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After the onset of COVID-19 pandemic, a sharp surge in the usage of the face-masks throughout the globe has been observed. Pre-experiment survey of 252 individuals indicated a higher use of cotton-make masks (41%), followed by N-95 make (31%), and surgical disposable masks (26%). It was also further revealed that a higher fraction of individuals wear a face-mask more than 3 times (37%) before its disposal. In order to assess the potential usability of different mask types as forensic DNA evidence, a study was conducted on 50 healthy individuals. DNA content of different fractions such as the portion of mask covering the mouth region and the ear-piece showed a good source of host DNA. Though no statistically significant difference (P 0.05) was found in the DNA quantity obtained from different face mask types, an increasing trend was obtained in the order: cloth make type (7.031 ± 0.31 ng), N-95 make (4.711 ± 0.15 ng), and surgical disposable type (2.17 ± 0.13 ng). The time of wearing of a face-mask showed a positive correlation with the yield of DNA irrespective of the face-mask type used. Samples retrieved from both the portions covering the mouth area and the ear-piece showed a good source of genomic DNA yielding an average of 4.82 ± 0.11 ng and 4.44 ± 0.10 ng of DNA, respectively. Irrespective of the face-mask types, number of reuse, and the portion of the mask, 66.66-96.11% of samples showed a complete autosomal STR DNA profile. This suggests that if a face-mask is found at the crime scene, it should be collected and preserved as a potential source of DNA evidence for routine forensic DNA analysis.

CRISPR-Cas technology has revolutionized the field of biotechnology with its precise therapeutic use from genetic as well as infectious diseases point of view. This technology is rapidly evolving to single tool enabling site-directed cut in the genome and highly specific activation or inhibition of gene expression or the exchange of single bases. Besides clinical applications, CRISPR-Cas technology has also shown promising use in the field of forensic DNA analysis. Enrichment of targeted genetic marker for identification followed by sequencing and non-PCR-dependent technique ensures the use of CRISPR-Cas technology in challenging forensic biological samples. The use of this advanced technology is also deemed helpful in mixed profile attribution, mostly in LCN contributors and the generation of a useful DNA profile in degraded samples. Besides its useful applications in forensic DNA analysis, CRISPR-Cas technology poses a huge threat from the generation of ghost DNA profiles by modification/alteration of target genetic markers. Forensic DNA analysts should carry out analysis of additional markers such as non-CODIS markers, Y-, X-chromosome markers, and mitochondrial DNA sequencing in a suspected ghost DNA profile case. KEY POINTS: • CRISPR-Cas9 technique is useful in analyzing LCN, mixed and degraded samples • Alteration of DNA using this technique can lead to generation of ghost DNA profiles • Alternative genetic markers and methylation pattern may detect a ghost DNA profile.

Capillary electrophoresis-based analysis does not reflect the exact allele number variation at the STR loci due to the non-availability of the data on sequence variation in the repeat region and the SNPs in flanking regions. Herein, this study reports the length-based and sequence-based allelic data of 138 central Indian individuals at 31 autosomal STR loci by NGS. The sequence data at each allele was compared to the reference hg19 sequence. The length-based allelic results were found in concordance with the CE-based results. 20 out of 31 autosomal STR loci showed an increase in the number of alleles by the presence of sequence variation and/or SNPs in the flanking regions. The highest gain in the heterozygosity and allele numbers was observed in D5S2800, D1S1656, D16S539, D5S818, and vWA. rs25768 (A/G) at D5S818 was found to be the most frequent SNP in the studied population. Allele no. 15 of D3S1358, allele no. 19 of D2S1338, and allele no. 22 of D12S391 showed 5 isoalleles each with the same size and with different intervening sequences. Length-based determination of the alleles showed Penta E to be the most useful marker in the central Indian population among 31 STRs studied; however, sequence-based analysis advocated D2S1338 to be the most useful marker in terms of various forensic parameters. Population genetics analysis showed a shared genetic ancestry of the studied population with other Indian populations. This first-ever study to the best of our knowledge on sequence-based STR analysis in the central Indian population is expected to prove the use of NGS in forensic case-work and in forensic DNA laboratories.

Detection of the body fluid present at a crime scene is essential for any forensic investigation. Amongst all the body fluids (sweat, semen, vaginal fluid, saliva, etc.,) blood is the most frequently encountered evidence at the crime scene. Currently, reagents like benzidine, orthotoluidine, tetramethylbenzidine, phenolphthalein, leucomalachite green, luminol, and fluorescein are used to screen the presence of blood on different surfaces (porous/nonporous). Majority of these tests are based on colorimetric changes owing to the nature of hemoglobin to catalyze the oxidation of chromogenic compounds. Apart from aiding the investigation, these reagents show toxic behavior (DNA damage, carcinogenic, etc.) and false-positive results. Hence, to circumvent this issue, the present study attempts to develop a state-of-art methodology for preliminary blood detection and screening using fluorescein-derived 2’,7’-dichlorofluorescein di-acetate (DCFDA) dye. It is hereby proposed that the fluorescein-based dye can successfully detect blood and bloodstains aged up to 20 days. Moreover, supplemental experiments have suggested that the dye doesn’t interfere with DNA integritycausing any damage to DNA. Parallelly, no false-positive reactions have been observed as tested against similar-looking substances.

Background Many countries have developed their core set of STR loci for forensic application and database generation, which India lacks. Aim To assess the usefulness of various combinations of autosomal STR marker sets for their superior use in the central Indian population for forensic and paternity applications. Subjects and methods 19 STR marker sets were analysed on 200 central Indian populations and 20 paternity cases to assess their usefulness. Results Two marker sets each comprising 19 STR markers are found to be superior to 20 expanded CODIS loci in the studied population. These marker sets also showed their effectiveness in 20 paternity cases having CPI values of 7.62 × 1011 and 7.16 × 1011. Three non-CODIS STR markers Penta E, Penta D, and SE33 showed amplification in 50 challenging samples with >0.80 heterozygosity. Conclusion Population-specific STR marker sets are useful in forensic and paternity applications, as well as database generation, and it is envisioned that Penta E, Penta D, and SE33 markers will be included in the list of core STR loci in the central Indian population.

The human body provides a complex ecosystem for symbiotic habitation of a huge number of microorganisms. These commensal microorganisms provide a huge benefit to the living host by acting against many deadly infections. Once the host dies, many changes in the complex ecosystem of the human body take place. The personalized microbes of a human body undergo successional change as many exogenous microbes attack the nutrient-rich cadaver after death. The succession pattern change of microbes in human cadaver allows postulating different models for estimation of Postmortem time interval (PMI). Estimation of PMI has a broad prospect from the criminal investigation point of view. Though many techniques are being used nowadays to estimate PMI, all of them have their pros and cons. With the advent of advanced molecular biological techniques, studies on the thanatomicrobiome of a human cadaver have gained pace and provide a superior alternative for conventional methods of PMI estimation. This chapter summarizes the recent advancements in the changes in signature microflora postmortem with change in human microenvironment to postulate a consensus model for estimation of PMI.

Forensic DNA typing and subsequent molecular methods of sex determination in humans have been proven to be an imperious tool to criminal justice system. In current practice, most of the short tandem repeat (STR) based commercial kits contain amelogenin as the sexing marker. Amelogenin gene which contributes to the tooth enamel formation is present on both X and Y chromosome with a variation in base pair size. However, huge discrepancies have been observed with amelogenin based sex determination mostly due to X and Y deletion in the population and mutation in primer binding sites. Some ethnicities such as those in Indian population are affected badly with inappropriate sex determination by amelogenin marker due to the presence of high frequency of Y deletion in the population. Presence of PCR inhibitors, degradation in the DNA samples and presence of mixed DNA also contribute to the discrepancy in results obtained by amelogenin analysis. To overcome this problem, many alternative markers/techniques such as STS, SRY, TSPY, DXYS156, SNPs, DYZ1 and Next generation sequencing have been discussed in much detail with their respective pros and cons. In this regard, inclusion of one or more alternative markers along with amelogenin will decrease the anomalies in sex determination observed while using the amelogenin marker alone in forensic sample analysis.

The STR typing has been regarded as the most reliable and robust genetic tool having a pivotal role in the criminal justice system. High mutation rates have led to widespread polymorphism in the STRs which increases the probability of divergence of a specific population. Therefore, two tetra- and two pentanucleotide repeat STR loci were evaluated for their informativeness and expediency in the central Indian population. Two hundred unrelated individuals of the central India were included in this study for DNA isolation followed by multiplex PCR and genotyping using four STR markers, i.e., D2S1338, D19S433, Penta E and Penta D. All STR markers followed the Hardy–Weinberg equilibrium in the studied population. Out of all, Penta E (15p15-39; AAAGA) was found to be the most polymorphic (25–120 bp), highest heterozygosity (92.0%), lowest matching probability (0.025), highest power of discrimination (0.975), polymorphic information content (PIC) (0.91), power of exclusion (0.936) and typical paternity index (6.25). The aptness of the Penta E STR marker in context to its forensic and paternity parameters strongly suggests its applicability in the central Indian population.

With the advent of next-generation sequencing technology, SNP markers are being explored as a useful alternative to conventional capillary electrophoresis–based STR typing. Low mutation rate and short-sized amplicons are added advantages of SNP markers over the STRs. However, to achieve a sufficient level of discrimination among individuals, a higher number of SNPs need to be characterized simultaneously. Hence, the NGS technique is highly useful to analyze a sufficiently higher number of SNPs simultaneously. Though the technique is in its nascent stage, an attempt has been made to assess its usability in the central Indian population by analyzing 124 SNPs (90 autosomal and 34 Y-chromosome) in 95 individuals. Various quality parameters such as locus balance, locus strand balance, heterozygosity balance, and noise level showed a good quality sequence obtained from the Ion GeneStudio S5 instrument. Obtained frequency of SNP alleles ranged from 0.001 to 0.377 in autosomal SNPs. rs9951171 was found to be the most informative SNP in the studied population with the highest PD and lowest MP value. The cumulative MP of 90 SNPs was found to be 4.76698 × 10–37. Analysis of 34 Y-chromosome SNPs reveals 11 unique haplogroups in 54 male samples with R1a1 as the most frequent haplogroup found in 22.22% of samples. Interpopulation comparison by FST analysis, PCA plot, and STRUCTURE analysis showed genetic stratification of the studied population suggesting the utility of SNP markers present in the Precision ID Identity Panel for forensic demands of the Indian population.

Background: Two cases involving father-daughter incest, a rare report in the Indian population, have been analyzed in the current study. STR markers on both autosomal and sex chromosomes were employed to expound the cases. Objective: To confirm the identity of the fetus as a product of father-daughter incest and to study the inheritance pattern of alleles in such cases. Results: In both cases, the aborted fetus was found to be the product of an incestuous father-daughter relationship. The probability of paternity as well as maternity was found to be >99.9999% in both cases. Analysis of other paternity and forensic parameters also substantiated the inclusion of the alleged individuals. Father-daughter incest had a tremendous effect on the genome as evidenced from the dramatical decrease in unrelated alleles between father/child [16.66% (Case 1), 20% (Case 2)] and mother/child [26.66% (Case 1), 21.66% (Case 2)]. Genetic evidence also suggested an increased biallelic match i.e., 26.66% (Case 1) and 33.33% (Case 2) between mother and fetus which are at par/ above the normal siblings’ values i.e., 26.66%. Conclusion: A significant increase in the percentage of homozygous alleles (53.33% in both cases) was observed in the product of father-daughter incest. Both daughters share the same X chromosome from the father, which also suggested the case to be of father-daughter incest. Similarly, the same Y-STR profile between the male fetus and alleged father confirmed the correct pattern of inherit1ance of the Y chromosome in this case.

Ever since the inception of STR-based forensic DNA analysis for human Identification and DNA profiling, the approach developed continuously. Most of these developments are pertaining to achieve the best polymorphic loci set for analysis, high inhibitor tolerance capability, increase in sensitivity, reduction in turnaround time, and cost-effectiveness. On the similar line, the SF25TM PCR amplification kit, a 6 fluorescent dye-chemistry based autosomal STR kit was developed, which analyses 25 STR loci viz., FAM fluorescent dye-labelled D3S1358, D13S317, D7S820, D16S539, D1S1656, and Penta E; HEX fluorescent dye-labelled TPOX, TH01, D2S1338, CSF1PO, and Penta D; SUM fluorescent dye-labeled D19S433, vWA, D21S11, D18S51, and D6S1043; LYN fluorescent dye-labelled Amelogenin, D8S1179, D5S818, D12S391, and FGA; PUR fluorescent dye-labelled D22S1045, Y indel; D2S441 and D10S1248, The developmental validation of the SF25 PCR Amplification reagents were carried out in this study to analyze its specificity, sensitivity, and concordance. This multiplex kit showed higher sensitivity with 125pg of DNA template generating a complete profile (with 100% allele call). Out of 83 samples, 10 samples showed aberrant triallelic pattern/aberrant heterozygous pattern at D16S539 locus. The possible discrepant homozygous condition at locus D1S1656 might be due to the invasion of alleles at D1S1656 locus present adjacent to D16S539 locus. Such invasion resulted due to the shortening of the allelic bin at the D1S1656 locus. The allelic ladder of the SF25TM PCR amplification kit reveals the allelic range of D1S1656 from 11 to 19.3 which can be interpreted according to the casework as deemed by the end-users for their samples.

In order to find out the genetic diversity in the eastern Indian population of Odisha consisting of various linguistic and ethnic groups, we undertook a study on 508 unrelated healthy individuals belonging to Odisha, India. We assessed genetic variation and compared the data with published literature of Indian population consisting of different ethnic groups from different geographical areas using 21 autosomal STR markers. The most polymorphic and discriminatory STR locus in the studied population was found to be SE33 with the calculated values of 0.94 and 0.991 respectively for both the parameters. The combined power of discrimination (CPD) and combined power of exclusion (CPE) were found to be 1 and 0.999999999704865 respectively. The combined probability of match (CPm) and combined paternity index (CPI) for all 21 autosomal STR loci were found to be 8.01 × 10−26 and 3.45 × 109 respectively. Though, the studied eastern Indian population of Odisha shared its closest genetic affinity with nearest Indian geographical regions, i.e., the population of Jharkhand which is geographically located in eastern India as well as the Central Indian population.

Sediment and water samples were collected during monsoon and summer seasons for 2 years from four study sites, viz. Paradeep, Chilika, Gopalpur, and Rushikulya, along the Bay of Bengal, Odisha, India. Samples were analysed for abiotic parameters such as pH, salinity, temperature and total mercury content. Similarly, total heterotrophic bacterial load and mercury-resistant marine bacterial load were analysed in the collected samples. The pH of water samples in all the study sites varied from 6.41 ± 0.014 to 8.4 ± 0.141 during the summer season, whereas during the monsoon season it varied from 6.535 ± 0.077 to 8.55 ± 0.070. Similarly, the salinity in the study sites ranged from 9 ± 1.414 psu to 36.5 ± 0.707 psu during the summer season and 4.5 ± 0.707 psu to 34.5 ± 0.707 psu during the monsoon season. The temperature of the water also followed the same trend that varied from 26.55 ± 1.343 °C to 38.5 ± 0.141 °C in the summer season, and during the monsoon season the range was 21.85 ± 0.494 °C to 28.95 ± 0.636 °C. Sediment samples showed to contain a higher amount of mercury at Rushikulya (2.48 and 2.26 ppb) among the study sites in both seasons followed by Paradeep, Chilika and Gopalpur. Huge fractions of marine bacteria were found to be mercury resistant in nature, and a strong positive correlation (r = 0.94 and 0.93 in water and sediment samples) was obtained between mercury content and the mercury-resistant marine bacterial populations in the Bay of Bengal, India.

Mercury (Hg) is a highly toxic element that occurs at low concentrations in nature. However, various anthropogenic and natural sources contribute around 5000 to 8000 metric tons of Hg per year, rapidly deteriorating the environmental conditions. Mercury-resistant bacteria that possess the mer operon system have the potential for Hg bioremediation through volatilization from the contaminated milieus. Thus, bacterial mer operon plays a crucial role in Hg biogeochemistry and bioremediation by converting both reactive inorganic and organic forms of Hg to relatively inert, volatile, and monoatomic forms. Both the broad-spectrum and narrow-spectrum bacteria harbor many genes of mer operon with their unique definitive functions. The presence of mer genes or proteins can regulate the fate of Hg in the biogeochemical cycle in the environment. The efficiency of Hg transformation depends upon the nature and diversity of mer genes present in mercury-resistant bacteria. Additionally, the bacterial cellular mechanism of Hg resistance involves reduced Hg uptake, extracellular sequestration, and bioaccumulation. The presence of unique physiological properties in a specific group of mercury-resistant bacteria enhances their bioremediation capabilities. Many advanced biotechnological tools also can improve the bioremediation efficiency of mercury-resistant bacteria to achieve Hg bioremediation.

This study was conducted to explore the genomic diversity and forensic characterization of 15 autosomal microsatellite markers in the East Indian Tripuri population. In the studied population, we observed 158 different alleles with the average 10.53 alleles per locus. The locus D2S1338 (PIC= 0.862) was found to be the most polymorphic wheres locus TPOX (PIC= 0.647) as the least polymorphic, among all the studied loci. The locus FGA was found with the highest number of effective alleles (Nall=19) whereas locus TH01 showed least number of effective alleles (Nall=6). The cumulative values for matching probability (CPm), power of discrimination (CPD), power of exclusion CPE), and paternity index (CPI) were found as 1.94×10-18, 1, 0.999998, and 4.8×105 respectively. The studied population showed genetic closeness with the Gorkha population. In neighbor-joining tree, Tripura population pooled with the population of Nepal and Tibet. The genetic data obtained from the present study will not only enrich the existing autosomal STR database but will also be useful for forensic DNA application and genealogical studies.

Forensic characterization and genetic evaluation study in the 539 randomly selected unrelated adult healthy individuals belonging to the Central Indian population was undertaken. The study was performed using a multiplex of 27 Y-STRs incoporated in Yfiler™ Plus multiplex kit. Out of 539 samples, 6 samples were observed for large deletion and tri-allelic patterns, which were removed from the analysis, and out of 533 samples, a total of 507 haplotypes were found, and out of these haplotypes, 482 unique haplotypes were found in this piece of work. The forensically important parameters, i.e., gene diversity (GD) and discrimination capacity (DC), were found to be 0.669 and 0.951, respectively, for the tested Y STR loci. The genetic data of this study will enrich the Y STR data bank and being used as a potential tool for forensic DNA and various genetic studies.

Estimation of post-mortem time interval (PMI) is a key parameter in the forensic investigation which poses a huge challenge to the medico-legal experts. The succession of microbes within different parts of the human body after death has shown huge potential in the determination of PMI. Human body harbors trillions of microorganisms as commensals. With the death of an individual when biological functions are stopped, these microorganisms behave contrarily along with the invasion of degrading microbes from the environment. Human cadaver becomes a rich source of nutrients due to autolysis of cells, which attracts various invading microorganisms as well as macroorganisms. At different stages of degradation, the succession of microorganisms differs significantly which can be explored for accurate PMI estimation. With the advent of microbial genomics technique and reduction in the cost of DNA sequencing, thanatomicrobiome and epinecrotic community analysis have gained huge attention in PMI estimation. The article summarizes different sources of microorganisms in a human cadaver, their succession pattern, and analytical techniques for application in the field of microbial forensics. KEY POINTS: • Thanatomicrobiome and epinecrotic microbiome develop in postmortem human body. • Lack of metabolic, immune, neuroendocrine systems facilitate microbial succession. • Analysis of postmortem microbial communities predicts accurate PMI.

Autosomal STRs are the gold standard and are the most commonly used STR markers in forensic DNA typing. Most of the autosomal STRs present at the surrounding of the centromere of an autosomal chromosome are responsible for a unique DNA fingerprint in an individual. The updated information about the autosomal STR based kits is discussed along with the case studies to showcase the importance and utility of autosomal STR markers in forensic DNA typing. With the advancement in the technology, not only the number of STR markers has been increased but the inhibitor tolerance of the multiplex, reduced time of polymerase chain reaction (PCR), and the inclusion of one or more Y chromosomal markers have increased its utility in many folds.

Forensic DNA typing has overpowered all other known methods in forensics. Starting with the method which required a reasonably high amount of good quality of DNA, time taking and a complex process, this little more than three decade old technology has gone through much advancement to overcome these issues. The chapter details different steps involved in forensic DNA typing from its inception to the present including the advancements.