genes related to antibiotic resistance, biosynthesis, transport, and degradation processes were significantly downregulated in the WG group. Finally, through PCR, qPCR, and metagenomic sequencing, we were unable to detect iridovirus in Larimichthys crocea, further suggesting that the causes of WGD may differ across aquaculture regions compared to previous reports. This study indicates that the etiology of WGD may involve complex ecological and metabolic mechanisms, rather than being merely the result of a single pathogen infection. This research provides a comprehensive analysis of the microbial communities in WGD-affected Larimichthys crocea from multiple aquaculture regions for the first time, providing a theoretical basis for further elucidating the causes of WGD and developing preventive measures.

Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products

Genetically modified microorganisms (GMM) are frequently employed for the production of microbial fermentation products such as food enzymes. Although presence of the GMM or its recombinant DNA in the final product is not authorized, contaminations occur frequently. Insight into the contamination source of a GMM is of crucial importance to allow the competent authorities to take appropriate action. The aim of this study was to explore the feasibility of a metagenomic shotgun sequencing approach to investigate microbial contamination in fermentation products, focusing on source tracing of GMM strains using innovative strain deconvolution and phylogenomic approaches. In most cases, analysis of 16 GMM-contaminated food enzyme products supported finding the same GM producer strains in different products, while often multiple GMM contaminations per product were detected. Presence of AMR genes in the samples was strongly associated with GMM contamination, emphasizing the potential public health risk. Additionally, a variety of other microbial contaminations were detected, identifying a group of samples with a conspicuously similar contamination profile, which suggested that these samples originated from the same production facility or batch. Together, these findings highlight the need for guidelines and quality control for traceability of these products to ensure the safety of consumers. This study demonstrates the added value of metagenomics to obtain insight in the microbial contamination profiles, as well as their underlying relationships, in commercial microbial fermentation products. The proposed approach may be applied to other types of microbial fermentation products and/or to other (genetically modified) producer strains.

Genetic and transcriptomic analysis of lentil seed imbibition and dormancy in relation to its domestication

Seed dormancy is an adaptation that delays germination to prevent the start of this process during unsuitable conditions. It is crucial in wild species but its loss was selected during crop domestication to ensure a fast and uniform germination. Water uptake, or imbibition, is the first step of germination. In the Fabaceae family, seeds have physical dormancy, in which seed coats are impermeable to water. We used an interspecific cross between an elite lentil line (Lens culinaris) and a wild lentil (L. orientalis) to investigate the genetic basis of imbibition capacity through quantitative trait locus (QTL) mapping and by using RNA from embryos and seed coats at different development stages, and phenotypic data of seed coat thickness (SCT) and proportion of imbibed seeds (PIS). Both characteristics were consistent throughout different years and locations, suggesting a hereditary component. QTL results suggest that they are each controlled by relatively few loci. Differentially expressed genes (DEGs) within the QTL were considered candidate genes. Two glycosyl-hydrolase genes (a β-glucosidase and a β-galactosidase), which degrade complex polysaccharides in the cell wall, were found among the candidate genes, and one of them had a positive correlation (β-glucosidase) between gene expression and imbibition capacity, and the other gene (β-galactosidase) presented a negative correlation between gene expression and SCT.

Whole-genome sequences revealed genomic diversity and selection signatures of Dermacentor silvarum in Shaanxi, China

Dermacentor silvarum (D. silvarum) is an arthropod that feeds on blood. It is a primary tick species found in northern China that poses a significant security risk to the health and life of the host, as it has the potential to transmit a variety of pathogens to humans and animals. Through ongoing research on tick genome sequences, researchers have successfully assembled and reported reference genomes for numerous tick species. These significant advances have greatly accelerated the study of tick biology and population genomics. D. silvarum samples were obtained from the body surface of free-range goats in Yulin, Shaanxi Province, China. The whole genomes of the samples were resequenced and merged with preexisting data from the National Genomics Data Center database (project ID: PRJCA002242) to analyze the genetic structure, genetic diversity, mitochondrial genetic structure, and selection signatures of D. silvarum in the Shaanxi Province. Based on the available data, the D.silvarum species in China could be classified into two main branches. These populations exhibited low nucleotide diversity. A slight discrepancy was noted between the mitochondrial phylogenetic tree and the autosomal whole-genome phylogenetic tree of D. silvarum, consistent with a previous study. In the selected analysis of D. silvarum in the Shaanxi Province, China, genes linked to immunity, iron storage, fatty acid biosynthesis, pesticide defense, and blood digestion were identified. Leutriene A4 hydrolase (LOC119466376) was also identified, although its function remains unknown. This information is crucial for understanding the biology of D. silvarum and developing management measures.

Natural mackinawite-based elimination of vanadium and ammonium from wastewater in autotrophic biosystem

Vanadium (V) production results in significant amounts of wastewater, which often co-contains considerable ammonium (NH4+) after being used as precipitants. Both pentavalent V [V(V)] and NH4+ can be removed independently through biological process. However, internal interactive biotechnology for one-step elimination of V(V) and NH4+ remains an enigma. In this study, we proposed biologically removing V(V) and NH4+ simultaneously with natural mineral mackinawite as electron donor and its oxidation products as electron acceptors. Our bioreactor achieved a V(V) removal efficiency of 99.5 ± 0.22 % and an NH4+-N removal capacity of 49.5 ± 0.40 g/m3·d. V(V) was reduced to tetravalent V precipitates, while mackinawite was bio-oxidized to Fe(III) and sulfate. Metagenomic binning analysis indicated Sulfurivermis sp. mediated mackinawite oxidation and V(V) reduction. Putative Pseudomonas sp. conducted NH4+ assimilation, anaerobic ammonium oxidation coupled to Fe(III) reduction (Feammox), and denitrification, achieving complete NH4+-N removal. Real-time qPCR validated the upregulation of functional genes involved in V(V) reduction and nitrogen metabolisms, with improved functional enzyme activities. Cytochrome c, nicotinamide adenine dinucleotide, and extracellular polymeric substances promoted electron transfer, facilitating the elimination of both V(V) and NH4+-N from wastewater. This study offers a novel and sustainable biological strategy for one-step treating V industrial wastewater.

Genetic insights into progressive myoclonic epilepsies: A case study of KCTD7 mutation in an Iranian-Azeri-Turkish family

Progressive Myoclonic Epilepsies (PMEs) are a rare and heterogeneous group of epileptic disorders often with progressive neurologic deterioration. The intensity of the clinical features varies depending on the underlying genetic etiology. This study aims to identify the genetic mutation associated with PME in a family belonging to the Iranian-Azeri-Turkish ethnic population. A 5-year-old boy and his 8-year-old sister, presenting with PME-related electroclinical features such as myoclonic seizures and progressive cognitive and motor decline, underwent comprehensive clinical evaluations, including pedigree analysis, laboratory tests, and EEG assessments, followed by Whole-Exome Sequencing (WES) to identify potential disease-causing mutations. We identified a novel homozygous mutation (c.14C > T) in the KCTD7 gene in both siblings, confirmed through Sanger sequencing. This mutation was not observed in a cohort of 430 healthy individuals from the same Iranian-Azeri-Turkish ethnic background, providing strong evidence for its pathogenic role. This finding advances our understanding of the genetic basis and phenotypic diversity of PMEs, but further research is needed to elucidate how KCTD7 mutations contribute to epilepsy and neurodegeneration.

Differential gene expression in uterine endometrioid cancer cells and adjusted normal tissue

Endometrial cancer is a significant public health concern with rising incidence rates globally. Understanding the molecular mechanisms underlying this disease is crucial for developing effective therapeutic strategies. Our study aimed to characterize transcriptional changes in endometrial cancer tissues compared to adjusted healthy tissue. Using RNA sequencing, we identified 2483 differentially expressed genes (DEGs), including protein-coding genes, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs). Notably, several known cancer-related genes were differentially expressed, such as MYC, AKT3, CCND1, and CDKN2A. Pathway analysis revealed significant alterations in cell cycle regulation, several signaling pathways, and metabolic processes. These findings provide valuable insights into the molecular pathways dysregulated in endometrial cancer. Our results may contribute to the development of novel therapeutic targets and biomarkers for this disease.

Endophytic bacteriome data of Litchi chinensis established by metagenomic 16S rRNA gene sequencing

This work reported the diversity profiling and predicted metabolic function of the endophytic bacteriome of lychee (Litchi chinensis S.) cultivated in Dak Lak Province of Vietnam for the first time. Roots of lychee were collected from three different fields in Krong Ana District in Dak Lak. 16S rRNA primers were used to sequence the metagenomic library. Kraken 2 was used to analyze the taxonomic distribution, while the MetaCyc database was used to predict the metabolic function. We identified 10 phyla, 14 classes, 27 orders, 30 families, and 27 genera of the endophytic bacteria from the sample. Actinomycetota was the most predominant phylum (84.49%), and biosynthesis was the bacteriome's primary function (75.42%). Data provided insight into the taxonomic distribution and metabolic function of lychee endophytic bacteria and might be helpful for the next steps concerning sustainable lychee cultivation using endophytic bacteria.

The Crucial Roles of Phloem Companion Cells in Response to Phosphorus Deficiency

Mineral deficiency is a major problem in agriculture. Plant adaption to low mineral environments involves signaling between shoots and roots, via the food transport cells, the sieve elements. However, due to the sequestered position of the sieve elements in the vascular bundles, identifying shoot-to-root mobile signals is challenging. In herbaceous species, sieve elements and companion cells (CCs) are isolated from other leaf tissues. We hypothesize that phloem CCs play an essential role by synthesizing shoot-to-root signals in response to mineral deficiency. To test this hypothesis, we analyzed gene expression responses in Arabidopsis CCs under phosphorus deficiency using TRAP-Seq. Phosphorus was chosen for its importance in plant growth and the known role of shoot-to-root signaling in regulating root phosphate transporters during deficiency. Our findings revealed that CCs exhibit more dramatic molecular responses than other leaf cells. We also found that many genes altered in CCs have potential functions in regulating root growth. This is unexpected because it has been widely believed that shoot-to-root signaling is not involved in root growth regulation under P deficiency. The importance of CCs in regulating mineral deficiency may extend beyond phosphorus because shoot-to-root signaling is a common response to the deficiency of various minerals.

Carposphere microbiota alters grape volatiles and shapes the wine grape typicality

While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe-metabolite relationship. These results provide novel insight into how the environment-microbiome-plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision-making in vineyard microbial management.

ROS-induced stress promotes enrichment and emergence of antibiotic resistance in conventional activated sludge processes

Since the Great Oxidation Event 2.4 billion years ago, microorganisms have evolved sophisticated responses to oxidative stress. These ancient adaptations remain relevant in modern engineered systems, particularly in conventional activated sludge (CAS) processes, which serve as significant reservoirs of antibiotic resistance genes (ARGs). While ROS-induced stress responses are known to promote ARG enrichment/emergence in pure cultures, their impact on ARG dynamics in wastewater treatment processes remains unexplored. Shotgun-metagenomics analysis of two hospital wastewater treatment plants showed that only 35-53 % of hospital effluent resistome was retained in final effluent. Despite this reduction, approximately 29-36 % of ARGs in CAS showed higher abundance than upstream stages, of which 20-22 % emerged de novo. Beta-lactamases and efflux pumps constituted nearly 47-53 % of these enriched ARGs. These ARGs exhibited significant correlations (p < 0.05) with ROS stress response genes (oxyR, soxR, sodAB, katG and ahpCF). The CAS resistome determined 58-75 % of the effluent ARG profiles, indicating treatment processes outweigh influent composition in shaping final resistome. Proof-of-concept batch reactor experiments confirmed increased ROS and ARG levels under high dissolved oxygen (8 mg/L) compared to low oxygen (2 mg/L) concentrations. Untargeted metaproteomics revealed higher expression of resistant proteins (e.g., OXA-184, OXA-576, PME-1, RpoB2, Tet(W/32/O)) under elevated ROS levels. Our findings demonstrate that CAS processes actively shape effluent resistome through ROS-mediated selection, indicating that treatment processes, rather than initial wastewater composition, determine final ARG profiles. This study indicates that the emergence of ARGs needs to be considered as an integral aspect of wastewater treatment design and operation to prevent antibiotic resistance dissemination.

Revisiting toxins with transcriptomics-informed proteomics of venom glands and crude venom from Centruroides bicolor from Panama

The sting of the scorpion Centruroides bicolor causes a large morbidity in Panama. To characterize its venom, transcriptomic and proteomic analyses of the venom glands and the crude venom were performed. These two approaches utilized high-throughput sequencing to enhance the likelihood of detecting a wide range of venom proteins correlated with the venom proteome. After RNA venom gland extraction, a cDNA library was constructed and sequenced by RNA-seq. Also, the crude venom was digested using trypsin and chymotrypsin, and the resulting peptides were analyzed using a nano-LC-MS/MS. Notably, transcriptomic and proteomic venom approaches identified a hyaluronidase, alpha- and beta-neurotoxins that affect Na+ channels, CRISP proteins, metalloproteinases, transferrin, monooxygenase alpha-peptidyl-glycine, serine proteases, alpha pancreatic amylase, lysozyme, neurotoxins targeting K+ channels, neprilysin, scorpine, angiotensin-converting enzyme, insulin-like growth factor-binding domain proteins, nucleobindin-like proteins, and uncharacterized proteins. Interestingly, some of the venom proteins such as nucleobindin and angiotensin-converting enzymes have been not reported in the proteome, their predicted presence has only been previously derived from the genomic sequence of Centruroides sculpturatus and C. vittatus. These newly identified components enhance the understanding of the venomous nature of C. bicolor. SIGNIFICANCE: The proteins and peptides found in Centruroides bicolor venom by transcriptomic and proteomic analyses were assessed according to the protein and toxin databases available on public domains. Notably, some of the venom proteins such as nucleobindin and angiotensin-converting enzymes have been not reported in the proteome, their predicted presence has only been previously derived from the genomic sequence of Centruroides sculpturatus and C. vittatus. Moreover, enzymatic assays, including hyaluronidase, phospholipase A2, and proteolytic activity were conducted to confirm the presence or absence of those enzymes. Interestingly, neurotoxins from C. limbatus, a related species in the region, were found in the proteome but no mRNAs were identified in the transcriptome. These newly identified components enhance the understanding of the venomous nature of Centruroides bicolor.

Natural Variation in Sexual Traits and Gene Expression between Selfing and Outcrossing Arabidopsis lyrata Suggests Sexual Selection at Work

Flowering plants show significant diversity in sexual strategies, profoundly impacting the evolution of sexual traits and associated genes. Sexual selection is one of the primary evolutionary forces driving sexual trait variation, particularly evident during pollen-pistil interactions, where pollen grains compete for fertilization and females select mating partners. Multiple mating may intensify competition among pollen donors for siring, while in contrast, self-fertilization reduces sire-sire competition, relaxing the sexual selection pressure. Traits involved in male-male competition and female choice are well described, and molecular mechanisms underlying pollen development and pollen-pistil interactions have been extensively studied in the model species Arabidopsis thaliana. However, whether these molecular mechanisms are involved in sexual selection in nature remains unclear. To address this gap, we measured intrinsic pollen performance and its interaction with female choice and investigated the associated gene expression patterns in a selfing and an outcrossing population of Arabidopsis lyrata. We found that pollen germination and pollen tube growth were significantly higher in outcrossers than selfers, and this difference was accompanied by changes in the expression of genes involved in vesicle transport and cytoskeleton. Outcrosser mother plants showed a negative impact on pollen tube growth compared to selfer mother plants, together with a difference of expression for genes involved in auxin and stress response, suggesting a potential mechanism for female choice through molecular cross talk at the post-pollination stage. Our study provides insight into the impact of sexual selection on the evolution of sexual gene expression in plants.

Population Genomics Reveals Demographic History and Climate Adaptation in Japanese Arabidopsis halleri

Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (∼50, 000 years ago). The ecological niche modeling predicted the geographic or distribution range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.

Cold suppresses virus accumulation and alters the host transcriptomic response in the turnip mosaic virus-Arabidopsis halleri system

Since plant viruses cause lifelong infections, virus-plant interactions are exposed to large temperature fluctuations in evergreen perennials. In such circumstances, virus-plant interactions are expected to change significantly between the warm and cold seasons. However, few studies have investigated the effects of cold temperatures on virus-plant interactions. Here, we show that in a persistent infection system of the turnip mosaic virus (TuMV)-Arabidopsis halleri, cold temperatures lead to slow viral replication/spreading within the host, attenuated host symptoms, and cold-specific transcriptomic responses. Many differentially expressed genes (DEGs) were detected between virus-inoculated and mock-inoculated plants under warm and cold conditions; however, the sets of DEGs and response timings were temperature-dependent. At cold temperatures, the expression of photosynthesis-related genes decreased in the early stages of infection. However, it recovered to the same level as that in uninfected plants in the later stages. In contrast, the transcriptomic changes under warm conditions suggest that viral infections cause auxin signaling disruption. These responses coincided with the inhibition of host growth. We identified 6 cold- and 38 warm-specific DEGs, which changed their expression in response to TuMV infection under more than half of the conditions for either cold or warm temperatures. Further validation of the putative relationships between transcriptomic and phenotypic responses of the host is required. Our findings on temperature-dependent host responses at both symptomatic and transcriptomic levels help us understand how warm and cold temperatures affect virus-plant interactions in seasonal environments.

Characterization of transferable antibiotic resistance plasmids in airborne particulate matter from ICU environments

Intensive care units (ICUs) are critical environments for the emergence of antibiotic-resistant bacteria, with numerous studies focusing on resistant pathogens in these settings. However, transferable antibiotic resistance plasmids (TARPs)-regardless of their origin from pathogenic or non-pathogenic bacteria-are key drivers of resistance gene dissemination and the emergence of resistant strains. This study investigated TARPs in ICU air. Air samples were directly used to isolate resistant plasmids using Escherichia coli CV601 as the recipient. Plasmid types, antibiotic resistance genes (ARGs), and virulence factors were identified through sequencing, and resistance phenotypes were validated. A total of 30 distinct plasmid types were detected, with IncX3 being the most prevalent. Among 245 ARGs identified, bla NDM-53, bla SHV-12, and BRP(MBL) were dominant. Phylogenetic analysis indicated that these TARPs originated from bacteria commonly colonizing human mucosa. ICU airborne TARPs may significantly contribute to the spread of ARGs and antibiotic resistance transmission.

Sheep serve as amplifying hosts of Japanese encephalitis virus, increasing the risk of human infection

The transmission cycle of Japanese encephalitis virus (JEV), involving pigs and birds as amplifying hosts and mosquitoes as vectors, was elucidated in the 1950s. However, factors contributing to this cycle remain unclear. Here, sheep were infected with a JEV strain isolated from sheep exhibiting neurological symptoms. The results revealed that sheep are susceptible to JEV infection and develop viremia, with levels and duration comparable to those observed in pigs, a known JEV-amplifying host. Mosquitoes fed viremic sheep blood showed an infection rate of 40.6 to 57.1%. These findings indicate that sheep can serve as amplifying hosts for JEV, potentially contributing to JEV transmission and increasing the public health risk of human infections. We propose an alternative, sheep-associated rural domestic JEV transmission cycle, which may be prevalent in specific regions where sheep are bred but pigs are not. This cycle exists along with the well-known pig-associated rural domestic and bird-associated wild cycles.

Ultraconserved Elements Reveal the Relationship Between Facultative Keratinophagy and Synanthropic Evolution in Clothes Moths

Synanthropic species live in close association with, or benefit from, humans. Despite their potential impacts to human health, little is known about the mechanisms driving synanthropic life-history evolution, evolutionary forces shaping diet among synanthropes, or how these combined factors affect population dynamics and/or speciation. The Tineidae moth family contains several synanthropic species, including the globally distributed pest species Tineola bissellellia, that contribute to the ~$1 billion worth of damage caused annually by keratinophagous synanthropes. Synanthropy among Tineidae is associated with a wide range of dietary strategies. While most tineids display obligate detritivory, synanthropic species are typically either facultatively or obligately keratinophagous. However, little is known about evolutionary relationships within Tineidae, hampering efforts to investigate the relationship between synanthropy and diet evolution. Here, to address this challenge, we extracted DNA from 39 tineid samples and two outgroups, including the closely related Tineola and Tinea genera, and generated genome-wide sequence data for thousands of ultraconserved elements (UCEs). Our phylogenetic analyses, using a concatenated maximum-likelihood-based approach, resulted in a well-supported, fully resolved phylogeny that demonstrates synanthropy has evolved multiple times and is consistently associated with facultative and obligate keratinophagy. Bayesian divergence time estimation indicates Cretaceous divergence among deep-branching tineid lineages, an ancestral origin of facultative keratinophagy, and a recent origin of the most economically important synanthropic pest, Tineola bissellellia, from within genus Tinea. Taken together, our results suggest that a shift to facultative keratinophagy was a key evolutionary innovation that has fuelled the repeated evolution of synanthropic life histories among this deep-diverging moth family.

Efficacy of Erwinia amylovora and Xanthomonas campestris pv campestris phages to control fire blight and black rot in vivo

Phytopathogens, such as Erwinia amylovora and Xanthomonas campestris, pose significant threats to agriculture, leading to substantial economic losses. Traditional chemical pesticides can harm soil fertility, contaminate water, and impact non-target organisms such as natural predators and pollinators, highlighting the need for sustainable pest control methods. This study explores the use of bacteriophages as biocontrol agents against E. amylovora, which causes fire blight, and X. campestris pv. campestris, responsible for black rot in cruciferous vegetables. Bacteriophages were isolated from urban wastewater and tested for their lytic activity against these pathogens. Three virulent phages were identified: ɸEF1 and ɸEF2 against E. amylovora and ɸXF1 against X. campestris pv. campestris. Genetic analysis confirmed the absence of known lysogeny-related genes, indicating that these phages are ideal candidates for biocontrol applications. In vitro assays demonstrated significant bacterial population reductions. Specifically, ɸEF1 killed 92.1% of the E. amylovora population at a multiplicity of infection (MOI) of 1 after 3 h, while ɸEF2 reduced the population by 98.1%. When combined in a 1:1 ratio, the two phages reduced E. amylovora populations by 99.7%, and no regrowth of resistant cells was observed, which was not the case when the phages were applied individually. ɸXF1 killed 99.9% of X. campestris pv. campestris populations at an MOI of 1 after 5 h. In vivo experiments using pears and kohlrabi as infection models further validated the phage effectiveness. Treated pears showed reduced fire blight symptoms, and kohlrabi plants exhibited markedly less necrosis from black rot compared to untreated controls.IMPORTANCEThree new virulent phages have been isolated: two targeting Erwinia amylovora and one targeting Xanthomonas campestris pv. campestris. All phages were able to rapidly reduce the population of their corresponding phytopathogens and alleviate disease symptoms in in vivo plant models. These findings highlight the potential of these phages as biocontrol agents for managing bacterial plant diseases, offering an alternative to traditional chemical treatments.

Multiple perinatal characteristics affect the association between maternal diabetes status and early neonatal gut microbiota

Increasing evidence has suggested that maternal gestational diabetes mellitus (GDM) can influence the neonatal gut microbiota. However, the initial microbial colonization of neonates is still unclear. The discrepancy in results between studies may be due to many other prenatal characteristics. This study aimed to investigate whether perinatal characteristics affect the association between maternal GDM status and early neonatal gut microbiota. This nested case-control study was based on a cohort of mothers and children (2016YFC1000304). Meconium samples were collected from neonates of mothers with (n = 114) and without GDM (n = 133) within 24 h after birth, and then assessed via 16S rRNA gene amplicon sequencing. Differences in the diversity and composition of the neonatal gut microbiota were compared according to maternal GDM status and other perinatal characteristics. The gut microbiota of neonates born to mothers with GDM presented lower alpha diversity with the Chao1 index (P = 0.0235). Principal coordinate analysis revealed that the meconium samples were clustered by maternal GDM status only with unweighted UniFrac distances (R2 = 0.011, P = 0.003). In other groups, such as maternal age ≥ 35 years old and maternal prepregnancy BMI ≥ 24 kg/m2, meconium was not clustered by maternal GDM status. Linear discriminant analysis revealed that 81 taxa were significantly different between the GDM group and the control group. Based on delivery mode, there were 226 representative taxa in the control group, whereas in the GDM group, there were no representative taxa. In addition, based on neonatal sex, there were 79 representative taxa in the GDM group and seven in the control group. Other perinatal characteristics, such as maternal prepregnancy BMI, age, gestational weight gain, and birth weight also influenced the differential taxa of the neonatal gut microbiota between the two groups. In our cohort, newborns from mothers with GDM and without GDM had similar composition but different abundances of the gut microbiota. Maternal prepregnancy BMI, age, gestational weight gain, and neonatal delivery mode, sex, and birth weight had different influences on the diversity and differential taxa of the neonatal gut microbiota. The results of this study suggest that when studying the association between GDM and neonatal gut microbiota, it is necessary to consider the concomitant perinatal characteristics.

IMPORTANCE

This study uses 16S rRNA gene amplicon sequencing to analyze 247 meconium samples with or without maternal gestational diabetes mellitus (GDM) and make a multi-group comparison. We found that newborns from mothers with GDM and normoglycemic mothers had similar compositions but different abundances of the gut microbiota. Other than the maternal diabetes status, maternal body mass index, age, gestational weight gain, and neonatal delivery mode, gender and birth weight all contribute to neonatal gut microbiota. Compared with former related studies, our sample size was larger, and meconium was collected within 24 h after birth to avoid the influence of the living environment, feeding methods, mother's lifestyle, or diet. The results of this study will provide some information on the association between maternal GDM and neonatal gut microbiota colonization in early life and highlight the influence of non-negligible concomitant perinatal characteristics.

Genomic characterization of the novel bacteriophage PfAn1 from Lake Baikal, infecting Pseudomonas fluorescens

We isolated a novel bacteriophage from Lake Baikal that infects Pseudomonas fluorescens. Transmission electron microscopy revealed that phage PfAn1 has a head with a diameter of 50 nm and a short tail. Its genome is 39,156 bp in length with a GC content of 57%. It is predicted to contain 53 open reading frames (ORFs). The results of evolutionary analysis suggest that phage PfAn1 should be considered a new member of the class Caudoviricetes.

Oral microbiota dysbiosis in pediatric patients undergoing treatment for acute lymphoid leukemia a preliminary study

Acute lymphoblastic leukemia (ALL) stands out as the most prevalent neoplasm during childhood, characterized by the rapid production of abnormal lymphoid cells. Chemotherapy administered to these patients may induce a substantial imbalance in the oral microbiota. A prospective pediatric study encompassing a control group (without ALL) and ALL patients at two treatment stages (pre-induction and consolidation) was conducted. Clinical and laboratory data were meticulously collected. Moreover, DNA from saliva samples was extracted for 16S rRNA sequencing. Clinical data revealed a heightened incidence of oral mucositis during the consolidation phase. Analysis of alpha biodiversity (observed taxa) exhibited a significant reduction in bacterial richness among patients in the consolidation phase. Network analysis identified key taxa during this phase, namely Neisseria flavescens, Prevotella melaninogenica and Porphyromonas. The findings underscore the substantial impact of ALL treatment on the oral microbiota composition, indicating diminished bacterial diversity and an elevated prevalence of oral mucositis.