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International Journal of Molecular... Mar 2024Body fluid identification plays a crucial role in criminal investigations. Because of their presence in many cases, blood and semen are the most relevant body fluids in...
Body fluid identification plays a crucial role in criminal investigations. Because of their presence in many cases, blood and semen are the most relevant body fluids in forensic sciences. Based on antigen-antibody reactions binding unique proteins for each body fluid, serological assays represent one of the most rapid and highly specific tests for blood and semen. Currently, few studies have assessed the factors affecting body fluid identification by applying these assays. This work aimed to study the effect of different fabrics from clothes and time since deposition on identification through immunochromatographic tests for blood and semen, DNA isolation, and STR profiling from these samples. Body fluids were deposited on black- and white-dyed denim and cotton fabrics, and on leather. Afterward, blood and semen were sampled at 1 day, 30 days, and 90 days after deposition and identified by using the SERATEC HemDirect Hemoglobin Test and the PSA Semiquant and SERATEC BLOOD CS and SEMEN CS tests, respectively. Laboratory and crime scene tests presented similar performances for the detection of blood and semen stains on every tested fabric. No differences were found on band intensities between timepoints for all fabrics. It was possible to recover and identify blood and semen samples up to three months after deposition and to obtain full STR profiles from all the tested fabrics. Both body fluid STR profiles showed differences in their quality between 1 and 90 days after deposition for all fabrics except for black cotton for semen samples. Future research will expand the results, assessing body fluid identification on other substrates and under different environmental conditions.
Topics: Humans; Seeds; Body Fluids; Bodily Secretions; Semen Analysis; DNA; Saliva; DNA Fingerprinting
PubMed: 38542494
DOI: 10.3390/ijms25063522 -
Genes Feb 2024Maize( L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While...
Maize( L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines.
Topics: Polymorphism, Single Nucleotide; Chromosome Mapping; Genetic Markers; Zea mays; Genotype; Phylogeny; Genome, Chloroplast; Genome, Plant; Plant Breeding
PubMed: 38540352
DOI: 10.3390/genes15030293 -
Genes Feb 2024DNA analysis of traces from commonly found objects like knives, smartphones, tapes and garbage bags related to crime in aquatic environments is challenging for forensic...
DNA analysis of traces from commonly found objects like knives, smartphones, tapes and garbage bags related to crime in aquatic environments is challenging for forensic DNA laboratories. The amount of recovered DNA may be affected by the water environment, time in the water, method for recovery, transport and storage routines of the objects before the objects arrive in the laboratory. The present study evaluated the effect of four storage conditions on the DNA retrieved from bloodstains, touch DNA, fingerprints and hairs, initially deposited on knives, smartphones, packing tapes, duct tapes and garbage bags, and submerged in lake water for three time periods. After retrieval, the objects were stored either through air-drying at room temperature, freezing at -30 °C, in nitrogen gas or in lake water. The results showed that the submersion time strongly influenced the amount and degradation of DNA, especially after the longest submersion time (21 days). A significant variation was observed in success for STR profiling, while mtDNA profiling was less affected by the submersion time interval and storage conditions. This study illustrates that retrieval from water as soon as possible and immediate storage through air-drying or freezing before DNA analysis is beneficial for the outcome of DNA profiling in crime scene investigations.
Topics: DNA Fingerprinting; DNA, Mitochondrial; Lakes; Water; Humans
PubMed: 38540338
DOI: 10.3390/genes15030279 -
Animals : An Open Access Journal From... Mar 2024The DKK family is a canonical small family of WNT antagonists. Though recent studies have suggested that the DKK gene family may be involved in sex differentiation in ,...
The DKK family is a canonical small family of WNT antagonists. Though recent studies have suggested that the DKK gene family may be involved in sex differentiation in , there are still a lot of things about the DKK gene family that we do not know. In this study, we used bioinformatics methods to identify members of the DKK gene family in and analyzed their phylogeny, covariance, gene structure, structural domains, promoter conserved sites, signal peptides, gonadal transcription factors, transcriptional profiles, and tissue expression profiles. Additionally, qRT-PCR results were utilized for the validation and preliminary investigation of the function of the DKK gene family in . The results showed that the DKK gene family is divided into six subfamilies, distributed on six different chromosomal scaffolds containing different gene structures and conserved motifs with the same structural domains, and all of the members were secreted proteins. Our transcriptional profiling and embryonic expression analysis showed that and were significantly expressed in the testes, whereas and were significantly upregulated in the ovaries. This suggests a potential function in sex differentiation in . Our results may provide a basic theoretical basis for the sex differentiation process in .
PubMed: 38540029
DOI: 10.3390/ani14060931 -
Genetics in Medicine : Official Journal... Mar 2024DISP1 encodes a transmembrane protein that regulates the secretion of the morphogen, Sonic hedgehog, a deficiency of which is a major cause of holoprosencephaly (HPE)....
PURPOSE
DISP1 encodes a transmembrane protein that regulates the secretion of the morphogen, Sonic hedgehog, a deficiency of which is a major cause of holoprosencephaly (HPE). This disorder covers a spectrum of brain and midline craniofacial malformations. The objective of the present study was to better delineate the clinical phenotypes associated with division transporter dispatched-1 (DISP1) variants.
METHODS
This study was based on the identification of at least 1 pathogenic variant of the DISP1 gene in individuals for whom detailed clinical data were available.
RESULTS
A total of 23 DISP1 variants were identified in heterozygous, compound heterozygous or homozygous states in 25 individuals with midline craniofacial defects. Most cases were minor forms of HPE, with craniofacial features such as orofacial cleft, solitary median maxillary central incisor, and congenital nasal pyriform aperture stenosis. These individuals had either monoallelic loss-of-function variants or biallelic missense variants in DISP1. In individuals with severe HPE, the DISP1 variants were commonly found associated with a variant in another HPE-linked gene (ie, oligogenic inheritance).
CONCLUSION
The genetic findings we have acquired demonstrate a significant involvement of DISP1 variants in the phenotypic spectrum of midline defects. This underlines its importance as a crucial element in the efficient secretion of Sonic hedgehog. We also demonstrated that the very rare solitary median maxillary central incisor and congenital nasal pyriform aperture stenosis combination is part of the DISP1-related phenotype. The present study highlights the clinical risks to be flagged up during genetic counseling after the discovery of a pathogenic DISP1 variant.
PubMed: 38529886
DOI: 10.1016/j.gim.2024.101126 -
Forensic Science International. Genetics Jul 2024The genetic characterization and identification of individuals who contributed to biological mixtures are complex and mostly unresolved tasks. These tasks are relevant...
The genetic characterization and identification of individuals who contributed to biological mixtures are complex and mostly unresolved tasks. These tasks are relevant in various fields, particularly in forensic investigations, which frequently encounters crime scene stains generated by more than one person. Currently, forensic mixture deconvolution is mostly performed subsequent to forensic DNA profiling at the level of the mixed DNA profiles, which comes with several limitations. Some previous studies attempted at separating single cells prior to forensic DNA profiling. However, these approaches are biased at selection of the cells and, due to their targeted DNA analysis on low template DNA, provide incomplete and unreliable forensic DNA profiles. We recently demonstrated the feasibility of performing mixture deconvolution prior to forensic DNA profiling through the utilization of a non-targeted single-cell transcriptome sequencing (scRNA-seq). In addition to individual-specific mixture deconvolution, this approach also allowed accurate characterisation of biological sex, biogeographic ancestry and individual identification of the separated mixture contributors. However, RNA has the forensic disadvantage of being prone to degradation, and sequencing RNA - focussing on coding regions - limits the number of single nucleotide polymorphisms (SNPs) utilized for genetic mixture deconvolution, characterization, and identification. These limitations can be overcome by performing single-cell sequencing on the level of DNA instead of RNA. Here, for the first time, we applied non-targeted single-cell DNA sequencing (scDNA-seq) by applying the scATAC-seq (Assay for Transposase-Accessible Chromatin with sequencing) technique to address the challenges of mixture deconvolution in the forensic context. We demonstrated that scATAC-seq, together with our recently developed De-goulash data analysis pipeline, is capable of deconvoluting complex blood mixtures of five individuals from both sexes with varying biogeographic ancestries. We further showed that our approach achieved correct genetic characterization of the biological sex and the biogeographic ancestry of each of the separated mixture contributors and established their identity. Furthermore, by analysing in-silico generated scATAC-seq data mixtures, we demonstrated successful individual-specific mixture deconvolution of i) highly complex mixtures of 11 individuals, ii) balanced mixtures containing as few as 20 cells (10 per each individual), and iii) imbalanced mixtures with a ratio as low as 1:80. Overall, our proof-of-principle study demonstrates the general feasibility of scDNA-seq in general, and scATAC-seq in particular, for mixture deconvolution, genetic characterization and individual identification of the separated mixture contributors. Furthermore, it shows that compared to scRNA-seq, scDNA-seq detects more SNPs from fewer cells, providing higher sensitivity, that is valuable in forensic genetics.
Topics: Humans; Single-Cell Analysis; Polymorphism, Single Nucleotide; DNA Fingerprinting; Sequence Analysis, DNA; Female; Male; Forensic Genetics; DNA
PubMed: 38513339
DOI: 10.1016/j.fsigen.2024.103030 -
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 -
Scientific Reports Mar 2024Four common Patrinia species, including P. heterophylla, P. monandra, P. scabiosifolia and P. villosa, have been documented as herbal medicines with various clinical...
Four common Patrinia species, including P. heterophylla, P. monandra, P. scabiosifolia and P. villosa, have been documented as herbal medicines with various clinical applications, such as anti-cancer, anti-diarrhea and sedative. However, the authentication of medicinal Patrinia species poses a problem, particularly with the processed herbal materials. This study aimed to systematically authenticate the four medicinal Patrinia species in the market using morphological and chemical characterization, as well as DNA markers. We found the species identity authenticated by traditional morphologies were in good agreement with both chemical and molecular results. The four species showed species-specific patterns in chromatographic profiles with distinct chemical markers. We also revealed the power of complete chloroplast genomes in species authentication. The sequences of targeted loci, namely atpB, petA, rpl2-rpl23 and psaI-ycf4, contained informative nucleotides for the species differentiation. Our results also facilitate authentication of medicinal Patrinia species using new DNA barcoding markers. To the best of our knowledge, this is the first report on the application of morphology, chemical fingerprinting, complete chloroplast genomes and species-specific Insertion-Deletions (InDels) in differentiating Patrinia species. This study reported on the power of a systematic, multidisciplinary approach in authenticating medicinal Patrinia species.
Topics: Patrinia; Plants, Medicinal
PubMed: 38503940
DOI: 10.1038/s41598-024-57115-w -
Cureus Feb 2024Background and objective Human teeth have a significant forensic importance. As they are the hardest of all human tissues, they are not just chemically stable but also...
Detection of ABO Blood Groups From Dentin and Pulp by Using the Absorption-Elution Technique: A Forensic Cross-Sectional Study Among the Population of the Al Jouf Province, Saudi Arabia.
Background and objective Human teeth have a significant forensic importance. As they are the hardest of all human tissues, they are not just chemically stable but also their characteristics are maintained for a long time after death even in the most harsh environmental conditions. Despite the advances made in DNA analysis, fingerprinting, etc., ABO blood grouping still plays a significant role in the forensic practice in the field of personal identification, paternity disputes, and several other scenarios including the identification of mass disaster victims The term blood groups refers to inherited antigens on the surface of red blood cells (RBCs) detected by specific antibodies. Since tooth pulp contains numerous blood vessels, blood group antigens are most certainly bound to be present in tooth pulp. Various studies have shown that blood group antigens in the pulp and dentin are preserved as long as up to two years after the demise of an individual. Absorption-elution technique has been proven to be the most sensitive, reliable, and consistent method to determine the ABO blood group from both the pulp and dentine. This study aimed to ascertain the ABO blood group from both the hard (dentin) as well as the soft tissue (pulp) of the tooth by using the absorption-elution (AE) technique and also to determine if there are any variations in identifying the blood groups from the teeth based on age and gender. Material and methods After obtaining due consent, we included patients of both genders aged between 16-60 years visiting the outpatient department (OPD) clinics at the College of Dentistry for periodontal or orthodontic extractions. One patient's blood type was determined by using the slide agglutination technique before any capillary blood extraction was performed; this patient served as a control. For this investigation, we used the pulp and powdered dentin samples taken from the dental extractions to test for the presence of ABO and Rhesus (Rh) factor antigens by using the AE method. The study samples were compared with the control for blood group determination. Statistical analysis was carried out using the chi-square test with Monte Carlo (MC) simulation to check for any correlation of blood grouping with age and gender. Results The dentin and pulp were shown to have positive blood group antigens for the ABO and Rh factors. While neither pulp nor dentin performed significantly differently in identifying the blood group antigens, pulp showed marginally higher accuracy. There was no discernible difference regarding gender or age in the dentin or pulp of any of the 45 samples studied. Conclusions For determining an individual's blood type and Rh factor, both the hard (dentin) and soft (pulp) tissues of a tooth are valid sources. This is particularly helpful in forensic medicine cases where teeth are the only remains that can be viably used to find out a person's identity.
PubMed: 38500947
DOI: 10.7759/cureus.54340 -
Fa Yi Xue Za Zhi Feb 2024To establish and forensically verify a 42 microhaplotypes (mircohaps, MHs) multiplex assay system based on next-generation sequencing (NGS), and to explore the...
OBJECTIVES
To establish and forensically verify a 42 microhaplotypes (mircohaps, MHs) multiplex assay system based on next-generation sequencing (NGS), and to explore the application value of this system in the practice of forensic genetics.
METHODS
A total of 42 highly polymorphic MHs were selected from previous studies, and sequenced by the MiSeq FGx platform to verify the repeata-bility, sensitivity, specificity, stability, and mixture analysis ability of the detection system. Through population genetic investigation of 102 unrelated Chinese Han individuals in Liyang City, Jiangsu Province, China, the application value of this system in forensic genetics was evaluated.
RESULTS
The sequencing repeatability of the 42-plex MHs assay was 100% and the sensitivity was as low as 0.062 5 ng. The system had the ability to withstand the interference of indigo (≤2 500 ng/μL), humic acid (≤9 ng/μL), hemoglobin(≤20 μmol), and urea (≤200 ng/μL) and to detect mixtures of 2 people (1∶19), 3 people (1∶1∶9) and 4 people (1∶1∶1∶9). Based on 102 individual data, the combined power of discrimination and the combined power of exclusion were 1-3.45×10 and 1-3.77×10, respectively, and the average effect value of alleles was 2.899.
CONCLUSIONS
The 42-plex MHs assay was successfully established in this study and this system has high repeatability and sensitivity, good anti-jamming ability and mixture analysis ability. The 42 MHs are highly polymorphism and have good application value in individual identification and paternity testing.
Topics: Humans; Gene Frequency; Genetics, Population; Forensic Genetics; Genotype; Polymorphism, Genetic; High-Throughput Nucleotide Sequencing; Polymorphism, Single Nucleotide; DNA Fingerprinting; Microsatellite Repeats
PubMed: 38500461
DOI: 10.12116/j.issn.1004-5619.2023.530803