Startseite Distinguish Dianthus species or varieties based on chloroplast genomes
Artikel Open Access

Distinguish Dianthus species or varieties based on chloroplast genomes

  • Dong Meng , Liu Yang , Zhao Yunlin , Yang Guiyan , Chen Shuwen und Xu Zhenggang EMAIL logo
Veröffentlicht/Copyright: 28. November 2023
Artikel downloaden (PDF)
Open Life Sciences
Aus der Zeitschrift Open Life Sciences Band 18 Heft 1

Abstract

Most plants belonging to the widely distributed genus Dianthus are used for gardening. Interspecific hybridization of different Dianthus species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among Dianthus species, the chloroplast genomes of 12 Dianthus species, including nine Dianthus gratianopolitanus varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474–149,735 bp), with Dianthus caryophyllus having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of Dianthus, we identified 124–126 annotated genes, including 83–84 protein-coding genes. Notably, D. caryophyllus had 83 protein-coding genes but lacked rpl2. The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of Dianthus indicated that D. caryophyllus and D. gratianopolitanus were most closely related, suggesting that the degree of variation within nine Dianthus varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within Dianthus species.

Keywords: comparative analysis; simple sequence repeat; phylogenetic analysis; molecular markers

1 Introduction

Dianthus is a genus comprising approximately 300 species in the Caryophyllaceae family. Species within this genus are widely distributed across Europe and Asia, particularly in the Mediterranean region, as well as in America and Africa [1]. Several species, notably Dianthus caryophyllus L., D. barbatus Linn., D. chinensis L., D. plumarius L., and D. superbus L., find extensive use in horticulture because of their beautiful flowers [1]. Moreover, many Dianthus species have been used in traditional Chinese medicine [2]. Two novel triterpenoid saponins with antimicrobial activity have been isolated from D. erinaceus Boiss. [3]. Furthermore, recent years have witnessed progress in research on Dianthus species, encompassing investigations into their morphological structure [4], molecular markers [5,6], environmental adaptation [7], and breeding techniques [1,8]. Because of the extensive utilization of Dianthus plants, the most commercially vital cultivars are hybrids that undergo vegetative propagation, and there has also been the development of transgenic varieties [8,9]. The use of advanced breeding technologies has expanded the diversity of Dianthus species, resulting in challenges when distinguishing these variations. This study underscores that morphological traits are the least effective means of identification, emphasizing the necessity for genetic markers in this regard [5].

Chloroplasts are vital organelles within green plant cells, closely involved in processes such as photosynthesis, carbon fixation, amino acid synthesis, and various other cellular functions [10]. In recent years, chloroplast DNA (CpDNA) has garnered increasing attention. According to the endosymbiotic theory, CpDNA is assumed to have originated from primordial photosynthetic prokaryotic cells associated with cyanobacteria [11]. CpDNA typically exhibits four regions: one large single-copy (LSC) region, one small single-copy (SSC) region, and a pair of inverted repeats (IRa and IRb) [12]. The absence of IRs in CpDNA is also widespread in many species, such as Vicia sepium [13]. CpDNA has single-parent genetic characteristics. Previous studies have shown that most gymnosperms inherit their chloroplasts paternally [14], whereas in angiosperms, chloroplast inheritance is primarily maternal [15]. Because of the lower replacement rates of CpDNA than that of nuclear genomes, CpDNA is frequently employed in the construction of evolutionary trees [16,17]. Extensive gene exchange occurs between the chloroplast genome, mitochondrial genome, and nuclear genomes, further diversifying the functions of chloroplasts [18–20]. The expression of genes encoded by CpDNA largely depends on a comprehensive set of factors of nuclear origin [21]. In recent years, CpDNA has been used to distinguish closely related species via comparative analysis [22–26].

D. caryophyllus, commonly known as carnation, is one the best-known species within the Dianthus genus [27]. The flowers of D. caryophyllus are renowned for their vibrant colors with strong aromas, including red, white, yellow, and green. The original natural flower color is a bright, pinkish-purple. They not only have ornamental value as cut flowers but also have medicinal properties. Our research team reported the characteristic CpDNA of D. caryophyllus, which is 147,604 bp long [28]. D. gratianopolitanus Vill., an endangered plant species, has a highly fragmented distribution range comprising numerous isolated populations [29]. To date, nine CpDNA sequences of D. gratianopolitanus varieties have been listed in the National Center for Biotechnology Information Database (https://www.ncbi.nlm.nih.gov/). However, there have been limited studies focusing on the genetic relationships and phylogenesis of Dianthus species. To explore the genetic characteristics of Dianthus species, a comprehensive comparison of CpDNA was conducted among different species and varieties of Dianthus. This study aims to test the hypothesis that differences in CpDNA characteristics among different species are greater than those among different varieties. The results of this study will not only enhance our understanding of the chloroplast genome characteristics of Dianthus but also provide valuable insights into their genetic diversity.

2 Materials and methods

2.1 Data collection and structure comparison

The CpDNA of D. caryophyllus was previously sequenced and published by our research team, under the accession number MG989277 [28]. A circular diagram was generated using OGDRAW 1.31 [30]. Similarly, 11 other Dianthus species were selected based on their nucleotide sequence similarity score using a BLAST search (https://blast.ncbi.nlm.nih.gov/). These species include D. gratianopolitanus (dg1602), D. gratianopolitanus (dg1869), D. gratianopolitanus (dg3051), D. gratianopolitanus (dg2134), D. gratianopolitanus (dg1856), D. gratianopolitanus (dg2769), D. gratianopolitanus (dg1255), D. gratianopolitanus (dg1370), D. gratianopolitanus (dg2868), D. longicalyx Miq., and D. moravicus Kovanda. The accession numbers for the CpDNA of all these plants are listed in Table 1. The GC content and length of the CpDNA as well as the LSC, SSC, and IR regions of these 12 species were calculated using BioEdit V7.0 [31]. The number of protein-coding genes was counted. Structural variations were detected using mVista in the shuffle-LAGAN model [32]. The sequences were visually checked for their identity using BLAST Ring Image Generator by aligning the 12 Dianthus species genomes with D. caryophyllus as a reference [33]. Simultaneous visual comparisons of the IR/LSC and IR/SSC border regions of the CpDNA from nine species were conducted using the drawing software Visio 2013, following the method described by Zhang et al. [34].

Table 1

Summary of chloroplast genomic for D. caryophyllus and other 11 Dianthus plants

Species (accession number) LSC SSC IR Total Protein-coding genes
Length (bp) GC (%) Length (%) Length (bp) GC (%) Length (%) Length (bp) GC (%) Length (%) Length (bp) GC (%)
D. caryophyllus (MG989277) 84,774 34.13 57.43 17,100 29.77 11.59 22,865 42.78 15.49 149,604 36.30 83
D. gratianopolitanus dg1602 (LN877389) 82,954 33.98 55.40 17,123 29.75 11.44 24,829 42.44 16.58 149,735 36.30 84
D. gratianopolitanus dg1869 (LN877391) 82,938 33.97 55.39 17,168 29.66 11.47 24,809 42.44 16.57 149,724 36.29 84
D. gratianopolitanus dg3051 (LN877395) 82,959 33.98 55.43 17,121 29.77 11.44 24,795 42.46 16.57 149,670 36.31 84
D. gratianopolitanus dg2134 (LN877392) 82,906 33.99 55.39 17,131 29.69 11.45 24,814 42.44 16.58 149,665 36.30 84
D. gratianopolitanus dg1856 (LN877390) 82,945 33.99 55.42 17,117 29.77 11.44 24,800 42.45 16.57 149,662 36.31 84
D. gratianopolitanus dg2769 (LN877393) 82,871 34.01 55.40 17,095 29.83 11.43 24,815 42.45 16.59 149,596 36.33 84
D. gratianopolitanus dg1255 (LN877387) 82,831 34.01 55.37 17,138 29.81 11.46 24,808 42.45 16.58 149,585 36.33 84
D. gratianopolitanus dg1370 (LN877388) 82,805 34.02 55.38 17,120 29.70 11.45 24,793 42.45 16.58 149,511 36.32 84
D. gratianopolitanus dg2868 (LN877394) 82,768 34.03 55.37 17,118 29.71 11.45 24,794 42.45 16.59 149,474 36.33 84
D. longicalyx (MT001881) 82,804 34.04 55.37 17,127 29.78 11.45 24,804 42.44 16.59 149,539 36.34 84
D. moravicus (LN877396) 82,756 34.01 55.35 17,122 29.77 11.45 24,823 42.45 16.60 149,524 36.33 84

2.2 Analysis of simple sequence repeats (SSRs) and long repeat sequences

Repeat sequences are either identical or complementary, and occur repeatedly at different positions within the genome. Forward, reverse, complementary, and palindromic repeat sequences in CpDNA were predicted using REPuter software, with the minimal repeat size set to 20 bp [35]. Simultaneously, SSRs, also known as microsatellite repeat sequence were detected in the CpDNA of these plants, including hexanucleotide SSRs, using MISA (https://webblast.ipk-gatersleben.de/misa/) [36]. The minimum repeat units of genes were set as 10, 4, 4, 3, 3, and 3 for mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide unit sizes, respectively (Table 2).

Table 2

List of genes encoded by D. caryophyllus chloroplast genome

Group of genes Gene names
Photosystem I psaA, psaB, psaC, psaI, psaJ
Photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
Cytochrome b/f complex petA, petB, petD, petG, petL, petN
ATP synthase atpA, atpB, atpE, atpF (a), atpH, atpI
NADH dehydrogenase ndhA (a), ndhB (×2) (a), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
RubisCO large subunit rbcL
RNA polymerase rpoA, rpoB, rpoC1 (a), rpoC2
Ribosomal proteins (SSU) rps11, rps12 (×2), rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7 (×2), rps8
Ribosomal proteins (LSU) rpl14, rpl16, rpl2 (a), rpl20, rpl22, rpl32, rpl33, rpl36
Proteins of unknown function ycf1 (×2) (a), ycf2 (×2), ycf3 (b), ycf4
Transfer RNAs trnA-UGC (×2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-UCC, trnH-GUG, trnI-GAU (×2), trnK-UUU, trnL-CAA (×2), trnL-UAA,trnL-UAG, trnM-CAU, trnN-GUU (×2), trnP-UGG, trnQ-UUG, trnR-ACG (×2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC (×2), trnV-UAC, trnY-GUA, trnY-GUA
Ribosomal RNAs rrn16 (×2), rrn23 (×2), rrn4.5 (×2), rrn5 (×2)
Other genes infA, matK, clpP (b), accD, ccsA, cemA

Note: (×2) means two gene copies; (a) means gene containing a single intron; (b) means gene containing two introns.

2.3 Analysis of codon usage bias

Codon usage bias reflects the balance between mutation bias and natural selection. In this study, we described the codon usage bias of CpDNA in all 12 selected plants using the relatively synonymous codon usage (RSCU) values, which were determined using DAMBE software [37]. An RSCU value of 1.00 indicated that the codons had no usage bias, whereas a value greater than 1.00 indicated a higher than expected usage frequency of the codon. To illustrate the distribution of codon usage preferences among these plants more clearly and intuitively, a heatmap based on the RSCU values using HemI software (version 1.0) was constructed [38].

2.4 Analysis of molecular evolution

Ka/Ks represents the ratio between the number of nonsynonymous substitutions per non-synonymous site (Ka) and the number of synonymous substitutions per synonymous site (Ks) in two protein-coding genes. It is used to determine whether there is selective pressure on the protein-coding gene [17]. If Ka/Ks > 1, the gene is considered to have undergone positive selection. If Ka/Ks = 1, the gene is considered to have evolved neutrally. If Ka/Ks < 1, the gene is considered to have undergone purify selection. Ka/Ks was calculated using D. caryophyllus as the reference, and the DnaSP v5 software was employed [39].

2.5 Phylogenetic analysis

The MEGA 7 software was employed to construct the phylogenetic tree using the neighbor-joining method, which is a simplified version of the minimal evolution method, for the aforementioned 12 CpDNAs [40]. The Kimura two-parameter model was selected using the corrected Akaike information criterion, and the bootstrap number was set to 100,000. The minimum value of the sum of all branches (S) was used as an estimate of the correct phylogenetic tree.

3 Results and discussion

3.1 CpDNA characteristics of Dianthus species

A comparison of the nine different varieties of D. gratianopolitanus revealed that although there were similarities in genome length, GC content, and the number of CpDNA genes, some differences persisted (Table 1). The CpDNA lengths of these nine varieties ranged from 149,474 bp (D. gratianopolitanus dg2868) to 149,735 bp (D. gratianopolitanus dg1602), with minimal variation. Moreover, the GC content of the nine CpDNAs ranged from 36.29 to 36.33%, with the IR regions showing relatively high GC content. D. gratianopolitanus (dg1869) had 124 genes, whereas the other eight varieties had 125 genes. All D. gratianopolitanus varieties contained 84 protein-encoding genes. It is worth mentioning that although the IR region of D. caryophyllus was the shortest in all 12 CpDNA, it exhibited the highest GC content. D. caryophyllus had the lowest number of protein-coding genes, totaling 83, and lacked the rpl2 gene. Conversely, the largest number of genes was observed for D. longicalyx, with 126 genes.

3.2 Comparative genomic analysis of the Dianthus complete chloroplast genomes

Via multiple sequence alignment analysis of the nine D. gratianopolitanus varieties (Figure 1), we observed significant deviations primarily in the conserved non-coding sequences (CNS), tRNA, and rRNA. Notably, variant sites in the protein-coding sequences were primarily concentrated in the atpF gene in D. gratianopolitanus (dg1255) and D. gratianopolitanus (dg1370), the ycf3 and petD genes in D. gratianopolitanus (dg3051), and the clpP gene in D. gratianopolitanus (dg1602) and D. gratianopolitanus (dg2868). Compared to the protein-coding sequence of D. caryophyllus, which exhibited notable distinctions in clpP, atpF, ycf3, the most significant divergence was observed in rpl16. Analyzed accessions of other 11 Dianthus species displayed conspicuous deletions in these gene. Overall, the dissimilarities between D. caryophyllus and D. gratianopolitanus (dg1869) were relatively minor, and their gene sequences are high degree of similarity. A comparative circular graph visually highlights the presence of genes, deletions, and sequence variations. The results indicate a high degree of sequence conservation, among the genomes (Figure 2).

Figure 1 Circular map of the chloroplast genome of the D. caryophyllus. Genes drawn within the circle are transcribed clockwise, while genes drawn outside are transcribed counterclockwise. Genes belonging to different functional groups are color coded. Dark bold lines show inverted repeats (IRa, and IRb). The dashed area in the inner circle indicates GC content in the chloroplast genome. The map is drawn by OGDRAW.
Figure 1

Circular map of the chloroplast genome of the D. caryophyllus. Genes drawn within the circle are transcribed clockwise, while genes drawn outside are transcribed counterclockwise. Genes belonging to different functional groups are color coded. Dark bold lines show inverted repeats (IRa, and IRb). The dashed area in the inner circle indicates GC content in the chloroplast genome. The map is drawn by OGDRAW.

Figure 2 Visual alignments of chloroplast genome sequences using the D. caryophyllus as the reference genomes. Arrows indicate the annotated genes and their transcriptional direction, and genome regions are color coded as exon, tRNA or rRNA, CNS (conserved non-coding sequences), and mRNA.
Figure 2

Visual alignments of chloroplast genome sequences using the D. caryophyllus as the reference genomes. Arrows indicate the annotated genes and their transcriptional direction, and genome regions are color coded as exon, tRNA or rRNA, CNS (conserved non-coding sequences), and mRNA.

Comparing the genes at the boundaries of the LSC, SSC, and IR regions (Figure 3), it becomes evident that the most significant difference among the nine D. gratianopolitanus varieties lies in the psbA (1,062 bp) within the LSC region of D. gratianopolitanus (dg1869). This same position was observed for trnH in eight other varieties. Although there were minor variations in the CpDNA of the nine D. gratianopolitanus species, overall, the CpDNA exhibited a high degree of conservation.

Figure 3 Comparative circle graph of similarity of the chloroplast genome sequences. The central ring represents the D. caryophyllus as the reference genome. There are 11 close related species plants from the inside to the outside. The outermost circle is the protein-coding gene of the D. caryophyllus.
Figure 3

Comparative circle graph of similarity of the chloroplast genome sequences. The central ring represents the D. caryophyllus as the reference genome. There are 11 close related species plants from the inside to the outside. The outermost circle is the protein-coding gene of the D. caryophyllus.

Figure 3 also highlights substantial differences between D. caryophyllus and the other 11 species in terms of genes at the boundaries of different regions. Notably, the LSC/IRa junction features ycf2, whereas rps19 occupied this position in the other 11 species and had a similar segmentation length. In the IRb/LSC junctions, a duplicated ycf2 gene replaces the rpl2 gene, whereas the rpl2 gene appears at the same connections as in other species. The ycf1 gene in the IRb region is slightly longer in D. caryophyllus, differing by just 3 bp among the other 11 analyzed accessions chloroplast genomes (Figure 4).

Figure 4 Comparison of the junctions of the four different constituent sequences in the chloroplast genome.
Figure 4

Comparison of the junctions of the four different constituent sequences in the chloroplast genome.

3.3 Repeat sequence features

Repeat sequence analysis was conducted on the CpDNA of the nine D. gratianopolitanus varieties, resulting in the identification of 49, 49, 49, 49, 49, 49, 42, 44, and 42 repeat sequences, respectively. These numbers were similar to those found in D. longicalyx (49) and D. moravicus (47) but were generally higher than those of the reference species, D. caryophyllus, which had only 42 repeat sequences (Figure 5a). Not all species contain all four types of repeat sequences. For instance, D. caryophyllus had only 10 forward, 20 palindromic, and 12 reverse repeat sequences. Only five species contained a very limited number of complementary repeat sequences, with D. gratianopolitanus (dg2769) having the most, but still only up to four. In contrast, the average numbers of forward, reverse, and palindromic repeats detected in the 12 CpDNAs were as high as 14, 12, and 20, respectively. As depicted in Figure 5b–d, palindromic repeat sequences were the most numerous, followed by forward and reverse repeats. Additionally, the sequence length of palindromic, forward, and reverse repeats was primarily concentrated in the 20–29 bp, followed by the 30–39 bp range. Repeat sequences longer than 59 bp, which are exclusively forward repeated sequences, were detected in D. gratianopolitanus (dg1602) and D. gratianopolitanus (dg3051).

Figure 5 Long repeat sequence analysis in the chloroplast genome: (a) number of four different directions, (b) number of the palindrome directions repeat length, (c) number of the forward directions repeat length, and (d) number of the reverse directions repeat length.
Figure 5

Long repeat sequence analysis in the chloroplast genome: (a) number of four different directions, (b) number of the palindrome directions repeat length, (c) number of the forward directions repeat length, and (d) number of the reverse directions repeat length.

SSR analysis identified a total of 134 SSRs with 13 combined types in D. caryophyllus CpDNA (Figure 6a). Among these 134 SSRs, 55 mononucleotide, 56 dinucleotide, 8 trinucleotide, 12 tetranucleotide, and 3 pentanucleotide repeats but no hexanucleotide repeats were detected. Furthermore, the frequencies of short polyadenine or polythymine repeats were significantly higher than those of tandem cytosine (C) or guanine (G) repeats. The most frequent composed dinucleotide repeat was AT/TA. In addition, the CpDNA of the nine D. gratianopolitanus varieties contained 142, 150, 141, 149, 144, 142, 140, 146, and 146 SSRs, which were similar in number to those in D. longicalyx (145) and D. moravicus (147). Among the six types of SSR sequences in the 12 species, mononucleotide and dinucleotide repeats were the most common, with the largest numbers ranging from 55 to 67 (Figure 6b). The numbers of trinucleotide and tetranucleotide repeats were similar, whereas pentanucleotide repeats were less frequent, with each species averaging only approximately four. Hexanucleotide repeats were detected in the CpDNA of only four species, with each species having only one, except for D. caryophyllus, which did not contain any hexanucleotide repeats.

Figure 6 Comparison of the repeat sequence features of the chloroplast genome. (a) SSR types and corresponding cumulative frequency in D. caryophyllus. (b) Differences of the chloroplast genomic SSR between D. caryophyllus and other 11 close related species.
Figure 6

Comparison of the repeat sequence features of the chloroplast genome. (a) SSR types and corresponding cumulative frequency in D. caryophyllus. (b) Differences of the chloroplast genomic SSR between D. caryophyllus and other 11 close related species.

3.4 Codon usage

The codon usage bias of the 20 amino acids and stop codons in D. caryophyllus is depicted by the RSCU value (Figure 7). The RSCU value of each synonymous codon exhibited significant variation. Nearly all of the amino acids in protein-coding regions contained synonymous codons, except methionine and tryptophan. Among these, arginine and leucine displayed the highest codon usage preferences, with identical RSCU values, followed by serine. The heat map of all 12 species reveals variations in codon usage preferences between species and varieties (Figure 8). Notably, more than half of the codons exhibited RSCU values greater than 1. Additionally, we observed a preference for codons ending with A or U over those ending with C or G.

Figure 7 RSCU value of amino acid and stop codon in the chloroplast genome of D. caryophyllus. The color of the histogram corresponds to the color of the codon.
Figure 7

RSCU value of amino acid and stop codon in the chloroplast genome of D. caryophyllus. The color of the histogram corresponds to the color of the codon.

Figure 8 Heat map of codons usage of 12 species. Different colors represent different RSCU values, red indicates a higher RSCU value and blue indicates a lower RSCU value.
Figure 8

Heat map of codons usage of 12 species. Different colors represent different RSCU values, red indicates a higher RSCU value and blue indicates a lower RSCU value.

3.5 Evolutionary rate analyses

In the evolutionary comparison of protein-coding genes with these 11 species (Figure 9), we observed that the Ka/Ks ratios among the nine D. gratianopolitanus varieties were similar. A significant proportion of protein-coding genes had Ka/Ks ratios less than 1, indicating that the non-synonymous sites were fewer than the synonymous sites, and these protein-coding genes underwent purify selection. Among all these species, only four genes (atpB, ndhF, psbB, and ycf1) had a value greater than 1, indicating positive selection. Comparatively, the ccsA of D. moravicus had a ratio greater than 1, whereas the ratios of the other species were slightly less than 1. A similar pattern was observed for rpoC2 of D. gratianopolitanus (dg1869) and D. gratianopolitanus (dg2134). Additionally, none of the protein-coding genes exhibited evidence of neutral evolution. Worth noting is that the Ka/Ks ratios of rpoA, associated with RNA polymerases in D. gratianopolitanus (dg1602), D. gratianopolitanus (dg3051), and D. gratianopolitanus (dg2769) varieties were notably high, indicating strong positive selection.

Figure 9 Ka/Ks comparison of protein genes with selective stress. The Ka/Ks values of other unlisted genes are zero.
Figure 9

Ka/Ks comparison of protein genes with selective stress. The Ka/Ks values of other unlisted genes are zero.

3.6 Phylogenetic analysis

Phylogenetic analysis is a common method for studying species evolution and phylogenetic classification, forming the core of our understanding of biodiversity, evolution, and genomics. The phylogenetic tree divided these species into three major evolutionary branches (Figure 9). Specifically, D. gratianopolitanus (dg2134), D. gratianopolitanus (dg1370), D. gratianopolitanus (dg2868), and D. longicalyx formed one evolutionary branch, with a 100% bootstrap value. Meanwhile, D. caryophyllus and D. gratianopolitanus (dg1869) were divided into two main branches that diverged from another evolutionary branch. Similar to the trend of the RSCU cluster trend, although most plants within a species exhibited similarity, some plants showed closer evolutionary relationships between species (Figure 10).

Figure 10 Phylogenetic analysis of the D. caryophyllus and 11 close relationship species by neighbor-joining method. The number indicates the NJ bootstrap value. The ruler indicates the genetic distance.
Figure 10

Phylogenetic analysis of the D. caryophyllus and 11 close relationship species by neighbor-joining method. The number indicates the NJ bootstrap value. The ruler indicates the genetic distance.

4 Conclusion

In this study, we analyzed the structure, size, number, and type of genes and the codon usage and repeat sequences of CpDNA for 12 Dianthus species, including nine different varieties of D. gratianopolitanus. The size and GC content of CpDNA were similar among Dianthus species. Notably, D. caryophyllus had the smallest cpDNA, with significant contraction, but possessed the largest LSC region. D. caryophyllus was an exception, having 83 protein-coding genes because of the lack of the rpl2 gene, whereas the other 11 species had all 84 protein-coding genes. Comparative analysis showed that the 12 CpDNAs of Dianthus species were highly conserved and that only a few sites of subtle variation existed. Gene analysis of the boundary regions showed that there were evident differences in the genes. The hypothesis is not supported by the data, as the differences within species were not less than the intra-species differences. More CpDNA data from Dianthus plants may be needed to explore molecular markers for distinguishing between different species.

# These authors contributed equally to this work.

Acknowledgements

The authors are grateful to Zhang Wan, Li Chaoyang, and Peng Jiao for their insightful assistance in writing this manuscript. They would like to thank Editage (www.editage.cn) for English language editing.

  1. Funding information: This research was funded by the Natural Science Foundation of Hunan Province (2022JJ50264), the Research Foundation of the Education Bureau of Hunan Province (21B0711, 21C0664), and the Key Projects of the National Forestry and Grassland Bureau (201801).

  2. Author contributions: Liu Yang, Xu Zhenggang, Yang Guiyan, and Zhao Yunlin contributed to the study conception and experimental design. Liu Yang and Chen Shuwen collected and analyzed the data. The first draft of the manuscript was written by Liu Yang and Dong Meng, and all authors commented on previous versions of the manuscript.

  3. Conflict of interest: Authors state no conflicts of interest.

  4. Data availability statement: The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

References

[1] Tanase K, Nishitani C, Hirakawa H, Isobe S, Tabata S, Ohmiya A, et al. Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology. BMC Genomics. 2012;13(1):292.10.1186/1471-2164-13-292Suche in Google Scholar PubMed PubMed Central

[2] Chandra S, Rawat DS. Medicinal plants of the family Caryophyllaceae: a review of ethno-medicinal uses and pharmacological properties. Integr Med Res. 2015;4(3):123–31.10.1016/j.imr.2015.06.004Suche in Google Scholar PubMed PubMed Central

[3] Mutlu K, Sarikahya NB, Yasa I, Kirmizigul S. Dianthus erinaceus var. erinaceus: extraction, isolation, characterization and antimicrobial activity investigation of novel saponins. Phytochemistry Lett. 2016;16:219–24.10.1016/j.phytol.2016.04.020Suche in Google Scholar

[4] Guo X-M, Yu Y-Y, Bai L, Gao R-F. Dianthus chinensis L.: the structural difference between vascular bundles in the placenta and ovary wall suggests their different origin. Front Plant Sci. 2017;8:1986.10.3389/fpls.2017.01986Suche in Google Scholar PubMed PubMed Central

[5] Fu X, Ning G, Gao L, Bao M. Genetic diversity of Dianthus accessions as assessed using two molecular marker systems (SRAPs and ISSRs) and morphological traits. Sci Horticulturae. 2008;117(3):263–70.10.1016/j.scienta.2008.04.001Suche in Google Scholar

[6] Yagi M, Shirasawa K, Waki T, Kume T, Isobe S, Tanase K, et al. Construction of an SSR and RAD marker-based genetic linkage map for carnation (Dianthus caryophyllus L.). Plant Mol Biol Report. 2017;35(1):110–7.10.1007/s11105-016-1010-2Suche in Google Scholar

[7] Wójcik M, Dresler S, Tukiendorf A. Physiological mechanisms of adaptation of Dianthus carthusianorum L. to growth on a Zn–Pb waste deposit – the case of chronic multi-metal and acute Zn stress. Plant Soil. 2015;390(1):237–50.10.1007/s11104-015-2396-6Suche in Google Scholar

[8] Noman A, Aqeel M, Deng J, Khalid N, Sanaullah T, Shuilin H. Biotechnological advancements for improving floral attributes in ornamental plants. Front Plant Sci. 2017;8:530.10.3389/fpls.2017.00530Suche in Google Scholar PubMed PubMed Central

[9] Casanova E, Valdés AE, Zuker A, Fernández B, Vainstein A, Trillas MI, et al. rolC-transgenic carnation plants: adventitious organogenesis and levels of endogenous auxin and cytokinins. Plant Sci. 2004;167(3):551–60.10.1016/j.plantsci.2004.04.029Suche in Google Scholar

[10] Hu S, Ding Y, Zhu C. Sensitivity and responses of chloroplasts to heat stress in plants. Front Plant Sci. 2020;11:11.10.3389/fpls.2020.00375Suche in Google Scholar PubMed PubMed Central

[11] Zimorski V, Ku C, Martin WF, Gould SB. Endosymbiotic theory for organelle origins. Curr Open Microbiol. 2014;22:38–48.10.1016/j.mib.2014.09.008Suche in Google Scholar PubMed

[12] Ravi V, Khurana JP, Tyagi AK, Khurana P. An update on chloroplast genomes. Plant Syst Evol. 2008;271(1):101–22.10.1007/s00606-007-0608-0Suche in Google Scholar

[13] Li C, Zhao Y, Xu Z, Yang G, Peng J, Peng X. Initial characterization of the chloroplast genome of Vicia sepium, an important wild resource plant, and related inferences about its evolution. Front Genet. 2020;11:73.10.3389/fgene.2020.00073Suche in Google Scholar PubMed PubMed Central

[14] Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci. 1995;92(17):7759–63.10.1073/pnas.92.17.7759Suche in Google Scholar PubMed PubMed Central

[15] Stegemann S, Hartmann S, Ruf S, Bock R. High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci U S A. 2003;100(15):8828–33.10.1073/pnas.1430924100Suche in Google Scholar PubMed PubMed Central

[16] Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, Kowallik KV. Gene transfer to the nucleus and the evolution of chloroplasts. Nature. 1998;393(6681):162–5.10.1038/30234Suche in Google Scholar PubMed

[17] Peng J, Zhao Y, Dong M, Liu S, Hu Z, Zhong X, et al. Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes. BMC Ecol Evolution. 2021;21(1):71.10.1186/s12862-021-01800-1Suche in Google Scholar PubMed PubMed Central

[18] Park S, Jansen RK, Park S. Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and transfer of the rpl32 gene to the nucleus in the ancestor of the subfamily Thalictroideae. BMC Plant Biol. 2015;15(1):40.10.1186/s12870-015-0432-6Suche in Google Scholar PubMed PubMed Central

[19] Choi K-S, Park S. Complete plastid and mitochondrial genomes of Aeginetia indica reveal intracellular gene transfer (IGT), horizontal gene transfer (HGT), and cytoplasmic male sterility (CMS). Int J Mol Sci. 2021;22(11):22.10.3390/ijms22116143Suche in Google Scholar PubMed PubMed Central

[20] Li J, Li J, Ma Y, Kou L, Wei J, Wang W. The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules. BMC Genomics. 2022;23(1):481.10.1186/s12864-022-08706-2Suche in Google Scholar PubMed PubMed Central

[21] Dobrogojski J, Adamiec M, Luciński R. The chloroplast genome: a review. Acta Physiol Plant. 2020;42(6):98.10.1007/s11738-020-03089-xSuche in Google Scholar

[22] Sheng J, Yan M, Wang J, Zhao L, Zhou F, Hu Z, et al. The complete chloroplast genome sequences of five Miscanthus species, and comparative analyses with other grass plastomes. Ind Crop Products. 2021;162:113248.10.1016/j.indcrop.2021.113248Suche in Google Scholar

[23] Wang X, Zhang R, Yun Q, Xu Y, Zhao G, Liu J, et al. Comprehensive analysis of complete mitochondrial genome of Sapindus mukorossi Gaertn.: an important industrial oil tree species in China. Ind Crop Products. 2021;174:114210.10.1016/j.indcrop.2021.114210Suche in Google Scholar

[24] Chong X, Li Y, Yan M, Wang Y, Li M, Zhou Y, et al. Comparative chloroplast genome analysis of 10 Ilex species and the development of species-specific identification markers. Ind Crop Products. 2022;187:115408.10.1016/j.indcrop.2022.115408Suche in Google Scholar

[25] Xu W, Lu R, Li J, Xia M, Chen G, Li P. Comparative plastome analyses and evolutionary relationships of all species and cultivars within the medicinal plant genus Atractylodes. Ind Crop Products. 2023;201:116974.10.1016/j.indcrop.2023.116974Suche in Google Scholar

[26] Zhao J, Chen J, Xiong Y, He W, Xiong Y, Xu Y, et al. Organelle genomes of Indigofera amblyantha and Indigofera pseudotinctoria: comparative genome analysis, and intracellular gene transfer. Ind Crop Products. 2023;198:116674.10.1016/j.indcrop.2023.116674Suche in Google Scholar

[27] Hu D, Zhang X, Xue P, Nie Y, Liu J, Li Y, et al. Exogenous melatonin ameliorates heat damages by regulating growth, photosynthetic efficiency and leaf ultrastructure of carnation. Plant Physiol Biochem. 2023;198:107698.10.1016/j.plaphy.2023.107698Suche in Google Scholar PubMed

[28] Chen S, Xu Z, Zhao Y, Zhong X, Li C, Yang G. Structural characteristic and phylogenetic analysis of the complete chloroplast genome of Dianthus caryophyllus. Mitochondrial DNA Part B-Resources. 2018;3(2):1131–2.10.1080/23802359.2018.1521313Suche in Google Scholar PubMed PubMed Central

[29] Putz CM, Schmid C, Reisch C. Living in isolation – population structure, reproduction, and genetic variation of the endangered plant species Dianthus gratianopolitanus (Cheddar pink). Ecol Evolution. 2015;5(17):3610–21.10.1002/ece3.1611Suche in Google Scholar PubMed PubMed Central

[30] Greiner S, Lehwark P, Bock R. Organellar genome DRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019;47(W1):W59–64.10.1093/nar/gkz238Suche in Google Scholar PubMed PubMed Central

[31] Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–8.Suche in Google Scholar

[32] Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004;32(suppl_2):W273–W9.10.1093/nar/gkh458Suche in Google Scholar PubMed PubMed Central

[33] Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA. BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12(1):402.10.1186/1471-2164-12-402Suche in Google Scholar PubMed PubMed Central

[34] Zhang W, Zhao Y, Yang G, Peng J, Chen S, Xu Z. Determination of the evolutionary pressure on Camellia oleifera on Hainan Island using the complete chloroplast genome sequence. Peerj. 2019;7:e8115.10.7717/peerj.7210Suche in Google Scholar PubMed PubMed Central

[35] Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001;29(22):4633–42.10.1093/nar/29.22.4633Suche in Google Scholar PubMed PubMed Central

[36] Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA-web: a web server for microsatellite prediction. Bioinformatics. 2017;33(16):2583–5.10.1093/bioinformatics/btx198Suche in Google Scholar PubMed PubMed Central

[37] Xia X, Xie Z. DAMBE: Software package for data analysis in molecular biology and evolution. J Heredity. 2001;92(4):371–3.10.1093/jhered/92.4.371Suche in Google Scholar PubMed

[38] Deng W, Wang Y, Liu Z, Cheng H, Xue Y. HemI: a Toolkit for illustrating heatmaps. PLoS One. 2014;9(11):e111988.10.1371/journal.pone.0111988Suche in Google Scholar PubMed PubMed Central

[39] Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25(11):1451–2.10.1093/bioinformatics/btp187Suche in Google Scholar PubMed

[40] Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evolution. 2016;33(7):1870–4.10.1093/molbev/msw054Suche in Google Scholar PubMed PubMed Central

Received: 2023-04-22
Revised: 2023-09-12
Accepted: 2023-10-19
Published Online: 2023-11-28

© 2023 the author(s), published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 International License.

Artikel in diesem Heft

  1. Biomedical Sciences
  2. Systemic investigation of inetetamab in combination with small molecules to treat HER2-overexpressing breast and gastric cancers
  3. Immunosuppressive treatment for idiopathic membranous nephropathy: An updated network meta-analysis
  4. Identifying two pathogenic variants in a patient with pigmented paravenous retinochoroidal atrophy
  5. Effects of phytoestrogens combined with cold stress on sperm parameters and testicular proteomics in rats
  6. A case of pulmonary embolism with bad warfarin anticoagulant effects caused by E. coli infection
  7. Neutrophilia with subclinical Cushing’s disease: A case report and literature review
  8. Isoimperatorin alleviates lipopolysaccharide-induced periodontitis by downregulating ERK1/2 and NF-κB pathways
  9. Immunoregulation of synovial macrophages for the treatment of osteoarthritis
  10. Novel CPLANE1 c.8948dupT (p.P2984Tfs*7) variant in a child patient with Joubert syndrome
  11. Antiphospholipid antibodies and the risk of thrombosis in myeloproliferative neoplasms
  12. Immunological responses of septic rats to combination therapy with thymosin α1 and vitamin C
  13. High glucose and high lipid induced mitochondrial dysfunction in JEG-3 cells through oxidative stress
  14. Pharmacological inhibition of the ubiquitin-specific protease 8 effectively suppresses glioblastoma cell growth
  15. Levocarnitine regulates the growth of angiotensin II-induced myocardial fibrosis cells via TIMP-1
  16. Age-related changes in peripheral T-cell subpopulations in elderly individuals: An observational study
  17. Single-cell transcription analysis reveals the tumor origin and heterogeneity of human bilateral renal clear cell carcinoma
  18. Identification of iron metabolism-related genes as diagnostic signatures in sepsis by blood transcriptomic analysis
  19. Long noncoding RNA ACART knockdown decreases 3T3-L1 preadipocyte proliferation and differentiation
  20. Surgery, adjuvant immunotherapy plus chemotherapy and radiotherapy for primary malignant melanoma of the parotid gland (PGMM): A case report
  21. Dosimetry comparison with helical tomotherapy, volumetric modulated arc therapy, and intensity-modulated radiotherapy for grade II gliomas: A single‑institution case series
  22. Soy isoflavone reduces LPS-induced acute lung injury via increasing aquaporin 1 and aquaporin 5 in rats
  23. Refractory hypokalemia with sexual dysplasia and infertility caused by 17α-hydroxylase deficiency and triple X syndrome: A case report
  24. Meta-analysis of cancer risk among end stage renal disease undergoing maintenance dialysis
  25. 6-Phosphogluconate dehydrogenase inhibition arrests growth and induces apoptosis in gastric cancer via AMPK activation and oxidative stress
  26. Experimental study on the optimization of ANM33 release in foam cells
  27. Primary retroperitoneal angiosarcoma: A case report
  28. Metabolomic analysis-identified 2-hydroxybutyric acid might be a key metabolite of severe preeclampsia
  29. Malignant pleural effusion diagnosis and therapy
  30. Effect of spaceflight on the phenotype and proteome of Escherichia coli
  31. Comparison of immunotherapy combined with stereotactic radiotherapy and targeted therapy for patients with brain metastases: A systemic review and meta-analysis
  32. Activation of hypermethylated P2RY1 mitigates gastric cancer by promoting apoptosis and inhibiting proliferation
  33. Association between the VEGFR-2 -604T/C polymorphism (rs2071559) and type 2 diabetic retinopathy
  34. The role of IL-31 and IL-34 in the diagnosis and treatment of chronic periodontitis
  35. Triple-negative mouse breast cancer initiating cells show high expression of beta1 integrin and increased malignant features
  36. mNGS facilitates the accurate diagnosis and antibiotic treatment of suspicious critical CNS infection in real practice: A retrospective study
  37. The apatinib and pemetrexed combination has antitumor and antiangiogenic effects against NSCLC
  38. Radiotherapy for primary thyroid adenoid cystic carcinoma
  39. Design and functional preliminary investigation of recombinant antigen EgG1Y162–EgG1Y162 against Echinococcus granulosus
  40. Effects of losartan in patients with NAFLD: A meta-analysis of randomized controlled trial
  41. Bibliometric analysis of METTL3: Current perspectives, highlights, and trending topics
  42. Performance comparison of three scaling algorithms in NMR-based metabolomics analysis
  43. PI3K/AKT/mTOR pathway and its related molecules participate in PROK1 silence-induced anti-tumor effects on pancreatic cancer
  44. The altered expression of cytoskeletal and synaptic remodeling proteins during epilepsy
  45. Effects of pegylated recombinant human granulocyte colony-stimulating factor on lymphocytes and white blood cells of patients with malignant tumor
  46. Prostatitis as initial manifestation of Chlamydia psittaci pneumonia diagnosed by metagenome next-generation sequencing: A case report
  47. NUDT21 relieves sevoflurane-induced neurological damage in rats by down-regulating LIMK2
  48. Association of interleukin-10 rs1800896, rs1800872, and interleukin-6 rs1800795 polymorphisms with squamous cell carcinoma risk: A meta-analysis
  49. Exosomal HBV-DNA for diagnosis and treatment monitoring of chronic hepatitis B
  50. Shear stress leads to the dysfunction of endothelial cells through the Cav-1-mediated KLF2/eNOS/ERK signaling pathway under physiological conditions
  51. Interaction between the PI3K/AKT pathway and mitochondrial autophagy in macrophages and the leukocyte count in rats with LPS-induced pulmonary infection
  52. Meta-analysis of the rs231775 locus polymorphism in the CTLA-4 gene and the susceptibility to Graves’ disease in children
  53. Cloning, subcellular localization and expression of phosphate transporter gene HvPT6 of hulless barley
  54. Coptisine mitigates diabetic nephropathy via repressing the NRLP3 inflammasome
  55. Significant elevated CXCL14 and decreased IL-39 levels in patients with tuberculosis
  56. Whole-exome sequencing applications in prenatal diagnosis of fetal bowel dilatation
  57. Gemella morbillorum infective endocarditis: A case report and literature review
  58. An unusual ectopic thymoma clonal evolution analysis: A case report
  59. Severe cumulative skin toxicity during toripalimab combined with vemurafenib following toripalimab alone
  60. Detection of V. vulnificus septic shock with ARDS using mNGS
  61. Novel rare genetic variants of familial and sporadic pulmonary atresia identified by whole-exome sequencing
  62. The influence and mechanistic action of sperm DNA fragmentation index on the outcomes of assisted reproduction technology
  63. Novel compound heterozygous mutations in TELO2 in an infant with You-Hoover-Fong syndrome: A case report and literature review
  64. ctDNA as a prognostic biomarker in resectable CLM: Systematic review and meta-analysis
  65. Diagnosis of primary amoebic meningoencephalitis by metagenomic next-generation sequencing: A case report
  66. Phylogenetic analysis of promoter regions of human Dolichol kinase (DOLK) and orthologous genes using bioinformatics tools
  67. Collagen changes in rabbit conjunctiva after conjunctival crosslinking
  68. Effects of NM23 transfection of human gastric carcinoma cells in mice
  69. Oral nifedipine and phytosterol, intravenous nicardipine, and oral nifedipine only: Three-arm, retrospective, cohort study for management of severe preeclampsia
  70. Case report of hepatic retiform hemangioendothelioma: A rare tumor treated with ultrasound-guided microwave ablation
  71. Curcumin induces apoptosis in human hepatocellular carcinoma cells by decreasing the expression of STAT3/VEGF/HIF-1α signaling
  72. Rare presentation of double-clonal Waldenström macroglobulinemia with pulmonary embolism: A case report
  73. Giant duplication of the transverse colon in an adult: A case report and literature review
  74. Ectopic thyroid tissue in the breast: A case report
  75. SDR16C5 promotes proliferation and migration and inhibits apoptosis in pancreatic cancer
  76. Vaginal metastasis from breast cancer: A case report
  77. Screening of the best time window for MSC transplantation to treat acute myocardial infarction with SDF-1α antibody-loaded targeted ultrasonic microbubbles: An in vivo study in miniswine
  78. Inhibition of TAZ impairs the migration ability of melanoma cells
  79. Molecular complexity analysis of the diagnosis of Gitelman syndrome in China
  80. Effects of maternal calcium and protein intake on the development and bone metabolism of offspring mice
  81. Identification of winter wheat pests and diseases based on improved convolutional neural network
  82. Ultra-multiplex PCR technique to guide treatment of Aspergillus-infected aortic valve prostheses
  83. Virtual high-throughput screening: Potential inhibitors targeting aminopeptidase N (CD13) and PIKfyve for SARS-CoV-2
  84. Immune checkpoint inhibitors in cancer patients with COVID-19
  85. Utility of methylene blue mixed with autologous blood in preoperative localization of pulmonary nodules and masses
  86. Integrated analysis of the microbiome and transcriptome in stomach adenocarcinoma
  87. Berberine suppressed sarcopenia insulin resistance through SIRT1-mediated mitophagy
  88. DUSP2 inhibits the progression of lupus nephritis in mice by regulating the STAT3 pathway
  89. Lung abscess by Fusobacterium nucleatum and Streptococcus spp. co-infection by mNGS: A case series
  90. Genetic alterations of KRAS and TP53 in intrahepatic cholangiocarcinoma associated with poor prognosis
  91. Granulomatous polyangiitis involving the fourth ventricle: Report of a rare case and a literature review
  92. Studying infant mortality: A demographic analysis based on data mining models
  93. Metaplastic breast carcinoma with osseous differentiation: A report of a rare case and literature review
  94. Protein Z modulates the metastasis of lung adenocarcinoma cells
  95. Inhibition of pyroptosis and apoptosis by capsaicin protects against LPS-induced acute kidney injury through TRPV1/UCP2 axis in vitro
  96. TAK-242, a toll-like receptor 4 antagonist, against brain injury by alleviates autophagy and inflammation in rats
  97. Primary mediastinum Ewing’s sarcoma with pleural effusion: A case report and literature review
  98. Association of ADRB2 gene polymorphisms and intestinal microbiota in Chinese Han adolescents
  99. Tanshinone IIA alleviates chondrocyte apoptosis and extracellular matrix degeneration by inhibiting ferroptosis
  100. Study on the cytokines related to SARS-Cov-2 in testicular cells and the interaction network between cells based on scRNA-seq data
  101. Effect of periostin on bone metabolic and autophagy factors during tooth eruption in mice
  102. HP1 induces ferroptosis of renal tubular epithelial cells through NRF2 pathway in diabetic nephropathy
  103. Intravaginal estrogen management in postmenopausal patients with vaginal squamous intraepithelial lesions along with CO2 laser ablation: A retrospective study
  104. Hepatocellular carcinoma cell differentiation trajectory predicts immunotherapy, potential therapeutic drugs, and prognosis of patients
  105. Effects of physical exercise on biomarkers of oxidative stress in healthy subjects: A meta-analysis of randomized controlled trials
  106. Identification of lysosome-related genes in connection with prognosis and immune cell infiltration for drug candidates in head and neck cancer
  107. Development of an instrument-free and low-cost ELISA dot-blot test to detect antibodies against SARS-CoV-2
  108. Research progress on gas signal molecular therapy for Parkinson’s disease
  109. Adiponectin inhibits TGF-β1-induced skin fibroblast proliferation and phenotype transformation via the p38 MAPK signaling pathway
  110. The G protein-coupled receptor-related gene signatures for predicting prognosis and immunotherapy response in bladder urothelial carcinoma
  111. α-Fetoprotein contributes to the malignant biological properties of AFP-producing gastric cancer
  112. CXCL12/CXCR4/CXCR7 axis in placenta tissues of patients with placenta previa
  113. Association between thyroid stimulating hormone levels and papillary thyroid cancer risk: A meta-analysis
  114. Significance of sTREM-1 and sST2 combined diagnosis for sepsis detection and prognosis prediction
  115. Diagnostic value of serum neuroactive substances in the acute exacerbation of chronic obstructive pulmonary disease complicated with depression
  116. Research progress of AMP-activated protein kinase and cardiac aging
  117. TRIM29 knockdown prevented the colon cancer progression through decreasing the ubiquitination levels of KRT5
  118. Cross-talk between gut microbiota and liver steatosis: Complications and therapeutic target
  119. Metastasis from small cell lung cancer to ovary: A case report
  120. The early diagnosis and pathogenic mechanisms of sepsis-related acute kidney injury
  121. The effect of NK cell therapy on sepsis secondary to lung cancer: A case report
  122. Erianin alleviates collagen-induced arthritis in mice by inhibiting Th17 cell differentiation
  123. Loss of ACOX1 in clear cell renal cell carcinoma and its correlation with clinical features
  124. Signalling pathways in the osteogenic differentiation of periodontal ligament stem cells
  125. Crosstalk between lactic acid and immune regulation and its value in the diagnosis and treatment of liver failure
  126. Clinicopathological features and differential diagnosis of gastric pleomorphic giant cell carcinoma
  127. Traumatic brain injury and rTMS-ERPs: Case report and literature review
  128. Extracellular fibrin promotes non-small cell lung cancer progression through integrin β1/PTEN/AKT signaling
  129. Knockdown of DLK4 inhibits non-small cell lung cancer tumor growth by downregulating CKS2
  130. The co-expression pattern of VEGFR-2 with indicators related to proliferation, apoptosis, and differentiation of anagen hair follicles
  131. Inflammation-related signaling pathways in tendinopathy
  132. CD4+ T cell count in HIV/TB co-infection and co-occurrence with HL: Case report and literature review
  133. Clinical analysis of severe Chlamydia psittaci pneumonia: Case series study
  134. Bioinformatics analysis to identify potential biomarkers for the pulmonary artery hypertension associated with the basement membrane
  135. Influence of MTHFR polymorphism, alone or in combination with smoking and alcohol consumption, on cancer susceptibility
  136. Catharanthus roseus (L.) G. Don counteracts the ampicillin resistance in multiple antibiotic-resistant Staphylococcus aureus by downregulation of PBP2a synthesis
  137. Combination of a bronchogenic cyst in the thoracic spinal canal with chronic myelocytic leukemia
  138. Bacterial lipoprotein plays an important role in the macrophage autophagy and apoptosis induced by Salmonella typhimurium and Staphylococcus aureus
  139. TCL1A+ B cells predict prognosis in triple-negative breast cancer through integrative analysis of single-cell and bulk transcriptomic data
  140. Ezrin promotes esophageal squamous cell carcinoma progression via the Hippo signaling pathway
  141. Ferroptosis: A potential target of macrophages in plaque vulnerability
  142. Predicting pediatric Crohn's disease based on six mRNA-constructed risk signature using comprehensive bioinformatic approaches
  143. Applications of genetic code expansion and photosensitive UAAs in studying membrane proteins
  144. HK2 contributes to the proliferation, migration, and invasion of diffuse large B-cell lymphoma cells by enhancing the ERK1/2 signaling pathway
  145. IL-17 in osteoarthritis: A narrative review
  146. Circadian cycle and neuroinflammation
  147. Probiotic management and inflammatory factors as a novel treatment in cirrhosis: A systematic review and meta-analysis
  148. Hemorrhagic meningioma with pulmonary metastasis: Case report and literature review
  149. SPOP regulates the expression profiles and alternative splicing events in human hepatocytes
  150. Knockdown of SETD5 inhibited glycolysis and tumor growth in gastric cancer cells by down-regulating Akt signaling pathway
  151. PTX3 promotes IVIG resistance-induced endothelial injury in Kawasaki disease by regulating the NF-κB pathway
  152. Pancreatic ectopic thyroid tissue: A case report and analysis of literature
  153. The prognostic impact of body mass index on female breast cancer patients in underdeveloped regions of northern China differs by menopause status and tumor molecular subtype
  154. Report on a case of liver-originating malignant melanoma of unknown primary
  155. Case report: Herbal treatment of neutropenic enterocolitis after chemotherapy for breast cancer
  156. The fibroblast growth factor–Klotho axis at molecular level
  157. Characterization of amiodarone action on currents in hERG-T618 gain-of-function mutations
  158. A case report of diagnosis and dynamic monitoring of Listeria monocytogenes meningitis with NGS
  159. Effect of autologous platelet-rich plasma on new bone formation and viability of a Marburg bone graft
  160. Small breast epithelial mucin as a useful prognostic marker for breast cancer patients
  161. Continuous non-adherent culture promotes transdifferentiation of human adipose-derived stem cells into retinal lineage
  162. Nrf3 alleviates oxidative stress and promotes the survival of colon cancer cells by activating AKT/BCL-2 signal pathway
  163. Favorable response to surufatinib in a patient with necrolytic migratory erythema: A case report
  164. Case report of atypical undernutrition of hypoproteinemia type
  165. Down-regulation of COL1A1 inhibits tumor-associated fibroblast activation and mediates matrix remodeling in the tumor microenvironment of breast cancer
  166. Sarcoma protein kinase inhibition alleviates liver fibrosis by promoting hepatic stellate cells ferroptosis
  167. Research progress of serum eosinophil in chronic obstructive pulmonary disease and asthma
  168. Clinicopathological characteristics of co-existing or mixed colorectal cancer and neuroendocrine tumor: Report of five cases
  169. Role of menopausal hormone therapy in the prevention of postmenopausal osteoporosis
  170. Precisional detection of lymph node metastasis using tFCM in colorectal cancer
  171. Advances in diagnosis and treatment of perimenopausal syndrome
  172. A study of forensic genetics: ITO index distribution and kinship judgment between two individuals
  173. Acute lupus pneumonitis resembling miliary tuberculosis: A case-based review
  174. Plasma levels of CD36 and glutathione as biomarkers for ruptured intracranial aneurysm
  175. Fractalkine modulates pulmonary angiogenesis and tube formation by modulating CX3CR1 and growth factors in PVECs
  176. Novel risk prediction models for deep vein thrombosis after thoracotomy and thoracoscopic lung cancer resections, involving coagulation and immune function
  177. Exploring the diagnostic markers of essential tremor: A study based on machine learning algorithms
  178. Evaluation of effects of small-incision approach treatment on proximal tibia fracture by deep learning algorithm-based magnetic resonance imaging
  179. An online diagnosis method for cancer lesions based on intelligent imaging analysis
  180. Medical imaging in rheumatoid arthritis: A review on deep learning approach
  181. Predictive analytics in smart healthcare for child mortality prediction using a machine learning approach
  182. Utility of neutrophil–lymphocyte ratio and platelet–lymphocyte ratio in predicting acute-on-chronic liver failure survival
  183. A biomedical decision support system for meta-analysis of bilateral upper-limb training in stroke patients with hemiplegia
  184. TNF-α and IL-8 levels are positively correlated with hypobaric hypoxic pulmonary hypertension and pulmonary vascular remodeling in rats
  185. Stochastic gradient descent optimisation for convolutional neural network for medical image segmentation
  186. Comparison of the prognostic value of four different critical illness scores in patients with sepsis-induced coagulopathy
  187. Application and teaching of computer molecular simulation embedded technology and artificial intelligence in drug research and development
  188. Hepatobiliary surgery based on intelligent image segmentation technology
  189. Value of brain injury-related indicators based on neural network in the diagnosis of neonatal hypoxic-ischemic encephalopathy
  190. Analysis of early diagnosis methods for asymmetric dementia in brain MR images based on genetic medical technology
  191. Early diagnosis for the onset of peri-implantitis based on artificial neural network
  192. Clinical significance of the detection of serum IgG4 and IgG4/IgG ratio in patients with thyroid-associated ophthalmopathy
  193. Forecast of pain degree of lumbar disc herniation based on back propagation neural network
  194. SPA-UNet: A liver tumor segmentation network based on fused multi-scale features
  195. Systematic evaluation of clinical efficacy of CYP1B1 gene polymorphism in EGFR mutant non-small cell lung cancer observed by medical image
  196. Rehabilitation effect of intelligent rehabilitation training system on hemiplegic limb spasms after stroke
  197. A novel approach for minimising anti-aliasing effects in EEG data acquisition
  198. ErbB4 promotes M2 activation of macrophages in idiopathic pulmonary fibrosis
  199. Clinical role of CYP1B1 gene polymorphism in prediction of postoperative chemotherapy efficacy in NSCLC based on individualized health model
  200. Lung nodule segmentation via semi-residual multi-resolution neural networks
  201. Evaluation of brain nerve function in ICU patients with Delirium by deep learning algorithm-based resting state MRI
  202. A data mining technique for detecting malignant mesothelioma cancer using multiple regression analysis
  203. Markov model combined with MR diffusion tensor imaging for predicting the onset of Alzheimer’s disease
  204. Effectiveness of the treatment of depression associated with cancer and neuroimaging changes in depression-related brain regions in patients treated with the mediator-deuterium acupuncture method
  205. Molecular mechanism of colorectal cancer and screening of molecular markers based on bioinformatics analysis
  206. Monitoring and evaluation of anesthesia depth status data based on neuroscience
  207. Exploring the conformational dynamics and thermodynamics of EGFR S768I and G719X + S768I mutations in non-small cell lung cancer: An in silico approaches
  208. Optimised feature selection-driven convolutional neural network using gray level co-occurrence matrix for detection of cervical cancer
  209. Incidence of different pressure patterns of spinal cerebellar ataxia and analysis of imaging and genetic diagnosis
  210. Pathogenic bacteria and treatment resistance in older cardiovascular disease patients with lung infection and risk prediction model
  211. Adoption value of support vector machine algorithm-based computed tomography imaging in the diagnosis of secondary pulmonary fungal infections in patients with malignant hematological disorders
  212. From slides to insights: Harnessing deep learning for prognostic survival prediction in human colorectal cancer histology
  213. Ecology and Environmental Science
  214. Monitoring of hourly carbon dioxide concentration under different land use types in arid ecosystem
  215. Comparing the differences of prokaryotic microbial community between pit walls and bottom from Chinese liquor revealed by 16S rRNA gene sequencing
  216. Effects of cadmium stress on fruits germination and growth of two herbage species
  217. Bamboo charcoal affects soil properties and bacterial community in tea plantations
  218. Optimization of biogas potential using kinetic models, response surface methodology, and instrumental evidence for biodegradation of tannery fleshings during anaerobic digestion
  219. Understory vegetation diversity patterns of Platycladus orientalis and Pinus elliottii communities in Central and Southern China
  220. Studies on macrofungi diversity and discovery of new species of Abortiporus from Baotianman World Biosphere Reserve
  221. Food Science
  222. Effect of berrycactus fruit (Myrtillocactus geometrizans) on glutamate, glutamine, and GABA levels in the frontal cortex of rats fed with a high-fat diet
  223. Guesstimate of thymoquinone diversity in Nigella sativa L. genotypes and elite varieties collected from Indian states using HPTLC technique
  224. Analysis of bacterial community structure of Fuzhuan tea with different processing techniques
  225. Untargeted metabolomics reveals sour jujube kernel benefiting the nutritional value and flavor of Morchella esculenta
  226. Mycobiota in Slovak wine grapes: A case study from the small Carpathians wine region
  227. Elemental analysis of Fadogia ancylantha leaves used as a nutraceutical in Mashonaland West Province, Zimbabwe
  228. Microbiological transglutaminase: Biotechnological application in the food industry
  229. Influence of solvent-free extraction of fish oil from catfish (Clarias magur) heads using a Taguchi orthogonal array design: A qualitative and quantitative approach
  230. Chromatographic analysis of the chemical composition and anticancer activities of Curcuma longa extract cultivated in Palestine
  231. The potential for the use of leghemoglobin and plant ferritin as sources of iron
  232. Investigating the association between dietary patterns and glycemic control among children and adolescents with T1DM
  233. Bioengineering and Biotechnology
  234. Biocompatibility and osteointegration capability of β-TCP manufactured by stereolithography 3D printing: In vitro study
  235. Clinical characteristics and the prognosis of diabetic foot in Tibet: A single center, retrospective study
  236. Agriculture
  237. Biofertilizer and NPSB fertilizer application effects on nodulation and productivity of common bean (Phaseolus vulgaris L.) at Sodo Zuria, Southern Ethiopia
  238. On correlation between canopy vegetation and growth indexes of maize varieties with different nitrogen efficiencies
  239. Exopolysaccharides from Pseudomonas tolaasii inhibit the growth of Pleurotus ostreatus mycelia
  240. A transcriptomic evaluation of the mechanism of programmed cell death of the replaceable bud in Chinese chestnut
  241. Melatonin enhances salt tolerance in sorghum by modulating photosynthetic performance, osmoregulation, antioxidant defense, and ion homeostasis
  242. Effects of plant density on alfalfa (Medicago sativa L.) seed yield in western Heilongjiang areas
  243. Identification of rice leaf diseases and deficiency disorders using a novel DeepBatch technique
  244. Artificial intelligence and internet of things oriented sustainable precision farming: Towards modern agriculture
  245. Animal Sciences
  246. Effect of ketogenic diet on exercise tolerance and transcriptome of gastrocnemius in mice
  247. Combined analysis of mRNA–miRNA from testis tissue in Tibetan sheep with different FecB genotypes
  248. Isolation, identification, and drug resistance of a partially isolated bacterium from the gill of Siniperca chuatsi
  249. Tracking behavioral changes of confined sows from the first mating to the third parity
  250. The sequencing of the key genes and end products in the TLR4 signaling pathway from the kidney of Rana dybowskii exposed to Aeromonas hydrophila
  251. Development of a new candidate vaccine against piglet diarrhea caused by Escherichia coli
  252. Plant Sciences
  253. Crown and diameter structure of pure Pinus massoniana Lamb. forest in Hunan province, China
  254. Genetic evaluation and germplasm identification analysis on ITS2, trnL-F, and psbA-trnH of alfalfa varieties germplasm resources
  255. Tissue culture and rapid propagation technology for Gentiana rhodantha
  256. Effects of cadmium on the synthesis of active ingredients in Salvia miltiorrhiza
  257. Cloning and expression analysis of VrNAC13 gene in mung bean
  258. Chlorate-induced molecular floral transition revealed by transcriptomes
  259. Effects of warming and drought on growth and development of soybean in Hailun region
  260. Effects of different light conditions on transient expression and biomass in Nicotiana benthamiana leaves
  261. Comparative analysis of the rhizosphere microbiome and medicinally active ingredients of Atractylodes lancea from different geographical origins
  262. Distinguish Dianthus species or varieties based on chloroplast genomes
  263. Comparative transcriptomes reveal molecular mechanisms of apple blossoms of different tolerance genotypes to chilling injury
  264. Study on fresh processing key technology and quality influence of Cut Ophiopogonis Radix based on multi-index evaluation
  265. An advanced approach for fig leaf disease detection and classification: Leveraging image processing and enhanced support vector machine methodology
  266. Erratum
  267. Erratum to “Protein Z modulates the metastasis of lung adenocarcinoma cells”
  268. Erratum to “BRCA1 subcellular localization regulated by PI3K signaling pathway in triple-negative breast cancer MDA-MB-231 cells and hormone-sensitive T47D cells”
  269. Retraction
  270. Retraction to “Protocatechuic acid attenuates cerebral aneurysm formation and progression by inhibiting TNF-alpha/Nrf-2/NF-kB-mediated inflammatory mechanisms in experimental rats”
https://doi.org/10.1515/biol-2022-0772
Schlagwörter für diesen Artikel
comparative analysis; simple sequence repeat; phylogenetic analysis; molecular markers
Creative Commons
BY 4.0

Artikel in diesem Heft

  1. Biomedical Sciences
  2. Systemic investigation of inetetamab in combination with small molecules to treat HER2-overexpressing breast and gastric cancers
  3. Immunosuppressive treatment for idiopathic membranous nephropathy: An updated network meta-analysis
  4. Identifying two pathogenic variants in a patient with pigmented paravenous retinochoroidal atrophy
  5. Effects of phytoestrogens combined with cold stress on sperm parameters and testicular proteomics in rats
  6. A case of pulmonary embolism with bad warfarin anticoagulant effects caused by E. coli infection
  7. Neutrophilia with subclinical Cushing’s disease: A case report and literature review
  8. Isoimperatorin alleviates lipopolysaccharide-induced periodontitis by downregulating ERK1/2 and NF-κB pathways
  9. Immunoregulation of synovial macrophages for the treatment of osteoarthritis
  10. Novel CPLANE1 c.8948dupT (p.P2984Tfs*7) variant in a child patient with Joubert syndrome
  11. Antiphospholipid antibodies and the risk of thrombosis in myeloproliferative neoplasms
  12. Immunological responses of septic rats to combination therapy with thymosin α1 and vitamin C
  13. High glucose and high lipid induced mitochondrial dysfunction in JEG-3 cells through oxidative stress
  14. Pharmacological inhibition of the ubiquitin-specific protease 8 effectively suppresses glioblastoma cell growth
  15. Levocarnitine regulates the growth of angiotensin II-induced myocardial fibrosis cells via TIMP-1
  16. Age-related changes in peripheral T-cell subpopulations in elderly individuals: An observational study
  17. Single-cell transcription analysis reveals the tumor origin and heterogeneity of human bilateral renal clear cell carcinoma
  18. Identification of iron metabolism-related genes as diagnostic signatures in sepsis by blood transcriptomic analysis
  19. Long noncoding RNA ACART knockdown decreases 3T3-L1 preadipocyte proliferation and differentiation
  20. Surgery, adjuvant immunotherapy plus chemotherapy and radiotherapy for primary malignant melanoma of the parotid gland (PGMM): A case report
  21. Dosimetry comparison with helical tomotherapy, volumetric modulated arc therapy, and intensity-modulated radiotherapy for grade II gliomas: A single‑institution case series
  22. Soy isoflavone reduces LPS-induced acute lung injury via increasing aquaporin 1 and aquaporin 5 in rats
  23. Refractory hypokalemia with sexual dysplasia and infertility caused by 17α-hydroxylase deficiency and triple X syndrome: A case report
  24. Meta-analysis of cancer risk among end stage renal disease undergoing maintenance dialysis
  25. 6-Phosphogluconate dehydrogenase inhibition arrests growth and induces apoptosis in gastric cancer via AMPK activation and oxidative stress
  26. Experimental study on the optimization of ANM33 release in foam cells
  27. Primary retroperitoneal angiosarcoma: A case report
  28. Metabolomic analysis-identified 2-hydroxybutyric acid might be a key metabolite of severe preeclampsia
  29. Malignant pleural effusion diagnosis and therapy
  30. Effect of spaceflight on the phenotype and proteome of Escherichia coli
  31. Comparison of immunotherapy combined with stereotactic radiotherapy and targeted therapy for patients with brain metastases: A systemic review and meta-analysis
  32. Activation of hypermethylated P2RY1 mitigates gastric cancer by promoting apoptosis and inhibiting proliferation
  33. Association between the VEGFR-2 -604T/C polymorphism (rs2071559) and type 2 diabetic retinopathy
  34. The role of IL-31 and IL-34 in the diagnosis and treatment of chronic periodontitis
  35. Triple-negative mouse breast cancer initiating cells show high expression of beta1 integrin and increased malignant features
  36. mNGS facilitates the accurate diagnosis and antibiotic treatment of suspicious critical CNS infection in real practice: A retrospective study
  37. The apatinib and pemetrexed combination has antitumor and antiangiogenic effects against NSCLC
  38. Radiotherapy for primary thyroid adenoid cystic carcinoma
  39. Design and functional preliminary investigation of recombinant antigen EgG1Y162–EgG1Y162 against Echinococcus granulosus
  40. Effects of losartan in patients with NAFLD: A meta-analysis of randomized controlled trial
  41. Bibliometric analysis of METTL3: Current perspectives, highlights, and trending topics
  42. Performance comparison of three scaling algorithms in NMR-based metabolomics analysis
  43. PI3K/AKT/mTOR pathway and its related molecules participate in PROK1 silence-induced anti-tumor effects on pancreatic cancer
  44. The altered expression of cytoskeletal and synaptic remodeling proteins during epilepsy
  45. Effects of pegylated recombinant human granulocyte colony-stimulating factor on lymphocytes and white blood cells of patients with malignant tumor
  46. Prostatitis as initial manifestation of Chlamydia psittaci pneumonia diagnosed by metagenome next-generation sequencing: A case report
  47. NUDT21 relieves sevoflurane-induced neurological damage in rats by down-regulating LIMK2
  48. Association of interleukin-10 rs1800896, rs1800872, and interleukin-6 rs1800795 polymorphisms with squamous cell carcinoma risk: A meta-analysis
  49. Exosomal HBV-DNA for diagnosis and treatment monitoring of chronic hepatitis B
  50. Shear stress leads to the dysfunction of endothelial cells through the Cav-1-mediated KLF2/eNOS/ERK signaling pathway under physiological conditions
  51. Interaction between the PI3K/AKT pathway and mitochondrial autophagy in macrophages and the leukocyte count in rats with LPS-induced pulmonary infection
  52. Meta-analysis of the rs231775 locus polymorphism in the CTLA-4 gene and the susceptibility to Graves’ disease in children
  53. Cloning, subcellular localization and expression of phosphate transporter gene HvPT6 of hulless barley
  54. Coptisine mitigates diabetic nephropathy via repressing the NRLP3 inflammasome
  55. Significant elevated CXCL14 and decreased IL-39 levels in patients with tuberculosis
  56. Whole-exome sequencing applications in prenatal diagnosis of fetal bowel dilatation
  57. Gemella morbillorum infective endocarditis: A case report and literature review
  58. An unusual ectopic thymoma clonal evolution analysis: A case report
  59. Severe cumulative skin toxicity during toripalimab combined with vemurafenib following toripalimab alone
  60. Detection of V. vulnificus septic shock with ARDS using mNGS
  61. Novel rare genetic variants of familial and sporadic pulmonary atresia identified by whole-exome sequencing
  62. The influence and mechanistic action of sperm DNA fragmentation index on the outcomes of assisted reproduction technology
  63. Novel compound heterozygous mutations in TELO2 in an infant with You-Hoover-Fong syndrome: A case report and literature review
  64. ctDNA as a prognostic biomarker in resectable CLM: Systematic review and meta-analysis
  65. Diagnosis of primary amoebic meningoencephalitis by metagenomic next-generation sequencing: A case report
  66. Phylogenetic analysis of promoter regions of human Dolichol kinase (DOLK) and orthologous genes using bioinformatics tools
  67. Collagen changes in rabbit conjunctiva after conjunctival crosslinking
  68. Effects of NM23 transfection of human gastric carcinoma cells in mice
  69. Oral nifedipine and phytosterol, intravenous nicardipine, and oral nifedipine only: Three-arm, retrospective, cohort study for management of severe preeclampsia
  70. Case report of hepatic retiform hemangioendothelioma: A rare tumor treated with ultrasound-guided microwave ablation
  71. Curcumin induces apoptosis in human hepatocellular carcinoma cells by decreasing the expression of STAT3/VEGF/HIF-1α signaling
  72. Rare presentation of double-clonal Waldenström macroglobulinemia with pulmonary embolism: A case report
  73. Giant duplication of the transverse colon in an adult: A case report and literature review
  74. Ectopic thyroid tissue in the breast: A case report
  75. SDR16C5 promotes proliferation and migration and inhibits apoptosis in pancreatic cancer
  76. Vaginal metastasis from breast cancer: A case report
  77. Screening of the best time window for MSC transplantation to treat acute myocardial infarction with SDF-1α antibody-loaded targeted ultrasonic microbubbles: An in vivo study in miniswine
  78. Inhibition of TAZ impairs the migration ability of melanoma cells
  79. Molecular complexity analysis of the diagnosis of Gitelman syndrome in China
  80. Effects of maternal calcium and protein intake on the development and bone metabolism of offspring mice
  81. Identification of winter wheat pests and diseases based on improved convolutional neural network
  82. Ultra-multiplex PCR technique to guide treatment of Aspergillus-infected aortic valve prostheses
  83. Virtual high-throughput screening: Potential inhibitors targeting aminopeptidase N (CD13) and PIKfyve for SARS-CoV-2
  84. Immune checkpoint inhibitors in cancer patients with COVID-19
  85. Utility of methylene blue mixed with autologous blood in preoperative localization of pulmonary nodules and masses
  86. Integrated analysis of the microbiome and transcriptome in stomach adenocarcinoma
  87. Berberine suppressed sarcopenia insulin resistance through SIRT1-mediated mitophagy
  88. DUSP2 inhibits the progression of lupus nephritis in mice by regulating the STAT3 pathway
  89. Lung abscess by Fusobacterium nucleatum and Streptococcus spp. co-infection by mNGS: A case series
  90. Genetic alterations of KRAS and TP53 in intrahepatic cholangiocarcinoma associated with poor prognosis
  91. Granulomatous polyangiitis involving the fourth ventricle: Report of a rare case and a literature review
  92. Studying infant mortality: A demographic analysis based on data mining models
  93. Metaplastic breast carcinoma with osseous differentiation: A report of a rare case and literature review
  94. Protein Z modulates the metastasis of lung adenocarcinoma cells
  95. Inhibition of pyroptosis and apoptosis by capsaicin protects against LPS-induced acute kidney injury through TRPV1/UCP2 axis in vitro
  96. TAK-242, a toll-like receptor 4 antagonist, against brain injury by alleviates autophagy and inflammation in rats
  97. Primary mediastinum Ewing’s sarcoma with pleural effusion: A case report and literature review
  98. Association of ADRB2 gene polymorphisms and intestinal microbiota in Chinese Han adolescents
  99. Tanshinone IIA alleviates chondrocyte apoptosis and extracellular matrix degeneration by inhibiting ferroptosis
  100. Study on the cytokines related to SARS-Cov-2 in testicular cells and the interaction network between cells based on scRNA-seq data
  101. Effect of periostin on bone metabolic and autophagy factors during tooth eruption in mice
  102. HP1 induces ferroptosis of renal tubular epithelial cells through NRF2 pathway in diabetic nephropathy
  103. Intravaginal estrogen management in postmenopausal patients with vaginal squamous intraepithelial lesions along with CO2 laser ablation: A retrospective study
  104. Hepatocellular carcinoma cell differentiation trajectory predicts immunotherapy, potential therapeutic drugs, and prognosis of patients
  105. Effects of physical exercise on biomarkers of oxidative stress in healthy subjects: A meta-analysis of randomized controlled trials
  106. Identification of lysosome-related genes in connection with prognosis and immune cell infiltration for drug candidates in head and neck cancer
  107. Development of an instrument-free and low-cost ELISA dot-blot test to detect antibodies against SARS-CoV-2
  108. Research progress on gas signal molecular therapy for Parkinson’s disease
  109. Adiponectin inhibits TGF-β1-induced skin fibroblast proliferation and phenotype transformation via the p38 MAPK signaling pathway
  110. The G protein-coupled receptor-related gene signatures for predicting prognosis and immunotherapy response in bladder urothelial carcinoma
  111. α-Fetoprotein contributes to the malignant biological properties of AFP-producing gastric cancer
  112. CXCL12/CXCR4/CXCR7 axis in placenta tissues of patients with placenta previa
  113. Association between thyroid stimulating hormone levels and papillary thyroid cancer risk: A meta-analysis
  114. Significance of sTREM-1 and sST2 combined diagnosis for sepsis detection and prognosis prediction
  115. Diagnostic value of serum neuroactive substances in the acute exacerbation of chronic obstructive pulmonary disease complicated with depression
  116. Research progress of AMP-activated protein kinase and cardiac aging
  117. TRIM29 knockdown prevented the colon cancer progression through decreasing the ubiquitination levels of KRT5
  118. Cross-talk between gut microbiota and liver steatosis: Complications and therapeutic target
  119. Metastasis from small cell lung cancer to ovary: A case report
  120. The early diagnosis and pathogenic mechanisms of sepsis-related acute kidney injury
  121. The effect of NK cell therapy on sepsis secondary to lung cancer: A case report
  122. Erianin alleviates collagen-induced arthritis in mice by inhibiting Th17 cell differentiation
  123. Loss of ACOX1 in clear cell renal cell carcinoma and its correlation with clinical features
  124. Signalling pathways in the osteogenic differentiation of periodontal ligament stem cells
  125. Crosstalk between lactic acid and immune regulation and its value in the diagnosis and treatment of liver failure
  126. Clinicopathological features and differential diagnosis of gastric pleomorphic giant cell carcinoma
  127. Traumatic brain injury and rTMS-ERPs: Case report and literature review
  128. Extracellular fibrin promotes non-small cell lung cancer progression through integrin β1/PTEN/AKT signaling
  129. Knockdown of DLK4 inhibits non-small cell lung cancer tumor growth by downregulating CKS2
  130. The co-expression pattern of VEGFR-2 with indicators related to proliferation, apoptosis, and differentiation of anagen hair follicles
  131. Inflammation-related signaling pathways in tendinopathy
  132. CD4+ T cell count in HIV/TB co-infection and co-occurrence with HL: Case report and literature review
  133. Clinical analysis of severe Chlamydia psittaci pneumonia: Case series study
  134. Bioinformatics analysis to identify potential biomarkers for the pulmonary artery hypertension associated with the basement membrane
  135. Influence of MTHFR polymorphism, alone or in combination with smoking and alcohol consumption, on cancer susceptibility
  136. Catharanthus roseus (L.) G. Don counteracts the ampicillin resistance in multiple antibiotic-resistant Staphylococcus aureus by downregulation of PBP2a synthesis
  137. Combination of a bronchogenic cyst in the thoracic spinal canal with chronic myelocytic leukemia
  138. Bacterial lipoprotein plays an important role in the macrophage autophagy and apoptosis induced by Salmonella typhimurium and Staphylococcus aureus
  139. TCL1A+ B cells predict prognosis in triple-negative breast cancer through integrative analysis of single-cell and bulk transcriptomic data
  140. Ezrin promotes esophageal squamous cell carcinoma progression via the Hippo signaling pathway
  141. Ferroptosis: A potential target of macrophages in plaque vulnerability
  142. Predicting pediatric Crohn's disease based on six mRNA-constructed risk signature using comprehensive bioinformatic approaches
  143. Applications of genetic code expansion and photosensitive UAAs in studying membrane proteins
  144. HK2 contributes to the proliferation, migration, and invasion of diffuse large B-cell lymphoma cells by enhancing the ERK1/2 signaling pathway
  145. IL-17 in osteoarthritis: A narrative review
  146. Circadian cycle and neuroinflammation
  147. Probiotic management and inflammatory factors as a novel treatment in cirrhosis: A systematic review and meta-analysis
  148. Hemorrhagic meningioma with pulmonary metastasis: Case report and literature review
  149. SPOP regulates the expression profiles and alternative splicing events in human hepatocytes
  150. Knockdown of SETD5 inhibited glycolysis and tumor growth in gastric cancer cells by down-regulating Akt signaling pathway
  151. PTX3 promotes IVIG resistance-induced endothelial injury in Kawasaki disease by regulating the NF-κB pathway
  152. Pancreatic ectopic thyroid tissue: A case report and analysis of literature
  153. The prognostic impact of body mass index on female breast cancer patients in underdeveloped regions of northern China differs by menopause status and tumor molecular subtype
  154. Report on a case of liver-originating malignant melanoma of unknown primary
  155. Case report: Herbal treatment of neutropenic enterocolitis after chemotherapy for breast cancer
  156. The fibroblast growth factor–Klotho axis at molecular level
  157. Characterization of amiodarone action on currents in hERG-T618 gain-of-function mutations
  158. A case report of diagnosis and dynamic monitoring of Listeria monocytogenes meningitis with NGS
  159. Effect of autologous platelet-rich plasma on new bone formation and viability of a Marburg bone graft
  160. Small breast epithelial mucin as a useful prognostic marker for breast cancer patients
  161. Continuous non-adherent culture promotes transdifferentiation of human adipose-derived stem cells into retinal lineage
  162. Nrf3 alleviates oxidative stress and promotes the survival of colon cancer cells by activating AKT/BCL-2 signal pathway
  163. Favorable response to surufatinib in a patient with necrolytic migratory erythema: A case report
  164. Case report of atypical undernutrition of hypoproteinemia type
  165. Down-regulation of COL1A1 inhibits tumor-associated fibroblast activation and mediates matrix remodeling in the tumor microenvironment of breast cancer
  166. Sarcoma protein kinase inhibition alleviates liver fibrosis by promoting hepatic stellate cells ferroptosis
  167. Research progress of serum eosinophil in chronic obstructive pulmonary disease and asthma
  168. Clinicopathological characteristics of co-existing or mixed colorectal cancer and neuroendocrine tumor: Report of five cases
  169. Role of menopausal hormone therapy in the prevention of postmenopausal osteoporosis
  170. Precisional detection of lymph node metastasis using tFCM in colorectal cancer
  171. Advances in diagnosis and treatment of perimenopausal syndrome
  172. A study of forensic genetics: ITO index distribution and kinship judgment between two individuals
  173. Acute lupus pneumonitis resembling miliary tuberculosis: A case-based review
  174. Plasma levels of CD36 and glutathione as biomarkers for ruptured intracranial aneurysm
  175. Fractalkine modulates pulmonary angiogenesis and tube formation by modulating CX3CR1 and growth factors in PVECs
  176. Novel risk prediction models for deep vein thrombosis after thoracotomy and thoracoscopic lung cancer resections, involving coagulation and immune function
  177. Exploring the diagnostic markers of essential tremor: A study based on machine learning algorithms
  178. Evaluation of effects of small-incision approach treatment on proximal tibia fracture by deep learning algorithm-based magnetic resonance imaging
  179. An online diagnosis method for cancer lesions based on intelligent imaging analysis
  180. Medical imaging in rheumatoid arthritis: A review on deep learning approach
  181. Predictive analytics in smart healthcare for child mortality prediction using a machine learning approach
  182. Utility of neutrophil–lymphocyte ratio and platelet–lymphocyte ratio in predicting acute-on-chronic liver failure survival
  183. A biomedical decision support system for meta-analysis of bilateral upper-limb training in stroke patients with hemiplegia
  184. TNF-α and IL-8 levels are positively correlated with hypobaric hypoxic pulmonary hypertension and pulmonary vascular remodeling in rats
  185. Stochastic gradient descent optimisation for convolutional neural network for medical image segmentation
  186. Comparison of the prognostic value of four different critical illness scores in patients with sepsis-induced coagulopathy
  187. Application and teaching of computer molecular simulation embedded technology and artificial intelligence in drug research and development
  188. Hepatobiliary surgery based on intelligent image segmentation technology
  189. Value of brain injury-related indicators based on neural network in the diagnosis of neonatal hypoxic-ischemic encephalopathy
  190. Analysis of early diagnosis methods for asymmetric dementia in brain MR images based on genetic medical technology
  191. Early diagnosis for the onset of peri-implantitis based on artificial neural network
  192. Clinical significance of the detection of serum IgG4 and IgG4/IgG ratio in patients with thyroid-associated ophthalmopathy
  193. Forecast of pain degree of lumbar disc herniation based on back propagation neural network
  194. SPA-UNet: A liver tumor segmentation network based on fused multi-scale features
  195. Systematic evaluation of clinical efficacy of CYP1B1 gene polymorphism in EGFR mutant non-small cell lung cancer observed by medical image
  196. Rehabilitation effect of intelligent rehabilitation training system on hemiplegic limb spasms after stroke
  197. A novel approach for minimising anti-aliasing effects in EEG data acquisition
  198. ErbB4 promotes M2 activation of macrophages in idiopathic pulmonary fibrosis
  199. Clinical role of CYP1B1 gene polymorphism in prediction of postoperative chemotherapy efficacy in NSCLC based on individualized health model
  200. Lung nodule segmentation via semi-residual multi-resolution neural networks
  201. Evaluation of brain nerve function in ICU patients with Delirium by deep learning algorithm-based resting state MRI
  202. A data mining technique for detecting malignant mesothelioma cancer using multiple regression analysis
  203. Markov model combined with MR diffusion tensor imaging for predicting the onset of Alzheimer’s disease
  204. Effectiveness of the treatment of depression associated with cancer and neuroimaging changes in depression-related brain regions in patients treated with the mediator-deuterium acupuncture method
  205. Molecular mechanism of colorectal cancer and screening of molecular markers based on bioinformatics analysis
  206. Monitoring and evaluation of anesthesia depth status data based on neuroscience
  207. Exploring the conformational dynamics and thermodynamics of EGFR S768I and G719X + S768I mutations in non-small cell lung cancer: An in silico approaches
  208. Optimised feature selection-driven convolutional neural network using gray level co-occurrence matrix for detection of cervical cancer
  209. Incidence of different pressure patterns of spinal cerebellar ataxia and analysis of imaging and genetic diagnosis
  210. Pathogenic bacteria and treatment resistance in older cardiovascular disease patients with lung infection and risk prediction model
  211. Adoption value of support vector machine algorithm-based computed tomography imaging in the diagnosis of secondary pulmonary fungal infections in patients with malignant hematological disorders
  212. From slides to insights: Harnessing deep learning for prognostic survival prediction in human colorectal cancer histology
  213. Ecology and Environmental Science
  214. Monitoring of hourly carbon dioxide concentration under different land use types in arid ecosystem
  215. Comparing the differences of prokaryotic microbial community between pit walls and bottom from Chinese liquor revealed by 16S rRNA gene sequencing
  216. Effects of cadmium stress on fruits germination and growth of two herbage species
  217. Bamboo charcoal affects soil properties and bacterial community in tea plantations
  218. Optimization of biogas potential using kinetic models, response surface methodology, and instrumental evidence for biodegradation of tannery fleshings during anaerobic digestion
  219. Understory vegetation diversity patterns of Platycladus orientalis and Pinus elliottii communities in Central and Southern China
  220. Studies on macrofungi diversity and discovery of new species of Abortiporus from Baotianman World Biosphere Reserve
  221. Food Science
  222. Effect of berrycactus fruit (Myrtillocactus geometrizans) on glutamate, glutamine, and GABA levels in the frontal cortex of rats fed with a high-fat diet
  223. Guesstimate of thymoquinone diversity in Nigella sativa L. genotypes and elite varieties collected from Indian states using HPTLC technique
  224. Analysis of bacterial community structure of Fuzhuan tea with different processing techniques
  225. Untargeted metabolomics reveals sour jujube kernel benefiting the nutritional value and flavor of Morchella esculenta
  226. Mycobiota in Slovak wine grapes: A case study from the small Carpathians wine region
  227. Elemental analysis of Fadogia ancylantha leaves used as a nutraceutical in Mashonaland West Province, Zimbabwe
  228. Microbiological transglutaminase: Biotechnological application in the food industry
  229. Influence of solvent-free extraction of fish oil from catfish (Clarias magur) heads using a Taguchi orthogonal array design: A qualitative and quantitative approach
  230. Chromatographic analysis of the chemical composition and anticancer activities of Curcuma longa extract cultivated in Palestine
  231. The potential for the use of leghemoglobin and plant ferritin as sources of iron
  232. Investigating the association between dietary patterns and glycemic control among children and adolescents with T1DM
  233. Bioengineering and Biotechnology
  234. Biocompatibility and osteointegration capability of β-TCP manufactured by stereolithography 3D printing: In vitro study
  235. Clinical characteristics and the prognosis of diabetic foot in Tibet: A single center, retrospective study
  236. Agriculture
  237. Biofertilizer and NPSB fertilizer application effects on nodulation and productivity of common bean (Phaseolus vulgaris L.) at Sodo Zuria, Southern Ethiopia
  238. On correlation between canopy vegetation and growth indexes of maize varieties with different nitrogen efficiencies
  239. Exopolysaccharides from Pseudomonas tolaasii inhibit the growth of Pleurotus ostreatus mycelia
  240. A transcriptomic evaluation of the mechanism of programmed cell death of the replaceable bud in Chinese chestnut
  241. Melatonin enhances salt tolerance in sorghum by modulating photosynthetic performance, osmoregulation, antioxidant defense, and ion homeostasis
  242. Effects of plant density on alfalfa (Medicago sativa L.) seed yield in western Heilongjiang areas
  243. Identification of rice leaf diseases and deficiency disorders using a novel DeepBatch technique
  244. Artificial intelligence and internet of things oriented sustainable precision farming: Towards modern agriculture
  245. Animal Sciences
  246. Effect of ketogenic diet on exercise tolerance and transcriptome of gastrocnemius in mice
  247. Combined analysis of mRNA–miRNA from testis tissue in Tibetan sheep with different FecB genotypes
  248. Isolation, identification, and drug resistance of a partially isolated bacterium from the gill of Siniperca chuatsi
  249. Tracking behavioral changes of confined sows from the first mating to the third parity
  250. The sequencing of the key genes and end products in the TLR4 signaling pathway from the kidney of Rana dybowskii exposed to Aeromonas hydrophila
  251. Development of a new candidate vaccine against piglet diarrhea caused by Escherichia coli
  252. Plant Sciences
  253. Crown and diameter structure of pure Pinus massoniana Lamb. forest in Hunan province, China
  254. Genetic evaluation and germplasm identification analysis on ITS2, trnL-F, and psbA-trnH of alfalfa varieties germplasm resources
  255. Tissue culture and rapid propagation technology for Gentiana rhodantha
  256. Effects of cadmium on the synthesis of active ingredients in Salvia miltiorrhiza
  257. Cloning and expression analysis of VrNAC13 gene in mung bean
  258. Chlorate-induced molecular floral transition revealed by transcriptomes
  259. Effects of warming and drought on growth and development of soybean in Hailun region
  260. Effects of different light conditions on transient expression and biomass in Nicotiana benthamiana leaves
  261. Comparative analysis of the rhizosphere microbiome and medicinally active ingredients of Atractylodes lancea from different geographical origins
  262. Distinguish Dianthus species or varieties based on chloroplast genomes
  263. Comparative transcriptomes reveal molecular mechanisms of apple blossoms of different tolerance genotypes to chilling injury
  264. Study on fresh processing key technology and quality influence of Cut Ophiopogonis Radix based on multi-index evaluation
  265. An advanced approach for fig leaf disease detection and classification: Leveraging image processing and enhanced support vector machine methodology
  266. Erratum
  267. Erratum to “Protein Z modulates the metastasis of lung adenocarcinoma cells”
  268. Erratum to “BRCA1 subcellular localization regulated by PI3K signaling pathway in triple-negative breast cancer MDA-MB-231 cells and hormone-sensitive T47D cells”
  269. Retraction
  270. Retraction to “Protocatechuic acid attenuates cerebral aneurysm formation and progression by inhibiting TNF-alpha/Nrf-2/NF-kB-mediated inflammatory mechanisms in experimental rats”
Jetzt anmelden und 20% sparen
Institutioneller Zugang
Wie funktioniert Authentifizierung?
Haben Sie eine Idee, wie wir unsere Website verbessern können?
Bitte schreiben Sie uns.
© 2025 De Gruyter Brill
Heruntergeladen am 6.9.2025 von https://www.degruyterbrill.com/document/doi/10.1515/biol-2022-0772/html?lang=de
Button zum nach oben scrollen