Genome evolution in Oryza allopolyploids of various ages: Insights into the process of diploidization.

The prevalence and recurrence of whole-genome duplication in plants and its major role in evolution have been well recognized. Despite great efforts, many aspects of genome evolution, particularly the temporal progression of genomic responses to allopolyploidy and the underlying mechanisms, remain poorly understood. The rice genus Oryza consists of both recently formed and older allopolyploid species, representing an attractive system for studying the genome evolution after allopolyploidy. In this study, through screening BAC libraries and sequencing and annotating the targeted BAC clones, we generated orthologous genomic sequences surrounding the DEP1 locus, a major grain yield QTL in cultivated rice, from four Oryza polyploids of various ages and their likely diploid genome donors or close relatives. Based on sequenced DEP1 region and published data from three other genomic regions, we investigated the temporal evolutionary dynamics of four polyploid genomes at both genetic and expression levels. In the recently formed BBCC polyploid, Oryza minuta, genome dominance was not observed and its short-term responses to allopolyploidy are mainly manifested as a high proportion of homoeologous gene pairs showing unequal expression. This could partly be explained by parental legacy, rewiring of divergent regulatory networks and epigenetic modulation. Moreover, we detected an ongoing diploidization process in this genus, and suggest that the expression divergence driven by changes of selective constraint probably plays a big role in the long-term diploidization. These findings add novel insights into our understanding of genome evolution after allopolyploidy, and could facilitate crop improvements through hybridization and polyploidization.

Infectious shock after liposuction.

BACKGROUND: Liposuction has become one of the most popular cosmetic surgeries in China. However, few studies have discussed infectious shock caused by C. perfringens as one of the causes of death after liposuction. CASE PRESENTATION: A 24-year-old woman was brought to the emergency department (ED) of Guangzhou Chinese Overseas Hospital for treatment. The patient had undergone liposuction in her bilateral lower limbs two days prior. At the ED, the patient was unconscious, and had bilateral equal-sized (diameter, 6 mm) round pupils, no light reflex, a blood pressure (BP) of 71/33 mmHg, a heart rate of 133 bpm, and an SpO2 of 70%. She had bilateral limb swelling, extensive ecchymoses in her lower abdomen and bilateral thighs, local crepitus, blisters, weak pulses on her femoral artery and dorsalis pedis, high skin tension, and hemoglobin of 32 g/L. The patient was diagnosed with Clostridium perfringens infection, and she underwent debridement surgery and supportive treatment. But the patient's BP could not improve. At 8:28 pm on the day of admission, the patient was declared clinically dead after the electrocardiograph showed a horizontal line and spontaneous respiration ceased. CONCLUSIONS: Failure to meet surgical disinfection and environmental standards may be the cause of infection of C. perfringens through wounds. Therefore, it is necessary to strengthen the environmental disinfection of the operating room, and standardize the sterile conditions of the operation staff and patients before and during operation. Liposuction surgery necrotizing fasciitis is a rare but fatal complications, especially if diagnosis delay, therefore it is critical for early diagnosis and treatment of gas gangrene.

Precise Control of Selenium Functionalization in Non-Fullerene Acceptors Enabling High-Efficiency Organic Solar Cells.

Central π-core engineering of non-fullerene small molecule acceptors (NF-SMAs) is effective in boosting the performance of organic solar cells (OSCs). Especially, selenium (Se) functionalization of NF-SMAs is considered a promising strategy but the structure-performance relationship remains unclear. Here, we synthesize two isomeric alkylphenyl-substituted selenopheno[3,2-b]thiophene-based NF-SMAs named mPh4F-TS and mPh4F-ST with different substitution positions, and contrast them with the thieno[3,2-b]thiophene-based analogue, mPh4F-TT. When placing Se atoms at the outer positions of the π-core, mPh4F-TS shows the most red-shifted absorption and compact molecular stacking. The PM6 : mPh4F-TS devices exhibit excellent absorption, high charge carrier mobility, and reduced energy loss. Consequently, PM6 : mPh4F-TS achieves more balanced photovoltaic parameters and yields an efficiency of 18.05 %, which highlights that precisely manipulating selenium functionalization is a practicable way toward high-efficiency OSCs.

DNA barcoding of Oryza: conventional, specific, and super barcodes.

KEY MESSAGE: We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

Regio-Regular Polymer Acceptors Enabled by Determined Fluorination on End Groups for All-Polymer Solar Cells with 15.2 % Efficiency.

Polymerization sites of small molecule acceptors (SMAs) play vital roles in determining device performance of all-polymer solar cells (all-PSCs). Different from our recent work about fluoro- and bromo- co-modified end group of IC-FBr (a mixture of IC-FBr1 and IC-FBr2), in this paper, we synthesized and purified two regiospecific fluoro- and bromo- substituted end groups (IC-FBr-o & IC-FBr-m), which were then employed to construct two regio-regular polymer acceptors named PYF-T-o and PYF-T-m, respectively. In comparison with its isomeric counterparts named PYF-T-m with different conjugated coupling sites, PYF-T-o exhibits stronger and bathochromic absorption to achieve better photon harvesting. Meanwhile, PYF-T-o adopts more ordered inter-chain packing and suitable phase separation after blending with the donor polymer PM6, which resulted in suppressed charge recombination and efficient charge transport. Strikingly, we observed a dramatic performance difference between the two isomeric polymer acceptors PYF-T-o and PYF-T-m. While devices based on PM6:PYF-T-o can yield power conversion efficiency (PCE) of 15.2 %, devices based on PM6:PYF-T-m only show poor efficiencies of 1.4 %. This work demonstrates the success of configuration-unique fluorinated end groups in designing high-performance regular polymer acceptors, which provides guidelines towards developing all-PSCs with better efficiencies.

Parallel Speciation of Wild Rice Associated with Habitat Shifts.

The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a "magic" trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.

Immunological Methods for the Detection of Binders in Ancient Tibetan Murals.

Tibetan mural samples from the Jiazhaer mountain cave were studied using enzyme-linked immunosorbent assays (ELISA) and immunofluorescence microscopy (IFM). Samples containing protein binders were first identified using ELISA, and then IFM was used to determine the location of protein binders. Using these methods, we discovered gelatin and casein in samples from wall murals, distributed in both red and black pigments. We excluded the possibility of contamination by conducting further experiments where simulated samples were spiked with milk. We conclude that both gelatin and casein were used as binders in the pigments of the Tibetan Buddhist murals in the Jiazhaer (Transliteration from Tibetan) mountain cave. This is the first evidence of casein being used as a binder in Chinese mural pigments.

Multilocus species tree analyses resolve the ancient radiation of the subtribe Zizaniinae (Poaceae).

The phylogeny of the subtribe Zizaniinae of rice tribe (Oryzeae) has not been well resolved, particularly for the monotypic Hygroryza whose systematic position was inconsistent in previous studies. Here, we used the concatenation approach and coalescent-based species tree methods to reconstruct the phylogeny of Zizaniinae based on sequences of 14 nuclear single-copy loci and concatenated chloroplast fragments. Despite the low resolution of the tree from concatenated data and substantial topological incongruence of individual gene trees, the species trees inferred from three coalescent-based methods were fully concordant and highly supported. Importantly, the genus Hygroryza was consistently recovered with strong support by all coalescent-based methods. Further various phylogenetic analyses indicated that incomplete lineage sorting was the most likely process that generated pervasive discordance among individual gene trees, although hybridization and introgression cannot be excluded completely. Our species tree inferences based on multilocus data successfully resolved the phylogenetic relationships of the Zizaniinae lineages and confirmed that ancient rapid radiation has taken place in the diversification history of Zizaniinae. This study demonstrates that coalescent-based species tree approaches outperformed the concatenation method and could effectively decipher ancient rapid radiations as long as well resolved individual gene trees were sufficiently sampled.

Multiple species of wild tree peonies gave rise to the 'king of flowers', Paeonia suffruticosa Andrews.

The origin of cultivated tree peonies, known as the 'king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.

Sugar import mediated by sugar transporters and cell wall invertases for seed development in Camellia oleifera.

Seed development and yield depend on the transport and supply of sugar. However, an insufficient supply of nutrients from maternal tissues to embryos results in seed abortion and yield reduction in Camellia oleifera. In this study, we systematically examined the route and regulatory mechanisms of sugar import into developing C. oleifera seeds using a combination of histological observations, transcriptome profiling, and functional analysis. Labelling with the tracer carboxyfluorescein revealed a symplasmic route in the integument and an apoplasmic route for postphloem transport at the maternal-filial interface. Enzymatic activity and histological observation showed that at early stages [180-220 days after pollination (DAP)] of embryo differentiation, the high hexose/sucrose ratio was primarily mediated by acid invertases, and the micropylar endosperm/suspensor provides a channel for sugar import. Through Camellia genomic profiling, we identified three plasma membrane-localized proteins including CoSWEET1b, CoSWEET15, and CoSUT2 and one tonoplast-localized protein CoSWEET2a in seeds and verified their ability to transport various sugars via transformation in yeast mutants and calli. In situ hybridization and profiling of glycometabolism-related enzymes further demonstrated that CoSWEET15 functions as a micropylar endosperm-specific gene, together with the cell wall acid invertase CoCWIN9, to support early embryo development, while CoSWEET1b, CoSWEET2a, and CoSUT2 function at transfer cells and chalazal nucellus coupled with CoCWIN9 and CoCWIN11 responsible for sugar entry in bulk into the filial tissue. Collectively, our findings provide the first comprehensive evidence of the molecular regulation of sugar import into and within C. oleifera seeds and provide a new target for manipulating seed development.

Selenium substitution for dielectric constant improvement and hole-transfer acceleration in non-fullerene organic solar cells.

Dielectric constant of non-fullerene acceptors plays a critical role in organic solar cells in terms of exciton dissociation and charge recombination. Current acceptors feature a dielectric constant of 3-4, correlating to relatively high recombination loss. We demonstrate that selenium substitution on acceptor central core can effectively modify molecule dielectric constant. The corresponding blend film presents faster hole-transfer of ~5 ps compared to the sulfur-based derivative (~10 ps). However, the blends with Se-acceptor also show faster charge recombination after 100 ps upon optical pumping, which is explained by the relatively disordered stacking of the Se-acceptor. Encouragingly, dispersing the Se-acceptor in an optimized organic solar cell system can interrupt the disordered aggregation while still retain high dielectric constant. With the improved dielectric constant and optimized fibril morphology, the ternary device exhibits an obvious reduction of non-radiative recombination to 0.221 eV and high efficiency of 19.0%. This work unveils heteroatom-substitution induced dielectric constant improvement, and the associated exciton dynamics and morphology manipulation, which finally contributes to better material/device design and improved device performance.

Charge Injection and Auger Recombination Modulation for Efficient and Stable Quasi-2D Perovskite Light-Emitting Diodes.

The inefficient charge transport and large exciton binding energy of quasi-2D perovskites pose challenges to the emission efficiency and roll-off issues for perovskite light-emitting diodes (PeLEDs) despite excellent stability compared to 3D counterparts. Herein, alkyldiammonium cations with different molecular sizes, namely 1,4-butanediamine (BDA), 1,6-hexanediamine (HDA) and 1,8-octanediamine (ODA), are employed into quasi-2D perovskites, to simultaneously modulate the injection efficiency and recombination dynamics. The size increase of the bulky cation leads to increased excitonic recombination and also larger Auger recombination rate. Besides, the larger size assists the formation of randomly distributed 2D perovskite nanoplates, which results in less efficient injection and deteriorates the electroluminescent performance. Moderate exciton binding energy, suppressed 2D phases and balanced carrier injection of HDA-based PeLEDs contribute to a peak external quantum efficiency of 21.9%, among the highest in quasi-2D perovskite based near-infrared devices. Besides, the HDA-PeLED shows an ultralong operational half-lifetime T50 up to 479 h at 20 mA cm‒2, and sustains the initial performance after a record-level 30 000 cycles of ON-OFF switching, attributed to the suppressed migration of iodide anions into adjacent layers and the electrochemical reaction in HDA-PeLEDs. This work provides a potential direction of cation design for efficient and stable quasi-2D-PeLEDs.

Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus.

· Despite substantial investigations into Oryza phylogeny and evolution, reliable estimates of the divergence times and ancestral effective population sizes of major lineages in Oryza are challenging. · We sampled sequences of 106 single-copy nuclear genes from all six diploid genomes of Oryza to investigate the divergence times through extensive relaxed molecular clock analyses and estimated the ancestral effective population sizes using maximum likelihood and Bayesian methods. · We estimated that Oryza originated in the middle Miocene (c. 13-15 million years ago; Ma) and obtained an explicit time frame for two rapid diversifications in this genus. The first diversification involving the extant F-/G-genomes and possibly the extinct H-/J-/K-genomes occurred in the middle Miocene immediately after (within < 1 Myr) the origin of Oryza. The second giving rise to the A-/B-/C-genomes happened c. 5-6 Ma. We found that ancestral effective population sizes were much larger than those of extant species in Oryza. · We suggest that the climate fluctuations during the period from the middle Miocene to Pliocene may have contributed to the two rapid diversifications of Oryza species. Such information helps better understand the evolutionary history of Oryza and provides further insights into the pattern and mechanism of diversification in plants in general.

Modification and Expression of mRNA m6A in the Lateral Habenular of Rats after Long-Term Exposure to Blue Light during the Sleep Period.

Artificial lighting, especially blue light, is becoming a public-health risk. Excessive exposure to blue light at night has been reported to be associated with brain diseases. However, the mechanisms underlying neuropathy induced by blue light remain unclear. An early anatomical tracing study described the projection of the retina to the lateral habenula (LHb), whereas more mechanistic reports are available on multiple brain functions and neuropsychiatric disorders in the LHb, which are rarely seen in epigenetic studies, particularly N6-methyladenosine (m6A). The purpose of our study was to first expose Sprague-Dawley rats to blue light (6.11 ± 0.05 mW/cm2, the same irradiance as 200 lx of white light in the control group) for 4 h, and simultaneously provide white light to the control group for the same time to enter a sleep period. The experiment was conducted over 12 weeks. RNA m6A modifications and different mRNA transcriptome profiles were observed in the LHb. We refer to this experimental group as BLS. High-throughput MeRIP-seq and mRNA-seq were performed, and we used bioinformatics to analyze the data. There were 188 genes in the LHb that overlapped between differentially m6A-modified mRNA and differentially expressed mRNA. The Kyoto Encyclopedia of Genes and Genomes and gene ontology analysis were used to enrich neuroactive ligand-receptor interaction, long-term depression, the cyclic guanosine monophosphate-dependent protein kinase G (cGMP-PKG) signaling pathway, and circadian entrainment. The m6A methylation level of the target genes in the BLS group was disordered. In conclusion, this study suggests that the mRNA expression and their m6A of the LHb were abnormal after blue light exposure during the sleep period, and the methylation levels of target genes related to synaptic plasticity were disturbed. This study offers a theoretical basis for the scientific use of light.

Improved photovoltaic performance and robustness of all-polymer solar cells enabled by a polyfullerene guest acceptor.

Fullerene acceptors typically possess excellent electron-transporting properties and can work as guest components in ternary organic solar cells to enhance the charge extraction and efficiencies. However, conventional fullerene small molecules typically suffer from undesirable segregation and dimerization, thus limiting their applications in organic solar cells. Herein we report the use of a poly(fullerene-alt-xylene) acceptor (PFBO-C12) as guest component enables a significant efficiency increase from 16.9% for binary cells to 18.0% for ternary all-polymer solar cells. Ultrafast optic and optoelectronic studies unveil that PFBO-C12 can facilitate hole transfer and suppress charge recombination. Morphological investigations show that the ternary blends maintain a favorable morphology with high crystallinity and smaller domain size. Meanwhile, the introduction of PFBO-C12 reduces voltage loss and enables all-polymer solar cells with excellent light stability and mechanical durability in flexible devices. This work demonstrates that introducing polyfullerenes as guest components is an effective approach to achieving highly efficient ternary all-polymer solar cells with good stability and mechanical robustness.

Auxiliary sequential deposition enables 19%-efficiency organic solar cells processed from halogen-free solvents.

High-efficiency organic solar cells are often achieved using toxic halogenated solvents and additives that are constrained in organic solar cells industry. Therefore, it is important to develop materials or processing methods that enabled highly efficient organic solar cells processed by halogen free solvents. In this paper, we report an innovative processing method named auxiliary sequential deposition that enables 19%-efficiency organic solar cells processed by halogen free solvents. Our auxiliary sequential deposition method is different from the conventional blend casting or sequential deposition methods in that it involves an additional casting of dithieno[3,2-b:2',3'-d]thiophene between the sequential depositions of the donor (D18-Cl) and acceptor (L8-BO) layers. The auxiliary sequential deposition method enables dramatic performance enhancement from 15% to over 18% compared to the blend casting and sequential deposition methods. Furthermore, by incorporating a branched-chain-engineered acceptor called L8-BO-X, device performance can be boosted to over 19% due to increased intermolecular packing, representing top-tier values for green-solvent processed organic solar cells. Comprehensive morphological and time-resolved characterizations reveal that the superior blend morphology achieved through the auxiliary sequential deposition method promotes charge generation while simultaneously suppressing charge recombination. This research underscores the potential of the auxiliary sequential deposition method for fabricating highly efficient organic solar cells using environmentally friendly solvents.

Multiple domestications of Asian rice.

The origin of domesticated Asian rice (Oryza sativa L.) has been controversial for more than half a century. The debates have focused on two leading hypotheses: a single domestication event in China or multiple domestication events in geographically separate areas. These two hypotheses differ in their predicted history of genes/alleles selected during domestication. Here we amassed a dataset of 1,578 resequenced genomes, including an expanded sample of wild rice from throughout its geographic range. We identified 993 selected genes that generated phylogenetic trees on which japonica and indica formed a monophyletic group, suggesting that the domestication alleles of these genes originated only once in either japonica or indica. Importantly, the domestication alleles of most selected genes (~80%) stemmed from wild rice in China, but the domestication alleles of a substantial minority of selected genes (~20%) originated from wild rice in South and Southeast Asia, demonstrating separate domestication events of Asian rice.

A Vinylene-Linker-Based Polymer Acceptor Featuring a Coplanar and Rigid Molecular Conformation Enables High-Performance All-Polymer Solar Cells with Over 17% Efficiency.

State-of-art Y-series polymer acceptors are typically based on a mono-thiophene linker, which can cause some twisted molecular conformations and thus limit the performance of all-polymer solar cells (all-PSCs). Here, a high-performance polymer acceptor based on vinylene linkers is reported, which leads to surprising changes in the polymers' molecular conformations, optoelectronic properties, and enhanced photovoltaic performance. It is found that the polymer acceptors based on thiophene or bithiophene linkers (PY-T-γ and PY-2T-γ) display significant molecular twisting between end-groups and linker units, while the vinylene-based polymer (PY-V-γ) exhibits a more coplanar and rigid molecular conformation. As a result, PY-V-γ demonstrates a better conjugation and tighter interchain stacking, which results in higher mobility and a reduced energetic disorder. Furthermore, detailed morphology investigations reveal that the PY-V-γ-based blend exhibits high domain purity and thus a better fill factor in its all-PSCs. With these, a higher efficiency of 17.1% is achieved in PY-V-γ-based all-PSCs, which is the highest efficiency reported for binary all-PSCs to date. This work demonstrates that the vinylene-linker is a superior unit to build polymer acceptors with more coplanar and rigid chain conformation, which is beneficial for polymer aggregation and efficient all-PSCs.

Solution-Processed, Inverted AgBiS2 Nanocrystal Solar Cells.

AgBiS2 nanocrystals are a promising nontoxic alternative to PbS, CsPbI3, and CdS quantum dots for solution-fabricated nanocrystal photovoltaics. In this work, we fabricated the first inverted (p-i-n) structure AgBiS2 nanocrystal solar cells. We selected spray-coated NiO as the hole-transporting material and used PCBM/BCP as the electron-transporting material. Combining transient photocurrent and photovoltage measurements with femtosecond transient absorption spectroscopy, we investigated the charge collection process on metal oxide/AgBiS2 interfaces and demonstrated that the NiO/AgBiS2 NC junction in the p-i-n configuration is more efficient for charge carrier collection. The fabricated p-i-n solar cells exhibited a 4.3% power conversion efficiency (PCE), which was higher than that of conventional n-i-p solar cells fabricated using the same sample. Additionally, inverted devices showed an ultrahigh short-circuit current (JSC) over 20.7 mA cm-2 and 0.38 V open-circuit voltage (VOC), suggesting their potential for further improvements in efficiency and, eventually, for large-scale production.