Primary Enrichment Research Articles

Design of a duplex Loop-mediated isothermal amplification assay suitable for real-time, and end-point, colorimetric detection of Vibrio parahaemolyticus, and a universal Internal Amplification Control, in mussel samples

Vibrio parahaemolyticus remains as one of the most important foodborne pathogens worldwide, causing gastrointestinal disease in humans due to the consumption of raw, or undercooked, seafood. Even though molecular techniques, like PCR and qPCR, have allowed to overcome most of the limitations associated to culture-based methods, some persist such as the need for highly trained personnel, or the need to acquire expensive equipment. Loop-mediated isothermal amplification, LAMP, has emerged as a promising tool to solve these issues. The present study reports the development of a novel LAMP-based method for the detection of V. parahaemolyticus in mussels. This assay targets the gene toxR, and implements a novel, universal, freely available Internal Amplification Control (IAC) which was detected in a multiplex real-time LAMP format, where it is differentiated by melt curve analysis (86.70 ± 0.32 °C and 90.24 ± 0.34 °C for toxR and IAC respectively) and did not impact the analytical sensitivity of the target. Alternatively, the IAC was also applied in a parallel reaction and the assays performed by end-point, colorimetric LAMP. This novel IAC allowed to identify reaction inhibition due to matrix effect, and rule out false negative results. This new assay was combined with the ISO 21872 enrichment protocol, and the evaluation of spiked mussel samples indicated that an LOD95 of 14.5 and 10.8 CFU/25g could be reached after the primary 6h and secondary 24h enrichment steps by real-time LAMP, and 27.9 and 10.9 CFU/25g by naked-eye, color LAMP. It was important to note that in addition to these differences in terms of LOD95, a higher number of samples presenting reaction inhibition was observed after the primary enrichment, compared to the secondary, all successfully identified thanks to the new IAC; and also that statistically longer amplification times were required (Cq values of 19.47 ± 7.87 and 7.90 ± 1.20 respectively). The overall evaluation of the method returned values of diagnostic sensitivity, specificity and accuracy of 100 % along with an index of concordance of 1.00. These results were consistent regardless if the real-time, or the colorimetric, LAMP strategy was followed.

SPECC1 as a pan-cancer biomarker: unraveling its role in drug sensitivity and resistance mechanisms

Previous studies have shown a relationship between SPECC1 and the prognosis of breast cancer, indicating a potential function for SPECC1 in the initiation and progression of cancer. However, the role played by SPECC1 in other tumors is not yet known. Therefore, we used bioinformatics techniques to conduct a thorough investigation into the possible mechanism of SPECC1 in pan-cancer, analyzing data reported in the literature as well as databases such as GTEx and CCLE, cBioportal, TCGA, and UCSC XENA. Comparing the results with matching normal tissues, the majority of cancers, including pancreatic adenocarcinoma (PAAD) and breast invasive carcinoma (BRCA), exhibited higher levels of SPECC1, while hepatocellular carcinoma (HCC) showed lower expression levels. SPECC1 was also found to be genetically mutated in endometrial cancer, sarcoma, and esophageal cancer. The prognosis of lung adenocarcinoma, kidney papillary cell carcinoma, and breast cancer is highly correlated with dysregulation of SPECC1 expression. This work helps guide clinical therapy by highlighting the sensitivity of tumor-treating medicines and the prognostic importance of SPECC1 in various malignancies. KEGG pathway enrichment analysis revealed focused adhesion, collagen-containing extracellular matrix (collagen), and the primary enrichment domains for SPECC1-related genes. These findings were obtained through gene annotation (GO) examination of SPECC1 expression. Primary mediators of the cytokine-cytokine receptor interaction include PICOC1-associated genes, cell-substrate junction genes, and extracellular matrix containing collagen. PICOC1-associated genes primarily mediate the PI3K-AKT signaling pathway. Drug sensitivity assay showed that SPECC1 high-expressing cell lines were more sensitive to docetaxel, doxorubicin, etc. In conclusion, the current study shows how SPECC1 is expressed in different cancers and how this expression relates to the prognosis of the tumor. It also revealed the mutations and copy number variations of SPECC1 in various tumors and its potential involvement in cellular pathway regulatory networks and cytological processes. This study examines the relationship between immune genes, cellular infiltration, and immunological scores in the tumor microenvironment, which explain the severity of the disease. This study looks at the response of SPEC1 expression to anticancer therapy. Explains the prognostic significance and drug response of SPECC-1.

Garnet as a carrier of HREEs in highly fractionated peraluminous granite: Implications for the formation of ion-absorption HREE deposits

Ion-absorption rare earth element (REE) deposits in South China are the world’s most important source of heavy REEs (HREEs). These deposits were formed by the weathering of granitic rocks whose formation involved primary HREE enrichment. Previous studies have identified the key role of late-stage magmatic evolution, especially the magmatic–hydrothermal transition stage played in HREE enrichment, but the detailed processes need further investigation. Garnet is a common HREE carrier in parent rocks and also a main contributor of these elements in formation of ion-absorption HREE deposits. Here, we investigate textural and compositional variations in garnets from parent rock (muscovite granite) of the Dabu ion-absorption HREE deposit to constrain the primary HREE enrichment of the parent rock during late-stage magmatic evolution. Mass-balance calculations reveal that garnet accounts for ∼67 % of the Y and 64 % of the REEs in the Dabu muscovite granite. The garnets can be classified into three types: i) magmatic garnets (Grt-1A) are intergrown with plagioclase, K-feldspar, and quartz, host both melt and mineral inclusions, and have high REE + Y contents (6488–19,215 ppm); ii) magmatic–hydrothermal garnets (Grt-1B) occur as overgrowths on Grt-1A, host both melt and fluid inclusions, and have intermediate REE + Y contents (2681–8683 ppm); and iii) hydrothermal garnets (Grt-2) are intergranular with quartz and altered biotite, host primary fluid inclusions, and have the lowest REE + Y contents (476–1247 ppm). The texture and composition of the three types of garnet indicate that the magma have undergone a transition from a volatile-undersaturated to a volatile-oversaturated aqueous system. The fluid, from which some REE minerals precipitated, present in the magma system was derived from the magma itself rather than from an external source, as evidenced by the similarity in Nd isotopic composition between the REE minerals and the whole-rock samples. During this transition, the presence of high-HREE garnet prevents the HREE partitioning into refractory minerals (e.g., zircon, REE-bearing phosphate) or extracting from the magma system by the fluid. Our findings show that granites containing high-HREE garnet have high potential for forming ion-absorption HREE deposits and that garnet can reliably record their magmatic evolution.

Expression characteristics of TBC1D4 activating protein molecule and identification of key module genes for preventing thyroid cancer progression

Endocrine tumors like thyroid carcinoma are becoming more frequent. No clinically informative predictors were found. Thus, effective gene networks and representative biomarkers can illuminate thyroid cancer prevention molecular mechanisms. TBC1D4 is an activating protein molecule that plays an important role in regulating cell metabolism and signal transduction. The aim of this study was to investigate the expression characteristics of TBC1D4 activating protein molecules and identify key module genes that prevent thyroid cancer progression. GSE65144 data were downloaded from GEO. “limma” in R found DEGs with a false discovery rate < 0.05 and a log2 fold change <1. WGCNA builds gene co-expression networks, screens key modules, and filters hub genes. Overlapping genes become hub genes. Hub genes underwent GO and KEGG pathway enrichment analysis. We used Lasso to extract hub gene expression results' distinctive genes. Key genes. GEPIA database determined expression and survival impact. A total of 3220 DEGs. Thyroid cancer was mostly associated with darkred, darkturquoise, and green modules. Venn screened 639 hub genes. Cytokine-cytokine receptor interaction was the primary KEGG enrichment. Hub genes were 14. Finally, ARHGAP6, TBC1D4, and TC2N were important genes. Through gene screening and functional enrichment analysis, we identified a group of genes related to TBC1D4 activating protein and constructed the corresponding protein interaction network.

Cobalt remobilization during tectonic–hydrothermal overprinting: A case from the Tuolugou Co(–Au) deposit in East Kunlun Orogenic Belt, China

Stratiform Cu-Co deposits hosted in (meta-) sedimentary and volcaniclastic rocks contribute two-thirds of the global Co supply. However, the mechanisms driving Co remobilization during tectonic-hydrothermal overprinting events remain poorly understood. As a dominant Co repository, pyrite can provide valuable insights into mineralization history due to its refractory nature. Here, we present the first micro-analytical investigation of pyrite from the Tuolugou Co(–Au) deposit in East Kunlun Orogenic Belt. Ore textures indicate that Co mineralization is attributed to two distinct stages: primary enrichment and subsequent overprinting processes. The former is characterized by pyrite (PyI with up to 3.92 wt% Co) remnants exhibiting oscillatory zones, while the latter is marked by deformation of pyrite (PyII) ores. Three overprinting episodes, namely Da, Db, and Dc, are further distinguished according to varying extents of deformation and mineral assemblages. The Da is characterized by synkinematic PyIIa (up to 4.18 wt% Co) augens, which were most likely formed via pressure–solution mechanism. The Db is represented by polygonal PyIIb (up to 4.75 wt% Co) and siegenite with 120° triple–point junctions. The random orientation and rare intragrain misorientation of cobaltiferous sulfides at Db suggest their formation by recrystallization without plastic strains. The Dc resulted in the formation of Co ± As–rich PyIIc (up to 5.36 wt% Co) along with minor occurrence of cobaltite–gersdorffite, pyrrhotite (up to 1.25 wt% Co), and marcasite (up to 1.28 wt% Co). The PyIIc replacing PyI underscores the role of fluid-coupled dissolution and precipitation during fluid–rock interactions in the formation of these cobaltiferous sulfide assemblages at Dc. The presence of PyIIc infilling within the PyI fissures, in conjunction with the transition from siegenite to cobaltite–gersdorffite, suggests a shift towards low fO2 and low temperature conditions under relatively brittle setting. There is a discernible disparity in sulfur isotope compositions between the two mineralization stages. The PyI exhibits a narrow range of δ34SV–CDT values from –2.14 to 1.35 ‰, indicating a magmatic sulfur origin. In contrast, PyII displays a wide δ34SV–CDT range of –5.22 to 6.16 ‰, suggesting an involvement of strata sulfur during the overprinting stage. Monazite U-Pb dating has effectively constrained two mineralization events. The ca. 453 Ma age implies a potential correlation of the primary Co mineralization with the Late Ordovician to Early Silurian exhalative-syngenetic processes in a Proto–Tethyan-related post–collisional extension setting. Conversely, the ca. 190 Ma age indicates that Co remobilization was instigated by the early Mesozoic ductile–brittle deformation associated with the Paleo-Tethyan orogenesis. Finally, geochemical modeling was performed by simulating the interaction of a Co-rich acidic, reducing fluid with typical quartz-albitite rocks. The simulations demonstrate the appearance of independent Co minerals such as Co-pentlandite during the reaction progression, greatly supporting ore upgrading via tectonic-hydrothermal overprinting.

Anomalous cobalt enrichment in pyrite from an altered mafic dike in the Linglong gold deposit, Jiaodong Peninsula, China: Mechanisms and implications

Traditionally, gold deposits in the Jiaodong gold province of China have been regarded as gold-only deposits lacking economic base metals. However, recent studies found some cobalt (Co) enrichment in those deposits. The mechanisms of this Co enrichment remain poorly understood. In this study, we identified a type of pyrite highly enriched in Co (concentrations up to 32800 ppm) at the Linglong gold deposit, Jiaodong gold province. The pyrite was collected from a hydrothermally altered mafic dike contacting with gold ore veins. To decipher the enrichment mechanisms of Co, in-situ textural, elemental and sulfur isotopic analyses were conducted on the pyrite. The pyrite typically exhibits core-mantle-rim textures. The cores (Py-m1) have high Co concentrations (up to 5950 ppm) with homogeneous texture and elemental distribution, which could be the primary pyrite formed by pyritization of the mafic dike. The mantles (Py-m2) have the highest Co concentrations (up to 32800 ppm) and contain abundant mineral inclusions (chalcopyrite, galena, and sphalerite) and pores, showing the formation through coupled dissolution-reprecipitation (CDR) reactions. The rims (Py-m3) have low concentrations of Co (0.14–559 ppm) and show cubic shapes, forming directly from hydrothermal fluids. The δ34S values increase from the cores (4.2 ‰ to 9.1 ‰, mean of 8.0 ‰) to the mantles (8.9 ‰ to 11.9 ‰), but vary between the above two in the rims (4.2 ‰ to 12.2 ‰, mean of 9.0 ‰). The sulfur isotopic compositions of the Py-m are similar to those of pyrite (4.8 ‰ to 9.5 ‰) from the neighboring auriferous quartz-sulfide veins at Linglong in previous study. Combined with the geological and textural features, it is inferred that hydrothermal fluids during gold mineralization extracted abundant Co from the mafic dikes, leading to the primary enrichment of Co in the Py-m1. The Py-m1 was dissolved and re-precipitated during subsequent hydrothermal activities, forming Py-m2 with enhanced re-enrichment of Co. Basically, the Co-rich mafic dike provided the initial enrichment of Co while the gold-bearing hydrothermal fluids contributed to concentrate Co further. Considering the widespread mafic rocks and extensive hydrothermal activities during gold mineralization throughout the Jiaodong gold province, there might be a considerable Co resource formed through the above processes.

Lactiplantibacillus plantarum N4 ameliorates lipid metabolism and gut microbiota structure in high fat diet-fed rats.

Lowing blood lipid levels with probiotics has good application prospects. This study aimed to isolate probiotics with hypolipidemic efficacy from homemade na dish and investigate their mechanism of action. In vitro experiments were conducted to determine the cholesterol-lowering ability of five isolates, with results showing that Lactiplantibacillus plantarum N4 exhibited a high cholesterol-lowering rate of 50.27% and significant resistance to acid (87%), bile salt (51.97%), and pepsin (88.28%) in simulated gastrointestinal fluids, indicating promising application prospects for the use of probiotics in lowering blood lipids. The findings from the in vivo experiment demonstrated that the administration of N4 effectively attenuated lipid droplet accumulation and inflammatory cell infiltration in the body weight and liver of hyperlipidemic rats, leading to restoration of liver tissue morphology and structure, as well as improvement in lipid and liver biochemical parameters. 16S analysis indicated that the oral administration of N4 led to significant alterations in the relative abundance of various genera, including Sutterella, Bacteroides, Clostridium, and Ruminococcus, in the gut microbiota of hyperlipidemia rats. Additionally, fecal metabolomic analysis identified a total of 78 metabolites following N4 intervention, with carboxylic acids and their derivatives being the predominant compounds detected. The transcriptomic analysis revealed 156 genes with differential expression following N4 intervention, leading to the identification of 171 metabolic pathways through Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Notably, the glutathione metabolism pathway, PPAR signaling pathway, and bile secretion pathway emerged as the primary enrichment pathways. The findings from a comprehensive multi-omics analysis indicate that N4 influences lipid metabolism and diminishes lipid levels in hyperlipidemic rats through modulation of fumaric acid and γ-aminobutyric acid concentrations, as well as glutathione and other metabolic pathways in the intestinal tract, derived from both the gut microbiota and the host liver. This research offers valuable insights into the therapeutic potential of probiotics for managing lipid metabolism disorders and their utilization in the development of functional foods.

Silencing METTL14 alleviates liver injury in non-alcoholic fatty liver disease by regulating mitochondrial homeostasis.

Mitochondrial dysfunction is an important pathogenic factor in non-alcoholic fatty liver disease (NAFLD). Methyltransferase-like 14 (METTL14) has been implicated in mitochondrial fission processes. This research aimed to investigate the mechanism of METTL14 in the mitochondrial function of NAFLD. We first established NAFLD mouse models and cell models, recording body and liver weights and examining pathological changes in liver tissues. Subsequently, serum levels of liver function indices (aspartate aminotransferase [AST], alanine aminotransferase [ALT], total cholesterol [TC], and triglycerides [TG]), inflammatory markers (tumor necrosis factor-alpha [TNF-α], interleukin [IL]-6, and IL-1β), and mitochondrial dysfunction indicators (fission 1 protein [Fis1], dynamin-related protein 1 [Drp1], mitofusin 2 [Mfn2], SID1 transmembrane family member 2 [SIDT2], and mitochondrial membrane potential [MMP]) in the liver and cells were evaluated. The N6-methyladenosine (m6A) modification level of primary microRNA (pri-miRNA) and m6A enrichment on pri-miR-34a were quantified. Co-immunoprecipitation and dual-luciferase reporter gene assays were utilized to validate gene interactions. Our findings revealed highly elevated METTL14 expression in NAFLD mouse and cell models. Silencing METTL14 reduced weight gain and mitigated adverse liver function indices, inflammation, hepatic steatosis, and structural damage in NAFLD mice. It also led to a decrease in Fis1/Drp1 levels and an increase in MMP/Mfn2 in the liver and cells. Moreover, METTL14 increased the m6A level, promoting the binding of DiGeorge syndrome critical region 8 (DGCR8) to pri-miR-34a, which enhanced miR-34a-5p expression. Databases and dual-luciferase reporter gene assays indicated that miR-34a-5p could suppress SIDT2 expression. The overexpression of miR-34a-5p or inhibition of SIDT2 expression negated the alleviative effects of METTL14 silencing on mitochondrial homeostasis imbalance. In conclusion, METTL14, through m6A modification, modulates the miR-34a-5p/SIDT2 axis, impairing mitochondrial homeostasis in NAFLD.

Abstract 141: Lesion Site-specific Mass Spectrometry Analysis Of Human Carotid Plaques Reveals Strongest Association Of The Necrotic Core And Fibrous Cap Proteome With Plaque Stability

The spatial impact of the plaque proteome on atherosclerotic plaque stability remains largely unknown. In this study, we performed mass spectrometry-based proteomics of various carotid plaque subregions (media, necrotic core, fibrous cap), using guided laser capture micro-dissections (LCM) of FFPE tissue in a matched cohort of 112 patients undergoing carotid endarterectomy (CEA) to study the impact of the plaque proteome, not only on lesion stability, but also on subregional changes of expression. Further, we performed a histological analysis according to the AHA classification and combined the data with clinical information on risk factors, comorbidities, and patient symptoms. Our LCM mass spectrometry analysis yielded over 3000 proteins for each plaque subregion. Gene set enrichment analysis revealed a high abundance of extracellular proteins and vice versa for cellular proteins. Subregion analysis identified the necrotic core and the fibrous cap to display the most significant changes in proteins associated with the stability status, whereas the media proteome remained largely unaffected. Primary and secondary enrichment analysis revealed synthetic vascular smooth muscle cells as the major source of these proteins. In addition, we analyzed the serum proteome of more than 500 patients (including non-athero control patients) with overlap from the tissue cohort. We combined these with histological evaluation and a complete set of clinical data. We used these two datasets for developing tissue and serological markers associated with plaque stability. In summary, our approach utilized LCM mass spectrometry, histological evaluation, and clinical data to analyze the association of different lesion subregions on plaque stability. We are able to demonstrate a high through-put method to identify potential protein markers relevant to atherosclerotic plaque stability.

Integrative analysis unveils ECM signatures and pathways driving hepatocellular carcinoma progression: A multi-omics approach and prognostic model development.

Liver hepatocellular carcinoma (LIHC) is a highly lethal form of cancer that is among the deadliest cancer types globally. In terms of cancer-related mortality rates, liver cancer ranks among the top three, underscoring the severity of this disease. Insufficient analysis has been conducted to fully understand the potential value of the extracellular matrix (ECM) in immune infiltration and the prognostic stratification of LIHC, despite its recognised importance in the development of this disease. The scRNA-seq data of GSE149614 was used to conduct single-cell analysis on 10 LIHC samples. CellChat scores were calculated for seven cell populations in the descending cohort to investigate cellular communication, while PROGENy scores were calculated to determine tumour-associated pathway scores in different cell populations. The pathway analysis using GO and KEGG revealed the enrichment of ECM-associated genes in the pathway, highlighting the potential role of the ECM in LIHC development. By utilizing the TCGA-LIHC cohort, an ECM-based prognostic model for LIHC was developed using Lasso regression. Immune infiltration scores were calculated using two methods, and the performance of the ECM-related risk score was evaluated using an independent cohort from the CheckMate study. To determine the precise expression of ECM-associated risk genes in LIHC, we evaluated hepatocellular carcinoma cell lines using a range of assays, including Western blotting, invasion assays and Transwell assays. Using single-cell transcriptome analysis, we annotated the spatially-specific distribution of major immune cell types in single-cell samples of LIHC. The main cell types identified and annotated included hepatocytes, T cells, myeloid cells, epithelial cells, fibroblasts, endothelial cells and B cells. The utilisation of cellchat and PROGENy analyses enabled the investigation and unveiling of signalling interactions, protein functionalities and the prominent influential pathways facilitated by the primary immune cell types within the LIHC. Numerous tumour pathways, including PI2K, EGFR and TGFb, demonstrated a close correlation with the involvement of ECM in LIHC. Moreover, an evaluation was conducted to assess the primary ECM-related functional changes and biological pathway enrichment in LIHC. Differential genes associated with ECM were identified and utilised to create prognostic models. The prognostic stratification value of these models for LIHC patients was confirmed through validation in multiple databases. Furthermore, through immune infiltration analysis, it was discovered that ECM might be linked to the irregular expression and regulation of numerous immune cells. Additionally, histone acetylation was mapped against gene mutation frequencies and differential expression profiles. The prognostic stratification efficacy of the ECM prediction model constructed in the context of PD-1 inhibitor therapy was also examined, and it exhibited strong stratification performance. Cellular experiments, including Western blotting, invasion and Transwell assays, revealed that ECM-associated risk genes have a promoting effect on the development of LIHC. The creation of biomarkers for LIHC using ECM-related genes unveiled substantial correlations with immune microenvironmental infiltration and functional mutations in various tumour pathways. This enlightens us to the possibility that the influence of ECM on tumours may extend beyond simply promoting the fibrotic process and the stromal composition of tumours.

Elucidating the molecular mechanisms of sepsis: Identifying key aging-related biomarkers and potential therapeutic targets in the treatment of sepsis.

Sepsis remains a crucial global health issue characterized by high mortality rates and a lack of specific treatments. This study aimed to elucidate the molecular mechanisms underlying sepsis and to identify potential therapeutic targets and compounds. High-throughput sequencing data from the GEO database (GSE26440 as the training set and GSE13904 and GSE32707 as the validation sets), weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, alongside a combination of PPI and machine learning methods (LASSO and SVM) were utilized. WGCNA identified the black module as positively correlated, and the green module as negatively correlated with sepsis. Further intersections of these module genes with age-related genes yielded 57 sepsis-related genes. GO and KEGG pathway enrichment analysis, PPI, LASSO, and SVM selected six hub aging-related genes: BCL6, FOS, ETS1, ETS2, MAPK14, and MYC. A diagnostic model was constructed based on these six core genes, presenting commendable performance in both the training and validation sets. Notably, ETS1 demonstrated significant differential expression between mild and severe sepsis, indicating its potential as a biomarker of severity. Furthermore, immune infiltration analysis of these six core genes revealed their correlation with most immune cells and immune-related pathways. Additionally, compounds were identified in the traditional Chinese medicine Danshen, which upon further analysis, revealed 354 potential target proteins. GO and KEGG enrichment analysis of these targets indicated a primary enrichment in inflammation and immune-related pathways. A Venn diagram intersects these target proteins, and our aforementioned six core genes yielded three common genes, suggesting the potential efficacy of Danshen in sepsis treatment through these genes. This study highlights the pivotal roles of age-related genes in the molecular mechanisms of sepsis, offers potential biomarkers, and identifies promising therapeutic compounds, laying a robust foundation for future studies on the treatment of sepsis.

The Snow Lake Deposits in Manitoba, Canada: Formation of Metamorphosed Amphibolite Facies Orogenic Gold Deposits During a Progressive and Prograde Orogenic Event

Abstract The Snow Lake camp is located in the ca. 1.89 Ga Flin Flon-Glennie Complex in the Paleoproterozoic Trans-Hudson orogen, Manitoba, Canada. The Flin Flon-Glennie Complex is bordered by the ca. 1.855 to 1.84 Ga metasedimentary Kisseynew domain to the north and by the Archean Superior craton to the east and is underlain by the Archean Sask microcraton. It hosts several orogenic gold deposits, including the No. 3 zone, Boundary zone, and New Britannia deposit (Toots, Dick, Hogg, Ruttan, and Mine East zones), which formed during thrusting of the Flin Flon-Glennie Complex and Kisseynew domain over the Sask microcraton. The New Britannia deposit produced 1.6 Moz Au and is the largest orogenic gold deposit in the Trans-Hudson orogen in Manitoba. The deposits consist of quartz ± carbonate veins surrounded by alteration zones of biotite, hornblende, plagioclase ± carbonate, diopside, orthoclase, and garnet. The veins and ore zones are folded within the hinge of the synthrusting Nor-Acme anticline, which has an axial plane cleavage defined by biotite and hornblende, but they also cut across the hinge of the anticline and contain foliated fragments of the wall rocks. These mutually overprinting relationships suggest that the veins and ore zones are synfolding. Garnet, diopside, and amphibole porphyroblasts grew during folding because they overgrow the foliation, which also wraps around them. Inclusions of gold and sulfide minerals within the porphyroblasts indicate that mineralization was emplaced early during folding at greenschist or lower amphibolite metamorphic conditions prior to the growth of the porphyroblasts at peak middle amphibolite metamorphic conditions. These observations are corroborated by laser ablation-inductively coupled plasma-mass spectrometry element maps of arsenopyrite grains. These maps reveal a primary internal enrichment of gold in arsenopyrite grains from the Toots, No. 3, and Boundary zones and a lack of primary lattice-bound gold in arsenopyrite grains of the Dick, Ruttan, and Mine East zones. The latter results from the deposition or remobilization of gold during a second hydrothermal event that occurred during shearing of these ore zones along a structure, the Howe Sound fault, which acted as a detachment surface during folding. The Snow Lake deposits are examples of orogenic gold deposits that formed early during a major thrusting and folding event and were later modified and metamorphosed at middle amphibolite facies conditions during the same progressive orogenic event.

Enriched Regions of 228Ra Along the U.S. GEOTRACES Pacific Meridional Transect (GP15)

AbstractThe half‐life of 228Ra (5.7 years) aligns well with near‐surface and near‐bottom ocean mixing timescales. Because 228Ra is sourced from sediments, regions of enhanced activity represent water that has recently interacted with sediments on the continental margin or seabed. The GP15 meridional transect from Alaska to Tahiti along152°W encountered several regions in the upper ocean where 228Ra was enriched. These enrichments follow surface and subsurface ocean current patterns and pair with earlier measurements of 228Ra and transient radionuclides to reveal the origins of these enriched regions. An enriched region at Alaska margin stations 1–3 was sourced locally but did not extend to the Alaskan trench at station 4. A large shallow region between 47° and 32°N. was sourced from the west by the North Pacific Current; another shallow enriched region between 11° and 5° N was also sourced from the west by the North Equatorial Countercurrent. Subsurface enrichments (100–400 m) between 18 and 47°N were associated with Central Mode Water and North Pacific Intermediate Water. The 228Ra activities in the upper Pacific were six times lower than activities in the Atlantic. In deep waters the primary enrichment was 27°–47°N. Two stations (32° and 37°N) were especially enriched, having near‐bottom inventories several times greater than other stations. With these two exceptions the remaining Pacific stations exhibited averaged inventories lower than those in the Atlantic. There was one region of enriched 223Ra (half‐life = 11 days) above the Puna Ridge near Hawaii.

Targeted Next-Generation Sequencing Assay for Direct Detection and Serotyping of Salmonella from Enrichment

In this study, an automated, targeted next-generation sequencing (tNGS) assay to detect and serotype Salmonella from sample enrichments was evaluated. The assay generates millions of reads to detect multiple Salmonella-specific genes and serotype-specific alleles, detecting all Salmonella spp. tested to date, and serotyping 62 common Salmonella serotypes. Accuracy was tested on 291 pure reference cultures (251 Salmonella, 40 non-Salmonella), 21 artificially contaminated poultry carcass rinse samples, and 363 naturally contaminated poultry environmental samples. Among the 291 pure reference cultures, the automated tNGS assay resulted in 100% detection accuracy, 100% serotyping accuracy for the claimed serotypes, and 0% false positives. The limit of detection was estimated at 5 × 104 CFU/mL by testing enumerated cultures of strains representative of six serotypes. In cocontamination studies with mixtures of two serotypes (Enteritidis, Typhimurium, Kentucky, Infantis, and Newport) at a 1:1 ratio, tNGS detected both serotypes with 100% accuracy. The assay demonstrated 100% accuracy in artificially contaminated poultry carcass rinse sample enrichments. Targeted NGS was highly effective in detecting Salmonella in samples collected from poultry production facilities. Results demonstrated that tNGS could detect Salmonella and provide accurate serotyping information consistent with conventional serology. These findings highlight the reliable and efficient performance of a fully automated tNGS Salmonella assay in detecting and identifying Salmonella strains in complex matrices, reducing the time to results from 4 to 5 days required by the traditional isolation and serotyping to 10–12 h for tNGS after primary enrichment.

Comprehensive analysis of co-expressed genes with TDP-43: prognostic and therapeutic potential in lung adenocarcinoma

BackgroundTransactivating DNA-binding protein 43 (TDP-43) is intimately associated with tumorigenesis and progression by regulating mRNA splicing, transport, stability, and non-coding RNA molecules. The exact role of TDP-43 in lung adenocarcinoma (LUAD) has not yet been fully elucidated, despite extensive research on its function in various cancer types. An imperative aspect of comprehending the underlying biological characteristics associated with TDP-43 involves investigating the genes that are co-expressed with this protein. This study assesses the prognostic significance of these co-expressed genes in LUAD and subsequently explores potential therapeutic strategies based on these findings.MethodsTranscriptomic and clinical data pertaining to LUAD were retrieved from open-access databases to establish an association between mRNA expression profiles and the presence of TDP-43. A risk-prognosis model was developed to compare patient survival rates across various groups, and its accuracy was also assessed. Additionally, differences in tumor stemness, mutational profiles, tumor microenvironment (TME) characteristics, immune checkpoints, and immune cell infiltration were analyzed in the different groups. Moreover, the study entailed predicting the potential response to immunotherapy as well as the sensitivity to commonly employed chemotherapeutic agents and targeted drugs for each distinct group.ResultsThe TDP-43 Co-expressed Gene Risk Score (TCGRS) model was constructed utilizing four genes: Kinesin Family Member 20A (KIF20A), WD Repeat Domain 4 (WDR4), Proline Rich 11 (PRR11), and Glia Maturation Factor Gamma (GMFG). The value of this model in predicting LUAD patient survival is effectively illustrated by both the Kaplan–Meier (K–M) survival curve and the area under the receiver operating characteristic curve (AUC-ROC). The Gene Set Enrichment Analysis (GSEA) revealed that the high TCGRS group was primarily enriched in biological pathways and functions linked to DNA replication and cell cycle; the low TCGRS group showed primary enrichment in immune-related pathways and functions. The high and low TCGRS groups showed differences in tumor stemness, mutational burden, TME, immune infiltration level, and immune checkpoints. The predictions analysis of immunotherapy indicates that the Tumor Immune Dysfunction and Exclusion (TIDE) score (p < 0.001) and non-response rate (74% vs. 51%, p < 0.001) in the high TCGRS group are higher than those in the low TCGRS group. The Immune Phenotype Score (IPS) in the high TCGRS group is lower than in the low TCGRS group (p < 0.001). The drug sensitivity analysis revealed that the half-maximal inhibitory concentration (IC50) values for cisplatin, docetaxel, doxorubicin, etoposide, gemcitabine, paclitaxel, vincristine, erlotinib, and gefitinib (all p < 0.01) in the high TCGRS group are lower than those in the low TCGRS group.ConclusionsThe TCGRS derived from the model exhibits a reliable biomarker for evaluating both prognosis and treatment effectiveness among patients with LUAD. This study is anticipated to offer valuable insights into developing effective treatment strategies for this patient population. It is believed that this study is anticipated to contribute significantly to clinical diagnostics, the development of therapeutic drugs, and the enhancement of patient care.

Relevance of Secondary Enrichment in the Detection of Salmonella spp. in Food Samples by qPCR According to DIN 10135.

When detecting Salmonella spp. in food samples, unlike with culture-based procedures where there are solid standards, PCR techniques are generally dominated by commercial solutions, often backed by the conformity of reference organizations, and based on rigorous validation studies. The few independent standards that exist are not subject to revision and improvement to the same extent as the manufacturer's methods. Moreover, since commercial networks do not promote them, they are implemented less in everyday practice. The German standard DIN 10135 is an example of this. In this method, before PCR detection, a primary enrichment (16-20 h) followed by a secondary selective enrichment of at least 6 h is needed. Nevertheless, it allows the possibility of only applying the first step if evidence of their correct operation is provided. To evaluate how necessary is the secondary enrichment for DIN 10135 standard. Short and complete enrichment steps were compared in the context of the evaluation of the limit of detection for 11 types of food. Additionally, a blind assay was performed with 75 food samples. The data show that a simple primary enrichment may be sufficient and that the second selective enrichment with the tested matrixes would not be strictly essential. The blind study obtained a 98.6% of trueness and precision of 100%. At least for the end consumer products, a secondary enrichment of 6 h is not necessary for all the products tested. In the context of the DIN 10135 standard, the primary enrichment (16-20 h, 37 ± 1°C) can be enough for detecting Salmonella spp.

StRAB4 gene is required for filamentous growth, conidial development, and pathogenicity in Setosphaeria turcica.

Setosphaeria turcica, the fungal pathogen responsible for northern corn leaf blight in maize, forms specialized infectious structures called appressoria that are critical for fungal penetration of maize epidermal cells. The Rab family of proteins play a crucial role in the growth, development, and pathogenesis of many eukaryotic species. Rab4, in particular, is a key regulator of endocytosis and vesicle trafficking, essential for filamentous growth and successful infection by other fungal pathogens. In this study, we silenced StRAB4 in S. turcica to gain a better understanding the function of Rab4 in this plant pathogen. Phenotypically, the mutants exhibited a reduced growth rate, a significant decline in conidia production, and an abnormal conidial morphology. These phenotypes indicate that StRab4 plays an instrumental role in regulating mycelial growth and conidial development in S. turcica. Further investigations revealed that StRab4 is a positive regulator of cell wall integrity and melanin secretion. Functional enrichment analysis of differentially expressed genes highlighted primary enrichments in peroxisome pathways, oxidoreductase and catalytic activities, membrane components, and cell wall organization processes. Collectively, our findings emphasize the significant role of StRab4 in S. turcica infection and pathogenicity in maize and provide valuable insights into fungal behavior and disease mechanisms.

К ПЕРСПЕКТИВАМ УТИЛИЗАЦИИ ХВОСТОВ ОБОГАЩЕНИЯ РУД

The experience of utilization of tailings of metal ore enrichment in the process of extracting metals from them to the required level is summarized. Leaching of metals from the tailings of primary enrichment and poor raw materials in a disintegrator with mechanical and chemical activation of processes allows reducing the residual content to a level that allows the disposal of waste from mining and related industries without restriction.

Processes controlling rare earth element distribution in sedimentary apatite: Insights from spectroscopy, in situ geochemistry and O and Sr isotope composition

ABSTRACTIn phosphorites, the content and distribution of rare earth elements are linked to the environment of phosphogenesis. This paper focuses on the question of sources and processes controlling the rare earth element content of apatite from Belgian phosphorites formed during three major phosphogenic events in the Lower Palaeozoic, Late Cretaceous and Cenozoic. To constrain sources and processes, new data include petrological, mineralogical (including cathodoluminescence and Raman spectroscopy) and in situ trace element and Sr and O isotope analyses of apatite. Fluorapatite from Lower Palaeozoic P‐rich conglomerates has the greatest rare earth element enrichment. It is affected by metamorphism that led to deformation of apatite nodules and formation of garnet porphyroblast inclusions. The role of Fe‐oxyhydroxides in element scavenging is highlighted by some apatite nodules that maintain their primary middle rare earth element enrichment, while others are characterized by altered rare earth element patterns resulting from competition for these elements between co‐crystallizing minerals during deformation. A systematic shift towards lower δ18O and radiogenic Sr isotopic composition compared to contemporaneous seawater indicate interaction with 18O‐depleted meteoric fluids and a crustal component. By contrast, carbonate‐rich fluorapatite from the Late Cretaceous phosphatic chalk mostly keeps its primary trace element and isotopic signatures (close to seawater), although an external rare earth element addition is noted, as well as rare earth element redistribution induced by diagenetic alteration. Cenozoic carbonate fluorapatite nodules mostly present flat rare earth element patterns that are indicative of a detrital influence. Slight changes in rare earth element distribution are assigned to post‐depositional alteration, which also led to an increase in radiogenic Sr, with unchanged δ18O compared to seawater. The methodology followed here efficiently helps in deciphering the processes that modified the chemistry of apatite in the frame of major phosphogenic events.

Growth assessment of Salmonella enterica multi-serovar populations in poultry rinsates with commonly used enrichment and plating media

Isolation of Salmonella from enrichment cultures of food or environmental samples is a complicated process. Numerous factors including fitness in various selective enrichment media, relative starting concentrations in pre-enrichment, and competition among multi-serovar populations and associated natural microflora, come together to determine which serovars are identified from a given sample. A recently developed approach for assessing the relative abundance (RA) of multi-serovar Salmonella populations (CRISPR-SeroSeq or Deep Serotyping, DST) is providing new insight into how these factors impact the serovars observed, especially when different selective enrichment methods are used to identify Salmonella from a primary enrichment sample. To illustrate this, we examined Salmonella-positive poultry pre-enrichment samples through the selective enrichment process in Tetrathionate (TT) and Rappaport Vassiliadis (RVS) broths and assessed recovery of serovars with each medium. We observed the RA of serovars detected post selective enrichment varied depending on the medium used, initial concentration, and competitive fitness factors, all which could result in minority serovars in pre-enrichment becoming dominant serovars post selective enrichment. The data presented provide a greater understanding of culture biases and lays the groundwork for investigations into robust enrichment and plating media combinations for detecting Salmonella serovars of greater concern for human health.