scholarly journals Messenger RNA biomarker signatures for forensic body fluid identification revealed by targeted RNA sequencing

2018 ◽  
Author(s):  
E Hanson ◽  
S Ingold ◽  
C Haas ◽  
J Ballantyne
Keyword(s):  
Sensitivity And Specificity ◽  
Biological Material ◽  
Body Fluid ◽  
Body Fluids ◽  
The Body ◽  
Menstrual Blood ◽  
Dna Profile ◽  
Fluid Identification ◽  
Biomarker Panel ◽  
Vaginal Secretions

AbstractThe recovery of a DNA profile from the perpetrator or victim in criminal investigations can provide valuable ‘source level’ information for investigators. However, a DNA profile does not reveal the circumstances by which biological material was transferred. Some contextual information can be obtained by a determination of the tissue or fluid source of origin of the biological material as it is potentially indicative of some behavioral activity on behalf of the individual that resulted in its transfer from the body. Here, we sought to improve upon established RNA based methods for body fluid identification by developing a targeted multiplexed next generation mRNA sequencing assay comprising a panel of approximately equal sized gene amplicons. The multiplexed biomarker panel includes several highly specific gene targets with the necessary specificity to definitively identify most forensically relevant biological fluids and tissues (blood, semen, saliva, vaginal secretions, menstrual blood and skin). In developing the biomarker panel we evaluated 66 gene targets, with a progressive iteration of testing target combinations that exhibited optimal sensitivity and specificity using a training set of forensically relevant body fluid samples. The current assay comprises 33 targets: 6 blood, 6 semen, 6 saliva, 4 vaginal secretions, 5 menstrual blood and 6 skin markers. We demonstrate the sensitivity and specificity of the assay and the ability to identify body fluids in single source and admixed stains. A 16 sample blind test was carried out by one lab with samples provided by the other participating lab. The blinded lab correctly identified the body fluids present in 15 of the samples with the major component identified in the 16th. Various classification methods are being investigated to permit inference of the body fluid/tissue in dried physiological stains. These include the percentage of reads in a sample that are due to each of the 6 tissues/body fluids tested and inter-sample differential gene expression revealed by agglomerative hierarchical clustering.

scholarly journals Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets

2014 ◽  
Author(s):  
Patrick Danaher ◽  
Robin Lynn White ◽  
Erin Hanson ◽  
Jack Ballantyne
Keyword(s):  
Gene Expression ◽  
Body Fluid ◽  
Body Fluids ◽  
Menstrual Blood ◽  
Body Fluid Identification ◽  
Fluid Identification ◽  
Mrna Profiling ◽  
Mrna Targets ◽  
Vaginal Secretions ◽  
Specific Mrna

A DNA profile from the perpetrator does not reveal, per se, the circumstances by which it was transferred. Body fluid identification by mRNA profiling may allow extraction of contextual 'activity level' information from forensic samples. Here we describe the development of a prototype multiplex digital gene expression (DGE) method for forensic body fluid/tissue identification based upon solution hybridization of color-coded NanoString® probes to 23 tissue/body fluid specific mRNA targets. The body fluids/tissues targeted were peripheral blood, semen, saliva, vaginal secretions, menstrual blood and skin. We tested and compared a simple 5 minute room temperature cellular lysis protocol against standard RNA isolation from same source material as a means to facilitate ease-of-use in forensic sample processing. We first describe a model for gene expression in a sample from a single body fluid and then extend that model to mixtures of body fluids. We then describe calculation of maximum likelihood estimates (MLEs) of body fluid quantities in a sample, and we describe the use of likelihood ratios to test for the presence of each body fluid in a sample. Known single source blood, semen, vaginal secretions, menstrual blood and skin samples all demonstrated the expected tissue specific gene expression for at least two of the chosen biomarkers. Saliva samples were more problematic, with their previously identified characteristic genes exhibiting poor specificity. Nonetheless the most specific saliva biomarker, HTN3, was expressed at a higher level in saliva than in any of the other tissues. As a preliminary indication of the ability of the method to discern admixtures of body fluids, five mixtures were prepared. Two of the five mixtures were called perfectly using the assay algorithm, and one of the component fluids was identified in the each of the 'false negative' mixtures. Crucially, our algorithm produced zero false positive fluid identifications across this study's 98 samples. Further optimization of the biomarker 'Codeset' will be required before it can be used in casework, particularly with respect to increasing the signal to noise ratio of the saliva biomarkers. With suitable modifications, this simplified protocol with minimal hands on requirement should facilitate routine use of mRNA profiling in casework laboratories.

A systematic analysis of miRNA markers and classification algorithms for forensic body fluid identification

2020 ◽  
Author(s):  
Yang Liu ◽  
Hongxia He ◽  
Zhi-Xiong Xiao ◽  
Anquan Ji ◽  
Jian Ye ◽  
...  
Keyword(s):  
Criminal Behavior ◽  
Body Fluid ◽  
Tissue Specificity ◽  
Random Perturbation ◽  
Crime Scene ◽  
Body Fluids ◽  
The Body ◽  
Systematic Analysis ◽  
Fluid Identification ◽  
Extreme Stability

Abstract Identifying the types of body fluids left at the crime scene can be essential to reconstructing the crime scene and inferring criminal behavior. MicroRNA (miRNA) molecule extracted from the trace of body fluids is one of the most promising biomarkers for the identification due to its high expression, extreme stability and tissue specificity. However, the detection of miRNA markers is not the answer to a yes–no question but the probability of an assumption. Therefore, it is a crucial task to develop complicated methods combining multi-miRNAs as well as computational algorithms to achieve the goal. In this study, we systematically analyzed the expression of 10 most probable body fluid-specific miRNA markers (miR-451a, miR-205-5p, miR-203a-3p, miR-214-3p, miR-144-3p, miR-144-5p, miR-654-5p, miR-888-5p, miR-891a-5p and miR-124-3p) in 605 body fluids-related samples, including peripheral blood, menstrual blood, saliva, semen and vaginal secretion. We introduced the kernel density estimation (KDE) method and six well-established methods to classify the body fluids in order to find the most optimal combinations of miRNA markers as well as the corresponding classifying method. The results show that the combination of miR-451a, miR-891a-5p, miR-144-5p and miR-203a-3p together with KDE can achieve the most accurate and robust performance according to the cross-validation, independent tests and random perturbation tests. This systematic analysis suggests a reference scheme for the identification of body fluids in an accurate and stable manner.

Semen-specific miRNAs: Suitable for the distinction of infertile semen in the body fluid identification?

2018 ◽  
Vol 33 ◽  
pp. 161-167 ◽  
Author(s):  
Huan Tian ◽  
Meili Lv ◽  
Zhilong Li ◽  
Duo Peng ◽  
Yu Tan ◽  
...  
Keyword(s):  
Body Fluid ◽  
The Body ◽  
Body Fluid Identification ◽  
Fluid Identification

scholarly journals The Mechanism of Urine Formation in Invertebrates

1936 ◽  
Vol 13 (3) ◽  
pp. 309-328
Author(s):  
L. E. R. PICKEN
Keyword(s):  
Hydrostatic Pressure ◽  
Osmotic Pressure ◽  
Body Fluid ◽  
External Medium ◽  
Carcinus Maenas ◽  
Colloid Osmotic Pressure ◽  
Body Fluids ◽  
The Body ◽  
Small Animals ◽  
Urine Formation

1. In Carcinus maenas: (a) The blood may be hypertonic, isotonic or hypotonic to the external medium. (b) The urine may be hypertonic, isotonic or hypotonic to the blood, and its concentration may differ in the two antennary glands. (c) The hydrostatic pressure of the body fluid is c. 13 cm. of water. (d) The colloid osmotic pressure of the blood is c. 11 cm. of water. (e) The urine probably contains protein and has a colloid osmotic pressure of c. 3 cm. of water. 2. In Potamobius fluviatilis: (a) The blood is hypertonic to the external medium. (b) The urine is hypotonic to the blood but hypertonic to the external medium and its concentration may differ in the two antennary glands. (c) The hydrostatic pressure of the body fluid is c. 20 cm. of water. (d) The colloid osmotic pressure of the blood is c. 15 cm. of water. (e) The urine may contain protein and has a colloid osmotic pressure (calculated) of c. 2 cm. of water. 3. In Peripatopsis spp.: (a) The blood is hypertonic to the urine. (b) The hydrostatic pressure of the body fluid is c. 10 cm. of water. (c) The colloid osmotic pressure (calculated) of the blood is c. 5 cm. of water. (d) The urine may contain protein and has a colloid osmotic pressure (calculated) of c. 2.5 cm. of water. 4. It is concluded that filtration is possible and that secretion and resorption almost certainly occur in the formation of the urine. 5. A microthermopile is described. 6. Methods are described for measuring the hydrostatic pressure and the colloid osmotic pressures of the body fluids in small animals.

Osmotic Regulation in the Brackish-Water Rotifer Brachionus Plicatilis (Muller)

1977 ◽  
Vol 68 (1) ◽  
pp. 151-156
Author(s):  
R. W. EPP ◽  
P. W. WINSTON
Keyword(s):  
Brackish Water ◽  
Body Fluid ◽  
Brachionus Plicatilis ◽  
Body Fluids ◽  
The Body ◽  
Osmotic Regulation ◽  
External Concentration ◽  
Brackish Waters ◽  
Low Concentrations ◽  
Rotifer Brachionus Plicatilis

The body fluid osmolarity of individual rotifers was measured at 12 external concentrations ranging from 32 to 957 m-osmol/1. Brachionus plicatilis is essentially an osmoconformer, since a change in the concentration of the medium results in a corresponding change in the concentration of the body fluids. Most animals were, however, slightly hyperosmotic throughout the range tested. The lowest body fluid osmolarity was 59 m-osmol/1 at an external concentration of 32 m-osmol/1. It appears that B. plicatilis is unable to tolerate the low concentrations that are frequently associated with acid water environments and this is responsible for the restriction of this species to alkaline and brackish waters.

scholarly journals Distinct spectrum of microRNA expression in forensically relevant body fluids and probabilistic discriminant approach

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shuntaro Fujimoto ◽  
Sho Manabe ◽  
Chie Morimoto ◽  
Munetaka Ozeki ◽  
Yuya Hamano ◽  
...  
Keyword(s):  
Body Fluid ◽  
Posterior Probability ◽  
Venous Blood ◽  
Body Fluids ◽  
Microrna Expression ◽  
Identification System ◽  
Vaginal Secretion ◽  
Fluid Identification ◽  
Discriminant Model ◽  
Probabilistic Evaluation

Abstract MicroRNA is attracting worldwide attention as a new marker for the identification of forensically relevant body fluids. A probabilistic discriminant model was constructed to identify venous blood, saliva, semen, and vaginal secretion, based on microRNA expression assessed via RT-qPCR. We quantified 15 candidate microRNAs in four types of body fluids by RT-qPCR and found that miR-144-3p, miR-451a-5p, miR-888-5p, miR-891a-5p, miR-203a-3p, miR-223-3p and miR-1260b were helpful to discriminate body fluids. Using the relative expression of seven candidate microRNAs in each body fluid, we implemented a partial least squares-discriminant analysis (PLS-DA) as a probabilistic discriminant model and distinguished four types of body fluids. Of 14 testing samples, 13 samples were correctly identified with >90% posterior probability. We also investigated the effects of microRNA expression in skin, semen infertility, and vaginal secretion during different menstrual phases. Semen infertility and menstrual phases did not affect our body fluid identification system. Therefore, the selected microRNAs were effective in identifying the four types of body fluids, indicating that probabilistic evaluation may be practical in forensic casework.

UF-1000i: validation of the body fluid mode for counting cells in body fluids

2014 ◽  
Vol 52 (12) ◽  
Author(s):  
Chérina Fleming ◽  
Rob Brouwer ◽  
Adriaan van Alphen ◽  
Jan Lindemans ◽  
Robert de Jonge
Keyword(s):  
Body Fluid ◽  
Method Comparison ◽  
Body Fluids ◽  
The Body ◽  
Comparison Results

Abstract: We evaluated the new body fluid mode on the UF-1000: We collected 154 body fluid samples, and compared the results of the UF-1000: Method comparison results showed acceptable WBC agreement between UF-1000: The UF-1000

scholarly journals Finger-Actuated Microneedle Array for Sampling Body Fluids

2021 ◽  
Vol 11 (12) ◽  
pp. 5329
Author(s):  
Misagh Rezapour Sarabi ◽  
Abdollah Ahmadpour ◽  
Ali K. Yetisen ◽  
Savas Tasoglu
Keyword(s):  
Minimally Invasive ◽  
Body Fluid ◽  
Interstitial Fluid ◽  
Biological Fluid ◽  
Body Fluids ◽  
The Body ◽  
Microneedle Array ◽  
User Friendly ◽  
Finger Pressure ◽  
Fluid Sampling

The application of microneedles (MNs) for minimally invasive biological fluid sampling is rapidly emerging, offering a user-friendly approach with decreased insertion pain and less harm to the tissues compared to conventional needles. Here, a finger-powered microneedle array (MNA) integrated with a microfluidic chip was conceptualized to extract body fluid samples. Actuated by finger pressure, the microfluidic device enables an efficient approach for the user to collect their own body fluids in a simple and fast manner without the requirement for a healthcare worker. The processes for extracting human blood and interstitial fluid (ISF) from the body and the flow across the device, estimating the amount of the extracted fluid, were simulated. The design in this work can be utilized for the minimally invasive personalized medical equipment offering a simple usage procedure.

Identification of Cancer Biomarkers in Human Body Fluids by Using Enhanced Physicochemical-incorporated Evolutionary Conservation Scheme

2020 ◽  
Vol 20 (21) ◽  
pp. 1888-1897
Author(s):  
Jian Zhang ◽  
Yu Zhang ◽  
Yanlin Li ◽  
Song Guo ◽  
Guifu Yang
Keyword(s):  
Human Body ◽  
Body Fluid ◽  
Cancer Biomarkers ◽  
Evolutionary Conservation ◽  
Body Fluids ◽  
The Body ◽  
Selection Strategy ◽  
Feature Subset ◽  
Scoring Matrices ◽  
Related Proteins

Objective: Cancer is one of the most serious diseases affecting human health. Among all current cancer treatments, early diagnosis and control significantly help increase the chances of cure. Detecting cancer biomarkers in body fluids now is attracting more attention within oncologists. In-silico predictions of body fluid-related proteins, which can be served as cancer biomarkers, open a door for labor-intensive and time-consuming biochemical experiments. Methods: In this work, we propose a novel method for high-throughput identification of cancer biomarkers in human body fluids. We incorporate physicochemical properties into the weighted observed percentages (WOP) and position-specific scoring matrices (PSSM) profiles to enhance their attributes that reflect the evolutionary conservation of the body fluid-related proteins. The least absolute selection and shrinkage operator (LASSO) feature selection strategy is introduced to generate the optimal feature subset. Results: The ten-fold cross-validation results on training datasets demonstrate the accuracy of the proposed model. We also test our proposed method on independent testing datasets and apply it to the identification of potential cancer biomarkers in human body fluids. Conclusion: The testing results promise a good generalization capability of our approach.

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