scholarly journals Genetic Identification: A Review on Autosomal Single Nucleotide Polymorphism’s as Diagnostic Tool for Identifying Human

2021 ◽  
pp. 25-33
Author(s):  
Fahmida Kahtoon ◽  
Ruba Mustafa Elsaid Ahmed ◽  
Naveed Iqbal ◽  
Zahid Balouch ◽  
Fahad Saleh Alenazi
Keyword(s):  
Forensic Science ◽  
Molecular Genetics ◽  
Crime Scene ◽  
The Body ◽  
Genetic Identification ◽  
Forensic Sciences ◽  
Nucleotide Polymorphisms ◽  
Human Beings ◽  
Autosomal Snps ◽  
Single Nucleotide

Single Nucleotide polymorphisms are biological markers, helping researchers  to locate genes that are associated with various  diseases. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene's function. Most SNPs have no effect on health or development.Advancement in the field of genetics has resulted in the application of several techniques of molecular genetics in Pharmacogenomics. Nucleotide Polymorphisms (SNPs) holds the key in defining the risk of an individual’s susceptibility to various illnesses and response to drugs The body of human beings is composed of DNA which is a chemical molecule responsible for imparting phenotypic and genotypic characteristics to the individuals. The most recent advancement of molecular genetics, which has found application in forensic science, is the use of autosomal SNPs because they can provide information about the ancestral genetics of human beings.The primary aim of this research is to explore the significance of autosomal SNPs in forensic science through the identification of humans at a crime scene. A secondary qualitative research design has been selected for conducting this study. This secondary research is based on a systematic review of the studies which have provided an insight in the significance of autosomal SNPs in forensic sciences by using various Data search Engine. SNPs can be used in the forensic investigation for the identification of individuals present at the crime scene.

scholarly journals RECENT TECHNIQUES BASED ON THE UTILIZATION OF DNA AND AUTOSOMAL SINGLE NUCLEOTIDE POLYMORPHISMS FOR IDENTIFYING HUMANS

2019 ◽  
Vol 17 (2) ◽  
pp. 58-62
Author(s):  
Fahmida Khatoon
Keyword(s):  
Forensic Science ◽  
Biological Samples ◽  
Crime Scene ◽  
The Body ◽  
Degraded Dna ◽  
Nucleotide Polymorphisms ◽  
Autosomal Snps ◽  
Significant Information ◽  
Dead Person ◽  
Crime Scene Investigators

The biological samples used in forensics can contain DNA which is highly fragmented as a consequence of exposure to any of the numerous degrading factors. Analysis of the sequence or size of the products of Polymerase chain reaction is at present responsible for the analysis of remains of humans in forensics. Despite the effectiveness of protocols based on PCR, there are certain limitations that are presented by the low numbers of copies of the template and the variations that are imposed by the decaying process to the template. The primary aim of this research is to explore the significance of autosomal SNPs in forensic science through the identification of humans at a crime scene. This study provides an exploration of the applicability of autosomal SNPs for the identification of humans at crime scene. This would fill the gap present in the current literature regarding the significance of autosomal SNPs in the identification of humans during crime scene investigation. It will also enable the identification of the criminals involved in several types of the crimes ranging from general theft to rape and sexual assault, murder, and robberies. It will also allow the identification of dead bodies in cases where it is difficult to identify the dead person due to unrecognizable condition of the body. This study will facilitate the improvement of the investigation of crime scene investigators. It will provide a significant way for the incorporation of recent techniques of the molecular genetics into forensics. Reduction in the workload of the crime scene investigators would also occur through the implementation of outcomes of this study into the field of forensic science. There are several studies which have demonstrated the applicability of SNPs in forensic investigations for identifying the humans at crime scene. Several effective and efficient technological systems have been developed by the researchers which are capable of performing analysis of biological samples containing degraded DNA because SNPs can be obtained from these samples. Physical characteristics of the individuals can be predicted through the analysis of SNPs. This can provide significant information about the color of eye, hair and skin of the individuals involved in crime.

scholarly journals RECENT TECHNIQUES BASED ON THE UTILIZATION OF DNA AND AUTOSOMAL SINGLE NUCLEOTIDE POLYMORPHISMS FOR IDENTIFYING HUMANS

2019 ◽  
Vol 17 (2) ◽  
Author(s):  
Fahmida Khatoon
Keyword(s):  
Forensic Science ◽  
Biological Samples ◽  
Crime Scene ◽  
The Body ◽  
Degraded Dna ◽  
Nucleotide Polymorphisms ◽  
Autosomal Snps ◽  
Significant Information ◽  
Dead Person ◽  
Crime Scene Investigators

The biological samples used in forensics can contain DNA which is highly fragmented as a consequence of exposure to any of the numerous degrading factors. Analysis of the sequence or size of the products of Polymerase chain reaction is at present responsible for the analysis of remains of humans in forensics. Despite the effectiveness of protocols based on PCR, there are certain limitations that are presented by the low numbers of copies of the template and the variations that are imposed by the decaying process to the template. The primary aim of this research is to explore the significance of autosomal SNPs in forensic science through the identification of humans at a crime scene. This study provides an exploration of the applicability of autosomal SNPs for the identification of humans at crime scene. This would fill the gap present in the current literature regarding the significance of autosomal SNPs in the identification of humans during crime scene investigation. It will also enable the identification of the criminals involved in several types of the crimes ranging from general theft to rape and sexual assault, murder, and robberies. It will also allow the identification of dead bodies in cases where it is difficult to identify the dead person due to unrecognizable condition of the body. This study will facilitate the improvement of the investigation of crime scene investigators. It will provide a significant way for the incorporation of recent techniques of the molecular genetics into forensics. Reduction in the workload of the crime scene investigators would also occur through the implementation of outcomes of this study into the field of forensic science. There are several studies which have demonstrated the applicability of SNPs in forensic investigations for identifying the humans at crime scene. Several effective and efficient technological systems have been developed by the researchers which are capable of performing analysis of biological samples containing degraded DNA because SNPs can be obtained from these samples. Physical characteristics of the individuals can be predicted through the analysis of SNPs. This can provide significant information about the color of eye, hair and skin of the individuals involved in crime.

scholarly journals Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function

2020 ◽  
Vol 21 (8) ◽  
pp. 2764
Author(s):  
Taremekedzwa Allan Sanyanga ◽  
Özlem Tastan Bishop
Keyword(s):  
Carbonic Anhydrase ◽  
Binding Site ◽  
Cross Correlation ◽  
Structure And Function ◽  
The Body ◽  
Conformational Sampling ◽  
Nucleotide Polymorphisms ◽  
Ip3 Receptor ◽  
Single Nucleotide ◽  
And Function

Human carbonic anhydrase 8 (CA-VIII) is an acatalytic isoform of the α -CA family. Though the protein cannot hydrate CO2, CA-VIII is essential for calcium (Ca2+) homeostasis within the body, and achieves this by allosterically inhibiting the binding of inositol 1,4,5-triphosphate (IP3) to the IP3 receptor type 1 (ITPR1) protein. However, the mechanism of interaction of CA-VIII to ITPR1 is not well understood. In addition, functional defects to CA-VIII due to non-synonymous single nucleotide polymorphisms (nsSNVs) result in Ca2+ dysregulation and the development of the phenotypes such as cerebellar ataxia, mental retardation and disequilibrium syndrome 3 (CAMRQ3). The pathogenesis of CAMRQ3 is also not well understood. The structure and function of CA-VIII was characterised, and pathogenesis of CAMRQ3 investigated. Structural and functional characterisation of CA-VIII was conducted through SiteMap and CPORT to identify potential binding site residues. The effects of four pathogenic nsSNVs, S100A, S100P, G162R and R237Q, and two benign S100L and E109D variants on CA-VIII structure and function was then investigated using molecular dynamics (MD) simulations, dynamic cross correlation (DCC) and dynamic residue network (DRN) analysis. SiteMap and CPORT analyses identified 38 unique CA-VIII residues that could potentially bind to ITPR1. MD analysis revealed less conformational sampling within the variant proteins and highlighted potential increases to variant protein rigidity. Dynamic cross correlation (DCC) showed that wild-type (WT) protein residue motion is predominately anti-correlated, with variant proteins showing no correlation to greater residue correlation. DRN revealed variant-associated increases to the accessibility of the N-terminal binding site residues, which could have implications for associations with ITPR1, and further highlighted differences to the mechanism of benign and pathogenic variants. SNV presence is associated with a reduction to the usage of Trp37 in all variants, which has implications for CA-VIII stability. The differences to variant mechanisms can be further investigated to understand pathogenesis of CAMRQ3, enhancing precision medicine-related studies into CA-VIII.

scholarly journals Structural and Functional Features of the P2X4 Receptor: An Immunological Perspective

2021 ◽  
Vol 12 ◽  
Author(s):  
Jean M. Kanellopoulos ◽  
Cássio Luiz Coutinho Almeida-da-Silva ◽  
Sirje Rüütel Boudinot ◽  
David M. Ojcius
Keyword(s):  
Plasma Membrane ◽  
P2y Receptors ◽  
Potential Interaction ◽  
The Body ◽  
Extracellular Nucleotides ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Functional Features ◽  
G Protein Coupled

Extracellular nucleotides are important mediators of activation, triggering various responses through plasma membrane P2 and P1 receptors. P2 receptors are further subdivided into ionotropic P2X receptors and G protein-coupled P2Y receptors. P2X4 is an ATP-gated cation channel broadly expressed in most tissues of the body. Within the P2X family, P2X4 has a unique subcellular distribution, being preferentially localized in lysosomes. In these organelles, high ATP concentrations do not trigger P2X4 because of the low pH. However, when the pH increases to 7.4, P2X4 can be stimulated by intra-lysosomal ATP, which is in its active, tetra-anionic form. Elucidation of P2X4, P2X3 and P2X7 structures has shed some light on the functional differences between these purinergic receptors. The potential interaction between P2X4 and P2X7 has been extensively studied. Despite intensive effort, it has not been possible yet to determine whether P2X4 and P2X7 interact as heterotrimers or homotrimers at the plasma membrane. However, several publications have shown that functional interactions between P2X4 and P2X7 do occur. Importantly, these studies indicate that P2X4 potentiates P2X7-dependent activation of inflammasomes, leading to increased release of IL-1β and IL-18. The role of P2X4 in various diseases could be beneficial or deleterious even though the pathophysiological mechanisms involved are still poorly defined. However, in diseases whose physiopathology involves activation of the NLRP3 inflammasome, P2X4 was found to exacerbate severity of disease. The recent production of monoclonal antibodies specific for the human and mouse P2X4, some of which are endowed with agonist or antagonist properties, raises the possibility that they could be used therapeutically. Analysis of single nucleotide polymorphisms of the human P2RX4 gene has uncovered the association of P2RX4 gene variants with susceptibility to several human diseases.

scholarly journals Forensic Anthropology

2021 ◽  
Author(s):  
Purva Wagisha Upadhyay ◽  
Amarnath Mishra
Keyword(s):  
Forensic Science ◽  
Ethnic Groups ◽  
Cause Of Death ◽  
Forensic Anthropology ◽  
Crime Scene ◽  
Physical Anthropology ◽  
Skeletal Remains ◽  
The Body ◽  
Time Since Death ◽  
Characteristic Features

Physical anthropology has been making progress in the field of forensic science. Forensic anthropology is the study of identifying and establishing identity of the skeletal remains present at the crime scene. The purpose of the chapter is to throw a light on the field of forensic anthropology as it seeks data like age, sex, ethnic groups, and other characteristic features after the examination of the skeletal remains. Forensic anthropology helps in determining the manner and cause of death, and if the body is still in the decompositions stage, time since death can also be estimated. Advancement in forensic anthropology will not only help to solve the case but it will also increase the opportunity to work in this area. In this chapter, there is an explanation of some of the methods used in forensic anthropology for the analysis of identification and other purposes.

Prognostic Assessment of Three Single Nucleotide Polymorphisms (BCL2–938C>A, MTHFR 677C>T, GNAS1 T393C) in Chronic Lymphocytic Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2080-2080
Author(s):  
Thorsten Zenz ◽  
Ulrich Duehrsen ◽  
Harald Dohner ◽  
Winfried Siffert ◽  
Stephan Stilgenbauer ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Single Nucleotide Polymorphisms ◽  
Molecular Genetics ◽  
Association Studies ◽  
Lymphocytic Leukemia ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Gnas1 T393c

Abstract A number of single nucleotide polymorphisms (SNP) have been implicated to impact on the disease course in chronic lymphocytic leukemia (CLL). Nonetheless, there have been few polymorphisms for which replications of association were done in different studies. We genotyped three recently described SNPs (BCL2 –938C>A, MTHFR 677C>T, GNAS1 T393C) in a large group of CLL patients (n=273) with mature follow up and detailed analysis of molecular genetics. The cohort had a median follow-up of over 150 months and the known poor risk molecular genetics (17p–, 11q– and unmutated VH-status) were associated with poor prognosis. The allele frequencies for all three SNPs were in Hardy Weinberg equilibrium and we could not identify imbalances when we stratified for subgroups (genomic aberrations, VH status, stage according to Binet). Moreover, the polymorphisms did not affect clinical outcome (time to first treatment and overall survival) in univariate or multivariate analysis in the current cohort. Comparing CLL patients with over 100 healthy controls we found no significant differences in allele frequencies or genotype distributions for all three polymorphisms. While there have been reports showing the molecular effects and clinical consequences of the polymorphisms we studied, we did not find SNP genotype-dependent effects in a large cohort of CLL patients. Potential reasons for the discrepancy of the results are numerous. Because of the advancement of genotyping technologies, a large number of SNPs can be evaluated (multiple testing). The sample sizes of the reported association studies are often too small and frequently only one patient cohort is investigated. Moreover, negative results are often not published (publication bias). One major reason for the different results is the different genetic background of the populations due to ethnicity (selection bias). Summarized, this study supports the importance of confirmation of initial findings in an independent data set. However, results of genome-wide association studies will soon be reported with additional novel genes identified and will help making great strides in identifying the genetic determinants of CLL risk.

scholarly journals Interaction between genes and lifestyle factors on obesity

2008 ◽  
Vol 67 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Amelia Marti ◽  
Miguel Angel Martinez-González ◽  
J. Alfredo Martinez
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Candidate Genes ◽  
Weight Control ◽  
Lifestyle Factors ◽  
The Body ◽  
Energy Regulation ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Leptin Receptors ◽  
Body Weight Control

Obesity originates from a failure of the body-weight control systems, which may be affected by changing environmental influences. Basically, the obesity risk depends on two important mutually-interacting factors: (1) genetic variants (single-nucleotide polymorphisms, haplotypes); (2) exposure to environmental risks (diet, physical activity etc.). Common single-nucleotide polymorphisms at candidate genes for obesity may act as effect modifiers for environmental factors. More than 127 candidate genes for obesity have been reported and there is evidence to support the role of twenty-two genes in at least five different populations. Gene–environment interactions imply that the synergy between genotype and environment deviates from either the additive or multiplicative effect (the underlying model needs to be specified to appraise the nature of the interaction). Unravelling the details of these interactions is a complex task. Emphasis should be placed on the accuracy of the assessment methods for both genotype and lifestyle factors. Appropriate study design (sample size) is crucial in avoiding false positives and ensuring that studies have enough power to detect significant interactions, the ideal design being a nested case–control study within a cohort. A growing number of studies are examining the influence of gene–environmental interactions on obesity in either epidemiological observational or intervention studies. Positive evidence has been obtained for genes involved in adiposity, lipid metabolism or energy regulation such as PPARγ2 (Pro12Ala), β-adrenoceptor 2 (Gln27Glu) or uncoupling proteins 1, 2 and 3. Variants on other genes relating to appetite regulation such as melanocortin and leptin receptors have also been investigated. Examples of some recently-identified interactions are discussed.

scholarly journals A Multidisciplinary Fingerprinting Approach for Authenticity and Geographical Traceability of Portuguese Wines

Foods ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1044
Author(s):  
Rui J. S. Teixeira ◽  
Sónia Gomes ◽  
Vitorino Malheiro ◽  
Leonor Pereira ◽  
José R. Fernandes ◽  
...  
Keyword(s):  
Clay Content ◽  
Two Dimensions ◽  
Added Value ◽  
Genetic Identification ◽  
Isotopic Ratios ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Isotopic Signatures ◽  
Anthocyanin Pathway ◽  
Varietal Identification

The interest in developing reliable wine authenticity schemes is a hot-topic, especially for wines with recognized added-value. In order to accomplish this goal, two dimensions need to be considered: the grapevine variety determination and the geographical provenance. The aim of this study was to develop a multidisciplinary approach applicable to wines from the sub region Melgaço and Monção of the demarcated Vinho Verde region and from the demarcated Douro region. The proposed scheme consists on the use of DNA-based assays to detect Single Nucleotide Polymorphisms (SNPs) on three genes of the anthocyanin pathway (UFGT, F3H and LDOX) coupled with High-resolution melting (HRM) analysis aiming the varietal identification. The Alvarinho wines revealed to have the same haplotype using this marker set, demonstrating its applicability for genetic identification. In addition, to assess their geographical provenance, a multi-elemental approach using Sr and Pb isotopic ratios of wine, soil and bedrock samples was used. The isotopic data suggest a relation between Sr and Pb uptake by vine roots and soil’s texture and clay content, rather than with the whole rock’s isotopic ratios, but also highlights the potential of a discriminating method based on the combination of selected isotopic signatures.

scholarly journals Using deep learning to analyze the compositeness of musculoskeletal aging reveals that spine, hip and knee age at different rates, and are associated with different genetic and non-genetic factors

2021 ◽  
Author(s):  
Alan Le Goallec ◽  
Samuel Diai ◽  
Sasha Collin ◽  
Theo Vincent ◽  
Chirag J Patel
Keyword(s):  
Musculoskeletal System ◽  
Genetic Factors ◽  
Pearson Correlation ◽  
The Body ◽  
World Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
X Ray ◽  
The Uk ◽  
Full Body

With age, the musculoskeletal system undergoes significant changes, leading to diseases such as arthritis and osteoporosis. Due to the aging of the world population, the prevalence of such diseases is therefore expected to starkly increase in the coming decades. While numerous biological age predictors have been developed to assess musculoskeletal aging, it remains unclear whether these different approaches and data capture a single aging process, or if the diverse joints and bones in the body age at different rates. In the following, we leverage 42,000 full body, spine, hip and knee X-ray images and musculoskeletal biomarkers from the UK Biobank and use artificial intelligence to build the most accurate musculoskeletal aging predictor to date (RMSE=2.65+/-0.01 years; R-Squared=87.6+/-0.1%). Our predictor is composite and can be used to assess spine age, hip age and knee age, in addition to general musculoskeletal aging. We find that accelerated musculoskeletal aging is moderately correlated between these different musculoskeletal dimensions (e.g hip vs. knee: Pearson correlation=.351+/-.004). Musculoskeletal aging is heritable at more than 35%, and the genetic factors are partially shared between joints (e.g hip vs. knee: genetic correlation=.52+/-.04). We identified single nucleotide polymorphisms associated with accelerated musculoskeletal aging in approximately ten genes for each musculoskeletal dimension. General musculoskeletal aging is for example associated with a TBX15 variant linked to Cousin syndrome and acromegaloid facial appearance syndrome. Finally, we identified biomarkers, clinical phenotypes, diseases, environmental and socioeconomic variables associated with accelerated musculoskeletal aging in each dimension. We conclude that, while the aging of the different components of the musculoskeletal system is connected, each bone and joint can age at significantly different rates.

scholarly journals Host- and Species-Dependent Quasispecies Divergence of Severe Acute Respiratory Syndrome Coronavirus-2 in Non-human Primate Models

2021 ◽  
Vol 12 ◽  
Author(s):  
Eun-Ha Hwang ◽  
Hoyin Chung ◽  
Green Kim ◽  
Hanseul Oh ◽  
You Jung An ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Rhesus Macaques ◽  
Vero Cells ◽  
Frequency Variation ◽  
Nucleotide Polymorphisms ◽  
Human Beings ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Variant Analysis

Recently, newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been continuously reported worldwide. However, the precise evaluation of SARS-CoV-2 microevolution in host is very limited because the exact genetic information of infected virus could not be acquired in human researches. In this report, we performed deep sequencing for seed virus and SARS-CoV-2 isolated in eight cynomolgus and rhesus macaques at 3 days postinoculation and evaluated single-nucleotide polymorphisms (SNPs) in SARS-CoV-2 by variant analysis. A total of 69 single-nucleotide variants (SNVs) were present in the 5′-untranslated region (UTR), 3′-UTR, ORF1ab, S, ORF3a, ORF8, and N genes of the seed virus passaged in VERO cells. Between those present on the seed virus and those on each SARS-CoV-2 isolated from the lungs of the macaques, a total of 29 variants was identified in 4 coding proteins (ORF1ab, S, ORF3a, and N) and non-coding regions (5′- and 3′-UTR). Variant number was significantly different according to individuals and ranged from 2 to 11. Moreover, the average major frequency variation was identified in six sites between the cynomolgus monkeys and rhesus macaques. As with diverse SNPs in SARS-CoV-2, the values of viral titers in lungs were significantly different according to individuals and species. Our study first revealed that the genomes of SARS-CoV-2 differ according to individuals and species despite infection of the identical virus in non-human primates (NHPs). These results are important for the interpretation of longitudinal studies evaluating the evolution of the SARS-CoV-2 in human beings and development of new diagnostics, vaccine, and therapeutics targeting SARS-CoV-2.

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