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Yi Chuan = Hereditas Apr 2024With the increasing number of complex forensic cases in recent years, it's more important to combine the different types of genetic markers such as short tandem repeats...
With the increasing number of complex forensic cases in recent years, it's more important to combine the different types of genetic markers such as short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (InDels), and microhaplotypes (MHs) to provide more genetic information. In this study, we selected totally 201 genetic markers, including 24 autosomes STRs (A-STRs), 24 Y chromosome STRs (Y-STRs), 110 A-SNPs, 24 Y-SNPs, 9 A-InDels, 1 Y-InDel, 8 MHs, and Amelogenin to establish the HID_AM Panel v1.0, a Next-Generation Sequencing (NGS) detection system. According to the validation guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), the repeatability, accuracy, sensitivity, suitability for degraded samples, species specificity, and inhibitor resistance of this system were assessed. The typing results on 48 STRs and Amelogenin of this system were completely consistent with those obtained using capillary electrophoresis. This system accurately detected 79 SNPs as parallelly confirmed by a FGx sequencer with the ForenSeq™ DNA Signature Prep Kit. Complete allele typing results could be obtained with a DNA input of no less than 200 pg. The detection success rate of this system was significantly higher than that of the GlobalFiler™ kit when the degradation index of mock degraded sample was greater than 15.87. When the concentration of hematin in the amplification system was ≤40 µmol/L, indigo blue was ≤2 mmol/L, or humic acid was ≤15 ng/µL, amplification was not significantly inhibited. The system barely amplified the DNA extract from duck, mouse, cow, rabbit, and chick. The detection rate of STRs on routine samples of this panel is 99.74%, while all the SNPs, InDels, and MHs were successfully detected. In summary, we setup a NGS individual typing panel including 201 genetic markers with the high accuracy, sensitivity, species specificity, and inhibitors resistance, which is applicable for individual identification of degraded samples.
Topics: Female; Cattle; Animals; Mice; Rabbits; DNA Fingerprinting; Genetic Markers; Amelogenin; Genotype; Polymerase Chain Reaction; Reproducibility of Results; Polymorphism, Single Nucleotide; High-Throughput Nucleotide Sequencing; Microsatellite Repeats; DNA; Sequence Analysis, DNA
PubMed: 38632093
DOI: 10.16288/j.yczz.23-253 -
BMC Genomics Apr 2024Previously, a novel multiplex system of 64 loci was constructed based on capillary electrophoresis platform, including 59 autosomal insertion/deletions (A-InDels), two...
Joint application of A-InDels and miniSTRs for forensic personal, full and half sibling identifications, and genetic differentiation analyses in two populations from China.
BACKGROUND
Previously, a novel multiplex system of 64 loci was constructed based on capillary electrophoresis platform, including 59 autosomal insertion/deletions (A-InDels), two Y-chromosome InDels, two mini short tandem repeats (miniSTRs), and an Amelogenin gene. The aim of this study is to evaluate the efficiencies of this multiplex system for individual identification, paternity testing and biogeographic ancestry inference in Chinese Hezhou Han (CHH) and Hubei Tujia (CTH) groups, providing valuable insights for forensic anthropology and population genetics research.
RESULTS
The cumulative values of power of discrimination (CDP) and probability of exclusion (CPE) for the 59 A-InDels and two miniSTRs were 0.99999999999999999999999999754, 0.99999905; and 0.99999999999999999999999999998, 0.99999898 in CTH and CHH groups, respectively. When the likelihood ratio thresholds were set to 1 or 10, more than 95% of the full sibling pairs could be identified from unrelated individual pairs, and the false positive rates were less than 1.2% in both CTH and CHH groups. Biogeographic ancestry inference models based on 35 populations were constructed with three algorithms: random forest, adaptive boosting and extreme gradient boosting, and then 10-fold cross-validation analyses were applied to test these three models with the average accuracies of 86.59%, 84.22% and 87.80%, respectively. In addition, we also investigated the genetic relationships between the two studied groups with 33 reference populations using population statistical methods of F, D, phylogenetic tree, PCA, STRUCTURE and TreeMix analyses. The present results showed that compared to other continental populations, the CTH and CHH groups had closer genetic affinities to East Asian populations.
CONCLUSIONS
This novel multiplex system has high CDP and CPE in CTH and CHH groups, which can be used as a powerful tool for individual identification and paternity testing. According to various genetic analysis methods, the genetic structures of CTH and CHH groups are relatively similar to the reference East Asian populations.
Topics: Humans; Phylogeny; Siblings; Genetics, Population; China; INDEL Mutation; Microsatellite Repeats; Forensic Genetics; Gene Frequency
PubMed: 38566035
DOI: 10.1186/s12864-024-10187-4 -
Biomedicines Mar 2024Dental caries is an avoidable and complex condition impacting billions of individuals worldwide, posing a specific concern among younger generations, despite the...
Dental caries is an avoidable and complex condition impacting billions of individuals worldwide, posing a specific concern among younger generations, despite the progress of oral hygiene products. This deterioration occurs due to the acid demineralization of tooth enamel, leading to the loss of minerals from the enamel subsurface. The remineralisation of early enamel carious lesions could prevent the cavitation of teeth. The enamel protein amelogenin constitutes 90% of the total enamel matrix protein and plays a key role in the bio mineralisation process. The aim of this study is to investigate the self-assembly microstructure and reticulation behaviour of a newly developed bioactive hydrogel with leucine-rich amelogenin peptide (LRAP) intended for enamel remineralisation. SEM, AFM, UV-VIS, and FTIR analyses emphasize the ability of peptides to promote cell adhesion and the treatment of early carious lesions. In conclusion, short-chain peptides can be used in hydrogels for individual or professional use.
PubMed: 38540307
DOI: 10.3390/biomedicines12030694 -
Cureus Feb 2024The purpose of the study was to compare and histologically investigate pulpal response and dentin bridge formation after direct pulp capping using recombinant amelogenin...
The purpose of the study was to compare and histologically investigate pulpal response and dentin bridge formation after direct pulp capping using recombinant amelogenin and mineral trioxide aggregate (MTA). Recombinant amelogenin protein and MTA were used as pulp capping materials in 120 teeth from eight mongrel dogs. Dogs were sacrificed at two different evaluation times. Regenerative changes were evaluated histologically. At two weeks, in contrast to the MTA group, most of the amelogenin group showed moderately formed hard tissue formation and the pulp tissue was completely filling the entire pulp chamber. These results were statistically significant. At two months, all the samples of the amelogenin group showed complete dentin bridge formation and the pulp chamber was filled entirely with tissue-mimicking the authentic pulp in all the specimens of the amelogenin group. These results were statistically significant. In conclusion, direct pulp capping by recombinant amelogenin protein resulted in significantly better regeneration of the dentin-pulp complex than MTA.
PubMed: 38516479
DOI: 10.7759/cureus.54560 -
International Journal of Legal Medicine Jul 2024Forensic DNA analysis in compromised skeletal remains may pose challenges due to DNA degradation, often resulting in partial or negative autosomal STRs profiles. To...
Forensic DNA analysis in compromised skeletal remains may pose challenges due to DNA degradation, often resulting in partial or negative autosomal STRs profiles. To address this issue, alternative approaches such as mitochondrial DNA or SNPs typing may be employed; however, they are labour-intensive and costly. Insertion-null alleles (INNULs), short interspersed nuclear elements, have been suggested as a valuable tool for human identification in challenging samples due to their small amplicon size. A commercial kit including 20 INNULs markers along with amelogenin (InnoTyper® 21) has been developed. This study assesses its utility using degraded skeletal remains, comparing the results obtained (the number of detected alleles, RFU values, PHR, and the number of reportable markers) to those obtained using GlobalFiler™. Subsequently, the random match probability of the two profiles for each sample was determined using Familias version 3 to evaluate the power of discrimination of the results obtained from each kit. In every sample, InnoTyper® 21 yielded more alleles, higher RFU values, and a greater number of reportable loci. However, in most cases, both profiles were similarly informative. In conclusion, InnoTyper® 21 serves as a valuable complement to the analysis of challenging samples in cases where a poor or negative profile was obtained.
Topics: Humans; Genetic Markers; DNA Fingerprinting; Body Remains; Amelogenin; Alleles; DNA Degradation, Necrotic; Microsatellite Repeats; Short Interspersed Nucleotide Elements; Polymerase Chain Reaction; Male
PubMed: 38509248
DOI: 10.1007/s00414-024-03205-3 -
Cytogenetic and Genome Research Mar 2024Introduction Parthenogenetic chimera is an extremely rare condition in human. Very few patients with parthenogenetic chimerism with XX/XY cells have been identified....
Introduction Parthenogenetic chimera is an extremely rare condition in human. Very few patients with parthenogenetic chimerism with XX/XY cells have been identified. Case Presentation We report the clinical findings and molecular analysis of chimerism with a 46,XX/46,XY karyotype in a patient presenting idiopathic oligoasthenoteratozoospermia (OAT). To clarify the mechanism of chimera formation, short tandem repeat (STR) analysis using 21 loci was carried out. Quantitation of alleles in D6S1043, D12S391, fibrinogen alpha chain (FGA) and Amelogenin revealed double paternal and one maternal genetic contribution to the patient, which is consistent with a parthenogenetic chimerism. The likely mechanism of chimerism formation was also discussed, followed by a literature review. Conclusion This is the first documented case of parthenogenetic chimerism in an adult male with XX/XY cells presenting OAT. Improved cell sampling and more sensitive and specific detection methods are necessary to identify more patients with XX/XY chimerism for systematic studies on this condition in the future.
PubMed: 38498988
DOI: 10.1159/000538396 -
Journal of Periodontal Research Jun 2024In order to evaluate the effect of methacrylated hyaluronic acid (HAMA) hydrogels containing the recombinant human amelogenin (rhAm) in vitro and in vivo.
OBJECTIVES
In order to evaluate the effect of methacrylated hyaluronic acid (HAMA) hydrogels containing the recombinant human amelogenin (rhAm) in vitro and in vivo.
BACKGROUND
The ultimate goal in treating periodontal disease is to control inflammation and achieve regeneration of periodontal tissues. In recent years, methacrylated hyaluronic acid (HAMA) containing recombinant human amyloid protein (rhAm) has been widely used as a new type of biomaterial in tissue engineering and regenerative medicine. However, there is a lack of comprehensive research on the periodontal regeneration effects of this hydrogel. This experiment aims to explore the application of photoresponsive recombinant human amelogenin-loaded hyaluronic acid hydrogel for periodontal tissue regeneration and provide valuable insights into its potential use in this field.
MATERIALS AND METHODS
The effects of rhAm-HAMA hydrogel on the proliferation of human periodontal ligament cells (hPDLCs) were assessed using the CCK-8 kit. The osteogenic differentiation of hPDLCs was evaluated through ALP staining and real-time PCR. Calvarial parietal defects were created in 4-week-old Sprague Dawley rats and implanted with deproteinized bovine bone matrix in different treatment groups. The animals were euthanized after 4 and 8 weeks of healing. The bone volume of the defect was observed by micro-CT and histological analysis.
RESULTS
Stimulating hPDLCs with rhAm-HAMA hydrogel did not significantly affect their proliferation (p > .05). ALP staining and real-time PCR results demonstrated that the rhAm-HAMA group exhibited a significant upregulation of osteoclastic gene expression (p < .05). Micro-CT results revealed a significant increase in mineralized tissue volume fraction (MTV/TV%), trabecular bone number (Tb.N), and mineralized tissue density (MTD) of the bone defect area in the rhAm-HAMA group compared to the other groups (p < .05). The results of hematoxylin and eosin staining and Masson staining at 8 weeks post-surgery further supported the results of the micro-CT.
CONCLUSIONS
The results of this study indicate that rhAm-HAMA hydrogel could effectively promote the osteogenic differentiation of hPDLCs and stabilize bone substitutes in the defects that enhance the bone regeneration in vivo.
Topics: Hyaluronic Acid; Animals; Bone Regeneration; Amelogenin; Humans; Rats, Sprague-Dawley; Periodontal Ligament; Rats; Hydrogels; Cell Proliferation; Cell Differentiation; Recombinant Proteins; Osteogenesis; Male; X-Ray Microtomography; Cells, Cultured; Methacrylates; Biocompatible Materials
PubMed: 38481308
DOI: 10.1111/jre.13235 -
International Journal of Legal Medicine Jul 2024Massively parallel sequencing allows for integrated genotyping of different types of forensic markers, which reduces DNA consumption, simplifies experimental processes,...
Massively parallel sequencing allows for integrated genotyping of different types of forensic markers, which reduces DNA consumption, simplifies experimental processes, and provides additional sequence-based genetic information. The STRseqTyper122 kit genotypes 63 autosomal STRs, 16 X-STRs, 42 Y-STRs, and the Amelogenin locus. Amplicon sizes of 117 loci were below 300 bp. In this study, MiSeq FGx sequencing metrics for STRseqTyper122 were presented. The genotyping accuracy of this kit was examined by comparing to certified genotypes of NIST standard reference materials and results from five capillary electrophoresis-based kits. The sensitivity of STRseqTyper122 reached 125 pg, and > 80% of the loci were correctly called with 62.5 pg and 31.25 pg input genomic DNA. Repeatability, species specificity, and tolerance for DNA degradation and PCR inhibitors of this kit were also evaluated. STRseqTyper122 demonstrated reliable performance with routine case-work samples and provided a powerful tool for forensic applications.
Topics: Humans; Microsatellite Repeats; High-Throughput Nucleotide Sequencing; DNA Fingerprinting; Amelogenin; Reproducibility of Results; Sequence Analysis, DNA; Genotype; Polymerase Chain Reaction; Species Specificity; Male; Animals; DNA Degradation, Necrotic; Electrophoresis, Capillary; Female
PubMed: 38416217
DOI: 10.1007/s00414-024-03195-2 -
BMC Oral Health Feb 2024Several methods were introduced for enamel biomimetic remineralization that utilize a biomimetic analogue to interact and absorb bioavailable calcium and phosphate ions...
BACKGROUND
Several methods were introduced for enamel biomimetic remineralization that utilize a biomimetic analogue to interact and absorb bioavailable calcium and phosphate ions and induce crystal nucleation on demineralized enamel. Amelogenin is the most predominant enamel matrix protein that is involved in enamel biomineralization. It plays a major role in developing the enamel's hierarchical microstructure. Therefore, this study was conducted to evaluate the ability of an amelogenin-inspired peptide to promote the remineralization potential of fluoride and a supersaturated calcium phosphate solution in treating artificially induced enamel carious lesions under pH-cycling regimen.
METHODS
Fifty enamel slices were prepared with a window (4*4 mm ) on the surface. Five samples were set as control healthy enamel and 45 samples were subjected to demineralization for 3 days. Another 5 samples were set as control demineralized enamel and 40 enamel samples were assigned into 8 experimental groups (n=5) (P/I, P/II, P/III, P/AS, NP/I, NP/II, NP/III and NP/AS) according to peptide treatment (peptide P or non-peptide NP) and remineralizing solution used (I; calcium phosphate solution, II; calcium phosphate fluoride solution, III; fluoride solution and AS; artificial saliva). Samples were then subjected to demineralization/remineralization cycles for 9 days. Samples in all experimental groups were evaluated using Raman spectroscopy for mineral content recovery percentage, microhardness and nanoindentation as healthy, demineralized enamel and after pH-cycling. Data were statistically analysed using two-way repeated measures Anova followed by Bonferroni-corrected post hoc test for pairwise multiple comparisons between groups. Statistical significance was set at p= 0.05. Additionally, XRD, FESEM and EDXS were used for crystal orientation, surface morphology and elemental analysis after pH-cycling.
RESULTS
Nanocrystals clumped in a directional manner were detected in peptide-treated groups. P/II showed the highest significant mean values in mineral content recovery (63.31%), microhardness (268.81±6.52 VHN), elastic modulus (88.74±2.71 GPa), nanohardness (3.08±0.59 GPa) and the best crystal orientation with I/ (1.87±0.08).
CONCLUSION
Despite pH changes, the tested peptide was capable of remineralizing enamel with ordered crystals. Moreover, the supplementary use of calcium phosphate fluoride solution with peptide granted an enhancement in enamel mechanical properties after remineralization.
Topics: Humans; Fluorides; Amelogenin; Cariostatic Agents; Biomimetics; Calcium Phosphates; Dental Caries; Minerals; Phosphates; Tooth Remineralization; Hydrogen-Ion Concentration
PubMed: 38413983
DOI: 10.1186/s12903-024-04008-z -
European Archives of Paediatric... Apr 2024Genetic variants of AMELX gene can affect the protein content, organization of enamel prisms, microstructure and microhardness of the enamel, thus altering the caries...
PURPOSE
Genetic variants of AMELX gene can affect the protein content, organization of enamel prisms, microstructure and microhardness of the enamel, thus altering the caries susceptibility. The present study aims to assess the association between polymorphisms rs17878486, rs5934997, and rs5933871 of AMELX gene and Early Childhood Caries (ECC).
MATERIALS AND METHODS
This case-control study was conducted on 200 participants, aged 3-6 years, with 100 controls and 100 children with ECC. A questionnaire was used to collect demographic data, birth-weight, type of delivery, oral hygiene practices, feeding history and 24-h diet diary. DNA was isolated from blood and subjected to PCR followed by Sanger sequencing.
RESULTS
The CC genotype of rs17878486 showed an OR of 1.93 (0.34-10.81; P = 0.73). In a recessive model, the CC genotype of rs17878486 reported an OR of 2.04 (0.36-11.40; P = 0.68); rs5593871 reported an OR of 1.00 (0.31-3.21). Statistically significant differences (P ≤ 0.05) between genotype and allele frequencies of rs17878486, rs5934997, and rs5933871 were not observed between children with ECC and the controls.
CONCLUSION
Polymorphisms of AMELX gene did not show a significant association with ECC in this population. However, documentation of genetic data in a global context of ECC may be essential for the future.
Topics: Humans; Case-Control Studies; Dental Caries; Child; Child, Preschool; Female; Male; India; Polymorphism, Single Nucleotide; Genotype; Amelogenin; Genetic Predisposition to Disease
PubMed: 38409576
DOI: 10.1007/s40368-024-00866-x