Simulation of the Resonance Raman Spectrum for Uracil

The resonance Raman spectrum of uracil is simulated using the Herzberg–Teller short-time dynamics formalism. The ground-state geometry is optimized at the levels of PBE0/aug-cc-pVTZ and B3LYP/aug-cc-pVTZ, respectively. The gradient of the bright excited state is computed using time-dependent density functional theory and spin-flip time-dependent density functional theory. The excited-state calculations are carried out in both the gas phase and implicit water using the conductor-like polarizable continuum model. The ground-state equilibrium structure is found to impact the resulting resonance Raman spectrum significantly. The simulated resonance Raman spectrum using the long-range corrected functionals, that is, CAMB3LYP and LC-BLYP, and based on the PBE0/aug-cc-pVTZ optimized ground-state structure shows better agreement with the experimental spectrum than using standard hybrid functionals, that is, PBE0 and B3LYP. The solvation effect leads to a change in the energetic order of the <i>n</i> → π* and π → π* excited states, and it improves the agreement with the experimental spectrum, especially with regard to the relative intensities of the peaks with frequencies greater than 1600 cm^–1

Simulation of the Resonance Raman Spectra for 5‑Halogenated (F, Cl, and Br) Uracils

The resonance Raman spectra of the 5-halogenated (F, Cl, and Br) uracils are simulated via the Herzberg–Teller (HT) short-time dynamics formalism. The gradient of the S₁ excited state is computed at the CAMB3LYP/aug-cc-pVTZ level of theory in the conductor-like polarizable continuum model for water (C-PCM, H₂O), based on the equilibrium geometry determined using PBE0/aug-cc-pVTZ in H₂O (C-PCM). The simulated resonance Raman spectra show good agreement with the experimental spectra in terms of both peak positions and intensities. The differences between the resonance Raman spectra of the three 5-halogenated uracils, caused by the effect of halogen substitution, are examined in terms of ground-state normal-mode eigenvectors and excited-state Cartesian gradients, according to the HT formalism. The differences in the normal-mode eigenvectors and excited-state Cartesian gradients between 5-fluorouracil and 5-chlorouracil are used to interpret the dissimilarity between their resonance Raman spectra. Meanwhile, the similarity between the spectra of 5-chlorouracil and 5-bromouracil is explained by the correspondence between their normal modes and excited-state gradients

DataSheet_1_Bibliometric analysis of global research trends on small-cell lung cancer (2012–2021).docx

BackgroundSmall-cell lung cancer (SCLC) is a recalcitrant tumor with a poor prognosis. With the rise of SCLC research in the past decade, this study aims to analyze the foundation and frontiers of SCLC research through bibliometric analysis.MethodsRelevant publications from the Web of Science Core Collection were retrieved on January 3, 2022. R package bibliometrix and EXCEL2019 were used to analyze quantitative variables. Bibliometric mapping was constructed by VOS viewer and CiteSpace software to visualize citation, co-authorship, co-occurrence, and co-citation analysis of countries/regions, organizations, authors, references, and keywords.ResultsA total of 2,361 publications related to SCLC were identified with the total amount of articles steadily increasing, where China is the most productive country with 859 papers. Scholars and organizations from the United States, China, and Europe are primary sources of this research, among which the University of Texas MD Anderson Cancer Center made the most contribution to the field with 122 papers. Lung Cancer published the highest number of SCLC-related articles with a total of 121, while the Journal of Thoracic Oncology received the most citations totaling 3,098. Rudin, Charles M., and Sage, Julien are the most creative author. Leora, Horn, 2018, New Engl J Med and Rudin, Charles M., Nat Genet, 2012 can be categorized as classic literature owing to their high citations or strong sigma value. “Heterogeneity & Subtypes” and “Immunotherapy” may be the new frontiers in the SCLC domain.ConclusionResearch on SCLC showed an upward trend based on the current global situation. Moreover, the current scope of collaboration in SCLC research is chiefly regional, which should further focus on transnational cooperation in the future. More attention should be devoted to “Heterogeneity & Subtypes” and “Immunotherapy”, which will be the hotspots in future research.</p

Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (<i>Oryza</i>)

<div><p>Background</p><p>Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica) and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown.</p><p>Methodology/Principal Findings</p><p>We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of <i>Oryza</i> by genomic in situ hybridization (GISH) and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs) and methylation stability of their flanking regions were also assessed. We made the following principle findings: (<i>i</i>) all three triploid hybrids are stable in both chromosome number and gross structure; (<i>ii</i>) stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (<i>iii</i>) alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (<i>iv</i>) transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner.</p><p>Conclusions/Significance</p><p>Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus <i>Oryza</i> are chromosomally stable but show immediate and highly stochastic genetic and epigenetic instabilities at the molecular level. These novel hybrids might provide a rich resource of genetic and epigenetic diversities for potential utilization in rice genetic improvements.</p></div

Frequencies and chromosomal location of genetic and DNA methylation changes detected by AFLP and MSAP.

<p>(A) Frequencies of genetic changes detected by AFLP analysis and revealed by various patterns of variant bands in the three F1 hybrids. (B) Frequencies of DNA methylation changes detected by MSAP analysis and revealed by various patterns of cytosine methylation in the three F1 hybrids. In both (A) and (B), the variant bands in the hybrids were determined by comparison with the parental mix. (C) Chromosomal location of the variant AFLP and MSAP bands. The three colors (red, green and purple) denote origins of variant bands from Hybrid 1, Hybrid 2 and Hybrid 3, respectively.</p

Frequencies and chromosomal locations of DNA methylation changes occurred in <i>mPing</i> and <i>Dasheng</i> flanking sequence.

<p>(A) Frequencies of DNA methylation changes in the 5’ flanks of <i>mPing</i> detected by MSTD in the three F1 hybrids. (B) Frequencies of DNA methylation changes in the 3’ flanks of <i>Dasheng</i> detected by MSTD in the three F1 hybrids. (C) Chromosomal locations of <i>mPing</i>, <i>Dasheng</i> innate copies in the Nipponbare genome and variant MSTD bands in the three F1 hybrids. Horizontal lines represent chromsomes of rice, triangles below the horizontal lines indicate the innate <i>mPing</i> and <i>Dasheng</i> copies, and triangles above the horizontal lines indicate the locations of DNA methylation changes.</p

Examples of TE mobility, DNA methylation alterations, and transcriptional activation in the three F1 hybrids.

<p>(A) Southern blot hybridization patterns of three TEs in the three hybrids, respectively, along with the corresponding parents and their mix. The DNA samples were digested with <i>Xba</i>I and a pair of cytosine methylation-sensitive isoschizomers, <i>Hpa</i>II and <i>Msp</i>I, respectively. (a) <i>Osr7</i>, which showed transpositional activation in several individuals of Hybrid 1; (b) <i>Lullaby</i>, which showed CG hypomethylation in several individuals of Hybrid 2; (c) <i>Tos17</i>, which showed immobility in all individuals of Hybrid 3. Red arrow indicates novel bands, blue arrow indicates loss of bands. (B) Transcriptional activation of TEs in the three F1 hybrids based on semi-quentitative RT-PCR analysis. A cDNA sample from callus of Nipponbare (six-month old) was included as a positive control, red arrows indicate transcriptional activation in the hybrids relative to their parents and mix (the <i>invitro</i> "hybrids").</p

Additional file 1 of A pretreatment prediction model of grade 3 tumors classed by the IASLC grading system in lung adenocarcinoma

Additional file 1: Supplementary Table 1. Baseline characteristics of training and validation set

Hybrid weakness in a rice interspecific hybrid is nitrogen-dependent, and accompanied by changes in gene expression at both total transcript level and parental allele partitioning

<div><p>Background</p><p>Hybrid weakness, a phenomenon opposite to heterosis, refers to inferior growth and development in a hybrid relative to its pure-line parents. Little attention has been paid to the phenomenological or mechanistic aspect of hybrid weakness, probably due to its rare occurrence.</p><p>Methodology/Principal findings</p><p>Here, using a set of interspecific triploid F1 hybrids between <i>Oryza sativa</i>, ssp. <i>japonica</i> (genome AA) and a tetraploid wild rice species, <i>O</i>. <i>alta</i> (genome, CCDD), we investigated the phenotypic and physiological differences between the F1 hybrids and their parents under normal and nitrogen-limiting conditions. We quantified the expression levels of 21 key genes involved in three important pathways pertinent to the assayed phenotypic and physiological traits by real-time qRT-PCR. Further, we assayed expression partitioning of parental alleles for eight genes in the F1 hybrids relative to the <i>in silico</i> “hybrids” (parental cDNA mixture) under both normal and N-limiting conditions by using locus-specific cDNA pyrosequencing.</p><p>Conclusions/Significance</p><p>We report that the F1 hybrids showed weakness in several phenotypic traits at the final seedling-stage compared with their corresponding mid-parent values (MPVs). Nine of the 21 studied genes showed contrasted expression levels between hybrids and parents (MPVs) under normal vs. N-limiting conditions. Interestingly, under N-limiting conditions, the overtly enhanced partitioning of maternal allele expression in the hybrids for eight assayed genes echo their attenuated hybrid weakness in phenotypes, an observation further bolstered by more resemblance of hybrids to the maternal parent under N-limiting conditions compared to normal conditions in a suite of measured physiological traits. Our observations suggest that both overall expression level and differential partitioning of parental alleles of critical genes contribute to condition-specific hybrid weakness.</p></div

Cytology and typical phenotypes of the F1 triploid hybrid plants between <i>Oryza sativa</i> ssp. <i>japonica</i> (<i>2n</i> = 2x = 24, genome AA) and <i>O</i>. <i>alta</i> (<i>2n</i> = 4x = 48, genome, CCDD) under both normal and N-limiting conditions.

<p>(<b>A</b>) Diagrams showing genesis of the F1 triploid rice hybrids; (<b>B</b>) Typical chromosomal constitution of the triploid hybrids based on multicolor GISH analysis (Bar = 10 μm). The pink-colored chromosomes belong to the A genome, green-colored chromosomes are the C genome and blue-colored chromosomes are the D genome; (<b>C</b>) Whole plant dry weight of parental plants (MPVs) and F1 hybrids under normal and N-limiting conditions, WPDW stands for whole plant dry weight. Different letters among genotypes of the same treatment denote statistical differences (based on the least significant difference or LSD test, <i>P</i> < 0.05). The capital and small letters refer to corresponding indices of normal and N-limiting conditions, respectively, Error bars indicate s.d., n (replicates) = 3 to 4; (<b>D-G</b>) The growth rates and whole plant fresh weight of parental plants (MPVs) and F1 hybrids under normal and N-limiting conditions after the treatment for 4 weeks, the blue-dotted lines represent normal conditions and the yellow-dotted lines N-limiting conditions, WPFW stands for whole plant fresh weight, error bars indicate s.d., n (replicates) = 3 to 4; (<b>H</b>) Whole plant phenotypic differences between normal and N-limiting conditions at the final seedling stage (Bar = 10 cm).</p