1
|
Javan GT, Singh K, Finley SJ, Green RL, Sen CK. Complexity of human death: its physiological, transcriptomic, and microbiological implications. Front Microbiol 2024; 14:1345633. [PMID: 38282739 PMCID: PMC10822681 DOI: 10.3389/fmicb.2023.1345633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Human death is a complex, time-governed phenomenon that leads to the irreversible cessation of all bodily functions. Recent molecular and genetic studies have revealed remarkable experimental evidence of genetically programmed cellular death characterized by several physiological processes; however, the basic physiological function that occurs during the immediate postmortem period remains inadequately described. There is a paucity of knowledge connecting necrotic pathologies occurring in human organ tissues to complete functional loss of the human organism. Cells, tissues, organs, and organ systems show a range of differential resilience and endurance responses that occur during organismal death. Intriguingly, a persistent ambiguity in the study of postmortem physiological systems is the determination of the trajectory of a complex multicellular human body, far from life-sustaining homeostasis, following the gradual or sudden expiry of its regulatory systems. Recent groundbreaking investigations have resulted in a paradigm shift in understanding the cell biology and physiology of death. Two significant findings are that (i) most cells in the human body are microbial, and (ii) microbial cell abundance significantly increases after death. By addressing the physiological as well as the microbiological aspects of death, future investigations are poised to reveal innovative insights into the enigmatic biological activities associated with death and human decomposition. Understanding the elaborate crosstalk of abiotic and biotic factors in the context of death has implications for scientific discoveries important to informing translational knowledge regarding the transition from living to the non-living. There are important and practical needs for a transformative reestablishment of accepted models of biological death (i.e., artificial intelligence, AI) for more precise determinations of when the regulatory mechanisms for homeostasis of a living individual have ceased. In this review, we summarize mechanisms of physiological, genetic, and microbiological processes that define the biological changes and pathways associated with human organismal death and decomposition.
Collapse
Affiliation(s)
- Gulnaz T. Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Kanhaiya Singh
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sheree J. Finley
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Robert L. Green
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Chandan K. Sen
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| |
Collapse
|
2
|
Delgado SL, Perilla PM, Salgado DM, Rojas MC, Narváez CF. Efficiency of Automated Viral RNA Purification for Pediatric Studies of Dengue and Zika in Hyperendemic Areas. J Trop Med 2023; 2023:1576481. [PMID: 37810169 PMCID: PMC10560119 DOI: 10.1155/2023/1576481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
The isolation of nucleic acids is a critical and limiting step for molecular assays, which prompted the arrival in Colombia of automated purification instruments during the SARS-CoV-2 pandemic. The local application of this technology in the study of tropical diseases, such as dengue and zika, is beginning to be tested. We evaluated the efficiency of the automated extraction of viral RNA for studies of pediatric dengue and zika. Clinical samples of children with dengue that were well characterized through RNA isolation by silica columns and serotype-specific nested RT-PCR (DENV-1 n = 7, DENV-2 n = 5, and negatives n = 8) in addition to 40 pediatric plasma samples spiked with ZIKV (strain PRVA BC59) and 209 from negative pre-epidemic children were analyzed. RNA from patients was extracted by two automated standard and high-throughput protocols on the KingFisher™ Flex instrument. The isolated RNA was evaluated for concentration and purity by spectrophotometry, for structural and functional integrity by electrophoresis and expression of the RNase P gene, and usefulness in serotype-specific DENV detection by conventional and real-time RT-PCR. For the evaluation of ZIKV RNA, the commercial TaqMan Triplex® assay was used, along with a well-tested in-house RT-qPCR assay. The concentration of RNA (5.2 vs. 7.5 ng/μL, P=0.03) and the number of integral bands (9 vs. 11) were higher with the high-throughput protocol. However, the number of specimens serotyped for DENV by RT-qPCR was comparable for both protocols. The cycle thresholds of the TaqMan Triplex® commercial kit and the in-house assay for the detection of plasma ZIKV RNA isolated with the standard protocol showed a strong association (r = 0.93, P < 0.0001) and a Cohen Kappa index of 0.98 when all 249 samples were analyzed. These preliminary results suggest that automated instruments could be used in studies of cocirculating flaviviruses that have represented a public health problem in recent decades in Colombia. They boast advantages such as efficiency, precision, time savings, and lower risk of cross-contamination.
Collapse
Affiliation(s)
- Sandra L. Delgado
- División de Inmunología, Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, Huila, Colombia
| | - Piedad M. Perilla
- División de Inmunología, Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, Huila, Colombia
| | - Doris M. Salgado
- Área de Pediatría, Universidad Surcolombiana, Neiva, Huila, Colombia
| | - María Clemencia Rojas
- Laboratorio de Salud Pública, Secretaría de Salud Departamental del Huila, Neiva, Huila, Colombia
| | - Carlos F. Narváez
- División de Inmunología, Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, Huila, Colombia
- Área de Pediatría, Universidad Surcolombiana, Neiva, Huila, Colombia
| |
Collapse
|
3
|
Hänggi NV, Bleka Ø, Haas C, Fonneløp AE. Quantitative PCR analysis of bloodstains of different ages. Forensic Sci Int 2023; 350:111785. [PMID: 37527614 DOI: 10.1016/j.forsciint.2023.111785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 07/15/2023] [Indexed: 08/03/2023]
Abstract
An accurate method to estimate the age of a stain or the time since deposition (TsD) would represent an important tool in police investigations for evaluating the true relevance of a stain. In this study, two laboratories reproduced an mRNA-based method for TsD estimation published by another group. The qPCR-based assay includes four transcripts (B2M, LGALS2, CLC, and S100A12) and showed preferential degradation of the 5' end over the 3' end. In this study, the blood-specific marker ALAS2 was added to examine whether it would show the same degradation pattern. Based on our qPCR data several elastic net models with different penalty combinations were created, using training data from the two laboratories separately and combined. Each model was then used to estimate the age of bloodstains from two independent test sets each laboratory had prepared. The elastic net model built on both datasets with training samples up to 320 days old displayed the best prediction performance across all test samples (MAD=18.9 days). There was a substantial difference in the prediction performance for the two laboratories: Restricting TsD to up to 100 days for test data, one laboratory obtained an MAD of 2.0 days when trained on its own data, whereas the other laboratory obtained an MAD of 15 days.
Collapse
Affiliation(s)
| | - Øyvind Bleka
- Department of Forensic Sciences, Oslo University Hospital, Norway
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
| | - Ane Elida Fonneløp
- Department of Forensic Sciences, Oslo University Hospital, Norway; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| |
Collapse
|
4
|
Zhang J, Ryu JY, Tirado SR, Dickinson LD, Abosch A, Aziz-Sultan MA, Boulos AS, Barrow DL, Batjer HH, Binyamin TR, Blackburn SL, Chang EF, Chen PR, Colby GP, Cosgrove GR, David CA, Day AL, Folkerth RD, Frerichs KU, Howard BM, Jahromi BR, Niemela M, Ojemann SG, Patel NJ, Richardson RM, Shi X, Valle-Giler EP, Wang AC, Welch BG, Williams Z, Zusman EE, Weiss ST, Du R. A Transcriptomic Comparative Study of Cranial Vasculature. Transl Stroke Res 2023:10.1007/s12975-023-01186-w. [PMID: 37612482 DOI: 10.1007/s12975-023-01186-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/06/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023]
Abstract
In genetic studies of cerebrovascular diseases, the optimal vessels to use as controls remain unclear. Our goal is to compare the transcriptomic profiles among 3 different types of control vessels: superficial temporal artery (STA), middle cerebral arteries (MCA), and arteries from the circle of Willis obtained from autopsies (AU). We examined the transcriptomic profiles of STA, MCA, and AU using RNAseq. We also investigated the effects of using these control groups on the results of the comparisons between aneurysms and the control arteries. Our study showed that when comparing pathological cerebral arteries to control groups, all control groups presented similar responses in the activation of immunological processes, the regulation of intracellular signaling pathways, and extracellular matrix productions, despite their intrinsic biological differences. When compared to STA, AU exhibited upregulation of stress and apoptosis genes, whereas MCA showed upregulation of genes associated with tRNA/rRNA processing. Moreover, our results suggest that the matched case-control study design, which involves control STA samples collected from the same subjects of matched aneurysm samples in our study, can improve the identification of non-inherited disease-associated genes. Given the challenges associated with obtaining fresh intracranial arteries from healthy individuals, our study suggests that using MCA, AU, or paired STA samples as controls are feasible strategies for future large-scale studies investigating cerebral vasculopathies. However, the intrinsic differences of each type of control should be taken into consideration when interpreting the results. With the limitations of each control type, it may be most optimal to use multiple tissues as controls.
Collapse
Affiliation(s)
- Jianing Zhang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Jee-Yeon Ryu
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Selena-Rae Tirado
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | | | - Aviva Abosch
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, USA
| | - M Ali Aziz-Sultan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Alan S Boulos
- Department of Neurosurgery, Albany Medical Center, Albany, NY, USA
| | - Daniel L Barrow
- Department of Neurosurgery, Emory University, Atlanta, GA, USA
| | - H Hunt Batjer
- Department of Neurosurgery, University of Texas Southwestern, Dallas, TX, USA
| | | | - Spiros L Blackburn
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Edward F Chang
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - P Roc Chen
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Geoffrey P Colby
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - G Rees Cosgrove
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Carlos A David
- Department of Neurosurgery, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Arthur L Day
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Rebecca D Folkerth
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Kai U Frerichs
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Brian M Howard
- Department of Neurosurgery, Emory University, Atlanta, GA, USA
| | - Behnam R Jahromi
- Department of Neurosurgery, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Mika Niemela
- Department of Neurosurgery, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Steven G Ojemann
- Department of Neurosurgery, University of Colorado, Denver, CO, USA
| | - Nirav J Patel
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - R Mark Richardson
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Xiangen Shi
- Department of Neurosurgery, Affiliated Fuxing Hospital, Capital Medical University, Beijing, China
| | | | - Anthony C Wang
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Babu G Welch
- Department of Neurosurgery, University of Texas Southwestern, Dallas, TX, USA
| | - Ziv Williams
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | | | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rose Du
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
| |
Collapse
|
5
|
Żarczyńska M, Żarczyński P, Tomsia M. Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics. Genes (Basel) 2023; 14:1643. [PMID: 37628694 PMCID: PMC10454188 DOI: 10.3390/genes14081643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.
Collapse
Affiliation(s)
- Małgorzata Żarczyńska
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Piotr Żarczyński
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Marcin Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland
| |
Collapse
|
6
|
Harl J, Himmel T, Ilgūnas M, Valkiūnas G, Weissenböck H. The 18S rRNA genes of Haemoproteus (Haemosporida, Apicomplexa) parasites from European songbirds with remarks on improved parasite diagnostics. Malar J 2023; 22:232. [PMID: 37563610 PMCID: PMC10416517 DOI: 10.1186/s12936-023-04661-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND The nuclear ribosomal RNA genes of Plasmodium parasites are assumed to evolve according to a birth-and-death model with new variants originating by duplication and others becoming deleted. For some Plasmodium species, it has been shown that distinct variants of the 18S rRNA genes are expressed differentially in vertebrate hosts and mosquito vectors. The central aim was to evaluate whether avian haemosporidian parasites of the genus Haemoproteus also have substantially distinct 18S variants, focusing on lineages belonging to the Haemoproteus majoris and Haemoproteus belopolskyi species groups. METHODS The almost complete 18S rRNA genes of 19 Haemoproteus lineages of the subgenus Parahaemoproteus, which are common in passeriform birds from the Palaearctic, were sequenced. The PCR products of 20 blood and tissue samples containing 19 parasite lineages were subjected to molecular cloning, and ten clones in mean were sequenced each. The sequence features were analysed and phylogenetic trees were calculated, including sequence data published previously from eight additional Parahaemoproteus lineages. The geographic and host distribution of all 27 lineages was visualised as CytB haplotype networks and pie charts. Based on the 18S sequence data, species-specific oligonucleotide probes were designed to target the parasites in host tissue by in situ hybridization assays. RESULTS Most Haemoproteus lineages had two or more variants of the 18S gene like many Plasmodium species, but the maximum distances between variants were generally lower. Moreover, unlike in most mammalian and avian Plasmodium species, the 18S sequences of all but one parasite lineage clustered into reciprocally monophyletic clades. Considerably distinct 18S clusters were only found in Haemoproteus tartakovskyi hSISKIN1 and Haemoproteus sp. hROFI1. The presence of chimeric 18S variants in some Haemoproteus lineages indicates that their ribosomal units rather evolve in a semi-concerted fashion than according to a strict model of birth-and-death evolution. CONCLUSIONS Parasites of the subgenus Parahaemoproteus contain distinct 18S variants, but the intraspecific variability is lower than in most mammalian and avian Plasmodium species. The new 18S data provides a basis for more thorough investigations on the development of Haemoproteus parasites in host tissue using in situ hybridization techniques targeting specific parasite lineages.
Collapse
Affiliation(s)
- Josef Harl
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Tanja Himmel
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | - Herbert Weissenböck
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| |
Collapse
|
7
|
Sun Y, Qu X, Qiu P, Mao C. A nanoparticle-based molecular beacon for directly detecting attomolar small RNA from plasma without purification. Talanta 2023; 260:124602. [PMID: 37148690 DOI: 10.1016/j.talanta.2023.124602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/08/2023]
Abstract
Molecular beacons (MBs) are DNA-based probes that detect DNA or RNA fragments and hold promise for monitoring diseases and studying protein-nucleic acid interactions. MBs usually use fluorescent molecules as fluorophores for reporting the target detection event. However, the fluorescence of the traditional fluorescent molecules can bleach and even be interfered with the background autofluorescence, reducing the detection performance. Hence, we propose to develop a nanoparticle-based MB (NPMB) that uses upconversion nanoparticles (UCNPs) as a fluorophore, which can be excited by near-infrared light to avoid background autofluorescence and thus enables us to detect small RNA from complicated clinical samples such as plasma. Specifically, we employ a DNA hairpin structure, with one segment complementary to the target RNA, to position a quencher (gold nanoparticles, Au NPs) and the UCNP fluorophore in close proximity, leading to the quenching of the fluorescence of UCNPs in the absence of a target nucleic acid. Only when the hairpin structure is complementary with the detection target, will the hairpin structure be destroyed to separate Au NPs and UCNPs, resulting in the instant recovery of the fluorescence signal of UCNPs and the consequent ultrasensitive detection of the target concentrations. The NPMB has an ultra-low background signal because UCNPs can be excited with NIR light with a wavelength longer than the emitted visible light. We demonstrate that the NPMB can successfully detect a small (22-nt) RNA (using a microRNA cancer biomarker, miR-21, as an example) and a small single-stranded DNA (complementing the cDNA of miR-21) in aqueous solutions from 1 aM to 1 pM, with the linear detection range being 10 aM to 1 pM for the former and 1 aM to 100 fM for the latter. We further show that the NPMB can be used to detect unpurified small RNA (miR-21) in clinical samples such as plasma with the same detection region. Our work suggests that the NPMB is a promising label-free and purification-free method for detecting small nucleic acid biomarkers in clinical samples with a detection limit as low as the aM level.
Collapse
Affiliation(s)
- Yueyi Sun
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Xuewei Qu
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Penghe Qiu
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Chuanbin Mao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, PR China.
| |
Collapse
|
8
|
Wenzlow N, Mills D, Byrd J, Warren M, Long MT. Review of the current and potential use of biological and molecular methods for the estimation of the postmortem interval in animals and humans. J Vet Diagn Invest 2023; 35:97-108. [PMID: 36744749 PMCID: PMC9999395 DOI: 10.1177/10406387231153930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We provide here an overview of the state of applied techniques in the estimation of the early period of the postmortem interval (PMI). The biological methods included consist of body cooling, CSF potassium, body cooling combined with CSF potassium, and tissue autolysis. For each method, we present its application in human and veterinary medicine and provide current methodology, strengths, and weaknesses, as well as target areas for improvement. We examine current and future molecular methods as they pertain to DNA and primarily to messenger RNA degradation for the estimation of the PMI, as well as the use of RNA in aging wounds, aging blood stains, and the identification of body fluids. Various types of RNA have different lengths, structures, and functions in cells. These differences in RNAs determine various intrinsic properties, such as their half-lives in cells, and, hence, their decay rate as well as their unique use for specific forensic tests. Future applications and refinements of RNA-based techniques provide opportunities for the use of molecular methods in the estimation of PMI and other general forensic applications.
Collapse
Affiliation(s)
- Nanny Wenzlow
- Louisiana Animal Disease Diagnostic Laboratory, Louisiana State University, Baton Rouge, LA, USA
| | - DeEtta Mills
- Department of Biological Sciences and International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - Jason Byrd
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Mike Warren
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Maureen T. Long
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, Gainesville, FL, USA
| |
Collapse
|
9
|
Amarilla-Stevens HN, Stevens RD, Phillips CD, Bradley RD. Temporal rate of postmortem DNA degradation in archived tissue samples: evidence from liver and muscle. J Mammal 2022. [DOI: 10.1093/jmammal/gyac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Guidelines identifying best practices for harvesting tissues that lead to optimal DNA preservation are few but are important curatorial concerns for genetic resource collections. We conducted a temporal study to establish rate of DNA degradation of tissue samples extracted from field-caught museum specimens. Five individuals of Sigmodon hispidus were collected and their liver and muscle tissues were harvested. Each tissue type was sectioned into 15 subsamples, and each was preserved in liquid nitrogen at different time intervals (2, 4, 8, 16, and 32 min; 1, 2, 4, 8, and 16 h; and 1, 2, 4, 8, and 16 days) following death. DNA was extracted using an automated robotic instrument and molecular mass profiles were determined fluorometrically. Postmortem DNA degradation was continuous and dependent on time, but also was significantly affected by differences among individual cotton rats. DNA fragments of ≥10,000 base pairs in length were present in muscle samples across all time intervals, whereas DNA fragments of this size in liver samples were no longer present after 8–16 h postmortem. DNA molecular mass profiles showed that muscle samples retained 80% of their longest fragments (≥10,000 base pairs) until 1 day postmortem, whereas liver samples retained the same percentage only until 8 min after death. Although rates of decay were measured from samples in a laboratory (not field) setting, rates of decay presented here can guide field and museum workers in best practices. Results suggest that opportunistic samples, such as those from roadkill specimens, are more likely to be of use for a variety of molecular methods when muscle is preserved. Considerations of differences in rates of degradation may also guide selection of tissue types housed in genetic resource collections, especially under space-limited circumstances.
Collapse
Affiliation(s)
- Heidi N Amarilla-Stevens
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Richard D Stevens
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Natural Resources Management, Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Caleb D Phillips
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Biological Sciences, Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Robert D Bradley
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Biological Sciences, Texas Tech University , Lubbock, Texas 79409-3131 , USA
| |
Collapse
|
10
|
Morikawa K, Kida H, Handa H, Inoue T, Saji H, Koike J, Nakamura S, Sato Y, Ueda Y, Suzuki F, Matoba R, Mineshita M. A Prospective Validation Study of Lung Cancer Gene Panel Testing Using Cytological Specimens. Cancers (Basel) 2022; 14:cancers14153784. [PMID: 35954448 PMCID: PMC9367394 DOI: 10.3390/cancers14153784] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary The gold standard for genetic panel test samples is considered to be tissue specimens. However, in clinical practice, tissue specimens are often unavailable. Therefore, using an amplicon-based high-sensitivity next-generation sequencing panel test capable of measuring eight druggable genes, we enrolled patients who underwent diagnostic procedures to evaluate analysis accuracy, nucleic acid yield, and quality using cytological specimens. Cytological specimens were suitable for both nucleic acid yield and specimen quality due to the ease of collection and processing. Cytological sample analysis detected gene mutations in 68.7% of lung adenocarcinomas, and these samples were consistent with companion diagnostic tests 99.5% of the time. Moreover, the allele frequency of gene mutations in cytological specimens showed a high correlation with tissue specimens. This is the first study to prospectively evaluate the feasibility of a lung cancer gene panel test using cytological specimens. Abstract Background: Genetic panel tests require sufficient tissue samples, and therefore, cannot always be performed. Although collecting cytological specimens is easier than tissue collection, there are no validation studies on the diagnostic accuracy of lung cancer gene panel tests using cytology samples. Methods: Using an amplicon-based high-sensitivity next-generation sequencing panel test capable of measuring eight druggable genes, we prospectively enrolled consecutive patients who underwent diagnostic procedures. We evaluated the analysis accuracy rate, nucleic acid yield, and the quality of cytological specimens under brushing, needle aspiration, and pleural effusion. We then compared these specimens with collected tissue samples. Results: In 163 prospectively enrolled cases, nucleic acid extraction and analysis accuracy was 100% in cases diagnosed with adenocarcinoma. Gene mutations were found in 68.7% of cases with 99.5% (95% CI: 98.2–99.9) concordance to companion diagnostics. The median DNA/RNA yield and DNA/RNA integrity number were 475/321 ng and 7.9/5.7, respectively. The correlation coefficient of the gene allele ratio in 64 cases compared with tissue samples was 0.711. Conclusion: The success of gene analysis using cytological specimens was high, and the yield and quality of the extracted nucleic acid were sufficient for panel analysis. Moreover, the allele frequency of gene mutations in cytological specimens showed high correlations with tissue specimens.
Collapse
Affiliation(s)
- Kei Morikawa
- Division of Respiratory Diseases, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8513, Japan; (H.K.); (H.H.); (T.I.); (M.M.)
- Correspondence: ; Tel.: +81-44-977-8111; Fax: +81-44-976-5792
| | - Hirotaka Kida
- Division of Respiratory Diseases, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8513, Japan; (H.K.); (H.H.); (T.I.); (M.M.)
| | - Hiroshi Handa
- Division of Respiratory Diseases, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8513, Japan; (H.K.); (H.H.); (T.I.); (M.M.)
| | - Takeo Inoue
- Division of Respiratory Diseases, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8513, Japan; (H.K.); (H.H.); (T.I.); (M.M.)
| | - Hisashi Saji
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki 216-8513, Japan;
| | - Junki Koike
- Department of Pathological Diagnosis, St. Marianna University School of Medicine, Kawasaki 216-8513, Japan;
| | - Seiji Nakamura
- DNA Chip Research Inc., Tokyo 105-0022, Japan; (S.N.); (Y.S.); (Y.U.); (F.S.); (R.M.)
| | - Yoshiharu Sato
- DNA Chip Research Inc., Tokyo 105-0022, Japan; (S.N.); (Y.S.); (Y.U.); (F.S.); (R.M.)
| | - Yumi Ueda
- DNA Chip Research Inc., Tokyo 105-0022, Japan; (S.N.); (Y.S.); (Y.U.); (F.S.); (R.M.)
| | - Fumihiko Suzuki
- DNA Chip Research Inc., Tokyo 105-0022, Japan; (S.N.); (Y.S.); (Y.U.); (F.S.); (R.M.)
| | - Ryo Matoba
- DNA Chip Research Inc., Tokyo 105-0022, Japan; (S.N.); (Y.S.); (Y.U.); (F.S.); (R.M.)
| | - Masamichi Mineshita
- Division of Respiratory Diseases, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki 216-8513, Japan; (H.K.); (H.H.); (T.I.); (M.M.)
| |
Collapse
|
11
|
Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
Collapse
Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
| |
Collapse
|
12
|
Buijs SB, Weehuizen JM, Jensen TK, Boye M, Hermans MH, Nooijen PT, Hoepelman AI, Bleeker-Rovers CP, Oosterheert JJ, Wever PC. Fluorescence in situ hybridization for detecting Coxiella burnetii in tissue samples from chronic Q fever patients. Clin Microbiol Infect 2022; 28:1502.e1-1502.e5. [PMID: 35724869 DOI: 10.1016/j.cmi.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/06/2022] [Accepted: 06/14/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVE Detection of the intracellular bacterium Coxiella burnetii, causative agent of chronic Q fever, is notoriously difficult. Diagnosis of and duration of antibiotic treatment for chronic Q fever is partly determined by detection of the bacterium with polymerase chain reaction (PCR). Fluorescence in situ hybridization (FISH) might be a promising technique for detecting C. burnetii in tissue samples from chronic Q fever patients, but its value in comparison with PCR is uncertain. We aim to assess the value of FISH for detecting C. burnetii in tissue of chronic Q fever patients. METHODS FISH and PCR were performed on tissue samples from Dutch chronic Q fever patients collected during surgery or autopsy. Sensitivity, specificity, and overall diagnostic accuracy were calculated. Additionally, data on patient and disease characteristics were collected from electronic medical records. RESULTS In total, 49 tissue samples from mainly vascular walls, heart valves, or placentas, obtained from 39 chronic Q fever patients, were examined by FISH and PCR. The sensitivity and specificity of FISH compared to PCR for detecting C. burnetii in tissue samples from chronic Q fever patients was 45.2% (95% CI, 27.3% - 64.0%) and 84.6% (95% CI, 54.6% - 98.1%), respectively. The overall diagnostic accuracy was 56.8% (95% CI, 42.2% - 72.3%). Two C. burnetii PCR negative placentas were FISH positive. Four FISH results (8.2%) were deemed inconclusive because of autofluorescence. CONCLUSION With an overall diagnostic accuracy of 57.8%, we conclude that FISH has limited value in the routine diagnostics of chronic Q fever.
Collapse
Affiliation(s)
- Sheila B Buijs
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jesper M Weehuizen
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Tim K Jensen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
| | - Mette Boye
- Norwegian Veterinary Institute, Ås, Norway
| | - Mirjam Ha Hermans
- Department of Medical Microbiology and Infection Control, Jeroen Bosch Hospital, 's-Hertogenbosch, the Netherlands
| | - Peet Tga Nooijen
- Department of Pathology, Pathologie-DNA, location Jeroen Bosch Hospital, 's-Hertogenbosch, the Netherlands
| | - Andy Im Hoepelman
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Chantal P Bleeker-Rovers
- Department of Internal Medicine and Infectious Diseases, Radboud university medical center and Radboud Expertise Center for Q fever, Nijmegen, the Netherlands
| | - Jan Jelrik Oosterheert
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Peter C Wever
- Department of Medical Microbiology and Infection Control, Jeroen Bosch Hospital, 's-Hertogenbosch, the Netherlands
| |
Collapse
|
13
|
Evaluation of the Effects of Different Sample Collection Strategies on DNA/RNA Co-Analysis of Forensic Stains. Genes (Basel) 2022; 13:genes13060983. [PMID: 35741745 PMCID: PMC9222428 DOI: 10.3390/genes13060983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
The aim of this study was to evaluate the impact of different moistening agents (RNase-free water, absolute anhydrous ethanol, RNAlater®) applied to collection swabs on DNA/RNA retrieval and integrity for capillary electrophoresis applications (STR typing, cell type identification by mRNA profiling). Analyses were conducted on whole blood, luminol-treated diluted blood, saliva, semen, and mock skin stains. The effects of swab storage temperature and the time interval between sample collection and DNA/RNA extraction were also investigated. Water provided significantly higher DNA yields than ethanol in whole blood and semen samples, while ethanol and RNAlater® significantly outperformed water in skin samples, with full STR profiles obtained from over 98% of the skin samples collected with either ethanol or RNAlater®, compared to 71% of those collected with water. A significant difference in mRNA profiling success rates was observed in whole blood samples between swabs treated with either ethanol or RNAlater® (100%) and water (37.5%). Longer swab storage times before processing significantly affected mRNA profiling in saliva stains, with the success rate decreasing from 91.7% after 1 day of storage to 25% after 7 days. These results may contribute to the future development of optimal procedures for the collection of different types of biological traces.
Collapse
|
14
|
Poma AM, Bonuccelli D, Giannini R, Macerola E, Vignali P, Ugolini C, Torregrossa L, Proietti A, Pistello M, Basolo A, Santini F, Toniolo A, Basolo F. COVID-19 autopsy cases: detection of virus in endocrine tissues. J Endocrinol Invest 2022; 45:209-214. [PMID: 34191258 PMCID: PMC8243303 DOI: 10.1007/s40618-021-01628-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/25/2021] [Indexed: 01/06/2023]
Abstract
PURPOSE The SARS-CoV-2 genome has been detected in a variety of human samples including blood, urine, semen, and faeces. However, evidence of virus presence in tissues other than lung are limited. METHODS We investigated whether SARS-CoV-2 could be detected in 50 autoptic specimens of endocrine organs from 29 patients who died of COVID-19. RESULTS The virus was detected in 25 specimens including ten abdominal subcutaneous adipose tissue samples (62%), six testes (67%), and nine thyroid (36%) samples. The analysis of multiple endocrine organ samples obtained from the same patients showed that, in virus-positive cases, the viral genome was consistently detected in all but two matched specimens. CONCLUSION Our findings show that the virus spread into endocrine organs is a common event in severe cases. Further studies should assess the rate of the phenomenon in clinically mild cases. The potential long-term effects of COVID-19 on endocrine functions should be taken into consideration.
Collapse
Affiliation(s)
- A M Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi,10, 56126, Pisa, Italy
| | - D Bonuccelli
- Department of Forensic Medicine, Azienda USL Toscana Nordovest, Lucca, Italy
| | - R Giannini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi,10, 56126, Pisa, Italy
| | - E Macerola
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi,10, 56126, Pisa, Italy
| | - P Vignali
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi,10, 56126, Pisa, Italy
| | - C Ugolini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi,10, 56126, Pisa, Italy
| | - L Torregrossa
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi,10, 56126, Pisa, Italy
| | - A Proietti
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi,10, 56126, Pisa, Italy
| | - M Pistello
- Retrovirus Center and Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A Basolo
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - F Santini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - A Toniolo
- Global Virus Network, University of Insubria, Varese, Italy
| | - F Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi,10, 56126, Pisa, Italy.
| |
Collapse
|
15
|
Abstract
The RNA-dependent RNA polymerase (RdRp) of all known double-stranded RNA viruses is located within the viral particle and is responsible for the transcription and replication of the viral genome. Through an RT-PCR assay, we determined that purified virions, in vitro translated RdRp proteins, and purified recombinant RdRp proteins of partitiviruses also have reverse transcriptase (RT) function. We show that partitivirus RdRps 1) synthesized DNA from homologous and heterologous dsRNA templates; 2) are active using both ssRNA and dsRNA templates; and 3) are active at lower temperatures compared to an optimal reaction temperature of commercial RT enzymes. This finding poses an intriguing question: why do partitiviruses, with dsRNA genomes, have a polymerase with RT functions? In comparison, 3Dpol, the RdRp of poliovirus, did not show any RT activity. Our findings lead us to propose a new evolutionary model for RNA viruses where the RdRp of dsRNA viruses could be the ancestor of RdRps.
Collapse
Affiliation(s)
- Mahtab Peyambari
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, PA, USA
| | | | - Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
16
|
Salzmann AP, Russo G, Kreutzer S, Haas C. Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces. Forensic Sci Int Genet 2021; 53:102524. [PMID: 34015741 DOI: 10.1016/j.fsigen.2021.102524] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022]
Abstract
Knowledge about the age of a stain, also termed as time since deposition (TsD), would provide law-enforcing authorities with valuable information for the prosecution of criminal offenses. Yet, there is no reliable method for the inference / assessment of TsD available. The aim of this study was to gain further insight into the RNA degradation pattern of forensically relevant body fluids and to find candidate markers for TsD estimation. Blood, menstrual blood, saliva, semen and vaginal secretion samples were exposed to indoor (dark, room temperature) and outdoor (exposed to sun, wind, etc. but protected from rain) conditions for up to 1.5 years. Based on expression and degradation analyses, we were able to identify body fluid specific signatures and RNA degradation patterns. The indoor samples showed a marked drop in RNA integrity after 6 months, while the outdoor samples were difficult to interpret and therefore excluded for some of the analyses. Up to 4 weeks, indoor samples showed more stable and less degrading transcripts than outdoor samples. Stable transcripts tended to be significantly shorter than degrading ones or transcripts, which are neither degrading nor stable. We reinforced the body fluid specific and the housekeeping gene nature of previously reported markers. With an unbiased approach, we selected stable and degrading genes for each body fluid in the short term and assessed their integrity during extended storage. We identified several stable and degrading gene transcripts, which could be tested in a targeted assay to assess the TsD interval e.g. by analyzing the ratio of degrading vs stable transcripts. In conclusion, we were able to detect RNA degradation patterns in samples being aged up to 1.5 years and identified several candidate markers, which could be evaluated for TsD estimation.
Collapse
Affiliation(s)
| | - Giancarlo Russo
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
| |
Collapse
|
17
|
Schyma C, Madea B, Müller R, Zieger M, Utz S, Grabmüller M. DNA-free does not mean RNA-free-The unwanted persistence of RNA. Forensic Sci Int 2020; 318:110632. [PMID: 33302243 DOI: 10.1016/j.forsciint.2020.110632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022]
Abstract
Contact shots to the head often provoke a transfer of biological traces into firearm barrels, which are not visible at endoscopic inspection. STR-PCR can amplify these latent traces and assign them to the victim. Via RNA-DNA-co-extraction also miRNA can be detected, which allow a conclusion to be drawn about the body fluid or tissue. Molecular genetic analysis of experimental stains in firearm barrels requires the guarantee that the barrel is initially free of any nucleic acid. Twelve shots were fired to so-called "reference cubes" (10 % gelatine, 12 cm edge length, embedded paint-blood-pad) using three current handguns: from 20 and 30 cm distance, four at close range (1-2.5 cm) and six contact shots. After endoscopic examination and swabbing of the barrels, a previously described mechanical and chemical cleaning using DNAExitusPlus™ was performed. The inner surface of the barrel was thoroughly wiped off using moistened forensic swabs, which were submitted to RNA-DNA-co-extraction. The combined thorough mechanical cleaning with Ballistol® and the application of DNAExitusPlus™ eliminated any profilable DNA in all samples. However, in 10 of 12 samples RNA concentrations between 0.11 - 0.79 ng/μl were measured. Furthermore, in 9 of 12 samples blood-specific miRNA (miR-451a) was detected. Summarizing, none of the experimentally contaminated barrels was RNA-free despite the performed cleaning procedure. Further investigation showed, that even "professional" cleaning by a gunsmith did not remove RNA.
Collapse
Affiliation(s)
- Christian Schyma
- Institute of Forensic Medicine of the University of Bern, Bühlstrasse 20, 3012 Bern, Switzerland.
| | - Burkhard Madea
- Institute of Legal Medicine, University Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Rolf Müller
- Criminal Investigation Service of the Cantonal Police Department of Bern, Nordring 30, 3013 Bern, Switzerland
| | - Martin Zieger
- Institute of Forensic Medicine of the University of Bern, Bühlstrasse 20, 3012 Bern, Switzerland
| | - Silvia Utz
- Institute of Forensic Medicine of the University of Bern, Bühlstrasse 20, 3012 Bern, Switzerland
| | - Melanie Grabmüller
- Institute of Legal Medicine, University Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| |
Collapse
|
18
|
Fattorini P, Bonin S, Marrubini G, Bertoglio B, Grignani P, Recchia E, Pitacco P, Zupanič Pajnič I, Sorçaburu-Ciglieri S, Previderè C. Highly degraded RNA can still provide molecular information: An in vitro approach. Electrophoresis 2020; 41:386-393. [PMID: 31967656 DOI: 10.1002/elps.201900200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 01/01/2023]
Abstract
The long-term survival of RNA in postmortem tissues is a tricky topic. Many aged/forensic specimens show, in fact, high rates of null/inconclusive PCR-based results, while reliable outcomes were sometimes achieved from archaeological samples. On the other hand, several data show that the RNA is a molecule that survives even to several physical-chemical stresses. In the present study, a simple protocol, which was already developed for the prolonged hydrolysis of DNA, was applied to a RNA sample extracted from blood. This protocol is based on the heat-mediated (70°C) hydrolysis for up to 36 h using ultrapure water and di-ethyl-pyro-carbonate-water as hydrolysis medium. Measurable levels of depurination were not found even if microfluidic devices showed a progressive pattern of degradation. The reverse transcription/quantitative PCR analysis of two (60 bp long) housekeeping targets (glyceraldehyde-3-phosphate dehydrogenase and porphobilinogen deaminase) showed that the percentage of amplifiable target (%AT) decreased in relation to the duration of the damaging treatment (r2 > 0.973). The comparison of the %AT in the degraded RNA and in the DNA samples that underwent the same damaging treatment showed that the %AT is always higher in RNA, reaching up to three orders of magnitude. Lastly, even the end-point PCR of blood-specific markers gave reliable results, which is in agreement with the body fluid origin of the sample. In conclusion, all the PCR-based results show that RNA maintains the ability to be retro-transcribed in short cDNA fragments even after 36 h of incubation at 70°C in mildly acidic buffers. It is therefore likely that the long-term survival of RNA samples depends mainly on the protection against RNAase attacks rather than on environmental factors (such as humidity and acidity) that are instead of great importance for the stability of DNA. As a final remark, our results suggest that the RNA analysis can be successfully performed even when DNA profiling failed.
Collapse
Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Serena Bonin
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | | | - Barbara Bertoglio
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Pierangela Grignani
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Elisa Recchia
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Paola Pitacco
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| |
Collapse
|
19
|
Salzmann AP, Russo G, Aluri S, Haas C. Transcription and microbial profiling of body fluids using a massively parallel sequencing approach. Forensic Sci Int Genet 2019; 43:102149. [DOI: 10.1016/j.fsigen.2019.102149] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022]
|
20
|
An Optimized Method of RNA Isolation from Goat Milk Somatic Cells for Transcriptomic Analysis. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2019-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
The goat (Capra hircus) is a perfect animal model for analyzing the transcriptome of milk somatic cells (MSCs), as sufficient numbers of somatic cells in goat milk, i.e., exfoliated epithelial cells, can be obtained using noninvasive methods. RNA integrity and purity are the first and most important parameters qualifying samples for transcriptomic tests and next-generation sequencing, as RNA quality influences experimental results. The aim of this study was to optimize a method for obtaining high-quality RNA from goat MSCs, irrespective of effects like breed, lactation stage, health status (e.g., with or without small ruminant lentivirus [SRLV] infection), or number of somatic cells. Milk samples were obtained from goats of two Polish breeds in various lactation stages and in different parities, and from goats infected and not infected with SRLV. Altogether, 412 MSC samples were examined: 206 using method A with fenozol and 206 using method B with QIAzol. Though the overall purity (measured as absorbance ratios at 260 nm/280 nm and 260 nm/230 nm) of the RNA material was comparable, the average yield of RNA isolated using method A was 11.9 µg, while method B’s average yield was 29.9 µg. Moreover, method B resulted in good quality RNA suitable for transcriptome analysis. Results were confirmed by RT-qPCR, using 18S rRNA and RPLP0 as the reference genes. The application of our modified treatment method was successful in obtaining high-integrity samples for transcriptomic or next-generation sequencing analysis. Using a 400 mL milk sample cooled in ice directly after milking, securing the cooling chain process from milking to MSC isolation, and applying method B to isolate RNA, we obtained good RNA quality irrespective of the goats’ breed, lactation stage, parity, milk yield, SRLV infection, and even milk yield and number of somatic cells in milk.
Collapse
|
21
|
Smith O, Dunshea G, Sinding MHS, Fedorov S, Germonpre M, Bocherens H, Gilbert MTP. Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. PLoS Biol 2019; 17:e3000166. [PMID: 31361744 PMCID: PMC6667121 DOI: 10.1371/journal.pbio.3000166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data’s authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology. Ancient DNA is known to survive in cold environments for tens of millennia, but it is assumed that ancient RNA could not persist in such a way due to its relative instability. However, this study shows that under permafrost conditions, ancient RNA can survive well enough to show tissue specificity even in mammalian soft tissues.
Collapse
Affiliation(s)
- Oliver Smith
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Glenn Dunshea
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Holger S. Sinding
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, Yakutsk, Russia
| | - Mietje Germonpre
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Science, Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - M. T. P. Gilbert
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| |
Collapse
|
22
|
A method to estimate the age of bloodstains using quantitative PCR. Forensic Sci Int Genet 2019; 39:103-108. [DOI: 10.1016/j.fsigen.2018.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/10/2018] [Accepted: 12/13/2018] [Indexed: 01/03/2023]
|
23
|
Peyambari M, Warner S, Stoler N, Rainer D, Roossinck MJ. A 1,000-Year-Old RNA Virus. J Virol 2019; 93:e01188-18. [PMID: 30305356 PMCID: PMC6288340 DOI: 10.1128/jvi.01188-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/26/2018] [Indexed: 11/20/2022] Open
Abstract
Only a few RNA viruses have been discovered from archaeological samples, the oldest dating from about 750 years ago. Using ancient maize cobs from Antelope house, Arizona, dating from ca. 1,000 CE, we discovered a novel plant virus with a double-stranded RNA genome. The virus is a member of the family Chrysoviridae that infect plants and fungi in a persistent manner. The extracted double-stranded RNA from 312 maize cobs was converted to cDNA, and sequences were determined using an Illumina HiSeq 2000. Assembled contigs from many samples showed similarity to Anthurium mosaic-associated virus and Persea americana chrysovirus, putative species in the Chrysovirus genus, and nearly complete genomes were found in three ancient maize samples. We named this new virus Zea mays chrysovirus 1. Using specific primers, we were able to recover sequences of a closely related virus from modern maize and obtained the nearly complete sequences of the three genomic RNAs. Comparing the nucleotide sequences of the three genomic RNAs of the modern and ancient viruses showed 98, 96.7, and 97.4% identities, respectively. Hence, in 1,000 years of maize cultivation, this virus has undergone about 3% divergence.IMPORTANCE A virus related to plant chrysoviruses was found in numerous ancient samples of maize, with nearly complete genomes in three samples. The age of the ancient samples (i.e., about 1,000 years old) was confirmed by carbon dating. Chrysoviruses are persistent plant viruses. They infect their hosts from generation to generation by transmission through seeds and can remain in their hosts for very long time periods. When modern corn samples were analyzed, a closely related chrysovirus was found with only about 3% divergence from the ancient sequences. This virus represents the oldest known plant virus.
Collapse
Affiliation(s)
- Mahtab Peyambari
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sylvia Warner
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Nicholas Stoler
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Drew Rainer
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| |
Collapse
|
24
|
"The acid test"-validation of the ParaDNA® Body Fluid ID Test for routine forensic casework. Int J Legal Med 2018; 133:751-757. [PMID: 30460509 DOI: 10.1007/s00414-018-1971-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/12/2018] [Indexed: 01/18/2023]
Abstract
The identification of the cellular origin and composition of crime scene-related traces can provide crucial insight into a crime scene reconstruction. In the last decade, especially mRNA-based body fluid and tissue identification (BFI) has been vigorously examined. Besides capillary electrophoretic (CE) and real-time quantitative PCR (RT-qPCR)-based approaches for mRNA detection, melt curve analysis bears potential as a simple-to-use method for BFI. The ParaDNA® Body Fluid ID Test relies on HyBeacon® probes and was developed as a rapid test for mRNA-based BFI of six different body fluids: vaginal fluid, seminal fluid, sperm cells, saliva, menstrual, and peripheral blood. The herein presented work was performed as an "acid test" of the system and should clarify whether the approach matches the requirements of forensic routine casework in German police departments. Tested samples consisted of single source as well as of mixed samples.
Collapse
|
25
|
Otte JM, Blackwell N, Soos V, Rughöft S, Maisch M, Kappler A, Kleindienst S, Schmidt C. Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples? FEMS Microbiol Ecol 2018; 94:5104375. [DOI: 10.1093/femsec/fiy189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/18/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Julia M Otte
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Viktoria Soos
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Saskia Rughöft
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Markus Maisch
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
- Geomicrobiology, Center for Geomicrobiology, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| |
Collapse
|
26
|
The thanatotranscriptome: Gene expression of male reproductive organs after death. Gene 2018; 675:191-196. [PMID: 30180965 DOI: 10.1016/j.gene.2018.06.090] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 11/23/2022]
Abstract
The prostate gland is one of the last internal organs to deteriorate during human decomposition; however, this phenomenon is still mysterious. Gene expression in antemortem cases has been widely studied and a majority of the analyses concentrate on discovering basic physiological processes. The question of "What happens to gene expression after a human dies?" is a novel and emerging topic. Thanatotranscriptome (thanatos-, Greek for death) involves research on mRNA transcript abundances and gene expression in human tissues after death. Our previous studies have shown that RNA is a suitable and stable molecule in postmortem liver samples up to two days. Consequently, we hypothesized that there are also measurable and significant differences in mRNA transcript abundances in prostate tissues from human remains. In the current study, the goal was to identify apoptotic molecular markers (i.e., pro- and/or anti-apoptosis genes) that provide accurate gene expression profiles regarding the time of death. Tissue samples were removed by a medical examiner from the prostate of five cadavers during autopsy. After RNA extraction, cDNA was synthesized and the concentration was determined. The cDNA was reacted in apoptosis-related gene expression profiling by human PCR Array. The PCR Array results showed that at 38 h after death, a majority of the genes for apoptosis induction and positive regulation (i.e., caspases) were over-expressed more than at five days. The expression of anti-apoptotic genes such as BAG1, BCL2, and negative regulator of apoptosis, XIAP, was significantly elevated in a time-dependent manner. However, pro-apoptotic gene expression such as TP53 and TNFSF10 was not significantly upregulated. Therefore, postmortem prostate cells counteract programmed cell death with its anti-apoptotic machinery; yet as time progresses, pro-apoptotic mechanisms dominate. In conclusion, our study implies that over-expression of genes in male reproductive organs still occurs during decomposition, which may play substantial roles in forensic research and clinical application. These findings demonstrate that there is still active postmortem gene expression; however, our future research question will be, "When does gene expression terminate after death?"
Collapse
|
27
|
|
28
|
Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R. The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Nat Commun 2018; 9:490. [PMID: 29440659 PMCID: PMC5811508 DOI: 10.1038/s41467-017-02772-x] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 12/22/2017] [Indexed: 12/05/2022] Open
Abstract
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues. RNA levels in post-mortem tissue can differ greatly from those before death. Studying the effect of post-mortem interval on the transcriptome in 36 human tissues, Ferreira et al. find that the response to death is largely tissue-specific and develop a model to predict time since death based on RNA data.
Collapse
Affiliation(s)
- Pedro G Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal. .,Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-625, Portugal.
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain.,Departament d'Estadística i Investigació Operativa, Universitat Politècnica de Catalunya, Barcelona, E-08034, Catalonia, Spain
| | - Ferran Reverter
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain.,Universitat de Barcelona, Barcelona, E-08028, Catalonia, Spain
| | - Caio P Sá Godinho
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-902, Brazil
| | - Abel Sousa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-625, Portugal.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, CB10 1 SD, UK
| | - Alicia Amadoz
- Department of Bioinformatics, Igenomix S.A, Valencia, 46980, Spain
| | - Reza Sodaei
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - Marta R Hidalgo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
| | - Dmitri Pervouchine
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain.,Skolkovo Institute of Science and Technology, 100 Novaya Street, Skolkovo, Moscow Region, 143025, Russia
| | - Jose Carbonell-Caballero
- Chromatin and Gene expression Lab, Gene Regulation, Stem Cells and Cancer Program, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, PRBB, Barcelona, 08003, Spain
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - Alessandra Breschi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - Raziel Amador
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - Patrícia Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-625, Portugal
| | - Cankut Çubuk
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
| | - João Curado
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Carla Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-625, Portugal
| | - Joaquin Dopazo
- Department of Bioinformatics, Igenomix S.A, Valencia, 46980, Spain.,Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain.,Functional Genomics Node (INB), FPS, Hospital Virgen del Rocio, Sevilla, 41013, Spain.,Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Sevilla, 41013, Spain
| | - Michael Sammeth
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-902, Brazil
| | - Kristin G Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003, Catalonia, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Catalonia, Spain. .,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, E-08003, Catalonia, Spain.
| |
Collapse
|
29
|
Elghamry HA, Mohamed MI, Hassan FM, Abdelfattah DS, Abdelaal AG. Potential use of GAPDH m-RNA in estimating PMI in brain tissue of albino rats at different environmental conditions. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2017. [DOI: 10.1186/s41935-017-0024-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
|
30
|
Butzelaar L, Niessen FB, Talhout W, Schooneman DPM, Ulrich MM, Beelen RHJ, Mink van der Molen AB. Different properties of skin of different body sites: The root of keloid formation? Wound Repair Regen 2017; 25:758-766. [PMID: 28846161 DOI: 10.1111/wrr.12574] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/03/2017] [Indexed: 01/24/2023]
Abstract
The purpose of this study was to examine extracellular matrix composition, vascularization, and immune cell population of skin sites prone to keloid formation. Keloids remain a complex problem, posing esthetical as well as functional difficulties for those affected. These scars tend to develop at anatomic sites of preference. Mechanical properties of skin vary with anatomic location and depend largely on extracellular matrix composition. These differences in extracellular matrix composition, but also vascularization and resident immune cell populations might play a role in the mechanism of keloid formation. To examine this hypothesis, skin samples of several anatomic locations were taken from 24 human donors within zero to 36 hours after they had deceased. Collagen content and cross-links were determined through high-performance liquid chromatography. The expression of several genes, involved in extracellular matrix production and degradation, was measured by means of real-time PCR. (Immuno)histochemistry was performed to detect fibroblasts, collagen, elastin, blood vessels, Langerhans cells, and macrophages. Properties of skin of keloid predilections sites were compared to properties of skin from other locations (nonpredilection sites [NPS]). The results indicated that there are site specific variations in extracellular matrix properties (collagen and cross-links) as well as macrophage numbers. Moreover, predilection sites (PS) for keloid formation contain larger amounts of collagen compared to NPS, but decreased numbers of macrophages, in particular classically activated CD40 positive macrophages. In conclusion, the altered (histological, protein, and genetic) properties of skin of keloid PS may cause a predisposition for and contribute to keloid formation.
Collapse
Affiliation(s)
- Liselotte Butzelaar
- Department of Plastic, Reconstructive and Hand Surgery, VU University Medical Center, Amsterdam, The Netherlands
| | - Frank B Niessen
- Department of Plastic, Reconstructive and Hand Surgery, VU University Medical Center, Amsterdam, The Netherlands
| | - Wendy Talhout
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | - Dennis P M Schooneman
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | - Magda M Ulrich
- Department of Plastic, Reconstructive and Hand Surgery, VU University Medical Center, Amsterdam, The Netherlands.,Association of Dutch Burn Centers, Beverwijk, The Netherlands
| | - Robert H J Beelen
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | | |
Collapse
|
31
|
Reiman M, Laan M, Rull K, Sõber S. Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples. FASEB J 2017; 31:3298-3308. [PMID: 28446590 DOI: 10.1096/fj.201601031rr] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 04/05/2017] [Indexed: 01/10/2023]
Abstract
RNA degradation is a ubiquitous process that occurs in living and dead cells, as well as during handling and storage of extracted RNA. Reduced RNA quality caused by degradation is an established source of uncertainty for all RNA-based gene expression quantification techniques. RNA sequencing is an increasingly preferred method for transcriptome analyses, and dependence of its results on input RNA integrity is of significant practical importance. This study aimed to characterize the effects of varying input RNA integrity [estimated as RNA integrity number (RIN)] on transcript level estimates and delineate the characteristic differences between transcripts that differ in degradation rate. The study used ribodepleted total RNA sequencing data from a real-life clinically collected set (n = 32) of human solid tissue (placenta) samples. RIN-dependent alterations in gene expression profiles were quantified by using DESeq2 software. Our results indicate that small differences in RNA integrity affect gene expression quantification by introducing a moderate and pervasive bias in expression level estimates that significantly affected 8.1% of studied genes. The rapidly degrading transcript pool was enriched in pseudogenes, short noncoding RNAs, and transcripts with extended 3' untranslated regions. Typical slowly degrading transcripts (median length, 2389 nt) represented protein coding genes with 4-10 exons and high guanine-cytosine content.-Reiman, M., Laan, M., Rull, K., Sõber, S. Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples.
Collapse
Affiliation(s)
- Mario Reiman
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristiina Rull
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia.,Women's Clinic of Tartu University Hospital, Tartu, Estonia
| | - Siim Sõber
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; .,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| |
Collapse
|
32
|
DNA and RNA profiling of excavated human remains with varying postmortem intervals. Int J Legal Med 2016; 130:1471-1480. [PMID: 27627902 DOI: 10.1007/s00414-016-1438-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/09/2016] [Indexed: 01/03/2023]
Abstract
When postmortem intervals (PMIs) increase such as with longer burial times, human remains suffer increasingly from the taphonomic effects of decomposition processes such as autolysis and putrefaction. In this study, various DNA analysis techniques and a messenger RNA (mRNA) profiling method were applied to examine for trends in nucleic acid degradation and the postmortem interval. The DNA analysis techniques include highly sensitive DNA quantitation (with and without degradation index), standard and low template STR profiling, insertion and null alleles (INNUL) of retrotransposable elements typing and mitochondrial DNA profiling. The used mRNA profiling system targets genes with tissue specific expression for seven human organs as reported by Lindenbergh et al. (Int J Legal Med 127:891-900, 27) and has been applied to forensic evidentiary traces but not to excavated tissues. The techniques were applied to a total of 81 brain, lung, liver, skeletal muscle, heart, kidney and skin samples obtained from 19 excavated graves with burial times ranging from 4 to 42 years. Results show that brain and heart are the organs in which both DNA and RNA remain remarkably stable, notwithstanding long PMIs. The other organ tissues either show poor overall profiling results or vary for DNA and RNA profiling success, with sometimes DNA and other times RNA profiling being more successful. No straightforward relations were observed between nucleic acid profiling results and the PMI. This study shows that not only DNA but also RNA molecules can be remarkably stable and used for profiling of long-buried human remains, which corroborate forensic applications. The insight that the brain and heart tissues tend to provide the best profiling results may change sampling policies in identification cases of degrading cadavers.
Collapse
|
33
|
A 17-month time course study of human RNA and DNA degradation in body fluids under dry and humid environmental conditions. Int J Legal Med 2016; 130:1431-1438. [DOI: 10.1007/s00414-016-1373-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/29/2016] [Indexed: 12/20/2022]
|
34
|
Raffort J, Lareyre F, Clement M, Mallat Z. Micro-RNAs in abdominal aortic aneurysms: insights from animal models and relevance to human disease. Cardiovasc Res 2016; 110:165-77. [PMID: 26965051 DOI: 10.1093/cvr/cvw046] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/28/2016] [Indexed: 01/09/2023] Open
Abstract
Abdominal aortic aneurysm (AAA) is a major health concern and may be associated with high rates of mortality linked to acute complications. Diagnosis and treatment are, respectively, based on imaging and surgical techniques. Drug-based therapies are still mostly ineffective, which highlight a real unmet need. Major pathophysiological mechanisms leading to aneurysm formation involve inflammatory processes, degradation of the extracellular matrix, and loss of smooth muscle cells. However, the precise cellular and molecular pathways are still poorly understood. Recently, microRNAs have emerged as major intracellular players in a wide range of biological processes, and their stability in extracellular medium within microvesicles has led to propose them as mediators of intercellular crosstalk and as potential biomarkers and therapeutic targets in a variety of disease settings. To date, several studies have been performed to address the involvement of micro-RNAs (miRs) in aneurysm formation and complications. Here, we discuss the roles and implications of miRs in animal models and their relevance to human AAA.
Collapse
Affiliation(s)
- Juliette Raffort
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge CB20 SZ, UK University of Nice-Sophia Antipolis, Medical School, Nice 06107, France INSERM U1081, CNRS UMR7284, IRCAN, Nice, France Clinical Chemistry Laboratory, University Hospital of Nice, Nice, France
| | - Fabien Lareyre
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge CB20 SZ, UK University of Nice-Sophia Antipolis, Medical School, Nice 06107, France INSERM U1081, CNRS UMR7284, IRCAN, Nice, France Department of Vascular Surgery, University Hospital of Nice, Nice, France
| | - Marc Clement
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge CB20 SZ, UK
| | - Ziad Mallat
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge CB20 SZ, UK Institut National de la Santé et de la Recherche Médicale (Inserm), Unit 970, Paris Cardiovascular Research Center, Paris 75015, France
| |
Collapse
|
35
|
Palladino R, Cigliero SS, Bonin S, Pitacco P, Nicolin V, Previderè C, Vatta P, Marrubini G, Fattorini P. Reliability of RT-qPCR from degraded RNA samples: An in vitro model. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
36
|
Poór VS, Lukács D, Nagy T, Rácz E, Sipos K. The rate of RNA degradation in human dental pulp reveals post-mortem interval. Int J Legal Med 2015; 130:615-9. [PMID: 26608472 DOI: 10.1007/s00414-015-1295-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/17/2015] [Indexed: 01/29/2023]
Abstract
Post-mortem interval (PMI) is the amount of time elapsed since the time of death. Over the years, many methods were developed to assess PMI, but their precision and time frame of applicability are often limited. Our present pilot study aimed to prove if RNA degradation of human dental pulp can be used for PMI estimation. RNA was isolated from the pulps of healthy wisdom teeth and premolars. RNA degradation was determined as RNA integrity number (RIN) with Agilent Bioanalyzer and subsequently by amplification of different length products by PCR after reverse transcription. The RNA integrity analysis allowed us to determine the time of post-mortem interval with high confidence level in the first 21 days. With the PCR-based method, we were able to perform a crude estimation of incubation time of teeth between 20 and 42 days post extraction. These results show that this method might be a promising new tool for PMI estimation despite the limitations.
Collapse
Affiliation(s)
- Viktor S Poór
- Department of Forensic Medicine, Faculty of Medicine, University of Pécs, Hungary Szigeti Street 12, Pécs, Hungary
| | - Dénes Lukács
- Dentoalveolar Division of Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Pécs, Dischka Győző Street 5, Pécs, Hungary
| | - Tamás Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Pécs, Ifjúság Street 13, Pécs, Hungary
| | - Evelin Rácz
- Department of Forensic Medicine, Faculty of Medicine, University of Pécs, Hungary Szigeti Street 12, Pécs, Hungary
| | - Katalin Sipos
- Department of Forensic Medicine, Faculty of Medicine, University of Pécs, Hungary Szigeti Street 12, Pécs, Hungary.
| |
Collapse
|
37
|
Comparative analysis of microRNA expression in mouse and human brown adipose tissue. BMC Genomics 2015; 16:820. [PMID: 26482036 PMCID: PMC4617708 DOI: 10.1186/s12864-015-2045-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 10/09/2015] [Indexed: 11/26/2022] Open
Abstract
Background In small mammals brown adipose tissue (BAT) plays a predominant role in regulating energy expenditure (EE) via adaptive thermogenesis. New-born babies require BAT to control their body temperature, however its relevance in adults has been questioned. Active BAT has recently been observed in adult humans, albeit in much lower relative quantities than small mammals. Comparing and contrasting the molecular mechanisms controlling BAT growth and development in mice and humans will increase our understanding or how human BAT is developed and may identify potential therapeutic targets to increase EE. MicroRNAs are molecular mechanisms involved in mouse BAT development however, little is known about the miRNA profile in human BAT. The aims of this study were to establish a mouse BAT-enriched miRNA profile and compare this with miRNAs measured in human BAT. To achieve this we firstly established a mouse BAT enriched-miRNA profile by comparing miRNAs expressed in mouse BAT, white adipose tissue and skeletal muscle. Following this the BAT-enriched miRNAs predicted to target genes potentially involved in growth and development were identified. Methods MiRNA levels were measured using PCR-based miRNA arrays. Results were analysed using ExpressionSuite software with the global mean expression value of all expressed miRNAs in a givensample used as the normalisation factor. Bio-informatic analyses was used to predict gene targets followed by Ingenuity Pathway Analysis. Results We identified 35 mouse BAT-enriched miRNAs that were predicted to target genes potentially involved in growth and development. We also identified 145 miRNAs expressed in both mouse and human BAT, of which 25 were enriched in mouse BAT. Of these 25 miRNAs, miR-20a was predicted to target MYF5 and PPARγ, two important genes involved in brown adipogenesis, as well as BMP2 and BMPR2, genes involved in white adipogenesis. For the first time, 69 miRNAs were identified in human BAT but absent in mouse BAT, and 181 miRNAs were expressed in mouse but not in human BAT. Conclusion The present study has identified a small sub-set of miRNAs common to both mouse and human BAT. From this sub-set bioinformatics analysis suggested a potential role of miR-20a in the control of cell fate and this warrants further investigation. The large number of miRNAs found only in mouse BAT or only in human BAT highlights the differing molecular profile between species that is likely to influence the functional role of BAT across species. Nevertheless the BAT-enriched miRNA profiles established in the present study suggest targets to investigate in the control BAT development and EE. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2045-8) contains supplementary material, which is available to authorized users.
Collapse
|
38
|
Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses. ISME JOURNAL 2015; 10:678-92. [PMID: 26394007 PMCID: PMC4817681 DOI: 10.1038/ismej.2015.145] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/29/2015] [Accepted: 07/05/2015] [Indexed: 01/15/2023]
Abstract
To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5′-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no 15NH4+ assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. 15N2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, 15N2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced 15N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations.
Collapse
|
39
|
Javan GT, Can I, Finley SJ, Soni S. The apoptotic thanatotranscriptome associated with the liver of cadavers. Forensic Sci Med Pathol 2015; 11:509-16. [PMID: 26318598 DOI: 10.1007/s12024-015-9704-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2015] [Indexed: 01/08/2023]
Abstract
Gene expression investigations are well-established components of ante mortem studies with broad applications ranging from elucidating basic mechanisms responsible for normal physiological processes to discovering therapeutic targets in pathophysiological conditions. However, gene expression studies and their application in the medico-legal field are still in their infancy. Therefore, the present study focuses on RNA using PCR array in the analysis of gene expression associated with tissues taken from actual criminal cases. RNA was extracted from the liver tissues of bodies with PMIs between 6 and 48 h. The results demonstrated that mRNA was stable up to 48 h postmortem. Further, as cell death is an indispensable and necessary part of the biological life cycle, apoptotic gene expression profiles were investigated. The gene expression related to the programmed cell death found in body tissues after death is defined as the apoptotic thanatotranscriptome (thanatos-, Greek for death). On comparison of control and decaying tissues, the results show that with time, pro-apoptotic genes such as caspases are up-regulated and the expression of genes responsible for anti-apoptosis such as BCL2 and BAG3 were down-regulated. Thus, this current work gives a unique perspective of the apoptotic thanatotranscriptome that is affected after death. Up to the present time, gene expression in bodies from criminal cases has not been reported in literature using PCR array techniques. Thus, this thanatotranscriptome study provides insight into postmortem gene activity with potential applications in medico-legal investigations.
Collapse
Affiliation(s)
- Gulnaz T Javan
- Forensic Science Program, Alabama State University, Montgomery, AL, 36104, USA.
| | - Ismail Can
- Forensic Science Program, Alabama State University, Montgomery, AL, 36104, USA.
| | | | - Shivani Soni
- Department of Biological Sciences, Alabama State University, Montgomery, AL, 36101, USA.
| |
Collapse
|
40
|
Sidova M, Tomankova S, Abaffy P, Kubista M, Sindelka R. Effects of post-mortem and physical degradation on RNA integrity and quality. BIOMOLECULAR DETECTION AND QUANTIFICATION 2015; 5:3-9. [PMID: 27077037 PMCID: PMC4822212 DOI: 10.1016/j.bdq.2015.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 01/06/2023]
Abstract
The precision and reliability of quantitative nucleic acid analysis depends on the quality of the sample analyzed and the integrity of the nucleic acids. The integrity of RNA is currently primarily assessed by the analysis of ribosomal RNA, which is the by far dominant species. The extrapolation of these results to mRNAs and microRNAs, which are structurally quite different, is questionable. Here we show that ribosomal and some nucleolar and mitochondrial RNAs, are highly resistant to naturally occurring post-mortem degradation, while mRNAs, although showing substantial internal variability, are generally much more prone to nucleolytic degradation. In contrast, all types of RNA show the same sensitivity to heat. Using qPCR assays targeting different regions of mRNA molecules, we find no support for 5' or 3' preferentiality upon post-mortem degradation.
Collapse
Affiliation(s)
- Monika Sidova
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic
- Charles University in Prague, Faculty of Science, Department of Cell Biology, Vinicna 7, 128 43, Prague, Czech Republic
| | - Silvie Tomankova
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic
| | - Pavel Abaffy
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic
- TATAA Biocenter AB, Odinsgatan 28, 411 03 Göteborg, Sweden
| | - Radek Sindelka
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic
- Corresponding author. Fax: +420 241 063 610.
| |
Collapse
|
41
|
Allaby RG, Gutaker R, Clarke AC, Pearson N, Ware R, Palmer SA, Kitchen JL, Smith O. Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130377. [PMID: 25487329 PMCID: PMC4275885 DOI: 10.1098/rstb.2013.0377] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.
Collapse
Affiliation(s)
- Robin G Allaby
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Rafal Gutaker
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Andrew C Clarke
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Neil Pearson
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Roselyn Ware
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Sarah A Palmer
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - James L Kitchen
- Rothamsted Research Station, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Oliver Smith
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| |
Collapse
|
42
|
Tappe D, Alquezar-Planas DE. Medical and molecular perspectives into a forgotten epidemic: encephalitis lethargica, viruses, and high-throughput sequencing. J Clin Virol 2014; 61:189-95. [PMID: 25129855 DOI: 10.1016/j.jcv.2014.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 01/06/2023]
Abstract
The emergence of encephalitis lethargica (EL), an acute-onset polioencephalitis of unknown etiology as an epidemic in the years 1917-1925 is still unexplainable today. Questioned by the first descriptor of EL himself, Constantin von Economo, there has been much debate shrouding a possible role of the "Spanish" H1N1 influenza A pandemic virus in the development of EL. Previous molecular studies employing conventional PCR for the detection of influenza A virus RNA in archived human brain samples from patients who died of acute EL were negative. However, the clinical and laboratory characteristics of EL and its epidemiology are consistent with an infectious disease, and recently a possible enterovirus cause was investigated. With the rapid development of high-throughput sequencing, new information about a possible viral etiology can be obtained if sufficient specimens for analysis were still available today. Here, we discuss the implications of these technologies for the investigation of a possible infectious cause of EL from archived material, as well as a prospectus for future work for acquiring viral nucleic acids from these sources.
Collapse
Affiliation(s)
- Dennis Tappe
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark.
| |
Collapse
|
43
|
Smith O, Clapham A, Rose P, Liu Y, Wang J, Allaby RG. A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Sci Rep 2014; 4:4003. [PMID: 24499968 PMCID: PMC3915304 DOI: 10.1038/srep04003] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/20/2014] [Indexed: 01/12/2023] Open
Abstract
The origins of many plant diseases appear to be recent and associated with the rise of domestication, the spread of agriculture or recent global movements of crops. Distinguishing between these possibilities is problematic because of the difficulty of determining rates of molecular evolution over short time frames. Heterochronous approaches using recent and historical samples show that plant viruses exhibit highly variable and often rapid rates of molecular evolution. The accuracy of estimated evolution rates and age of origin can be greatly improved with the inclusion of older molecular data from archaeological material. Here we present the first reconstruction of an archaeological RNA genome, which is of Barley Stripe Mosaic Virus (BSMV) isolated from barley grain ~750 years of age. Phylogenetic analysis of BSMV that includes this genome indicates the divergence of BSMV and its closest relative prior to this time, most likely around 2000 years ago. However, exclusion of the archaeological data results in an apparently much more recent origin of the virus that postdates even the archaeological sample. We conclude that this viral lineage originated in the Near East or North Africa, and spread to North America and East Asia with their hosts along historical trade routes.
Collapse
Affiliation(s)
- Oliver Smith
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL
| | - Alan Clapham
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL
| | - Pam Rose
- The Austrian Archaeological Institute; Cairo Branch, Zamalek, Sharia Ismail Muhammed, Apt 62/72, Cairo, Egypt
| | - Yuan Liu
- BGI-Europe-UK, 9 Devonshire Square, London, EC2M 4YF, UK
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Robin G Allaby
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL
| |
Collapse
|