GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified "baiting and iterative ...mapping" approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).
Regulations currently in force enable to claim that the lead content in perovskite solar cells is low enough to be safe, or no more dangerous, than other electronics also containing lead. However, ...the actual environmental impact of lead from perovskite is unknown. Here we show that the lead from perovskite leaking into the ground can enter plants, and consequently the food cycle, ten times more effectively than other lead contaminants already present as the result of the human activities. We further demonstrate that replacing lead with tin represents an environmentally-safer option. Our data suggest that we need to treat the lead from perovskite with exceptional care. In particular, we point out that the safety level for lead content in perovskite-based needs to be lower than other lead-containing electronics. We encourage replacing lead completely with more inert metals to deliver safe perovskite technologies.
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In ...this study, 785 single‐copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian‐western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, provide insights into the complex biogeographic history in the Northern Hemisphere, and inspire a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming datasets.
Transition metal catalyzed C−H phosphorylation remains an unsolved challenge. Reported methods are generally limited in scope and require stoichiometric silver salts as oxidants. Reported here is an ...electrochemically driven RhIII‐catalyzed aryl C−H phosphorylation reaction that proceeds through H2 evolution, obviating the need for stoichiometric metal oxidants. The method is compatible with a variety of aryl C−H and P−H coupling partners and particularly useful for synthesizing triarylphosphine oxides from diarylphosphine oxides, which are often difficult coupling partners for transition metal catalyzed C−H phosphorylation reactions. Experimental results suggest that the mechanism responsible for the C−P bond formation involves an oxidation‐induced reductive elimination process.
Electric cell: Reported herein is an electrochemically driven RhIII‐catalyzed aryl C−H phosphorylation reaction which proceeds through H2 evolution. The method is compatible with a variety of aryl C−H and P−H coupling partners and particularly useful for synthesizing triarylphosphine oxides from diarylphosphine oxides. Experimental results suggest that the mechanism responsible for the C−P bond formation involves an oxidation‐induced reductive elimination process. DG=directing group.
Tunability and stability in the electrical properties of 2D semiconductors pave the way for their practical applications in logic devices. A robust layered indium selenide (InSe) field‐effect ...transistor (FET) with superior controlled stability is demonstrated by depositing an indium (In) doping layer. The optimized InSe FETs deliver an unprecedented high electron mobility up to 3700 cm2 V−1 s−1 at room temperature, which can be retained with 60% after 1 month. Further insight into the evolution of the position of the Fermi level and the microscopic device structure with different In thicknesses demonstrates an enhanced electron‐doping behavior at the In/InSe interface. Furthermore, the contact resistance is also improved through the In insertion between InSe and Au electrodes, which coincides with the analysis of the low‐frequency noise. The carrier fluctuation is attributed to the dominance of the phonon scattering events, which agrees with the observation of the temperature‐dependent mobility. Finally, the flexible functionalities of the logic‐circuit applications, for instance, inverter and not‐and (NAND)/not‐or (NOR) gates, are determined with these surface‐doping InSe FETs, which establish a paradigm for 2D‐based materials to overcome the bottleneck in the development of electronic devices.
A robust layered indium selenide (InSe) field‐effect transistor (FET) with superior high mobility (3700 cm2 V−1 s−1 at room temperature) is demonstrated by depositing an indium doping layer. With tunable carrier transport, the surface‐doped InSe FETs present flexible operations to realize various logic circuits, such as inverters and not‐or and not‐and gates.
The NLRP3 (nucleotide-binding oligomerization domain-like receptor NLR family pyrin domain-containing 3) inflammasome is a member of the NLR family of innate immune cell sensors. These are crucial ...regulators of cytokine secretions, which promote ischemic cell death and insulin resistance. This review summarizes recent progress regarding the NLRP3 inflammasome as a potential treatment for ischemic stroke in patients with diabetes, two complicated diseases that often occur together. Stroke worsens glucose metabolism abnormalities, and the outcomes after stroke are more serious for diabetic patients compared with those without diabetes. Inflammation contributes to organ injury after ischemic stroke and diabetes. Recent research has focused on inhibiting the activation of inflammasomes and thus reducing the maturation of proinflammatory cytokines such as interleukin (IL)-1β and IL-18. Studies suggest that inhibition of NLRP3 prevents or alleviates both ischemic stroke and diabetes. Targeting against the assembly and activity of the NLRP3 inflammasome is a potential and novel therapy for inflammasome-associated diseases, including ischemic stroke concomitant with diabetes.
Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly ...impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades.
Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation.
We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.
Sensing of benzene vapor is a hot spot due to the volatile drastic carcinogen even at trace concentration. However, achieving convenient and rapid detection is still a challenge. As a sort of ...functional porous material, metal‐organic frameworks (MOFs) have been developed as detection sensors by adsorbing benzene vapor and converting it into other signals (fluorescence intensity/wavelength, chemiresistive, weight or color, etc.). Supramolecular interaction between benzene molecules and the host framework, aperture size/shape and structural flexibility are influential factors in the performance of MOF‐based sensors. Therefore, enhancing the host‐guest interactions between the host framework and benzene molecules, or regulating the diffusion rate of benzene molecules by changing the aperture size/shape and flexibility of the host framework to enhance the detection signal are effective strategies for constructing MOF‐based sensors. This concept highlights several types of MOF‐based sensors for the detection of benzene vapor.
The development and challenges of benzene vapor sensors based on metal‐organic frameworks (MOFs), which achieve effective detection by virtue of the singal changes in weight, chemiresistive, fluorescence or color after adsorption.
With the widespread application of low-dose computed tomography (LDCT) technology, pulmonary nodules have aroused more attention. Significant alteration in plasma metabolite levels, mainly amino acid ...and lipid, have been observed in patients of PNs. However, evidence on the association between central carbon metabolism and PNs are largely unknown. The aim of this study was to investigate the underlying association of PNs and plasma central carbon metabolites. We measured the levels of 16 plasma central carbon metabolites in 1954 participants who gained LDCT screening in MALSC cohort. The inverse probability weighting (IPW) technique was used to control for bias due to self-selection for LDCT in the assessed high-risk population. The least absolute shrinkage and selection operator (LASSO) penalized regression was used to deal with the problem of multicollinearity among metabolites and the combined association of central carbon metabolites with PNs was estimated by using quantile g-computation (QgC) models. A quartile increase in 3-hydroxybutyric acid, gluconic acid, succinic acid and hippuric acid was positively associated with the PNs risk, whereas a quartile increase in 2-oxadipic acid and fumaric acid was negatively associated with the risk of PNs in multiple-metabolite models. A positive but insignificant joint associations of the mixture of 16 metabolites with PNs was observed by using QgC models analyses. Further studies are warranted to clarify the association between circulating metabolites and PNs and the biological mechanisms.
Natural killer/T cell lymphoma (NKTCL) is an aggressive and heterogeneous entity of non-Hodgkin lymphoma, strongly associated with Epstein-Barr virus (EBV) infection. To identify molecular subtypes ...of NKTCL based on genomic structural alterations and EBV sequences, we performed multi-omics study on 128 biopsy samples of newly diagnosed NKTCL and defined three prominent subtypes, which differ significantly in cell of origin, EBV gene expression, transcriptional signatures, and responses to asparaginase-based regimens and targeted therapy. Our findings thus identify molecular networks of EBV-associated pathogenesis and suggest potential clinical strategies on NKTCL.
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•Integrated analysis provides insight into the molecular classification in NKTCL•EBV lytic genes play an important role on NKTCL pathogenesis•Genomic alteration-based molecular subtypes associate with clinical outcomes•MYC, histone acetylation, and PD-L1/2 are potential therapeutic targets of NKTCL
Xiong et al. propose an updated molecular subtyping scheme based on integrated analysis of the genomic and transcriptomic features of natural killer/T cell lymphoma from patient biopsies, and provide insights into pathogenesis and therapeutic targeting of the disease.
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