High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We ...used a newly developed pool of 96 synthetic RNAs with various lengths, and GC content covering a 2(20) concentration range as spike-in controls to measure sensitivity, accuracy, and biases in RNA-seq experiments as well as to derive standard curves for quantifying the abundance of transcripts. We observed linearity between read density and RNA input over the entire detection range and excellent agreement between replicates, but we observed significantly larger imprecision than expected under pure Poisson sampling errors. We use the control RNAs to directly measure reproducible protocol-dependent biases due to GC content and transcript length as well as stereotypic heterogeneity in coverage across transcripts correlated with position relative to RNA termini and priming sequence bias. These effects lead to biased quantification for short transcripts and individual exons, which is a serious problem for measurements of isoform abundances, but that can partially be corrected using appropriate models of bias. By using the control RNAs, we derive limits for the discovery and detection of rare transcripts in RNA-seq experiments. By using data collected as part of the model organism and human Encyclopedia of DNA Elements projects (ENCODE and modENCODE), we demonstrate that external RNA controls are a useful resource for evaluating sensitivity and accuracy of RNA-seq experiments for transcriptome discovery and quantification. These quality metrics facilitate comparable analysis across different samples, protocols, and platforms.
Ethylene response factor (ERF) gene family plays an important role in abiotic stress responses. In this study, we isolated a salt-inducible ERF gene,
ERF38
(Potri.006G138900.1), from the 84K poplar (
...Populus alba × Populus glandulosa
) and investigated its functions in salt and osmotic tolerance. We identified that ERF38 protein was targeted to nucleus and had no self-activation. Results from yeast-one-hybrid indicated that the ERF38 protein can specifically bind to the dehydration responsive element (DRE). We then successfully transferred the
ERF38
gene into the 84K poplar. Under respective salt and polyethylene glycol (PEG)-6000 stresses, four of the physiological traits, including peroxidase (POD) and superoxide dismutase (SOD) activities, soluble protein content, and proline content, increased significantly in the transgenic plants, compared to the wild type. Regarding the other two parameters, hydrogen peroxide (H
2
O
2
) and malondialdehyde (MDA) content, their increments in the transgenic lines under the stresses, which were compared to the water control, were significantly low than that of the wild type. In addition, reactive oxygen species (ROS) are scavenged in the transgenic lines under the stresses, but not in the wild type (WT). Interestingly, when challenged with the stresses, expression levels of a few genes associated with POD and SOD metabolism were significantly increased in the transgenic poplars. In all, evidence from morphological, physiological, and biochemical analyses indicated that over-expression of
ERF38
gene can improve salt and osmotic tolerance in the transgenic poplar.
NAC (NAM/ATAF/CUC) is one of the largest plant-specific transcription factor (TF) families known to play significant roles in wood formation. Acting as master gene regulators, a few NAC genes can ...activate secondary wall biosynthesis during wood formation in woody plants.
In the present study, firstly, we screened 110 differentially expressed NAC genes in the leaves, stems, and roots of di-haploid Populus simonii×P. nigra by RNA-Seq. Then we identified a nucleus-targeted gene, NAC15 gene, which was one of the highly expressed genes in the stem among 110 NAC family members. Thirdly, we conducted expression pattern analysis of NAC15 gene, and observed NAC15 gene was most highly expressed in the xylem by RT-qPCR. Moreover, we transferred NAC15 gene into tobacco and obtained 12 transgenic lines overexpressing NAC15 gene (TLs). And the relative higher content of hemicellulose, cellulose and lignin was observed in the TLs compared to the control lines containing empty vector (CLs). It also showed darker staining in the culms of the TLs with phloroglucinol staining, compared to the CLs. Furthermore, the relative expression level of a few lignin- and cellulose-related genes was significantly higher in the TLs than that in the CLs.
The overall results indicated that NAC15 gene is highly expressed in the xylem of poplar and may be a potential candidate gene playing an important role in wood formation in transgenic tobacco.
A high-quality remote sensing interpretation dataset has become crucial for driving an intelligent model, i.e., deep learning (DL), to produce land-use/land-cover (LULC) products. The existing remote ...sensing datasets face the following issues: the current studies (1) lack object-oriented fine-grained information; (2) they cannot meet national standards; (3) they lack field surveys for labeling samples; and (4) they cannot serve for geographic engineering application directly. To address these gaps, the national-standards- and DL-oriented raster and vector benchmark dataset (RVBD) is the first to be established to map LULC for conducting soil water erosion assessment (SWEA). RVBD has the following significant innovation and contributions: (1) it is the first second-level object- and DL-oriented dataset with raster and vector data for LULC mapping; (2) its classification system conforms to the national industry standards of the Ministry of Water Resources of the People’s Republic of China; (3) it has high-quality LULC interpretation accuracy assisted by field surveys rather than indoor visual interpretation; and (4) it could be applied to serve for SWEA. Our dataset is constructed as follows: (1) spatio-temporal-spectrum information is utilized to perform automatic vectorization and label LULC attributes conforming to the national standards; and (2) several remarkable DL networks (DenseNet161, HorNet, EfficientNetB7, Vision Transformer, and Swin Transformer) are chosen as the baselines to train our dataset, and five evaluation metrics are chosen to perform quantitative evaluation. Experimental results verify the reliability and effectiveness of RVBD. Each chosen network achieves a minimum overall accuracy of 0.81 and a minimum Kappa of 0.80, and Vision Transformer achieves the best classification performance with overall accuracy of 0.87 and Kappa of 0.86. It indicates that RVBD is a significant benchmark, which could lay a foundation for intelligent interpretation of relevant geographic research about SWEA in the Yangtze River Basin and promote artificial intelligence technology to enrich geographical theories and methods.
The poor stability of CsPbX
3
(X = Cl, Br, I) perovskite nanocrystals is the most impediment to its application in the field of photoelectrics. In this work, monodisperse CsPbBr
3
/TiO
2
nanocrystals ...are successfully prepared by coating titanium precursor on the surface of colloidal CsPbBr
3
nanocrystals at room temperature. The CsPbBr
3
/TiO
2
nanocomposites exhibit excellent stability, remaining the identical particle size (9.2 nm), crystal structures and optical properties. Time-resolved photoluminescence decay shows that the lifetime of CsPbBr
3
/TiO
2
nanocrystals is about 4.04 ns and keeps great stability after lasting two months in the air. Results show that the coating of TiO
2
on CsPbBr
3
NCs greatly suppressed the anion exchange and photodegradation, which are the main reasons for dramatically improving their chemical stability and photostability. The results provide an effective method to solve the stability problem of perovskite nanostructures and are expected to have a promising application in optoelectronic fields
Article highlights
1. Prepared the all-inorganic CsPbBr
3
/TiO
2
core/shell perovskite nanocrystals by an easy method.
2. Explored its essences of PL and lifetime of the synthesized CsPbBr
3
/TiO
2
perovskite nanocrystals.
3. CsPbBr
3
/TiO
2
nanocrystals show the great thermal stability after the post-annealing.
4. The CsPbBr
3
/TiO
2
nanocrystals have a high PLQY and have a promising application in solar cells.
Wound healing is a complex system including such key players as host, microbe, and treatments. However, little is known about their dynamic interactions. Here we explored the interplay between: (1) ...bacterial bioburden and host immune responses, (2) bacterial bioburden and wound size, and (3) treatments and wound size, using murine models and various treatment modalities: Phosphate buffer saline (PBS or vehicle, negative control), doxycycline, and two doses of
A. baumannii
phage mixtures. We uncovered that the interplay between bacterial bioburden and host immune system may be bidirectional, and that there is an interaction between host CD3
+
T-cells and phage dosage, which significantly impacts bacterial bioburden. Furthermore, the bacterial bioburden and wound size association is significantly modulated by the host CD3
+
T-cells. When the host CD3
+
T-cells (x on log10 scale) are in the appropriate range (1.35 < x < = 1.5), we observed a strong association between colony forming units (CFU) and wound size, indicating a hallmark of wound healing. On the basis of the findings and our previous work, we proposed an integrated parallel systems biology model.
D. melanogaster is increasingly used as a lipid metabolism model, but the D. melanogaster metabolome is not well studied. A number of studies strongly suggest that lipid metabolism is linked to ...sexual behavior and gametogenesis.
We determined the levels of 400 different lipids in the non-gonadal soma of D. melanogaster females and males. We found higher levels of saturated cholesterol esters and lysophosphatidylcholine in males, and higher levels of polyunsaturated cholesterol esters in females. We also determined the levels of these lipids in females and males without a germline to determine if the absence of gamete "sinks" for metabolic products, such as yolk and lipid deposits in eggs, altered somatic lipid profiles. We observed little change in lipid profiles between these samples.
Overall lipid compositions are similar between the sexes, although there are differences in saturation states of two lipid classes, where saturated fatty acids were male-biased and polyunsaturated fatty acids were female-biased. The presence of a germline did not significantly influence lipid profiles, raising the possibility that germline-dependent changes in metabolic gene expression patterns serve a homeostatic purpose.
Protein-DNA interactions play a significant role in gene regulation and expression. In order to identify transcription factor binding sites (TFBS) of double sex (DSX)-an important transcription ...factor in sex determination, we applied the DNA adenine methylation identification (DamID) technology to the fat body tissue of Drosophila, followed by deep sequencing (DamID-Seq). One feature of DamID-Seq data is that induced adenine methylation signals are not assured to be symmetrically distributed at TFBS, which renders the existing peak calling algorithms for ChIP-Seq, including SPP and MACS, inappropriate for DamID-Seq data. This challenged us to develop a new algorithm for peak calling. A challenge in peaking calling based on sequence data is estimating the averaged behavior of background signals. We applied a bootstrap resampling method to short sequence reads in the control (Dam only). After data quality check and mapping reads to a reference genome, the peaking calling procedure compromises the following steps: 1) reads resampling; 2) reads scaling (normalization) and computing signal-to-noise fold changes; 3) filtering; 4) Calling peaks based on a statistically significant threshold. This is a non-parametric method for peak calling (NPPC). We also used irreproducible discovery rate (IDR) analysis, as well as ChIP-Seq data to compare the peaks called by the NPPC. We identified approximately 6,000 peaks for DSX, which point to 1,225 genes related to the fat body tissue difference between female and male Drosophila. Statistical evidence from IDR analysis indicated that these peaks are reproducible across biological replicates. In addition, these peaks are comparable to those identified by use of ChIP-Seq on S2 cells, in terms of peak number, location, and peaks width.
Alloxan (AL)-generated Reactive Oxygen Species (ROS) selectively destroy insulin-producing pancreatic β-cells. A previous genome-wide scan (GWS) using a cohort of 296 F2 hybrids between NOD ...(AL-sensitive) and ALR (AL-resistant) mice identified linkages contributing to β-cell susceptibility or resistance to AL-induced diabetes on Chromosomes (Chr) 2, 3, 8, and a single nucleotide polymorphism in
mt-Nd2
of the mitochondrial genome (mtDNA). AL treatment of congenic and consomic NOD mouse stocks confirmed resistance linked to both the mtDNA and the Chr 8 locus from ALR NOD.mt
ALR
.ALR-(
D8Mit293-D8Mit137
). To identify possible epistatic interactions, the GWS analysis was expanded to 678 F2 mice. ALR-derived diabetes-resistance linkages on Chr 8 as well as the
mt-Nd2
a
allele were confirmed and novel additional linkages on Chr 4, 5, 6, 7, and 13 were identified. Epistasis was observed between the linkages on Chr 8 and 2 and Chr 8 and 6. Furthermore, the
mt-Nd2
genotype affected the epistatic interactions between Chr 8 and 2. These results demonstrate that a combination of nuclear-cytoplasmic genome interactions regulates β-cell sensitivity to ROS-mediated ALD.
The BCS then underwent systemic treatment in the Breast Cancer Center of Chongqing and were then followed up in the outpatient clinic from October 2019 to June 2020. ...we enrolled a total of 370 BCS ...and 3700 age- and sex-matched normal healthy subjects in the proportion of 1:10. The high-density lipoprotein (HDL)–cholesterol was significantly lower in the cancer group (1.49 mmol/L) compared to 1.56 mmol/L in the non-cancer controls (1.56 mmol/L); the level of HDL-cholesterol was obviously lower in the cancer group (1.49 mmol/L). The total cholesterol and low-density lipoprotein-cholesterol level among BCS were significantly lower (5.00 mmol/L IQR 4.37–5.63) and (2.77 mmol/L IQR 2.16–3.43) compared to the controls ((5.01 mmol/L IQR 4.39–5.66) and (3.07 mmol/L IQR 2.52–3.66), respectively.
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