Post-hybridization introgression and natural selection promoted genomic divergence of Aegilops speltoides and the four S*-genome diploid species.

Understanding how different driving forces have promoted biological divergence and speciation is one of the central issues in evolutionary biology. The Triticum/Aegilops species complex contains 13 diploid species belonging to the A-, B- and D-lineages and offers an ideal system to address the evolutionary dynamics of lineage fusion and splitting. Here, we sequenced the whole genomes of one S-genome species (Aegilops speltoides) of the B-lineage and four S*-genome diploid species (Aegilops bicornis, Aegilops longissima, Aegilops sharonensis and Aegilops searsii) of the D-lineage at the population level. We performed detailed comparisons of the five species and with the other four representative A-, B- and D-lineage species. Our estimates identified frequent genetic introgressions from A- and B-lineages to the D-lineage species. A remarkable observation is the contrasting distributions of putative introgressed loci by the A- and B-lineages along all the seven chromosomes to the extant D-lineage species. These genetic introgressions resulted in high levels of genetic divergence at centromeric regions between Ae. speltoides (B-lineage) and the other four S*-genome diploid species (D-lineage), while natural selection is a potential contributor to divergence among the four S*-genome species at telomeric regions. Our study provides a genome-wide view on how genetic introgression and natural selection acted together yet chromosome-regionally divided to promote genomic divergence among the five S- and S*-genome diploid species, which provides new and nuanced insights into the evolutionary history of the Triticum/Aegilops species complex.

Two-Fold Interpenetrated Binuclear Nickel Metal-Organic Framework as a Heterogeneous Catalyst for N-Heterocycle Synthesis.

A binuclear Ni(II)-based metal-organic framework {[Ni2(btb)1.333(H2O)3.578(py)1.422]·(DMF)(H2O)3.25}n (Nibtb) was solvothermally synthesized (H3btb = 1,3,5-tri(4-carboxylphenyl)benzene, py = pyridine, DMF = N,N-dimethylformamide). Nibtb shows a rare 2-fold interpenetrating (3,4)-connected 3D network with a point symbol of (83)4(86)3 based on binuclear Ni(II) clusters. Nibtb as a heterogeneous catalyst combines the high stability of MOFs and excellent catalytic activity of nickel, which exhibits excellent catalytic activity for the synthesis of benzimidazoles and pyrazoles under mild conditions. Moreover, the catalyst can be easily separated and reused for seven successive cycles and maintains high catalytic activity.

Ultrasensitive detection of UO2 2+ based on dopamine-functionalized MoOx quantum dots.

Uranium is an important nuclear fuel and the risk of human exposure to uranium increases as increasing amounts of uranium-containing waste enter the environment due to the rapid growth of nuclear power. Therefore, rapid, sensitive, and portable uranium detection is a promising approach to effectively control and monitor uranium contamination. To achieve this goal, abundant oxygen- and nitrogen-containing groups were introduced to molybdenum oxide quantum dot (MoOx QDs) surfaces with dopamine (DA) modification. Due to the excellent coordination ability of oxygen- and nitrogen-containing groups with uranium, the obtained DA-functionalized MoOx QDs (DA-MoOx QDs) showed a strong binding affinity for uranium and sensitivity was increased nearly 1000-fold compared with MoOx QDs alone. The limit of detection was 3.85 nM, which is higher than most of the reported nanomaterials. Moreover, the DA-MoOx QD-based method showed high selectivity and uranium could be clearly detected under masking with ethylenediaminetetraacetic acid even when the concentration of other metal ions was 100-fold higher than that of uranium, showing a very promising method for uranium contamination control and monitoring.

CT image crack segmentation method based on linear feature enhancement.

Industrial computed tomography (CT) crack segmentation is a key technology in industrial CT image processing. Unfortunately, the interference of artifact and noise in CT image often bring great trouble to the crack segmentation. In order to improve the segmentation accuracy of cracks in CT images, we propose to develop and test a new crack segmentation algorithm based on linear feature enhancement by analyzing the features of cracks in CT images. Firstly, the total variational model is used to denoise the input image. Next, a Frangi multiscale filter is used to extract linear structures in the image, and then the extracted linear structures are used to enhance the contrast of the image. Finally, the cracks in the image are detected and segmented by Otsu algorithm. By comparing with the manual segmentation results, the average intersection-over-union (IOU) reaches 86.10% and the average F1 score reaches 92.44%, which verifies the effectiveness and correctness of the algorithm developed in this study. Overall, experiments demonstrate that the new algorithm improves the accuracy of crack segmentation and it is effective applying to industry CT images.

Rapid and sensitive detection of Mycobacterium tuberculosis based on strand displacement amplification and magnetic beads.

Tuberculosis is one of the main infectious diseases threatening public health, and the development of simple, rapid, and cost-saving methods for tuberculosis diagnosis is of profound importance for tuberculosis prevention and treatment. The bacterium Mycobacterium tuberculosis (MTB) is the pathogen that causes tuberculosis, and assaying for MTB is the only criterion for tuberculosis diagnosis. A new enzyme-free method based on strand displacement amplification and magnetic beads was developed for simple, rapid, and cost-saving MTB detection. Under optimum conditions, a good linear relationship could be observed between fluorescence and MTB specific DNA concentration ranging from 0.05 to 150 nM with a correlation coefficient of 0.993 (n = 8) and a detection limit of 47 pM (3σ/K). The present method also distinguished a one base mismatch from MTB specific DNA, showing great promise for MTB genome single base polymorphism analysis. MTB specific DNA content in polymerase chain reaction samples was successfully detected using the new method, and recoveries were 97.8-100.8%, indicating that the present method had high accuracy and shows good potential for the early diagnosis of tuberculosis.

New Helvolic Acid Derivatives with Antibacterial Activities from Sarocladium oryzae DX-THL3, an Endophytic Fungus from Dongxiang Wild Rice (Oryza rufipogon Griff.).

Three new helvolic acid derivatives (named sarocladilactone A (1), sarocladilactone B (2) and sarocladic acid A (3a)), together with five known compounds (6,16-diacetoxy-25-hy- droxy-3,7-dioxy-29-nordammara-1,17(20)-dien-21-oic acid (3b), helvolic acid (4), helvolinic acid (5), 6-desacetoxy-helvolic acid (6) and 1,2-dihydrohelvolic acid (7)), were isolated from the endophytic fungus DX-THL3, obtained from the leaf of Dongxiang wild rice (Oryza rufipogon Griff.). The structures of the new compounds were elucidated via HR-MS, extensive 1D and 2D NMR analysis and comparison with reported data. Compounds 1, 2, 4, 5, 6 and 7 exhibited potent antibacterial activities. In particular, sarocladilactone B (2), helvolinic acid (5) and 6-desacetoxy-helvolic acid (6) exhibited strongly Staphylococcus aureus inhibitory activity with minimum inhibitory concentration (MIC) values of 4, 1 and 4 µg/mL, respectively. The structure-activity relationship (SAR) of these compounds was primarily summarized.

Transcriptome analysis of the dimorphic transition induced by pH change and lipid biosynthesis in Trichosporon cutaneum.

Trichosporon cutaneum, a dimorphic oleaginous yeast, has immense biotechnological potential, which can use lignocellulose hydrolysates to accumulate lipids. Our preliminary studies on its dimorphic transition suggested that pH can significantly induce its morphogenesis. However, researches on dimorphic transition correlating with lipid biosynthesis in oleaginous yeasts are still limited. In this study, the unicellular yeast cells induced under pH 6.0-7.0 shake flask cultures resulted in 54.32% lipid content and 21.75 g/L dry cell weight (DCW), so lipid production was over threefold than that in hypha cells induced by acidic condition (pH 3.0-4.0). Furthermore, in bioreactor batch cultivation, the DCW and lipid content in unicellular yeast cells can reach 21.94 g/L and 58.72%, respectively, both of which were also more than twofold than that in hypha cells. Moreover, the activities of isocitrate dehydrogenase (IDH), malic enzyme (MAE), isocitrate lyase (ICL) and ATP citrate lyase (ACL) in unicellular cells were all higher than in the hyphal cells. In the meanwhile, the transcriptome data showed that the genes related to fatty acid biosynthesis, carbon metabolism and encoded Rim101 and cAMP-PKA signaling transduction pathways were significantly up-regulated in unicellular cells, which may play an important role in enhancing the lipid accumulation. In conclusion, our results provided insightful information focused on the molecular mechanism of dimorphic transition and process optimization for enhancing lipid accumulation in T. cutaneum.

Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing.

The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.

On Monolayer Formation of Pyrenebutyric Acid on Graphene.

As a two-dimensional material with high charge carrier mobility, graphene may offer ultrahigh sensitivity in biosensing. To realize this, the first step is to functionalize the graphene. This is commonly done by using 1-pyrenebutyric acid (PBA) as a linker for biomolecules. However, the adsorption of PBA on graphene remains poorly understood despite reports of successful biosensors functionalized via this route. Here, the PBA adsorption on graphene is characterized through a combination of Raman spectroscopy, ab initio calculations, and spectroscopic ellipsometry. The PBA molecules are found to form a self-assembled monolayer on graphene, the formation of which is self-limiting and Langmuirian. Intriguingly, in concentrated solutions, the PBA molecules are found to stand up and stack horizontally with their edges contacting the graphene surface. This morphology could facilitate a surface densely populated with carboxylic functional groups. Spectroscopic analyses show that the monolayer saturates at 5.3 PBA molecules per nm2 and measures ∼0.7 nm in thickness. The morphology study of this PBA monolayer sheds light on the π-π stacking of small-molecule systems on graphene and provides an excellent base for optimizing functionalization procedures.

Mitochondrial Genomes of Two Pygmy Grasshoppers (Orthoptera: Tetrigoidea) and a Comparative Analysis of Caelifera Mitogenomes.

The nearly complete mitogenomes of Bolivaritettix sikkinensis and Bolivaritettix yuanbaoshanensis were determined and compared with the mitogenomes of other 29 caeliferans. These two newly determined mitogenomes displayed the typical gene organization and composition, codon usage and AT skew of most Caelifera mitogenomes. A comparison of 31 orthopteran sequences revealed that the main causes of the differences in total length are an A+T-rich region and the length of IGS, even the rRNAs, and an AT content proportional to the value of AT-skew in the third position of PCGs. In Tetrigoidea, several tRNA were found to possess smaller TΨC or DHC loops and a number of special and conserved regions or motifs were found in tRNA genes and IGS, which may be useful as a molecular synapomorphy for this genus. ML and BI methods used in phylogenetic analysis revealed that Acridoidea species may have a close relationship with Tetrigoidea species.

Protective role of normothermic machine perfusion during reduced-size liver transplantation in pigs.

The purpose of this study is to explore whether normothermic machine perfusion (NMP) preservation is superior to cold preservation during reduced-size liver transplantation (RSLT) in pigs. Twenty-four healthy Ba-Ma mini pigs were used (aged >13 months; weight 25-35 kg; regardless of sex). The animals were randomized into 2 groups. In group A (NMP), donor livers were harvested without warm ischemia time and heartbeats and then were connected to the NMP system to reduce the livers' size under the normothermic condition. In group B (University of Wisconsin [UW] solution), donor livers were harvested without warm ischemia time and heartbeats after being perfused by UW solution and were then preserved in 0°C-4°C UW solution to reduce the livers' size under cold conditions. After that, liver transplantation without venovenous bypass was performed. General RSLT information of the pigs from the 2 groups was recorded; the serological indices were measured; and routine pathological examination of liver tissue was observed. A significant difference was observed in the intraoperative bleeding between the 2 groups (P < 0.05), whereas no significant difference was found in the other indices (all P > 0.05). Significant differences of alanine aminotransferase levels, aspartate aminotransferase levels, and lactate dehydrogenase levels between the 2 groups were observed between postoperative days 3 and 5 (P < 0.05). Significant differences of lactic acid levels between the 2 groups were observed between postoperative days 2 and 5 (P < 0.05). Compared with the cold preservation group, the liver tissues of the NMP preservation group only rarely experienced liver cell necrosis and maintained integrities in the hepatic sinusoid spaces and endothelial cells. In conclusion, NMP preservation is superior to cold preservation during RSLT in pigs. Liver Transplantation 22 968-978 2016 AASLD.

Isolation, diversity and acetylcholinesterase inhibitory activity of the culturable endophytic fungi harboured in Huperzia serrata from Jinggang Mountain, China.

Huperzia serrata has many important medicinal properties with proven pharmacological potential. Some of these properties may be mediated by its endophytic fungi. To test this hypothesis, in the present study, we provided a first insights into evaluating the species composition and acetylcholinesterase (AChE) inhibitory activity of the culturable endophytic fungi of H. serrata from the regional at Jinggang Mountain in southeastern China. A total number of 885 fungal isolates distributed across 44 genera and 118 putative species were obtained from 1422 fragments of fine H. serrata roots, stems and leaves base on ITS-rDNA sequences BLAST analysis. The endophytic fungi were phylogenetically diverse and species-rich, with high rate of colonization and isolation. The assemble of endophytic fungi consisted mainly of Ascomycota (97.15%), followed by Basidiomycota (1.92%) and unknown fungal species (0.90%). Colletotrichum (64.29%), Phyllosticta (3.39%), Hypoxylon (2.81%), Xylaria (2.25%) and Nigrospora (2.04%) were the most abundant genera, whereas the remaining genera were infrequent groups. Although, roots yielded low abundance strains, the diverse and species-rich were both higher than that of stems and leaves. In addition, out of the 247 endophytic fungi strains determinated, 221 fungal extracts showed AChE inhibition activities in vitro. Among them, 22 endophytic fungi strains achieved high inhibitory activity (≥50%) on AChE which belongs to 13 genera and five incertae sedis strains. Four endophytic fungi designated as JS4 (Colletotrichum spp.), FL14 (Ascomycota spp.), FL9 (Sarcosomataceae spp.) and FL7 (Dothideomycetes spp.) were displayed highly active (≥80%) against AChE, which the inhibition effects were even more intense than the positive control. Our findings highlight that H. serrata grown in Jinggang Mountain harbors a rich and fascinating endophytic fungus community with potential AChE inhibitory activity, which could further broaden the natural acetylcholinesterase inhibitors resources used for Alzheimer's disease treatment.

Spike timing-based coding in neuromimetic tactile system enables dynamic object classification.

Rapid processing of tactile information is essential to human haptic exploration and dexterous object manipulation. Conventional electronic skins generate frames of tactile signals upon interaction with objects. Unfortunately, they are generally ill-suited for efficient coding of temporal information and rapid feature extraction. In this work, we report a neuromorphic tactile system that uses spike timing, especially the first-spike timing, to code dynamic tactile information about touch and grasp. This strategy enables the system to seamlessly code highly dynamic information with millisecond temporal resolution on par with the biological nervous system, yielding dynamic extraction of tactile features. Upon interaction with objects, the system rapidly classifies them in the initial phase of touch and grasp, thus paving the way to fast tactile feedback desired for neuro-robotics and neuro-prosthetics.

Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model.

The coronavirus disease 2019 (COVID-19) pandemic has greatly damaged human society, but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen remain unclear. Here, we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations. We explored the position (i.e., root, middle, or tip) of early detected samples in the evolutionary tree of SARS-CoV-2. In total, 6 799 transmission chains and 1 766 transmission networks were reconstructed, with chain lengths ranging from 1-9 nodes. The root node samples of the 1 766 transmission networks were from 58 countries or regions and showed no common ancestor, indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected (i.e., all samples were located at the tip position of the evolutionary tree). No root node sample was found in any sample ( n=31, all from the Chinese mainland) collected in the first 15 days from 24 December 2019. Results using six-month data or RaTG13-referenced mutation data were similar. The reconstruction method was verified using a simulation approach. Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan, China. Thus, a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.

Novel metal peroxide nanoboxes restrain Clostridioides difficile infection beyond the bactericidal and sporicidal activity.

Clostridioides difficile spores are considered as the major source responsible for the development of C. difficile infection (CDI), which is associated with an increased risk of death in patients and has become an important issue in infection control of nosocomial infections. Current treatment against CDI still relies on antibiotics, which also damage normal flora and increase the risk of CDI recurrence. Therefore, alternative therapies that are more effective against C. difficile bacteria and spores are urgently needed. Here, we designed an oxidation process using H2O2 containing PBS solution to generate Cl- and peroxide molecules that further process Ag and Au ions to form nanoboxes with Ag-Au peroxide coat covering Au shell and AgCl core (AgAu-based nanoboxes). The AgAu-based nanoboxes efficiently disrupted the membrane structure of bacteria/spores of C. difficile after 30-45 min exposure to the highly reactive Ag/Au peroxide surface of the nano structures. The Au-enclosed AgCl provided sustained suppression of the growth of 2 × 107 pathogenic Escherichia coli for up to 19 days. In a fecal bench ex vivo test and in vivo CDI murine model, biocompatibility and therapeutic efficacy of the AuAg nanoboxes to attenuate CDI was demonstrated by restoring the gut microbiota and colon mucosal structure. The treatment successfully rescued the CDI mice from death and prevented their recurrence mediated by vancomycin treatment. The significant outcomes indicated that the new peroxide-derived AgAu-based nanoboxes possess great potential for future translation into clinical application as a new alternative therapeutic strategy against CDI.

A new "fully reduced" polyoxovanadate constructed from nanosized triangle-shaped [V(III)3V(IV)18P6O60(DACH)3]}9- cluster anions exhibiting ferrimagnetic interactions.

Magnetic personality: A pentavalent vanadium source was employed to prepare the largest highly reduced polyoxovanadate cluster by virtue of the reducing power of 1,2-diaminocyclohexane under hydrothermal conditions. The new non-classical triangle-shaped cluster shows good catalytic selectivity for the oxidation of styrene and exhibits ferrimagnetic interactions that could make it a promising magnetic material.

Self-Driven Electrochromic Window System Cu/WOx-Al3+/GR with Dynamic Optical Modulation and Static Graph Display Functions.

Electrochromic devices with unique advantages of electrical/optical bistability are highly desired for energy-saving and information storage applications. Here, we put forward a self-driven Al-ion electrochromic system, which utilizes WOx films, Cu foil, and graphite rod as electrochromic optical modulation and graph display electrodes, coloration potential supplying electrodes, and bleaching potential supplying electrodes, respectively. The inactive Cu electrode can not only realize the effective Al3+ cation intercalation into electrochromic WOx electrodes but also eliminate the problem of metal anode consumption. The electrochromic WOx electrodes cycled in Al3+ aqueous media exhibit a wide potential window (∼1.5 V), high coloration efficiency (36.0 cm2/C), and super-long-term cycle stability (>2000 cycles). The dynamic optical modulation and static graph display function can be achieved independently only by switching the electrode connection mode, thus bringing more features to this electrochromic system. For a large-area electrochromic system (10 × 10 cm2), the absolute transmittance value in its color-neutral state can reach about 41% (27%) at 633 nm (780 nm) by connecting the Cu and WOx electrodes for 140 s. The original transparent state can be readily recovered by replacing the Cu foil with the graphite rod. This work throws light on next-generation electrochromic applications for optical/thermal modulation, privacy protection, and information display.

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To explore the effects of different electron acceptors on soil methane emission and responses of soil microorganisms to different light conditions, a strict anaerobic 20-day incubation experiment was conducted with eight treatments: darkness + Fe3+ (DF); darkness + NO3- (DN); darkness +SO42- (DS); darkness + distilled water (DCK); light + Fe3+ (LF); light + NO3- (LN); light +SO42- (LS); light + distilled water (LCK). The changes of methane concentration in the anaerobic incubation flask and the variation of the abundance of bacteria, archaea, fungi and six soil functional genes were analyzed. Results showed that soil methane emission under NO3-, SO42- addition and control (CK) was significantly lower under light conditions than dark, except the Fe3+ treatment. DN, DCK and LF treatments had the highest abundance of bacteria, fungi and archaea genes, respectively. The gene abundance of methanogenic mcrA, sulfate-reducing bacteria Dsr, and carbon-fixing CbbL were significantly up-regulated in the LF, while that of methanotrophs pmoA, iron-reducing bacteria Geo, and denitrifying bacteria nosZ were significantly up-regulated in the LN, DCK and LCK, respectively. Results of Pearson correlation and RDA analysis showed that CH4 emission was significantly positively correlated with CO2 concentration, pH, ammonium-nitrogen, and total N contents, and negatively correlated with N2O concentration, Eh, nitrate, and total C contents. Under dark condition, methane emission was positively correlated with archaea and pmoA genes abundance, and negatively correlated with other genes abundance. Under light condition, methane emission was negatively correlated with the abundance of soil microbe and functional genes. In general, methane emission under light condition was significantly lower than that under dark condition (except for the Fe3+ treatment). These results showed that it was helpful to reduce methane emission under light condition, but the increase or decrease of methane emission was closely related to the type of electron acceptors and the functional responses of soil micro-organisms.

An inner-filter-effect based ratiometric fluorescent sensor for the detection of uranyl ions in real samples.

In this work, a ratiometric fluorescence system was designed for the detection of trace UO22+ in water based on the inner filter effect (IFE) between gold nanoparticles (AuNPs) and gold nanoclusters (AuNCs). IFE-induced fluorescence quenching was achieved due to the enhanced complementary overlap between the absorption spectra of AuNPs and the emission spectrum of AuNCs after the addition of UO22+. Blue carbon dots (B-CDs) were added to serve as reference fluorophores to expand the color tonality and make human eye recognition easier. The ratiometric fluorescent sensor demonstrated a unique fluorescence color change from red to blue when different doses of UO22+ were added, with a detection limit of 8.4 nM. Furthermore, the ratiometric fluorescent sensor was effectively used for UO22+ determination in real-world water samples, with acceptable recoveries.

Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome.

Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.