We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment ...indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets,
N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.
Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the ...sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2-149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.
Abstract
We carefully investigate the comprehensive impact of atom-cavity interaction and artificial magnetic fields on quantum phase transitions of anti-Jaynes-Cummings triangle model in the ...infinite frequency limit. We discover that ground states of the optical field can be a gapped normal phase (NP) or three kinds of gapless superradiant phases with infinite degeneracy. When the atom-cavity coupling is weak, the optical field is in a NP, which is a vacuum with no photons. Otherwise, it will stay at one of the superradiant phases: a normal superradiant phase without photon currents and another two chiral superradiant phases with opposite photon currents. The former only breaks the continuous
U
(1) symmetry and its gapless excitations are normal Goldstone modes. Nevertheless, the latter, mainly induced by an external synthetic gauge field, break both the continuous
U
(1) symmetry and chiral symmetry, thereby corresponding gapless excitations are chiral Goldstone modes. In addition, we also propose a detecting scheme to distinguish these superradiant phases.
Development of new porous materials as hosts to suppress the dissolution and shuttle of lithium polysulfides is beneficial for constructing highly efficient lithium–sulfur batteries (LSBs). Although ...2D covalent organic frameworks (COFs) as host materials exhibit promising potential for LSBs, their performance is still not satisfactory. Herein, we develop polyimide COFs (PI-COF) with a well-defined lamellar structure, which can be exfoliated into ultrathin (∼1.2 nm) 2D polyimide nanosheets (PI-CONs) with a large size (∼6 μm) and large quantity (40 mg/batch). Explored as new sulfur host materials for LSBs, PI-COF and PI-CONs deliver high capacities (1330 and 1205 mA h g–1 at 0.1 C, respectively), excellent rate capabilities (620 and 503 mA h g–1 at 4 C, respectively), and superior cycling stability (96% capacity retention at 0.2 C for PI-CONs) by virtue of the synergy of robust conjugated porous frameworks and strong oxygen–lithium interactions, surpassing the vast majority of organic/polymeric lithium–sulfur battery cathodes ever reported. Our finding demonstrates that ultrathin 2D COF nanosheets with carbonyl groups could be promising host materials for LSBs with excellent electrochemical performance.
Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent ...differentiation of ancient plants.
Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2-8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47-53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf.
We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize.
(Mont.) de Bary, the oomycotic pathogen responsible for potato late blight, is the most devastating disease of potato production. The primary pesticides used to control oomycosis are phenyl amide ...fungicides, which cause environmental pollution and toxic residues harmful to both human and animal health. To address this, an antimicrobial peptide, NoPv1, has been screened to target
cellulose synthase 2 (PvCesA2) to inhibit the growth of
(
). In this study, we employed AlphaFold2 to predict the three-dimensional structure of PvCesA2 along with NoPv peptides. Subsequently, utilizing computational methods, we dissected the interaction mechanism between PvCesA2 and these peptides. Based on this analysis, we performed a saturation mutation of NoPv1 and successfully obtained the double mutants DP1 and DP2 with a higher affinity for PvCesA2. Meanwhile, dynamics simulations revealed that both DP1 and DP2 utilize a mechanism akin to the barrel-stave model for penetrating the cell membrane. Furthermore, the predicted results showed that the antimicrobial activity of DP1 was superior to that of NoPv1 without being toxic to human cells. These findings may offer insights for advancing the development of eco-friendly pesticides targeting various oomycete diseases, including late blight.
Abstract
We propose to protect fluxonium qubits that are away from half flux quantum against environmental noises, especially
1
/
f
flux noise, by adopting a modulated flux with ...tunable-complex-amplitude. Using open-system Floquet theory, we derive a Lindblad equation and extract decoherent rates for pure-dephasing, excitation and relaxation. After examining intrinsic attributes of the flux driven fluxonium qubit, we put forward an analytic manner to locate dynamical sweet spots for fast and weak driving. Continuous families of dynamical sweet spots are found in the parameter plane of relative amplitude factor and relative phase. Around a family of dynamical sweet spots or between two families of dynamical sweet spots, there exist continuous regions with long coherent times that exceed
100
μ
s
. Taking advantage of the two noise-insensitive channels: relative amplitude factor and relative phase, a flux driven fluxonium qubit can become immune to flux noises from both the dc and ac flux amplitudes. And the optimal driving amplitudes are no longer isolated at a certain driving frequency, but become continuous. This is in sharp contrast to the usual schemes based on flux modulation with real-amplitude. As a result, there are plenty of manipulating flexibility in our flux driving scheme with tunable-complex-amplitude, which may be useful in logical operations among flux driven fluxonium qubits or other flux qubits.
Purpose
Breast cancer is the most common type of cancer with high incidence in women. Currently, identifying new therapies that selectively inhibit tumor growth without damaging normal tissue are a ...major challenge of cancer research. One of the features of cancer cells is that they do not consume more oxygen even under normal oxygen circumstances but prefer to aerobic glycolysis through the enhanced catabolism of glucose and glutamine. In this study, we investigate the mechanisms of the radioresistance in breast cancer cells.
Methods
Human breast cancer cells MDA-MB-231 and MCF-7 were treated with radiation alone, Glut1 inhibitor alone or the combination of both to evaluate cell glucose metabolism and apoptosis. By the establishment of radioresistant cell line, we investigate the mechanisms of the combined treatments of radiation with Glut1 inhibitor in the radioresistant cells.
Results
The glucose metabolism and the expression of Glut1 are significantly stimulated by radiotherapy. We report the radioresistant breast cancer cells exhibit upregulated Glut1 expression and glucose metabolism. In addition, we observed overexpression of Glut1 renders breast cancer cells resistant to radiation and knocking down of Glut1 sensitizes breast cancer cells to radiation. We treated breast cancer cells with radiation and WZB117 which inhibits Glut1 expression and glucose metabolism and found the combination of WZB117 and radiation exhibits synergistically inhibitory effects on breast cancer cells. Finally, we demonstrate the inhibition of Glut1 re-sensitizes the radioresistant cancer cells to radiation.
Conclusions
This study reveals the roles of Glut1 in the radiosensitivity of human breast cancer. It will provide new mechanisms and strategies for the sensitization of cancer cells to radiotherapy through regulation of glucose metabolism.
STUDY DESIGN.A retrospective study.
OBJECTIVE.The purpose of this study was to identify the independent risk factors for postoperative surgical site infection (SSI) after posterior lumbar spinal ...surgery based on the perioperative factors analysis.
SUMMARY OF BACKGROUND DATA.SSI is one of the most common complications after spinal surgery. Previous studies have identified different risk factors for postoperative SSI after lumbar spinal surgery. However, most of the studies were focused on the patient and procedure-related factors. Few studies reported the correlation between laboratory tests and postoperative SSI.
METHODS.A retrospective study was carried out in a single institution. Patients who underwent posterior lumbar spinal surgery between January 2010 and August 2016 were included in this study. All patients’ medical records were reviewed and patients with postoperative SSI were identified. Perioperative variables were included to determine the risk factors for SSI by univariate and multivariate regression analysis.
RESULTS.A total of 2715 patients undergoing posterior lumbar spinal surgery were included in this study. Of these patients, 64 (2.4%) were detected with postoperative SSI, including 46 men and 18 women. Diabetes mellitus (P = 0.026), low preoperative serum level of calcium (P = 0.009), low preoperative and postoperative albumin (P = 0.025 and 0.035), high preoperative serum glucose (P = 0.029), multiple fusion segments (P < 0.001), increased surgical time and estimated blood loss (P = 0.023 and 0.005), decreased postoperative hemoglobin (P = 0.008), and prolonged drainage duration (P = 0.016) were found to be the independent risk factors for SSI. Multilevel fusion and a history of diabetes mellitus were the two strongest risk factors (odds ratio = 2.329 and 2.227) for SSI.
CONCLUSION.Based on a large population analysis, previous reported risk factors for SSI were confirmed in this study while some new independent risk factors were identified significantly associated with SSI following lumbar spinal surgery, including preoperative low serum level of calcium, decreased preoperative and postoperative albumin, and decreased postoperative hemoglobin.Level of Evidence4
Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for ...all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.
This study reports two gap-free reference genomes for Oryza sativa xian/indica varieties ZS97 and MH63, which are used as a model system for studying rice heterosis and yield. Further genomic analyses show that the architectures of functional centromeres are extensively variable at the sequence level. These two gap-free rice genomes provide a new standard for assembling reference genomes of other plant species.
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