PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects.

Congenital diaphragmatic hernia (CDH) is a relatively common and genetically heterogeneous structural birth defect associated with high mortality and morbidity. We describe eight unrelated families with an X-linked condition characterized by diaphragm defects, variable anterior body-wall anomalies, and/or facial dysmorphism. Using linkage analysis and exome or genome sequencing, we found that missense variants in plastin 3 (PLS3), a gene encoding an actin bundling protein, co-segregate with disease in all families. Loss-of-function variants in PLS3 have been previously associated with X-linked osteoporosis (MIM: 300910), so we used in silico protein modeling and a mouse model to address these seemingly disparate clinical phenotypes. The missense variants in individuals with CDH are located within the actin-binding domains of the protein but are not predicted to affect protein structure, whereas the variants in individuals with osteoporosis are predicted to result in loss of function. A mouse knockin model of a variant identified in one of the CDH-affected families, c.1497G>C (p.Trp499Cys), shows partial perinatal lethality and recapitulates the key findings of the human phenotype, including diaphragm and abdominal-wall defects. Both the mouse model and one adult human male with a CDH-associated PLS3 variant were observed to have increased rather than decreased bone mineral density. Together, these clinical and functional data in humans and mice reveal that specific missense variants affecting the actin-binding domains of PLS3 might have a gain-of-function effect and cause a Mendelian congenital disorder.

Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene.

Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.

Rationalization of passivation strategies toward high-performance perovskite solar cells.

Lead halide perovskite solar cells (PSCs) have shown unprecedented development in efficiency and progressed relentlessly in improving stability. All the achievements have been accompanied by diverse passivation strategies to circumvent the pervasive defects in perovskite materials, which play crucial roles in the process of charge recombination, ion migration, and component degradation. Among the tremendous efforts made to solve these issues and achieve high-performance PSCs, we classify and review both well-established and burgeoning passivation strategies to provide further guidance for the passivation protocols in PSCs, including chemical passivation to eliminate defects by the formation of chemical bonds, physical passivation to eliminate defects by strain relaxation or physical treatments, energetic passivation to improve the stability toward light and oxygen, and field-effect passivation to regulate the interfacial carrier behavior. The subtle but non-trivial consequences from various passivation strategies need advanced characterization techniques combining synchrotron-based X-ray analysis, capacitance-based measurements, spatially resolved imaging, fluorescent molecular probe, Kelvin probe force microscope, etc., to scrutinize the mechanisms. In the end, challenges and prospective research directions on advancing these passivation strategies are proposed. Judicious combinations among chemical, physical, energetic, and field-effect passivation deserve more attention for future high-efficiency and stable perovskite photovoltaics.

In Situ Transformation of an Amorphous Supramolecular Coating to a Hydrogen-Bonded Organic Framework Membrane to Trigger Selective Gas Permeation.

We introduce a "solution-processing-transformation" strategy, deploying solvent vapor as scaffolds, to fabricate high-quality hydrogen-bonded organic framework (HOF) membranes. This strategy can overcome the mismatch in processing conditions and crystal growth thermodynamics faced during the facile solution processing of the membrane. The procedure includes the vapor-trigged in situ transformation of dense amorphous supramolecules to crystalline HOF-16, with HOF-11 as the transient state. The mechanism involves a vapor-activated dissolution-precipitation equilibrium shifting and hydrogen bonding-guided molecule rearrangement, elucidated through combined experimental and theoretical analysis. Upon removal of the molecular scaffolds, the resulting HOF-16 membranes showcase significant improvement in hydrogen separation performance over their amorphous counterparts and previously reported HOF membranes. The method's broad applicability is evidenced by successfully extending it to other substrates and HOF structures. This study provides a fundamental understanding of guest-induced ordered supramolecular assembly and paves the way for the advanced manufacture of high-performance HOF membranes for gas separation processes.

Experimental 61-partite entanglement on a three-dimensional photonic chip.

Multipartite entanglements are essential resources for proceeding tasks in quantum information science and technology. However, generating and verifying them present significant challenges, such as the stringent requirements for manipulations and the need for a huge number of building-blocks as the systems scale up. Here, we propose and experimentally demonstrate the heralded multipartite entanglements on a three-dimensional photonic chip. Integrated photonics provide a physically scalable way to achieve an extensive and adjustable architecture. Through sophisticated Hamiltonian engineering, we are able to control the coherent evolution of shared single photon in the multiple spatial modes, dynamically tuning the induced high-order W-states of different orders in a single photonic chip. Using an effective witness, we successfully observe and verify 61-partite quantum entanglements in a 121-site photonic lattice. Our results, together with the single-site-addressable platform, offer new insights into the accessible size of quantum entanglements and may facilitate the developments of large-scale quantum information processing applications.

Experimental Boson Sampling Enabling Cryptographic One-Way Function.

Boson sampling is a computational problem, which is commonly believed to be a representative paradigm for attaining the milestone of quantum advantage. So far, massive efforts have been made to the experimental large-scale boson sampling for demonstrating this milestone, while further applications of the machines remain a largely unexplored area. Here, we investigate experimentally the efficiency and security of a cryptographic one-way function that relies on coarse-grained boson sampling, in the framework of a photonic boson-sampling machine fabricated by a femtosecond laser direct writing technique. Our findings demonstrate that the implementation of the function requires moderate sample sizes, which can be over 4 orders of magnitude smaller than the ones predicted by the Chernoff bound; whereas for numbers of photons n≥3 and bins d∼poly(m,n), the same output of the function cannot be generated by nonboson samplers. Our Letter is the first experimental study that deals with the potential applications of boson sampling in the field of cryptography and paves the way toward additional studies in this direction.

Suppressing Oxygen-Induced Deterioration of Metal Halide Perovskites by Alkaline Earth Metal Doping: A Quantum Dynamics Study.

Exposure to oxygen undermines stability and charge transport in metal halide perovskites, because molecular oxygen, as well as photogenerated superoxide and peroxide, erodes the perovskite lattice and creates charge traps. We demonstrate that alkaline earth metals passivate the oxygen species in CH3NH3PbI3 by breaking the O-O bond and forming new bonds with the oxygen atoms, shifting the trap states of the antibonding O-O orbitals from inside the bandgap into the bands. In addition to eliminating the oxidizing species and the charge traps, doping with the alkaline earth metals slightly increases the bandgap and partially localizes the electron and hole wavefunctions, weakening the electron-hole and charge-phonon interactions and making the charge carrier lifetimes longer than even those in pristine CH3NH3PbI3. Relative to CH3NH3PbI3 exposed to oxygen and light, the charge carrier lifetime of the passivated CH3NH3PbI3 increases by 2-3 orders of magnitude. The ab initio quantum dynamics simulations demonstrate that alkaline earth metals passivate efficiently not only intrinsic perovskite defects, but also the foreign species, providing a viable strategy to suppress perovskite degradation.

SEPHS1 is dispensable for pluripotency maintenance but indispensable for cardiac differentiation in mouse embryonic stem cells.

Embryonic stem cells (ESCs) are derived from the inner cell mass of developing blastocysts, which have self-renewal ability and have the potential to develop or reconstitute into all embryonic lineages. Selenophosphate synthetase 1 (SEPHS1) is an essential protein in mouse early embryo development. However, the role of SEPHS1 in mouse ESCs remains to be elucidated. In this study, we generated Sephs1 KO ESCs and found that deficiency of SEPSH1 has little effect on pluripotency maintenance and proliferation. Notably, SEPHS1 deficiency impaired differentiation into three germ layers and gastruloid aggregation in vitro. RNA-seq analysis showed SEPHS1 is involved in cardiogenesis, verified by no beating signal in Sephs1 KO embryoid body at d10 and low expression of cardiac-related and contraction markers. Taken together, our results suggest that SPEHS1 is dispensable in ESC self-renewal, but indispensable in subsequent germ layer differentiation especially for functional cardiac lineage.

Substitutional alkaline earth metals delay nonradiative charge recombination in CH3NH3PbI3 perovskite: A time-domain study.

Experiments reported that alkaline earth metal dopants greatly prolong carrier lifetime and improve the performance of perovskite solar cells. Using state-of-the-art ab initio time-domain nonadiabatic molecular dynamics (NAMD), we demonstrate that incorporation of alkaline earth metals, such as Sr and Ba, into MAPbI3 (MA = CH3NH3 +) lattice at the lead site is energetically favorable due to the largely negative formation energies about -7 eV. The replacement widens the bandgap and increases the open-circuit voltage by creating no trap states. More importantly, the substitution reduces the mixing of electron and hole wave functions by pushing the hole charge density away from the dopant together with no contribution of Sr and Ba to the conduction band edge state, thus decreasing the NA coupling. The high frequency phonons generated by enhanced atomic motions and symmetry breaking accelerate phonon-induced loss of coherence. The synergy of the three factors reduces the nonradiative recombination time by a factor of about 2 in the Sr- and Ba-doped systems with respect to pristine MAPbI3, which occurs over 1 ns and agrees well with the experiment. The study highlights the importance of various factors affecting charge carrier lifetime, establishes the mechanism of reduction of nonradiative electron-hole recombination in perovskites upon alkaline earth metal doping, and provides meaningful insights into the design of high performance of perovskite solar cells and optoelectronics.

LaDAL1 Coordinates Age and Environmental Signals in the Life Cycle of Larix kaempferi.

Perennial woody plants are long-lived, and their life-cycle events occur in order in each generation, but what drives the occurrence and restart of these events in their offspring is unknown. Based on its age-dependent expression pattern and function, Larix kaempferi DEFICIENS-AGAMOUS-LIKE 1 (LaDAL1), a MADS transcription factor has been suggested to be a time recorder and life-cycle event coordinator. Here, we studied the dynamic spatiotemporal expression pattern of LaDAL1 in the life cycle of L. kaempferi to analyze the molecular mechanism of life-cycle progression. In full view of the life cycle, LaDAL1 transcription was related with life-cycle progression, and its transcript level increased sharply from age 3 to 5 years, which might be the molecular characteristic of the vegetative phase change, and then stayed at a high level. During sexual reproduction, LaDAL1 transcript level decreased sequentially during meiosis and embryogenesis, suggesting that meiosis rapidly lowers the age signal, and after fertilization, the age signal was reset to "0" with the embryogenesis. When a seed germinates, the next generation restarts, and the age is re-counted. Altogether, these results not only provide important and novel insights into the life-cycle progression and transgeneration in perennial woody plants, but also advance our understanding of age recording.

Drought Stress Stimulates the Terpenoid Backbone and Triterpenoid Biosynthesis Pathway to Promote the Synthesis of Saikosaponin in Bupleurum chinense DC. Roots.

Bupleurum chinense is an important medicinal plant in China; however, little is known regarding how this plant transcribes and synthesizes saikosaponins under drought stress. Herein, we investigated how drought stress stimulates the transcriptional changes of B. chinense to synthesize saikosaponins. Short-term drought stress induced the accumulation of saikosaponins, especially from the first re-watering stage (RD_1 stage) to the second re-watering stage (RD_2 stage). Saikosaponin-a and saikosaponin-d increased by 84.60% and 75.13%, respectively, from the RD_1 stage to the RD_2 stage. Drought stress also stimulated a rapid increase in the levels of the hormones abscisic acid, salicylic acid, and jasmonic acid. We screened 49 Unigenes regarding the terpenoid backbone and triterpenoid biosynthesis, of which 33 differential genes were significantly up-regulated during drought stress. Moreover, one P450 and two UGTs are possibly involved in the synthesis of saikosaponins, while some transcription factors may be involved in regulating the expression of key enzyme genes. Our study provides a reference for the cultivation of B. chinense and a practical means to ensure the quality (safety and effectiveness) of B. chinense for medicinal use, as well as insights into the modernization of the China Agriculture Research System.

ARL4C might serve as a prognostic factor and a novel therapeutic target for gastric cancer: bioinformatics analyses and biological experiments.

The ADP-ribosylation factor-like proteins (ARLs) have been proved to regulate the malignant phenotypes of several cancers. However, the exact role of ARLs in gastric cancer (GC) remains elusive. In this study, we systematically investigate the expression status, interactive relations, potential pathways, genetic variations and clinical values of ARLs in GC. We find that ARLs are significantly dysregulated in GC and involved in various cancer-related pathways. Subsequently, machine learning models identify ARL4C as one of the two most significant clinical indicators among ARLs for GC. Furthermore, ARL4C silencing remarkably inhibits the growth and metastasis of GC cells both in vitro and in vivo. Moreover, enrichment analysis indicates that ARL4C is highly correlated with TGF-ß1 signalling. Correspondingly, TGF-ß1 treatment dramatically increases ARL4C expression and ARL4C knockdown inhibits the phosphorylation level of Smads, downstream factors of TGF-ß1. Meanwhile, the coexpression of ARL4C and TGF-ß1 worsens the prognosis of GC patients. Our work comprehensively demonstrates the crucial role of ARLs in the carcinogenesis of GC and the specific mechanisms underlying the GC-promoting effects of TGF-ß1. More importantly, we uncover the great promise of ARL4C-targeted therapy in improving the efficacy of TGF-ß1 inhibitors for GC patients.

Elimination of Charge Recombination Centers in Metal Halide Perovskites by Strain.

Metal halide perovskites exhibit enhanced photoluminescence and long-lived carriers in experiments under strain. Using ab initio nonadiabatic molecular dynamics, we demonstrate that compressive and tensile strain can eliminate charge recombination centers created by defect states, by shifting traps from bandgap into bands. A compressive strain enhances coupling of Pb-s and I-p orbitals, pushes the valence band (VB) up in energy, and moves the trap state due to iodine interstitial (Ii) into the VB. The strain distorts the system and breaks the I-dimer responsible for the Ii trap. A tensile strain increases Pb-Pb distance, weakens overlap of Pb-p orbitals, and pushes the conduction band (CB) down in energy. The trap state created by replacement of iodine with methylammonium (MAI) is moved into the CB. Application of strain to the defective systems not only eliminates midgap traps but also creates moderate disorder that reduces overlap of electron and hole wave functions, activates phonon modes accelerating coherence loss within the electronic subsystem, and extends carrier lifetimes even beyond those in pristine MAPbI3. Our investigation rationalizes the high performance of perovskites solar cells under strain and reveals how strain passivates Ii and MAI defects in MAPbI3, providing a new nonchemical strategy for defect control and engineering.

Genome-wide identification of cotton GRAM family proteins reveals that GRAM31 regulates fiber length.

The glucosyltransferases, Rab-like GTPase activators and myotubularins (GRAM) domain is highly conserved in eukaryotic cells and is found in proteins involved in membrane-associated processes. GRAM domain proteins have not yet been functionally characterized in cotton. In this study, we identified 164 genes encoding GRAM domain proteins in four cotton species, comprising two subfamilies. In Gossypium hirsutum, our transcriptome data showed that GhGRAM31 was predominantly expressed during the rapid elongation stage of fiber development and that it might control fiber length. GhGRAM31-RNAi transgenic cotton lines showed inhibition of fiber elongation and produced shorter mature fibers, and this was coupled with expression changes of genes related to fiber development. In addition, lint percentage and seed size were also decreased in the RNAi lines. Further examination revealed that GhGRAM31 directly interacts with two other GRAM-domain proteins, GhGRAM5 and GhGRAM35. GhGRAM5 also interacts with the transcription factor GhTTG1, while GhGRAM35 interacts with the transcription factors GhHOX1 and GhHD1. Co-expression of GhGRAM31 and GhGRAM35 was able to promote GhHD1 transcription activity in cotton protoplasts. Our results provide new insights into the biological function of the GRAM-domain protein family in cotton, and selected genes have the potential to be utilized in future programs for the genetic improvement of fibers.

Experimentally Detecting Quantized Zak Phases without Chiral Symmetry in Photonic Lattices.

Symmetries play a major role in identifying topological phases of matter and in establishing a direct connection between protected edge states and topological bulk invariants via the bulk-boundary correspondence. One-dimensional lattices are deemed to be protected by chiral symmetry, exhibiting quantized Zak phases and protected edge states, but not for all cases. Here, we experimentally realize an extended Su-Schrieffer-Heeger model with broken chiral symmetry by engineering one-dimensional zigzag photonic lattices, where the long-range hopping breaks chiral symmetry but ensures the existence of inversion symmetry. By the averaged mean displacement method, we detect topological invariants directly in the bulk through the continuous-time quantum walk of photons. Our results demonstrate that inversion symmetry protects the quantized Zak phase but edge states can disappear in the topological nontrivial phase, thus breaking the conventional bulk-boundary correspondence. Our photonic lattice provides a useful platform to study the interplay among topological phases, symmetries, and the bulk-boundary correspondence.

Symmetry-Induced Error Filtering in a Photonic Lieb Lattice.

Quantum computation promises intrinsically parallel information processing capacity by harnessing the superposition and entanglement of quantum states. However, it is still challenging to realize universal quantum computation due that the reliability and scalability are limited by unavoidable noises on qubits. Nontrivial topological properties like quantum Hall phases are found capable of offering protection, but require stringent conditions of topological band gaps and broken time-reversal symmetry. Here, we propose and experimentally demonstrate a symmetry-induced error filtering scheme, showing a more general role of geometry in protection mechanism and applications. We encode qubits in a superposition of two spatial modes on a photonic Lieb lattice. The geometric symmetry endows the system with topological properties featuring a flat band touching, leading to distinctive transmission behaviors of π-phase qubits and 0-phase qubits. The geometry exhibits a significant effect on filtering phase errors, which also enables it to monitor phase deviations in real time. The symmetry-induced error filtering can be a key element for encoding and protecting quantum states, suggesting an emerging field of symmetry-protected universal quantum computation and noisy intermediate-scale quantum technologies.

Autophagic Flux Detection: Significance and Methods Involved.

Macroautophagy is an important biological process in eukaryotic cells by which longevity proteins, misfolded proteins, and damaged organelles are degraded. The autophagy process consists of three key steps: (1) the formation of autophagosomes; (2) the fusion of the autophagosomes with lysosomes; and (3) the degradation of the contents of autolysosomes. If any of the three steps is impaired, autophagy will not be able to complete its biological function. Dysfunctional or blocked autophagy is closely involved in the pathogenesis of a variety of diseases. The accurate determination of the autophagy activity in vivo and in vitro has become a challenge in the field of autophagy research. At present, the most widely used detection method to determine autophagy activity in mammalian cells is to quantify LC3B in the cells by Western blot, or to observe the formation and changes of autophagosomes and autolysosomes by immunofluorescence and electron microscopy. However, ignoring the dynamic characteristics of autophagy and only evaluating the number of autophagosomes or the presence of LC3B cannot completely reflect the activation or a blockage of the autophagy system, and objectively analyze its real role in the occurrence and development of a disease. For example, the accumulation of autophagosomes and autolysosomes can occur through an increase in substrate to be degraded after the activation of autophagy, or it may be caused by the partial obstruction or blockage of autophagy. In this chapter, new and familiar ways to detect the autophagic flux are methodically summarized to provide researchers with a multi-angled viewpoint.

Constitutive Oxidative Stress by SEPHS1 Deficiency Induces Endothelial Cell Dysfunction.

The primary function of selenophosphate synthetase (SEPHS) is to catalyze the synthesis of selenophosphate that serves as a selenium donor during selenocysteine synthesis. In eukaryotes, there are two isoforms of SEPHS (SEPHS1 and SEPHS2). Between these two isoforms, only SEPHS2 is known to contain selenophosphate synthesis activity. To examine the function of SEPHS1 in endothelial cells, we introduced targeted null mutations to the gene for SEPHS1, Sephs1, in cultured mouse 2H11 endothelial cells. SEPHS1 deficiency in 2H11 cells resulted in the accumulation of superoxide and lipid peroxide, and reduction in nitric oxide. Superoxide accumulation in Sephs1-knockout 2H11 cells is due to the induction of xanthine oxidase and NADPH oxidase activity, and due to the decrease in superoxide dismutase 1 (SOD1) and 3 (SOD3). Superoxide accumulation in 2H11 cells also led to the inhibition of cell proliferation and angiogenic tube formation. Sephs1-knockout cells were arrested at G2/M phase and showed increased gamma H2AX foci. Angiogenic dysfunction in Sephs1-knockout cells is mediated by a reduction in nitric oxide and an increase in ROS. This study shows for the first time that superoxide was accumulated by SEPHS1 deficiency, leading to cell dysfunction through DNA damage and inhibition of cell proliferation.

Identification of Signaling Pathways for Early Embryonic Lethality and Developmental Retardation in Sephs1-/- Mice.

Selenophosphate synthetase 1 (SEPHS1) plays an essential role in cell growth and survival. However, the underlying molecular mechanisms remain unclear. In the present study, the pathways regulated by SEPHS1 during gastrulation were determined by bioinformatical analyses and experimental verification using systemic knockout mice targeting Sephs1. We found that the coagulation system and retinoic acid signaling were most highly affected by SEPHS1 deficiency throughout gastrulation. Gene expression patterns of altered embryo morphogenesis and inhibition of Wnt signaling were predicted with high probability at E6.5. These predictions were verified by structural abnormalities in the dermal layer of Sephs1-/- embryos. At E7.5, organogenesis and activation of prolactin signaling were predicted to be affected by Sephs1 knockout. Delay of head fold formation was observed in the Sephs1-/- embryos. At E8.5, gene expression associated with organ development and insulin-like growth hormone signaling that regulates organ growth during development was altered. Consistent with these observations, various morphological abnormalities of organs and axial rotation failure were observed. We also found that the gene sets related to redox homeostasis and apoptosis were gradually enriched in a time-dependent manner until E8.5. However, DNA damage and apoptosis markers were detected only when the Sephs1-/- embryos aged to E9.5. Our results suggest that SEPHS1 deficiency causes a gradual increase of oxidative stress which changes signaling pathways during gastrulation, and afterwards leads to apoptosis.

Likely damaging de novo variants in congenital diaphragmatic hernia patients are associated with worse clinical outcomes.

PURPOSE: Congenital diaphragmatic hernia (CDH) is associated with significant mortality and long-term morbidity in some but not all individuals. We hypothesize monogenic factors that cause CDH are likely to have pleiotropic effects and be associated with worse clinical outcomes. METHODS: We enrolled and prospectively followed 647 newborns with CDH and performed genomic sequencing on 462 trios to identify de novo variants. We grouped cases into those with and without likely damaging (LD) variants and systematically assessed CDH clinical outcomes between the genetic groups. RESULTS: Complex cases with additional congenital anomalies had higher mortality than isolated cases (P = 8 × 10-6). Isolated cases with LD variants had similar mortality to complex cases and much higher mortality than isolated cases without LD (P = 3 × 10-3). The trend was similar with pulmonary hypertension at 1 month. Cases with LD variants had an estimated 12-17 points lower scores on neurodevelopmental assessments at 2 years compared with cases without LD variants, and this difference is similar in isolated and complex cases. CONCLUSION: We found that the LD genetic variants are associated with higher mortality, worse pulmonary hypertension, and worse neurodevelopment outcomes compared with non-LD variants. Our results have important implications for prognosis, potential intervention and long-term follow up for children with CDH.