Soil ecosystems harbor the most complex prokaryotic and eukaryotic microbial communities on Earth. Experimental approaches studying these systems usually focus on either the soil community's taxonomic structure or its functional characteristics. Many methods target DNA as marker molecule and use PCR for amplification.

Histone methylation and demethylation play important roles in plant growth and development, but the involvement of histone demethylation during meiosis is poorly understood. Here we show that disruption of Arabidopsis thaliana INCREASE IN BONSAI METHYLATION 1 (IBM1) causes incomplete synapsis, chromosome entanglement and reduction of recombination during meiosis, leading to sterility. Interestingly, these ibm1 meiotic defects are rescued by mutations in either SUVH4/KYP or CMT3. Using transcriptomic analyses we show that mutation of IBM1 down-regulates thousands of genes expressed in meiocytes, and that expression of about 38% of these genes are restored to wild type levels in ibm1 cmt3 double mutants. Changes in the expression of 437 of these, including the ARABIDOPSIS MEI2-LIKE AML3-5 genes, are correlated with a significant reduction of gene body CHG methylation. Consistently, the aml3 aml4 aml5 triple have defects in synapsis and chromosome entanglement similar to ibm1. Genetic analysis shows that aml3 aml4 aml5 ibm1 quadruple mutants resembles the ibm1 single mutant. Strikingly, over expression of AML5 in ibm1 can partially rescue the ibm1 meiotic defects. Taken together, our results demonstrate that histone demethylase IBM1 is required for meiosis likely via coordinated regulation of meiocyte gene expression during meiosis.

The solvation shell structures of Ca2+ in aqueous and organic solutions probed by calcium L-edge soft X-ray absorption spectroscopy (XAS) and DFT/MD simulations show the coordination number of Ca2+ to be negatively correlated with the electrolyte concentration and the steric hindrance of the solvent molecule. In this work, the calcium L-edge soft XAS demonstrates its sensitivity to the surrounding chemical environment. Additionally, the total electron yield (TEY) mode is surface sensitive because the electron penetration depth is limited to a few nanometers. Thus this study shows its implications for future battery studies, especially for probing the electrolyte/electrode interface for electrochemical reactions under in situ/operando conditions.

The spread of Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), resulting in a global pandemic with around four million deaths. Although there are a variety of nucleic acid-based tests for detecting SARS-CoV-2, these methods have a relatively high cost and require expensive supporting equipment. To overcome these limitations and improve the efficiency of SARS-CoV-2 diagnosis, we developed a microfluidic platform that collected serum by a pulling-force spinning top and paper-based microfluidic enzyme-linked immunosorbent assay (ELISA) for quantitative IgA/IgM/IgG measurements in an instrument-free way. We further validated the paper-based microfluidic ELISA analysis of SARS-CoV-2 receptor-binding domain (RBD)-specific IgA/IgM/IgG antibodies from human blood samples as a good measurement with higher sensitivity compared with traditional IgM/IgG detection (99.7% vs 95.6%) for early illness onset patients. In conclusion, we provide an alternative solution for the diagnosis of SARS-CoV-2 in a portable manner by this smart integration of pulling-force spinning top and paper-based microfluidic immunoassay.

The local structure of a transition metal (TM) ion is a function of cation elements and valence states. More than that, in this work, by employing a trove of first-principles data of TM oxides, the local structures of TM cations are statistically analyzed to extract detailed information about cation site preference, bond length, site structural distortion, and cation magnetization. It is found that cation radius alone poorly describes the local structure of a transition metal oxide, while the statistics of coordination number as well as the TMO bond length distribution, especially that of the 3d TMs, can provide comprehensive knowledge for understanding the behavior of TM elements. Based on these statistics, the interplay of site distortion due to the Jahn-Teller effect, cation site similarity, and a new set of ionic radii are all obtained to chart the "persona" of transition metal ions in solids.

Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.

In this study, a novel polysaccharide (SPN) was extracted by high-temperature pressure method and purified by a DEAE-52 column and a Sephadx G-100 gel column. PPN was obtained after phosphorylation of SPN. The differences of structural features, antioxidant activity, and anti-inflammatory effect of the two polysaccharides were investigated by chemical methods and RAW 264.7 cell model. SPN (Mw = 15.8 kDa) and PPN (Mw = 27.7 kDa) are an acidic polysaccharide with β-pyranose configuration, mainly containing rhamnose, mannose, glucose, arabinose, and galacose. FI-IR, NMR, and SEM spectra showed phosphorylation of SPN changed its structure. In methylation analysis, the major chains of SPN and PPN were 1,4-linked Glcp, 1,6-linked Galp, 1,2-linked Rhap, and 1.6-linked Manp with terminals of t-linked Glcp, t-linked Araf. The side chain of SPN was 1,4,6-linked Galp, 1,2,5-linked Araf, while the side chain of PPN was 1,4,6-linked Galp, 1,2,4-linked Glcp. In antioxidant activity experiments, the free radical scavenging rate of PPN was stronger than that of SPN. Also, PPN always has better anti-inflammatory on RAW 264.7 cells induced by LPS than that of SPN in same concentration, and it plays an anti-inflammatory role by inhibiting PI3K/AKT/mTOR pathway. The results indicated polysaccharide could significantly improve its antioxidant and anti-inflammatory function after phosphorylation. This study provides a potentially antioxidant and anti-inflammatory health food and drug.

Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about 10% of angiosperm species, is thus undoubtedly one of the most successful lineages and paleopolyploidization was suggested early in this family using a small number of datasets. Here, we used genes from 64 new transcriptome datasets and others to reconstruct a robust Asteraceae phylogeny, covering 73 species from 18 tribes in six subfamilies. We estimated their divergence times and further identified multiple potential ancient WGDs within several tribes and shared by the Heliantheae alliance, core Asteraceae (Asteroideae-Mutisioideae), and also with the sister family Calyceraceae. For two of the WGD events, there were subsequent great increases in biodiversity; the older one proceeded the divergence of at least 10 subfamilies within 10 My, with great variation in morphology and physiology, whereas the other was followed by extremely high species richness in the Heliantheae alliance clade. Our results provide different evidence for several WGDs in Asteraceae and reveal distinct association among WGD events, dramatic changes in environment and species radiations, providing a possible scenario for polyploids to overcome the disadvantages of WGDs and to evolve into lineages with high biodiversity.

Kluyveromyces marxianus is a promising host for producing bioethanol and heterologous proteins. It displays many superior traits to a conventional industrial yeast species, Saccharomyces cerevisiae, including fast growth, thermotolerance and the capacity to assimilate a wider variety of sugars. However, little is known about the mechanisms underlying the fast-growing feature of K. marxianus. In this study, we performed a comparative genomic analysis between K. marxianus and other Saccharomycetaceae species. Genes involved in flocculation, iron transport, and biotin biosynthesis have particularly high copies in K. marxianus. In addition, 60 K. marxianus specific genes were identified, 45% of which were upregulated during cultivation in rich medium and these genes may participate in glucose transport and mitochondrion related functions. Furthermore, the transcriptomic analysis revealed that under aerobic condition, normalized levels of genes participating in TCA cycles, respiration chain and ATP biosynthesis in the lag phase were higher in K. marxianus than those in S. cerevisiae. Levels of highly copied genes, genes involved in the respiratory chain and mitochondrion assembly, were upregulated in K. marxianus, but not in S. cerevisiae, in later time points during cultivation compared with those in the lag phase. Notably, during the fast-growing phase, genes involved in the respiratory chain, ATP synthesis and glucose transport were co-upregulated in K. marxianus. A few shared motifs in upstream sequences of relevant genes might result in the co-upregulation. Specific features in the co-regulations of gene expressions might contribute to the fast-growing phenotype of K. marxianus. Our study underscores the importance of genome-wide rewiring of the transcriptional network during evolution.

The anterior cruciate ligament (ACL) is an important structure maintaining stability of the knee joints. Deficits in physical stability and the proprioceptive capabilities of the knee joints are observed, when the ACL is damaged. Additionally, a unilateral ACL injury can affect bilateral knee proprioception; therefore, proprioception of the ACL may play a key role in stability. Electroacupuncture therapy has a definite effect nerve regeneration. In this study, cynomolgus monkeys were randomly divided into 4 groups: the model control group, intervention of the injured knee with electroacupuncture (IIKE) group, intervention of the bilateral knees with electroacupuncture (IBKE) group, and the blank control group. The unilateral ACL injury model was developed in IIKE and IBKE groups; acupuncture points around the knees underwent intervention similarly in the IIKE and IBKE groups. Then, mRNA and protein expressions of NT-3 and TrkC in the dorsal root ganglion and of growth-associated protein-43 in the ACL increased according to reverse-transcription quantitative polymerase chain reaction and Western blotting results. Decreased incubations and increased amplitudes were found for somatosensory-evoked potentials and motor nerve conduction velocity. The finding indicates that electroacupuncture may play an important role in the recovery of proprioception in the ACL by activating the NT-3/TrkC signalling pathway.

Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene duplication events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.

Despite the importance of studying the instability of delithiated cathode materials, it remains difficult to underpin the degradation mechanism of lithium-rich cathode materials due to the complication of combined chemical and structural evolutions. Herein, we use state-of-the-art electron microscopy tools, in conjunction with synchrotron X-ray techniques and first-principle calculations to study a 4d-element-containing compound, Li2Ru0.5Mn0.5O3. We find surprisingly, after cycling, ruthenium segregates out as metallic nanoclusters on the reconstructed surface. Our calculations show that the unexpected ruthenium metal segregation is due to its thermodynamic insolubility in the oxygen deprived surface. This insolubility can disrupt the reconstructed surface, which explains the formation of a porous structure in this material. This work reveals the importance of studying the thermodynamic stability of the reconstructed film on the cathode materials and offers a theoretical guidance for choosing manganese substituting elements in lithium-rich as well as stoichiometric layer-layer compounds for stabilizing the cathode surface.

Rechargeable solid-state sodium-ion batteries (SSSBs) hold great promise for safer and more energy-dense energy storage. However, the poor electrochemical stability between current sulfide-based solid electrolytes and high-voltage oxide cathodes has limited their long-term cycling performance and practicality. Here, we report the discovery of the ion conductor Na3-xY1-xZrxCl6 (NYZC) that is both electrochemically stable (up to 3.8 V vs. Na/Na+) and chemically compatible with oxide cathodes. Its high ionic conductivity of 6.6 × 10-5 S cm-1 at ambient temperature, several orders of magnitude higher than oxide coatings, is attributed to abundant Na vacancies and cooperative MCl6 rotation, resulting in an extremely low interfacial impedance. A SSSB comprising a NaCrO2 + NYZC composite cathode, Na3PS4 electrolyte, and Na-Sn anode exhibits an exceptional first-cycle Coulombic efficiency of 97.1% at room temperature and can cycle over 1000 cycles with 89.3% capacity retention at 40 °C. These findings highlight the immense potential of halides for SSSB applications.

A solid with larger sound speeds usually exhibits higher lattice thermal conductivity. Here, we report an exception that CuP2 has a quite large mean sound speed of 4155 m s-1, comparable to GaAs, but single crystals show very low lattice thermal conductivity of about 4 W m-1 K-1 at room temperature, one order of magnitude smaller than GaAs. To understand such a puzzling thermal transport behavior, we have thoroughly investigated the atomic structures and lattice dynamics by combining neutron scattering techniques with first-principles simulations. This compound crystallizes in a layered structure where Cu atoms forming dimers are sandwiched in between P atomic networks. In this work, we reveal that Cu atomic dimers vibrate as a rattling mode with frequency around 11 meV, which is manifested to be remarkably anharmonic and strongly scatters acoustic phonons to achieve the low lattice thermal conductivity.

Cohesin, a multisubunit protein complex, is required for holding sister chromatids together during mitosis and meiosis. The recruitment of cohesin by the sister chromatid cohesion 2/4 (SCC2/4) complex has been extensively studied in Saccharomyces cerevisiae mitosis, but its role in mitosis and meiosis remains poorly understood in multicellular organisms, because complete loss-of-function of either gene causes embryonic lethality. Here, we identified a weak allele of Atscc2 (Atscc2-5) that has only minor defects in vegetative development but exhibits a significant reduction in fertility. Cytological analyses of Atscc2-5 reveal multiple meiotic phenotypes including defects in chromosomal axis formation, meiosis-specific cohesin loading, homolog pairing and synapsis, and AtSPO11-1-dependent double strand break repair. Surprisingly, even though AtSCC2 interacts with AtSCC4 in vitro and in vivo, meiosis-specific knockdown of AtSCC4 expression does not cause any meiotic defect, suggesting that the SCC2-SCC4 complex has divergent roles in mitosis and meiosis. SCC2 homologs from land plants have a unique plant homeodomain (PHD) motif not found in other species. We show that the AtSCC2 PHD domain can bind to the N terminus of histones and is required for meiosis but not mitosis. Taken together, our results provide evidence that unlike SCC2 in other organisms, SCC2 requires a functional PHD domain during meiosis in land plants.

Organic near-infrared (NIR) emitters with simultaneously high absorption coefficient and photoluminescence quantum yield (PLQY) are highly desirable for biomedical imaging yet seldom reported because these two aspects are usually contradictory. The conjugated planar structures exhibit strong absorption but the emission is seriously quenched in aggregate state, whereas the twisted unplanar molecules display opposite phenomena. Herein, we report a kind of dragonfly-shaped NIR aggregation-induced emission luminogen (AIEgen) with both high absorption coefficient (6.24 × 104 M-1 cm-1) and superior PLQY (51.2%) for precise image-guided cancer surgery. The compound possessing a conjugated structure with vibrational substitutes has been synthesized, in which the good conjugation enables strong absorption, and the molecular vibration affords AIE signature. Moreover, the nonfluorescent processes are significantly suppressed, making every effort to boost fluorescence. The highly bright and stable AIE nanoparticles warrant efficient in vitro cellular imaging and in vivo tumor imaging. Moreover, the fluorescence imaging-guided cancer surgery helps to precisely delineate tiny tumor nodules, significantly improving the cancer surgery outcome. This work will inspire more insights into the development of organic NIR emitters with high brightness for biomedical applications.

The standard-of-care for the detection of laryngeal pathologies involves distinguishing suspicious lesions from surrounding healthy tissue via contrasts in colour and texture captured by white-light endoscopy. However, the technique is insufficiently sensitive and thus leads to unsatisfactory rates of false negatives. Here we show that laryngeal lesions can be better detected in real time by taking advantage of differences in the light-polarization properties of cancer and healthy tissues. By measuring differences in polarized-light retardance and depolarization, the technique, which we named 'surgical polarimetric endoscopy' (SPE), generates about one-order-of-magnitude greater contrast than white-light endoscopy, and hence allows for the better discrimination of cancerous lesions, as we show with patients diagnosed with squamous cell carcinoma. Polarimetric imaging of excised and stained slices of laryngeal tissue indicated that changes in the retardance of polarized light can be largely attributed to architectural features of the tissue. We also assessed SPE to aid routine transoral laser surgery for the removal of a cancerous lesion, indicating that SPE can complement white-light endoscopy for the detection of laryngeal cancer.

The ongoing COVID-19 pandemic produced far-reaching effects throughout society, and science is no exception. The scale, speed, and breadth of the scientific community's COVID-19 response lead to the emergence of new research at the remarkable rate of more than 250 papers published per day. This posed a challenge for the scientific community as traditional methods of engagement with the literature were strained by the volume of new research being produced. Meanwhile, the urgency of response lead to an increasingly prominent role for preprint servers and a diffusion of relevant research through many channels simultaneously. These factors created a need for new tools to change the way scientific literature is organized and found by researchers. With this challenge in mind, we present an overview of COVIDScholar https://covidscholar.org, an automated knowledge portal which utilizes natural language processing (NLP) that was built to meet these urgent needs. The search interface for this corpus of more than 260,000 research articles, patents, and clinical trials served more than 33,000 users at an average of 2,000 monthly active users and a peak of more than 8,600 weekly active users in the summer of 2020. Additionally, we include an analysis of trends in COVID-19 research over the course of the pandemic with a particular focus on the first 10 months, which represents a unique period of rapid worldwide shift in scientific attention.

The physical states and chemical components of bulk sludge determine the occurrence and development of membrane fouling in membrane bioreactors. Thus, regulation of sludge suspensions can provide new strategies for fouling control. In this study, we used "top-down" enrichment to construct a synthetic anti-fouling consortium (SAC) from bio-cake and evaluate its roles in preventing membrane fouling. The SAC was identified as Massilia-dominated and could almost wholly degrade the alginate solution (1,000 mg/L) within 72 h. Two-dimensional Fourier transformation infrared correlation spectroscopy (2D-FTIR-CoS) analysis demonstrated that the SAC induced the breakage of glycosidic bond in alginates. The co-cultivation of sludge with a low dosage of SAC (ranging from 0 to 1%) led to significant fouling mitigation, increased sludge floc size, and decreased unified membrane fouling index value (0.55 ± 0.06 and 0.11 ± 0.05). FTIR spectra and X-ray spectroscopy analyses demonstrated that the addition of SAC decreased the abundance of the O-acetylation of polysaccharides in extracellular polymeric substances. Secondary derivatives analysis of amide I spectra suggested a strong reduction in the α-helix/(β-sheet + random coil) ratio in the presence of SAC, which was expected to enhance cell aggregation. Additionally, the extracellular secretions of SAC could both inhibit biofilm formation and strongly disperse the existing biofilm strongly during the biofilm incubation tests. In summary, this study illustrates the feasibility and benefits of using SAC for fouling control and provides a new strategy for fouling control.

Microsatellite primers were developed to investigate population genetic structure in Lindera glauca (Lauraceae).