Single-cell RNA sequencing illuminates the ontogeny, conservation and diversification of cartilaginous and bony fish lymphocytes.

Elucidating cellular architecture and cell-type evolution across species is central to understanding immune system function and susceptibility to disease. Adaptive immunity is a shared trait of the common ancestor of cartilaginous and bony fishes. However, evolutionary features of lymphocytes in these two jawed vertebrates remain unclear. Here, we present a single-cell RNA sequencing atlas of immune cells from cartilaginous (white-spotted bamboo shark) and bony (zebrafish and Chinese tongue sole) fishes. Cross-species comparisons show that the same cell types across different species exhibit similar transcriptional profiles. In the bamboo shark, we identify a phagocytic B cell population expressing several pattern recognition receptors, as well as a T cell sub-cluster co-expressing both T and B cell markers. In contrast to a division by function in the bony fishes, we show close linkage and poor functional specialization among lymphocytes in the cartilaginous fish. Our cross-species single-cell comparison presents a resource for uncovering the origin and evolution of the gnathostome immune system.

Genetic and epigenetic signatures for improved breeding of cultivated blueberry.

Blueberry belongs to the Vaccinium genus and is a highly popular fruit crop with significant economic importance. It was not until the early twentieth century that they began to be domesticated through extensive interspecific hybridization. Here, we collected 220 Vaccinium accessions from various geographical locations, including 154 from the United States, 14 from China, eight from Australia, and 29 from Europe and other countries, comprising 164 Vaccinium corymbosum, 15 Vaccinium ashei, 10 lowbush blueberries, seven half-high blueberries, and others. We present the whole-genome variation map of 220 accessions and reconstructed the hundred-year molecular history of interspecific hybridization of blueberry. We focused on the two major blueberry subgroups, the northern highbush blueberry (NHB) and southern highbush blueberry (SHB) and identified candidate genes that contribute to their distinct traits in climate adaptability and fruit quality. Our analysis unveiled the role of gene introgression from Vaccinium darrowii and V. ashei into SHB in driving the differentiation between SHB and NHB, potentially facilitating SHB's adaptation to subtropical environments. Assisted by genome-wide association studies, our analysis suggested VcTBL44 as a pivotal gene regulator governing fruit firmness in SHB. Additionally, we conducted whole-genome bisulfite sequencing on nine NHB and 12 SHB cultivars, and characterized regions that are differentially methylated between the two subgroups. In particular, we discovered that the ß-alanine metabolic pathway genes were enriched for DNA methylation changes. Our study provides high-quality genetic and epigenetic variation maps for blueberry, which offer valuable insights and resources for future blueberry breeding.

Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding.

To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.

Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis.

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice.

The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

Light control of three-dimensional chromatin organization in soybean.

Higher-order chromatin structure is critical for regulation of gene expression. In plants, light profoundly affects the morphogenesis of emerging seedlings as well as global gene expression to ensure optimal adaptation to environmental conditions. However, the changes and functional significance of chromatin organization in response to light during seedling development are not well documented. We constructed Hi-C contact maps for the cotyledon, apical hook and hypocotyl of soybean subjected to dark and light conditions. The resulting high-resolution Hi-C contact maps identified chromosome territories, A/B compartments, A/B sub-compartments, TADs (Topologically Associated Domains) and chromatin loops in each organ. We observed increased chromatin compaction under light and we found that domains that switched from B sub-compartments in darkness to A sub-compartments under light contained genes that were activated during photomorphogenesis. At the local scale, we identified a group of TADs constructed by gene clusters consisting of different numbers of Small Auxin-Upregulated RNAs (SAURs), which exhibited strict co-expression in the hook and hypocotyl in response to light stimulation. In the hypocotyl, RNA polymerase II (RNAPII) regulated the transcription of a SAURs cluster under light via TAD condensation. Our results suggest that the 3D genome is involved in the regulation of light-related gene expression in a tissue-specific manner.

Roflumilast inhibits tumor growth and migration in STK11/LKB1 deficient pancreatic cancer.

Pancreatic cancer is a malignant tumor of the digestive system. It is highly aggressive, easily metastasizes, and extremely difficult to treat. This study aimed to analyze the genes that might regulate pancreatic cancer migration to provide an essential basis for the prognostic assessment of pancreatic cancer and individualized treatment. A CRISPR knockout library directed against 915 murine genes was transfected into TB 32047 cell line to screen which gene loss promoted cell migration. Next-generation sequencing and PinAPL.py- analysis was performed to identify candidate genes. We then assessed the effect of serine/threonine kinase 11 (STK11) knockout on pancreatic cancer by wound-healing assay, chick agnosia (CAM) assay, and orthotopic mouse pancreatic cancer model. We performed RNA sequence and Western blotting for mechanistic studies to identify and verify the pathways. After accelerated Transwell migration screening, STK11 was identified as one of the top candidate genes. Further experiments showed that targeted knockout of STK11 promoted the cell migration and increased liver metastasis in mice. Mechanistic analyses revealed that STK11 knockout influences blood vessel morphogenesis and is closely associated with the enhanced expression of phosphodiesterases (PDEs), especially PDE4D, PDE4B, and PDE10A. PDE4 inhibitor Roflumilast inhibited STK11-KO cell migration and tumor size, further demonstrating that PDEs are essential for STK11-deficient cell migration. Our findings support the adoption of therapeutic strategies, including Roflumilast, for patients with STK11-mutated pancreatic cancer in order to improve treatment efficacy and ultimately prolong survival.

Photochemical Transformation of Dissolved Organic Matter in Surface Water Augmented the Formation of Disinfection Byproducts.

Sunlight may lead to changes in disinfection byproducts (DBPs) formation potentials of source water via transforming dissolved organic matter (DOM); however, the underlying mechanisms behind these changes remain unclear. This work systematically investigated the effect of photochemical transformation of DOM from reservoir water (DOMRe) and micropolluted river water (DOMRi) after 36 h of simulated sunlight irradiation (equivalent to one month under natural sunlight) on DBPs formation. Upon irradiation, high molecular weight (MW) and aromatic molecules tended to be mineralized or converted into low-MW and highly oxidized (O/C > 0.5) ones which might react with chlorine to generate high levels of DBPs, resulting in an elevation in the yields (µg DBP/mg C) of almost all the measured DBPs and the quantities of unknown DBPs in both DOM samples after chlorination. Additionally, DOMRi contained more aromatic molecules susceptible to photooxidation than DOMRe. Consequently, irradiated DOMRi exhibited a greater increase in the formation potentials of haloacetonitriles, halonitromethanes, and specific regulated DBPs, with nitrogenous DBPs being responsible for the overall rise in the calculated cytotoxicity following chlorination. This work emphasized the importance of a comprehensive removal of phototransformation products that may serve as DBPs precursors from source waters, especially from micropolluted source waters.

Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids.

In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col × C24 and C24 × Col in Arabidopsis using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of CURLY LEAF (clf) mutants clfCol × clfC24 and clfC24 × clfCol , the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.

Novel multiplexed alkali enzyme lysis coupled with EDTA pretreatment for RNA virus extraction from wastewater sludge: Optimization, recovery, and detection.

RNA viruses are readily enriched in wastewater sludge owing to adsorption by extracellular polymeric substances (EPS) during wastewater treatment, causing pathogenicity. However, conventional wastewater extraction methods often fail to fully extract these viruses from sludge. In this study, three methods: enzymatic (ENP), alkaline (ALP), and ethylenediaminetetraacetic acid (EDTA) pretreatments were applied to sludges and promote the RNA virus extraction from sludge. Our results show that the total recovery rate of RNA viruses increased by 87.73% after ENP pretreatment, whereas ALP pretreatment inhibited virus extraction. The highest recovery rate of viruses from sludge, reaching 296.80%, was achieved with EDTA pretreatment (EDP) coupled with ENP. Notably, the most significant increase was observed in the abundance of Astroviruses, which increased from 7.60 × 107 to 7.86 × 108 copies/g TSS after EDP + ENP treatment. Our investigations revealed that virus extraction was affected by a class of short-wavelength protein substances, as opposed to tryptophan or tyrosine, which were eluted by proteins with beef paste buffer by substitution after EDP + ENP treatment. The results of this study provide essential insights for sludge-based epidemiology with the required sensitivity for managing the extraction of RNA epidemic viruses to control viral transmission.

Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.

Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.

Hot Deformation Behavior and Processing Maps of 26CrMo7S Steel Used in Oil Exploration.

The hot deformation behavior and flow stress characteristics of experimental 26CrMo7S steel were analyzed using a thermal simulator under a range of conditions, including a strain rate range of 0.01~10 s-1, a temperature range of 850~1250 °C, and a maximum deformation amount of 70%. The Arrhenius constitutive model was built for the corresponding conditions, and the model's accuracy was verified through error analysis. Additionally, hot processing maps were constructed to analyze the processing zone of the steel under different hot deformation conditions. Finally, the microstructure of the processing zones was observed and verified using the electron backscattered diffraction (EBSD). The results indicate that the interaction of work hardening and dynamic softening influences the hot deformation behavior of 26CrMo7S steel. The Arrhenius constitutive equation with a value of the correlation coefficient (r = 0.99523) accurately predicts the flow behavior of 26CrMo7S steel under different strains. The optimal processing zone obtained with the hot processing maps is within a deformation range of 1010~1190 °C and a strain rate range of 0.01~10-1.5 s-1, and the obtained microstructure is in good agreement with the analysis results.

Corrigendum: Triticeae crop genome biology: an endless frontier.

[This corrects the article DOI: 10.3389/fpls.2023.1222681.].

Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings.

Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs at this time. Although several studies have reported about organ-specific development and expression induced by light, a systematic analysis of cell-type-specific differentiation and the associated transcriptional regulation is still lacking. Here we obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis thaliana seedlings. Informative cells from shoot and root tissues were grouped into 48 different cell clusters and finely annotated using multiple markers. With the determination of comprehensive developmental trajectories, we demonstrate light modulation of cell fate determination during guard cell specialization and vasculature development. Comparison of expression atlases between wild type and the pifq mutant indicates that phytochrome-interacting factors (PIFs) are involved in distinct developmental processes in endodermal and stomatal lineage cells via controlling cell-type-specific expression of target genes. These results provide information concerning the light signalling networks at the cell-type resolution, improving our understanding of how light regulates plant development at the cell-type and genome-wide levels. The obtained information could serve as a valuable resource for comprehensively investigating the molecular mechanism of cell development and differentiation in response to light.

The Impact of Diabetes Mellitus on Patient-Reported Outcomes of Chronic Low Back Pain with Modic Changes at One Year: A Prospective Cohort Study.

STUDY DESIGN: Prospective cohort study. OBJECTIVES: Diabetes mellitus (DM) is associated with unfavourable patient-reported outcomes after spine surgery. Chronic low back pain (CLBP) with Modic Changes (MCs) in the lumbar vertebrae, as observed on MRI, forms a specific subgroup. This study aims to investigate the potential influence of DM on CLBP with MCs. METHODS: This study involved 259 patients with CLBP accompanied MCs. We recorded the patient-reported outcomes (visual analogue scale (VAS), Oswestry Disability Index (ODI), and Roland-Morris Disability Questionnaire (RMDQ)) at baseline, 3, 6, and 12 months. Multivariable linear regression analyses were performed to determine predictors of patient-reported outcomes. RESULTS: 103 patients had DM. Patients with DM exhibited higher VAS (P < .05), ODI (P < .001), and RMDQ (P < .001) scores at 3, 6, and 12 months, while patients without DM experienced more significant improvements in the scores over time (P < .001). Patients with DM reported longer durations of physical exercise (P = .007). Additionally, patients without DM had a significantly higher patient satisfaction index (P < .001) and a lower prevalence of hypertension (P < .001). Notably, significant differences were observed in the distribution of MCs of lumbar vertebrae (P = .034) and Pfirrmann grades of intervertebral disc degeneration between two groups (P < .001). CONCLUSION: Patients with DM demonstrated poorer patient-reported outcomes compared to those without DM in 1-year. DM emerged as an independent predictor of adverse patient-reported outcomes. It can be utilized to enhance the management and treatment of CLBP in patients with MCs.

Environmental impact and optimization suggestions of pig manure and wastewater treatment systems from a life cycle perspective.

With the rapid development of the pig farming industry in China, a large amount of pig manure is inevitably generated. The management and utilization of pig manure in a sustainable approach require a systematic analysis of the environmental impacts generated from the existing pig manure treatment and disposal routes. In this study, three typical pig manure treatment and disposal routes: pig manure solid-liquid separation, i) wastewater biological treatment, direct land application of manure/sludge; ii) black-film anaerobic digestion of wastewater, mono-composting of manure/sludge and land use; iii) wastewater biological treatment, co-composting of manure/sludge and land use, were comparatively assessed in terms of their environmental impacts using the life cycle assessment. The results show that the added chemicals in wastewater treatment and the consumed electricity in composting the manure/sludge are the two main contributors to all environmental impacts. Thus, using green chemicals, controlling the dosage of added chemicals accurately, and selecting composting types with low energy consumption will significantly reduce the environmental burden of pig manure treatment and disposal routes. For the global warming potential of the evaluated three pig manure treatment and disposal routes, direct emissions of greenhouse gases during the composting process contribute the most, accounting for 77 %, 95 %, and 79 %, respectively. Furthermore, the struvite recovery with anaerobic digestion from pig manure will bring excellent environmental benefits, which will markedly offset the toxicity impacts and carbon emissions derived from pig manure treatment and disposal process. Overall, this work quantitatively evaluates the potential environmental impacts of the existing pig manure treatment and disposal routes, providing insights on optimization for future technical improvement and development.

Design of carbazole-based platinum complexes with steric hindrance for efficient organic light-emitting diodes.

The construction of platinum complexes with high steric hindrance is expected to suppress triple-triplet annihilation and π-π stacking to achieve high-performance organic light-emitting diodes (OLEDs) with low efficiency roll-off. Herein, two large steric hindrance platinum complexes (N-CzPhPtacac and N-CzCF3PhPtacac) were prepared by taking advantage of steric hindrance between the phenyl group on carbazole and the functional group (phenyl and trifluoromethyl substituted phenyl) at the 3-position of a pyridine moiety. Due to the similar electron cloud distribution and gap difference between the HOMO and LUMO, the two complexes showed similar orange-red emission peaks at 590 and 596 nm with high PL quantum yields of 90% and 92% and short excited state lifetimes of 2.77 and 3.08 µs in doped films, respectively. Consequently, OLEDs based on N-CzPhPtacac and N-CzCF3PhPtacac showed maximum external quantum efficiency (EQEmax) values of 15.4% and 18.9%, respectively. Importantly, benefitting from the more stretched spatial configuration from the -CF3 effect, the corresponding OLED exhibited a lower efficiency roll-off, with an EQE of 18.1% at 1000 cd m-2.

Effects of dissolved organic matter removal and molecular transformation in different water treatment processes on formation of disinfection byproducts.

Alterations in molecular composition of dissolved organic matter (DOM) during water treatments can influence the composition and toxicity of disinfection by-products (DBPs) in subsequent chlorination disinfection process. In this study, the impacts of DOM composition after various water treatment techniques (coagulation, adsorption, nanofiltration, biological aerated filter (BAF), and their integrated processes) on the generation mechanisms of DBPs were comprehensively explored by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with GC-MS and LC-MS analysis. The results indicated that coagulation preferentially removed unsaturated (low H/C) and oxidized (high O/C) compounds, whereas adsorption was prone to remove the reduced (low O/C) component that was more reactive with chlorine, leading to lower yields (µg DBP/mg DOC) of trihalomethanes (THMs) and haloacetic acids (HAAs) during subsequent chlorination. The coagulation-adsorption technique exhibited a relatively high removal of both known and unknown DBPs, demonstrating that coagulation and adsorption were complementary for DOM removal at the molecular level. Nanofiltration selectively removed molecules with relatively high O/C, however, those with very low O/C that were more reactive with chlorine could pass through the nanofiltration membrane, resulting in the highest yields of THMs and HAAs. Although BAF was inefficient in removing DBPs precursors, it could convert molecules with low degree of oxidation and unsaturation into highly oxidized and unsaturated ones, thereby significantly enhancing the removal of DBPs precursors in the subsequent coagulation-adsorption process. These findings are instrumental in developing and selecting more effective techniques to minimize the formation of DBPs in water treatment.

Should we initiate vasopressors earlier in patients with septic shock: A mini systemic review.

Septic shock treatment remains a major challenge for intensive care units, despite the recent prominent advances in both management and outcomes. Vasopressors serve as a cornerstone of septic shock therapy, but there is still controversy over the timing of administration. Specifically, it remains unclear whether vasopressors should be used early in the course of treatment. Here, we provide a systematic review of the literature on the timing of vasopressor administration. Research was systematically identified through PubMed, Embase and Cochrane searching according to PRISMA guidelines. Fourteen studies met the eligibility criteria and were included in the review. The pathophysiological basis for early vasopressor use was classified, with the exploration on indications for the early administration of mono-vasopressors or their combination with vasopressin or angiotensinII. We found that mortality was 28.1%-47.7% in the early vasopressors group, and 33.6%-54.5% in the control group. We also investigated the issue of vasopressor responsiveness. Furthermore, we acknowledged the subsequent challenge of administration of high-dose norepinephrine via peripheral veins with early vasopressor use. Based on the literature review, we propose a possible protocol for the early initiation of vasopressors in septic shock resuscitation.

Triticeae crop genome biology: an endless frontier.

Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley, rye, and oat, which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.