Abundance Levels Research Articles

4D-DIA Proteomics Uncovers New Insights into Host Salivary Response Following SARS-CoV-2 Omicron Infection.

Since late 2021, Omicron variants have dominated the epidemiological scenario as the most successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineages, driving new and breakthrough infections globally over the past two years. In this study, we investigated for the first time the host salivary response of COVID-19 patients infected with Omicron variants (BA.1, BA.2, and BA.4/5) by using an untargeted four-dimensional data-independent acquisition (4D-DIA)-based proteomics approach. We identified 137 proteins whose abundance levels differed between the COVID-19 positive and negative groups. Salivary signatures were mainly enriched in ribosomal proteins, linked to mRNAviral translation, protein synthesis and processing, immune innate, and antiapoptotic signaling. The higher abundance of 14-3-3 proteins (YWHAG, YWHAQ, YWHAE, and SFN) in saliva, first reported here, may be associated with increased infectivity and improved viral replicative fitness. We also identified seven proteins (ACTN1, H2AC2, GSN, NDKA, CD109, GGH, and PCYOX) that yielded comprehension into Omicron infection and performed outstandingly in screening patients with COVID-19 in a hospital setting. This panel also presented an enhanced anti-COVID-19 and anti-inflammatory signature, providing insights into disease severity, supported by comparisons with other proteome data sets. The salivary signature provided valuable insights into the host's response to SARS-CoV-2 Omicron infection, shedding light on the pathophysiology of COVID-19, particularly in cases associated with mild disease. It also underscores the potential clinical applications of saliva for disease screening in hospital settings. Data are available via ProteomeXchange with the identifier PXD054133.

Prenylation-dependent membrane localization of a deubiquitinating enzyme and its role in regulating G protein-mediated signaling in yeast.

Miy1 is a highly conserved de-ubiquitinating enzyme in yeast with MINDY1 as its human homolog. Miy1 is known to act on K48-linked polyubiquitin chain, but its biological function is unknown. Miy1 has a putative prenylation site, suggesting it as a membrane-associated protein that may contribute to the regulation of cell signaling. Here, we demonstrate that Miy1 is localized in the plasma membrane and nuclear periphery. Mutating the putative prenylation site in Miy1 or disrupting the farnesyltransferase activity impairs its localization. Consistent with a role of Miy1 in regulating the ubiquitination status of membrane proteins, the miy1Δ mutants exhibit a higher level of ubiquitinated conjugates at the plasma membrane. To examine a role of Miy1 in regulating cell signaling across plasma membrane, we focused on the pheromone response, as both Ste2, the receptor for mating pheromone, and Gpa1, the cognate Gα protein of Ste2, are well-known to be regulated by ubiquitination. We find that Miy1 interacts with Gpa1, regulates its level of ubiquitination and abundance. Pheromone-induced MAP kinase Fus3 activation is also altered in the MIY1-disrupted mutants. The findings demonstrate that Miy1 is a membrane-associated deubiquitinating enzyme and a regulator of G protein-mediated signaling.

In Situ Phytoremediation of Mine Tailings with High Concentrations of Cadmium and Lead Using Dodonaea viscosa (Sapindaceae).

The waste generated during metal mining activities contains mixtures of heavy metals (HM) that are not biodegradable and can accumulate in the surrounding biota, increasing risk to human and environmental health. Plant species with the capacity to grow and develop on mine tailings can be used as a model system in phytoremediation studies. Dodonaea viscosa (L.) Jacq. is a shrub with wide geographical distribution and the ability to establish itself in mine tailings. The Sierra de Huautla Biosphere Reserve in Mexico contains a metallurgic district where mining activities have generated 780 million kg of waste with large concentrations of toxic heavy metals, mainly cadmium and lead. The present study evaluated the phytoremediation potential of D. viscosa in in situ conditions on soils contaminated with HMs (exposed) and reference sites (non-exposed) for one year. Also, the effects of cadmium (Cd) and lead (Pb) exposure in D. viscosa were analyzed via DNA damage (comet assay) morphological and physiological characters in exposed vs non-exposed individuals. The concentration of Cd and Pb was measured through atomic absorption spectrophotometry in the roots and leaves of plants. In total, 120 D. viscosa individuals were established, 60 growing in exposed and 60 in non-exposed soils. Exposed individuals of D. viscosa hyperaccumulated Cd and Pb in roots and leaves. At the end of the experiment, eight out of twelve characters under evaluation decreased significantly in HM-exposed plants in relation to individuals growing in non-exposed soils, except for stomatal index, stomatal coverage, and fresh leaf biomass. The micro-morphological and physiological traits of D. viscosa were not influenced by Cd and Pb bioaccumulation. In contrast, the bioaccumulation of Cd and Pb significantly influenced the macro-morphological characters and genetic damage; this last biomarker was 3.2 times higher in plants growing in exposed sites. The bioconcentration factor (BCF) of Cd and Pb in root and leaf tissue increased significantly over time. The mean BCF in root and leaf tissue was higher for Pb (877.58 and 798.77) than for Cd (50.86 and 23.02). After 12 months of exposure, D. viscosa individuals growing on mine tailing substrate showed that the total HM phytoextraction capacity was 7.56 kg∙ha-1 for Pb and 0.307 kg∙ha-1 for Cd. D. viscosa shows potential for phytoremediation of soils contaminated with Cd and Pb, given its capacity for establishing and developing naturally in contaminated soils with HM. Along with its bioaccumulation, biomass production, abundance, and high levels of bioconcentration factors, but without affecting plant development and not registering associated herbivores, it may incorporate HM into the trophic chain.

Predation by marine mammals explains recent trends in natural mortality of Pacific Herring (Clupea pallasii) and changes expectations for future biomass

Abstract The recovery of marine mammals from historical over-exploitation in the 1970s represents one of the largest changes in trophic structure in the northeast Pacific Ocean over the last century, for which the impacts on key forage species such as Pacific Herring (Clupea pallasii) are poorly understood. This has prompted hypotheses that increasing marine mammal populations are the primary cause for productivity declines for some fish stocks and their lack of recovery to historical abundance levels. In this study, we evaluate such a hypothesis for Pacific Herring by quantifying historical predation rates by key predators, including cetaceans (Pacific Humpbacks, Grey Whales), pinnipeds (Steller Sea Lions, Harbour Seals), and piscivorous fish (Pacific Hake). Predation mortality is quantified via a novel approach that integrates a single-species catch-at-age model with estimates of predator consumption derived from bioenergetic models. We found that predator consumption, largely driven by Humpback Whales, explained increasing Pacific Herring natural mortality rates in recent years and could be used to forecast future mortality. Incorporating higher future natural mortality rates produced higher estimates of current stock status (1.09–1.2$B_0$) based on lower estimates of equilibrium unfished biomass (17.5–20.3 kt). Conversely, models that assumed mortality was more like the historical average had lower stock status (0.63$B_0$) and higher estimates of unfished biomass (32.4 kt). We demonstrate a practical approach for ecosystem modelling that can be used to develop operating model scenarios for management strategy evaluation, improving scientific defensibility by removing an element of analyst choice for future mortality scenarios. We discuss how simpler modifications to single-species model assumptions can be more pragmatic for providing fisheries management advice, while more complex multi-species or ecosystem models might provide more nuanced insights for exploring research questions related to multi-species ecosystems and fisheries interactions.

Common Species in the Subtropical Evergreen Broad-Leaved Forest: Dominance in Adaptation Mechanisms and Resource Utilization Capabilities

When species of different abundance coexist, their ecological strategies remain uncertain. Assessing the functional diversity and niche characteristics of species with different levels of abundance contributes to understanding vegetation properties and is essential for species conservation. Based on the species abundance of 380 plots in the Gutianshan subtropical evergreen broad-leaved forest in the Zhejiang Province of China, woody plants were categorized as common species (86 species), occasional species (87 species), and rare species (79 species). Plant functional traits, including maximum height, seed dispersal modes, first flowering stage, flowering duration, and fruit length, were used to assess the functional diversity of the community of common, occasional, and rare species, while 15 environmental factors were used to evaluate their Levins’ niche breadth and Pianka’s niche overlap. The results showed that rare species have the highest functional evenness, while functional dispersion and Rao’s quadratic entropy were higher for common species (2.05 and 5.07, respectively) compared to occasional species (1.57 and 3.10) and rare species (1.35 and 2.48). Furthermore, the 15-dimensional mean value of niche breadth of common species (ranging from 0.277 to 0.955) was also higher than that of occasional (ranging from 0.193 to 0.710) and rare species (ranging from 0.100 to 0.345), and the same trend was also observed in niche overlap. The results suggest that common species have diverse functional traits and a greater ability to adapt to the environment and use resources, whereas occasional species have a limited ability to use the environment. Rare species are evenly distributed within functional space to reduce direct competition with other species, but they thrive only under specific environmental conditions, mainly following a K reproductive strategy. Niche differentiation mechanisms are important determinants of species coexistence in subtropical evergreen broad-leaved forests. In summary, more attention and greater efforts should be paid to the conservation of rare species. Our findings could help forest managers in the restoration and conservation of subtropical forests.

Chlorine and UV combination sequence: Effects on antibiotic resistance control and health risks of ARGs.

The effective control of antibiotic resistance in aquatic environments is urgent. The combined chlorine and UV processes (Cl2-UV, UV/Cl2, and UV-Cl2) are considered potential control processes for controlling antibiotic resistance. This study compared the effectiveness of these three processes in real water bodies and the potential health risks associated with antibiotic resistance genes (ARGs) after treatments. The removal of various antibiotic-resistant bacteria (ARB) and ARGs by the combined processes was analysed. The UV/Cl2 process was less effective than the others in inactivating β-lactam-resistant bacteria (BRB) and sulfamethoxazole-resistant bacteria (SRB), which are more challenging to remove, though its performance might improve with increased UV fluence. Nevertheless, the UV/Cl2 process showed an advantage in removing ARGs. The absolute abundance of aminoglycoside resistance genes (AmRGs), sulfonamide resistance genes (SRGs), macrolide resistance genes (MRGs), and multidrug efflux-associated ARGs detected after the UV/Cl2 process was relatively low, and this process outperformed the others in removing a greater number of ARGs. Additionally, certain ARGs and bacterial genera were found to be enriched after the combined processes, with lower and more similar abundance levels of ARGs and genera observed after UV/Cl2 and UV-Cl2 processes compared to the Cl2-UV process. Health risk assessments indicated that the Cl2-UV process posed the highest risk, followed by UV/Cl2 and UV-Cl2 processes. Overall, the UV/Cl2 process may offer the most practical advantages for controlling antibiotic resistance.

Internal Doping and Surface Coating: Mn/La-HCF @ Fe-HCF Composites as High-Performance Cathode Materials for Sodium-Ion Batteries

Manganese-based Prussian blue analogue (Mn-HCF) has outstanding advantages such as a high discharge platform, high discharge capacity and high energy density compared with other PB and PBAs, which is a very valuable cathode material for sodium-ion batteries. However, the rapid decrease in capacity in the cycle process by the Jahn–Teller effect caused by [Formula: see text] is the main obstacle to the commercialization of Mn-HCF. In this work, Mn/La-HCF @ Fe-HCF was synthesized by doping La element into the Mn-HCF phase to suppress the Jahn–Teller effect of Mn ions and coating the Fe-HCF phase outside to protect the Mn-HCF phase from electrolyte corrosion. Benefiting from the inhibition of the Jahn–Teller effect of [Formula: see text] by the abundant electronic energy level structure of La element and the protection of Fe-HCF phase relative to Mn-HCF phase, the initial discharge capacity of Mn/La-HCF @ Fe-HCF can reach 135.6 mAh [Formula: see text] at current density of 0.1 C, and it still has a high discharge capacity of 112.2[Formula: see text]mAh [Formula: see text] at current density of 5 C. After 300 cycles at a current density of 2 C, the reversible capacity of 117.6[Formula: see text]mAh [Formula: see text] is maintained (capacity retention rate is 86.1%). The results show that this method of internal doping and outsourcing can greatly improve the electrochemical performance of Mn-HCF, and provide feasible ideas for the commercialization of Mn-HCF.

Combining two main NAL1 functional alleles can increase rice yield.

NARROW LEAF1 (NAL1) is one of the key genes in regulating photosynthesis and plant architecture. As the antagonistic effects of NAL1 have concurrent impacts on photosynthesis and yield component traits, how we can effectively utilize the NAL1 gene to further increase rice yield is not clear. In this study, we used two different main functional NAL1 alleles, each of which has previously been proven to have specifically advantageous traits, and tested whether the combined NAL1 alleles have a higher yield than the homozygous alleles. Our results exhibited that the combined NAL1 alleles had better parent heterosis (BPH) for panicle number and the total filled grain number per plant, and had middle parent heterosis (MPH) for spikelet number per panicle without affecting thousand-grain weight when compared with the homozygous alleles. In consequence, the NAL1 hybrid plants displayed highly increased grain yield compared with both homozygous parents. The hybrid plants also had better plant architecture and higher canopy photosynthesis. Western blot and proteomics results showed the hybrid plants had a middle abundant NAL1 protein level, and the upregulated proteins were mainly involved in the nucleus and DNA binding process but the downregulated proteins were mainly involved in the oxidation-reduction process, single-organism metabolic process, and fatty acid biosynthetic process. Furthermore, the hybrid vigor effect of NAL1 was confirmed by substituting the mutual male parent 9311 with 9311-NIL in two super hybrid rice varieties (LYP9 and YLY1). This study demonstrates that we can achieve a higher level of grain production in hybrid rice by using the heterosis of NAL1.

Using a knowledge representation logic to estimate the availability of Imbrasia epimethea (Lepidoptera: Saturniidae), an important edible insect in Subsaharan Africa

Based on monthly abundance patterns, we model the density of Imbrasia epimethea (Drury, 1773), an important edible insect in Africa. Categorical data was collected from various regions in Cameroon, and data analysis techniques were used to infer relationships between environmental variables and the level of insect abundance. Through fuzzy logic modeling, we identified the key environmental factors and rules that influence the density of the insect. To visualize the distribution of I. epimethea across African landscapes, interpolation techniques were used on the study area matrix of geographical coordinates based on the corresponding monthly predictor variables for the most recent available year (2022). The results suggested a clear dynamic across Africa through the different months of the year with potentially overlapping generations with relatively high accuracy (>90 %). A clear relationship between regional climatic conditions and the density of I. epimethea could be established across Africa. The models provide insights into the complex dynamics of insect populations and sheds light on the stability and transferability of our results across different African regions (during stability analysis). This research offers a foundation for further investigations on sustainable food production and the promotion of edible insects as a viable protein source.

Comparison of Anaerobic Culture Methods for Detecting Clostridioides difficile in Bovine Faeces.

The study of the epidemiology of Clostridioides difficile in populations is greatly facilitated by the ability to isolate and further characterize individual organisms, which requires effective culture protocols. In cattle, where little is known about the epidemiology of C. difficile, no studies have assessed or compared the performance of different assays for detecting C. difficile. This study compared two culture protocols for detecting C. difficile in bovine faeces from 121 gestating cows and 70 of their neonatal calves, while situating results obtained with each protocol relative to those obtained with shotgun metagenomic sequencing. Protocol 1 involved direct plating enrichment onto taurocholine-cycloserine-cefoxitin-fructose agar (TCCFA), while Protocol 2 included an ethanol shock step before plating on CCFA/ChromID agar. For both protocols, one aliquot underwent broth enrichment prior to plating, while the other aliquot did not. Clostridioides difficile was detected following broth enrichment in two of the same calf samples using both protocols, and an additional cow sample was found to be positive with Protocol 2, though the difference in detection rates was not statistically significant (p = 1.0). The detection of C. difficile in a much high number of these samples by shotgun metagenomics, albeit at low levels of relative abundance, suggests that neither of these culture protocols is sensitive when levels of abundance are low.

Multi-omics analysis reveals indicator features of microbe-host interactions during Candida albicans colonization and subsequent infection.

Candida albicans gastrointestinal (GI) colonization is crucial for the onset of invasive disease. This research encompassed 31 patients diagnosed with Candida spp. bloodstream infections during their admission to a university hospital in China. We explored risk factors associated with C. albicans GI colonization and ensuing translocated infection. Animal models were established via gavage with clinical isolates of C. albicans to induce GI tract colonization and subsequent kidney translocation infection. Our analysis is focused on 16S rRNA gene sequencing, metabolomics of colon contents, and transcriptomics of colon tissues, examining the intestinal barrier, inflammatory responses, and immune cell infiltration. This study observed that down-regulation of programmed cell death 1 (PD-1) in colon tissues is likely linked to the progression from C. albicans colonization to translocated infection. Notably, reductions in Dubosiella abundance and Short-chain fatty acids (SCFA) levels, coupled with increases in Mucispirillum and D-erythro-imidazolylglycerol phosphate, were indicator features during the advancement to translocated invasive infection in hosts with rectal colonization by C. albicans and lower serum protein levels. Given the similarity in intestinal bacterial communities and metabolome profiles, antifungal treatment may not be necessary for patients with nonpathogenic C. albicans colonization. The reduced expression of PD-1 in colon tissues may contribute to the transition from colonized C. albicans to subsequent translocated infection. The indicator features of decreased Dubosiella abundance and SCFA levels, coupled with increased Mucispirillum and D-erythro-imidazolylglycerol phosphate, are likely linked to the development of translocated invasive infection in hosts colonized rectally by C. albicans with lower serum protein levels. Candida albicans invasive infections pose a significant challenge to contemporary medicine, with mortality rates from such fungal infections remaining high despite antifungal treatment. Gastrointestinal colonization by potential pathogens is a critical precursor to the development of translocated infections. Consequently, there is an increasing demand to identify clinical risk factors, multi-omics profiles, and key indicators to prevent the progression to translocated invasive infections in patients colonized rectally by C. albicans.

Polycyclic Aromatic Hydrocarbons in exoplanet atmospheres: A detectability study

Abstract In this paper, we explore the detectability of polycyclic aromatic hydrocarbons (PAHs) under diverse planetary conditions, aiming to identify promising targets for future observations of planetary atmospheres. Our primary goal is to determine the minimum detectable mass fractions of PAHs on each studied planet. We integrate the one-dimensional self consistent model petitCODE with petitRADTRANS, a radiative transfer model, to simulate the transmission spectra of these planets. Subsequently, we employ the PandExo noise simulator using the NIRSpec PRISM instrument aboard the JWST to assess the observability. Then, we conduct a Bayesian analysis through the MULTINEST code. Our findings illustrate that variations in C/O ratios and planet temperatures significantly influence the transmission spectra and the detectability of PAHs. Our results show that planets with [Fe/H]=0 and 1, C/O=0.55, and temperatures around 1200 K are the most promising for detecting PAHs, with detectable mass fractions as low as 10−7, or one thousandth of the ISM abundance level. For colder planets with lower metallicities and C/O ratios, as well as hotter planets with carbon-rich atmospheres, PAHs can be detected at abundances around 10−6. These results aid our strategy for selecting targets to study PAHs in the atmospheres of exoplanets.

Population dynamics of defective viral genomes of tomato black ring virus during host-to-host transmission.

Defective viral genomes (DVGs) have been identified in vivo and in vitro for different virus species infecting humans, animals, and plants. The ability to form DVGs during the passaging of virus in one host has been demonstrated, i.e., for tomato black ring virus (TBRV). In our research, RNA-Seq data obtained after TBRV passaging through a combination of four distinct host species were analyzed. Our results indicate that the level of DVG abundance varied across host plant combinations. Deletions were the most prevalent class of DVGs, with the domination of longer species. Additionally, the conserved junction sites in the TBRV genome were identified, resulting in the generation of identical deletions in independently evolved viral lineages. In summary, our findings provide significant insights into the origin and structure of DVGs of plant viruses. The obtained results will help in understanding viral evolution and host-virus interactions.

High-fat diet stimulated butyric acid metabolism dysbiosis, altered microbiota, and aggravated inflammatory response in collagen-induced arthritis rats.

Research has demonstrated that obesity may be associated with rheumatoid arthritis (RA). In addition, Dysbiosis of intestinal microbiota and their metabolites has been linked to the occurrence and development of RA and obesity. However, the mechanism by which obesity affects RA remains unclear.In this study, we explored the impact of high fat diet(HFD) on collagen-induced arthritis (CIA) rats and revealed its mechanisms based on gut microbiota and metabolomics. Based on diet and modeling, rats were divided into normal group (Con), CIA model group, HFD group (HFD), and HFD + CIA group (HCIA). The effect of HFD on arthritis in CIA rats were investigated based on the arthritis index (AI), weight, blood lipid levels, and inflammatory cytokines. Moreover, HE staining and micro-CT were performed to evaluated the effect of HFD on the pathology of joints and synovial tissues in CIA rats.16S rRNA amplicon sequencing and liquid chromatography-mass spectrometry (LC-MS) were employed to explore changes in gut microbiota and short-chain fatty acids (SCFAs). The AI scores, inflammatory cytokines and bone destruction parameters in the HCIA group were significantly higher than those in the other three groups. The results of 16S rRNA amplicon sequencing and metabolomics showed that compared with the other three groups, the expression of g_Muribaculaceae and butyric acid were reduced in the HCIA group. Spearman and linear correlation analyses revealed a positive correlation between g_Muribaculaceae abundance and butyric acid levels. HFD stimulated butyric acid metabolism dysbiosis, altered microbiota, and aggravated inflammatory response in CIA rats.

Analysis of Plankton Abundance, Diversity and Dominance along the Siddo Coast in Barru Regency, Indonesia

This research aims to determine the level of abundance, diversity, uniformity, and dominance of plankton in the waters of Siddo Beach, Barru Regency. The research was carried out at three research locations, namely location 1, namely the hatchery location and Siddo Beach Bay; location 2, namely the location around the pier and mangroves; and location 3, namely the location around the community settlement in Toe hamlet, Barru Regency. Plankton in this location needs to be researched because there are many environmental forces that can disrupt the existence of plankton. Analisis plankton dilaksanakan di Laboratorium Kimia dan Air Politeknik Pertanian Negeri Pangkep. Data selanjutnya dianalisis dengan analisis deskriptif. The results showed that the abundance of plankton at location 1 was highest for plankton of the Navicula sp type; at location 2, the highest was for plankton of the Oscilatoria sp type; and the abundance of plankton at location 3 was highest for plankton of the type Acartia sp. The average diversity of plankton at the research location is in the range of 0.1526795-0.20716, the uniformity of plankton at the research location is in the range 0.06144279-0.10646145, and the dominance of plankton at location 1 is highest in Cosconidiscus sp type plankton, location 2 is dominated by Oscilatoria sp type plankton, and location 3 is dominated by plankton of the Acartis sp type. Thus, there is no type of plankton that has the highest abundance and dominance for all research locations.

Unstable pathogen profile in spotted seal (Phoca largha) gut microbiota and limited turnover with habitat microbiome.

It is vital that we monitor the gut microbiota of sentinel species such as spotted seals (Phoca largha) and their association with habitat microbiomes, which can provide critical data for assessing the health of marine mammals and their potential ecological influences. In this study, PacBio technology was used to sequence the full-length bacterial 16S rRNA gene from the feces of captive and wild spotted seals, as well as samples from a wild population and their habitats. Based on the pathogen identification results, the gut microbiota of wild and captive spotted seals showed similar levels of pathogen richness and abundance. In particular, the pathogen profiles in wild spotted seals were more variable, with a high risk of disease in a minority of individuals. Meanwhile, the gut microbiota of spotted seals was significantly less diverse than their habitat microbiomes. Firmicutes and Proteobacteria dominated the gut microbiota of spotted seals and their habitat microbiomes, respectively. Furthermore, network analysis revealed that the gut microbiota of spotted seals was simple and weak. The ratios of microbial turnover between spotted seal gut microbiota and their habitat microbiomes were further analyzed using SourceTracker, and the estimated values were low (< 0.1%). These results provide baseline data on pathogen profiles in spotted seals and their potential interactions with habitat microbiomes.

Toxoplasma gondii infection induces the expression of the chemokine CXCL16 in macrophages to promote chemoattraction of CXCR6+ cells.

CXCL16 is a multifaceted chemokine expressed by macrophages and other immune cells in response to viral and bacterial pathogens. However, few studies have investigated its role in parasitic infections. The obligate intracellular parasite Toxoplasma gondii (T. gondii) is the causative agent of toxoplasmosis, an infection with potentially deleterious consequences in immunocompromised individuals and the developing fetus of acutely infected pregnant women. Chemokines are critical mediators of host defense and, as such, dysregulation of their expression is a subversion strategy often employed by the parasite to ensure its survival. Herein, we report that types I and II T. gondii strains upregulated the expression of both transmembrane and soluble forms of CXCL16 in infected bone marrow-derived macrophages (BMDM). Exposure to soluble T. gondii antigens (STAg) and to excreted-secreted proteins (TgESP) led to the induction of CXCL16. Cxcl16 mRNA abundance and CXCL16 protein levels increased in a time-dependent manner upon T. gondii infection. Importantly, conditioned medium (CM) collected from T. gondii-infected wild-type (WT) macrophage cultures promoted the migration of RAW264.7 cells expressing CXCR6, the cognate receptor of CXCL16, an effect that was significantly reduced by a neutralizing anti-CXCL16 antibody or use of CM from CXCL16 knockout (KO) macrophages. Lastly, T. gondii-driven CXCL16 expression appeared to modulate cytokine-induced (IL-4 + IL-13) alternative macrophage activation and M2 phenotypic marker expression. Further investigation is required to determine whether this chemokine contributes to the pathogenesis of toxoplasmosis and to elucidate the underlying molecular mechanisms.

TMIC-42. CONQUERING SPP1+ MYELOID-DRIVEN RESISTANCE OF GLIOBLASTOMA TO IL13RA2-TARGETED CAR T CELL THERAPY

Abstract In the evolving landscape of glioblastoma (GBM) therapy, the recent proliferation of clinical trials exploring chimeric antigen receptor (CAR) T cell interventions has garnered attention, although their therapeutic efficacy remains limited. Despite recent progress in elucidating the role of the GBM microenvironment in immunotherapy resistance, particularly regarding intercellular networks and macrophages, significant ambiguities endure, impeding a comprehensive understanding of resistance mechanisms amidst the patient-specific heterogeneity of the tumor microenvironment (TME). In this study, we utilized single-cell RNA sequencing to analyze tumors from 41 glioma patients undergoing IL13Rα2-targeted CAR T cell therapy. Our findings unveiled heightened suppressive extracellular network signatures, particularly SPP-1, predominantly observed within myeloid cells from non-responsive patients. The clinical significance of both SPP1+ myeloid cell abundance and overall expression levels revealed associations with patient outcomes. Subsequently, transcriptomic insights were translated to myeloid cell functions in patients exhibiting high versus low SPP1 expression. SPP1-expressing macrophages displayed diminished antigen presentation, phagocytosis, and cell-mediated cytotoxicity, along with augmented extracellular matrix biogenesis and degradation, iron efflux, and suppressive interleukin pathways. Moreover, SPP1-high macrophages exhibited enhanced ligand-receptor interactions, implying a predisposition towards suppressive activities. Immunometabolism pathways, including lipid and ketone body biogenesis and regeneration, were upregulated in SPP1-expressing macrophages, indicating an increased reliance on non-glycolysis-mediated ATP production. To assess translational implications, the therapeutic efficacy of SPP1 blockade was evaluated in a syngeneic glioma model. Blockade of SPP1 with an anti-SPP1 antibody prior to CAR T cell infusion effectively mitigated the immunosuppressive milieu, reversing resistance in preclinical GBM models to murine IL13Rα2-targeted CAR T cell therapy. Subsequent profiling of tumors post-treatment provided insights into TME alterations following SPP1 blockade therapy. This investigation illuminates the intricate interplay between the TME and CAR T cell therapy resistance in GBM, underscoring SPP1 as a promising therapeutic target to surmount CAR T cell resistance and enhance treatment outcomes.

Kidney mRNA-protein expression correlation: what can we learn from the Human Protein Atlas?

The Human Protein Atlas, with more than 10 million immunohistochemical images showing tissue- and cell-specific protein expression levels and subcellular localization information, is widely used in kidney research. The Human Protein Atlas contains comprehensive data on multi-tissue transcript and protein abundance, allowing for comparisons across tissues. However, while visual and intuitive to interpret, immunohistochemistry is limited by its semi-quantitative nature. This can lead to mismatches in protein expression measurements across different platforms. We performed a comparison of the Human Protein Atlas' kidney-specific RNA sequencing and immunohistochemistry data to determine whether the mRNA and protein abundance levels are concordant. Our study shows that there is a discordance between mRNA and protein expression in the kidney based on the Human Protein Atlas data. Using an external validation mass spectrometry dataset, we show that more than 500 proteins undetected by immunohistochemistry are robustly measured by mass spectrometry. The Human Protein Atlas transcriptome data, on the other hand, exhibit similar transcript detection levels as other kidney RNA-seq datasets. Discordance in mRNA-protein expression could be due to both biological and technical reasons, such as transcriptional dynamics, translation rates, protein half-lives, and measurement errors. This is further complicated by the heterogeneity of the kidney tissue itself, which can increase the discordance if the cell populations or tissue compartment samples do not match. As such, shedding light on the mRNA-protein relationship of the kidney-specific Human Protein Atlas data can provide context to our scientific inferences onrenal gene and protein quantification.

Impact of prescribed fire on fungal communities in Scots pine (Pinus sylvestris) forests in Mediterranean transitional zones

The Mediterranean region is renowned for its natural susceptibility to wildfires. In recent years, this risk has intensified due to various factors, including climate change and rural abandonment. Castilla y Leon stands out as one of the most severely impacted areas grappling with rural exodus. This evolving scenario accentuates the urgency of implementing forest management strategies to mitigate the escalating threat of wildfires, with a primary focus on fuel reduction. Although prescribed fires represent an efficient and cost-effective tool for wildfire prevention, they remain a contentious subject in Europe. Fungi not only contribute significantly to rural economies but also play a pivotal role in maintaining the equilibrium of forest ecosystems. The main objective of this study was to examine the effects of prescribed burning on Pinus sylvestris soils, with a specific focus on the recovery of fungal populations after such fires. To assess the short-term effects of prescribed fires on soil fungal communities, we collected soil samples from both burned and unburned plots 12 months post-burning to perform genomic DNA analyses. Our findings indicate that prescribed burning does not significantly alter fungal diversity or composition, with only litter saprotrophs showing significantly higher levels of abundance in burned areas than in unburned areas. Valuable edible fungi persisted post-burning, suggesting that prescribed burning could be used to reduce wildfire fuel loads while preserving fungal biodiversity and valuable edible fungi. These results advocate for the use of prescribed burning as a viable, myco-friendly forest management practice, offering a balance between fire prevention and ecological conservation.