High Levels Of Abundance Research Articles

Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing.

In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray-finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups. Collectively, our results revealed reliable and sufficient information within metatranscriptomics sequencing to characterize not only RNA viruses, but also DNA and retro-transcribing viruses, and therefore established a key methodology that will help us to understand the composition and evolution of the total “infectome” within a diverse range of vertebrate hosts.

An artificial reef at the edge of the deep: An interdisciplinary case study

Just nearby the largest submarine canyon in Europe – off the western coast of Portugal – is located the Nazaré artificial reef (NAR) deployed in 2010 and the first of its kind in this coast. NAR aimed to improve social and economic resilience of the local communities, mainly by creating a safer and closer area for fishing and to enhance commercially exploitable marine resources. The innovative part of this research lies on the fact that for the first time was developed a multidisciplinary approach for NAR. Scientific evidence from fieldwork shows that in 2015 the reef was already mature and colonized by abundant and diversified macrobenthic assemblages. No evidence of negative impacts of NAR on the soft bottom macrofauna was observed, as assemblage composition in the NAR area and in the vicinity areas is similar. In relation to the primary producers that support the subsequent food chain, there also seems to be a balance between NAR and the surrounding area since phytoplankton was equally abundant throughout the area. Experimental fisheries and underwater visual census results on ichthyofaunal communities in the reef revealed high abundance and low levels of species richness, pouting, Trisopterus luscus Linnaeus, 1758 being the most common fish species found. Concerning NAR socio-economic impact, results from direct site observations (DSOs) showed that only some small-scale fishing vessels were eligible to operate on the NAR area. Thus, comparatively to non-AR areas nearby reef use by fishing vessels differs according to spatial and temporal strata. In what perception was concerned, the NAR has contributed to fish aggregation, though being populated mostly by small fish. Fishers have stated that some factors seemed to have changed after reef deployment. Notwithstanding, the NAR may have been a valuable contribution to an apparently overall socio-economic positive impact on the local fishing community that can be corroborated by the presence of good biological indicators.

Spatiotemporal patterns of variability in the abundance and distribution of winter-spawned pelagic juvenile rockfish in the California Current.

Rockfish are an important component of West Coast fisheries and California Current food webs, and recruitment (cohort strength) for rockfish populations has long been characterized as highly variable for most studied populations. Research efforts and fisheries surveys have long sought to provide greater insights on both the environmental drivers, and the fisheries and ecosystem consequences, of this variability. Here, variability in the temporal and spatial abundance and distribution patterns of young-of-the-year (YOY) rockfishes are described based on midwater trawl surveys conducted throughout the coastal waters of California Current between 2001 and 2019. Results confirm that the abundance of winter-spawning rockfish taxa in particular is highly variable over space and time. Although there is considerable spatial coherence in these relative abundance patterns, there are many years in which abundance patterns are very heterogeneous over the scale of the California Current. Results also confirm that the high abundance levels of YOY rockfish observed during the 2014–2016 large marine heatwave were largely coastwide events. Species association patterns of pelagic YOY for over 20 rockfish taxa in space and time are also described. The overall results will help inform future fisheries-independent surveys, and will improve future indices of recruitment strength used to inform stock assessment models and marine ecosystem status reports.

High levels of truncated RHAMM cooperate with dysfunctional p53 to accelerate the progression of pancreatic cancer.

Pancreatic cancer has the lowest survival rate out of all types of cancer. Pancreatic cancer patients are often diagnosed at advanced stages, hence an urgent need for a better therapeutic development of this devastating disease. Receptor for hyaluronan-mediated motility (RHAMM), not expressed in adult normal pancreas, has been suggested as a prognostic factor and a potential therapeutic target for pancreatic ductal adenocarcinoma (PDAC) and pancreatic neuroendocrine tumor (PNET). In this study, we initially sought to determine whether genetic deletion of RHAMM would slow down pancreatic cancer progression using Rhamm-/- mice. However, we found that Rhamm-/- mice expressed a truncated HMMRΔexon8-16 protein at higher abundance levels than wild-type RHAMM. While HMMRΔexon8-16 did not enable malignant progression of pancreatic intraepithelial neoplasia in p48-Cre; LSL-KRASG12D mice, it accelerated the formation of invasive PDAC and shortened the survival of p48-Cre; LSL-KRASG12D mice with heterozygous p53 knockout. KrasG12D PDAC mice with homozygous p53 knockout mice died around 10 weeks, and the effect of HMMRΔexon8-16 was not apparent in these short lifespan mice. In addition, HMMRΔexon8-16 shortened the survival of PNET-bearing RIP-Tag mice, which had inactivated p53. In our analysis of TCGA dataset, pancreatic cancer patients with mutant TP53 or loss of one copy of TP53 had higher RHAMM expression, which, combined, predicted worse outcomes. Taken together, by collaborating with dysfunctional p53, high levels of HMMRΔexon8-16 , which lacks the centrosome targeting domain and degrons for interaction with the Anaphase-Promoting Complex (APC), accelerated pancreatic cancer progression.

Extracellular microRNAs: key players to explore the outcomes of in vitro fertilization

BackgroundMicroRNAs (miRNAs) are small RNA molecules that modulate post-transcriptional gene regulation. They are often used as promising non-invasive biomarkers for the early diagnosis of cancer. However, their roles in assisted reproduction are still unknown.MethodsThis prospective study was designed to evaluate the expression profiles of seven extracellular miRNAs (miR-7-5p, miR-202-5p, miR-378-3p, miR-224, miR-320a, miR-212-3p, and miR-21-5p) in human follicular fluid (FF) to explore the outcomes of in vitro fertilization (IVF). Of 255 women, 145 were without polycystic ovary syndrome (PCOS), and their ovarian assets were normal (NOR), while 110 were with normo-androgenic PCOS.ResultsThe combination of six FF miRNAs expression profile discriminated between PCOS and NOR women with a sensitivity of 79.2% and a specificity of 87.32% (AUC = 0.881 [0.61; 0.92], p = 0.001). MiR-202-5p significantly had a lower abundance level, and miR-378-3p had a high abundance level in pooled FF samples from patients treated with human menopausal gonadotropin (hMG) than those treated with recombinant follicle-stimulating hormone (rFSH) (p < 0.001). Our results showed that miRNA-320a was significantly different in top-quality embryos versus non-top-quality embryos on day 3 in NOR patients with a sensitivity of 80% and specificity of 71%, (AUC = [0.753 (0.651; 0.855)], p = 0.001). For clinical pregnancy outcome prediction, FF miRNA-21 exhibited high sensitivity (74.8%) and specificity (83.7%) with the AUC value of 0.774 (0.682; 0.865).ConclusionConclusively, our results provide evidence that miR-7-5p, miR-378-3p, miR-224, miR-212-3p were a differentially high expression in normo-androgenic PCOS patients than NOR patients. While miRNA-320a was significantly different in top-quality embryos versus non-top-quality embryos on day 3 (p = 0.001). The expression level of FF miR-212-3p was significantly related to the probability of embryos to develop into a high-quality blastocyst in patients with normal ovarian reserve.

Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiation.

BMDMs are a key model system to study macrophage biology in vitro. Commonly used methods to differentiate macrophages from BM are treatment with either recombinant M-CSF or the supernatant of L929 cells, which secrete M-CSF. However, little is known about the composition of L929 cell-conditioned media (LCCM) and how it affects the BMDM phenotype. Here, we used quantitative mass spectrometry to characterise the kinetics of protein secretion from L929 cells over a 2-wk period, identifying 2,193 proteins. Whereas M-CSF is very abundant in LCCM, we identified several other immune-regulatory proteins such as macrophage migration inhibitory factor (MIF), osteopontin, and chemokines such as Ccl2 and Ccl7 at surprisingly high abundance levels. We therefore further characterised the proteomes of BMDMs after differentiation with M-CSF, M-CSF + MIF, or LCCM, respectively. Interestingly, macrophages differentiated with LCCM induced a stronger anti-inflammatory M1 phenotype that those differentiated with M-CSF. This resource will be valuable to all researchers using LCCM for the differentiation of BMDMs.

Comparative proteomic analysis reveals molecular differences between incompatible and compatible interaction of Erysiphe pisi in garden pea

Comparative proteome analysis of Erysiphe pisi-infected pea genotypes; JI-2480 carrying er2 resistant gene and Arkel, the susceptible genotype by liquid chromatography- mass spectrometry (LCMS/MS QTOF) at 72 h post inoculation (hpi) revealed several differentially abundant proteins (DAPs) of both the host and the pathogen. The functional annotation of proteins through gene enrichment and KEGG pathway analyses revealed strong up-regulation of pathogenesis related protein NPR1, proteins related to defense, transportation and signal transduction, hypersensitive response, cell wall modifications, phenylpropanoid and metabolic pathways in J-72. Significant abundance of membrane-related polypeptides, kinase domains and small GTPase signal transduction-related proteins suggested their major role in plant defense. The abundance of cellular antioxidant protein, catalase and its isozyme along with calreticulin-1 and 2 in J-72 confirmed their intervention in maintaining a redox balance in powdery mildew defense. High abundance levels of Glycolysis-related proteins indicated it as a major pathway for energy source during fungal growth. The majority of pathogenicity and virulence genes were downregulated in J-72 compared to A-72, while four EKA (Effectors homologues to Avk1 and Avra10) like avirulence proteins were significantly upregulated in incompatible interaction suggesting their role in eliciting hypersensitive response in pea against E. pisi.

English

Soil macro-fauna diversity and abundance greatly influence soil fertility. However, little has been done to confirm this hypothesis in cocoa-based agroforestry systems. It was in this light that this research work was undertaken in order to fill the knowledge gap. Through the use of a mixed research method for data collection and appropriate data analysis procedures, findings showed that diverse soil macro-fauna were identified by cocoa farmers in cocoa-based agroforestry systems with the main being earth worms (100%), ants (100%), termites (70%), millipedes (50%), centipedes (50%), and snails (60%). Most cocoa farmers perceived that soil macro-fauna diversity in cocoa-based agroforestry systems was high (58.3%) and very high (17%) respectively. Earth worms, ants, millipedes, centipedes, spiders, harvestmen and scorpions were perceived by most cocoa farmers (44%, 38.3%, 43.3%, 41.3%, 55.6%, 53.3% and 48% respectively) to have a high level of abundance in cocoa-based agroforestry systems. A statistically significant direct non-causal and causal relationship (p&lt;0.05) existed between soil macro-fauna diversity and soil fertility enhancement in cocoa-based agroforestry systems, implying that the higher the diversity, the higher the level of soil fertility and the lower the diversity, the lower the level of soil fertility enhancement. Concerning soil macro-fauna abundance, a statistically significant direct non-causal and causal relationship (p&lt;0.05) existed between soil macro-fauna abundance (i.e. for earth worms, ants, termites, beetles, crickets, woodlice, snails and slugs) and soil fertility enhancement in cocoa-based agroforestry systems, implying that the greater the abundance of these soil macro-fauna, the greater the fertility of the soil. It is recommended that measures be taken to ensure soil macro-fauna diversity and abundance in order to enhance the fertility of the soil in cocoa-based agroforestry systems. Key words: Cocoa, cocoa farmers, agroforestry, cocoa-based agroforestry systems, soil macro-fauna, macro-fauna, soil fertility, Cameroon.

Identification of inorganic waste at mangrove ecosystem, Gampong Jawa, Banda Aceh

The plastic pollution entering the ocean has been global concern. However, the research about the mangrove ecosystem poses the plastic waste in Aceh Province is limited. This study aims to investigate the inorganic waste based on type and its abundance in mangrove area at Gampong Jawa, Banda Aceh. Transect was installed along 6m x 100m at three stations. The total waste collected was 134 items with the most abundance was plastic (126 items). The most common type found at the three stations was plastic bags. Rubber and glass were also observed trapped in Gampong Jawa’s mangrove area. The high level of debris abundance at station 1 was suspected because station 1 has the highest mangrove density so that allows the debris trapped at the mangrove roots. Stations 2 and 3 have less debris abundance because the low density of mangroves.

&lt;span&gt;First researches of the underwater ecosystem communities of an underground channel built in 1950s (Balaklava bay, Sevastopol)&lt;/span&gt;

The results of the first studies of the ecosystem state of the underwater part of the channel, artificially created in the middle of the 20th century on the western shore of the Balaklava Bay (Sevastopol) as a naval base of the Black Sea Fleet for the submarines repair, are presented. Channel's ecosystem is determined by uniqueness of anthropogenic formation and considered as analogue of natural Black Sea cave. Hydrospelological survey of the channel and biological studies allowed assessing its current state, the nature of biofouling of its walls and anthropogenic and technical pollution of the bottom. Macrofauna of the channel wall biofouling is represented by the Mytilaster lineatus community, which has a high level of species abundance (about 80 species have been registered) and quantitative development. Both in taxonomic diversity and in quantitative terms, this community is comparable to the rocky substrate community near open Crimean coasts, but with a smaller share of crustacean group development. Due to weakened hydrodynamics, well developed fauna of bryozoans forming plurannual crusty structures and single sponges is observed on the channel's walls. In contrast to the channel walls biofouling, its bottom macrofauna has relatively lower quantitative and qualitative composition. Meiobenthos in the channel’s wall biofouling is represented by 18 higher taxa (type, class, order) of Protozoa and Metazoa with predominance of harpacticoids by abundance. Meiobenthos of the soft bottom of underground channel is represented by 15 higher taxa with predominance of free-living nematodes and harpacticoids by abundance. Average density of meiobenthos in the channel’s bottom sediments is comparable with similar parameters of its development in open water areas and Sevastopol bays.

Characteristics of expanded polystyrene microplastics on island beaches in the Pearl River Estuary: abundance, size, surface texture and their metals-carrying capacity.

While expanded polystyrene (EPS) microplastics have been widely recognized as one of the most important components of plastic litter in the intertidal zones of the global ocean, our understanding of their environmental fate on island beaches is insufficient. In this study, we intended to reveal that the latest EPS microplastic pollution status on 5 island beaches in the Pearl River Estuary, China, by comprehensively assessing the abundance, distribution, size, surface texture and carrying capacity of heavy metals (Cd, As, Cr, Ni, Cu, Pb, Mn, Fe, Al). High level of EPS microplastic abundance ranged from 328 to 82,276 particles m-2 was found, with the highest abundance at Guishan Island and the lowest at Dong'ao Island. Spatial distribution of EPS microplastic abundance was significantly different among different islands. EPS microplastics in the size range of 1-2 mm were the most abundant. The content of heavy metals in EPS microplastics collected on the beaches was greater than that in the new EPS products. The average concentrations of heavy metals in EPS microplastics from 5 islands are Cd (0.27 ± 0.19 μg g-1), As (5.50 ± 3.84 μg g-1), Cr (14.9 ± 8.25 μg g-1), Cu (15.0 ± 7.66 μg g-1), Ni (17.2 ± 17.6 μg g-1), Pb (24.8 ± 7.39 μg g-1), Mn (730 ± 797 μg g-1), Fe (8340 ± 4760 μg g-1), and Al (9624 ± 6187 μg g-1), respectively. The correlation between heavy metals in EPS microplastics and sediments was better than that between heavy metals in EPS microplastics and seawater. The study results indicated that EPS microplastics could act as a carrier for the transport of heavy metals, which might pose a threat to biological and human health.

Вплив евтрофікації на багаторічну динаміку угруповань молоді риб

The article reveals the patterns of the temporal dynamics of juvenile fish communities under conditions of eutrophication of water bodies. The study was conducted in the reservoirs of the nature reserve “Dniprovsko-Orilsky”. Ichthyological sampling was carried out according to standard methods used in the study of the quantitative and qualitative composition of fish communities. During the study period, representatives of 38 species of juvenile fish were established in the surveys. Numbers of fish communities showed temporal patterns and differed significantly between habitat types. At presence of the general temporary trends of abundance, each of types of biotopes is characterized by the features of temporary dynamics. The highest level of abundance was characteristic of the channel part of the Dnieper River. Lake ecosystems of the Dnieper River floodplain were characterized by a much lower level of fish abundance. Among lake ecosystems, the highest number of juvenile fish communities was established for the reservoirs of the Taromsky ledge. The highest biomass was established for the channel part of the Dnieper River. The biomass of juvenile fish communities was significantly lower in the lacustrine water bodies. Species diversity of juvenile fish communities statistically reliably depends on habitat type and year as a categorical variable. The number of species increases with the growth of community abundance up to a certain level, after which there is an exit to a plateau: the growth of abundance is not accompanied by a significant increase in the number of species in the community. Biotopes can be divided into three groups according to the level of diversity. It has been substantiated that the establishment of protected areas and the maintenance of a fish conservation regime within them is an important factor in stabilizing the temporal dynamics of abundance, diversity and sustainability of fish populations over a much larger area than the territory of the reserve itself. Young fish communities are a sensitive indicator of the temporal dynamics of the ecological state of water bodies and respond both to the negative impact of anthropogenic activities and to positive measures of protection of biological diversity in protected areas.

Environmental variables affect the diversity of adult damselflies (Odonata: Zygoptera) in western Amazonia

Our study evaluated the effects of environmental variables on the assemblages of the suborder Zygoptera, and tested the hypothesis that environmental variables are more important determinants of the structure of these assemblages than limnological variables in streams. We sampled 17 streams in the Carajás National Forest and tested our hypothesis using a linear regression analysis, with the zygopteran species composition, richness, and abundance as the response variables. Our findings indicate that both limnological and physical variables influence, independently, the characteristics of the zygopteran assemblages. The riparian forest maintains the stability of the environment and provides dispersal corridors, along which the zygopterans can reach alternative, suitable environments. The small scale of this study also implies that the continuity of the vegetation is essential for the dispersal of the zygopterans among different landscapes. The high levels of abundance recorded in the better-preserved environments may reflect the maintenance of specific habitats and resource availability. Riparian forest is crucial to the ecological equilibrium of the stream systems, although further research at a broader spatial scale that focuses on a greater diversity of variables should provide more robust insights into the phenomenon.

Exploring microbial community structure and metabolic gene clusters during silage fermentation of paper mulberry, a high-protein woody plant

To develop a new high-protein woody forage resource for livestock to alleviate feed shortages in the tropics, we applied PacBio single-molecule, real-time (SMRT) sequencing to explore the community structure, species diversity and metabolic gene clusters of natural microorganisms associated with paper mulberry (PM) silage fermentation. High levels of microbial diversity and abundance were observed in PM raw material, and these levels decreased with the progression of silage fermentation. During woody ensiling, the dominant bacteria shifted from pathogenic Gram-negative Proteobacteria to beneficial Gram-positive Firmicutes. Lactic acid bacteria became the most dominant bacteria that affected fermentation quality in terminal silages. Global and overview maps, carbohydrate metabolism and amino-acid metabolism were the important microbial metabolic pathways that impacted the final fermentation product of silage. PacBio SMRT sequencing revealed specific microbial-related information concerning silage. PM is rich in nutrients and macro mineral contents, which are preserved well during ensiling, indicating that PM silage can serve as a new woody resource suitable for ruminants.

Characterization of gut microbiota associated with clinical parameters in intrahepatic cholestasis of pregnancy

BackgroundIntrahepatic cholestasis of pregnancy (ICP) is a liver disorder that specifically occurs in pregnancy. Elevated levels of liver transaminases aspartate aminotransferase, alanine aminotransferase and serum bilirubin levels are common biochemical characteristics in ICP. The disorder is associated with an increased risk of premature delivery and stillbirth. The characterization of the potential microbiota in ICP could go a long way in the prevention and treatment of this pregnancy disease.MethodsA total of 58 patients were recruited for our study: 27 ICP patients and 31 healthy pregnant subjects with no ICP. The V3 and V4 regions of the 16S rDNA collected from fecal samples of both diseased and control groups were amplified. 16S rRNA gene amplicon sequencing was then performed on gut microbiota. Sequencing data were analyzed and the correlation between components of microbiota and patient ICP status was found. Related metabolic pathways, relative abundance and significantly different operational taxonomic units (OTUs) between ICP and controls were also identified.ResultsElevated levels of total bile acid, ALT, AST, Dbil and Tbil were recorded or observed in ICP subjects as compared to the control. Gut microbiota in pregnant women was dominated by four major phyla and 27 core genera. PCoA analysis results indicated that there was no significant clustering in Bray–Curtis distance matrices. Our results showed that there was a correlation between specific OTUs and measured clinical parameters of pregnant women. Comparison at the different taxonomy levels revealed high levels of abundance of Blautia and Citrobacter in ICP patients. At the family level, Enterobacteriaceae and Leuconostocaceae were higher in ICP patients. 638 KEGG Orthologs and 138 pathways significantly differed in the two groups. PLS-DA model with VIP plots indicated a total of eight genera and seven species were key taxa in ICP and control groups.ConclusionsOur research indicated that although there was no significant clustering by PCoA analysis, patients with ICP have increased rare bacteria at different phylogenetic levels. Our results also illustrated that all 638 KEGG Orthologs and 136 in 138 KEGG pathways were less abundant in ICP patients compared to the controls.

Annual Wildflower Strips as a Tool for Enhancing Functional Biodiversity in Rye Fields in an Organic Cultivation System

Ecological intensification of agriculture (e.g., with the use of wildflower strips) is being currently discussed as a mean for gaining high yields, preserving high biodiversity of farmland. The aim of this study was to assess the efficiency of annual wildflower strips (WFSs) established in rye field (RF) in (1) increasing species richness and abundance in terms of beneficial arthropod groups (carabids, ground spiders, plant spiders, butterflies, insect pollinators and plant-dwelling insect predators), (2) decreasing the abundance of insect pests, (3) decreasing damages of the crop, and (4) increasing the yield. The field survey was carried out in 2019, in two WFSs and in the adjacent crop field at the distances of 3, 9, 21 and 45 m. The study was not skewed by pesticide use as it was carried out on an organic farm. Mean “site” species numbers (α-diversity) and the abundance of most groups were found to be significantly higher in WFSs than in RF. A negative relationship was found in most groups between distance from WFSs and species numbers and abundance. The mean total abundance of all observed pest insects was positively related to distance from WFSs and increased by 83% at distances between 3 and 45 m from WFSs. There was a negative exponential relationship between aphid abundance and total predator abundance, which suggests a mechanism reducing aphid abundance resulting from high levels of predator abundance in the nearby WFSs. The study shows that annual WFSs can be an efficient measure for enhancing cropland biodiversity and should be taken into account in agri-environmental schemes in the Common Agricultural Policy after 2020.

Immune Cell Confrontation in the Papillary Thyroid Carcinoma Microenvironment.

BackgroundPapillary thyroid cancer has been associated with chronic inflammation. A systematic understanding of immune cell infiltration in PTC is essential for subsequent immune research and new diagnostic and therapeutic strategies.MethodsThree different algorithms, single-sample gene set enrichment analysis (ssGSEA), immune cell marker and CIBERSORT, were used to evaluate immune cell infiltration levels (abundance and proportion) in 10 data sets (The Cancer Genome Atlas [TCGA], GSE3467, GSE3678, GSE5364, GSE27155, GSE33630, GSE50901, GSE53157, GSE58545, and GSE60542; a total of 799 PTC and 194 normal thyroid samples). Consensus unsupervised clustering divided PTC patients into low-immunity and high-immunity groups. Weighted gene coexpression network analysis (WGCNA) and gene set enrichment analysis (GSEA) were used to analyze the potential mechanisms causing differences in the immune response.ResultsCompared with normal tissues, PTC tissues had a higher overall immune level and higher abundance levels and proportions of M2 macrophages, Tregs, monocytes, neutrophils, dendritic cells (DCs), mast cells (MCs), and M0 macrophages. Compared with early PTC, advanced PTC showed higher immune infiltration and higher abundance levels and proportions of M2 macrophages, Tregs, monocytes, neutrophils, DCs, MCs, and M0 macrophages. Compared to the low-immunity group, the high-immunity group exhibited more advanced stages, larger tumor sizes, greater lymph node metastases, higher tall-cell PTCs, lower follicular PTC proportions, more BRAF mutations, and fewer RAS mutations. Epstein-Barr virus (EBV) infection was the most significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for key module genes.ConclusionsIn human PTC, M2 macrophages, Tregs, monocytes, neutrophils, DCs, MCs, and M0 macrophages appear to play a tumor-promoting role, while M1 macrophages, CD8+ T cells, B cells, NK cells, and T follicular helper (TFH) cells (including eosinophils, γδ T cells, and Th17 cells with weak supporting evidence) appear to play an antitumor role. During the occurrence and development of PTC, the overall immune level was increased, and the abundance and proportion of tumor-promoting immune cells were significantly increased, indicating that immune escape had been aggravated. Finally, we speculate that EBV may play an important role in changing the immune microenvironment of PTC tumors.

Characteristics and controlling factors of LORS from the Chang 7–3 section of the Triassic Yanchang Formation in the Ordos Basin

Lacustrine organic-rich shale (LORS) developed in the Chang 7–3 section of the Triassic Yanchang Formation in the Ordos Basin. LORS has been proven to be a source of crude oil and tight oil, as well as a source and reservoir for shale oil in the basin. A total of 35 LORS samples were collected from Well Z233 and analysed by mineralogy and element geochemistry to reveal the characteristics and controlling factors of LORS. The following results were obtained: ① In the oil shale, the organic matter is composed of type I and type II kerogen, with a predominance of type II. The organic matter is mature and reaches high levels of abundance. ②Through further analysis. The values of w(U)/w(Th), w(V)/w(Cr), w(Ni)/w(Co), the size and morphology of pyrite, indicates that the lake water of the LORS deposition period in the study area is anoxic or suboxic state. the TOC of the samples was found to have significant positive correlations with the w(Mo) and w(Babio) contents. Paleoproductivity can be inferred to be the key factor controlling organic matter enrichment in the LORS. ③Volcanic and hydrothermal activities promote the development of LORS, provide nutrients needed by organisms, promote the growth of organisms, and improve paleoproductivity. Hydrothermal activity leads to the formation of an anoxic environment at the bottom of the lake, and tuff will cover the sediments, which promotes LORS preservation. This study reveals in detail paleoproductivity is the main factor in the formation of LORS during the evolution of the basin. Volcanic and hydrothermal activities promoted the increase of paleoproductivity, and finally the oil shale layers with the richest organic matter have been formed. And thereby deepens our theoretical understanding of organic matter enrichment.

Observation of microplastics in mariculture water of Longjiao Bay, southeast China: Influence by human activities

The fishery and mariculture industry contributes to social food supply and offers high-quality protein to humans. However, mariculture is recently regarded as an important source of marine microplastic pollution, which might even pose a threat to human health. Here we investigated a shrimp-culturing farm for 9 months in Longjiao Bay, a typical mariculture area in southeast China, to study the occurrence and seasonal variations of microplastics in the mariculture water. Results showed that microplastics were widely present (250–5150 particles/m3, mean 1594 particles/m3) in the water of culture ponds. Granules (41.36%) and fibers (34.93%) were the main components of microplastics and white (45.42%) is the dominant color, followed by yellow (32.13%) and black (19.55%). Most of microplastics had a particle size between 0.30 mm and 5.00 mm (92.03%). The proportions of PE (34.40%) and PET (30.18%) accounted for more than 60% of detected microplastics. The abundance of microplastics in mariculture water had a potential positive correlation with local seafood yield and a negative correlation with land areas. This study suggested that further research is needed to figure out the impact of the high levels of microplastic abundance in mariculture environments on organisms, especially cultured ones.

Ресурсы трески Курильских островов: запасы и современный промысел

The paper analyzes the long-term dynamics of stocks and annual catches&#x0D; of Pacific cod of the Kuril Islands, and also considers the structure of its&#x0D; modern fishery, taking into account the changes that have occurred in the&#x0D; organization of its coastal fishing in recent years. It was shown that the&#x0D; dynamics of commercial biomass of Pacific cod in the Northern and Southern&#x0D; Kuril Islands is comparable to that in 1975-2020 for groups in the southeastern&#x0D; part of the Bering Sea, the Karagin and Olyutor bays, on the shelf of Western&#x0D; Kamchatka, and in south-western Sakhalin. Development of the cod fishery in&#x0D; the North and South Kuril Islands in 1980-2019 went in accordance with the&#x0D; dynamics of stocks, the maximum catches were observed during the period&#x0D; of a high level of abundance of both groups in the 1980s. While the structure&#x0D; of the cod fishery on the shelf of the Northern Kuril Islands to date can be&#x0D; considered established, the development of fishing in the South Kuril Islands&#x0D; in the last two decades went by the gradual replacement of trawl fishing in the&#x0D; winter-spring period with snorkeling in the summer season.