De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions.

The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.

Competitive Uptake of Dimethylamine and Trimethylamine against Ammonia on Acidic Particles in Marine Atmospheres.

Alkaline gases such as NH3 and amines play important roles in neutralizing acidic particles in the atmosphere. Here, two common gaseous amines (dimethylamine (DMA) and trimethylamine (TMA)), NH3, and their corresponding ions in PM2.5 were measured semicontinuously using an ambient ion monitor-ion chromatography (AIM-IC) system in marine air during a round-trip cruise of approximately 4000 km along the coastline of eastern China. The concentrations of particulate DMA, detected as DMAH+, varied from <4 to 100 ng m-3 and generally decreased with increasing atmospheric NH3 concentrations. Combining observations with thermodynamic equilibrium calculations using the extended aerosol inorganics model (E-AIM) indicated that the competitive uptake of DMA against NH3 on acidic aerosols generally followed thermodynamic equilibria and appeared to be sensitive to DMA/NH3 molar ratios, resulting in molar ratios of DMAH+ to DMA + DMAH+ of 0.31 ± 0.16 (average ± standard deviation) at atmospheric NH3 concentrations over 1.8 µg m-3 (with a corresponding DMA/NH3 ratio of (1.8 ± 1.0) × 10-3), 0.80 ± 0.15 at atmospheric NH3 concentrations below 0.3 µg m-3 (with a corresponding DMA/NH3 ratio of (1.3 ± 0.6) × 10-2), and 0.56 ± 0.19 in the remaining cases. Particulate TMA concentrations, detected as TMAH+, ranged from <2 to 21 ng m-3 and decreased with increasing concentrations of atmospheric NH3. However, TMAH+ was depleted concurrently with the formation of NH4NO3 under low concentrations of atmospheric NH3, contradictory to the calculated increase in the equilibrated concentration of TMAH+ by the E-AIM.

Cajuputones A-C, ß-Triketone Flavanone Hybrids from the Branches and Leaves of Melaleuca cajuputi.

Three new ß-triketone flavanone hybrids, cajuputones A-C were obtained from Melaleuca cajuputi (the Australian 'tea tree'). The structures of cajuputones A-C were elucidated by 1D/2D NMR spectroscopy and HR-ESI-MS analyses; and their absolute configurations were established by electric circular dichroism (ECD) calculations using TDDFT method. Structurally, cajuputones A-C feature a rare 6/6/6/6 oxatetracyclic ring system fused between an acylphloroglucinol-derived ß-triketone and a pinocembrin or strobopinin moiety via an angle-type pyran-like motif. DFT-based conformational optimization in chloroform explained the similarity of the 1D NMR data of cajuputones B and C (C-2 epimers).

Recovery of non-reference sequences missing from the human reference genome.

BACKGROUND: The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of structure variations with NRS exist. RESULTS: Here, we compared 31 human de novo assemblies with the current reference genome to identify the NRS and their location. We resolved the precise location of 6113 NRS adding up to 12.8 Mb. Besides 1571 insertions, we detected 3041 alternate alleles, which were defined as having less than 90% (or none) identity with the reference alleles. These alternate alleles overlapped with 1143 protein-coding genes including a putative novel MHC haplotype. Further, we demonstrated that the alternate alleles and their flanking regions had high content of tandem repeats, indicating that their origin was associated with tandem repeats. CONCLUSIONS: Our study detected a large number of NRS including many alternate alleles which are previously uncharacterized. We suggested that the origin of alternate alleles was associated with tandem repeats. Our results enriched the spectrum of genetic variations in human genome.

New Structurally Diverse Limonoids from the Seeds of Khaya senegalensis.

Twelve new limonoids (khasenegasins O-Z; 1-12) with three different kinds of skeletons, including eight mexicanolides, two gedunins, and two andirobins, together with four known limonoids (13-16) were isolated from the seeds of Khaya senegalensis. Their structures were determined by extensive spectroscopic analyses (HR-ESI-MS, 1D/2D NMR), and the absolute configurations of 1 and 2 were established by the electronic circular dichroism exciton chirality method. Moreover, a new andirobin-type limonoid (12) showed significant neuroprotective activity against glutamate-induced injury in primary rat cerebellar granule neuronal cells with increased viability of 83.3 ± 6.0 % at 10 µM and 80.3 ± 3.2 % at 1 µM.

Synergy of Dendrites-Impeded Atomic Clusters Dissociation and Side Reactions Suppressed Inert Interface Protection for Ultrastable Zn Anode.

The sluggish ions-transfer and inhomogeneous ions-nucleation induce the formation of randomly oriented dendrites on Zn anode, while the chemical instability at anode-electrolyte interface triggers detrimental side reactions. Herein, this report in situ designs a multifunctional hybrid interphase of Bi/Bi2O3, for the first time resulting in a novel synergistic regulation mechanism involving: (i) chemically inert interface protection mechanism suppresses side reactions; and more fantastically, (ii) innovative thermodynamically favorable Zn atomic clusters dissociation mechanism impedes dendrites formation. Assisted by collaborative modulation behavior, the Zn@Bi/Bi2O3 symmetry cell delivers an ultrahigh cumulative plating capacity of 1.88 Ah cm-2 at 5 mA cm-2 and ultralong lifetimes of 300 h even at high current density and depth of discharge (10 mA cm-2, DODZn: 60%). Furthermore, under a low electrolyte-to-capacity ratio (E/C: 45 µL mAh-1) and negative-to-positive capacity ratio (N/P: 6.3), Zn@Bi/Bi2O3||MnO2 full-cell exhibits a superior capacity retention of 86.7% after 500 cycles at 1 A g-1, which outperforms most existing interphases. The scaled-up Zn@Bi/Bi2O3||MnO2 battery module (6 V, 1 Ah), combined with the photovoltaic panel, presents excellent renewable-energy storage ability and long output lifetime (12 h). This work provides a fantastic synergistic mechanism to achieve the ultrastable Zn anode and can be greatly promised to apply it into other metal-based batteries.

Correction: Effects of nurse-led transitional care interventions for patients with heart failure on healthcare utilization: A meta-analysis of randomized controlled trials.

[This corrects the article DOI: 10.1371/journal.pone.0261300.].

Effects of nurse-led transitional care interventions for patients with heart failure on healthcare utilization: A meta-analysis of randomized controlled trials.

BACKGROUND: Heart failure (HF) imposes a substantial burden on patients and healthcare systems. Hospital-to-home transitional care, involving time-limited interventions delivered predominantly by nurses, was introduced to lighten this burden. This study aimed to examine the effectiveness and dose-response of nurse-led transitional care interventions (TCIs) on healthcare utilization among patients with HF. METHODS: Health-related databases were systematically searched for articles published from January 2000 to June 2020. We included randomized controlled trials (RCTs) that compared nurse-led TCIs with usual care for adults hospitalized with HF and reported the following healthcare utilization outcomes: all-cause readmissions, HF-specific readmissions, emergency department visits, or length of hospital stay. Random-effects meta-analysis, meta-regression analysis, and dose-response analysis were performed to estimate the treatment effects and explain the heterogeneity. RESULTS: Twenty-five RCTs including 8422 patients with HF were included. Nurse-led TCIs for patients with HF resulted in a mean 9% (RR = 0.91; 95% CI = 0.82 to 0.99; p = 0.04; I2 = 46%) and 29% (RR = 0.71; 95% CI = 0.60 to 0.84; p < 0.0001; I2 = 0%) reduction in all-cause and HF-specific readmission risks respectively compared to usual care. The interventions were also effective in shortening the length of hospital stay (MD = -2.37; 95% CI = -3.16 to -1.58; p < 0.0001; I2 = 14%). However, no significant reduction was found for emergency department visits (RR = 0.96; 95% CI = 0.84 to 1.10; p = 0.58; I2 = 0%). The effect of meta-regression coefficients on all-cause and HF-specific readmissions was not statistically significant for any prespecified trial-level characteristic. Dose-response analysis revealed that the HF-specific readmission risk decreased in a dose-dependent manner with the complexity and intensity of nurse-led TCIs. CONCLUSIONS: Nurse-led TCIs were effective in decreasing all-cause and HF-specific readmission risks, as well as in reducing the length of hospital stay; however, the interventions were not effective in reducing the frequency of emergency department visits.

Fe2+ activating sodium percarbonate (SPC) to enhance removal of Microcystis aeruginosa and microcystins with pre-oxidation and in situ coagulation.

The frequent occurrence of cyanobacterial blooms has become a concern for drinking water safety. Common pre-oxidation, which was widely considered to enhance the followed coagulation, can cause the rupture of algae cell, leading to the undesirable release of intracellular organic matter. In this study, the Fe2+ activating sodium percarbonate (SPC/Fe2+) process for pre-oxidation and in situ coagulation was proved to effectively remove Microcystis aeruginosa without damaging cell integrity at optimal combined doses of SPC (0.2 mM) and Fe2+ (0.2 mM). Moreover, the SPC/Fe2+ process can not only control the release of MCs, but also reduce extracellular MCs from 5.22 µg/L to 1.50 µg/L, due to their moderate oxidation. Meanwhile, the SPC/Fe2+ treatment produces low levels of residual Fe after settling. During sludge ageing, owing to oxidation damage on cells arising from the SPC/Fe2+ treatment, cells continually suffered severe damage and lysed on day 4, leading to large release of intracellular organic matter and MCs, correspondingly. As a result, it is worth noting that the M. aeruginosa cells in stored sludge should be treated or disposed of early. These findings support the development of a green and cost-effective technology to handle cyanobacteria-containing water based on SPC/Fe2+ for ensuring water quality.

Dynamic metabolic and transcriptomic profiling reveals the biosynthetic characteristics of hydroxycinnamic acid amides (HCAAs) in sunflower pollen.

Sunflower pollen is a natural nutritious food with a long history and multiple functions, however, the main chemical components apart from flavonoids and their biosynthesis processes have not been thoroughly investigated. In this study, seven hydroxycinnamic acid amides (HCAAs) (1-7) abundant in sunflower pollen were isolated and identified as one type of the pollen's main chemicals. For a comprehensive understanding of HCAA biosynthesis in Helianthus annuus flowers, RNA-seq, metabolomics, and key genes related to biosynthesis in the sunflower were studied. A large number of compounds at different sunflower growth stages (the 7th, 14th, 21st, and 28th days) and high expression levels of related genes in the transcriptome were detected. A molecular network was constructed to clarify the synthetic pathway of HCAAs, which revealed high transcriptional levels of spermidine hydroxycinnamoyl transferase genes (HaSHT2795 and HaSHT2436) in 14-21-days-old flowers. HaSHT2795 enzymes catalyze tri-coumaroylspermidine formation, and virus-induced gene silencing to inhibit HaSHT2795 and HaSHT2436 could significantly reduce the synthesis of hydroxycinnamic acid amides in sunflower pollen. HCAAs were inferred to be related to the formation of pollen walls and the health effects of pollen. Analyzing HCAA biosynthesis and accumulation in H. annuus pollen will be helpful to understand the functions of HCAAs in the development of pollen and its nutritional value.

Toonasindiynes A-F, new polyacetylenes from Toona sinensis with cytotoxic and anti-inflammatory activities.

The plants of genus Toona are well known for diverse limonoid secondary metabolites, while polyacetylenes are rarely found from Toona species. In this work, six new polyacetylenes toonasindiynes A-F (1-6) and six known analogues (7-12) were isolated from the root bark of Toona sinensis. Their structures and absolute configurations were elucidated by HRESIMS, 1D and 2D NMR spectroscopic analysis, modified Mosher's method, and biosynthetic consideration. These polyacetylenes share the same 4,6-diyne moiety with different side chain length and different oxidation degree. Bioactivity screening revealed the cytotoxic activity of 3, 5, 9, and 11 against U2OS cells, and the inhibitory effects on nitric oxide (NO) production of 1, 2, 5, 8, 9, and 11 in lipopolysaccharide-induced RAW 264.7 cells.

Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data.

Pigs were domesticated independently in the Near East and China, indicating that a single reference genome from one individual is unable to represent the full spectrum of divergent sequences in pigs worldwide. Therefore, 12 de novo pig assemblies from Eurasia were compared in this study to identify the missing sequences from the reference genome. As a result, 72.5 Mb of non-redundant sequences (∼3% of the genome) were found to be absent from the reference genome (Sscrofa11.1) and were defined as pan-sequences. Of the pan-sequences, 9.0 Mb were dominant in Chinese pigs, in contrast with their low frequency in European pigs. One sequence dominant in Chinese pigs contained the complete genic region of the tazarotene-induced gene 3 (TIG3) gene which is involved in fatty acid metabolism. Using flanking sequences and Hi-C based methods, 27.7% of the sequences could be anchored to the reference genome. The supplementation of these sequences could contribute to the accurate interpretation of the 3D chromatin structure. A web-based pan-genome database was further provided to serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.

Highly oxygenated and rearranged limonoids from the stem barks of Entandrophragma utile.

Seventeen highly oxygenated and rearranged limonoids, including nine previously undescribed phragmalin-type limonoids with 1,8,9- and 8,9,30-orthesters (entanutilins C-K, 1-9), three undescribed limonoids with rare rearranged-6/6/7/5 skeleton (entanutilins L-N, 10-12), and 5 known limonoids, were isolated from the stem barks of Entandrophragma utile from Ghana (Africa). Their structures including absolute configurations were elucidated based on comprehensive spectroscopic analyses, such as HRESIMS, 1D/2D-NMR, CD exciton chirality method, time-dependent density functional theory (TDDFT)/ECD calculations, and single-crystal X-ray diffraction. Bioactivity screenings suggested that some of these compounds effectively reversed resistance in MCF-7/DOX cells at a nontoxic concentration of 30 µM with 6- to 19-fold enhancing effects.

New triterpenoids, steroids and lignan from the stem barks of Entandrophragma utile.

Eight new compounds (Entanutilins O-V; 1-8), including four limonoids, two steroids, one triterpenoid and one lignan were isolated from the stem barks of Entandrophragma utile. Their structures were determined by detailed spectroscopic analyses (HRESIMS and 1D/2D-NMR). Bioactivity screening indicated that compounds 1, 6 and 7 exhibited effective in reversing resistance in MCF-7/DOX cells at a nontoxic concentration of 30 µM with 18.18-, 7.43- and 7.94-fold enhancing effect, respectively, meanwhile, compounds 5 and 6 showed moderate NO inhibitory activities in LPS-activated RAW 264.7 macrophages.

Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome.

It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock. However, the rich diversity of worldwide goat breeds indicates that a genome from one individual would be insufficient to represent the whole genomic contents of goats. By comparing nine de novo assemblies from seven sibling species of domestic goat with ARS1 and using resequencing and transcriptome data from goats for verification, we identified a total of 38.3 Mb sequences that were absent in ARS1. The pan-sequences contain genic fractions with considerable expression. Using the pan-genome (ARS1 together with the pan-sequences) as a reference genome, variation calling efficacy can be appreciably improved. A total of 56,657 spurious SNPs per individual were repressed and 24,414 novel SNPs per individual on average were recovered as a result of better reads mapping quality. The transcriptomic mapping rate was also increased by ∼1.15%. Our study demonstrated that comparing de novo assemblies from closely related species is an efficient and reliable strategy for finding missing sequences from the reference genome and could be applicable to other species. Pan-genome can serve as an improved reference genome in animals for a better exploration of the underlying genomic variations and could increase the probability of finding genotype-phenotype associations assessed by a comprehensive variation database containing much more differences between individuals. We have constructed a goat pan-genome web interface for data visualization (http://animal.nwsuaf.edu.cn/panGoat).

Anti-inflammatory activity of Khayandirobilide A from Khaya senegalensis via NF-κB, AP-1 and p38 MAPK/Nrf2/HO-1 signaling pathways in lipopolysaccharide-stimulated RAW 264.7 and BV-2 cells.

BACKGROUND: Immunocytes-involved inflammation is considered to modulate the damage in various diseases. Herein, novel therapeutics suppressing over-activation of immunocytes could prove an effective strategy to prevent inflammation-related diseases. PURPOSE: The objective of this study is to evaluate the anti-inflammatory activity of Khayandirobilide A (KLA), a new andirobin-type limonoid with modified furan ring isolated from the Khaya senegalensis (Desr.) A. Juss., and to explore its potential underlying mechanisms in LPS-stimulated inflammatory models. METHODS: The structure of KLA was elucidated on the basis of 1D- and 2D-NMR spectroscopic data as well as HR-ESI-MS. As for its anti-inflammatory effect, the production of pro-inflammatory mediators and cytokines in LPS-stimulated RAW 264.7 and BV-2 cells were measured by Griess reagent, ELISA and qRT-PCR. The relevant proteins including nuclear factor κB (NF-κB), p-AKT, p-p38 and Nrf2/HO-1 were investigated by western blot. Nuclear localisations of NF-κB, activator protein-1 (AP-1) and Nrf2 were also examined by western blot and immunofluorescence. RESULTS: KLA could inhibit the production of LPS-induced NO with IC50 values of 5.04 ±â€¯0.14 µM and 4.97 ±â€¯0.5 µM in RAW 264.7 and BV-2 cells, respectively. KLA also attenuated interleukin-6 (IL-6), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) at the protein and mRNA levels. Further mechanistic studies demonstrated the activation of NF-κB and AP-1 were reduced by KLA. Moreover, KLA elevated expression of heme oxygenase-1(HO-1) via inducing Keap1 autophagic degradation and promoting Nrf2 nuclear translocation. Despite KLA induced the phosphorylation of mitogen-activated protein kinases (MAPKs) family, inhibiting the phosphorylation of p38 by its specific inhibitor SB203580 attenuated the degradation of KLA-induced Keap1, and then reduced KLA-induced Nrf2 nuclear translocation and HO-1 expression. Furthermore, SB203580, Brusatol (a Nrf2 specific inhibitor) and ZnPP (a HO-1 specific inhibitor) could partly reverse the suppressive effects of KLA on LPS-induced NO production and mRNA levels of pro-inflammatory genes. CONCLUSION: These data displayed that KLA possessed anti-inflammatory activity, which was attributed to inhibit the release of LPS-stimulated inflammatory mediators via suppressing the activation of NF-κB, AP-1, and upregulating the induction of p38 MAPK/Nrf2-mediated HO-1.