ZSWIM4 regulates embryonic patterning and BMP signaling by promoting nuclear Smad1 degradation.

The dorsoventral gradient of BMP signaling plays an essential role in embryonic patterning. Zinc Finger SWIM-Type Containing 4 (zswim4) is expressed in the Spemann-Mangold organizer at the onset of Xenopus gastrulation and is then enriched in the developing neuroectoderm at the mid-gastrula stages. Knockdown or knockout of zswim4 causes ventralization. Overexpression of zswim4 decreases, whereas knockdown of zswim4 increases the expression levels of ventrolateral mesoderm marker genes. Mechanistically, ZSWIM4 attenuates the BMP signal by reducing the protein stability of SMAD1 in the nucleus. Stable isotope labeling by amino acids in cell culture (SILAC) identifies Elongin B (ELOB) and Elongin C (ELOC) as the interaction partners of ZSWIM4. Accordingly, ZSWIM4 forms a complex with the Cul2-RING ubiquitin ligase and ELOB and ELOC, promoting the ubiquitination and degradation of SMAD1 in the nucleus. Our study identifies a novel mechanism that restricts BMP signaling in the nucleus.

The A2c111nt-dup variants of human metapneumovirus predominantly circulating in Qingdao, China, during 2018 and 2019.

Human metapneumovirus (HMPV) plays an important role in acute respiratory tract infections (ARTIs), especially in children. We investigated the epidemiology of HMPV associated with ARTIs among pediatric inpatients and identified HMPV genetic variations in Qingdao, China, from January 2018 to June 2019. HMPV-positive samples were identified from throat swabs by multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR). The G gene sequences of HMPV were obtained, followed by phylogenetic analysis. As a result, 71 out of 1051 (6.76%) patients were HMPV positive, and the HMPV-positive rate in children under 5 years of age was three times higher than that in those aged 5-17 years. The epidemic season of HMPV was in spring, with a peak mainly in March. Thirty-two nucleotide sequences of the HMPV G gene successfully obtained were clustered into three genotypes, A2c (25/32, 78.13%), B1 (3/32, 9.38%) and B2 (4/32, 12.50%). In addition, 76% (19/25) of A2c viruses were identified as the emerging A2c111nt-dup variants, which were predominantly circulating among pediatric inpatients with ARTIs between January 2018 and June 2019 in Qingdao. The emerging A2c111nt-dup variants have spread between countries and cities and might spread more widely in the future. Further prevalence monitoring of this duplication variant is needed to clarify the potentially expanding transmission and to provide a scientific basis for disease control and vaccine development.

Ultrathin multi-band coherent perfect absorber in graphene with high-contrast gratings.

High-contrast gratings (HCGs) can be designed as a resonator with high-quality factor and surface-normal emission, which are excellent characters for designing optical devices. In this work, we combine HCGs with plasmonic graphene structure to achieve an ultrathin five-band coherent perfect absorber (CPA). The presented CPA can achieve multi- and narrow-band absorption with high intensity under a relatively large incident angle. The good agreement between theoretical analysis and numerical simulated results demonstrates that our proposed HCGs-based structure is feasible to realize CPA. Besides, by dynamically adjusting the Fermi energy of graphene, we realize the active tunability of resonance frequency and absorption intensity simultaneously. Benefitting from the combination of HCGs and the one-atom thickness of graphene, the proposed device possesses an extremely thin feature. Our work proposes a novel method to manipulate coherent perfect absorption and is helpful to design tunable multi-band and ultrathin absorbers.

Measurement of the Acoustic Non-Linearity Parameter of Materials by Exciting Reversed-Phase Rayleigh Waves in Opposite Directions.

The acoustic non-linearity parameter of Rayleigh waves can be used to detect various defects (such as dislocation and micro-cracks) on material surfaces of thick-plate structures; however, it is generally low and likely to be masked by noise. Moreover, conventional methods used with non-linear Rayleigh waves exhibit a low detection efficiency. To tackle these problems, a method of exciting reversed-phase Rayleigh waves in opposite directions is proposed to measure the acoustic non-linearity parameter of materials. For that, two angle beam wedge transducers were placed at the two ends of the upper surface of a specimen to excite two Rayleigh waves of opposite phases, while a normal transducer was installed in the middle of the upper surface to receive them. By taking specimens of 0Cr17Ni4Cu4Nb martensitic stainless steel subjected to fatigue damage as an example, a finite element simulation model was established to test the proposed method of measuring the acoustic non-linearity parameter. The simulation results show that the amplitude of fundamentals is significantly reduced due to offset, while that of second harmonics greatly increases due to superposition because of the opposite phases of the excited signals, and the acoustic non-linearity parameter thus increases. The experimental research on fatigue damage specimens was carried out using this method. The test result was consistent with the simulation result. Thus, the method of exciting reversed-phase Rayleigh waves in opposite directions can remarkably increase the acoustic non-linearity parameter. Additionally, synchronous excitation with double-angle beam wedge transducers can double the detection efficiency.

Bidirectional and dynamically tunable THz absorber with Dirac semimetal.

Traditional absorbers are usually sandwich structures in which a metallic ground plane is employed to prevent the transmission. Such absorbers suffer from a major drawback that incident light can only irradiate from the front of the absorbers. In this paper, a novel absorber with bulk Dirac semimetal (BDS)-AlCuFe quasicrystals is proposed to realize bidirectional and dynamically tunable terahertz (THz) perfect absorption. The proposed structure consists of two layers of AlCuFe plates with rectangular apertures and a dielectric spacer. By adjusting transverse distance between the top and bottom rectangular apertures, perfect absorption could be realized under TM polarization. Simulation results show that perfect absorption can be obtained whether light irradiates from the front or back of the system, indicating a performance of bidirectional absorption. In addition, benefiting from the variable Fermi level of AlCuFe, the resonance frequency can be dynamically tuned in the THz range. Our work will stimulate more investigations on BDS-based bidirectional absorbers and optical modulators.

A sclerocornea-associated RAD21 variant induces corneal stroma disorganization.

Sclerocornea is a cornea opacification disorder. Disorganized corneal stroma fibrils are observed in patients' cornea. Previously we identified a RAD21C1348T variant that is associated with a peripheral sclerocornea pedigree. To explore whether this RAD21 variant can induce sclerocornea-related phenotype, and to investigate the possible mechanisms of such phenotype, the orthologous rad21 wild-type and variant mRNAs were injected into Xenopus laevis embryos and the developed eyes were subjected for histological examination. Transmission electron microscopy was applied for corneal stroma organization check. rad21 is highly expressed in the eye region during X. laevis development. Disrupted eye development was observed in the rad21 variant injected embryos. Disorganized corneal stroma and decreased diameters of collagen fibrils were observed in the rad21 variant injected X. laevis eyes. These eye defects can be rescued by overexpression of the wild-type rad21. Histological examination found stroma attracting center, a key structure in X. laevis corneal development, was impaired in rad21 variant injected embryos. Our results suggest a key role of RAD21 during corneal development. Our data indicates the RAD21R450C variant contributes to peripheral sclerocornea by disturbing collagen fibril organization in the corneal stroma.

Orexins increase the firing activity of nigral dopaminergic neurons and participate in motor control in rats.

Orexin is a member of neuropeptides which is involved in the central motor control. The substantia nigra pars compacta (SNc) is an important nucleus participating in motor control under both physiological and pathological conditions. Morphological studies reveal that orexinergic neurons located in lateral hypothalamus innervate the SNc. Both orexin-1 receptors (OX1 R) and orexin-2 receptors (OX2 R) are expressed in the SNc. To investigate the effects of orexins on SNc, single unit in vivo extracellular recordings and behavioral tests were performed in this study. Micro-pressure administration of orexin A and orexin B significantly increased the spontaneous firing rate of nigral DAergic neurons by 65.87 ± 7.73% and 90.49 ± 17.83%, respectively. The excitatory effects of orexin A on nigral DAergic neurons were mainly mediated by OX1 R, while OX2 R were involved in the increase in firing rate induced by orexin B. Selectively blocking OX1 R and OX2 R significantly decreased the firing rate of nigral DAergic neurons by 36.77 ± 6.26% and 32.04 ± 6.12%, respectively, which suggested that endogenous orexins modulated the spontaneous firing activity of nigral DAergic neurons. Finally, both elevated body swing test and haloperidol-induced postural behavioral test showed that unilateral microinjection of orexin A and orexin B induced significantly contralateral-biased swing and deflection behavior. Meanwhile, the specific OX1 R and OX2 R antagonists produced opposite effects. The present electrophysiological and behavioral studies suggested that orexins increased the firing activity of nigral DAergic neurons and participated in central motor control. Open Practices Open Science: This manuscript was awarded with the Open Materials Badge. For more information see: https://cos.io/our-services/open-science-badges/.

Hybridization induced metallic and magnetic edge states in noble transition-metal-dichalcogenides of PtX2 (X = S, Se) nanoribbons.

The semiconducting transition metal dichalcogenide (TMD) 2H-MoS2 zigzag nanoribbon has two different edges, and only one edge shows metallic properties due to symmetric protection. In the present work, a nanoribbon with two parallel metallic and magnetic edges was designed from a noble TMD 1T-PtX2 (X = S, Se) by employing first-principles calculations based on density functional theory (DFT). The band structure, density of states (DOS), and simulated scanning tunneling microscopy (STM) of three possible zigzag edge states of monolayer semiconducting PtX2 were systematically studied. Detailed calculations showed that the Pt-terminated edge state among the three zigzag edge states was metallic. The Pt-terminated edge state designed from monolayer PtS2 showed both metallic and magnetic properties. These metallic and magnetic properties were mainly contributed to by the hybridization of the 5d orbitals of Pt atoms and the 3p orbitals of S atoms located at the edges. However, hybridization of the 5d orbitals of Pt atoms and the 4p orbitals of Se atoms located at the edges does not bring magnetic properties to the zigzag metallic PtSe2 nanoribbon. The interesting electronic and magnetic properties of 1T-PtX2 nanoribbons indicate that they may have promising applications as zigzag nanoribbons in spin electronics and photovoltaic cells.

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels regulate firing of globus pallidus neurons in vivo.

The globus pallidus plays a significant role in motor control under both health and pathological states. Recent studies have revealed that hyperpolarization-activated cyclic nucleotide-gated (HCN) channels occupy a critical position in globus pallidus pacemaking activity. Morphological studies have shown the expression of HCN channels in the globus pallidus. To investigate the in vivo effects of HCN channels in the globus pallidus, extracellular recordings and behavioral tests were performed in the present study. In normal rats, micro-pressure ejection of 0.05mM ZD7288, the selective HCN channel blocker, decreased the frequency of spontaneous firing in 21 out of the 40 pallidal neurons. The average decrease was 50.4±5.4%. Interestingly, in another 18 out of the 40 pallidal neurons, ZD7288 increased the firing rate by 137.1±27.6%. Similar bidirectional modulation on the firing rate was observed by a higher concentration of ZD7288 (0.5mM) as well as another HCN channel blocker, CsCl. Furthermore, activation of HCN channels by 8-Br-cAMP increased the firing rate by 63.0±9.3% in 15 out of the 25 pallidal neurons and decreased the firing rate by 46.9±9.4% in another 8 out of the 25 pallidal neurons. Further experiments revealed that modulation of glutamatergic but not GABAergic transmission may be involved in ZD7288-induced increase in firing rate. Consistent with electrophysiological results, further studies revealed that modulation of HCN channels also had bidirectional effects on behavior. Taken together, the present studies suggest that HCN channels may modulate the activity of pallidal neurons by different pathways in vivo.

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice.

The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

Excited-State Dynamics in All-Polymer Blends with Polymerized Small-Molecule Acceptors.

Polymerizing small-molecular acceptors (SMAs) is a promising route to construct high performance polymer acceptors of all-polymer solar cells (all-PSCs). After SMA polymerization, the microstructure of molecular packing is largely modified, which is essential in regulating the excited-state dynamics during the photon-to-current conversion. Nevertheless, the relationship between the molecular packing and excited-state dynamics in polymerized SMAs (PSMAs) remains poorly understood. Herein, the excited-state dynamics and molecular packing are investigated in the corresponding PSMA and SMA utilizing a combination of experimental and theoretical methods. This study finds that the charge separation from intra-moiety delocalized states (i-DEs) is much faster in blends with PSMAs, but the loosed π-π molecular packing suppresses the excitation conversion from the local excitation (LE) to the i-DE, leading to additional radiative losses from LEs. Moreover, the increased aggregations of PSMA in the blends decrease donor: acceptor interfaces, which reduces triplet losses from the bimolecular charge recombination. These findings suggest that excited-state dynamics may be manipulated by the molecular packing in blends with PSMAs to further optimize the performance of all-PSCs.

Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes.

The biological function of the novel zinc-finger SWIM domain-containing protein family (ZSWIM) during embryonic development remains elusive. Here, we conducted a genome-wide analysis to explore the evolutionary processes of the ZSWIM gene family members in mice, Xenopus tropicalis, zebrafish, and humans. We identified nine putative ZSWIM genes in the human and mouse genome, eight in the Xenopus genome, and five in the zebrafish genome. Based on multiple sequence alignment, three members, ZSWIM5, ZSWIM6, and ZSWIM8, demonstrated the highest homology across all four species. Using available RNA sequencing (RNA-seq) data, ZSWIM genes were found to be widely expressed across different tissues, with distinct tissue-specific properties. To identify the functions of the ZSWIM protein family during embryogenesis, we examined temporal and spatial expression patterns of zswim family genes in Xenopus embryos. Quantitative real-time polymerase chain reaction (qRT-PCR) revealed that each member had a distinct expression profile. Whole-mount in situ hybridization showed that both zswim1 and zswim3 were maternally expressed genes; zswim5 and zswim6 were expressed throughout embryogenesis and displayed dynamic expression in the brain, eyes, somite, and bronchial arch at the late tailbud stages; zswim7 was detected in the eye area; zswim8 showed a dynamic expression pattern during the tailbud stages, with expression detected in the brain, eyes, and somite; zswim9 was faintly expressed throughout embryonic development. This study provides a foundation for future research to delineate the functions of ZSWIM gene members.

Intersystem Crossing in Acceptor-Donor-Acceptor Type Organic Photovoltaic Molecules Promoted by Symmetry Breaking in Polar Environments.

The intramolecular electron push-pulling effect has been widely applied to manipulate the excited states in organic photovoltaic (OPV) molecules toward efficient photocurrent generation in working devices with bias fields. However, the effect of field induced polar environments on the excited-state dynamics remains largely unexplored. Here, we investigate the polar environment effect on excited dynamics in acceptor-donor-acceptor type OPV molecules dissolved in solvents with different polarities. By combining ultrafast transient absorption spectroscopy and quantum chemical computation, we observe the stabilization of excited states induced by symmetry breaking in the polar solvent in the molecules exhibiting strong electron push-pulling effects. The stabilized excited states undergo faster intersystem crossing processes with reduced singlet-triplet energy gaps. The findings suggest that the dynamics of charge generation and recombination may be controlled by manipulating the polar environment and electron push-pulling effect to improve the device performance.

Epidemiologic and clinical characteristics of human bocavirus infection in children hospitalized for acute respiratory tract infection in Qingdao, China.

Persistent infection and prolonged shedding of human bocavirus 1 (HBoV1) in children have been reported, and the role of HBoV1 as a sole causative pathogen in acute respiratory infection (ARI) is yet to be established. While the reported prevalence of HBoV infection varies due to different detection methods and sampling criteria, determining the viral and bacterial etiology of HBoV infection using multiplex real-time PCR is yet to be reported. Herein, we aimed to further explore the pathogenicity of HBoV in patients with ARI by screening the viral and bacterial infections in children with ARI in Qingdao and comparing the epidemiological, clinical characteristics, and etiological results. Human bocavirus was identified in 28.1% of the samples, and further sequencing analysis of the detected HBoV confirmed 96.4% as HBoV1. The rate of HBoV as a single viral infection was 75%, and the rate of coinfection with bacteria was 66.1%, suggesting the need for continued monitoring of HBoV in children with ARIs. Clinical characterization suggested that HBoV infection may affect the function of organs, such as the liver, kidney, and heart, and the blood acid-base balance. Additionally, it is essential to promote awareness about the importance of disinfection and sterilization of the hospital environment and standardizing operations. The interactions between HBoV and other pathogens remain to be investigated in further detail in the future.

Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops.

Common weedy rice plants are important genetic resources for modern breeding programs because they are the closest relatives to rice cultivars and their genomes contain elite genes. Determining the utility and copy numbers of WRKY and nucleotide-binding site (NBS) resistance-related genes may help to clarify their variation patterns and lead to crop improvements. In this study, the weedy rice line LM8 was examined at the whole-genome level. To identify the Oryza sativa japonica subpopulation that LM8 belongs to, the single nucleotide polymorphisms (SNPs) of 180 cultivated and 23 weedy rice varieties were used to construct a phylogenetic tree and a principal component analysis and STRUCTURE analysis were performed. The results indicated that LM8 with admixture components from japonica (GJ) and indica (XI) belonged to GJ-admixture (GJ-adm), with more than 60% of its genetic background derived from XI-2 (22.98%), GJ-tropical (22.86%), and GJ-subtropical (17.76%). Less than 9% of its genetic background was introgressed from weedy rice. Our results also suggested LM8 may have originated in a subtropical or tropical geographic region. Moreover, the comparisons with Nipponbare (NIP) and Shuhui498 (R498) revealed many specific structure variations (SVs) in the LM8 genome and fewer SVs between LM8 and NIP than between LM8 and R498. Next, 96 WRKY and 464 NBS genes were identified and mapped on LM8 chromosomes to eliminate redundancies. Three WRKY genes (ORUFILM02g002693, ORUFILM05g002725, and ORUFILM05g001757) in group III and one RNL [including the resistance to powdery mildew 8 (RPW8) domain, NBS, and leucine rich repeats (LRRs)] type NBS gene (ORUFILM12g000772) were detected in LM8. Among the NBS genes, the RPW8 domain was detected only in ORUFILM12g000772. This gene may improve plant resistance to pathogens as previously reported. Its classification and potential utility imply LM8 should be considered as a germplasm resource relevant for rice breeding programs.

LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants.

LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations, lncRNA-phenotype correlations, and the similar non-coding regions of the queried sequence in multiple species. LncPheDB sorted out a total of 203,391 lncRNA sequences, 2000 phenotypes, and 120,271 variants of nine species (Zea mays L., Gossypium barbadense L., Triticum aestivum L., Lycopersicon esculentum Mille, Oryza sativa L., Hordeum vulgare L., Sorghum bicolor L., Glycine max L., and Cucumis sativus L.). By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis, a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits. More importantly, to facilitate the study of the functions of lncRNAs, we analyzed the possible target genes of lncRNAs, constructed a blast tool for performing similar fragmentation studies in all species, linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-modal convenient data search engine. We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-022-00084-3.

Genomic Analysis Provides Insights Into the Plant Architecture Variations in in situ Conserved Chinese Wild Rice (Oryza rufipogon Griff.).

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains.

The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl a/b cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F2 generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F2 populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl a/b cycle-related structural gene DVR (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl a/b-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the CTR (encoding an ethylene-responsive protein kinase) and ERF (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp.

Genome-wide selection and introgression of Chinese rice varieties during breeding.

China is the largest rice-producing country, but the genomic landscape of rice diversity has not yet been clarified. In this study, we re-sequence 1070 rice varieties collected from China (400) and other regions in Asia (670). Among the six major rice groups (aus, indica-I, indica-II, aromatic, temperate japonica, and tropical japonica), almost all Chinese varieties belong to the indica-II or temperate japonica group. Most Chinese indica varieties belong to indica-II, which consists of two subgroups developed during different phases of rice breeding. The genomic segments underlying the differences between these subgroups span 36.32 Mb. The Chinese japonica rice varieties fall into the temperate japonica group, consisting of two subgroups based on their geographical distribution. The genomic segments underlying the differences between these subgroups span 27.69 Mb. These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width. Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups. These findings provide new insights into rice diversity in China that will facilitate the molecular breeding.