Temporal dynamics and genomic programming of plasma cell fates.

Affinity-matured plasma cells (PCs) of varying lifespans are generated through a germinal center (GC) response. The developmental dynamics and genomic programs of antigen-specific PC precursors remain to be elucidated. Here, using a model antigen in mice, we demonstrate biphasic generation of PC precursors, with those generating long-lived bone marrow PCs preferentially produced in the late phase of GC response. Clonal tracing using single-cell RNA sequencing and B cell antigen receptor sequencing in spleen and bone marrow compartments, coupled with adoptive transfer experiments, reveals a new PC transition state that gives rise to functionally competent PC precursors. The latter undergo clonal expansion, dependent on inducible expression of TIGIT. We propose a model for the proliferation and programming of precursors of long-lived PCs, based on extended antigen encounters in the GC.

Coupled analysis of transcriptome and BCR mutations reveals role of OXPHOS in affinity maturation.

Antigen-activated B cells diversify variable regions of B cell antigen receptors by somatic hypermutation in germinal centers (GCs). The positive selection of GC B cells that acquire high-affinity mutations enables antibody affinity maturation. In spite of considerable progress, the genomic states underlying this process remain to be elucidated. Single-cell RNA sequencing and topic modeling revealed increased expression of the oxidative phosphorylation (OXPHOS) module in GC B cells undergoing mitoses. Coupled analysis of somatic hypermutation in immunoglobulin heavy chain (Igh) variable gene regions showed that GC B cells acquiring higher-affinity mutations had further elevated expression of OXPHOS genes. Deletion of mitochondrial Cox10 in GC B cells resulted in reduced cell division and impaired positive selection. Correspondingly, augmentation of OXPHOS activity with oltipraz promoted affinity maturation. We propose that elevated OXPHOS activity promotes B cell clonal expansion and also positive selection by tuning cell division times.

Early developing B cells undergo negative selection by central nervous system-specific antigens in the meninges.

Self-reactive B cell progenitors are eliminated through central tolerance checkpoints, a process thought to be restricted to the bone marrow in mammals. Here, we identified a consecutive trajectory of B cell development in the meninges of mice and non-human primates. The meningeal B cells were located predominantly at the dural sinuses, where endothelial cells expressed essential niche factors to support B cell development. Parabiosis experiments together with lineage tracing showed that meningeal developing B cells were replenished continuously from hematopoietic stem cell (HSC)-derived progenitors via a circulation-independent route. Autoreactive immature B cells that recognized myelin oligodendrocyte glycoprotein (MOG), a central nervous system-specific antigen, were eliminated specifically from the meninges. Furthermore, genetic deletion of the Mog gene restored the self-reactive B cell population in the meninges. These findings identify the meninges as a distinct reservoir for B cell development, allowing in situ negative selection to ensure a locally non-self-reactive immune repertoire.

Pseudocell Tracer-A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination.

Single cell RNA sequencing (scRNAseq) can be used to infer a temporal ordering of cellular states. Current methods for the inference of cellular trajectories rely on unbiased dimensionality reduction techniques. However, such biologically agnostic ordering can prove difficult for modeling complex developmental or differentiation processes. The cellular heterogeneity of dynamic biological compartments can result in sparse sampling of key intermediate cell states. To overcome these limitations, we develop a supervised machine learning framework, called Pseudocell Tracer, which infers trajectories in pseudospace rather than in pseudotime. The method uses a supervised encoder, trained with adjacent biological information, to project scRNAseq data into a low-dimensional manifold that maps the transcriptional states a cell can occupy. Then a generative adversarial network (GAN) is used to simulate pesudocells at regular intervals along a virtual cell-state axis. We demonstrate the utility of Pseudocell Tracer by modeling B cells undergoing immunoglobulin class switch recombination (CSR) during a prototypic antigen-induced antibody response. Our results revealed an ordering of key transcription factors regulating CSR to the IgG1 isotype, including the concomitant expression of Nfkb1 and Stat6 prior to the upregulation of Bach2 expression. Furthermore, the expression dynamics of genes encoding cytokine receptors suggest a poised IL-4 signaling state that preceeds CSR to the IgG1 isotype.

LOVD-DASH: A comprehensive LOVD database coupled with diagnosis and an at-risk assessment system for hemoglobinopathies.

Hemoglobinopathies are the most common monogenic disorders worldwide. Substantial effort has been made to establish databases to record complete mutation spectra causing or modifying this group of diseases. We present a variant database which couples an online auxiliary diagnosis and at-risk assessment system for hemoglobinopathies (DASH). The database was integrated into the Leiden Open Variation Database (LOVD), in which we included all reported variants focusing on a Chinese population by literature peer review-curation and existing databases, such as HbVar and IthaGenes. In addition, comprehensive mutation data generated by high-throughput sequencing of 2,087 hemoglobinopathy patients and 20,222 general individuals from southern China were also incorporated into the database. These sequencing data enabled us to observe disease-causing and modifier variants responsible for hemoglobinopathies in bulk. Currently, 371 unique variants have been recorded; 265 of 371 were described as disease-causing variants, whereas 106 were defined as modifier variants, including 34 functional variants identified by a quantitative trait association study of this high-throughput sequencing data. Due to the availability of a comprehensive phenotype-genotype data set, DASH has been established to automatically provide accurate suggestions on diagnosis and genetic counseling of hemoglobinopathies. LOVD-DASH will inspire us to deal with clinical genotyping and molecular screening for other Mendelian disorders.

Neoformation and summer arrest are common sources of tree plasticity in response to water stress of apple cultivars.

BACKGROUND AND AIMS: Depending on the species, water stress affects different growth and developmental processes, mainly due to changes in hydraulic properties and hormonal signalling. This study compared the impact of water stress on tree development and organ growth in three apple cultivars. METHODS: Trees were differentially irrigated to induce water stress or to provide well-watered conditions in their second and third years of growth. Effects of water stress were evaluated at tree scale by shoot number and proportions of the different types of shoots, and at shoot scale by metamer appearance rate, growth duration and arrest time, as well as organ size. KEY RESULTS: Water stress promoted early growth cessation, prolonged summer arrests and decreased growth resumptions, thus modifying within-tree shoot demography in favour of short shoots. Growth cessations occurred in mild water stress conditions before any difference in stem water potential appeared. No major impact was observed on organ size. Consistently with tree ontogeny, the number of shoots that resumed growth after summer arrest decreased with years, but more in water-stressed than well-watered conditions. CONCLUSIONS: Even though the impact of water stress differed slightly among cultivars, the reduction in neoformation and increase in summer arrest played a common role in apple tree morphological responses and led to stress avoidance by early reduction of tree leaf area.

[Research progress on uniparental disomy in cancer].

Uniparental disomy (UPD) refers to a chromosome defect that an individual's homologous chromosome or segments are inherited from one parent. UPD can cause either aberrant patterns of genomic imprinting or homozygosity of mutations, leading to various diseases, including cancer. The mechanisms of UPD formation are diverse but largely due to the incorrect chromosome separation during cell division. UPD does not alter the number of gene copies, thus is difficult to be detected by conventional cytogenetic techniques effectively. Assisted by the new techniques such as single nucleotide polymorphism arrays, more and more UPD-related cases have been reported recently. UPD events are non-randomly distributed across cancer types, which play important role in the occurrence, development and metastasis of cancer. Here we review the research progress on the formation mechanisms, detection methods, the involved chromosomal regions and genes, and clinical significance of UPD; and also discuss the directions for future studies in this field.

Survival and inflammation promotion effect of PTPRO in fulminant hepatitis is associated with NF-κB activation.

Previous investigations demonstrated that protein tyrosine phosphatase, receptor type, O (PTPRO) acts as a tumor suppressor in liver cancer; however, little is known about its role in liver inflammation. Thus, we investigated the role of PTPRO in fulminant hepatitis (FH) using a Con A-induced mouse model. Significantly more severe liver damage, but attenuated inflammation, was detected in PTPRO-knockout (KO) mice, and PTPRO deficiency could confer this phenotype to wild-type mice in bone marrow transplantation. Moreover, hepatocytes with PTPRO depletion were more sensitive to TNF-α-induced apoptosis, and secretion of cytokines was significantly decreased in both T and NK/NKT cells and led to marked impairment of NF-κB activation. Intriguingly, wild-type and PTPRO-KO cells responded equally to TNF-α in activation of IKK, but NF-κB activation was clearly decreased in PTPRO-KO cells. PTPRO associated with ErbB2, and loss of PTPRO potentiated activation of the ErbB2/Akt/GSK-3ß/ß-catenin cascade. Increased ß-catenin formed a complex with NF-κB and attenuated its nuclear translocation and activation. Importantly, in humans, PTPRO was much decreased in FH, and this was associated with enhanced ß-catenin accumulation but reduced IFN-γ secretion. Taken together, our study identified a novel PTPRO/ErbB2/Akt/GSK-3ß/ß-catenin/NF-κB axis in FH, which suggests that PTPRO may have therapeutic potential in this liver disease.

PTPRO plays a dual role in hepatic ischemia reperfusion injury through feedback activation of NF-κB.

BACKGROUND & AIMS: Nuclear factor-κB (NF-κB) activation in hepatocytes and macrophages appeared as a double-edged-sword in hepatic ischemia reperfusion (IR) injury. Protein tyrosine phosphatase receptor type O (PTPRO) was recently identified as a potential activator of c-Src, which can in turn activate the NF-κB pathway. In this study, we aimed to determine the change and function of PTPRO in hepatocytes and macrophages during IR. METHODS: Clinical patients with benign liver condition undergoing liver surgery were recruited in our study. Wild type (WT) and ptpro(-/-) C57BL/6 mice were processed to construct hepatic IR models. Isolated mouse hepatocytes and macrophages were treated with peroxide or TNFα in vitro. RESULTS: In human and mouse IR models, PTPRO level was decreased in the early phase but reversed in the late phase. In vitro studies demonstrated that NF-κB up-regulated PTPRO transcription. Using ptpro(-/-) mice and primary cells, we found that PTPRO deficiency resulted in reduction of NF-κB activation in both hepatocytes and macrophages and was correlated to c-Src phosphorylation; PTPRO in hepatocytes alleviated, but PTPROt in macrophages exacerbated IR injury. CONCLUSIONS: PTPRO activates NF-κB in a positive feedback manner, and plays a dual role in hepatic IR injury.

Copper catalyzed C-O bond formation via oxidative cross-coupling reaction of aldehydes and ethers.

A practical and efficient construction of C-O bonds via oxidative cross-coupling reaction of aldehydes and ethers has been realized under open air. When 2 mol% copper was used as the catalyst, various α-acyloxy ethers were obtained with up to 93% isolated yield.

Drought stimulus enhanced stress tolerance in winter wheat (Triticum aestivum L.) by improving physiological characteristics, growth, and water productivity.

The impact of drought events on the growth and yield of wheat plants has been extensively reported; however, limited information is available on the changes in physiological characteristics and their effects on the growth and water productivity of wheat after repeated drought stimuli. Moreover, whether appropriate drought stimulus can improve stress resistance in plants by improving physiological traits remains to be explored. Thus, in this study, a pot experiment was conducted to investigate the effects of intermittent and persistent mild [65%-75% soil water-holding capacity (SWHC)], moderate (55%-65% SWHC), and severe drought (45%-55% SWHC) stress on the growth, physiological characteristics, yield, and water-use efficiency (WUE) of winter wheat. After the second stress stimulus, persistent severe drought stress resulted in 30.98%, 234.62%, 53.80%, and 31.00% reduction in leaf relative water content, leaf water potential, photosynthetic rate (Pn), and indole-3-acetic acid content (IAA), respectively, compared to the control plants. However, abscisic acid content, antioxidant enzyme activities, and osmoregulatory substance contents increased significantly under drought stress, especially under persistent drought stress. After the second rehydration stimulus (ASRR), the actual and maximum efficiency of PSII and leaf water status in the plants exposed to intermittent moderate drought (IS2) stress were restored to the control levels, resulting in Pn being 102.56% of the control values; instantaneous WUE of the plants exposed to persistent severe drought stress was 1.79 times that of the control plants. In addition, the activities of superoxide dismutase, peroxidase, catalase, and glutathione reductase, as well as the content of proline, under persistent mild drought stress increased by 52.98%, 33.47%, 51.95%, 52.35%, and 17.07% at ASRR, respectively, compared to the control plants, which provided continuous antioxidant protection to wheat plants. This was also demonstrated by the lower H2O2 and MDA contents after rehydration. At ASRR, the IAA content in the IS2 and persistent moderate drought treatments increased by 36.23% and 19.61%, respectively, compared to the control plants, which favored increased aboveground dry mass and plant height. Compared to the control plants, IS2 significantly increased wheat yield, WUE for grain yield, and WUE for biomass, by 10.15%, 32.94%, and 33.16%, respectively. Collectively, IS2 increased grain growth, yield, and WUE, which could be mainly attributed to improved physiological characteristics after drought-stimulated rehydration.

Greenhouse gas emissions and drivers of the global warming potential of vineyards under different irrigation and fertilizer management practices.

In the context of global warming and low water and fertilizer utilization efficiency in vineyards, identifying the driving factors of global warming potential (GWP) and proper irrigation and fertilization management strategies are crucial for high grape yields and emission reduction. In this experiment, drip fertigation technology was used, including three irrigation levels (W3 (100% M, where M is the irrigation quota), W2 (75% M) and W1 (50% M)) and four fertilization levels (F3 (648 kg hm-2), F2 (486 kg hm-2), F1 (324 kg hm-2) and F0 (0 kg hm-2)). Traditional furrow irrigation and fertilization (CG) and rainfed (CK) treatments were used as control treatments. The results indicated that under the drip fertigation system, fertilization significantly increased the grape leaf chlorophyll relative content (SPAD) and leaf area index (LAI) within a fertilizer application of 0-486 kg hm-2. Irrigation primarily had a direct positive effect on the water-filled pore space (WFPS) in the 0-60 cm soil layer, and the residual soil nutrient content was mainly affected by fertilization. The vital stage for reducing greenhouse gas emissions was the fruit-inflating and fruit-rendering stages. The CG treatment not only failed to ensure high grape yield but also adversely affected the soil environment and the reduction of greenhouse gas emissions in the vineyard. Fertilization had a direct positive effect on the grape SPAD, LAI, yield, and soil residual nutrient content. GWP was primarily directly driven by SPAD, WFPS, and soil residual nutrient content, while grape yield was primarily directly driven by fertilization and SPAD. In conclusion, the W2F2 treatment (25 % reduced irrigation and 486 kg hm-2 of fertilization) of drip fertigation in the vineyard was the preferred irrigation and fertilizer management strategy for maintaining good vine vigor and balancing grape yield and environmental benefits.

Antibody Fc-receptor FcεR1γ stabilizes cell surface receptors in group 3 innate lymphoid cells and promotes anti-infection immunity.

Group 3 innate lymphoid cells (ILC3) are crucial for maintaining mucosal homeostasis and regulating inflammatory diseases, but the molecular mechanisms governing their phenotype and function are not fully understood. Here, we show that ILC3s highly express Fcer1g gene, which encodes the antibody Fc-receptor common gamma chain, FcεR1γ. Genetic perturbation of FcεR1γ leads to the absence of critical cell membrane receptors NKp46 and CD16 in ILC3s. Alanine scanning mutagenesis identifies two residues in FcεR1γ that stabilize its binding partners. FcεR1γ expression in ILC3s is essential for effective protective immunity against bacterial and fungal infections. Mechanistically, FcεR1γ influences the transcriptional state and proinflammatory cytokine production of ILC3s, relying on the CD16-FcεR1γ signaling pathway. In summary, our findings highlight the significance of FcεR1γ as an adapter protein that stabilizes cell membrane partners in ILC3s and promotes anti-infection immunity.

Individual and combined effects of heat and drought and subsequent recovery on winter wheat (Triticum aestivum L.) photosynthesis, nitrogen metabolism, cell osmoregulation, and yield formation.

Extreme temperatures and droughts are considered as the two main factors that limit wheat growth and production. Although responses of wheat plants to heat and drought stress have been extensively investigated, little is known about the extent to which wheat plants can recover after stress relief. In this study, a winter wheat pot experiment was conducted to evaluate the growth, physiological activities, and yield formation responses of wheat to stress and recovery periods under heat stress (36 °C, daily maximum temperature), drought (45-55% of soil water holding capacity), and combined stress conditions. Heat and drought stress significantly reduced photosynthesis, leaf relative water content (LRWC), leaf water potential (LWPnoon), and nitrogen metabolism enzyme activities and increased electrolyte leakage. These parameters showed significant interactions between heat and drought stress. Beneficial osmoregulation of membrane stability was observed in stressed plants because of the accumulation of proline and soluble sugars. Within a range of stresses, the abovementioned physiological processes of individual heat- and drought-stressed plants recovered to levels comparable to those of the control. The recovery capacities of the physiological traits decreased gradually with increasing stress duration, particularly under combined stress. The recovery of LWPnoon and LRWC contributed to the improved photosynthetic performance after stress relief. The combined stress caused greater yield losses than individual heat and drought stress, which was mainly attributed to low levels of thousand grain weight (TGW), the number of grains per ear, and the grain filling rate. After stress relief, the recovery of proline content, glutamine synthetase activity, photosynthetic rate, and LRWC were closely associated with grain yield and thousand grain weight. Collectively, these findings contribute to a better understanding of the coordinated responses of winter wheat during the combined heat and drought stress and recovery periods.

Photosynthetic, antioxidant activities, and osmoregulatory responses in winter wheat differ during the stress and recovery periods under heat, drought, and combined stress.

There will be longer and more intense periods of heat and drought stress in the future for terrestrial ecosystems. Although the responses of wheat plants to heat and drought stress alone have been extensively investigated, little is known about the extent to which their recovery can be assured after stress relief. In this study, a winter wheat pot experiment was conducted to investigate the changes in photosynthetic performance, antioxidant activity, osmoregulation, and membrane lipid peroxidation under heat stress (36 °C), drought (45-55% of soil water holding capacity), and combined stress conditions. The results showed that heat and drought stress significantly reduced the photosynthetic rate and the contents of chlorophyll and carotenoid. Superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutathione reductase (GR) activities were greatly activated by heat and drought stress to scavenge overproduced superoxide anion (O2-). Plants exhibited positive osmoregulation through the synthesis of soluble protein (SP), soluble sugar (SS), and proline (Pro) to improve membrane stability. Within a range of stress, combined heat and drought stress exhibited significant interactive effects in the above mentioned indicators. After stress relief, the majority of physiological processes were reversible, as indicated by the effective recovery of pigment contents, photosynthetic rate, antioxidant enzyme activities, osmoregulatory substance contents, and O2- production. Antioxidant enzyme activities tended to increase after recovering from 12 days of combined stress, whereas they were still not effective in mitigating oxidative damage. High levels of O2- and malondialdehyde (MDA) and a low relative growth rate during the recovery confirmed the irreversible damage caused by combined heat and drought stress. ROC (receiver operating characteristic) analysis indicated that GR and SS could accurately detect individual heat and drought stress that wheat plants were suffering or had suffered (AUC = 0.812-0.965), while POD and Pro had greater potential for diagnosing combined heat and drought stress (AUC = 0.871-0.958). Physiological indicators of stress tolerance were closely related to the photosynthetic rate during the stress, particularly Pro and GR. Collectively, the physiological processes of plants are reversible within a certain range of stress. POD, GR, Pro, and SS play vital roles in identifying and resisting heat, drought, and combined stress, and the recovery of these indicators contributed to improving photosynthesis and thereby increasing wheat growth. Our research contributes to the understanding of the underlying physiological mechanisms of plants in response to combined heat and drought stress and after stress relief.

Temporal dynamics and genomic programming of plasma cell fates.

Affinity-matured plasma cells (PCs) of varying lifespans are generated through a germinal center (GC) response. The developmental dynamics and genomic programs of antigen-specific PC precursors remain to be elucidated. Using a model antigen, we demonstrate biphasic generation of PC precursors, with those generating long-lived bone marrow PCs preferentially produced in the late phase of GC response. Clonal tracing using scRNA-seq+BCR-seq in spleen and bone marrow compartments, coupled with adoptive transfer experiments, reveal a novel PC transition state that gives rise to functionally competent PC precursors. The latter undergo clonal expansion, dependent on inducible expression of TIGIT. We propose a model for the proliferation and programming of precursors of long-lived PCs, based on extended antigen encounters followed by reduced antigen availability.

Complete Genome Sequence of Brevibacillus laterosporus Bl-zj, an Algicidal Bacterium Isolated from Soil.

Brevibacillus laterosporus can be used as a biocontrol agent for varieties of plants, as it is a pathogen of invertebrates and can also inhibit many bacteria and fungi. Here, we describe the complete genome sequence of B. laterosporus strain Bl-zj, an algicidal bacterium on cyanobacteria isolated from the soil in China.

PTPROt maintains T cell immunity in the microenvironment of hepatocellular carcinoma.

Intratumoral T cells play a central role in anti-tumor immunity, and the balance between T effector cells (Teff) and regulatory T cells (Treg) affects the prognosis of cancer patients. However, educated by tumor microenvironment, T cells frequently fail in their responsibility. In this study, we aimed to investigate the role of truncated isoform of protein tyrosine phosphatase receptor-type O (PTPROt) in T cell-mediated anti-tumor immunity. We recruited 70 hepatocellular carcinoma (HCC) patients and 30 healthy volunteers for clinical investigation, and analyzed cellular tumor immunity by using ptpro(-/-) C57BL/6 mice and NOD/SCID mice. PTPROt expression was significantly downregulated in human HCC-infiltrating T cells due to the hypoxia microenvironment; PTPROt expression highly correlated with the intratumoral Teff/Treg ratio and clinicopathologic characteristics. Moreover, PTPROt deficiency attenuated T cell-mediated anti-tumor immunity and remarkably promoted mouse HCC growth. Mechanistically, deletion of PTPROt decreased Teff quantity and quality through phosphorylation of lymphocyte-specific tyrosine kinase, but increased Treg differentiation through phosphorylation of signal transducer and activator of transcription 5. In support of the Teff/Treg homeostasis, PTPROt serves as an important tumor suppressor in HCC microenvironment.

Attenuated Listeria monocytogenes as a cancer vaccine vector for the delivery of CD24, a biomarker for hepatic cancer stem cells.

Attenuated Listeria monocytogenes (LM) is a promising candidate vector for the delivery of cancer vaccines. After phagocytosis by antigen-presenting cells, this bacterium stimulates the major histocompatibility complex (MHC)-I and MHC-II pathways and induces the proliferation of antigen-specific T lymphocytes. A new strategy involving genetic modification of the replication-deficient LM strain ΔdalΔdat (Lmdd) to express and secrete human CD24 protein has been developed. CD24 is a hepatic cancer stem cell biomarker that is closely associated with apoptosis, metastasis and recurrence of hepatocellular carcinoma (HCC). After intravenous administration in mice, Lmdd-CD24 was distributed primarily in the spleen and liver and did not cause severe organ injury. Lmdd-CD24 effectively increased the number of interferon (IFN)-γ-producing CD8(+) T cells and IFN-γ secretion. Lmdd-CD24 also enhanced the number of IL-4- and IL-10-producing T helper 2 cells. The efficacy of the Lmdd-CD24 vaccine was further investigated against Hepa1-6-CD24 tumors, which were inguinally inoculated into mice. Lmdd-CD24 significantly reduced the tumor size in mice and increased their survival. Notably, a reduction of T regulatory cell (Treg) numbers and an enhancement of specific CD8(+) T-cell activity were observed in the tumor-infiltrating lymphocytes (TILs). These results suggest a potential application of the Lmdd-CD24 vaccine against HCC.

Synthesis and properties of a novel quarternerized imidazolium [α-PW12O40]3- salt as a recoverable photo-polymerization catalyst.

A recoverable photo-polymerization catalyst based on an imidazolium and a polyoxometalate, viz., (BMIm)2(DMIm)PW12O40 (where, BMIm = 1-butyl-3-methylimidazolium, DMIm = 3,3'-dimethyl-1,1'-diimidazolium) is reported. It catalyzes photo-polymerization of several industrially important monomers like styrene, methyl methacrylate, butyl methacrylate and vinyl acetate. The catalyst is recoverable and hence can be reused. The molecular weight and polydispersity index can be controlled reasonably and a reaction pathway is proposed. The synthesis of this novel catalyst is reported and the catalyst has been characterized using standard techniques such as single crystal X-ray diffraction studies, cyclic voltammetry and various spectroscopic methods such as Fourier transform infrared spectroscopy, (1)H NMR spectroscopy, EPR spectroscopy and UV-Vis spectroscopy. DFT calculations have been used to explain the catalyst's photo-chemical activity.