Home Phylogenetic analysis of promoter regions of human Dolichol kinase (DOLK) and orthologous genes using bioinformatics tools
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Phylogenetic analysis of promoter regions of human Dolichol kinase (DOLK) and orthologous genes using bioinformatics tools

  • Nadia Farooqi , Ataur Rahman , Yasir Ali , Kishwar Ali , Muhammad Ezaz Hasan Khan , David Aaron Jones EMAIL logo , Mouadh Abdelkarim , Farman Ullah and Fazal Jalil
Published/Copyright: May 23, 2023

Abstract

The Dolichol kinase (DOLK) gene encodes the polytopic DOLK protein associated with the endoplasmic reticulum (ER) N-glycosylation pathway catalyzing the final step in the biosynthesis of dolichol phosphate. Dolichol phosphate is an oligosaccharide carrier required for N-glycosylation of DOLK protein, with its deficiency leading to a severe hypo glycosylation phenotype in humans which can cause congenital disorders of glycosylation and death in early infancy. The aim of the present study is to identify the phylogenetic relationship between human and ortholog species based on their conserved sequences in DOLK gene. Sequence alignment of DOLK was carried out in this study and the evolutionarily conserved regulatory sequences were identified using bioinformatics. Promoter sequence of human DOLK was compared with orthologous sequences from different organisms. Conserved non-coding sequences (CNS) and motifs in promoter regions were found by analyzing upstream promoter sequences of Homo sapiens DOLK and its orthologous genes in other organisms. Conserved sequences were predicted in the promoter regions in CNS1 and CNS2. Conserved protein sequences were also identified by alignment of the orthologous sequences. Organisms with similar gene sequences are assumed to be closely related and the ER N-glycosylation pathway is conserved in them.

1 Introduction

Metabolic disorders including congenital disorders of glycosylation (CDG) result from abnormal protein and lipid glycosylation in the endoplasmic reticulum (ER) and Golgi apparatus. Glycosylation is a co- and post-translational addition of oligosaccharides (glycans) which are important in supporting protein folding, stability, and cell–cell adhesion [1,2]. Genetic defects in the N-glycosylation pathway can result in multisystem disease. CDGs are inborn metabolic errors, which form a rapidly growing group of 170 rare familial inherited diseases [3,4]. A defect in Dolichol Kinase (DOLK; E.C. 2.7.1.108) was discovered in 2007 by Kranz et al. [5].

CDG patients present with seizures, muscle hypotonia, ataxia, failure to thrive, ophthalmologic anomalies, endocrine and coagulation abnormalities, dysmorphism, psychomotor, and intellectual disability. A rare case of dilated cardiomyopathy (DCM) was reported in one of the two families with DOLK deficiency (DOLK-CDG, MIM 610768). The patients present with multisystem muscular hypotonia, ichthyosis, nystagmus, epilepsy, and pulmonary infection. These cases result in death at early stages in infants [5,6] with liver involvement and those with cognitive delay [6].

A gene (SEC59) coding for DOLK was first identified in temperature-sensitive yeast cells. The mutant yeast, deficient in this protein, ceased dividing and became enlarged at the restrictive temperature of 37°C, with inactive and incompletely glycosylated secretory proteins accumulating in the cell [5]. Human DOLK gene (ID: 22845, 9q34.11) was characterized at the molecular level by Fernandez et al., Shridas and Waechter [7,8]. This gene was found to be located on chromosome No. 9, with the open reading frame encoding for a protein consisting of 538 amino acids [9,10].

DOLK catalyzes the final step in the biosynthesis of Dolichol phosphate (Dol-P). Its deficiency in this pathway was reported to cause a severe hypo glycosylation phenotype in humans [11]. Three variants (CM1110851, CM111850, and CM1110849) in the gene have been associated with DCM [9]. Two siblings with neurological disorder were reported to have a homozygous missense mutation (p.M1?; c.2T > C) in DOLK [12]. Four patients homozygous for either c.295TrA (99Cys > Ser) or c.1322ArC (441Tyr > Ser) mutations, died in early infancy [5]. Autosomal recessive DOLK mutations were reported in 11 young patients (5–13 years) with DCM [13]. Two newborn female siblings with DCM and sever ichthyosis were found to have novel compound heterozygous mutations in DOLK: c.951C > A (p.Tyr317Ter) and c.1558A. G (p.Thr520Ala) which resulted in their death [14,15]. Using next generation sequencing, patient’s fibroblasts were identified as having homozygous c.1447C > A (p.Q483K) DOLK mutations [16]. These patients demonstrated severe effects upon enzymatic functions verifying in silico predictions as damaging (SIFT score 0.003) and probably damaging (Polyphen-2 score 0.975) [17,18]. A novel DOLK mutation was identified in a child with neonatal asphyxia, ichthyoid rash, and congenital heart disease [19].

To our knowledge, there are few bioinformatics studies available on the evolutionary analysis of DOLK gene in various species. We selected this gene for our study to understand its evolutionary history, gene expression, its contribution to the pathogenesis of different genetic disorders including DCM and to identify the cis-regulatory elements. Therefore, we investigated whether evolutionary conserved sequences are present in DOLK gene of ortholog species. The current study was conducted to analyze the human DOLK and its orthologous genes in order to study the phylogenetic relationship and to find conserved non-coding sequences (CNS) in the promoter region across various species. A comprehensive analysis of tissue specific expression was performed with the help of available expression data in Ensembl for the DOLK gene. The use of various bioinformatics tools will help us better understand the expression and regulation of the DOLK gene across various species. Consequently, by understanding the regulation and evolution of the DOLK gene, this study may help improve the diagnosis and treatment of diseases caused by defects in the DOLK gene or the ER N-glycosylation pathway.

2 Methods

2.1 DOLK gene and its expression analysis

In silico expression profile of human DOLK gene was analyzed at the developmental stage with the help of the online database Ensembl (https://asia.ensembl.org/index.html). On the Ensembl homepage, our species of interest (Human) was chosen using the pull-down menu at the left of the search box and DOLK was typed in the search box. By clicking on the “Go” button, next page was opened. In the next step, DOLK (Human Gene) was selected. By clicking on gene expression on the right side, the expression profile of the DOLK gene was obtained. For identification of the DOLK gene ID, the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov/) was used. On the NCBI homepage, the pull-down menu was clicked to select the gene database. The gene name (DOLK) was typed in the text box and search button was clicked to obtain the gene ID. The workflow for the identification of conserved sequences in DOLK gene promoters of orthologous species is shown in Figure 1.

Figure 1 
                  Workflow for identification of conserved sequences in the promoters of DOLK gene in orthologous species.
Figure 1

Workflow for identification of conserved sequences in the promoters of DOLK gene in orthologous species.

2.2 Screening for human DOLK gene and its orthologous gene sequences

The FASTA sequence of Homo sapiens DOLK gene was downloaded from NCBI database. The obtained sequence was then used as a query sequence in NCBI Basic Local Alignment Search Tool (BLAST) (http://blast.ncbi.nlm.nih.gov) to find the orthologous gene sequences, total score, query cover, sequence identity, and accession number for different species. On the NCBI BLAST homepage, Nucleotide BLAST was clicked, and query sequence (human DOLK sequence) was entered in the text area, using default parameters for analysis. After clicking the BLAST button, a table showing sequences of significant alignments was obtained (results are displayed in a new window). On clicking the download button, FASTA (complete sequence) was selected to obtain a file with FASTA sequences.

2.3 Sequence alignment and construction of the phylogenetic tree

Genes from the 15 closest orthologous members were selected based on their sequence identity. Using the accession number of Homo sapiens DOLK gene (query sequence) and its orthologous genes, the gene annotations and FASTA sequence were obtained from NCBI for the phylogenetic analysis of Homo sapiens and its orthologous species. The FASTA sequences of all the orthologous species were aligned using the bioinformatics tools (MUSCLE, Gblocks, PhyML, TreeDyn in Phylogeny.fr (http://www.phylogeny.fr) [20] and then the phylogenetic tree was constructed. Using the Phylogeny.fr server, the “One Click” Mode was selected and a set of sequences in FASTA format was pasted in the text box. By clicking the submit button, the sequence data were processed to construct the tree. The analysis was performed on the Phylogeny.fr platform and comprised four steps, namely, alignment, curation, phylogeny, and tree rendering.

First the sequences were aligned with MUSCLE using default settings. Second, the regions containing gaps and poorly aligned were removed with Gblocks using the default parameters. In the third step, the phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML program. In the fourth step, graphical representation and edition of the phylogenetic tree were performed with TreeDyn.

2.4 Searching CNS in the promoter regions

The comparative analysis was performed using FASTA sequences of 15 orthologous genes with the help of EARS software (http://nero.wsbc.warwick.ac.uk/tools/user_case_form.php) [21]. A template sequence (human DOLK sequence) was selected, to which all other orthologous sequences were compared. The orthologous sequences were used as comparison sequences. The species names were entered in each case. A cut off P-value of 0.1 and window size of 90 bp were selected. The resulting EARS file for each pair of species (human and one ortholog species) was analyzed individually and the location of significant peaks in the promoter region was detected for Homo sapiens DOLK gene and its orthologous sequence. Similarly, the cumulative EARS file was obtained for all the species.

The conserved motif sequences were identified in promoters using MEME Suite (https://meme-suite.org/meme/) [22]. This server performs motif-based sequence analysis and provides MEME tool. Using the FASTA sequences of DOLK gene and default parameters, three conserved motifs were identified in the promoters of the orthologous species, representing binding sites for the regulatory proteins. The results were obtained as MEME HTML output.

2.5 Aligning multiple sequences of DOLK protein

The DOLK protein sequences of different species were analyzed and aligned using the Clustal Omega algorithm. The UniProt database (https://www.uniprot.org/) [23] provides a multiple sequence alignment tool for proteins called “Align.” This tool runs the Clustal Omega program to find the similarity in the sequences being aligned. On the UniProt homepage, the Align tab in the toolbar was clicked to align the protein sequences with the Clustal Omega program. Protein sequences in FASTA format were entered in the text area. Output sequence order was selected similar to that of the input. The “Run Align” button was clicked to obtain the alignment results.

3 Results

3.1 Selection and expression analysis of DOLK gene in the species

Gene expression analysis can help us to identify different genetic defects underlying human disorders. The Ensembl database was used to perform expression analysis of human DOLK gene in fetal and adult tissues. The highest expression level was found in fetal and adult brain tissue followed by adult heart, and fetal skeletal and heart tissues (Figure 2).

Figure 2 
                  Human DOLK mRNA expression analysis in fetal and adult tissues shown as fold change in comparison to tissue with lowest expression level [9].
Figure 2

Human DOLK mRNA expression analysis in fetal and adult tissues shown as fold change in comparison to tissue with lowest expression level [9].

3.2 DOLK sequence in human and other ortholog species

The FASTA sequence of Homo sapiens DOLK gene downloaded from NCBI was used as query sequence in NCBI BLAST to obtain its orthologous gene sequences. Closely related organisms will have more similar sequences than distantly related organisms. Therefore, those species were selected which showed sequence identity >95% and were more closely related. The orthologous sequences were downloaded and saved in a word file. The total score, query cover, sequence identity, and accession number for different orthologous genes were obtained, as indicated in Table 1.

Table 1

Total score and other information for DOLK and orthologous genes in different species

S. no. Source Total score Query cover (%) Identity (%) Accession
1. Homo sapiens 4,071 100 100 NM_014908.3
2 Gorilla gorilla 4,015 99 99 XM_004048710.2
3 Pan paniscus 3,976 99 99 XM_008975907.1
4 Nomascus leucogenys 3,890 99 99 XM_003264225.3
5 Pongo abelii 3,888 99 99 XM_009244938.1
6 Theropithecus gelada 3,810 100 98 XM_025358577.1
7 Piliocolobus tephrosceles 3,808 99 98 XM_023216989.2
8 Macaca mulatta 3,494 91 98 NM_001266918.1
9 Chlorocebus sabaeus 3,792 99 98 XM_008005998.1
10 Cercocebus atys 3,783 99 98 XM_012038908.1
11 Rhinopithecus bieti 3,771 99 98 XM_017848286.1
12 Colobus angolensis palliates 3,762 99 98 XM_011931244.1
13 Mandrillus leucophaeus 3,736 98 98 XM_011971196.1
14 Macaca fascicularis 3,602 94 98 NM_001283633.1
15 Aotus nancymaae 3,533 99 96 XM_012458008.1

3.3 Sequence alignment and phylogenetic tree

The promoter regions of the DOLK orthologous genes showed close association across various species in order to conserve the biological role and expression of the gene. Phylogenetic analysis helped in the prediction of conserved promoter regions in the species. The phylogenetic tree was constructed by aligning FASTA sequences from human DOLK and 14 orthologous genes obtained from BLAST. It was constructed via the neighbor-joining method showing the ancestral relationship among species. The results of phylogenetic analysis are given in bootstrap values. The higher the bootstrap values, the more closely are the organism related to each other. The tree consisted of a clade with a higher bootstrap value (0.98) and a high confidence level, showing that human and other species are genetically and evolutionarily related to each other (Figure 3).

Figure 3 
                  Phylogenetic tree for human DOLK gene and orthologous species using Phylogeny.fr.
Figure 3

Phylogenetic tree for human DOLK gene and orthologous species using Phylogeny.fr.

3.4 CNS in DOLK promoters

Promoter regions are functionally important for gene expression and are conserved during evolution. Promoter regions consisting of conserved sequences showed significant conservation between human and other species. EARS tool was used to compare the orthologous sequences to identify conserved regions in all the orthologs. After submitting sequences, EARS analysis was performed for each pair of species, and individual results (Figure 4) and cumulative results (Figure 5) were obtained. Cumulative results highlighted the conserved regions in all the species. In this study, two peaks were found above the significance threshold (P = 0.1) indicating a highly conserved match between human and other species. CNS1 and CNS2 were predicted in the promoter regions (Figure 5).

Figure 4 
                  Identification of evolutionarily conserved sequences and individual conservation profile of human DOLK and orthologous promoters. The sequences upstream of the translation start codon were aligned using the EARS tool with a 90-base window length. Peaks above significance threshold of P = 0.1 (dotted red line) show a highly conserved match between species. Regions of conservativity highlighted with RED bracket = CNS1 and BLACK bracket = CNS2.
Figure 4

Identification of evolutionarily conserved sequences and individual conservation profile of human DOLK and orthologous promoters. The sequences upstream of the translation start codon were aligned using the EARS tool with a 90-base window length. Peaks above significance threshold of P = 0.1 (dotted red line) show a highly conserved match between species. Regions of conservativity highlighted with RED bracket = CNS1 and BLACK bracket = CNS2.

Figure 5 
                  Cumulative conservation profile of human DOLK promoter and orthologous gene promoters from other species.
Figure 5

Cumulative conservation profile of human DOLK promoter and orthologous gene promoters from other species.

The promoter sequences upstream from the translation start codon were aligned using the EARS tool to identify the evolutionary conserved regulatory regions and a cumulative conservation profile was constructed for human DOLK promoter and promoters from all other orthologs (Figure 5).

Identification of the conserved motifs in the promoters was performed using MEME tool. A conserved motif in human DOLK promoter was found between positions −624 and −673. The second and third motifs were revealed in the promoter between positions −96 and −145, and between positions −560 and −609, respectively. Similarly, the motifs for other species were identified in their promoters. The sequences of these motifs in the orthologous species are shown as colored sequences in Supplementary File 1. These conserved motifs within the promoter of DOLK may represent the binding sites for the transcription factors, controlling the expression of DOLK gene. These results indicate that these promoter regions harboring conserved motifs are required for expression of DOLK.

3.5 Multiple protein sequence alignment

A set of FASTA sequences of the DOLK protein was pasted and aligned using the Clustal Omega program in UniProt database. The alignment results showed a significant similarity in the protein sequences of different species with only few different amino acid residues (Supplementary File 2). This shows that the DOLK protein is highly conserved in these species suggesting their role in phylogenetic analysis.

4 Discussion

In humans, the CNS in DOLK promoter involved in the ER N-glycosylation pathway can also be found in other organisms such as Gorilla sp., Pan paniscus, Nomascus leucogenys, Pongo abelii, Mandrillus leucophaeus, and Aotus nancymaae indicating a close evolutionary relationship between humans and other eukaryotes which can be correlated using the findings of Levy-Ontman et al. [24]. Sequence information is a transmutable phenomenon in living organisms, which is why conserved sequence shows the presence of a conserved gene. In the case of cross species conservation, this would indicate that a particular sequence has been unchanged by evolution as mutations in a highly conserved region results in non-viable life forms or a form quickly eliminated through natural selection.

Bioinformatics tools have been used to identify protein sequences involved in the ER N-glycosylation pathway of the red algae Porphyridium sp. These protein sequences were compared with ortholog protein sequences of other red algae, green algae, diatoms, mammals, and yeast which led to the identification of 24 encoded-genes homologous for known protein sequences in their ER pathways suggesting this pathway is conserved in animals, plants, yeasts, etc. [24]. Using a comparative genome-wide bioinformatics analysis, it was found that by analyzing upstream promoter sequences of glutamine synthetase cytosolic isozyme GS1;5 from Arabidopsis thaliana and its orthologous genes in various plant species, it was possible to identify CNS in promoter region [25]. Forty-two different enzymes in the N-linked glycan synthetic pathway or interactive pathways were found deficient in different types of CDG-N-linked disorders and multiple-pathway disorders [26,27]. DOLK variants have also been reported in patients showing a phenotype which overlaps CDG and dystroglycanopathy (DGpathy), with defective N-glycosylation and reduced O-mannosylation [28]. Neuromuscular disorders such as DGpathies have abnormal glycosylation of the glycoprotein dystroglycan [26]. Moreover, four genes DOLK (OMIM 610746), DPM1 (OMIM 603503), DPM2 (OMIM 603564), and DPM3 (OMIM 605951) encode for important enzymes involved in Dolichol metabolism [28] and mutations in them can cause some CDGs [29]. DGpathies have recently been associated with these four proteins and reported patients present with DCM, muscular dystrophy, and CDG diseases [29]. CDG-DOLK deficiency and cardiac pathology were reported in nine patients in three unrelated Israeli families with novel homozygous DOLK mutations. The cardiac symptoms ranged from discrete, mild DCM to overt heart failure with death [15,30]. Various studies have shown that DOLK is one of the candidate genes causing CDG, and mutations in this gene have also been associated with other genetic disorders such as DCM [13,26].

The present study is helpful in understanding the N-glycosylation pathway in different species. The conserved sequences have important biological functions. Their identification in human and lab organisms such as mice can be useful in predicting DOLK-related genetic anomalies. Besides its importance in the study of human diseases, phylogenetic analysis has a key role in identifying and characterizing newly discovered pathogens. As outlined above, the current information on evolutionary analysis of DOLK gene indicates that there are many gaps in our knowledge. The regulatory aspects of the N-linked glycan synthetic pathway and its interconnection within protein networks are still not well understood. Further studies on CDG patients will aid in finding some of the missing genes which cause the disease. Molecular and biochemical techniques will further help in our understanding of this diverse group of genetic disorders. Genome-wide association studies can be used to identify variations in conserved sequences associated with these diseases. Moreover, mechanism-based studies will help in monitoring the medication responses and in novel treatments in the future.

5 Conclusion

In conclusion, this study shows that human DOLK is closely related to orthologous genes in other species and has been found to express throughout the body. DOLK expression was found to be higher in both fetal and adult brain tissue with lower but still significant expression in adult heart, and fetal skeletal and heart muscle tissues. Evolutionary analysis of regulatory sequences using phylogenetic approach revealed highly conserved sequences and motifs in DOLK promoter region of human and orthologous species. In addition, sequence alignment of the orthologous proteins indicated conserved sequences with only few different amino acid residues. Currently, little is known about the evolutionary conserved sequences of DOLK gene in human and orthologous species. Going forward, it is recommended to screen the transcription factors binding sites for the DOLK gene promoter and to study other genes for evolutionary analysis. Gene expression studies on animal models will help us better understand the disease mechanisms and its treatment.

6 Web resources

Ensembl, https://asia.ensembl.org/index.html (17 June 2022).

NCBI, https://www.ncbi.nlm.nih.gov/(24 June 2022).

BLAST, http://blast.ncbi.nlm.nih.gov (3 July 2022).

Phylogeny.fr, http://www.phylogeny.fr (19 July 2022).

Evolutionary Analysis of Regulatory Sequences (EARS), http://nero.wsbc.warwick.ac.uk/tools/user_case_form.php (15 September 2022).

MEME Suite, https://meme-suite.org/meme/(2 February 2023).

UniProt, https://www.uniprot.org/(30 January 2023).

  1. Funding information: Open Access funding was provided by the Qatar National Library.

  2. Author contributions: N.F. analyzed the data, drafted the manuscript and designed the study. N.F. and F.U. performed the data curation and revised the manuscript. F.J. helped in study designing and writing and editing the manuscript. A.R., K.A., and D.A.J. helped in manuscript preparation, reviewing, and editing. Y.A., M.A., and M.E.H.K. revised the manuscript. All authors read and approved the final version of the manuscript.

  3. Conflict of interest: Authors state no conflict 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.

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Received: 2022-12-13
Revised: 2023-02-07
Accepted: 2023-03-12
Published Online: 2023-05-23

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

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

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  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”
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