Intrinsic targeting of host RNA by Cas13 constrains its utility.

Cas13 can be used for the knockdown, editing, imaging or detection of RNA and for RNA-based gene therapy. Here by using RNA immunoprecipitation sequencing, transcriptome profiling, biochemical analysis, high-throughput screening and machine learning, we show that Cas13 can intrinsically target host RNA in mammalian cells through previously unappreciated mechanisms. Different from its known cis/trans RNA-cleavage activity, Cas13 can also cleave host RNA via mechanisms that are transcript-specific, independent of the sequence of CRISPR RNA and dynamically dependent on the conformational state of Cas13, as we show for several Cas13-family effectors encoded in one-vector and two-vector lentiviral systems. Moreover, host genes involved in viral processes and whose transcripts are intrinsically targeted by Cas13 contribute to constraining the lentiviral delivery and expression of Cas13. Our findings offer guidance for the appropriate use of lentiviral Cas13 systems and highlight the need for caution regarding intrinsic RNA targeting in Cas13-based applications.

Decoding Heterogenous Single-cell Perturbation Responses.

Understanding diverse responses of individual cells to the same perturbation is central to many biological and biomedical problems. Current methods, however, do not precisely quantify the strength of perturbation responses and, more importantly, reveal new biological insights from heterogeneity in responses. Here we introduce the perturbation-response score (PS), based on constrained quadratic optimization, to quantify diverse perturbation responses at a single-cell level. Applied to single-cell transcriptomes of large-scale genetic perturbation datasets (e.g., Perturb-seq), PS outperforms existing methods for quantifying partial gene perturbation responses. In addition, PS presents two major advances. First, PS enables large-scale, single-cell-resolution dosage analysis of perturbation, without the need to titrate perturbation strength. By analyzing the dose-response patterns of over 2,000 essential genes in Perturb-seq, we identify two distinct patterns, depending on whether a moderate reduction in their expression induces strong downstream expression alterations. Second, PS identifies intrinsic and extrinsic biological determinants of perturbation responses. We demonstrate the application of PS in contexts such as T cell stimulation, latent HIV-1 expression, and pancreatic cell differentiation. Notably, PS unveiled a previously unrecognized, cell-type-specific role of coiled-coil domain containing 6 (CCDC6) in guiding liver and pancreatic lineage decisions, where CCDC6 knockouts drive the endoderm cell differentiation towards liver lineage, rather than pancreatic lineage. The PS approach provides an innovative method for dose-to-function analysis and will enable new biological discoveries from single-cell perturbation datasets.

Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches.

A major challenge in the application of the CRISPR-Cas13d system is to accurately predict its guide-dependent on-target and off-target effect. Here, we perform CRISPR-Cas13d proliferation screens and design a deep learning model, named DeepCas13, to predict the on-target activity from guide sequences and secondary structures. DeepCas13 outperforms existing methods to predict the efficiency of guides targeting both protein-coding and non-coding RNAs. Guides targeting non-essential genes display off-target viability effects, which are closely related to their on-target efficiencies. Choosing proper negative control guides during normalization mitigates the associated false positives in proliferation screens. We apply DeepCas13 to the guides targeting lncRNAs, and identify lncRNAs that affect cell viability and proliferation in multiple cell lines. The higher prediction accuracy of DeepCas13 over existing methods is extensively confirmed via a secondary CRISPR-Cas13d screen and quantitative RT-PCR experiments. DeepCas13 is freely accessible via http://deepcas13.weililab.org .

Temperature modulation of CAMTA3 gene induction activity is mediated through the DNA binding domain.

The calmodulin-binding transcription activator (CAMTA) proteins of Arabidopsis thaliana play a major role in cold acclimation, contributing to the rapid induction of the C-REPEAT BINDING FACTOR (CBF) genes and other genes that impart freezing tolerance in plants exposed to cold temperature (4°C). The goal of this study was to better understand how the gene induction activity of CAMTA3 is modulated by temperature. Our results indicate that a severely truncated version of CAMTA3, CAMTA3334 , which includes the N-terminal CG-1 DNA binding domain and a newly identified transcriptional activation domain (TAD), was able to rapidly induce the expression of CBF2 and two newly identified target genes, EXPANSIN-LIKE A1 (EXPL1) and NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3), in response to cold temperature. Additionally, CAMTA3334 was able to restore freezing tolerance when expressed in a camta23 double mutant. The ability of CAMTA3 and CAMTA3334 to induce target genes at cold temperature did not involve increased levels of these proteins or increased binding of these proteins to target gene promoters in cold-treated plants. Rather, domain-swapping experiments indicated that the CAMTA3 CG-1 domain conferred temperature dependence to the ability of the CAMTA3 TAD to induce gene expression. The CG-1 domain also enabled the TAD to induce the expression of target genes at a moderate temperature (22°C) in response to cycloheximide treatment, consistent with the TAD activity not being intrinsically temperature dependent. We propose a working model in which the temperature modulation of CAMTA3 gene induction activity occurs independently from the C-terminal calmodulin-binding domains that previously have been proposed to activate CAMTA3 transcriptional activity in response to cold temperature.

Ag85A, As an S2 Vaccine Carrier, Reduces the Toxicity of the S2 Vaccine and Enhances the Protective Ability of Mice against Brucella.

Brucella is a globally distributed zoonotic disease that can cause abortion and changes in immune function in humans and animals. At present, there is no good treatment plan for Brucella, and animals can only be treated harmlessly once they become ill, resulting in huge economic losses. Therefore, the prevention of Brucella infection is a very crucial step. Although a variety of Brucella vaccines have been widely used, they have varying degrees of shortcomings. For example, some Brucella vaccines have residual virulence, which leads to the emergence of Brucella in animals during the immunization process. Bacillus infection and other conditions occur. To further reduce the toxicity of the Brucella vaccine and enhance its protective effect on animals, this study used Antigen 85A (Ag85A) as a carrier of the Brucella vaccine to fuse with the Brucella S2 vaccine. The results of the study found that the S2-Ag85A oral Brucella vaccine could effectively reduce the toxicity residue of the S2 vaccine, stimulate the mice to produce a better immunogenic response, and effectively activate the expression levels of Brucella heterozygous IgG1 and IgG2a. Experiments have shown that the expression of IFN-γ in the peripheral blood serum and spleen of mice is significantly increased, and the expression levels of IL-1ß, TNF-α, and IL-6 are significantly reduced, which may indicate that S2-Ag85A oral Brucella vaccine could induce the expression of IFN-γ, thus downregulating the expression levels of IL-6 and TNF-α in the spleen tissue. The above results indicate that the S2-Ag85A oral vaccine is an effective attenuated vaccine for preventing Brucella infection.

CRISP-view: a database of functional genetic screens spanning multiple phenotypes.

High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides a wealth of knowledge about genotype-to-phenotype relationships and a valuable resource for the systematic analysis of gene functions. Here we present CRISP-view, a comprehensive database of CRISPR/Cas9 and RNAi screening datasets that span multiple phenotypes, including in vitro and in vivo cell proliferation and viability, response to cancer immunotherapy, virus response, protein expression, etc. By 22 September 2020, CRISP-view has collected 10 321 human samples and 825 mouse samples from 167 papers. All the datasets have been curated, annotated, and processed by a standard MAGeCK-VISPR analysis pipeline with quality control (QC) metrics. We also developed a user-friendly webserver to visualize, explore, and search these datasets. The webserver is freely available at http://crispview.weililab.org.

A novel way for high value-added application of lignosulfonate: Producing lignosulfonate nanosheets/graphene ultrathin film electrodes for electrochemical capacitors.

In this paper, a novel way for high value-added application of lignosulfonate is presented. In this study, we use lignosulfonate nanosheets to fabricate a free-standing, binder-free, ultrathin and light-weight conductive film electrode via vacuum filtration method. The results show that LS is a promising candidate material for the preparation of electrochemical capacitor film electrode. It is worth mentioning that we use non-toxic, pollution-free aqueous solution (water) over organic solvents as the dispersion during the reductive graphene oxide (RGO) preparation process. The electrochemical measurements exhibit that the resistivity of lignosulfonate nanosheets/RGO (LNRGO) film electrode is 0.66 × 10-3 kΩ cm-1. The specific capacitance of the LNRGO film electrode is calculated to be 120 mF cm-2 at the current density of 0.2 mA cm-2, which is approximately 6.67 times larger than that of RGO-water film electrode.

Arabidopsis CAMTA Transcription Factors Regulate Pipecolic Acid Biosynthesis and Priming of Immunity Genes.

The Arabidopsis thaliana Calmodulin-binding Transcription Activator (CAMTA) transcription factors CAMTA1, CAMTA2, and CAMTA3 (CAMTA123) serve as master regulators of salicylic acid (SA)-mediated immunity, repressing the biosynthesis of SA in healthy plants. Here, we show that CAMTA123 also repress the biosynthesis of pipecolic acid (Pip) in healthy plants. Loss of CAMTA123 function resulted in the induction of AGD2-like defense response protein 1 (ALD1), which encodes an enzyme involved in Pip biosynthesis. Induction of ALD1 resulted in the accumulation of high levels of Pip, which brought about increased levels of the SA receptor protein NPR1 without induction of NPR1 expression or requirement for an increase in SA levels. Pip-mediated induction of ALD1 and genes regulating the biosynthesis of SA-CBP60g, SARD1, PAD4, and EDS1-was largely dependent on NPR1. Furthermore, Pip-mediated increase in NPR1 protein levels was associated with priming of Pip and SA biosynthesis genes to induction by low levels of SA. Taken together, our findings expand the role for CAMTA123 in regulating key immunity genes and suggest a working model whereby loss of CAMTA123 repression leads to the induction of plant defense genes and initiation of SAR.

Arabidopsis Transcription Factors SPL1 and SPL12 Confer Plant Thermotolerance at Reproductive Stage.

Plant reproductive organs are vulnerable to heat, but regulation of heat-shock responses in inflorescence is largely uncharacterized. Here, we report that two of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcriptional factors in Arabidopsis, SPL1 and SPL12, act redundantly in thermotolerance at the reproductive stage. The spl1-1 spl12-1 inflorescences displayed hypersensitivity to heat stress, whereas overexpression of SPL1 or SPL12 enhanced the thermotolerance in both Arabidopsis and tobacco. RNA sequencing revealed 1939 upregulated and 1479 downregulated genes in wild-type inflorescence upon heat stress, among which one-quarter (1,040) was misregulated in spl1-1 spl12-1, indicating that SPL1 and SPL12 contribute greatly to the heat-triggered transcriptional reprogramming in inflorescence. Notably, heat stress induced a large number of abscisic acid (ABA) responsive genes, of which ∼39% were disturbed in heat induction in spl1-1 spl12-1 inflorescence. Preapplication of ABA and overexpression of SPL1 restored the inflorescence thermotolerance in spl1-1 spl12-1 and in the ABA biosynthesis mutant aba2-1, but not in the pyl sextuple mutant defective in ABA receptors PYR1/PYL1/PYL2/PYL4/PYL5/PYL8. Thus, inflorescence thermotolerance conferred by SPL1 and SPL2 involves PYL-mediated ABA signaling. The molecular network consisting of SPL1 and SPL12 illustrated here shed new light on the mechanisms of plant thermotolerance at the reproductive stage.

Effects of induced optical tunable and ferromagnetic behaviors of Ba doped nanocrystalline LaB6.

Multiple nanocrystalline rare-earth hexaborides La1-xBaxB6 have been synthesized via a single step solid-state reaction. The Ba doping effects on crystal structure, grain morphology, magnetic and optical absorption properties were investigated using XRD, FESEM, HRTEM, SQUID magnetometry and optical measurements. The results show that all the Ba-doped hexaborides crystallize in the CsCl-type single phase, indicating the Ba atoms occupied the lattice sites of LaB6. The optical absorption results indicate that the absorption valleys of LaB6 are red-shifted from 622 nm to 780 nm when the Ba doping content increases to x = 0.8. The first-principle calculation results reveal that Ba doping reduces the total kinetic energy of the electrons of LaB6, which lead to the absorption valleys moving toward a higher wavelength. Meanwhile, the band gap of BaB6 obtained from optical absorption is in good agreement with the theoretical calculation results. The magnetic measurements results showed that Ba doping lead to room-temperature ferromagnetism of LaB6 due to the different ionic radii of La(3+) and Ba(2+) causing intrinsic crystal defects, which is directly observed experimentally by HRTEM. This is the first time that we have found the tunable optical and ferromagnetic behavior of Ba doped nanocrystalline LaB6. Thus, nanocrystalline La1-xBaxB6, as multi-functional materials, should open up a new route to extend the optical and magnetic applications of LaB6 nanopowder.

[Light and temperature indices during the seeding stage of spring maize in Hetao irrigation district, Inner Mongolia, China].

We collected the experimental dataset of a spring-maize in Hetao irrigation district (Bayannaoer, Inner Mongolia) during 2012 and 2013, as well as the crop data observed in related agrometeorological stations to investigate the impacts of light and temperature variation on maize development during the seedling stage to derive adequate light and temperature indices for different suitability. Furthermore, polynomial fitting was applied to interpolate the temperature indices for each day of the whole seedling period to draw the dynamics of the temperature indices and to better characterize its influence on maize development during the seedling stage. The results suggested that the emergence and development rates increased by 11% and 12%, respectively when the average temperature increased 1 °C during the sowing-emergence period and emergence-jointing period, and the biological lowest temperature was 7.4 and 11.9°C , respectively. The optimum temperature at the sowing-emergence stage ranged from 16.0 to 18.0°C , and the leaf area index at the three-leaf stage reached 0.0172 and above. The optimum temperature at the emergence-jointing stage ranged from 21.6 to 23.0°0C , and the photosynthesis/growth of plant tissue was positively correlated with the temperature. The leaf area index in the jointing period could reach 2.15 and the plant height was 120 cm. At the emergence-jointing stage, when the sunshine percentage 74%, or the daily sunshine hours ≥11.0 h . d-1 , or the total sunshine hours ≥540 h, the dry mass of plant tissue could

Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3.

Cotton fibres are unusually long, single-celled epidermal seed trichomes and a model for plant cell growth, but little is known about the regulation of fibre cell elongation. Here we report that a homeodomain-leucine zipper (HD-ZIP) transcription factor, GhHOX3, controls cotton fibre elongation. GhHOX3 genes are localized to the 12th homoeologous chromosome set of allotetraploid cotton cultivars, associated with quantitative trait loci (QTLs) for fibre length. Silencing of GhHOX3 greatly reduces (>80%) fibre length, whereas its overexpression leads to longer fibre. Combined transcriptomic and biochemical analyses identify target genes of GhHOX3 that also contain the L1-box cis-element, including two cell wall loosening protein genes GhRDL1 and GhEXPA1. GhHOX3 interacts with GhHD1, another homeodomain protein, resulting in enhanced transcriptional activity, and with cotton DELLA, GhSLR1, repressor of the growth hormone gibberellin (GA). GhSLR1 interferes with the GhHOX3-GhHD1 interaction and represses target gene transcription. Our results uncover a novel mechanism whereby a homeodomain protein transduces GA signal to promote fibre cell elongation.

Interaction between two timing microRNAs controls trichome distribution in Arabidopsis.

The miR156-targeted squamosa promoter binding protein like (SPL) transcription factors function as an endogenous age cue in regulating plant phase transition and phase-dependent morphogenesis, but the control of SPL output remains poorly understood. In Arabidopsis thaliana the spatial pattern of trichome is a hallmark of phase transition and governed by SPLs. Here, by dissecting the regulatory network controlling trichome formation on stem, we show that the miR171-targeted lost meristems 1 (LOM1), LOM2 and LOM3, encoding GRAS family members previously known to maintain meristem cell polarity, are involved in regulating the SPL activity. Reduced LOM abundance by overexpression of miR171 led to decreased trichome density on stems and floral organs, and conversely, constitutive expression of the miR171-resistant LOM (rLOM) genes promoted trichome production, indicating that LOMs enhance trichome initiation at reproductive stage. Genetic analysis demonstrated LOMs shaping trichome distribution is dependent on SPLs, which positively regulate trichome repressor genes TRICHOMELESS 1 (TCL1) and TRIPTYCHON (TRY). Physical interaction between the N-terminus of LOMs and SPLs underpins the repression of SPL activity. Importantly, other growth and developmental events, such as flowering, are also modulated by LOM-SPL interaction, indicating a broad effect of the LOM-SPL interplay. Furthermore, we provide evidence that MIR171 gene expression is regulated by its targeted LOMs, forming a homeostatic feedback loop. Our data uncover an antagonistic interplay between the two timing miRNAs in controlling plant growth, phase transition and morphogenesis through direct interaction of their targets.

[Temporal change in annual air temperature and heat island effect in a coastal city and an inland city at mid-latitude in China during 1956-1998].

Temporal changes in air temperature and urban heat island (UHI) effects during 1956-1998 were compared between a coastal city, Ji' nan, and an inland city, Xi' an, which were similar in latitude, size and development. During 1956-1978, except that the annual mean minimum temperature in Ji' nan increased by 0.37 degrees C x 10 a(-1), the temperature variables in the two cities did not display any apparent trend. During 1979-1998, all temperature variables of the two cities showed an increasing trend. Comparing with that in Ji' nan, the increasing rate of annual mean maximum temperature and annual mean temperature in Xi' an was greater, but that of annual mean minimum temperature was smaller. In the two cities, heat island effect occurred during 1956-1978 but without any apparent trend, whereas during 1979-1998, this effect increased with time, especially in Xi' an where the annual mean minimum temperature and annual mean temperature increased by 0.22 degrees C x 10 a(-1) and 0.32 degrees C x 10 a(-1), respectively. Both the level and the inter-annual variation of the heat island effect were much greater in Ji' nan than in Xi' an, but the increasing rate of this effect was greater in Xi' an than in Ji' nan. Obvious differences were observed in the increasing rate of annual mean maximum air temperature, annual mean air temperature, and annual mean minimum temperature as well as the heat island effect in Ji' nan, whereas negligible differences were found in Xi' an. Among the three temperature variables, annual mean minimum temperature displayed the most obvious increasing trend and was most affected by heat island effect, while annual mean maximum temperature was most variable inter-annually. Geographical location not only affected the magnitude of urban warming, but also affected the mode of urban warming and the strength of heat island effect.

[Effects of electro-warmed needle of inner-Mongolian medicine on serum TNF-alpha, ACTH and corticosterone contents in fatigue rats].

OBJECTIVE: To observe the effect of electro-warmed needle (EWN, of Inner-Mongolian medicine) on fatigue rats' behavior, hypothalamic-pituitary-adrenocortex (HPA) axis activity and immune system so as to reveal its neuro-endocrino-immune mechanism. METHODS: Male SD rats were randomized into control (n=20), model (n=20) and EWN (n=19) groups. Fatigue model was established by forcing the rat to swim in a water pool till exhaustion, once daily, continuously for 21 days. "Dinghui" (central spot over the bregmatic bone) and "Xinxue" (the center of the depression beneath the 7th thoracic vertebra) were punctured with silver needles which were warmed electrically by using a MLY-I Electrical Needle-warming Apparatus, once every 3 days, 7 sessions altogether. On the 21st day of modeling, swim-exhaustion duration (SED), and immobility time and struggle times in tail suspension test were measured. Twenty-four hours after the last swim, the rats' serum TNF-alpha, ACTH an corticosterone contents were detected by enzyme linked immunosorbent assay (ELISA). RESULTS: Compared with control group SED, immobility time and struggle times in tail suspension test in model group decreased, increased and lowered respectively and significantly (P < 0.01, 0.05); while in comparison with model group, the first 2 indexes of EWN group increased and lowered respectively and significantly (P < 0.05). No significant difference was found between EWN and model groups in struggle times (P > 0.05). Compared with control group, serum TNF-alpha, ACTH and corticosterone contents in model group increased significantly (P < 0.01), while in comparison with model group, the 3 indexes of EWN group were significantly lower (P < 0.01, 0.05). CONCLUSION: EWN treatment can reduce fatigue-induced increase of serum TNF-alpha, ACTH and corticosterone levels, and raise motor ability, suggesting a favorable regulation of HPA axis and immune function after EWN and improvement of fatigue in fatigue