Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity

Animal venom systems have emerged as valuable models for investigating how novel polygenic phenotypes may arise from gene evolution by varying molecular mechanisms. However, a significant portion of venom genes produce alternative mRNA isoforms that have not been extensively characterized, hindering a comprehensive understanding of venom biology. In this study, we present a full-length isoform-level profiling workflow integrating multiple RNA sequencing technologies, allowing us to reconstruct a high-resolution transcriptome landscape of venom genes in the parasitoid wasp Pteromalus puparum Our findings demonstrate that more than half of the venom genes generate multiple isoforms within the venom gland. Through mass spectrometry analysis, we confirm that alternative splicing contributes to the diversity of venom proteins, acting as a mechanism for expanding the venom repertoire. Notably, we identified seven venom genes that exhibit distinct isoform usages between the venom gland and other tissues. Furthermore, evolutionary analyses of venom serpin3 and orcokinin further reveal that the co-option of an ancient isoform and a newly evolved isoform, respectively, contributes to venom recruitment, providing valuable insights into the genetic mechanisms driving venom evolution in parasitoid wasps. Overall, our study presents a comprehensive investigation of venom genes at the isoform level, significantly advancing our understanding of alternative isoforms in venom diversity and evolution and setting the stage for further in-depth research on venoms.

Reverse logistics planning research of building waste from perspective of closed supply chain in urban sustainable environment governance

The resource utilization of building waste in urban sustainable environment governance is significant, in view of the status of construction waste recycling; this article built a reverse logistics planning model in urban building waste from the perspective of a closed supply chain by means of a hybrid nonlinear programming model. Combining the simulated annealing algorithm with memory function and the genetic algorithm with global convergence performance, a new genetic simulated annealing algorithm is presented to optimize the model. The empirical study was then made for the system to verify the feasibility of the model. The proposed new planning method and its detailed steps can provide a meaningful reference value for resource utilization of building waste in urban sustainable environment governance.

The moderating effect of solar radiation on the association between human mobility and COVID-19 infection in Europe

The novel coronavirus disease 2019 (COVID-19) has caused a global pandemic. Some studies have suggested a negative association between sunlight intensity and COVID-19 infection, alluding to the belief that it might be safe to go out on sunny days. This paper examined whether solar radiation mitigated the association between human mobility and COVID-19 infection in Europe using a dynamic panel data model to investigate the effect of human mobility, solar radiation, and their interaction on COVID-19 infection. The results revealed that outgoing mobility was positively correlated and solar radiation was negatively correlated with COVID-19 infection at lag levels of 1, 2, and 3 weeks. The coefficients of the interaction items indicated that solar radiation negatively moderated the relationship between outgoing mobility and the number of daily new confirmed cases at 2- and 3-week lag levels. However, the moderating effect was limited and unable to eliminate the positive effect of outgoing mobility on COVID-19 infection. Thus, these results suggested that solar radiation only weakly mitigated the relationship between human mobility and COVID-19 infection, providing policy implications that mobility should still be restricted on sunny days during the COVID-19 pandemic.

Fungal-induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL-22

Incorporation of microbiome data has recently become important for prevention, diagnosis, and treatment of colorectal cancer, and several species of bacteria were shown to be associated with carcinogenesis. However, the role of commensal fungi in colon cancer remains poorly understood. Here, we report that mice lacking the c-type lectin Dectin-3 (Dectin-3-/- ) show increased tumorigenesis and Candida albicans burden upon chemical induction. Elevated C. albicans load triggered glycolysis in macrophages and interleukin-7 (IL-7) secretion. IL-7 induced IL-22 production in RORγt+ (group 3) innate lymphoid cells (ILC3s) via aryl hydrocarbon receptor and STAT3. Consistently, IL-22 frequency in tumor tissues of colon cancer patients positively correlated with fungal burden, indicating the relevance of this regulatory axis in human disease. These results establish a C. albicans-driven crosstalk between macrophages and innate lymphoid cells in the intestine and expand our understanding on how commensal mycobiota regulate host immunity and promote tumorigenesis.

Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies

HIV-1 latency is a major obstacle to achieving a functional cure for AIDS. Reactivation of HIV-1-infected cells followed by their elimination via immune surveillance is one proposed strategy for eradicating the viral reservoir. However, current latency-reversing agents (LRAs) show high toxicity and low efficiency, and new targets are needed to develop more promising LRAs. Here, we found that the histone chaperone CAF-1 (chromatin assembly factor 1) is enriched on the HIV-1 long terminal repeat (LTR) and forms nuclear bodies with liquid-liquid phase separation (LLPS) properties. CAF-1 recruits epigenetic modifiers and histone chaperones to the nuclear bodies to establish and maintain HIV-1 latency in different latency models and primary CD4+ T cells. Three disordered regions of the CHAF1A subunit are important for phase-separated CAF-1 nuclear body formation and play a key role in maintaining HIV-1 latency. Disruption of phase-separated CAF-1 bodies could be a potential strategy to reactivate latent HIV-1.

A positive feedback loop between mTORC1 and cathelicidin promotes skin inflammation in rosacea

Rosacea is a chronic inflammatory skin disorder whose pathogenesis is unclear. Here, several lines of evidence were provided to demonstrate that mTORC1 signaling is hyperactivated in the skin, especially in the epidermis, of both rosacea patients and a mouse model of rosacea-like skin inflammation. Both mTORC1 deletion in epithelium and inhibition by its specific inhibitors can block the development of rosacea-like skin inflammation in LL37-induced rosacea-like mouse model. Conversely, hyperactivation of mTORC1 signaling aggravated rosacea-like features. Mechanistically, mTORC1 regulates cathelicidin through a positive feedback loop, in which cathelicidin LL37 activates mTORC1 signaling by binding to Toll-like receptor 2 (TLR2) and thus in turn increases the expression of cathelicidin itself in keratinocytes. Moreover, excess cathelicidin LL37 induces both NF-κB activation and disease-characteristic cytokine and chemokine production possibly via mTORC1 signaling. Topical application of rapamycin improved clinical symptoms in rosacea patients, suggesting mTORC1 inhibition can serve as a novel therapeutic avenue for rosacea.

Global Observations and CMIP6 Simulations of Compound Extremes of Monthly Temperature and Precipitation

Compound climate extremes, such as events with concurrent temperature and precipitation extremes, have significant impacts on the health of humans and ecosystems. This paper aims to analyze temporal and spatial characteristics of compound extremes of monthly temperature and precipitation, evaluate the performance of the sixth phase of the Coupled Model Intercomparison Project (CMIP6) models in simulating compound extremes, and investigate their future changes under Shared Socioeconomic Pathways (SSPs). The results show a significant increase in the frequency of compound warm extremes (warm/dry and warm/wet) but a decrease in compound cold extremes (cold/dry and cold/wet) during 1985-2014 relative to 1955-1984. The observed upward trends of compound warm extremes over China are much higher than those worldwide during the period of interest. A multi-model ensemble (MME) of CMIP6 models performs well in simulating temporal changes of warm/wet extremes, and temporal correlation coefficients between MME and observations are above 0.86. Under future scenarios, CMIP6 simulations show substantial rises in compound warm extremes and declines in compound cold extremes. Globally, the average frequency of warm/wet extremes over a 30-yr period is projected to increase for 2070-2099 relative to 1985-2014 by 18.53, 34.15, 48.79, and 59.60 under SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5, respectively. Inter-model uncertainties for the frequencies of compound warm extremes are considerably higher than those of compound cold extremes. The projected uncertainties in the global occurrences of warm/wet extremes are 3.82 times those of warm/dry extremes during 2070-2099 and especially high for the Amazon and the Tibetan Plateau.

Modeling the Spatiotemporal Association Between COVID-19 Transmission and Population Mobility Using Geographically and Temporally Weighted Regression

The ongoing Coronavirus Disease 2019 (COVID-19) has posed a serious threat to human public health and global economy. Population mobility is an important factor that drives the spread of COVID-19. This study aimed to quantitatively evaluate the impact of population flow on the spread of COVID-19 from a spatiotemporal perspective. To this end, a case study was carried out in Hubei Province, which was once the most affected area of COVID-19 outbreak in Mainland China. The geographically and temporally weighted regression (GTWR) model was applied to model the spatiotemporal association between COVID-19 epidemic and population mobility. Two patterns of population flows, including the population inflow from Wuhan and intra-city population movement, were considered to construct explanatory variables. Results indicate that the GTWR model can reveal the spatial-temporal-varying relationships between COVID-19 and population mobility. Moreover, the association between COVID-19 case counts and population movements presented three stages of temporal variation characteristics due to the virus incubation period and implementation of strict lockdown measures. In the spatial dimension, evident geographical disparities were observed across Hubei Province. These findings can provide policymakers useful knowledge about the impact of population movement on the spatio-temporal transmission of COVID-19. Thus, targeted interventions, if necessary in certain time periods, can be implemented to restrict population flow in cities with high transmission risk.

Diurnal Variations of Size-Resolved Bioaerosols During Autumn and Winter Over a Semi-Arid Megacity in Northwest China

Bioaerosols have a major negative effect on air quality and on public health by causing the spread of diseases. This study evaluated the bioaerosol composition and variation in a semi-arid megacity of northwest China from October 2019 to January 2020 using an Andersen six-stage impactor sampler. The size distribution, diurnal variations of the concentrations of airborne bacteria, airborne fungi, and total airborne microbes (TAM) were investigated in autumn and winter. The mean concentrations of airborne bacteria, fungi, and TAM were 523.5 ± 301.1 colony-forming units (CFU)/m3, 1318.9 ± 447.8 CFU/m3, and (7.25 ± 1.90) × 106 cells/m3, respectively, in autumn and 581 ± 305.4 CFU/m3, 1234.4 ± 519.9 CFU/m3, and (5.96 ± 1.65) × 106 cells/m3, respectively, in winter. The mean bioaerosol concentrations were slightly higher on nonhaze days than on haze days, but the difference was not statistically significant. Higher ambient particulate matter levels and atmospheric oxidation capacity inhibited bacteria survival. The diurnal maximum bioaerosol concentration was observed in the morning in autumn, whereas in winter, bioaerosols did not exhibit such a distribution, the impact of human activities on bioaerosols was still uncertain. The size of airborne bacteria exhibited a bimodal distribution, whereas a unimodal pattern was observed for fungi and TAM. Most bacteria, fungi, and TAM were distributed in the respirable ranges from trachea and primary bronchi to alveoli, indicating that bioaerosols have a high risk of being inhaled and causing respiratory diseases in Xi'an.

Positive selection drives the evolution of a primate bitter taste receptor gene

Bitter taste perception is important in food choice of animals, and it is mediated by bitter taste receptor (T2R) containing three regions: extracellular regions (ECs), transmembrane regions (TMs), and intracellular regions (ICs). It is hypothesized that ECs, TMs, and ICs are under different selective pressures, with ECs being unstable while TMs and ICs being constrained. To test this hypothesis, we examined the selective pressures on one of the bitter taste receptor genes-T2R1 and its different areas from 35 primates and found that T2R1 was under neutral evolution but with some positively selected sites in it. Further analyses suggested that TMs, ICs, and the concatenated transmembrane region TM1237 were under purifying selection; in contrast, extracellular regions, the first and second extracellular loop (EL1, EL2), were subject to positive selection with several positively selected sites in them. Therefore, this study supported the above-mentioned hypothesis. The reason why EL1 and EL2 of T2R1 have positively selected sites is probably due to their participation in forming the cap-like structure involved in ligand binding. Positive selection acts as a driving force of the T2R1 functional differentiation and confers the ability to discern various bitter substances for primates, which could help them to adapt to the changing environment during the evolutionary course.

More Significant Impacts From New Particle Formation on Haze Formation During COVID-19 Lockdown

During the COVID-19 lockdown in 2020, large-scale industrial and transportation emissions were reduced, but high PM2.5 concentration still occurred. This study investigated the variation of particle number size distribution during the lockdown, and analyzed the characteristics of new particle formation (NPF) events and its potential impact on haze formation. Through measurement conducted in urban Beijing during the first 3 months of 2020, and comparison with year-over-year data, the decrease of primary Aitken-mode particles was observed. However, frequencies, formation rates and growth rates of NPF events remained stable between 2020 and 2019 in the same period. As a result, >25 nm particles produced by NPF events, would play a more important role in serving as the haze formation "seeds" compared to those produced by primary emissions. This finding emphasizes the significance on the understanding of NPF mechanisms when making pollution mitigation policy in the future.

ATAD3B is a mitophagy receptor mediating clearance of oxidative stress-induced damaged mitochondrial DNA

Mitochondrial DNA (mtDNA) encodes several key components of respiratory chain complexes that produce cellular energy through oxidative phosphorylation. mtDNA is vulnerable to damage under various physiological stresses, especially oxidative stress. mtDNA damage leads to mitochondrial dysfunction, and dysfunctional mitochondria can be removed by mitophagy, an essential process in cellular homeostasis. However, how damaged mtDNA is selectively cleared from the cell, and how damaged mtDNA triggers mitophagy, remain mostly unknown. Here, we identified a novel mitophagy receptor, ATAD3B, which is specifically expressed in primates. ATAD3B contains a LIR motif that binds to LC3 and promotes oxidative stress-induced mitophagy in a PINK1-independent manner, thus promoting the clearance of damaged mtDNA induced by oxidative stress. Under normal conditions, ATAD3B hetero-oligomerizes with ATAD3A, thus promoting the targeting of the C-terminal region of ATAD3B to the mitochondrial intermembrane space. Oxidative stress-induced mtDNA damage or mtDNA depletion reduces ATAD3B-ATAD3A hetero-oligomerization and leads to exposure of the ATAD3B C-terminus at the mitochondrial outer membrane and subsequent recruitment of LC3 for initiating mitophagy. Furthermore, ATAD3B is little expressed in m.3243A > G mutated cells and MELAS patient fibroblasts showing endogenous oxidative stress, and ATAD3B re-expression promotes the clearance of m.3243A > G mutated mtDNA. Our findings uncover a new pathway to selectively remove damaged mtDNA and reveal that increasing ATAD3B activity is a potential therapeutic approach for mitochondrial diseases.

CASB: a concanavalin A-based sample barcoding strategy for single-cell sequencing

Sample multiplexing facilitates single-cell sequencing by reducing costs, revealing subtle difference between similar samples, and identifying artifacts such as cell doublets. However, universal and cost-effective strategies are rather limited. Here, we reported a concanavalin A-based sample barcoding strategy (CASB), which could be followed by both single-cell mRNA and ATAC (assay for transposase-accessible chromatin) sequencing techniques. The method involves minimal sample processing, thereby preserving intact transcriptomic or epigenomic patterns. We demonstrated its high labeling efficiency, high accuracy in assigning cells/nuclei to samples regardless of cell type and genetic background, and high sensitivity in detecting doublets by three applications: 1) CASB followed by scRNA-seq to track the transcriptomic dynamics of a cancer cell line perturbed by multiple drugs, which revealed compound-specific heterogeneous response; 2) CASB together with both snATAC-seq and scRNA-seq to illustrate the IFN-γ-mediated dynamic changes on epigenome and transcriptome profile, which identified the transcription factor underlying heterogeneous IFN-γ response; and 3) combinatorial indexing by CASB, which demonstrated its high scalability.

Adapting to Changing Labor Productivity as a Result of Intensified Heat Stress in a Changing Climate

The intensification of heat stress reduces the labor capacity and hence poses a threat to socio-economic development. The reliable projection of the changing climate and the development of sound adaptation strategies are thus desired for adapting to the decreasing labor productivity under climate change. In this study, an optimization modeling approach coupled with dynamical downscaling is proposed to design the optimal adaptation strategies for improving labor productivity under heat stress in China. The future changes in heat stress represented by the wet-bulb globe temperature (WBGT) are projected with a spatial resolution of 25 × 25 km by a regional climate model (RCM) through the dynamical downscaling of its driving global climate model (GCM). Uncertain information such as system costs, environmental costs, and subsidies are also incorporated into the optimization process to provide reliable decision alternatives for improving labor productivity. Results indicate that the intensification of WBGT is overestimated by the GCM compared to the RCM. Such an overestimation can lead to more losses in working hours derived from the GCM than those from the RCM regardless of climate scenarios. Nevertheless, the overestimated heat stress does not alter the regional measures taken to adapt to decreasing labor productivity. Compared to inland regions, the monsoon-affected regions tend to improve labor productivity by applying air conditioning rather than working overtime due to the cost differences. Consequently, decision-makers need to optimally make a balance between working overtime and air conditioning measures to meet sustainable development goals.

The Golgi microtubules regulate single cell durotaxis

Current understandings on cell motility and directionality rely heavily on accumulated investigations of the adhesion-actin cytoskeleton-actomyosin contractility cycles, while microtubules have been understudied in this context. Durotaxis, the ability of cells to migrate up gradients of substrate stiffness, plays a critical part in development and disease. Here, we identify the pivotal role of Golgi microtubules in durotactic migration of single cells. Using high-throughput analysis of microtubule plus ends/focal adhesion interactions, we uncover that these non-centrosomal microtubules actively impart leading edge focal adhesion (FA) dynamics. Furthermore, we designed a new system where islands of higher stiffness were patterned within RGD peptide coated polyacrylamide gels. We revealed that the positioning of the Golgi apparatus is responsive to external mechanical cues and that the Golgi-nucleus axis aligns with the stiffness gradient in durotaxis. Together, our work unveils the cytoskeletal underpinning for single cell durotaxis. We propose a model in which the Golgi-nucleus axis serves both as a compass and as a steering wheel for durotactic migration, dictating cell directionality through the interaction between non-centrosomal microtubules and the FA dynamics.

Weakened Aerosol-PBL Interaction During COVID-19 Lockdown in Northern China

Anthropogenic emissions were greatly constrained during COVID-19 lockdown in China. Nevertheless, observations still showed high loadings of fine particles (PM2.5) over northern China with secondary aerosols increasing by 15 μg/m3 yet a ∼10% drop in light-absorbing black carbon (BC). Such a chemical transition in aerosol composition tended to make the atmosphere more scattering, indicated by satellite-retrieved aerosol absorption optical depth falling by 60%. Comparison between weather forecast and radiosonde observations illustrated that, without upper-level heating induced by BC, the stabilized stratification diminished, which was conducive for planetary boundary layer (PBL) mixing and thus near-surface pollution dispersion. Furthermore, coupled dynamic-chemistry simulations estimated that emission reduction during the lockdown weakened aerosol-PBL interaction and thus a reduction of 25 μg/m3 (∼50%) in PM2.5 enhancement. Based on the unique natural experiment, this work observationally confirmed and numerically quantified the importance of BC-induced meteorological feedback, further highlighting the priority of BC control in haze mitigation.

MOTS-c promotes phosphorodiamidate morpholino oligomer uptake and efficacy in dystrophic mice

Antisense oligonucleotide (AO)-mediated exon-skipping therapies show promise in Duchenne muscular dystrophy (DMD), a devastating muscular disease caused by frame-disrupting mutations in the DMD gene. However, insufficient systemic delivery remains a hurdle to clinical deployment. Here, we demonstrate that MOTS-c, a mitochondria-derived bioactive peptide, with an intrinsic muscle-targeting property, augmented glycolytic flux and energy production capacity of dystrophic muscles in vitro and in vivo, resulting in enhanced phosphorodiamidate morpholino oligomer (PMO) uptake and activity in mdx mice. Long-term repeated administration of MOTS-c (500 μg) and PMO at the dose of 12.5 mg/kg/week for 3 weeks followed by 12.5 mg/kg/month for 3 months (PMO-M) induced therapeutic levels of dystrophin expression in peripheral muscles, with up to 25-fold increase in diaphragm of mdx mice over PMO alone. PMO-M improved muscle function and pathologies in mdx mice without detectable toxicity. Our results demonstrate that MOTS-c enables enhanced PMO uptake and activity in dystrophic muscles by providing energy and may have therapeutic implications for exon-skipping therapeutics in DMD and other energy-deficient disorders.

Chromatin accessibility dynamics during cell fate reprogramming

Genome architecture and chromatin dynamics govern the fate and identify of a cell. Recent advances in mapping chromatin landscapes offer valuable tools for the acquisition of accurate information regarding chromatin dynamics. Here we discuss recent findings linking chromatin dynamics to cell fate control. Specifically, chromatin undergoes a binary off/on switch during iPSC reprogramming, closing and opening loci occupied by somatic and pluripotency transcription factors, respectively. This logic of a binary off/on switch may also be operational in cell fate control during normal development and implies that further approaches could potentially be developed to direct cell fate changes both in vitro and in vivo.

Enhanced PM2.5 Decreases and O3 Increases in China During COVID-19 Lockdown by Aerosol-Radiation Feedback

We apply an online-coupled meteorology-chemistry model (WRF-Chem) embedded with an improved process analysis to examine aerosol-radiation feedback (ARF) impacts on effectiveness of emission control due to Coronavirus Disease 2019 (COVID-19) lockdown over North China Plain. Emission reduction alone induces PM2.5 decrease by 16.3 μg m-3 and O3 increase by 10.2 ppbv during COVID-19 lockdown. The ARF enhances PM2.5 decrease by 2.7 μg m-3 (16.6%) and O3 increase by 0.8 ppbv (7.8%). The ARF-induced enhancement of PM2.5 decline is mostly attributed to aerosol chemistry process, while enhancement of O3 rise is ascribed to physical advection and vertical mixing processes. A set of sensitivity experiments with emission reductions in different degrees indicate that the ARF-induced enhancements of PM2.5 declines (O3 rises) follow a robust linear relationship with the emission-reduction-induced PM2.5 decreases. The fitted relationship has an important implication for assessing the effectiveness of emission abatement at any extent.

Dynamic folding modulation generates FGF21 variant against diabetes

Fibroblast growth factor 21 (FGF21) is a regulator of glucose and lipid metabolism. It has been widely considered as a promising candidate for the treatment of type 2 diabetes mellitus (T2DM) and other related metabolic disorders. However, lack of structural and dynamic information has limited FGF21-based drug development. Here, using nuclear magnetic resonance (NMR) spectroscopy, we determine the structure of FGF21 and find that its non-canonical flexible β-trefoil conformation affects the folding of β2-β3 hairpin and further overall protein stability. To modulate folding dynamics, we designed an FGF21-FGF19 chimera, FGF21SS . As expected, FGF21SS shows better thermostability without inducing hepatocyte proliferation. Functional characterization of FGF21SS shows its better insulin sensitivity, reduced inflammation in 3T3-L1 adipocytes, and lower blood glucose and insulin levels in ob/ob mice compared with wild type. Our dynamics-based rational design provides a promising approach for FGF21-based therapeutic development against T2DM.

OMA1 reprograms metabolism under hypoxia to promote colorectal cancer development

Many cancer cells maintain enhanced aerobic glycolysis due to irreversible defective mitochondrial oxidative phosphorylation (OXPHOS). This phenomenon, known as the Warburg effect, is recently challenged because most cancer cells maintain OXPHOS. However, how cancer cells coordinate glycolysis and OXPHOS remains largely unknown. Here, we demonstrate that OMA1, a stress-activated mitochondrial protease, promotes colorectal cancer development by driving metabolic reprogramming. OMA1 knockout suppresses colorectal cancer development in AOM/DSS and xenograft mice models of colorectal cancer. OMA1-OPA1 axis is activated by hypoxia, increasing mitochondrial ROS to stabilize HIF-1α, thereby promoting glycolysis in colorectal cancer cells. On the other hand, under hypoxia, OMA1 depletion promotes accumulation of NDUFB5, NDUFB6, NDUFA4, and COX4L1, supporting that OMA1 suppresses OXPHOS in colorectal cancer. Therefore, our findings support a role for OMA1 in coordination of glycolysis and OXPHOS to promote colorectal cancer development and highlight OMA1 as a potential target for colorectal cancer therapy.

BRLF1 suppresses RNA Pol III-mediated RIG-I inflammasome activation in the early EBV lytic lifecycle

Latent infection with herpesviruses constitutively activates inflammasomes, while lytic replication suppresses their activation through distinct mechanisms. However, how Epstein-Barr virus (EBV) lytic replication inhibits the activation of inflammasomes remains unknown. Here, we reveal that the EBV immediate-early protein BRLF1 inhibits inflammasome activation, and BRLF1 deficiency significantly increases the activation of inflammasomes and pyroptosis during early lytic lifecycle. BRLF1 interacts with RNA polymerase III subunits to suppress immunostimulatory small RNA transcription, RIG-I inflammasome activation, and antiviral responses. Consequently, BRLF1-deficient EBV primary infection induces robust T-cell and NK cell activation and killing through IL-1β and IL-18. A BRLF1-derived peptide that inhibits inflammasome activation is sufficient to suppress T-cell and NK cell responses during BRLF1-deficient EBV primary infection in lymphocytes. These results reveal a novel mechanism involved in the evasion of inflammasome activation and antiviral responses during EBV early lytic infection and provide a promising approach for the manipulation of inflammasomes against infection of oncogenic herpesviruses.

A Warm Summer is Unlikely to Stop Transmission of COVID-19 Naturally

The outbreak of coronavirus disease 2019 (COVID-19) showed various transmission rate (R t ) across different regions. The determination of the factors affecting transmission rate is urgent and crucial to combat COVID-19. Here we explored variation of R t between 277 regions across the globe and the associated potential socioeconomic, demographic, and environmental factors. At global scale, the R t started to decrease approximately 2 weeks after policy interventions initiated. This lag from the date of policy interventions initiation to the date when R t started to decrease ranges from 9 to 19 days, largest in Europe and North America. We find that proportion of elderly people or life expectancy can explain ~50% of variation in transmission rate across the 277 regions. The transmission rate at the point of inflection (R I ) increases by 29.4% (25.2-34.0%) for 1% uptick in the proportion of people aged above 65, indicating that elderly people face ~2.5 times higher infection risk than younger people. Air temperature is negatively correlated with transmission rate, which is mainly attributed to collinearities between air temperature and demographic factors. Our model predicted that temperature sensitivity of R I is only -2.7% (-5.2-0%) per degree Celsius after excluding collinearities between air temperature and demographic factors. This low temperature sensitivity of R I suggests that a warm summer is unlikely to impede the spread of COVID-19 naturally.

Programmable C-to-U RNA editing using the human APOBEC3A deaminase

Programmable RNA cytidine deamination has recently been achieved using a bifunctional editor (RESCUE-S) capable of deaminating both adenine and cysteine. Here, we report the development of "CURE", the first cytidine-specific C-to-U RNA Editor. CURE comprises the cytidine deaminase enzyme APOBEC3A fused to dCas13 and acts in conjunction with unconventional guide RNAs (gRNAs) designed to induce loops at the target sites. Importantly, CURE does not deaminate adenosine, enabling the high-specificity versions of CURE to create fewer missense mutations than RESCUE-S at the off-targets transcriptome-wide. The two editing approaches exhibit overlapping editing motif preferences, with CURE and RESCUE-S being uniquely able to edit UCC and AC motifs, respectively, while they outperform each other at different subsets of the UC targets. Finally, a nuclear-localized version of CURE, but not that of RESCUE-S, can efficiently edit nuclear RNAs. Thus, CURE and RESCUE are distinct in design and complementary in utility.

CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators

Cellular RNA is decorated with over 170 types of chemical modifications. Many modifications in mRNA, including m6 A and m5 C, have been associated with critical cellular functions under physiological and/or pathological conditions. To understand the biological functions of these modifications, it is vital to identify the regulators that modulate the modification rate. However, a high-throughput method for unbiased screening of these regulators is so far lacking. Here, we report such a method combining pooled CRISPR screen and reporters with RNA modification readout, termed CRISPR integrated gRNA and reporter sequencing (CIGAR-seq). Using CIGAR-seq, we discovered NSUN6 as a novel mRNA m5 C methyltransferase. Subsequent mRNA bisulfite sequencing in HAP1 cells without or with NSUN6 and/or NSUN2 knockout showed that NSUN6 and NSUN2 worked on non-overlapping subsets of mRNA m5 C sites and together contributed to almost all the m5 C modification in mRNA. Finally, using m1 A as an example, we demonstrated that CIGAR-seq can be easily adapted for identifying regulators of other mRNA modification.

NO x Emission Changes Over China During the COVID-19 Epidemic Inferred From Surface NO2 Observations

The COVID-19 epidemic has substantially limited human activities and affected anthropogenic emissions. In this work, daily NO x emissions are inferred using a regional data assimilation system and hourly surface NO2 measurement over China. The results show that because of the coronavirus outbreak, NO x emissions across the whole mainland China dropped sharply after 31 January, began to rise slightly in certain areas after 10 February, and gradually recover across the country after 20 February. Compared with the emissions before the outbreak, NO x emissions fell by more than 60% and ~30% in many large cities and most small to medium cities, respectively. Overall, NO x emissions were reduced by 36% over China, which were mainly contributed by transportation. Evaluations show that the inverted changes over eastern China are credible, whereas those in western China might be underestimated. These findings are of great significance for exploring the reduction potential of NO x emissions in China.

Oridonin ameliorates carbon tetrachloride-induced liver fibrosis in mice through inhibition of the NLRP3 inflammasome

Liver fibrosis is characterized by the activation of hepatic stellate cells (HSCs) and accumulation of the extracellular matrix. There are limitations in the current therapies for liver fibrosis. Recently, oridonin was shown to induce apoptosis in HSCs. Thus, we aimed to determine the roles of oridonin in chronic liver injury and fibrosis. Liver fibrosis was induced by CCl4 in mice injected intraperitoneally with oridonin for 6 weeks. The administration of oridonin significantly attenuated liver injury and reduced ALT levels. In addition, Sirius Red staining and the expression of α-smooth muscle actin (α-SMA) were significantly reduced by oridonin in murine livers with fibrosis. The expression of NLRP3, caspase-1, and IL-1β was downregulated with the oridonin treatment. Furthermore, the expression of F4/80 in liver tissues was also decreased by oridonin treatment. These results demonstrate that oridonin ameliorates chronic liver injury and fibrosis. Mechanically, oridonin may inhibit the activity of the NLRP3 inflammasome and inflammation in the liver. These results highlight the potential of oridonin as a therapeutic agent for liver fibrosis.

A point-to-point protein-protein interaction assay reveals the signaling interplays among plant hormones and environmental cues

As sessile organisms, plants must properly coordinate their growth and developmental programs with changes in the environment. The integration of exogenous environmental cues with endogenous plant hormone responses often occurs through physical protein-protein interactions (PPIs). However, a comprehensive PPI network that mediates environmental and hormonal responses has not been established. In this study, we initially cloned 113 phytohormone-related genes and 29 light signaling components of Arabidopsis and then individually tested their mutual interactions (in total 2,655 tests) using a yeast-two-hybrid approach to ultimately identify 141 interactions. Based on these interaction results, we next revealed the signaling cross talk between jasmonate and abscisic acid by characterizing the JAZ1-PYL4 and JAZ1-ABI1 interactions. Thus, we generated a useful resource for the community to explore the molecular mechanisms underlying signaling interactions between plant hormones and/or with light.

Improvement of the Irrigation Scheme in the ORCHIDEE Land Surface Model and Impacts of Irrigation on Regional Water Budgets Over China

In China, irrigation is widespread in 40.7% cropland to sustain crop yields. By its action on water cycle, irrigation affects water resources and local climate. In this study, a new irrigation module, including flood and paddy irrigation technologies, was developed in the ORCHIDEE-CROP land surface model which describes crop phenology and growth in order to estimate irrigation demands over China from 1982 to 2014. Three simulations were performed including NI (no irrigation), IR (with irrigation limited by local water resources), and FI (with irrigation demand fulfilled). Observations and census data were used to validate the simulations. Results showed that the estimated irrigation water withdrawal ( W ) based on IR and FI scenarios bracket statistical W with fair spatial agreements ( r = 0 . 68 ± 0 . 07 ; p < 0 . 01 ). Improving irrigation efficiency was found to be the dominant factor leading to the observed W decrease. By comparing simulated total water storage (TWS) with GRACE observations, we found that simulated TWS with irrigation well explained the TWS variation over China. However, our simulation overestimated the seasonality of TWS in the Yangtze River Basin due to ignoring regulation of artificial reservoirs. The observed TWS decrease in the Yellow River Basin caused by groundwater depletion was not totally captured in our simulation, but it can be inferred by combining simulated TWS with census data. Moreover, we demonstrated that land use change tended to drive W locally but had little effect on total W over China due to water resources limitation.

Crystallized and fluid intelligence are predicted by microstructure of specific white-matter tracts

Studies of the neural basis of intelligence have focused on comparing brain imaging variables with global scales instead of the cognitive domains integrating these scales or quotients. Here, the relation between mean tract-based fractional anisotropy (mTBFA) and intelligence indices was explored. Deterministic tractography was performed using a regions of interest approach for 10 white-matter fascicles along which the mTBFA was calculated. The study sample included 83 healthy individuals from the second wave of the Cuban Human Brain Mapping Project, whose WAIS-III intelligence quotients and indices were obtained. Inspired by the "Watershed model" of intelligence, we employed a regularized hierarchical Multiple Indicator, Multiple Causes model (MIMIC), to assess the association of mTBFA with intelligence scores, as mediated by latent variables summarizing the indices. Regularized MIMIC, used due to the limited sample size, selected relevant mTBFA by means of an elastic net penalty and achieved good fits to the data. Two latent variables were necessary to describe the indices: Fluid intelligence (Perceptual Organization and Processing Speed indices) and Crystallized Intelligence (Verbal Comprehension and Working Memory indices). Regularized MIMIC revealed effects of the forceps minor tract on crystallized intelligence and of the superior longitudinal fasciculus on fluid intelligence. The model also detected the significant effect of age on both latent variables.

Association of suboptimal health status with intestinal microbiota in Chinese youths

Suboptimal health status (SHS), a physical state between health and disease, is a subclinical and reversible stage of chronic disease. Previous studies have shown alterations in the intestinal microbiota in patients with some chronic diseases. This study aimed to investigate the association between SHS and intestinal microbiota in a case-control study with 50 SHS individuals and 50 matched healthy controls. Intestinal microbiota was analysed by MiSeq 250PE. Alpha diversity of intestinal microbiota in SHS individuals was higher compared with that of healthy controls (Simpson index, W = 2238, P = .048). Beta diversity was different between SHS and healthy controls (P = .018). At the phylum level, the relative abundance of Verrucomicrobia was higher in the SHS group than that in the controls (W = 2201, P = .049). Compared with that of the control group, nine genera were significantly higher and five genera were lower in abundance in the SHS group (all P < .05). The intestinal microbiota, analysed by a random forest model, was able to distinguish individuals with SHS from the controls, with an area under the curve of 0.79 (95% confidence interval: 0.77-0.81). We demonstrated that the alteration of intestinal microbiota occurs with SHS, an early stage of disease, which might shed light on the importance of intestinal microbiota in the primary prevention of noncommunicable chronic diseases.

Development of a 1550-nm InAs/GaAs Quantum Dot Saturable Absorber Mirror with a Short-Period Superlattice Capping Structure Towards Femtosecond Fiber Laser Applications

Low-dimensional III-V InAs/GaAs quantum dots (QDs) have been successfully applied to semiconductor saturable absorber mirrors (SESAMs) working at a 900-1310-nm wavelength range for ultrafast pulsed laser applications benefitting from their broad bandwidth, wavelength flexibility, and low saturation fluence. However, it is very challenging to obtain a high-performance QD-SESAM working at the longer wavelength range around 1550 nm due to the huge obstacle to epitaxy growth of the QD structures. In this work, for the first time, it is revealed that, the InAs/GaAs QD system designed for the 1550-nm light emission range, the very weak carrier relaxation process from the capping layers (CLs) to QDs is mainly responsible for the poor emission performance, according to which we have developed a short-period superlattice (In_0.20Ga_0.80As/In_0.30Ga_0.70As)₅ as the CL for the QDs and has realized ~ 10 times stronger emission at 1550 nm compared with the conventional InGaAs CL. Based on the developed QD structure, high-performance QD-SESAMs have been successfully achieved, exhibiting a very small saturation intensity of 13.7 MW/cm² and a large nonlinear modulation depth of 1.6 %, simultaneously, which enables the construction of a 1550-nm femtosecond mode-locked fiber lasers with excellent long-term working stability.

A Framework for Global Multicategory and Multiscalar Drought Characterization Accounting for Snow Processes

Drought indices do not always provide the most relevant information for water resources management as most of them neglect the role of snow in the land surface water balance. In this study, a physically based drought index, the Standardized Moisture Anomaly Index (SZI), was modified and improved by incorporating the effects of snow dynamics for drought characterization at multiple time scales. The new version of the SZI, called SZIsnow, includes snow in both the water supply and demand in drought characterization by using the water-energy budgets from the Global Land Data Assimilation Systems product. We compared and evaluated the performance of SZIsnow and SZI in drought identification globally across various time scales using observed multicategory drought evidences from several sources. Results show that the SZIsnow agrees better with the observed changes in hydrological and agricultural droughts than the SZI, particularly over basins with high snow accumulation. Furthermore, the SZIsnow is more consistent with the residual water-energy ratio than the SZI over snow-influenced regions. Overall, the SZIsnow can be either a complement or an improvement over the SZI for identifying, monitoring, and characterizing hydrological and agricultural droughts at various scales (e.g., 1-48 months) over high-latitude and high-elevation regions that receive snow.

The advanced strategy for enhancing biobutanol production and high-efficient product recovery with reduced wastewater generation

BACKGROUND

Butanol as an important chemical and potential fuel could be produced via ABE fermentation from lignocellulosic biomass. The use of food-related feedstocks such as maize and sugar cane may not be a sustainable solution to world's energy needs. Recently, Jerusalem artichoke tubers containing inulin have been used as feedstock for butanol production, but this bioprocess is not commercially feasible due to the great value of inulin as functional food. Till now, there is a gap on the utilization of Jerusalem artichoke stalk (JAS) as feedstock for microbial butanol production.

RESULTS

Biobutanol production from JAS was investigated in order to improve cellulose digestibility and efficient biobutanol fermentation. Compared with 9.0 g/L butanol (14.7 g/L ABE) production by 2% NaOH pretreatment of JAS, 11.8 g/L butanol (17.6 g/L ABE) was produced in the best scenario conditions of NaOH-H₂O₂ pretreatment, washing times and citrate buffer strengths etc. Furthermore, more than >64% water in washing pretreated JAS process could be saved, with improving butanol production by >25.0%. To mimic in situ product recovery for ABE fermentation, the vapor stripping-vapor permeation (VSVP) process steadily produced 323.4-348.7 g/L butanol (542.7-594.0 g/L ABE) in condensate, which showed more potentials than pervaporation for butanol recovery.

CONCLUSIONS

Therefore, the present study demonstrated an effective strategy on efficient biobutanol production using lignocellulosic biomass. The process optimization could contribute to significant reduction of wastewater emission and the improvement of lignocellulosic biomass digestibility and biobutanol production, which makes biobutanol production more efficient using JAS.

Transgenic studies reveal the positive role of LeEIL-1 in regulating shikonin biosynthesis in Lithospermum erythrorhizon hairy roots

BACKGROUND

The phytohormone ethylene (ET) is a key signaling molecule for inducing the biosynthesis of shikonin and its derivatives, which are secondary metabolites in Lithospermum erythrorhizon. Although ETHYLENE INSENSITIVE3 (EIN3)/EIN3-like proteins (EILs) are crucial transcription factors in ET signal transduction pathway, the possible function of EIN3/EIL1 in shikonin biosynthesis remains unknown. In this study, by targeting LeEIL-1 (L. erythrorhizon EIN3-like protein gene 1) at the expression level, we revealed the positive regulatory effect of LeEIL-1 on shikonin formation.

RESULTS

The mRNA level of LeEIL-1 was significantly up-regulated and down-regulated in the LeEIL-1-overexpressing hairy root lines and LeEIL-1-RNAi hairy root lines, respectively. Specifically, LeEIL-1 overexpression resulted in increased transcript levels of the downstream gene of ET signal transduction pathway (LeERF-1) and a subset of genes for shikonin formation, excretion and/or transportation (LePAL, LeC4H-2, Le4CL-1, HMGR, LePGT-1, LeDI-2, and LePS-2), which was consistent with the enhanced shikonin contents in the LeEIL-1-overexpressing hairy root lines. Conversely, LeEIL-1-RNAi dramatically repressed the expression of the above genes and significantly reduced shikonin production.

CONCLUSIONS

The results revealed that LeEIL-1 is a positive regulator of the biosynthesis of shikonin and its derivatives in L. erythrorhizon hairy roots. Our findings gave new insights into the molecular regulatory mechanism of ET in shikonin biosynthesis. LeEIL-1 could be a crucial target gene for the genetic engineering of shikonin biosynthesis.