Discovery and Characterization of the ddx41 Gene in Atlantic Salmon: Evolutionary Implications, Structural Functions, and Innate Immune Responses to Piscirickettsia salmonis and Renibacterium salmoninarum Infections.

The innate immune response in Salmo salar, mediated by pattern recognition receptors (PRRs), is crucial for defending against pathogens. This study examined DDX41 protein functions as a cytosolic/nuclear sensor for cyclic dinucleotides, RNA, and DNA from invasive intracellular bacteria. The investigation determined the existence, conservation, and functional expression of the ddx41 gene in S. salar. In silico predictions and experimental validations identified a single ddx41 gene on chromosome 5 in S. salar, showing 83.92% homology with its human counterpart. Transcriptomic analysis in salmon head kidney confirmed gene transcriptional integrity. Proteomic identification through mass spectrometry characterized three unique peptides with 99.99% statistical confidence. Phylogenetic analysis demonstrated significant evolutionary conservation across species. Functional gene expression analysis in SHK-1 cells infected by Piscirickettsia salmonis and Renibacterium salmoninarum indicated significant upregulation of DDX41, correlated with increased proinflammatory cytokine levels and activation of irf3 and interferon signaling pathways. In vivo studies corroborated DDX41 activation in immune responses, particularly when S. salar was challenged with P. salmonis, underscoring its potential in enhancing disease resistance. This is the first study to identify the DDX41 pathway as a key component in S. salar innate immune response to invading pathogens, establishing a basis for future research in salmonid disease resistance.

Influence on denitrifying community performance by the long-term exposure to sulfamethoxazole and chlortetracycline in the continuous-flow EGSB reactors.

The response of the denitrification community to long-term antibiotic exposure requires further investigation. Here, the significantly altered denitrifying community structure and function were observed by continuous exposure to 1 mg/L sulfamethoxazole (SMZ) or chlortetracycline (CTC) for 180 d in the expanded granular sludge bed reactors. Thaurea, positively correlated with SMZ and NO3- removal efficiency (NrE), was highly enriched in the SMZ-added reactor, while, Comamons and Acinetobacter were largely inhibited. The acute inhibited and then gradual-recovered NrE (87.17-90.38 %) was observed with highly expressed narG, indicating the adaptability of Thaurea to SMZ. However, the abundance of Thaurea and Comamonas greatly decreased, while Melioribacter and Acinetobacter were largely enriched in the CTC-added reactor. CTC created more serious and continuous inhibition of NO3- reduction (NrE of 64.53-66.95 %), with lowly expressed narG. Improved NO2- reduction capacity was observed in both reactors (70.16-95.42 %) with highly expressed nirS and nosZ, revealing the adaptability of NO2- reduction populations to antibiotics.

Effects of multiple drivers of ocean global change on the physiology and functional gene expression of the coccolithophore Emiliania huxleyi.

Ongoing ocean global change due to anthropogenic activities is causing multiple chemical and physical seawater properties to change simultaneously, which may affect the physiology of marine phytoplankton. The coccolithophore Emiliania huxleyi is a model species often employed in the study of the marine carbon cycle. The effect of ocean acidification (OA) on coccolithophore calcification has been extensively studied; however, physiological responses to multiple environmental drivers are still largely unknown. Here we examined two-way and multiple driver effects of OA and other key environmental drivers-nitrate, phosphate, irradiance, and temperature-on the growth, photosynthetic, and calcification rates, and the elemental composition of E. huxleyi. In addition, changes in functional gene expression were examined to understand the molecular mechanisms underpinning the physiological responses. The single driver manipulation experiments suggest decreased nitrate supply being the most important driver regulating E. huxleyi physiology, by significantly reducing the growth, photosynthetic, and calcification rates. In addition, the interaction of OA and decreased nitrate supply (projected for year 2100) had more negative synergistic effects on E. huxleyi physiology than all other two-way factorial manipulations, suggesting a linkage between the single dominant driver (nitrate) effects and interactive effects with other drivers. Simultaneous manipulation of all five environmental drivers to the conditions of the projected year 2100 had the largest negative effects on most of the physiological metrics. Furthermore, functional genes associated with inorganic carbon acquisition (RubisCO, AEL1, and δCA) and calcification (CAX3, AEL1, PATP, and NhaA2) were most downregulated by the multiple driver manipulation, revealing linkages between responses of functional gene expression and associated physiological metrics. These findings together indicate that for more holistic projections of coccolithophore responses to future ocean global change, it is necessary to understand the relative importance of environmental drivers both individually (i.e., mechanistic understanding) and interactively (i.e., cumulative effect) on coccolithophore physiology.

Tissue specific human fibroblast differential expression based on RNAsequencing analysis.

BACKGROUND: Physical forces, such as mechanical stress, are essential for tissue homeostasis and influence gene expression of cells. In particular, the fibroblast has demonstrated sensitivity to extracellular matrices with assumed adaptation upon various mechanical loads. The purpose of this study was to compare the vocal fold fibroblast genotype, known for its unique mechanically stressful tissue environment, with cellular counterparts at various other anatomic locales to identify differences in functional gene expression profiles. RESULTS: By using RNA-seq technology, we identified differentially expressed gene programs (DEseq2) among seven normal human fibroblast primary cell lines from healthy cadavers, which included: vocal fold, trachea, lung, abdomen, scalp, upper gingiva, and soft palate. Unsupervised gene expression analysis yielded 6216 genes differentially expressed across all anatomic sites. Hierarchical cluster analysis revealed grouping based on anatomic site origin rather than donor, suggesting global fibroblast phenotype heterogeneity. Sex and age-related effects were negligible. Functional enrichment analyses based on separate post-hoc 2-group comparisons revealed several functional themes within the vocal fold fibroblast related to transcription factors for signaling pathways regulating pluripotency of stem cells and extracellular matrix components such as cell signaling, migration, proliferation, and differentiation potential. CONCLUSIONS: Human fibroblasts display a phenomenon of global topographic differentiation, which is maintained in isolation via in vitro assays. Epigenetic mechanical influences on vocal fold tissue may play a role in uniquely modelling and maintaining the local environmental cellular niche during homeostasis with vocal fold fibroblasts distinctly specialized related to their anatomic positional and developmental origins established during embryogenesis.

A comprehensive insight into the functional bacteria and genes and their roles in simultaneous denitrification and anammox system at varying substrate loadings.

Simultaneous denitrification and anammox process are newly developed wastewater treatment processes with high-nitrogen removal efficiency, but little information is available regarding its optimal operational conditions and molecular mechanisms. In this study, a lab-scale up-flow anaerobic sludge blanket bioreactor fed with nitrate and ammonia was continuously operated for 180 days to establish the simultaneous denitrification and anammox system, so as to investigate the changing patterns of nitrogen removal efficiency and functional bacteria and genes at varying substrate loadings. Results showed that the optimal removal efficiency of total nitrogen (TN) reached 92.47%, corresponding to TN loading removal rate of 0.9 kg-N m-3 day-1 that was achieved at low influent substrate concentrations and short hydraulic retention time (HRT) (4 h). High-throughput sequencing of 16S rRNA gene amplicons revealed that the predominant denitrifying and anammox bacteria in the coupling system were Thauera (relative abundance of 25.30%) and Candidatus Brocadia (relative abundance of 6.85%), respectively. Quantitative real-time PCR showed that the anammox genes (hzsA, hzsB, and hzo) and denitrifying genes (narG, napA, and nirS) demonstrated high abundance in the optimized bioreactor. Batch experiments were also conducted to determine the temporal difference in the expression of the anammox and denitrifying genes. NarG was found to play a crucial role in nitrate reduction to produce nitrite for anammox bacteria, while nirS was identified as the key genes for nitrite reduction to produce nitric oxide, which acted as an important role in both denitrification and anammox reaction.

The effect of bioaugmentation of petroleum-contaminated soil with Rhodococcus erythropolis strains on removal of petroleum from soil.

The aim of the study was to assess the impact of inoculation of petroleum-contaminated soil with the hydrocarbon-degrading bacterial strains Rhodococcus erythropolis CD 130 and CD 167 or their consortium on the removal of hydrocarbons from the soil. Additionally, changes in the activity and structure of soil autochthonous bacterial communities were studied. At the end of the experiment, the fastest hydrocarbon removal was seen in the soil treated with the CD 167 strain (38.40%) and was statistically higher compared to the removal of total petroleum hydrocarbons (TPH) observed in soils inoculated with strain CD 130 (29.8%) or bacterial consortium CD 130 + CD 167 (29.72%). The rifampicin-resistant CD 130 and CD 167 strains, introduced as single strains or a consortium, survived in the soil for 42 days. The introduction of gram-positive strains of R. erythropolis primarily caused an increase in the biomass of branched phospholipid fatty acids (PLFAs), characteristic for gram-positive bacteria. Nevertheless, changes in the concentrations of gram-positive and gram-negative PLFA markers were periodic, and at the end of the experiment, significant changes were observed only in the case of the soil bioaugmented with the CD 167 strain. After the bioaugmentation, higher values of substrate-induced respiration (SIR) were observed in all the inoculated soils compared to the non-inoculated control. Nonetheless, after 91 days of incubation, a significant decrease in soil respiration was observed in the soil treated with single CD 130 or CD 167 strains or with their consortium. The number of transcripts of the CYP153 gene obtained on days 91 and 182 reflected the results of the hydrocarbon loss. The level of expression of the alkH gene in experimental soil was estimated and found to be higher than the level of expression of the CYP153 gene but did not coincide with the loss of hydrocarbons. The introduction of strains CD 130, CD 167, or CD 130 + CD 167 caused temporary changes in the composition of the soil autochthonous bacterial community, but it seems that these changes were needed for the enhanced removal of hydrocarbons from this soil.

Responses to phytoplankton community succession and expression of key functional genes in plateau lakes under 17ß-estradiol interference.

Steroid estrogens (SEs) have garnered global attention because of their potential hazards to human health and aquatic organisms at low concentrations (ng/L). The ecosystems of plateau freshwater lakes are fragile, the water lag time is long, and pollutants easily accumulate, making them more vulnerable to the impact of SEs. However, the knowledge of the impact of SEs on the growth and decomposition of phytoplankton communities in plateau lakes and the eutrophication process is limited. This study investigated the effects and mechanisms of SEs exposure on dominant algal communities and the expression of typical algal functional genes in Erhai Lake using indoor simulations and molecular biological methods. The results showed that phytoplankton were sensitive to 17ß-estradiol (E2ß) pollution, with a concentration of 50, and 100 ng/L E2ß exposure promoting the growth of cyanophyta and chlorophyta in the short term; this poses an ecological risk of inducing algal blooms. E2ß of 1000 ng/L exposure led to cross-effects of estrogenic effects and toxicity, with most phytoplankton being inhibited. However, small filamentous cyanobacteria and diatoms exhibited greater tolerance; Melosira sp. even exhibited "low inhibition, high promotion" behavior. Exposure to E2ß reduced the Shannon-Wiener diversity index (H'), Pielou index (J), and the number of dominant algal species (S) in phytoplankton communities, leading to instability in community succession. E2ß of 50 ng/L enhanced the expression levels of relevant functional genes, such as ftsH, psaB, atpB, and prx, related to Microcystis aeruginosa. E2ß of 50 ng/L and 5 mg/L can promote the transcription of Microcystis toxins (MC) related genes (mcyA), leading to more MC production by algal cells.

Development and performance evaluation of a novel elastic bacterial nanocellulose/polyurethane small caliber artificial blood vessels.

There is an increasing demand for small-diameter blood vessels. Currently, there is no clinically available small-diameter artificial vessel. Bacterial nanocellulose (BNC) has vast potential for applications in artificial blood vessels due to its good biocompatibility. At the same time, medical polyurethane (PU) is a highly elastic polymer material widely used in artificial blood vessels. This study reports a composite small-diameter BNC/PU conduit using a non-solvent-induced phase separation method with the highly hydrophilic BNC tube as the skeleton and the hydrophobic polycarbonate PU as the filling material. The results revealed that the compliance and mechanical matching of BNC/PU tubes were higher than BNC tubes; the axial/radial mechanical strength, burst pressure, and suture strength were significantly improved; the blood compatibility and cell compatibility were also excellent. The molecular and subcutaneous embedding tests showed that the composite tubes had lighter inflammatory reactions. The results of the animal substitution experiments showed that the BNC/PU tubes kept blood flow unobstructed without tissue proliferation after implantation in rats for 9 months. Thus, the BNC/PU small-diameter vascular prosthesis had the potential for long-term patency and acted as an ideal material for small-diameter vessels.

Gibberellin Positively Regulates Tomato Resistance to Tomato Yellow Leaf Curl Virus (TYLCV).

Tomato yellow leaf curl virus (TYLCV) is a prominent viral pathogen that adversely affects tomato plants. Effective strategies for mitigating the impact of TYLCV include isolating tomato plants from the whitefly, which is the vector of the virus, and utilizing transgenic lines that are resistant to the virus. In our preliminary investigations, we observed that the use of growth retardants increased the rate of TYLCV infection and intensified the damage to the tomato plants, suggesting a potential involvement of gibberellic acid (GA) in the conferring of resistance to TYLCV. In this study, we employed an infectious clone of TYLCV to inoculate tomato plants, which resulted in leaf curling and growth inhibition. Remarkably, this inoculation also led to the accumulation of GA3 and several other phytohormones. Subsequent treatment with GA3 effectively alleviated the TYLCV-induced leaf curling and growth inhibition, reduced TYLCV abundance in the leaves, enhanced the activity of antioxidant enzymes, and lowered the reactive oxygen species (ROS) levels in the leaves. Conversely, the treatment with PP333 exacerbated TYLCV-induced leaf curling and growth suppression, increased TYLCV abundance, decreased antioxidant enzyme activity, and elevated ROS levels in the leaves. The analysis of the gene expression profiles revealed that GA3 up-regulated the genes associated with disease resistance, such as WRKYs, NACs, MYBs, Cyt P450s, and ERFs, while it down-regulated the DELLA protein, a key agent in GA signaling. In contrast, PP333 induced gene expression changes that were the opposite of those caused by the GA3 treatment. These findings suggest that GA plays an essential role in the tomato's defense response against TYLCV and acts as a positive regulator of ROS scavenging and the expression of resistance-related genes.

Functional Gene Expression Signatures from On-Treatment Tumor Specimens Predict Anti-PD1 Blockade Response in Metastatic Melanoma.

Functional gene expression signatures (FGES) from pretreatment biopsy samples have been used to predict the responses of metastatic melanoma to immune checkpoint blockade (ICB) therapies. However, there are no predictive FGE signatures from patients receiving treatment. Here, using the Elastic Net Regression (ENLR) algorithm, we analyzed transcriptomic and matching clinical data from a dataset of patients with metastatic melanoma treated with ICB therapies and produced an FGE signature for pretreatment (FGES-PRE) and on-treatment (FGES-ON). Both the FGES-PRE and FGES-ON signatures are validated in three independent datasets of metastatic melanoma as the validation set, achieving area under the curve (AUC) values of 0.44-0.81 and 0.82-0.83, respectively. Then, we combined all test samples and obtained AUCs of 0.71 and 0.82 for the FGES-PRE and FGES-ON signatures, respectively. The FGES-ON signatures had a higher predictive value for prognosis than the FGES-PRE signatures. The FGES-PRE and FGES-ON signatures were divided into high- and low-risk scores using the signature score mean value. Patients with a high FGE signature score had better survival outcomes than those with low scores. Overall, we determined that the FGES-ON signature is an effective biomarker for metastatic melanoma patients receiving ICB therapy. This work would provide an important theoretical basis for applying FGE signatures derived from on-treatment tumor samples to predict patients' therapeutic response to ICB therapies.

Potential utilization of vitamin C industrial effluents in agriculture: Soil fertility and bacterial community composition.

The potential of industrial effluents from vitamin C (VC) production was assessed for agricultural applications by monitoring plant growth, soil properties, and microbial community structure. The results demonstrated that two types of effluents-residue after evaporation (RAE) and concentrated bacterial solution after ultrafiltration (CBS)-had positive effects on the yield and VC content of pak choi. The highest yield and VC content were achieved with a combined RAE-CBS treatment (55.82 % and 265.01 % increase, respectively). The soil fertility was also enhanced by the application of RAE and CBS. Nitrate nitrogen and organic carbon contents in the soil were positively correlated with the RAE addition, while ammonium nitrogen and available phosphorus were positively correlated with the CBS addition. The diversity of bulk and rhizosphere soil bacterial communities increased significantly after the addition of RAE-CBS. The abundance of Sphingomonas and Rhizobium significantly increased after the RAE-CBS treatment, which affected aromatic compound hydrolysis and nitrogen fixation positively. Changes in plant growth and soil fertility were closely related to the upregulation of functional gene expression related to C, N, and P cycling. RAE and CBS application exerted various positive synergistic effects on plant growth, soil fertility, and bacterial community structure. Consequently, the study results confirmed the potential of RAE and CBS application in agriculture. This study provides an innovative solution for utilizing VC industrial wastewater in agriculture in a resourceful and economically beneficial manner while alleviating the corresponding environmental burden.

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning.

Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on microbial functional gene expressions. Here, we applied functional gene array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA to assess expressed functional genes in active soil microbial communities after nine years of experimental warming in a tallgrass prairie. Our results showed that warming significantly altered the community wide gene expressions. Specifically, expressed genes for degrading more recalcitrant carbon were stimulated by warming, likely linked to the plant community shift toward more C4 species under warming and to decrease the long-term soil carbon stability. In addition, warming changed expressed genes in labile C degradation and N cycling in different directions (increase and decrease), possibly reflecting the dynamics of labile C and available N pools during sampling. However, the average abundances of expressed genes in phosphorus and sulfur cycling were all increased by warming, implying a stable trend of accelerated P and S processes which might be a mechanism to sustain higher plant growth. Furthermore, the expressed gene composition was closely related to both dynamic (e.g., soil moisture) and stable environmental attributes (e.g., C4 leaf C or N content), indicating that RNA analyses could also capture certain stable trends in the long-term treatment. Overall, this study revealed the importance of elucidating functional gene expressions of soil microbial community in enhancing our understanding of ecosystem responses to warming.

Co-liposomes having anisamide tagged lipid and cholesteryl tryptophan trigger enhanced gene transfection in sigma receptor positive cells.

Selective gene transfection could be strategy of interest for reducing off-target gene expression and toxicity. In this respect, sigma receptors are found to be over-expressed in many human tumors and liposomal formulations with ability to target these sigma receptors may improve the transfection efficiency to a significant level. To this direction, six novel lipids have been synthesized with different hydrophobic segments such as a long hydrophobic chain or a cholesteryl group and L-tryptophan as the head group. Three of them, Lipid 1, 3 and 5 possessed cationic Me3N(+) moiety at the distal end. In contrast each of the other three Lipid 2, 4 and 6 possessed sigma receptor targeting anisamide group with no cationic charge. Mixing of cationic and anisamide counterparts of the same lipid in a molar ratio of 1:1 produced co-liposomes L-M-1 (Lipid 1+2), L-M-2 (Lipid 3+4) and L-M-3 (Lipid 5+6). These co-liposomes, while keeping the sigma targeting anisamide tag intact, showed good DNA binding and release which were optimized from EB intercalation and gel electrophoresis assays. Inclusion of a zwitterionic, fusogenic natural lipid, DOPE, into the co-liposomes further improved the binding efficiencies of the lipid mixtures with DNA. These co-liposomes having cationic and anisamide lipids and DOPE were highly selective toward sigma positive HEK293 and HEK293T cells compared to the sigma negative HeLa cells. As evidenced from both FACS and luciferase assay, a lipid mixture comprising Lipid 3, 4 and DOPE in a molar ratio of 1:1:1 (L-M-2D1) was the best for transfection of reporter pEGFP-C3 and functional pCEP4-p53 gene plasmids. Anisamide mediated sigma receptor selectivity was further probed by pre-incubating the transfecting cells with lipids possessing anisamide and by quantification of the un-transfected plasmid DNA. Also each formulation was highly non-toxic in the cell lines examined.

Effect of particle size on the performance of autotrophic nitrogen removal in the granular sludge bed reactor and microbiological mechanisms.

The effect of particle size on the performance of autotrophic nitrogen removal in the granular sludge bed reactor (GSB-ANR) and microbiological mechanisms were investigated. The results indicated that performance of GSB-ANR process decreased gradually with the increase of the granular sludge size. Indeed small granules ranging between 0.5 and 0.9mm had a higher nitrogen removal capacity than large ones. The reasons of this effect were that (i) the aerobic ammonium oxidizing capacity of microorganisms was the bottle neck of nitrogen removal in GSB-ANR process, and the increase of aerobic ammonium oxidizing activity enhances nitrite production in nitrification and promotes subsequent nitrite consumption during anaerobic ammonia oxidation; (ii) the aerobic/anaerobic zone separation in granular sludge was the key factor affecting the aerobic ammonium oxidizing capacity of microorganisms. The small granules had a larger aerobic functional zone (75.1%) which was profitable for up-regulating the expression level of functional gene in aerobic ammonium oxidizing microorganisms.