Estimating trace deposition time with circadian biomarkers: a prospective and versatile tool for crime scene reconstruction

The Role of Molecular Investigations in Estimating the Time since Deposition (TSD) of Bloodstains: A Systematic Review of the Literature

At many crime scenes, investigators are able to trace and find traces of blood. For many years, it was believed that such traces could only be subjected to genetic investigations, such as those aimed at comparing DNA profiling with a suspect to verify his identity, and that it was therefore not possible to backdate the traces. In recent years, various works have used experimental models to investigate the possibility of identifying markers and methodologies for estimating the time since deposition (TSD) of bloodstains. Despite the results, these methods are still not part of standard procedures, and there is no univocal analysis methodology. In this work we carried out a systematic literature review of all the papers published in the last ten years on this topic, comparing the experimental models created. This review demonstrates the potential that different molecular approaches, such as transcriptomics, metabolomics, proteomics, and spectrometry, can have in the analysis of TSD, with notable sensitivity and specificity. This paper also analyzes the intrinsic and extrinsic limits of these models and emphasizes the need to continue research work on this topic, considering the importance that this parameter can assume in forensic investigations against a suspect.

A common framework to situate digital and physical traces in time

In this article, three main approaches to situate forensic traces in time were revisited under the prism of the Sydney Declaration and adapted to be applicable to a large range of physical and digital traces. The first approach is based on time tags which are time-based characteristics produced as the result of an activity at a specific time. They can either be directly related to time (i.e., time stamps) or indirectly (i.e., time indicators). While relatively straightforward, time tags require scientific knowledge to be correctly interpreted and to account for the risks of desynchronisation, anomalies and manipulation. The second approach is based on time dynamics and aim at measuring changes that occur as a function of time, such as caesium pulsation (i.e., on which international atomic time is based) or body cooling after death (i.e., from which time since death can be inferred). However, time dynamics phenomena are generally also influenced by other case-specific factors (e.g., environmental factors), and thus more difficult to reliably implement in practice. Finally, the third approach relies on relative sequences, using information unrelated to time, such as relative positions or dynamics of traces at the scene. As each approach has its potential and limitations, a combination of traces from different (both material and digital) sources and approaches is recommended to answer time questions in practice (When? How long? In which succession?) and enhance the reliability of the dating endeavours. It is strongly recommended to consider the principles of the Sydney Declaration when implementing or developing dating methods, as they point at potential issues that are often forgotten in forensic research and practice, such as uncertainties linked to the concept of trace, scene investigation, the asymmetry of time, the importance of context and the multiplicity of purposes. Future research should focus on improving the reliability of these dating approaches by combining and systematising their usage in investigative practice, as well as in broader intelligence processes.

Age-related changes in the gut melatonin levels and its possible role in the regulation of feeding and digestibility, with the development of the gut from fingerling to adult stages of carp, Catla catla

The present study aims to understand the feeding-related age-bound changes in gut histoarchitecture and its response to gut melatonin (GM) titer regulating major digestive enzymes in carp, Catla catla. Therefore, gut samples were collected from different growth stages of carp, viz. (i) fingerling (FL), body weight (BW) ≥ 3 g to ≤ 20 g; (ii) advanced fingerling (AFL), BW > 20 g to ≤ 40 g; (iii) early juvenile (EJv), BW > 40 g to ≤ 70 g; (iv) juvenile (Jv), BW > 70 g to ≤ 200 g; (v) late juvenile (LJv), BW > 200 g to ≤ 300 g; (vi) preadult (PA), BW > 300 g to ≤ 500 g; (vii) subadult (SA), BW > 500 g to ≤ 1.00 kg; and (viii) adult (AD), BW > 1 kg to ≤ 2.5 kg. Data analysis revealed that the highest titer of GM was noted in FL, moderate in AFL, Jv, and PA, lower in EJv, SA, and AD, and lowest in LJv. Results depicted a negative correlation between the development of the gut and its melatonin content. Moreover, GM was positively associated with feeding intensity and gastro-somatic index (GaSI) and negatively related to ovarian onset and development. Following correlation and principal component analysis, several pieces of evidence were recorded on the role of gut melatonin in regulating digestive physiology. Finally, it indicates that gut melatonin has a progressively influential role in improving digestion, particularly protein and microbial digestion, with the development of an adult gut from the fingerling stage.

TrACES of time: Transcriptomic analyses for the contextualization of evidential stains - Identification of RNA markers for estimating time-of-day of bloodstain deposition

Obtaining forensically relevant information beyond who deposited a biological stain on how and under which circumstances it was deposited is a question of increasing importance in forensic molecular biology. In the past few years, several studies have been produced on the potential of gene expression analysis to deliver relevant contextualizing information, e.g. on nature and condition of a stain as well as aspects of stain deposition timing. However, previous attempts to predict the time-of-day of sample deposition were all based on and thus limited by previously described diurnal oscillators. Herein, we newly approached this goal by applying current sequencing technologies and statistical methods to identify novel candidate markers for forensic time-of-day predictions from whole transcriptome analyses. To this purpose, we collected whole blood samples from ten individuals at eight different time points throughout the day, performed whole transcriptome sequencing and applied biostatistical algorithms to identify 81 mRNA markers with significantly differential expression as candidates to predict the time of day. In addition, we performed qPCR analysis to assess the characteristics of a subset of 13 candidate predictors in dried and aged blood stains. While we demonstrated the general possibility of using the selected candidate markers to predict time-of-day of sample deposition, we also observed notable variation between different donors and storage conditions, highlighting the relevance of employing accurate quantification methods in combination with robust normalization procedures.This study's results are foundational and may be built upon when developing a targeted assay for time-of-day predictions from forensic blood samples in the future.

Estimating the time since deposition (TsD) in saliva stains using temporal changes in microbial markers

Determining the time since deposition (TsD) of traces could be helpful in the investigation of criminal offenses. However, there are no reliable markers and models available for the inference of short-term TsD. The goal of this study was to investigate the potential of the succession pattern of human salivary microbial communities to serve as an efficiency TsD prediction tool in the resolution of the forensic cases. Saliva stains exposed to indoor conditions up to 20 days were collected and analyzed by 16S rRNA profiling using high-throughput sequencing technique. Noticeable differences in microbial composition were observed between different time points, and the indoor exposure time of saliva stains were inversely correlated with alpha diversity estimates across the measured time period. The sequencing results were used to identify TsD-dependent bacterial indicators to regress a generalized random forest model, resulting in a mean absolute deviation (MAD) of 1.41 days. Furthermore, a simplified TsD predictive model was also developed utilizing Enhydrobacter, Paenisporosarcina, and Janthinobacterium by quantitative PCR (qPCR) with a MAD of 1.32 days, and then forensic practice assessment were also performed by using mock samples with a MAD of 3.53 days. In conclusion, this study revealed significant changes in salivary microbial abundance as the prolongation of TsD. It demonstrated that the microbial biomarkers could be invoked as a "clock" for TsD estimation in human dried saliva stains.

Short and Long Time Bloodstains Age Determination by Colorimetric Analysis: A Pilot Study

Bloodstains found at crime scenes represent a crucial source of information for investigative purposes. However, in forensic practice, no technique is currently used to estimate the time from deposition of bloodstains. This preliminary study focuses on the age estimation of bloodstains by exploiting the color variations over time due to the oxidation of the blood. For this purpose, we used a colorimetric methodology in order to easily obtain objective, univocal and reproducible results. We developed two bloodstain age prediction algorithms: a short-term and a long-term useful model for the first 24h and 60 days, respectively. Both models showed high levels of classification accuracy, particularly for the long-term model. Although a small-scale study, these results improve the potential application of colorimetric analysis in the time-line reconstruction of violent criminal events.

Analytical Strategy for MS-Based Thanatochemistry to Estimate Postmortem Interval

An analytical strategy for a matrix-assisted laser desorption mass spectrometry-based untargeted metabolomic study on vitreous humor (VH) was developed, looking for statistically significant parameters correlated to death time estimation. Five incubation stages of VH, 0, 24, 48, 72, and 96 h, at physiological pH and controlled temperature, were adopted to monitor time-dependent changes and correlate them with the postmortem interval (PMI). Using two multivariate statistical approaches, principal component regression (PCR) and partial least squares regression (PLSR), the PMI was assessed, considering the m/z values from mass spectra and the incubation time (ISt) as predictors. An independent validation set was used to evaluate the predictive capability of the models through the coefficient of determination (R²) and the root-mean-square error (RMSE). Different pre-treatments were applied to the raw mass spectra, and their performance in assessing PMI was evaluated. Based on the best outcomes in terms of both R² and RMSE, multiplicative scatter correction combined with a logarithmic transformation was chosen. The results of PCR and PLSR based on the selected pre-treatment are encouraging because validation R² is about 0.95 for both models. Moreover, the prediction error is 6 h for both models, when PMI is lower than 1 day. Although these results are obtained by the uncritical application of the models, they are comparable to or even better than those reported in the literature. Notwithstanding, we consider that many in situ influences, such as passive diffusion, functional loss of tissues, and advanced autolytic processes, could not get captured in vitro. However, the developed approach was optimized using VH samples and overcomes the limitations of the vast majority of methods that require validation for serum and/or urine samples.

Metabolomic profiling of bloodstains on various absorbent and non-absorbent surfaces

Bloodstains found at crime scenes contain immense information about the crime; thus, studies involving analysis of small molecules in bloodstains have been conducted. However, most of these studies have not accounted for the difference in the results of small molecule analysis due to the surface of bloodstains. To evaluate the "surface effect," we prepared bloodstains on seven surfaces, including both absorbent and non-absorbent surfaces, and performed global small molecule analysis by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). We used three indicators: (1) count recovery rate (%) of molecular features (MFs), (2) the number of MFs extracted from the surface without bloodstains, and (3) difference in abundance recovery rate (%) of MFs, to determine the ranking of the seven surfaces in the order of their similarity with blood. We also confirmed the correlation between each surface and blood through multivariate analysis. We found that the non-absorbent surfaces ranked better than the absorbent surfaces; wooden flooring was ranked as the most efficient surface, followed by stainless, vinyl flooring, glass, tile, filter paper, and mixed cotton. This study will help in the selection of the most efficient surface for collection of bloodstains for small molecule analysis from a crime scene. This is the first study to identify the effects of surface on extraction of global small molecules from bloodstains; it will help forensic scientists in obtaining more accurate information from small molecules present in the bloodstains collected at the field. Graphical abstract.

Diagnostic Value of Salivary Markers in Neuropsychiatric Disorders

A growing interest in the usability of saliva has been observed recently. Using saliva as a diagnostic material is possible because it contains a varied range of composites, organic and inorganic like proteins, carbohydrates, and lipids, which are secreted into saliva. Moreover, this applies to drugs and their metabolites. Saliva collection is noninvasive, and self-collection is possible. There is a lack of risk of injuries related to injection with needle, and it is generally safe. Human saliva has been successfully used, for example, in the diagnosis of many systemic diseases like cancers, autoimmunological diseases, infectious diseases (HIV, hepatitis, and malaria), and endocrinological diseases, as well as diseases of the gastrointestinal tract. Also, it is used in toxicological diagnostics, drug monitoring, and forensic medicine. The usefulness of saliva as a biological marker has also been extended to psychiatry. The specificity of mental illness and patients limits or prevents cooperation and diagnosis. In many cases, the use of saliva as a marker seems to be the most sensible choice.

Internal standard metabolites for obtaining absolute quantitative information on the components of bloodstains by standardization of samples

Analysis of the components of bloodstains found at crime scenes can provide important information for solving the crime. However, components of blood and bloodstains vary with volume and various other unpredictable factors. Therefore, it is necessary to specify the volume of the initial liquid blood droplet and standardize the analysis. In this study, internal standard metabolites that remained constant in a certain amount of bloodstain, long after deposition of the stain, were identified. Liquid chromatography-electrospray ionization-tandem mass spectrometry of the metabolites extracted from the bloodstain samples at various time points (0, 7, 14, 21, and 28 days) was performed. The coefficient of variation (CV) of the obtained molecular features was calculated for each criterion: time point, subject, and all data (time and subject, triplicate of each). Five molecular features with average CVs of less than or equal to 5% were selected as candidates. Partial least squares discriminant analysis and principal component analysis showed that the effect on the candidates was very low over time. The fold-change value of abundances was confirmed according to time. Stigmasterol exhibited the most stable pattern; l-methionine remained stable until day 14 and after day 21. This study was the first attempt to identify internal standard metabolites that were maintained at a constant level in a bloodstain for a sufficiently long time. Analysis of internal standard metabolites in bloodstains will facilitate determination of the initial blood volume from which the bloodstain was made. Moreover, this method will provide an approach for standardization of bloodstains to obtain absolute quantitative information of bloodstain components at crime scenes.

Human saliva as a diagnostic material

Today blood biochemical laboratory tests are essential elements to the diagnosis and monitoring of the treatment of diseases. However, many researchers have suggested saliva as an preferable diagnostic material. The collection of saliva is simple, painless, cheap and safe, both for patients and medical staff. An additional advantage of saliva is the fact that it may be retrieved several times a day, which makes repeat analysis much easier. Furthermore, saliva has very high durability. Although 94-99% of salivary content is water, saliva also contains numerous cellular elements and many organic and inorganic substances, including most biological markers present in the blood and urine that may be used in the early detection and monitoring of many dental and general diseases.

Investigation of metabolites for estimating blood deposition time

Trace deposition timing reflects a novel concept in forensic molecular biology involving the use of rhythmic biomarkers for estimating the time within a 24-h day/night cycle a human biological sample was left at the crime scene, which in principle allows verifying a sample donor’s alibi. Previously, we introduced two circadian hormones for trace deposition timing and recently demonstrated that messenger RNA (mRNA) biomarkers significantly improve time prediction accuracy. Here, we investigate the suitability of metabolites measured using a targeted metabolomics approach, for trace deposition timing. Analysis of 171 plasma metabolites collected around the clock at 2-h intervals for 36 h from 12 male participants under controlled laboratory conditions identified 56 metabolites showing statistically significant oscillations, with peak times falling into three day/night time categories: morning/noon, afternoon/evening and night/early morning. Time prediction modelling identified 10 independently contributing metabolite biomarkers, which together achieved prediction accuracies expressed as AUC of 0.81, 0.86 and 0.90 for these three time categories respectively. Combining metabolites with previously established hormone and mRNA biomarkers in time prediction modelling resulted in an improved prediction accuracy reaching AUCs of 0.85, 0.89 and 0.96 respectively. The additional impact of metabolite biomarkers, however, was rather minor as the previously established model with melatonin, cortisol and three mRNA biomarkers achieved AUC values of 0.88, 0.88 and 0.95 for the same three time categories respectively. Nevertheless, the selected metabolites could become practically useful in scenarios where RNA marker information is unavailable such as due to RNA degradation. This is the first metabolomics study investigating circulating metabolites for trace deposition timing, and more work is needed to fully establish their usefulness for this forensic purpose.

Melatonin biosynthesizing enzyme genes and clock genes in ovary and whole brain of zebrafish (Danio rerio): Differential expression and a possible interplay

The present study on zebrafish (Danio rerio) is the first attempt to demonstrate the circadian mRNA expression of melatonin biosynthesizing enzyme genes (Tph1a, Aanat1, Aanat2 and Hiomt) and clock associated genes (Bmal1a, Clock1a, Per1b, Per2 and Cry2a) in the ovary with a comparison to whole brain in normal (LD=12h L:12h D) and altered photic conditions (continuous dark, DD; continuous light, LL). Moreover, the present study also confirmed the ability of zebrafish ovary to biosynthesize melatonin both in vivo and in vitro with a significant difference at day and night. qRT-PCR analysis of genes revealed a dark acrophase of Aanat2 in both organs while Tph1 is in whole brain in LD condition. On the contrary, Bmal1a and Clock1a giving their peak in light, thereby showing a negative correlation with Tph1a and Aanat2. In LD-ovary, the acrophase of Tph1a, Bmal1a and Clock1a is in light and thus display a positive correlation. This trend of relationship in respect to Tph1a is not changing in altered photic conditions in both organs (except in DD-ovary). On the other hand this association for Aanat2 is varying in ovary under altered photic conditions but only in DD-whole brain. Both in LD and LL the expression of Aanat2 in brain presenting an opposite acrophase with both Bmal1a and Clock1a of ovary and consequently displaying a strong negative correlation among them. Interestingly, all ovarian clock associated genes become totally arrhythmic in DD, representing a loss of correlation between the melatonin synthesizing genes in brain and clock associated genes in ovary. The result is also indicating the formation of two heterodimers namely Clock1a:Bmal1a and Per2:Cry2a in the functioning of clock genes in both organs, irrespective of photic conditions, as they are exhibiting a strong significant positive correlation. Collectively, our data suggest that ovary of zebrafish is working as peripheral oscillator having its own melatonin biosynthesizing machinery and signifying a possible correlation with central oscillating system in various photic conditions.

Recent applications of CE- and HPLC-MS in the analysis of human fluids

The present review intends to cover the literature on the use of CE-/LC-MS for the analysis of human fluids, from 2010 until present. It has been planned to provide an overview of the most recent practical applications of these techniques to less extensively used human body fluids, including, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate, tear fluid, breast fluid, amniotic fluid, and cerumen. Potential pitfalls related to fluid collection and sample preparation, with particular attention to sample clean-up procedures, and methods of analysis, from the research laboratory to a clinical setting will also be addressed. While being apparent that proteomics/metabolomics represent the most prominent approaches for global identification/quantification of putative biomarkers for a variety of human diseases, evidence is also provided of the suitability of these sophisticated techniques for the detection of heterogeneous components carried by these fluids.

Improving human forensics through advances in genetics, genomics and molecular biology

Forensic DNA profiling currently allows the identification of persons already known to investigating authorities. Recent advances have produced new types of genetic markers with the potential to overcome some important limitations of current DNA profiling methods. Moreover, other developments are enabling completely new kinds of forensically relevant information to be extracted from biological samples. These include new molecular approaches for finding individuals previously unknown to investigators, and new molecular methods to support links between forensic sample donors and criminal acts. Such advances in genetics, genomics and molecular biology are likely to improve human forensic case work in the near future.