Search Results (19)

An emerging area of microbial biology focuses on oligonucleotides excised from functional RNAs and subsequently fulfilling an independent cellular role. Some of these products are subjected to modifications that may expand their functional inventory. Here, we applied a differential analysis of intra- and extracellular RNA fragments produced by wild-type Escherichia coli and its dps-null mutant and discovered leucine tRNA fragments with random 3′-terminal extensions among oligonucleotides with Dps-dependent secretion. We observed an exclusive intracellular enrichment of modified LeuT(VPQ) tRNA fragments compared to secretomes, with abundance level dependent on growth medium and the presence of competing bacteria. To assess the pervasiveness of this phenomenon, we developed a custom computational pipeline for detecting variable RNA termini in RNA-seq data. Beyond LeuT(VPQ) tRNA fragments, several other genomic loci yielded oligos with highly heterogeneous ends, indicating that terminal elongation, most prevalent in LeuT(VPQ), is not exclusive to these fragments. Ex vivo testing using synthetic LeuT(VPQ) analogs revealed their stimulatory effect on the persistence of multiple taxa in an artificial microbiome, which was attenuated by 3′-end elongation. We propose that non-template extensions may serve to broaden the spectrum of target molecules for elimination of unused mRNAs by an interference-like mechanism or to generate sequences absent from the E. coli genome as part of a primitive defense system. Full article

Although Cervus elaphus (Linnaeus, 1758) has been well studied, the subspecific taxonomy of Cervus canadensis populations in Qinghai and Gansu, China, is still controversial, and the mitochondrial characteristics of Cervus elaphus (Linnaeus, 1758) remain incompletely understood. We assembled 89 mitogenomes of C. canadensis from five geographical populations across Qinghai and Gansu. Phylogenetic analysis confirmed that the 89 individuals are taxonomically classified as C. c. kansuensis. Nucleotide compositions showed a higher abundance of adenine and cytosine compared to guanine and thymine in both complete mitogenomes and mitochondrial PCGs. Codon usage analysis revealed a strong preference towards A-ending codons (68.04% of over-represented codons, RSCU > 1.6) in mitochondrial PCGs, with systemic avoidance of G-ending codons (53.30% of unused codons, RSCU = 0). The CAMs of 13 PCGs are reported for the first time. Furthermore, the ENC plot showed that the codon usage of all PCGs was biased except for gene ATP8. The PR2 bias plot showed that gene ND6 exhibited bias towards T3 and G3, whereas the other genes preferred A3 and C3. Both the ENC-plot and PR2 bias plot suggested that natural selection played an important role in the forces driving codon usage bias in mitochondrial PCGs. Our results demonstrate the subspecific status of C. canadensis distributed in Qinghai and Gansu as C. c. kansuensis, and provide insights into the mitochondrial characteristics of C. c. kansuensis. The mitogenome sequences assembled in this study provide valuable data for further understanding of the Cervus elaphus (Linnaeus, 1758) mitogenome. Full article

Tidal flats in eastern China have undergone various transformations into other land-use types. Understanding the impact of land-use conversion on soil properties and microbial communities is crucial for effective ecological conservation efforts. In this study, we compared soil chemical properties and the diversity, composition, and ecological functions of soil bacterial and fungal communities across four land-use types: natural bare land (BL), unused reclaimed tidal land (Phragmites, PL), agricultural land (maize, ML), and shelterbelt land (SL), utilizing next-generation sequencing technology. The results indicated that soil electrical conductivity decreased, while soil organic carbon (SOC) and nutrient contents increased in ML and SL compared to BL and PL. The bacterial Chao1 and fungal Chao1 and Shannon values vary across different land-use types. A higher relative abundance of Acidobacteriota, specifically RB41, was found in ML compared to BL. Principal coordinate and PerMANOVA analysis showed that the composition of bacterial and fungal communities differed significantly across the four land-use types. SOC explained the most variance in both bacterial and fungal communities. Carbon-related functional genes and fungal guilds exhibit greater diversity across the four land-use types compared to nitrogen-related functional genes. In conclusion, the transformation of natural land-use types to managed one greatly altered soil chemical and microbial properties. Our study offers foundational insights into the microbial communities in the typical land-use types of Eastern China’s coastal area. Future studies should emphasize the quantification of human interventions and their impact on soil microbial communities and ecological functions. Full article

Hypertrophic Cardiomyopathy (HCM) is a common inherited disorder that can lead to heart failure and sudden cardiac death, characterized at the histological level by focal areas of myocyte disarray, hypertrophy and fibrosis, and only a few disease-targeted therapies exist. To identify the focal and spatially restricted alterations in the transcriptional pathways and reveal novel therapeutic targets, we performed a spatial transcriptomic analysis of the areas of focal myocyte disarray compared to areas of normal tissue using a commercially available platform (GeoMx, nanoString). We analyzed surgical myectomy tissue from four patients with HCM and the control interventricular septum tissue from two unused organ donor hearts that were free of cardiovascular disease. Histological sections were reviewed by an expert pathologist, and 72 focal areas with varying degrees of myocyte disarray (normal, mild, moderate, severe) were chosen for analysis. Areas of interest were interrogated with the Human Cancer Transcriptome Atlas designed to profile 1800 transcripts. Differential expression analysis revealed significant changes in gene expression between HCM and the control tissue, and functional enrichment analysis indicated that these genes were primarily involved in interferon production and mitochondrial energetics. Within the HCM tissue, differentially expressed genes between areas of normal and severe disarray were enriched for genes related to mitochondrial energetics and the extracellular matrix in severe disarray. An analysis of the gene expression of the ligand–receptor pair revealed that the HCM tissue exhibited downregulation of platelet-derived growth factor (PDGF), NOTCH, junctional adhesion molecule, and CD46 signaling while showing upregulation of fibronectin, CD99, cadherin, and amyloid precursor protein signaling. A deconvolution analysis utilizing the matched single nuclei RNA-sequencing (snRNA-seq) data to determine cell type composition in areas of interest revealed significant differences in fibroblast and vascular cell composition in areas of severe disarray when compared to normal areas in HCM samples. Cell composition in the normal areas of the control tissue was also divergent from the normal areas in HCM samples, which was consistent with the differential expression results. Overall, our data identify novel and potential disease-modifying targets for therapy in HCM. Full article

Natural language generation (NLG) models combined with increasingly mature and powerful deep learning techniques have been widely used in recent years. Deployed NLG models in practical applications may be stolen or used illegally, and watermarking has become an important tool to protect the Intellectual Property (IP) of these deep models. Watermarking technique designs algorithms to embed watermark information and extracts watermark information for IP identification of NLG models can be seen as a symmetric signal processing problem. In terms of IP protection of NLG models, however, the existing watermarking approaches cannot provide reliable and timely model protection and prevent illegal users from utilizing the original performance of the stolen models. In addition, the quality of watermarked text sequences generated by some watermarking approaches is not high. In view of these, this paper proposes two embedding schemes to the hidden memory state of the RNN to protect the IP of NLG models for different tasks. Besides, we add a language model loss to the model decoder to improve the grammatical correctness of the output text sequences. During the experiments, it is proved that our approach does not compromise the performance of the original NLG models on the corresponding datasets and outputs high-quality text sequences, while forged secret keys will generate unusable NLG models, thus defeating the purpose of model infringement. Besides, we also conduct sufficient experiments to prove that the proposed model has strong robustness under different attacks. Full article

High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well. Full article

Methane (CH₄) has attracted attention as not only one of the hydrogen carriers in terms of energy density, but also synthetic natural gas. In nature, the decomposition of organic compounds is performed with bacterial ecosystems that can produce CH₄. Clostridium cellulovorans as a decomposer was cultivated with pig manure (PM) as an unused biomass in this study. As a result of high-performance liquid chromatography (HPLC) analysis, while formate and lactate were decreased in the C. cellulovorans medium containing 0.5% PM, acetate and butyrate were increased in it. Accordingly, in order to compare with the effect of carbon sources for methane production, the cocultivation of C. cellulovorans and the methanogenesis of Methanosarcina mazei or microbial flora of methane production (MFMP) was carried out in the C. cellulovorans medium. As a result, only the cocultivation with C. cellulovorans and MFMP showed methane production in 0.5% acetate medium. Moreover, in comparison with a carbon source in either 1% acetate or 1% methanol medium, MFMP was only cultivated after being precultivated with 0.5% glucose medium for 12 h. The results revealed that MFMP with a 1% methanol medium produced methane approximately eight times higher than with 1% acetate medium. After cultivation with 1% acetate or 1% methanol, next-generation sequencing (NGS) analysis of MFMP was carried out. Interestingly, Methanofollis (0.211%), belonging to methanogens through the CO₂ reduction pathway, was dominant in the 1% acetate medium for 72 h cultivation, while Methanosarcina siciliae (1.178%), M. barkeri (0.571%), and Methanofollis (0.490%) were major species in 1% methanol medium for 72 h cultivation. Since Methanosarcina spp. belong to acetoclasts (acetoclastic pathway), methanol could promote the growth of Methanosarcina spp., rather than acetate. Therefore, it seems that Methanosarcina spp. may play a key methanogenesis role in MFMP. Thus, these results will provide important information for low-cost biomethane production. Full article

In this study, we consider a production lot-sizing and scheduling problem found in the fruit juice production industry from an enhanced inventory management perspective. The problem can be classified as a P2SMM (two-stage multi-machine lot-scheduling) problem. We extended the classical P2SMM problem by incorporating an additional inventory management aspect of finished products to reflect a possible real-life case problem, specifically regarding the shelf-life concept and limited warehouse capacity, with a possibility of outsourcing the warehousing demand to a third-party logistics company. We developed the mixed integer linear programming (MILP) model to fully represent the considered problem (due to the NP-hard nature of the problem, only small-scale instances could be solved to optimality), and the hybrid variable neighborhood search with linear programming (VNS/LP) model to solve both small and real-life large-scale problem instances. The goal of the developed models is to minimize total costs that consist of the cost of backordering, the cost of planned minimum and maximum stock level violation, the cost of warehouse capacity overflow, the costs of production setup time and unused available production time. The main idea of the VNS/LP model is to solve the scheduling segment of P2SMM (the production sequence) via a VNS heuristic, and the lot-sizing segment of P2SMM via the linear programming (LP) model. Based on the results from five variants of the problem setup, a potential decision maker can have an overview of the impact of different important input parameters (production time costs, warehouse capacity and costs, inventory related costs and production demand) on the total cost of a production process and improve its efficiency in changing conditions. Full article

Hypertrophic cardiomyopathy (HCM) is the most common genetic cardiomyopathy. The molecular mechanisms determining HCM phenotypes are incompletely understood. Myocardial biopsies were obtained from a group of patients with obstructive HCM (n = 23) selected for surgical myectomy and from 9 unused donor hearts (controls). A subset of tissue-abundant myectomy samples from HCM (n = 10) and controls (n = 6) was submitted to laser-capture microdissection to isolate cardiomyocytes. We investigated the relationship among clinical phenotype, cardiac myosin proteins (MyHC6, MyHC7, and MyHC7b) measured by optimized label-free mass spectrometry, the relative genes (MYH7, MYH7B and MYLC2), and the MyomiR network (myosin-encoded microRNA (miRs) and long-noncoding RNAs (Mhrt)) measured using RNA sequencing and RT-qPCR. MyHC6 was lower in HCM vs. controls, whilst MyHC7, MyHC7b, and MyLC2 were comparable. MYH7, MYH7B, and MYLC2 were higher in HCM whilst MYH6, miR-208a, miR-208b, miR-499 were comparable in HCM and controls. These results are compatible with defective transcription by active genes in HCM. Mhrt and two miR-499-target genes, SOX6 and PTBP3, were upregulated in HCM. The presence of HCM-associated mutations correlated with PTBP3 in myectomies and with SOX6 in cardiomyocytes. Additionally, iPSC-derived cardiomyocytes, transiently transfected with either miR-208a or miR-499, demonstrated a time-dependent relationship between MyomiRs and myosin genes. The transfection end-stage pattern was at least in part similar to findings in HCM myectomies. These data support uncoupling between myosin protein/genes and a modulatory role for the myosin/MyomiR network in the HCM myocardium, possibly contributing to phenotypic diversity and providing putative therapeutic targets. Full article

A patient with oral squamous cell carcinoma (OSCC) underwent complex surgical tumor therapy, including the reconstruction of soft tissues using a radial forearm flap. Due to venous congestion that could only partly be resolved by revision surgery, leech therapy was started on the second postoperative day. The patient developed pneumonia and sepsis and died as a result of septic shock, despite having received targeted broad-spectrum antibiotic therapy since day 5. Aeromonas spp. were cultured from both the patient’s specimens and unused leeches. Biochemical identification and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) yielded inconsistent identification results. Finally, microbiological identification of Aeromonas spp. was performed via 16S rDNA sequencing and use of the basic local alignment search tool (BLAST), and strains from both the patient and the leeches were identified as Aeromonas veronii. Aeromonas spp. strains derived from the patient and leeches and independent laboratory strains were submitted to randomly amplified polymorphic DNA (RAPD) subtyping. RAPD of A. veronii strains from both sources revealed an identical pattern, strongly suggesting the transmission of A. veronii from the leeches to the patient. Physicians should be aware of the potential for severe lethal infections as a fatal side-effect of leech therapy in critically ill patients, which should be addressed using antibiotic prophylaxis. Full article

Next-generation sequencing has revolutionized entomological study, rendering it possible to analyze the genomes and transcriptomes of non-model insects. However, use of this technology is often limited to obtaining the nucleotide sequences of target or related genes, with many of the acquired sequences remaining unused because other available sequences are not sufficiently annotated. To address this issue, we have developed a functional annotation workflow for transcriptome-sequenced insects to determine transcript descriptions, which represents a significant improvement over the previous method (functional annotation pipeline for insects). The developed workflow attempts to annotate not only the protein sequences obtained from transcriptome analysis but also the ncRNA sequences obtained simultaneously. In addition, the workflow integrates the expression-level information obtained from transcriptome sequencing for application as functional annotation information. Using the workflow, functional annotation was performed on the sequences obtained from transcriptome sequencing of the stick insect (Entoria okinawaensis) and silkworm (Bombyx mori), yielding richer functional annotation information than that obtained in our previous study. The improved workflow allows the more comprehensive exploitation of transcriptome data and is applicable to other insects because the workflow has been openly developed on GitHub. Full article

Phosphorus (P), in the form of inorganic phosphate (Pi), is one of the most important macronutrients for all organisms, including fish. It is indispensable for the formation of hard tissues such as bones, but also for cell signalling and cell membrane formation, and energy transduction, among many other functions and is kept under well-controlled conditions, since its deficiency or overload may lead to skeletal malformation or ectopic calcification, disturbances of intermediary metabolism, growth and function impairment, endocrine dysfunction, and eventually death. Fish feeds used in aquaculture are therefore P-rich but excess/unused/excreted P in the effluents can lead to eutrophication and a consequent deleterious change in the aquatic ecosystem. The objective of this study was to evaluate the expression profiles and transcripts modified by dietary P, to identify pathways and mechanisms involved in P transport and regulation in the kidney and intestine. Juvenile Dicentrarchus labrax were fed using a commercial feed (1.1% P) or tailored-made feeds containing 0.05%, 1.1%, or 3% Pi. Fish (duplicate tanks, n = 10) were fed for 70 days and weighed periodically to evaluate growth changes. Kidney and intestine were used for RNA extraction. Next-Generation Sequencing and RNAseq library preparation were performed in an Illumina system following the manufacturer’s recommendations. Annotation was performed using the available sea bass genome assembly. Bioinformatic analysis showed significant differences in expression patterns among the three conditions tested in both tissues. In the kidney, increased P led to a total of 135 differentially expressed genes (DEGs; 82 up and 53 down), while only 54 (11 up and 43 down) genes responded to P restriction. In the intestine, high P affected the expression of 50 genes (16 up and 34 down) whereas only 26 (6 up and 20 down) were modified by low P. However, DEGs between high and low P were 156 in kidney and 154 in intestine. Preliminary analysis suggests the most affected pathways were those involved in cellular metabolism and phosphorylation but also on the structure of cell membranes, either for maintaining membrane integrity or in genes related to transmembrane ion transport. We expect this research to reveal the molecular implications of dietary P imbalance looking at specific targets such as membrane transporters and regulatory factors, but also to the larger metabolic pathways affected in these two key organs for P uptake and excretion. Full article

(1) Background: Abnormal repair after alveolar epithelial injury drives the progression of idiopathic pulmonary fibrosis (IPF). The maintenance of epithelial integrity is based on the self-renewal and differentiation of alveolar type 2 (AT2) cells, which require sufficient energy. However, the role of glutamine metabolism in the maintenance of the alveolar epithelium remains unclear. In this study, we investigated the role of glutamine metabolism in AT2 cells of patients with IPF and in mice with bleomycin-induced fibrosis. (2) Methods: Single-cell RNA sequencing (scRNA-seq), transcriptome, and metabolomics analyses were conducted to investigate the changes in the glutamine metabolic pathway during pulmonary fibrosis. Metabolic inhibitors were used to stimulate AT2 cells to block glutamine metabolism. Regeneration of AT2 cells was detected using bleomycin-induced mouse lung fibrosis and organoid models. (3) Results: Single-cell analysis showed that the expression levels of catalytic enzymes responsible for glutamine catabolism were downregulated (p < 0.001) in AT2 cells of patients with IPF, suggesting the accumulation of unusable glutamine. Combined analysis of the transcriptome (p < 0.05) and metabolome (p < 0.001) revealed similar changes in glutamine metabolism in bleomycin-induced pulmonary fibrosis in mice. Mechanistically, inhibition of the key enzymes involved in glucose metabolism, glutaminase-1 (GLS1) and glutamic-pyruvate transaminase-2 (GPT2) leads to reduced proliferation (p < 0.01) and differentiation (p < 0.01) of AT2 cells. (4) Conclusions: Glutamine metabolism is required for alveolar epithelial regeneration during lung injury. Full article

Construction companies are increasingly utilizing sensing technologies to automatically record different steps of the construction process in detail for effective monitoring and control. This generates a significant amount of event data that can be used to learn the underlying behavior of agents in a construction site using process mining. While process mining can be used to discover the real process and identify and analyze deviations and bottlenecks in operations, it is a backward-looking approach. On the other hand, discrete event simulation (DES) provides a means to forecast future performance from historical data to enable proactive decision-making by operation managers relating to their projects. However, this method is largely unused by the industry due to the specialized knowledge required to create the DES models. This paper thus proposes a framework that extends the utility of collecting event data and their process models, by transforming them into DES models for forecasting future performance. This framework also addresses another challenge of using DES relating to its inability to update itself as the project progresses. This challenge is addressed by using the Bayesian updating technique to continuously update the input parameters of the simulation model for the most up-to-date estimation based on data collected from the field. The proposed framework was validated on a real-world case study of an earthmoving operation. The results show that the process mining techniques could accurately discover the process model from the event data collected from the field. Furthermore, it was noted that continuous updating of DES model input parameters can provide accurate and reliable productivity estimates based on the actual data generated from the field. The proposed framework can help stakeholders to discover the underlying sequence of their operations, and enable timely, data-driven decisions regarding operations control. Full article

The dairy industry produces large amounts of wastewater, including white and cleaning wastewater originating principally from rinsing and cleaning-in-place procedures. Their valorization into process water and non-fat milk solids, in the case of white wastewater, or the renewal of cleaning solutions could be achieved using pressure-driven membrane processes. However, it is crucial to determine the intrinsic characteristics of wastewaters, such as proximate composition and bacterial composition, to optimize their potential for valorization. Consequently, white and cleaning wastewaters were sampled from industrial-scale pasteurizers located in two different Canadian dairy processing plants. Bacterial profiles of dairy wastewaters were compared to those of tap waters, pasteurized skim milk and unused cleaning solutions. The results showed that the physicochemical characteristics as well as non-fat milk solids contents differed drastically between the two dairy plants due to different processing conditions. A molecular approach combining quantitative real-time polymerase chain reaction (qPCR) and metabarcoding was used to characterize the bacteria present in these solutions. The cleaning solutions did not contain sufficient genomic DNA for sequencing. In white wastewater, the bacterial contamination differed depending on the dairy plant (6.91 and 7.21 log10 16S gene copies/mL). Psychrotrophic Psychrobacter genus (50%) dominated white wastewater from plant A, whereas thermophilic Anoxybacillus genus (56%) was predominant in plant B wastewater. The use of cold or warm temperatures during the pasteurizer rinsing step in each dairy plant might explain this difference. The detailed characterization of dairy wastewaters described in this study is important for the dairy sector to clearly identify the challenges in implementing strategies for wastewater valorization. Full article