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Understanding the genetic basis of the node of the first fruiting branch (NFFB) improves early-maturity cotton breeding. Here we report QTL mapping on 200 F2 plants and derivative F2:3 and F2:4 populations by genotyping by sequencing (GBS). BC1F2 population was constructed by backcrossing one F2:4 line with the maternal parent JF914 and used for BSA-seq for further QTL mapping. A total of 1,305,642 SNPs were developed between the parents by GBS, and 2,907,790 SNPs were detected by BSA-seq. A high-density genetic map was constructed containing 11,488 SNPs and spanning 4,202.12 cM in length. A total of 13 QTL were mapped in the 3 tested populations. JF914 conferred favorable alleles for 11 QTL, and JF173 conferred favorable alleles for the other 2 QTL. Two stable QTL were repeatedly mapped in F2:3 and F2:4, including qNFFB-D3-1 and qNFFB-D6-1. Only qNFFB-D3-1 contributed more than 10% of the phenotypic variation. This QTL covered about 24.7 Mb (17,130,008–41,839,226 bp) on chromosome D3. Two regions on D3 (41,779,195–41,836,120 bp, 41,836,768–41,872,287 bp) were found by BSA-seq and covered about 92.4 Kb. This 92.4 Kb region overlapped with the stable QTL qNFFB-D3-1 and contained 8 annotated genes. By qRT-PCR, Ghir_D03G012430 showed a lower expression level from the 1- to 2-leaf stage and a higher expression level from the 3- to 6-leaf stage in the buds of JF173 than that of JF914. Ghir_D03G012390 reached the highest level at the 3- and 5-leaf stages in the buds of JF173 and JF914, respectively. As JF173 has lower NFFB and more early maturity than JF914, these two genes might be important in cell division and differentiation during NFFB formation in the seedling stage. The results of this study will facilitate a better understanding of the genetic basis of NFFB and benefit cotton molecular breeding for improving earliness traits.

B-box (BBX) which are a class of zinc finger transcription factors, play an important role in regulating of photoperiod, photomorphogenesis, and biotic and abiotic stresses in plants. However, there are few studies on the involvement of BBX transcription factors in response to abiotic stresses in sweet potato. In this paper, we cloned the DNA and promoter sequences of IbBBX28. There was one B-box conserved domain in IbBBX28, and the expression of IbBBX28 was induced under drought stress. Under drought stress, compared to wild type Arabidopsis, the protective enzyme activities (SOD, POD, and CAT) were all decreased in IbBBX28-overexpression Arabidopsis but increased in the mutant line bbx28, while the MDA content was increased in the IbBBX28-overexpression Arabidopsis and decreased in the bbx28. Moreover, the expression levels of the resistance-related genes showed the same trend as the protective enzyme activities. These results showed that IbBBX28 negatively regulates drought tolerance in transgenic Arabidopsis. Additionally, the yeast two-hybrid and BiFC assays verified that IbBBX28 interacted with IbHOX11 and IbZMAT2. The above results provide important clues for further studies on the role of IbBBX28 in regulating the stress response in sweet potato.

Diacylglycerol acyltransferases (DGAT) function as the key rate-limiting enzymes in de novo biosynthesis of triacylglycerol (TAG) by transferring an acyl group from acyl-CoA to sn-3 of diacylglycerol (DAG) to form TAG. Here, two members of the type 3 DGAT gene family, GmDGAT3-1 and GmDGAT3-2, were identified from the soybean (Glycine max) genome. Both of them were predicted to encode soluble cytosolic proteins containing the typical thioredoxin-like ferredoxin domain. Quantitative PCR analysis revealed that GmDGAT3-2 expression was much higher than GmDGAT3-1's in various soybean tissues such as leaves, flowers, and seeds. Functional complementation assay using TAG-deficient yeast (Saccharomyces cerevisiae) mutant H1246 demonstrated that GmDGAT3-2 fully restored TAG biosynthesis in the yeast and preferentially incorporated monounsaturated fatty acids (MUFAs), especially oleic acid (C18:1) into TAGs. This substrate specificity was further verified by fatty-acid feeding assays and in vitro enzyme activity characterization. Notably, transgenic tobacco (Nicotiana benthamiana) data showed that heterogeneous expression of GmDGAT3-2 resulted in a significant increase in seed oil and C18:1 levels but little change in contents of protein and starch compared to the EV-transformed tobacco plants. Taken together, GmDGAT3-2 displayed a strong enzymatic activity to catalyze TAG assembly with high substrate specificity for MUFAs, particularly C18:1, playing an important role in the cytosolic pathway of TAG synthesis in soybean. The present findings provide a scientific reference for improving oil yield and FA composition in soybean through gene modification, further expanding our knowledge of TAG biosynthesis and its regulatory mechanism in oilseeds.

Additional file 8: Figure S2. Clustering diagram of enriched GO terms from 651 annotated differentially expressed genes (DEGs). Genes were assigned into three main categories: biological processes, cellular components or molecular functions.

Additional file 3 Fig. S1. Gene duplication analysis of potato genome. The local database of potato protein sequences was established by Makeblastdb program. And pairwise comparisons were made between potato protein sequences by Blastp with E-value ≤1e-10. The gene duplication analysis result was obtained by duplicate_gene_classifier program provided in MCScanX software. Singleton: single copy genes; Proximal: adjacent but discontinuous repetitive genes on the same chromosome; Tandem: tandem duplications; WGD or segmental: whole genome duplications or segmental duplications; Dispersed: dispersed genes. Fig. S2. Sequence logos of conserved motifs in StKFB proteins. The 20 conserved motifs of the putative StKFB proteins were identified by MEME software v5.3.0. Fig. S3. The correlation analysis between the expression patterns of StKFBs in diverse potato tissues (a), in potato plants with different treatments (b) and in three colored potato tubers (c). The correlation between the expression levels (FPKM values) of StKFBs was analyzed by Pearson’s correlation coefficient and plotted using the corrplot package v. 0.92 ( https://cran.r-project.org/web/packages/corrplot/ ). Fig. S4. Dissociation curves of primers for qRT-PCR. Dissolution curves were obtained by heating the amplicon from 60 °C (5 s) to 95 °C (50 s) on CFX96 PCR System (Bio-Rad, USA). Fig. S5. Comparison of the expression levels of the 9 selected StKFB genes determined by qRT-PCR and transcriptome sequencing. The boxplots were plotted using tidyverse v. 1.3.1, cowplot v. 1.1.1, ggplot2 v. 3.3.5 and ggsci v. 2.9 packages in RStudio. Values are means ± SD of three replicates in each experiment. Bars with different lowercase letters represent significant difference at p

Additional file 6: Figure S1. Functional annotation and classification of unigenes in V. galamensis. (a) Overall classification of 21,364 unigenes distributed into major GO categories. (b) Eukaryotic Orthologous Groups (KOG) analysis of 28,896 unigenes which were classified into 26 functional groups.

Supplemental material, sj-docx-1-tam-10.1177_17588359221133546 for Circulating tumour DNA biomarkers in savolitinib-treated patients with non-small cell lung cancer harbouring MET exon 14 skipping alterations: a post hoc analysis of a pivotal phase 2 study by Yongfeng Yu, Yongxin Ren, Jian Fang, Lejie Cao, Zongan Liang, Qisen Guo, Sen Han, Zimei Ji, Ye Wang, Yulan Sun, Yuan Chen, Xingya Li, Hua Xu, Jianying Zhou, Liyan Jiang, Ying Cheng, Zhigang Han, Jianhua Shi, Gongyan Chen, Rui Ma, Yun Fan, Sanyuan Sun, Longxian Jiao, Xiaoyun Jia, Linfang Wang, Puhan Lu, Qian Xu, Xian Luo, Weiguo Su and Shun Lu in Therapeutic Advances in Medical Oncology

Additional file 8: Figure S4. SNP and Indel mutations in the promoter regions of GhAPL and GhHDA5 genes. The red boxes represent the specific location of mutation sites.

Additional file 4: Figure S2. The distributions of 17 QTLs overlapped with the previous studies on chromosomes. The QTLs identified in this study are marked in green and red, and the QTLs located in hotspots are marked in red; The QTLs detected in previous studies are marked in gray.

Additional file 1: Figure S1. The library fragments distribution of G2005, RIL182, NFFB-L-bulk, and NFFB-H-bulk.

Additional file 9: Figure S5. Leaves whitening of the pCLCrVA::GhPDS plants.

Additional file 7: Figure S3. The relative expression of 10 genes from the two-leaf stage to five-leaf stage of RIL182 and G2005. Orange and green bar graphs show the relative expression of early-maturing cotton (RIL182) and late-maturing cotton (G2005), respectively. The error bars indicate the standard deviation of three biological replicates. *, differences at p

Aiming at the requirement of video surveillance and disease identification in modern greenhouse, this paper designed a system consisted by greenhouse intelligent monitoring and disease identification system. At first, this paper using OpenMV camera designed a disease monitoring system which could recognize and collect disease images automatically by multi-color thresholds tracking. Then, this paper designed a cuckoo search and BP neural network collaborative search (CSBP-CS) algorithm, the algorithm combined the global search capability of Cuckoo Search(CS) and back-propagation algorithm of BP algorithm to optimize weights and thresholds collaboratively. this paper took three tomato diseases and normal leaves as research objects, firstly step was to separate the disease spots from disease images, then was to extract 56 classification features and select 47 excellent classification features by relief F to construct CSBP-CS RF classifier. Finally, this paper compared the classification accuracy of CSBP-CS with CSBP-CS RF network and analyzed the effectiveness of relief F. The simulation results showed that the average correct recognition rate of the CSBP-CS RF was approximately equal to CSBP-CS under the same conditions, but CSBP-CS RF is more simple, so Relief F can help to speed up the efficiency of CSBP-CS.

Upper Carboniferous-Lower Permian volcanic event deposits from two cross sections in Nanpiao, Liaoning Province, and the Daqing Mountains, Inner Mongolia, were examined by systematic rock and mineral identification, differential thermal analysis, X-ray diffraction, scanning electron microscopy and trace element and rare earth element quantitative analysis. According to the results, twelve sequences of volcanic event deposits have been distinguished from bottom to top, including 34–39 volcanic event layers. As these layers each have their own distinctive petrological, mineralogical and geochemical characteristics and were derived from the same source, they provide new evidence for further ascertaining the distribution characteristics of volcanic event deposits on the northern margin of the North China plate and carrying out the stratigraphic correlation using volcanic event layers as marker beds.

A novel co-doped rare earth complex Gd05 Eu05 (TTA)3 Dipy was synthesized and chosen as the emitter material in the organic electroluminescent device ITO/PVK:Gd0.5 Eu0.5 (TTA)3 Dipy/PBD/A1. It was proved that there was Forster energy transfer from Gd3+ to Eu3+. The electroluminescent mechanism of the device was proposed by measuring and analyzing the emission and the excitation spectra of the emissive layer. Gd3+ might play the role of promoting the energy transfer from PVK to Eu3+ and inhibiting an intrinsic luminescence of PVK. The device displayed red light with good monochromaticity. The possible energy transfer process of the device was preliminarily discussed.

Our work strongly suggests that microRNA858 regulates anthocyanin biosynthesis in tomato by modulating the expression of two R2R3 MYB transcription factors, underscoring the importance of microRNAs in the gene regulatory network controlling specialized metabolism in plants. The biological functions of microRNA858 (miR858), a recently identified small RNA, are not well understood. Here, we identified miR858 as a negative regulator of anthocyanin biosynthesis in tomato (Solanum lycopersicum). RNA ligase-mediated 5′RACE cleavage assay showed that miR858 mediates the cleavage of SlMYB7-like and SlMYB48-like transcripts in tomato. Expression analysis revealed an inverse correlation between the accumulation of miR858 and its target SlMYB7-like mRNA, in different tissues of tomato. Subsequently, a small tandem target mimic construct for blocking miR858 (STTM858) was generated and transformed into tomato. The majority of endogenous miR858 was blocked in STTM858 over-expressing tomato plants, whereas SlMYB7-like transcripts increased significantly. Concomitantly, upregulated expression was detected for several anthocyanin biosynthetic genes, including PAL, CHS, DFR, ANS and 3GT. As a result, anthocyanins were highly accumulated in young seedlings, leaves, stems and leaf buds of the transgenic plants under normal growth conditions. In addition, over-expression of STTM858 in tomato activated another MYB transcription factor, SlMYB48, implicating the possible involvement of SlMYB48 in anthocyanin biosynthesis.

Based on the geological conditions of cut and cover tunnel of the South to North Water Transfer Project, lining temperature field for crack control is simulated by finite element software—ANSYS. Through simulation of hydration heat effects, large temperature difference areas can be identified quantitatively, thermal insulation and sprinkler maintenance can be carried on during the initial setting. Cracks can be controlled well by pouring concrete in different section, mixing amount of fly ash and controlling mold temperature reasonable. Thus, model can be optimized continuously, optimal solution will to be established to provide better reference for selecting the temperature control program of massive concrete.

Silicon nitride films were deposited by radio frequency (r.f.) magnetron sputtering in an Ar-N2 gas mixture at a low substrate temperature. Subsequently the samples were annealed in pure N2 ambience. Influences of the Ar/N2 gas flow ratio as well as annealing on the optical properties and structure were studied. The optical properties of the films before annealing were examined using transmittance spectra. The composition of the samples was investigated by Fourier transform infrared (FTIR) spectra. Microstructure of the films was investigated using atomic force microscope (AFM). The films after annealing compared to former present a more compact construct, which is very dependent on the hydrogen concentration in the film.

This paper presents an ultra-low-power area-efficient non-volatile memory (NVM) in a 0.18 μm single-poly standard CMOS process for passive radio frequency identification (RFID) tags. In the memory cell, a novel low-power operation method is proposed to realize bi-directional Fowler—Nordheim tunneling during write operation. Furthermore, the cell is designed with PMOS transistors and coupling capacitors to minimize its area. In order to improve its reliability, the cell consists of double floating gates to store the data, and the 1 kbit NVM was implemented in a 0.18 μm single-poly standard CMOS process. The area of the memory cell and 1 kbit memory array is 96 μm2 and 0.12 mm2, respectively. The measured results indicate that the program/erase voltage ranges from 5 to 6 V The power consumption of the read/write operation is 0.19 μW/0.69 μW at a read/write rate of (268 kb/s)/(3.0 kb/s).

Purpose To identify the genetic defect in a large Chinese family with autosomal dominant cerulean cataract. Methods Genomic DNA and clinical data were collected from the family. Candidate gene sequencing and genome-wide linkage analysis were used to disclose the molecular basis responsible for cerulean cataract in the family. Results Initially, sequencing analysis of the three genes (beta-B2-crystallin [CRYBB2], gamma-D-crystallin [CRYGD], and V-MAF avian musculoaponeurotic fibrosarcoma oncogene homolog [MAF]) known to cause cerulean cataract failed to find any mutation. Then, genome-wide linkage analysis mapped the disease to chromosome 12q13-q22 between D12S85 and D12S351, with a maximum lod score of 4.10 at θ=0. Sequence analysis of the major intrinsic protein of lens fiber gene (MIP), a gene known to cause other types of cataract in the linkage interval, detected a novel heterozygous initiation codon mutation, c.2T>C (p.Met1?). This mutation was present in all patients with cerulean cataract but was not present in any of the 13 unaffected family members nor in 96 control individuals. Conclusions Cerulean cataract was found in a large family and is caused by a novel initiation codon mutation in MIP. This study adds a new member in the existing list of genes causing cerulean cataract and expands the mutation spectrum and phenotypic association of MIP mutations.

Purpose Dominant optic atrophy (DOA) is the most common form of autosomal inherited optic neuropathy, mainly caused by mutations in the optic atrophy 1 (OPA1) gene. The purpose of this study was to detect OPA1 gene mutations and associated phenotypes in Chinese patients with suspected hereditary optic neuropathy. Methods A cohort of 193 Chinese families with suspected hereditary optic neuropathy was collected, which had been excluded from the three common primary mitochondrial DNA mutations associated with Leber hereditary optic neuropathy in our prior screening. Sanger sequencing was used to analyze variants in the coding and adjacent regions of OPA1. Results In this study, 11 heterozygous OPA1 mutations, among which eight were novel and three were known, were identified in 12 of the 193 families (6.2%) but in none of the 192 control individuals. These novel mutations consisted of two nonsense mutations (p.E707* and p.K797*), two missense mutations (p.T330S and p.V377I), two deletions (p.S64fs and p.L331fs), one small insertion (p.L17fs), and one splice site mutation (c.2614–2A>G). Of the 12 families, three had a family history of optic neuropathy while nine were sporadic cases. Analysis of the family members in the two sporadic cases demonstrated that one parent in each of the two families had the OPA1 mutation and mild phenotype of optic atrophy. A 4-year-old boy with severe ocular phenotype was found to be compound heterozygous for two OPA1 mutations, a p.S64fs frameshift deletion and a p.V377I missense mutation, possibly implying an additive effect. Conclusions This study implies that the frequency of DOA is much lower than that of Leber hereditary optic neuropathy in Chinese compared with other ethnic groups. Lack of awareness of the mild phenotype of DOA may contribute to the low frequency of OPA1-related DOA in Chinese. The phenotype associated with compound heterozygous OPA1 mutations may suggest a possible addictive effect.

Purpose To identify null mutations in novel genes associated with early-onset high myopia using whole exome sequencing. Methods Null mutations, including homozygous and compound heterozygous truncations, were selected from whole exome sequencing data for 298 probands with early-onset high myopia. These data were compared with those of 507 probands with other forms of eye diseases. Null mutations specific to early-onset high myopia were considered potential candidates. Candidate mutations were confirmed with Sanger sequencing and were subsequently evaluated in available family members and 480 healthy controls. Results A homozygous frameshift mutation (c.39dup; p.L14Afs*21) and a compound heterozygous frameshift mutation (c.39dup; p.L14Afs*21 and c.594delG; p.Q199Kfs*35) in LOXL3 were separately identified in two of the 298 probands with early-onset high myopia. These mutations were confirmed with Sanger sequencing and were not detected in 1,974 alleles of the controls from the same region (507 individuals with other conditions and 480 healthy control individuals). These two probands were singleton cases, and their parents had only heterozygous mutations. A homozygous missense mutation in LOXL3 was recently reported in a consanguineous family with Stickler syndrome. Conclusions Our results suggest that null mutations in LOXL3 are likely associated with autosomal recessive early-onset high myopia. LOXL3 is a potential candidate gene for high myopia, but this possibility should be confirmed in additional studies. LOXL3 null mutations in human beings are not lethal, providing a phenotype contrary to that in mice.

Purpose Mutations in 60 known genes were previously identified by exome sequencing in 79 of 157 families with retinitis pigmentosa (RP). This study analyzed variants in 129 genes associated with other forms of hereditary retinal dystrophy in the same cohort. Methods Apart from the 73 genes previously analyzed, a further 129 genes responsible for other forms of hereditary retinal dystrophy were selected based on RetNet. Variants in the 129 genes determined by whole exome sequencing were selected and filtered by bioinformatics analysis. Candidate variants were confirmed by Sanger sequencing and validated by analysis of available family members and controls. Results A total of 90 candidate variants were present in the 129 genes. Sanger sequencing confirmed 83 of the 90 variants. Analysis of family members and controls excluded 76 of these 83 variants. The remaining seven variants were considered to be potential pathogenic mutations; these were c.899A>G, c.1814C>G, and c.2107C>T in BBS2; c.1073C>T and c.1669C>T in INPP5E; and c.3582C>G and c.5704–5C>G in CACNA1F. Six of these seven mutations were novel. The mutations were detected in five unrelated patients without a family history, including three patients with homozygous or compound heterozygous mutations in BBS2 and INPP5E, and two patients with hemizygous mutations in CACNA1F. None of the patients had mutations in the genes associated with autosome dominant retinal dystrophy. Conclusions Only a small portion of patients with RP, about 3% (5/157), had causative mutations in the 129 genes associated with other forms of hereditary retinal dystrophy.

Purpose Mitochondrial DNA (mtDNA) haplogroups affect the clinical expression of Leber hereditary optic neuropathy, age-related macular degeneration, and other diseases. The objective of this study is to investigate whether an mtDNA background is associated with myopia. Methods Blood DNA was obtained from 192 college students, including 96 individuals with moderate-to-high myopia and 96 controls without myopia. All the subjects were from a well-known isolated population living in the Chaoshan area of east Guangdong Province and speaking one of the four major dialects in southern China. The mtDNA haplogroups in the 192 subjects were determined by sequencing the mtDNA control region and partial coding regions as well as by analysis of restriction fragment length polymorphisms. Each mtDNA was classified according to the updated version of the Eastern Asian haplogroup system. Results Sixteen mtDNA haplogroups were recognized in the 192 subjects. The overall matrilineal structures of the samples with and without myopia were similar and had genetic imprints showing their ethno-origin. There was no statistical difference in frequencies of haplogroup distribution between subjects with and without myopia (χ2 test, p=0.556). Conclusions We failed to identify clues that suggest an involvement of mtDNA background in the predisposition to myopia.