Roles of programmed death-1 and muscle innate lymphoid cell-derived interleukin 13 in sepsis-induced intensive care unit-acquired weakness.

BACKGROUND: Intensive care unit-acquired weakness (ICU-AW) is a syndrome characterized by a long-term muscle weakness often observed in sepsis-surviving patients during the chronic phase. Although ICU-AW is independently associated with increased mortality, effective therapies have yet to be established. Programmed death-1 (PD-1) inhibitors have attracted attention as potential treatments for reversing immune exhaustion in sepsis; however, its impact on ICU-AW remains to be elucidated. Here, we study how PD-1 deficiency affects sepsis-induced skeletal muscle dysfunction in a preclinical sepsis model. METHODS: Chronic sepsis model was developed by treating wild-type (WT) and PD-1 knockout (KO) mice with caecal slurry, followed by resuscitation with antibiotics and saline. Mice were euthanized on days 15-17. Body weights, muscle weights, and limb muscle strengths were measured. Interleukin 13 (IL-13) and PD-1 expressions were examined by flow cytometry. Messenger RNA (mRNA) expressions of slow-twitch muscles were measured by reverse transcription and quantitative polymerase chain reaction (RT-qPCR). In an in vitro study, C2C12 myotubes were treated with lipopolysaccharide (LPS) and recombinant IL-13 followed by gene expression measurements. RESULTS: WT septic mice exhibited decreased muscle weight (quadriceps, P < 0.01; gastrocnemius, P < 0.05; and tibialis anterior, P < 0.01) and long-term muscle weakness (P < 0.0001), whereas PD-1 KO septic mice did not exhibit any reduction in muscle weights and strengths. Slow-twitch specific mRNAs, including myoglobin (Mb), troponin I type 1 (Tnni1), and myosin heavy chain 7 (Myh7) were decreased in WT skeletal muscle (Mb, P < 0.0001; Tnni1, P < 0.05; and Myh7, P < 0.05) after sepsis induction, but mRNA expressions of Tnni1 and Myh7 were increased in PD-1 KO septic mice (Mb, not significant; Tnni1, P < 0.0001; and Myh7, P < 0.05). Treatment of C2C12 myotube cells with LPS decreased the expression of slow-twitch mRNAs, which was restored by IL-13 (Mb, P < 0.0001; Tnni1, P < 0.001; and Myh7, P < 0.05). IL-13 production was significantly higher in ILC2s compared to T cells in skeletal muscle (P < 0.05). IL-13-producing ILC2s in skeletal muscle were examined and found to increase in PD-1 KO septic mice, compared with WT septic mice (P < 0.05). ILC2-derived IL-13 was increased by PD-1 KO septic mice and thought to protect the muscles from experimental ICU-AW. CONCLUSIONS: Long-term muscle weakness in experimental ICU-AW was ameliorated in PD-1 KO mice. ILC2-derived IL-13 production in skeletal muscles was increased in PD-1 KO mice, thereby suggesting that IL-13 alleviates muscle weakness during sepsis. This study demonstrates the effects of PD-1 blockade in preserving muscle strength during sepsis through an increase in ILC2-derived IL-13 and may be an attractive therapeutic target for sepsis-induced ICU-AW.

miR-200c-3p regulates α4 integrin-mediated T cell adhesion and migration.

A microRNA miR-200c-3p is a regulator of epithelial-mesenchymal transition to control adhesion and migration of epithelial and mesenchymal cells. However, little is known about whether miR-200c-3p affects lymphocyte adhesion and migration mediated by integrins. Using TK-1 (a T lymphoblast cell) as a model of T cell, here we show that repressed expression of miR-200c-3p upregulated α4 integrin-mediated adhesion to and migration across mucosal addressin cell adhesion molecule-1 (MAdCAM-1). Conversely, overexpression of miR-200c-3p downregulated α4 integrin-mediated adhesion and migration. Unlike in epithelial cells, miR-200c-3p did not target talin, a conformation activator of integrin, but, targeted E26-transformation-specific sequence 1 (ETS1), a transcriptional activator of α4 integrin, in T cells. Treatment of the miR-200c-3p-low-expressing TK-1 cells that possessed elevated α4 integrin with ETS1 small interfering RNA (siRNA) resulted in the reversion of the α4 integrin expression, supporting that ETS1 is a target of miR-200c-3p. A potential proinflammatory immune-modulator retinoic acid (RA) treatment of TK-1 cells elicited a significant reduction of miR-200c-3p and simultaneously a marked increase in ETS1 and α4 integrin expression. An anti-inflammatory cytokine TGF-ß1 treatment elevated miR-200c-3p, thereby downregulating ETS1 and α4 integrin expression. These results suggest that miR-200c-3p is an important regulator of α4 integrin expression and functions and may be controlled by RA and TGF-ß1 in an opposite way. Overexpression of miR-200c-3p could be a novel therapeutic option for treatment of gut inflammation through suppressing α4 integrin-mediated T cell migration.

The complete mitochondrial genome of Zaomma eriococci (hymenoptera: encyrtidae).

The complete mitochondrial genome of the Zaomma eriococci (Ferrière, 1955) (Hymenoptera: Encyrtidae) was obtained through next-generation sequencing, making the first reported complete mitochondrial genome of the genus Zaomma. The mitochondrial genome is 15,648 bp in length and includes 37 classical eukaryotic mitochondrial genes along with an A + T rich region. All 13 protein-coding genes (PCGs) initiate with typical ATN codons. Of these, 10 PCG genes terminate with TAA, while three terminate with TAG. Additionally, there are 22 tRNA genes, ranging in size from 62 to 70 bp. The maximum likelihood phylogenetic tree was constructed based on 13 PCGs, indicates that Z. eriococci is closely related to Tassonia gloriae. This mitochondrial genome will serve as a valuable molecular resource for species identification, genetic analysis, and comparative genomic studies of Z. eriococci, contributing to the growing collection of mitochondrial genomes within the family Encyrtidae.

Gallstone Dissolution Effects of Combination Therapy with n-3 Polyunsaturated Fatty Acids and Ursodeoxycholic Acid: A Randomized, Prospective, Preliminary Clinical Trial.

Background/Aims: : Ursodeoxycholic acid (UDCA) is the only well-established and widely used agent for dissolving gallstones. Epidemiological and animal studies have suggested potential therapeutic benefits of n-3 polyunsaturated fatty acids (PUFA) for dissolving cholesterol gallstones. We evaluated whether adding PUFA to UDCA improves gallstone dissolution in patients with cholesterol gallstones. Methods: : This randomized, prospective, preliminary clinical trial compared the efficacy and safety of UDCA plus PUFA combination therapy (combination group) with those of UDCA monotherapy (monotherapy group). The inclusion criteria were a gallstone diameter ≤15 mm on ultrasonography, radiolucent stones on plain X-ray, and no to mild symptoms. Gallstone dissolution rates, response rates, and adverse events were evaluated. Results: : Of the 59 screened patients, 45 patients completed treatment (24 and 21 in the monotherapy and combination groups, respectively). The gallstone dissolution rate tended to be higher in the combination group than in the monotherapy group (45.7% vs 9.9%, p=0.070). The radiological response rate was also significantly higher in the combination group (90.5% vs 41.7%, p=0.007). In both groups, dissolution and response rates were higher in patients with gallbladder sludge than in those with distinct stones. Four adverse events (two in each group) were observed, none of which were study drug-related or led to drug discontinuation. The incidence of these adverse events was similar in both groups (combination vs monotherapy: 9.5% vs 8.3%, p=0.890). Conclusions: : UDCA plus PUFA therapy dissolves cholesterol gallstones more effectively than UDCA monotherapy, without significant complications. Further prospective, large-scale studies of this combination therapy are warranted.

Lactiplantibacillus plantarum-Derived Indole-3-lactic Acid Ameliorates Intestinal Barrier Integrity through the AhR/Nrf2/NF-κB Axis.

Our previous studies have shown that Lactiplantibacillus plantarum DPUL-S164-derived indole-3-lactic acid (ILA) ameliorates intestinal epithelial cell barrier injury by activating aryl hydrocarbon receptor (AhR) and nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathways and promoting tight junction protein expression. This study further explored the crucial substances of L. plantarum DPUL-S164 in alleviating intestinal barrier damage in mice through a dextran sodium sulfate-induced ulcerative colitis mouse model. Compared to dead L. plantarum DPUL-S164 (D-S164), live L. plantarum DPUL-S164 (S164) and its tryptophan metabolite, ILA, showed an effective ameliorating effect on the intestinal barrier injury of mice treated by antibiotic cocktail and sodium dextran sulfate, suggesting that the crucial substances of L. plantarum DPUL-S164 ameliorating intestinal barrier injury are its extracellular metabolites. Furthermore, S164 and its tryptophan metabolite, ILA, ameliorate intestinal barrier injury and suppress intestinal inflammation by activating the AhR-Nrf2 pathway and inhibiting the nuclear factor kappa-B (NF-κB) pathway. These results suggest that L. plantarum DPUL-S164 ameliorates intestinal epithelial barrier damage in mice, primarily by producing ILA as a ligand to activate the AhR pathway.

Assessment of prolonged proteasome inhibition through ixazomib-based oral regimen on newly diagnosed and first-relapsed multiple myeloma: A real-world Chinese cohort study.

OBJECTIVE: To evaluate the effectiveness, safety, and convenience of in-class transition (iCT) from intravenous bortezomib-based induction to ixazomib-based oral regimens. METHODS: This retrospective real-world study was conducted in 16 Chinese hospitals between October 2017 and April 2023 and analyzed newly diagnosed (NDMM) and first-line relapsed multiple myeloma (FRMM) patients who attained at least a partial response from bortezomib-based induction therapy, followed by an ixazomib-based oral regimen for 2 year or until disease progression or intolerable toxicity. RESULTS: The study enrolled 199 patients, median age: 63 years old, male 55.4%, 53% as high risk (HR), and 47% as standard risk. Cytogenetic risk stratification by metaphase fluorescence in situ hybridization (M-FISH), based on the Mayo Clinic risk stratification system. The median duration of total PI therapy was 11 months, with ixazomib-based treatment spanning 6 months. At the 20-month median follow-up, 53% of patients remained on therapy. The 24-month PFS rate was 84.3% from the initiation of bortezomib-based induction and 83.4% from the start of ixazomib-based treatment. Overall response rate (ORR) was 100% post-bortezomib induction and 90% following 6 cycles of the ixazomib-based regimen. Based on the Sankey diagrams, 89.51% of patients maintained or improved their disease response after 2 cycles of iCT, 6 cycles (90.14%), and 12 cycles (80%). The HR level of Mayo was found to be a significant independent factor in a worse remission (hazard ratio (HR) 2.55; p = 0.033). Ixazomib's safety profile aligned with previous clinical trial data, with 49% of patients experiencing at least one AE of any grade. The most common AEs included peripheral neuropathy, nausea and vomiting, diarrhea, thrombocytopenia, and granulocytopenia. CONCLUSION: In the real-world Chinese MM population, NDMM and FRMM patients responded favorably to PI-based continuous therapy, demonstrating substantial response rates. The ixazomib-based iCT allows for sustained PI-based treatment, offering promising efficacy and tolerable AEs.

Cryptic diversity begets challenges and opportunities in biodiversity research.

How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.

Assessing heavy metal contamination in Amomum villosum Lour. fruits from plantations in Southern China: Soil-fungi-plant interactions.

Amomum villosum Lour. fruit is a common healthy food widely cultivated in southern China. Heavy metal contamination of farmland soils has becomes a serious environmental concern in China. Heavy metals in soil can be introduced into the food chain and pose health risks to humans. However, microbial communities may play beneficial roles in plants grown in metal-polluted soils. This study aimed to assess the potential health risks of heavy metals in soils and A. villosum fruits from different production areas and to explore the soil-microbe-plant regulation pattern for heavy metals in A. villosum fruits. Soil and A. villosum fruit samples were collected from nine planting fields in four provinces of southern China. The results showed that soils from seven areas were polluted with heavy metals to different degrees. Cr and Mn were the most serious contaminating elements. However, the accumulation of heavy metals in A. villosum fruit was negligible with no expected human health risks. Partial least squares path analysis of structural equation modeling showed that the accumulation of heavy metals in A. villosum fruits was influenced by multiple factors. More importantly, the PLS-SEM revealed that the heavy metal content in A. villosum fruits was indirectly affected by soil heavy metals through the regulation of the microbial community. Furthermore, some fungal phyla (e.g., Ascomycota and Chytridiomycota) and genera (e.g., Mucor) were related to the heavy metal content in the soil and in A. villosum fruits. The results of this study verified that soil fungal community play an important role in the accumulation of heavy metals in A. villosum fruits. Using fungi provides a potential biological strategy for reducing the health risk posed by heavy metals in food.

Postoperative analgesic efficacy of nefopam after anorectal surgery: a retrospective observational study

Objective: To examine the effectiveness of nefopam on postoperative pain control after anorectal surgeries. Methods: We retrospectively reviewed the electronic medical records of patients who underwent anorectal surgeries from January 2019 to March 2022 at two medical centers. The data were divided into nefopam and conventional groups. The primary outcome was the number of patients who requested additional opioids in the 24-h postoperative period. The secondary outcomes were numeric rating pain scores (NRPS) within a 24-h postoperative period and analgesic drugs-related side effects. Results: Eighty-seven patients in the conventional group and 60 in the nefopam group were recruited. The nefopam group reported less additional opioid consumption than the conventional group in all dimensions of analysis, including overall, adjusted to anesthetic techniques and types of surgery. However, these did not reach statistical significance (P = 0.093). Only patients in the nefopam group who underwent hemorrhoidectomy under TIVA or spinal anesthesia significantly required fewer additional opioids (P = 0.016, 60% mean difference). Similarly, the 24-h postoperative morphine consumption was lower in the nefopam group (mean difference = -3.4, 95%CI: 0.72,6.08). Furthermore, significantly lower NRPS were reported in the nefopam group during the 12-18 h postoperative period (P = 0.009). On the other hand, analgesic drugs related side effects were similar in both groups. Conclusions: The administration of nefopam after major anorectal surgery is beneficially evident in reducing postoperative opioid requirements. (AU)

Indole-3-Lactic Acid, a Tryptophan Metabolite of Lactiplantibacillus plantarum DPUL-S164, Improved Intestinal Barrier Damage by Activating AhR and Nrf2 Signaling Pathways.

A growing body of evidence suggests that microbial tryptophan metabolites play a crucial role in maintaining intestinal barrier stability and modulating host immunity. Our previous study showed that the Lactiplantibacillus plantarum (L. plantarum ) DPUL-S164 intervention in mice with a high tryptophan (Trp) diet promotes indole-3-lactic acid (ILA) production in the mice's intestinal tract and ameliorates dextran sodium sulfate(DSS)-induced intestinal barrier damage in mice. In this study, we used the HT-29 cell monolayer model to evaluate the effect of the L. plantarum DPUL-S164 Trp metabolites (DPUL-S164-TM) on the intestinal barrier. We found that L. plantarum DPUL-S164-TM alleviated lipopolysaccharide (LPS)-induced intestinal barrier damage and inflammation of the HT-29 cell monolayer by promoting the expression of tight junction proteins (ZO-1, occludin, claudin1), activating the AhR and Nrf2 signaling pathways, and inhibiting the NF-κB signaling pathway. We found that the promotion of tight junction protein expression and the activation of the Nrf2 signaling pathway by L. plantarum DPUL-S164-TM were dependent on the AhR expression of HT-29 cells. Additionally, L. plantarum DPUL-S164-TM showed a dramatic increase in the ILA content. Therefore, we inferred that ILA in L. plantarum DPUL-S164-TM plays a key role in improving the intestinal barrier function and alleviating inflammation.

Tree communities and functional traits determine herbivore compositional turnover.

There are many factors known to drive species turnover, although the mechanisms by which these operate are less clear. Based on comprehensive datasets from the largest tree diversity experiment worldwide (BEF-China), we used shared herbivore species (zeta diversity) and multi-site generalized dissimilarity modelling to investigate the patterns and determinants of species turnover of Lepidoptera herbivores among study plots across a gradient in tree species richness. We found that zeta diversity declined sharply with an increasing number of study plots, with complete changes in caterpillar species composition observed even at the fine spatial scale of our study. Plant community characteristics rather than abiotic factors were found to play key roles in driving caterpillar compositional turnover, although these effects varied with an increasing number of study plots considered, due to the varying contributions of rare and common species to compositional turnover. Our study reveals details of the impact of phylogeny- and trait-mediated processes of trees on herbivore compositional turnover, which has implications for forest management and conservation and shows potential avenues for maintenance of heterogeneity in herbivore communities.

Recombinant soluble thrombomodulin attenuates cisplatin-induced intestinal injury by inhibiting intestinal epithelial cell-derived cytokine secretion.

BACKGROUND: Intestinal injury is one of the main side-effects of cisplatin chemotherapy, impairing the quality of life in patients with cancer. In this study, we investigated the protective effects of recombinant soluble thrombomodulin (rsTM), which is a potent anti-inflammatory agent, on cisplatin-induced intestinal injury. METHODS: We first evaluated the effects of rsTM on intestinal injury caused by cisplatin in mice in vivo. Disease progression was monitored by analyzing loss of body weight and histological changes in intestinal tissue. We then investigated the effects of rsTM on mouse intestinal organoid formation and growth in vitro. Gene expression levels were analyzed by quantitative real-time polymerase chain reaction and Western blotting. RESULTS: rsTM treatment significantly attenuated the loss of body weight, histological damage and gene expression levels of pro-inflammatory cytokines such as interleukin-6, tumor necrosis factor-α and high-mobility group box-1 in a cisplatin-treated mouse model. Furthermore, rsTM alleviated the inflammatory response and apoptosis in a cisplatin-treated intestinal epithelial organoid model. CONCLUSION: rsTM suppresses cisplatin-induced intestinal epithelial cell-derived cytokine production and alleviates intestinal mucositis.

Changes in Intracellular and Extracellular Metabolites of Mixed Lactobacillus Strains Enhance Inhibition of Pathogenic Bacterial Growth and Lipopolysaccharide-Induced Alleviation of RAW264.7 Cellular Inflammation.

It is important to explore whether there are antagonistic and synergistic effects between different strains of Lactobacillus when developing mixed Lactobacillus strain products. In this study, we investigated the antagonistic and symbiotic effects of co-cultured Lactobacillus strains, as well as their amelioratory effects on lipopolysaccharide (LPS)-induced inflammation and oxidative stress in RAW264.7 cells. The Lactobacillus strains tested in this paper showed no antagonism. Co-culture of Lactiplantibacillus plantarum Y44 and L. plantarum AKS-WS9 was found to show inhibiting effects on the growth of Escherichia coli and Staphylococcus aureus. Additionally, the co-cultured Lactiplantibacillus plantarum Y44 and L. plantarum AKS-WS9 relieved inflammation in RAW264.7 cells induced by LPS by inhibiting the activation of NF-κB and P38 signaling pathways and down-regulating the expression of pro-inflammatory cytokines NO, ROS, iNOs and TNF-α. And the co-cultured Lactobacillus strains activated the Nrf2 signaling pathway in the LPS-induced RAW264.7 cells to promote the expression of antioxidant enzymes in response to oxidative stress. There was a difference in intracellular and extracellular metabolites between single or co-cultured Lactobacillus strains, and the co-cultured Lactobacillus strains significantly increased extracellular metabolites 4-chlorobenzaldehyde, psoromic acid, and 2-dodecylbenzenesulfonic acid and intracellular metabolites 9(S)-HODE, pyocyanin, and LysoPA. We inferred that the better antibacterial and anti-inflammatory ability of the co-cultured Lactobacillus strains were related to the changes in the metabolites of the co-cultured Lactobacillus strains. The co-cultured L. plantarum Y44 and L. plantarum AKS-WS9 strains exhibited better anti-inflammatory abilities and had the potential to alleviate the symptoms of inflammatory diseases as mixed probiotics.

The impact of heavy metal pollution on wild bee communities in smallholder farmlands.

Wild bees provide important pollination services, but they face numerous stressors that threaten them and their ecosystem services. Wild bees can be exposed to heavy metal pollution through the consumption of nectar, pollen, and water, which might cause bee decline. While some studies have measured heavy metal concentrations in honeybees, few studies have monitored heavy metal concentrations in wild bees or explored their potential effects on wild bee communities. To investigate the impact of heavy metal pollution on wild bee communities, heavy metal concentrations, including vanadium (V), chromium (Cr), nickel (Ni), cadmium (Cd), Zinc (Zn) and lead (Pb) in multiple wild bee species were measured. Multiple wild bee species, including: Xylocopa tranquabaroroum, Eucera floralia, Apis cerana, and small bee mixtures (representing multiple small wild bee species) were sampled from 18 sites in Quzhou, Zhejiang Province, China. The findings demonstrated that there were significant differences in heavy metal concentrations among different bee species. The concentrations of V, Zn, Cd, and Pb in X. tranquabaroroum, the largest bee species in this study, were lower than that in the other three sample groups. Furthermore, there were significant negative correlations between heavy metal pollution and wild bee diversity and species richness, but not with abundance. Particularly, there was no significant relationship between heavy metal pollution and the abundance of small bees. Given these worrying findings, monitoring multiple heavy metals in wild bees should be conducted for protecting wild bee diversity and securing their pollination services.

Plantamajoside modulates immune dysregulation and hepatic lipid metabolism in rats with nonalcoholic fatty liver disease via AMPK/Nrf2 elevation.

Nonalcoholic fatty liver disease (NAFLD) is a hepatic metabolic syndrome with a rapidly increasing prevalence globally. Plantamajoside (PMS), a phenylethanoid glycoside component extracted from Plantago asiatica, has various biological properties. However, its effect on NAFLD remains unknown. The study aimed to explore the effect and mechanism of PMS on NAFLD in the high-fat diet (HFD)-feeding rats. PMS induced a decrease in body and liver weight, and the amelioration in the blood lipid parameters and pathological symptoms in HFD-feeding rats. The increase in the serum concentrations and the relative protein expressions of proinflammatory factors was decreased by the PMS treatment in HFD-induced NAFLD rats. Additionally, PMS reduced the excessive lipid vacuoles, and modified the relative expressions of proteins involved in the fatty acid synthesis and uptake in HFD-feeding rats. Mechanically, the downregulation of AMPK/Nrf2 pathway in HFD-feeding rats was restored by the PMS treatment. Inhibition of AMPK pathway reversed the PMS-induced the increase in the level of inflammatory factors, pathological symptoms, excessive lipid vacuoles, and the relative expression of proteins involved in the fatty acid synthesis and uptake. Collectively, PMS ameliorated immune dysregulation and abnormal hepatic lipid metabolism by activating AMPK/Nrf2 pathway in rats with NAFLD.

A Chromosome-level Genome Assembly and Evolution Analysis of Andrena camellia (Hymenoptera: Andrenidae).

Andrena camellia, an effective pollinator of the economicallysignificant crop Camellia oleifera, can withstand the toxic pollen of C. oleifera, making A. camellia a crucial for resource conservation and cultivation of C. oleifera. In this study, the whole genome of A. camellia was sequenced on the Oxford Nanopore platform. The assembled genome size was 340.73 Mb including 50 scaffolds (N50=47.435 Mb) and 131 contigs (N50=17.2 Mb). A total of 11, 258 protein-coding genes were annotated, in addition, 1,104 non-coding RNAs were identified. Further analysis that some chromosomes of A. camellia have a high level of synteny with those of Apis mellifera, Osmia bicornis and Andrena minutula. Thus, our reported genome of A. camellia serves as a valuable resource for studying species evolution, behavioral biology, and adaption to toxic pollen of C. oleifera.

The Whole Genome of Colletes collaris (Hymenoptera: Colletidae): An Important Step in Comparative Genomics of Cellophane Bees.

Gaining knowledge on bees is of the utmost importance due to the paramount role that they play in angiosperm pollination. Herein, we provide the first genome assembly of Colletes collaris, a pan-Eurasian cellophane bee. We sequenced 50.53 Gbp of long-read data plus 57.36 Gbp of short-read data in Oxford Nanopore Technologies and Illumina platforms, respectively. The genome assembly consisted of 374.75 Mbp distributed across 374 contigs, with L50 and N50 of 9 and 8.96 Mbp, respectively. We predicted the genome to comprise 20,399 protein-coding genes, 467,947 repeats, and 4,315 non-coding RNA genes. The transcriptome and mitochondrial genome of the species were also assembled. Gene family analysis with 15 insect species identified 14,417 families, 9,517 of them found in C. collaris. A dated phylogenomic analysis revealed high numbers of orthogroups experiencing rapid evolution within Colletes.

Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process.

Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].

MicroRNA Profiles in Intestinal Epithelial Cells in a Mouse Model of Sepsis.

Sepsis is a systemic inflammatory disorder that leads to the dysfunction of multiple organs. In the intestine, the deregulation of the epithelial barrier contributes to the development of sepsis by triggering continuous exposure to harmful factors. However, sepsis-induced epigenetic changes in gene-regulation networks within intestinal epithelial cells (IECs) remain unexplored. In this study, we analyzed the expression profile of microRNAs (miRNAs) in IECs isolated from a mouse model of sepsis generated via cecal slurry injection. Among 239 miRNAs, 14 miRNAs were upregulated, and 9 miRNAs were downregulated in the IECs by sepsis. Upregulated miRNAs in IECs from septic mice, particularly miR-149-5p, miR-466q, miR-495, and miR-511-3p, were seen to exhibit complex and global effects on gene regulation networks. Interestingly, miR-511-3p has emerged as a diagnostic marker in this sepsis model due to its increase in blood in addition to IECs. As expected, mRNAs in the IECs were remarkably altered by sepsis; specifically, 2248 mRNAs were decreased, while 612 mRNAs were increased. This quantitative bias may be possibly derived, at least partly, from the direct effects of the sepsis-increased miRNAs on the comprehensive expression of mRNAs. Thus, current in silico data indicate that there are dynamic regulatory responses of miRNAs to sepsis in IECs. In addition, the miRNAs that were increased with sepsis had enriched downstream pathways including Wnt signaling, which is associated with wound healing, and FGF/FGFR signaling, which has been linked to chronic inflammation and fibrosis. These modifications in miRNA networks in IECs may lead to both pro- and anti-inflammatory effects in sepsis. The four miRNAs discovered above were shown to putatively target LOX, PTCH1, COL22A1, FOXO1, or HMGA2, via in silico analysis, which were associated with Wnt or inflammatory pathways and selected for further study. The expressions of these target genes were downregulated in sepsis IECs, possibly through posttranscriptional modifications of these miRNAs. Taken together, our study suggests that IECs display a distinctive miRNA profile which is capable of comprehensively and functionally reshaping the IEC-specific mRNA landscape in a sepsis model.