Structural basis for self-cleavage prevention by tag:anti-tag pairing complementarity in type VI Cas13 CRISPR systems.

Bacteria and archaea apply CRISPR-Cas surveillance complexes to defend against foreign invaders. These invading genetic elements are captured and integrated into the CRISPR array as spacer elements, guiding sequence-specific DNA/RNA targeting and cleavage. Recently, in vivo studies have shown that target RNAs with extended complementarity with repeat sequences flanking the target element (tag:anti-tag pairing) can dramatically reduce RNA cleavage by the type VI-A Cas13a system. Here, we report the cryo-EM structure of Leptotrichia shahii LshCas13acrRNA in complex with target RNA harboring tag:anti-tag pairing complementarity, with the observed conformational changes providing a molecular explanation for inactivation of the composite HEPN domain cleavage activity. These structural insights, together with in vitro biochemical and in vivo cell-based assays on key mutants, define the molecular principles underlying Cas13a's capacity to target and discriminate between self and non-self RNA targets. Our studies illuminate approaches to regulate Cas13a's cleavage activity, thereby influencing Cas13a-mediated biotechnological applications.

AKT2 reduces IFNß1 production to modulate antiviral responses and systemic lupus erythematosus.

Interferon regulatory factor 3 (IRF3)-induced type I interferon (I-IFN) production plays key roles in both antiviral and autoimmune responses. IRF3 phosphorylation, dimerization, and nuclear localization are needed for its activation and function, but the precise regulatory mechanisms remain to be explored. Here, we show that the serine/threonine kinase AKT2 interacts with IRF3 and phosphorylates it on Thr207, thereby attenuating IRF3 nuclear translocation in a 14-3-3ε-dependent manner and reducing I-IFN production. We further find that AKT2 expression is downregulated in viral-infected macrophages or in monocytes and tissue samples from systemic lupus erythematosus (SLE) patients and mouse models. Akt2-deficient mice exhibit increased I-IFN induction and reduced mortality in response to viral infection, but aggravated severity of SLE. Overexpression of AKT2 kinase-inactive or IRF3-T207A mutants in zebrafish supports that AKT2 negatively regulates I-IFN production and antiviral response in a kinase-dependent manner. This negative role of AKT2 in IRF3-induced I-IFN production suggests that AKT2 may be therapeutically targeted to differentially regulate antiviral infection and SLE.

Structure and biochemical characterization of l-2-hydroxyglutarate dehydrogenase and its role in the pathogenesis of l-2-hydroxyglutaric aciduria.

l-2-hydroxyglutarate dehydrogenase (L2HGDH) is a mitochondrial membrane-associated metabolic enzyme, which catalyzes the oxidation of l-2-hydroxyglutarate (l-2-HG) to 2-oxoglutarate (2-OG). Mutations in human L2HGDH lead to abnormal accumulation of l-2-HG, which causes a neurometabolic disorder named l-2-hydroxyglutaric aciduria (l-2-HGA). Here, we report the crystal structures of Drosophila melanogaster L2HGDH (dmL2HGDH) in FAD-bound form and in complex with FAD and 2-OG and show that dmL2HGDH exhibits high activity and substrate specificity for l-2-HG. dmL2HGDH consists of an FAD-binding domain and a substrate-binding domain, and the active site is located at the interface of the two domains with 2-OG binding to the re-face of the isoalloxazine moiety of FAD. Mutagenesis and activity assay confirmed the functional roles of key residues involved in the substrate binding and catalytic reaction and showed that most of the mutations of dmL2HGDH equivalent to l-2-HGA-associated mutations of human L2HGDH led to complete loss of the activity. The structural and biochemical data together reveal the molecular basis for the substrate specificity and catalytic mechanism of L2HGDH and provide insights into the functional roles of human L2HGDH mutations in the pathogeneses of l-2-HGA.

A vitamin-C-derived DNA modification catalysed by an algal TET homologue.

Methylation of cytosine to 5-methylcytosine (5mC) is a prevalent DNA modification found in many organisms. Sequential oxidation of 5mC by ten-eleven translocation (TET) dioxygenases results in a cascade of additional epigenetic marks and promotes demethylation of DNA in mammals1,2. However, the enzymatic activity and function of TET homologues in other eukaryotes remains largely unexplored. Here we show that the green alga Chlamydomonas reinhardtii contains a 5mC-modifying enzyme (CMD1) that is a TET homologue and catalyses the conjugation of a glyceryl moiety to the methyl group of 5mC through a carbon-carbon bond, resulting in two stereoisomeric nucleobase products. The catalytic activity of CMD1 requires Fe(II) and the integrity of its binding motif His-X-Asp, which is conserved in Fe-dependent dioxygenases3. However, unlike previously described TET enzymes, which use 2-oxoglutarate as a co-substrate4, CMD1 uses L-ascorbic acid (vitamin C) as an essential co-substrate. Vitamin C donates the glyceryl moiety to 5mC with concurrent formation of glyoxylic acid and CO2. The vitamin-C-derived DNA modification is present in the genome of wild-type C. reinhardtii but at a substantially lower level in a CMD1 mutant strain. The fitness of CMD1 mutant cells during exposure to high light levels is reduced. LHCSR3, a gene that is critical for the protection of C. reinhardtii from photo-oxidative damage under high light conditions, is hypermethylated and downregulated in CMD1 mutant cells compared to wild-type cells, causing a reduced capacity for photoprotective non-photochemical quenching. Our study thus identifies a eukaryotic DNA base modification that is catalysed by a divergent TET homologue and unexpectedly derived from vitamin C, and describes its role as a potential epigenetic mark that may counteract DNA methylation in the regulation of photosynthesis.

Realizing multi-function absorptions through arbitrary octagonal meta-atoms.

Metasurface absorbers (MA) typically exhibit a single type of absorption function due to their regular structures. In this study, we propose an irregular MA structure with octagonal meta-atoms. The presence of eight vertices in each meta-atom allows for tunable coordinates and offers a multitude of degrees of freedom in terms of geometry. As a result, the proposed MA exhibits diverse functionalities, including perfect absorption, multi-peaks absorption, and high absorption with a filtering window. To predict the geometric parameters of the MA structure based on a given target absorption spectrum, as well as the inverse design of the structure using the absorption spectrum as input, we employ a deep neural network combined with the particle swarm optimization algorithm. Remarkably, the mean-square error for spectrum prediction and inverse design of the MA structure is found to be as low as 0.0008 and 0.0031, respectively. This study opens up new possibilities for designing irregular electromagnetic structures and holds great potential for applications in multifunctional metasurfaces and metamaterials.

Longitudinal manipulation of local nonseparability in vector beams.

The inherent nonseparability of vector beams presents a unique opportunity to explore novel optical functionalities, expanding new degrees of freedom for optical information processing. In this Letter, we introduce a novel, to the best of our knowledge, method for tailoring the local nonseparability along the propagation axis of vector beams. Employing higher-order Bessel vector beams, the longitudinal control over the local nonseparability is achieved through targeted amplitude modulation of constituent orthogonal polarization components within the main ring region. Experimental demonstrations of diverse longitudinal nonseparability profiles corroborate the efficacy and versatility of our approach, opening avenues for further exploration of the nonseparability manipulation in vector beams.

Achieving focal invariance in different background refractive indices through a dual-environment metalens.

A conventional metalens is designed with a fixed working environment, and its focal length depends on the background refractive index. In this study, we propose a dual-environment metalens that can maintain the same focal length in both media of air and water. The metalens consists of 16 types of meta-atoms with different geometries, which can cover the 0-2π phase range in both air and water. We perform finite-difference time-domain simulations to investigate the metalens and demonstrate that its focal length remains unchanged, regardless of whether the background medium is air or water. Furthermore, we investigated the optical forces within the focal field of the metalens in both air and water, indicating its potential trapping capability in these media. Our method provides a new insight into dual-environment metasurfaces and advances the methodology of electromagnetic structures in extensive applications.

Molecular insight into the potential functional role of pseudoenzyme GFOD1 via interaction with NKIRAS2.

The glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family includes a variety of oxidoreductases with a wide range of substrates that utilize NAD or NADP as redox cofactor. Human contains two members of this family, namely glucose-fructose oxidoreductase domain-containing protein 1 and 2 (GFOD1 and GFOD2). While GFOD1 exhibits low tissue specificity, it is notably expressed in the brain, potentially linked to psychiatric disorders and severe diseases. Nevertheless, the specific function, cofactor preference, and enzymatic activity of GFOD1 remain largely unknown. In this work, we find that GFOD1 does not bind to either NAD or NADP. Crystal structure analysis unveils that GFOD1 exists as a typical homodimer resembling other family members, but lacks essential residues required for cofactor binding, suggesting that it may function as a pseudoenzyme. Exploration of GFOD1-interacting partners in proteomic database identifies NK-κB inhibitor-interacting Ras-like 2 (NKIRAS2) as one potential candidate. Co-immunoprecipitation (co-IP) analysis indicates that GFOD1 interacts with both GTP- and GDP-bound forms of NKIRAS2. The predicted structural model of the GFOD1-NKIRAS2 complex is validated in cells using point mutants and shows that GFOD1 selectively recognizes the interswitch region of NKIRAS2. These findings reveal the distinct structural properties of GFOD1 and shed light on its potential functional role in cellular processes.

Biochemical properties of sheep colostrum and its potential benefits for lamb survival: a review.

Colostrum is the initial secretion of the mammary glands following parturition, which offers main food, protection, and biological active substances for the new born. The most threatening episode of neonate's life is the initial two weeks after birth. This period is associated with high neonatal mortality and morbidity. These worthwhile losses lead to a poor prolificacy rate, low profitability, and ultimately poor performance in animal production. Hence, both diseases and mortality cause valuable losses in terms of production and economic losses. The survival of neonate is correlated with their immune status and passive immune transfer (PIT). Colostrum provides the primary source of nutrition and immunity (PIT) that protects neonates against infections. It must be given as soon as possible after birth since its immunoglobulins are absorbed within the first 16-27 hours after birth, ideally within 2-4 hours. As a result, immunoglobulin (PIT) is the most important component of distressing infectious immunity, and a passable concentration of immunoglobulin in the blood of newborn lambs is linked to their health and survival rate. In this review, we summarized the importance of colostrum in early life and its association with neonatal lamb's survival, profitability and productivity of sheep farming.

Effects of probiotic supplementation on 12 min run performance, mood management, body composition and gut microbiota in amateur marathon runners: A double-blind controlled trial.

Background: Probiotic supplementation has a positive effect on endurance exercise performance and body composition in athletes, but the underlying mechanisms remain unclear. Gut microbiota can provide measurable markers of immune function in athletes, and microbial composition analysis may be sensitive enough to detect stress and metabolic disorders caused by exercise. Methods: Nineteen healthy active amateur marathon runners (15 male and 4 female) with a mean age of 29.11 years volunteered to participate in this double-blind controlled study. Based on the performance of the Cooper 12-min running test (CRT), the participants were allocated into two groups to receive either a probiotic formulation comprising lactobacillus acidophilus and bifidobacterium longum (n = 10) or placebo containing maltodextrin (n = 9) for five weeks. Consistency of diet and exercise was ensured throughout the experimental period. Before and after the intervention, all participants were assessed for CRT, emotional stability and gastrointestinal symptoms, gut microbiota composition, body composition and magnetic resonance imaging (MRI) indicators of skeletal muscle microcirculation. Results: Compared to before the intervention, the probiotics group showed an increase in CRT score (2.88 ± 0.57 vs 3.01 ± 0.60 km, P＜0.05), significant improvement in GSRS and GIQLI (9.20 ± 4.64 vs 7.40 ± 3.24, 118.90 ± 12.30 vs 127.50 ± 9.85, P＜0.05), while these indicators remained unchanged in the control group, with a significant time-group interaction effect on gastrointestinal symptoms. Additionally, some MRI metabolic cycling indicators of the thigh skeletal muscle also changed in the probiotics group (P＜0.05). Regarding microbiota abundance, the probiotics group exhibited a significant increase in the abundance of beneficial bacteria and a significant decrease in the abundance of harmful bacteria post-intervention (P＜0.05). Conclusion: As a sports nutritional supplement, probiotics have the potential to improve athletic performance by optimizing the balance of gut microbiota, alleviating gastrointestinal symptoms.

Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction.

Human NAD-dependent isocitrate dehydrogenase or IDH3 (HsIDH3) catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the tricarboxylic acid cycle. It consists of three types of subunits (α, ß, and γ) and exists and functions as the (αßαγ)2 heterooctamer. HsIDH3 is regulated allosterically and/or competitively by numerous metabolites including CIT, ADP, ATP, and NADH. Our previous studies have revealed the molecular basis for the activity and regulation of the αß and αγ heterodimers. However, the molecular mechanism for the allosteric activation of the HsIDH3 holoenzyme remains elusive. In this work, we report the crystal structures of the αß and αγ heterodimers and the (αßαγ)2 heterooctamer containing an α-Q139A mutation in the clasp domain, which renders all the heterodimers and the heterooctamer constitutively active in the absence of activators. Our structural analysis shows that the α-Q139A mutation alters the hydrogen-bonding network at the heterodimer-heterodimer interface in a manner similar to that in the activator-bound αγ heterodimer. This alteration not only stabilizes the active sites of both αQ139Aß and αQ139Aγ heterodimers in active conformations but also induces conformational changes of the pseudo-allosteric site of the αQ139Aß heterodimer enabling it to bind activators. In addition, the αQ139AICT+Ca+NADßNAD structure presents the first pseudo-Michaelis complex of HsIDH3, which allows us to identify the key residues involved in the binding of cofactor, substrate, and metal ion. Our structural and biochemical data together reveal new insights into the molecular mechanisms for allosteric regulation and the catalytic reaction of HsIDH3.

Breaking symmetry restriction of chirality through spin-decoupled phase modulation utilizing non-mirror-symmetric meta-atoms.

The geometric phase in metasurfaces follows a symmetry restriction of chirality, which dictates that the phases of two orthogonal circularly polarized waves are identical but have opposite signs. In this study, we propose a general mechanism to disrupt this symmetric restriction on the chirality of orthogonal circular polarizations by introducing mirror-symmetry-breaking meta-atoms. This mechanism introduces a new degree of freedom in spin-decoupled phase modulation without necessitating the rotation of the meta-atom. To demonstrate the feasibility of this concept, we design what we believe is a novel meta-atom with a QR-code structure and successfully showcase circular-polarization multiplexing metasurface holography. Our investigation offers what we believe to be a novel understanding of the chirality in geometric phase within the realm of nanophotonics. Moreover, it paves the way for the development of what we believe will be novel design methodologies for electromagnetic structures, enabling applications in arbitrary wavefront engineering.

Single-shot measurement of the Jones matrix for anisotropic media using four-channel digital polarization holography.

Dynamic measurement of the Jones matrix is crucial in investigating polarization light fields, which have wide applications in biophysics, chemistry, and mineralogy. However, acquiring the four elements of the Jones matrix instantly is difficult, hindering the characterization of random media and transient processes. In this study, we propose a single-shot measurement method of the Jones matrix for anisotropic media called "four-channel digital polarization holography" (FC-DPH). The FC-DPH system is created by a slightly off-axis superposition of reference light waves, which are modulated by a spatial light modulator (SLM), and signal light waves that pass through a Ronchi grating. The SLM enables flexible adjustment of the spatial carrier frequency, which can be adapted to different anisotropic media. The four elements of the Jones matrix can be obtained from the interferogram through the inverse Fourier transform. Optical experiments on anisotropic objects validate the feasibility and accuracy of the proposed method.

Spatio-temporal structuring control of a vectorial focal field.

Focal field modulation has attracted a lot of interest due to its potential in many applications such as optical tweezers or laser processing, and it has recently been facilitated by spatial light modulators (SLMs) owing to their dynamic modulation abilities. However, capabilities for manipulating focal fields are limited by the space-bandwidth product of SLMs. This difficulty can be alleviated by taking advantage of the high-speed modulation ability of digital micromirror devices (DMDs), i.e., trading time for space to achieve fine focus shaping. In this paper, we propose a new, to the best of our knowledge, technique for achieving four-dimensional focal field modulation, which allows for independent manipulation of the focal field's parameters (including amplitude, phase, and polarization) in both the space and time domains. This technique combines a DMD and a vector field synthesis system based on a 4-f system. The high-speed modulation ability of DMDs enables versatile focus patterns to be fast switchable during the exposure time of the detector, forming multiple patterns in a single recording frame. By generating different kinds of focal spots and lines at different moments during the exposure time of the detector, we can finally get complete multifocal spots and lines. Our proposed method is effective at improving the flexibility and speed of the focal field modulation, which is beneficial to applications.

HBO1 is a versatile histone acyltransferase critical for promoter histone acylations.

Recent studies demonstrate that histones are subjected to a series of short-chain fatty acid modifications that is known as histone acylations. However, the enzymes responsible for histone acylations in vivo are not well characterized. Here, we report that HBO1 is a versatile histone acyltransferase that catalyzes not only histone acetylation but also propionylation, butyrylation and crotonylation both in vivo and in vitro and does so in a JADE or BRPF family scaffold protein-dependent manner. We show that the minimal HBO1/BRPF2 complex can accommodate acetyl-CoA, propionyl-CoA, butyryl-CoA and crotonyl-CoA. Comparison of CBP and HBO1 reveals that they catalyze histone acylations at overlapping as well as distinct sites, with HBO1 being the key enzyme for H3K14 acylations. Genome-wide chromatin immunoprecipitation assay demonstrates that HBO1 is highly enriched at and contributes to bulk histone acylations on the transcriptional start sites of active transcribed genes. HBO1 promoter intensity highly correlates with the level of promoter histone acylation, but has no significant correlation with level of transcription. We also show that HBO1 is associated with a subset of DNA replication origins. Collectively our study establishes HBO1 as a versatile histone acyltransferase that links histone acylations to promoter acylations and selection of DNA replication origins.

Predicting the eigenstructures of metamaterials with QR-code meta-atoms by deep learning.

Deep neural networks (DNNs) facilitate the reverse design of metamaterial perfect absorbers (MPAs), usually by predicting the MPA structure from the input absorptivity. However, this suffers from the difficulty that the spectrum that actually exists is unknown before the structure is known. We propose an MPA structure with quick response (QR)-code meta-atoms and construct a novel DNN to predict and reverse design the eigenstructures by inputting designated eigenfrequencies. In addition, the meta-atom has a tremendous number of degrees of freedom, providing rich properties such as multiple absorption peaks. This work paves the way for the study of eigenproblems of complicated metamaterials and metasurfaces.

Radiographic measurement of the posterior tibial slope in normal Chinese adults: a retrospective cohort study.

BACKGROUND: Measurement of the posterior tibial slope (PTS) angle has important applications in total knee replacement surgery, high tibial osteotomy, and anterior cruciate ligament reconstruction. This study aimed to determine the mean PTS of knee joints in healthy Chinese adults, and provide data to guide knee surgery in China. METHODS: A retrospective analysis of 1257 (n = 1233, 50.4% male) plain X-ray films of participants aged 25-59 years was performed. The picture archiving and communication system was used for PTS measurement. The PTS was defined as the angle between the vertical line of the tangent of the anterior tibial cortex of the proximal tibia, and the tangent line of the tibial cortex. Two imaging physicians conducted the PTS measurements independently, and both the inter- and intraclass correlation coefficients (ICCs) were calculated. RESULTS: The mean PTS value was 7.68 ± 3.84° (range: 0-21°). The left PTS was significantly smaller in males than in females (7.22 ± 3.89 vs 8.05 ± 3.60; P = 0.005). Additionally, the PTS in participants aged 25-29 years was significantly larger than that in the other age groups (Left side: 8.64 ± 3.73 vs 6.92 ± 3.42, 7.42 ± 3.75, 7.53 ± 3.98; P <  0.001 and Right side: 8.68 ± 3.84 vs 7.48 ± 4.21, 7.13 ± 3.64, 7.66 ± 3.80; P = 0.004). There were no significant differences in PTS between the left and right sides. Two-way analysis of variance suggested that the differences in PTS between age groups were not affected by sex. The interobserver ICC was 0.91 (95% confidence interval [CI]: 0.85-0.94), and the intraobserver ICC was 0.90 (95% CI: 0.82-0.94). CONCLUSIONS: This study demonstrated that there were significant differences in PTS based on sex and age, highlighting the need to provide individualized treatment for knee surgery. It provided valuable information regarding the normal PTS values in Chinese adults and presented regionalised data to guide knee surgery.

Acute changes in knee cartilage and meniscus following long-distance running in habituate runners: a systematic review on studies using quantitative magnetic resonance imaging.

OBJECTIVE: Running is among the most popular recreational activities; nonetheless, the acute post-race changes of cartilage or meniscus have rarely been determined. The current study aimed to review the acute changes in knee cartilage and meniscus among habituate runners following long-distance running detected by using quantitative magnetic resonance imaging (MRI). MATERIALS AND METHODS: Systematic literature search was performed on those dominate clinical databases which including MEDLINE, Cochrane, Embase, ScienceDirect, and Web of Science. Included studies should be conducted on healthy marathon runners, and the participants should be examined before and after running by using MRI. Intervention studies were excluded. RESULTS: A total number of 14 studies were finally included in this review which all examined the cartilage or meniscus by using MRI functional sequences. Among them, six studies quantitatively measured the changes regarding volume of the knee cartilage or/and meniscus. Five studies found that the volume would decrease initially after running. Ten studies reported T2 (T2*) would decrease after running and returned to the baseline in a short term, while T1ρ may remain increased in months. Five studies measured subareas for T2 (T2*) value, and found that the superficial and medial subarea changed more vastly than other regions after running. CONCLUSION: Runners experience transient changes in the volume and signals of knee cartilage and meniscus after long-distance running. A liquid exchange and material interaction in cartilage and meniscus was observed after running. Superficial and medial areas of knee cartilage and meniscus might be more susceptible to mechanical loading.

Nonvolatile Optically Reconfigurable Radiative Metasurface with Visible Tunability for Anticounterfeiting.

Control of thermal emission underpins fundamental science, as it is related to both heat and infrared electromagnetic wave transport. However, realizing nonvolatile reconfigurable thermal emission is challenging due to the inherent complexity or limitation in conventional radiative materials or structures. Here, we experimentally demonstrate a nonvolatile optically reconfigurable mid-infrared coding radiative metasurface. By applying laser pulses, infrared emissive patterns are directly encoded into an ultrathin (∼25 nm) Ge2Sb2Te5 layer integrated into a planar optical cavity with the optically crystallized Ge2Sb2Te5 spots, and the peak spectral emissivity is repeatedly switched between low (∼0.1) and high (∼0.7) values. In addition, the visible scattering patterns are independently modulated with submicron-sized bumps generated by high-power laser pulses. An anticounterfeiting label is demonstrated with spatially different infrared emission and visible light scattering information encoded. This approach constitutes a new route toward thermal emission control and has broad applications in encryption, camouflage, and so on.

Metamaterial perfect absorber with morphology-engineered meta-atoms using deep learning.

Metamaterial perfect absorbers (MPAs) typically have regularly-shaped unit structures owing to constraints on conventional analysis methods, limiting their absorption properties. We propose an MPA structure with a general polygon-shaped meta-atom. Its irregular unit structure provides multiple degrees-of-freedom, enabling flexible properties, such as dual-band absorption. We constructed a deep neural network to predict the parameters of the corresponding MPA structure with a given absorptivity as input, and vice versa. The mean-square error was as low as 0.0017 on the validation set. This study provides a basis for the design of complicated artificial electromagnetic structures for application in metamaterials and metasurfaces.