Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution.

Synthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single-cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated peripheral blood mononuclear cells from 96 African American children. We used novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we showed that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and showed widespread genetic regulation of the transcriptional dynamics of the gene expression response.

Antiviral RISC mainly targets viral mRNA but not genomic RNA of tospovirus.

Antiviral RNA silencing/interference (RNAi) of negative-strand (-) RNA plant viruses (NSVs) has been studied less than for single-stranded, positive-sense (+)RNA plant viruses. From the latter, genomic and subgenomic mRNA molecules are targeted by RNAi. However, genomic RNA strands from plant NSVs are generally wrapped tightly within viral nucleocapsid (N) protein to form ribonucleoproteins (RNPs), the core unit for viral replication, transcription and movement. In this study, the targeting of the NSV tospoviral genomic RNA and mRNA molecules by antiviral RNA-induced silencing complexes (RISC) was investigated, in vitro and in planta. RISC fractions isolated from tospovirus-infected N. benthamiana plants specifically cleaved naked, purified tospoviral genomic RNAs in vitro, but not genomic RNAs complexed with viral N protein. In planta RISC complexes, activated by a tobacco rattle virus (TRV) carrying tospovirus NSs or Gn gene fragments, mainly targeted the corresponding viral mRNAs and hardly genomic (viral and viral-complementary strands) RNA assembled into RNPs. In contrast, for the (+)ssRNA cucumber mosaic virus (CMV), RISC complexes, activated by TRV carrying CMV 2a or 2b gene fragments, targeted CMV genomic RNA. Altogether, the results indicated that antiviral RNAi primarily targets tospoviral mRNAs whilst their genomic RNA is well protected in RNPs against RISC-mediated cleavage. Considering the important role of RNPs in the replication cycle of all NSVs, the findings made in this study are likely applicable to all viruses belonging to this group.

The Sw-5b NLR nucleotide-binding domain plays a role in oligomerization, and its self-association is important for activation of cell death signaling.

Plant and animal intracellular nucleotide-binding and leucine-rich repeat (NLR) receptors play important roles in sensing pathogens and activating defense signaling. However, the molecular mechanisms underlying the activation of host defense signaling by NLR proteins remain largely unknown. Many studies have determined that the coil-coil (CC) or Toll and interleukin-1 receptor/resistance protein (TIR) domain of NLR proteins and their dimerization/oligomerization are critical for activating downstream defense signaling. In this study, we demonstrated that, in tomato, the nucleotide-binding (NB) domain Sw-5b NLR alone can activate downstream defense signaling, leading to elicitor-independent cell death. Sw-5b NB domains can self-associate, and this self-association is crucial for activating cell death signaling. The self-association was strongly compromised after the introduction of a K568R mutation into the P-loop of the NB domain. Consequently, the NBK568R mutant induced cell death very weakly. The NBCΔ20 mutant lacking the C-terminal 20 amino acids can self-associate but cannot activate cell death signaling. The NBCΔ20 mutant also interfered with wild-type NB domain self-association, leading to compromised cell death induction. By contrast, the NBK568R mutant did not interfere with wild-type NB domain self-association and its ability to induce cell death. Structural modeling of Sw-5b suggests that NB domains associate with one another and likely participate in oligomerization. As Sw-5b-triggered cell death is dependent on helper NLR proteins, we propose that the Sw-5b NB domain acts as a nucleation point for the assembly of an oligomeric resistosome, probably by recruiting downstream helper partners, to trigger defense signaling.

Impacts of Urban Expansion on Terrestrial Carbon Storage in China.

Urban expansion is one of the main factors driving terrestrial carbon storage (TCS) changes. Accurate accounting of TCS and rigorous quantification of its changes caused by historical urban expansion may help us to better predict its changes in the future. This study focuses on the carbon impacts of urbanization in China where the share of the urban population has increased from 18% in 1978 to 59% in 2017 and the growing will continue in the coming decades. Our results show that China's TCS decreased at an accelerating pace over the past three decades with an average reduction of 0.72TgC/y in 1980-1990 and 8.72TgC/y in 2000-2010, mostly due to conversion from cropland and woodland to urban land. Through simulating urban expansion under four scenarios from 2010 to 2050, we found a potential increasing trend in land conversion from woodland to urban land. This conversion trend would result in carbon storage loss at an average rate of 9.31TgC/y ∼ 12.94TgC/y in 2010-2050. The increasing trend in both land conversion and carbon storage loss is especially visible in the population centers of the Yangtze River Delta and the Pearl River Delta. Considering that the indirect emission effects of urbanization, such as farmland displacement, population migration, and land degradation, may be much larger, the overall emission impact of forthcoming urban expansion in China would increase the uncertainty of the nation's carbon emissions and potentially undermine China's targets as committed in the Paris Climate Agreement.

Synthesis and Characterization of MnIn2S4/Single-Walled Carbon Nanotube Composites as an Anode Material for Lithium-Ion Batteries.

In this study, we synthesized a transition metal sulfide (TMS) with a spinel structure, i.e., MnIn2S4 (MIS), using a two-step hydrothermal and sintering process. In the context of lithium-ion battery (LIB) applications, ternary TMSs are being considered as interesting options for anode materials. This consideration arises from their notable attributes, including high theoretical capacity, excellent cycle stability, and cost-effectiveness. However, dramatic volume changes result in the electrochemical performance being severely limited, so we introduced single-walled carbon nanotubes (SWCNTs) and prepared an MIS/SWCNT composite to enhance the structural stability and electronic conductivity. The synthesized MIS/SWCNT composite exhibits better cycle performance than bare MIS. Undergoing 100 cycles, MIS only yields a reversible capacity of 117 mAh/g at 0.1 A/g. However, the MIS/SWCNT composite exhibits a reversible capacity as high as 536 mAh/g after 100 cycles. Moreover, the MIS/SWCNT composite shows a better rate capability. The current density increases with cycling, and the SWCNT composite exhibits high reversible capacities of 232 and 102 mAh/g at 2 A/g and 5 A/g, respectively. Under the same conditions, pristine MIS can only deliver reversible capacities of 21 and 4 mAh/g. The results indicate that MIS/SWCNT composites are promising anode materials for LIBs.

[Meta analysis of infection risks of anti-TNF-α treatment in rheumatoid arthritis].

OBJECTIVE: To systematically evaluate the risks of anti-TNF-α treatment-associated infection, severe infection and tuberculosis in rheumatoid arthritis (RA) patients, and to reduce the infection incidences associated with anti-TNF-α therapy. METHODS: We used Meta analysis to systematically review randomized controlled trials on anti- TNF-α treatment associated risks of infection, severe infection and tuberculosis in RA patients. RESULTS: Although no statistically significant differences were detected in TB risk between anit- TNF-α treatment and the control group (0.5% vs 0.07%; P=0.27, OR=1.85, 95% CI: 0.62-5.52), there still existed a clinically obvious elevation of TB risk in monoclonal anti-TNF-α treatment, which was illustrated by the results that no TB case was reported in the etanercept group, but 11 TBs in 2050 infliximab-treated cases, and 3 TBs in 722 adalimumab-treated cases. The total infection and severe infection risks were also significantly higher in patients receiving anti-TNF-α treatment (P<0.05). Subanalysis revealed that etanercept showed no significantly higher infection or severe infection risk than control group (P>0.05), while both kinds of monoclonal antibodies of TNF-α blockers showed a significantly elevated infection or severe infection risks (P<0.05). High doses of anti-TNF-α treatment were associated with statistically increased risks of severe infection (6.0% vs 2.8%, P=0.04, OR=1.68, 95% CI: 1.02-2.78). CONCLUSION: The TB risk of anti-TNF-α treatment deserves close attention, especially in places with high rate of BCG vaccination and MTb infection. Monoclonal anti-TNF-α treatment brings higher risks of infection and severe infection than soluble TNF-α receptor.

Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers.

BACKGROUND: The inhibition of poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) is a potential synthetic lethal therapeutic strategy for the treatment of cancers with specific DNA-repair defects, including those arising in carriers of a BRCA1 or BRCA2 mutation. We conducted a clinical evaluation in humans of olaparib (AZD2281), a novel, potent, orally active PARP inhibitor. METHODS: This was a phase 1 trial that included the analysis of pharmacokinetic and pharmacodynamic characteristics of olaparib. Selection was aimed at having a study population enriched in carriers of a BRCA1 or BRCA2 mutation. RESULTS: We enrolled and treated 60 patients; 22 were carriers of a BRCA1 or BRCA2 mutation and 1 had a strong family history of BRCA-associated cancer but declined to undergo mutational testing. The olaparib dose and schedule were increased from 10 mg daily for 2 of every 3 weeks to 600 mg twice daily continuously. Reversible dose-limiting toxicity was seen in one of eight patients receiving 400 mg twice daily (grade 3 mood alteration and fatigue) and two of five patients receiving 600 mg twice daily (grade 4 thrombocytopenia and grade 3 somnolence). This led us to enroll another cohort, consisting only of carriers of a BRCA1 or BRCA2 mutation, to receive olaparib at a dose of 200 mg twice daily. Other adverse effects included mild gastrointestinal symptoms. There was no obvious increase in adverse effects seen in the mutation carriers. Pharmacokinetic data indicated rapid absorption and elimination; pharmacodynamic studies confirmed PARP inhibition in surrogate samples (of peripheral-blood mononuclear cells and plucked eyebrow-hair follicles) and tumor tissue. Objective antitumor activity was reported only in mutation carriers, all of whom had ovarian, breast, or prostate cancer and had received multiple treatment regimens. CONCLUSIONS: Olaparib has few of the adverse effects of conventional chemotherapy, inhibits PARP, and has antitumor activity in cancer associated with the BRCA1 or BRCA2 mutation. (ClinicalTrials.gov number, NCT00516373.)

Relationship between the UPLC Fingerprints of Citrus reticulata "Chachi" Leaves and Their Antioxidant Activities.

Citrus reticulata "Chachi" (CRC) leaves contain abundant flavonoids, indicating that they possess good nutritional/pharmacological research and development potential. This study aims to explore chemical antioxidant quality markers based on the spectrum-effect relationship and quality control strategy of CRC leaves. The ultrahigh performance liquid chromatography (UPLC) system was used to establish chromatographic fingerprints of Citrus reticulata "Chachi" leaves. Simultaneously, they were evaluated by using similarity analysis (SA), hierarchical cluster analysis (HCA), and principal component analysis (PCA). Afterwards, the DPPH assay was adopted to study the antioxidant effects. The spectrum-effect relationship between UPLC fingerprints and DPPH radical-scavenging activities was studied with grey relational analysis (GRA). Analysis results indicated that there were twenty-one common peaks of fourteen batches of CRC leaves which were from different regions of Guangdong province, and their similarities ranged from 0.648 to 0.997. HCA results showed that fourteen batches of samples of CRC leaves could be divided into six classes at Euclidean distance of 5. The results from GRA showed that tangeretin and hesperidin were the main flavonoids responsible for the antioxidant activity in CRC leaves. In conclusion, this research established a chromatographic analysis method suitable for CRC leaves and demonstrated that chromatographic fingerprints analysis combined with the antioxidant activity could be used to evaluate the material basis of CRC leaves and may provide a reference to establish a quality standard.

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution.

Synthetic glucocorticoids, such as dexamethasone, have been used as treatment for many immune conditions, such as asthma and more recently severe COVID-19. Single cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated Peripheral Blood Mononuclear Cells from 96 African American children. We employed novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we demonstrated that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and demonstrated widespread genetic regulation of the transcriptional dynamics of the gene expression response.

Characterization of alphasatellites associated with monopartite begomovirus/betasatellite complexes in Yunnan, China.

BACKGROUND: Alphasatellites are single-stranded molecules that are associated with monopartite begomovirus/betasatellite complexes. RESULTS: Alphasatellites were identified in begomovirus-infected plant samples in Yunnan, China. All samples that contained alphasatellites also contained betasatellites, but only some samples that contained betasatellites contained alphasatellites. Thirty-three alphasatellites were sequenced, and they ranged from 1360 to 1376 nucleotides. All alphasatellites contain 3 conserved features: a single open reading frame (Rep), a conserved hairpin structure, and an adenine-rich (A-rich) region. On the basis of the phylogenetic tree of the complete nucleotide sequences, the alphasatellites were divided into 3 types with one exception. Type 1 was associated with Tomato yellow leaf curl China virus (TYLCCNV)/Tomato yellow leaf curl China betasatellite (TYLCCNB) complex. Type 2 was associated with Tobacco curly shoot virus (TbCSV)/Tobacco curly shoot betasatellite (TbCSB) complex. Type 3 was associated with TbCSV/Ageratum yellow vein betasatellite (AYVB) complex. Within each type, nucleotide sequence identity ranged from 83.4 to 99.7%, while 63.4-81.3% identity was found between types. Mixed infections of alphasatellites associated with begomovirus/betasatellite complexes were documented. CONCLUSIONS: Our results validate that alphasatellites are only associated with begomovirus/betasatellite complexes. Thirty-three sequenced alphasatellites isolated from Yunnan Province, China were divided into 3 types--each associated with a specific begomovirus/betasatellite complex. Mix-infections of alphasatellite molecules may not be unusual.

Heavy metal accumulation, risk assessment and integrated biomarker responses of local vegetables: A case study along the Le'an river.

In this research, Ganzhou Chinese Cabbage (Brassica rapa pekinensis), Native Purple Garlic (Allium sativum L) and Leping Radish (Raphanus sativus L) widely planted and distributed along the Le'an River were chosen in the present study. Soil physical-chemical properties, nutrients contents as well as heavy metals elements accumulated in both soils and vegetables collected from 24 sites were analyzed by lab analysis combined with statistical method which was also used for calculation of contamination factor, pollution indexes and hazardous index. Heavy metals accumulation in soils were revealed with higher level, and copper and cadmium exceeded the background values by 8.82 and 16.73 times on average, which were also significantly related with the distribution of nonferrous metal processing enterprises. Heavy metal elements accumulated in vegetables were fully consistent with the finding of pollution characteristics in soils. Peroxidase biomarkers in vegetables, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), reduced glutathione (GSH) and lipoperoxidation (as TBARS), as well as integrated biomarker responses (IBR) were determined to give a reliable response after exposing of contaminants. Heavy metals accumulation ability and biomarker responses for three vegetables were usually determined in the following decrease trend: Ganzhou Chinese Cabbage > Native Purple Garlic > Leping Radish. Compared with peroxidase biomarkers activities or contents of control site, all the measured biomarkers in polluted sites showed significantly responses, indicating potential relationship between pollutants stresses and biomarker responses. This study also revealed that the IBR values were coordinated well with the pollutants concentrations.

P-STAT1 mediates higher-order chromatin remodelling of the human MHC in response to IFNgamma.

Transcriptional activation of the major histocompatibility complex (MHC) by IFNgamma is a key step in cell-mediated immunity. At an early stage of IFNgamma induction, chromatin carrying the entire MHC locus loops out from the chromosome 6 territory. We show here that JAK/STAT signalling triggers this higher-order chromatin remodelling and the entire MHC locus becomes decondensed prior to transcriptional activation of the classical HLA class II genes. A single point mutation of STAT1 that prevents phosphorylation is sufficient to abolish chromatin remodelling, thus establishing a direct link between the JAK/STAT signalling pathway and human chromatin architecture. The onset of chromatin remodelling corresponds with the binding of activated STAT1 and the chromatin remodelling enzyme BRG1 at specific sites within the MHC, and is followed by RNA-polymerase recruitment and histone hyperacetylation. We propose that the higher-order chromatin remodelling of the MHC locus is an essential step to generate a transcriptionally permissive chromatin environment for subsequent activation of classical HLA genes.

Replication timing profile reflects the distinct functional and genomic features of the MHC class II region.

The timing of DNA replication generally correlates with transcription, gene density and sequence composition. How is the timing affected if a genomic region has a combination of features that individually correlate with either early or late replication? The major histocompatibility complex (MHC) class II region is an AT-rich isochore that would be expected to replicate late, but it also contains coordinately regulated genes that are highly expressed in antigen-presenting cells and are strongly inducible in other cell types. Using cytological and biochemical assays, we find that the entire MHC replicates within the first half of S-phase, and that the class II region replicates slightly later than the adjacent regions irrespective of gene expression. These data suggest that despite AT-richness, an early-to-middle replication time in the class II region is defined by an open chromatin conformation that allows rapid transcriptional activation as a defence against pathogens.

Interaction between a nanovirus-like component and the Tobacco curly shoot virus/satellite complex.

The biological role of DNA1, a nanovirus-like component shown to be associated with the begomovirus/satellite complex, has not yet been identified. Here, we demonstrated that DNA1 of Tobacco curly shoot virus isolate Y35 (TbCSV-Y35) attenuated leaf-curling symptoms induced by TbCSV-Y35 or TbCSV-Y35 plus Y35 DNAbeta in the early stage of symptom development and induced leaf cluster at a later stage of symptom development in Nicotiana benthamiana plants. The leaf disc assay demonstrated that TbCSV-Y35 DNA1 replicated autonomously. Southern blot analysis revealed that TbCSV-Y35 DNA1 reduced viral DNA accumulation. Viral DNA accumulation was not reduced when plants were co-inoculated with TbCSV-Y35 DNAbeta, but the TbCSV-Y35 DNAbeta level was dramatically reduced in the presence of TbCSV-Y35 DNA1. To determine whether the interaction between TbCSV/satellite complex and DNA1 had isolate specificity, DNA1 of TbCSV isolate Y132 was cloned and sequenced. It was found to have 75% nucleotide sequence identity with TbCSV-Y35 DNA1. Infectivity tests showed that TbCSV-Y132 DNA1 had no effect on the symptoms induced by TbCSV-Y35 or TbCSV-Y35 and Y35 DNAbeta in N. benthamiana plants, although Y132 DNA1 could replicate in these plants.