Barcoding for diatoms in the Yangtze River from the morphological observation and 18S rDNA polymorphic analysis

Optical microscopy is suitable for numerous applications ranging from various fields of research such as mineralogy, entomology, botany, medicine, surgery, and various sectors of industrial production. As far as forensic applications are concerned, it maintains a prominent position as an important tool for the examination of the evidence. Actually, optical microscopy has always been a key application in judicial investigations and, until the early 1900s, it has been the forensic scientists’ main tool. At present, although highly advanced analytical techniques support forensic scientists for characterizing and identifying traces linked to a particular offence, optical microscopy continues to play an important role, especially in the early stages of laboratory investigation. Optical microscopy can provide direct information when there are comparative materials associated with suspects, or indirect information when compared with databases dedicated to forensic science applications. The most used optical microscopy tools for forensic purposes on a wide range of materials are the stereoscopic microscope and the polarized light microscope (PLM).

First record of Teleogryllus (Brachyteleogryllus) marini Otte & Alexander, 1983 (Orthoptera: Gryllidae) in korea and discussion of its continued misidentification using DNA barcoding

Context: Visceral congestion is a characteristic autopsy finding of some causes of death, and the congestion changes the organ weight. Therefore, comparing the measured organ weights against standards can provide useful information. Aim: We sought to generate accurate organ weight standards according to the postmortem interval (PMI) and the cause of death, with particular focus on brain and lung weights. Settings and Design: Retrospective study. Cadavers and Methods: We included data from 489 (320 males and 169 females) forensic autopsy cases with known PMIs; within 4 days. We considered gender, age, height, body weight and PMI in our organ weight estimations. In addition, we used longitudinal (243 males and 131 females) and transverse (243 males and 130 females) skull diameters in constructing an equation for brain weight estimation. Statistical Analysis Used: Chi-square test, Welch's t-test and stepwise regression analysis. Results: Causes of death such as intracranial injury and bleeding, intoxication and drowning tended to increase lung weight; other causes tended to decrease lung weight. When we focused on cases with 1-day PMI, the brain and lung weights increased with longer PMIs, probably due to the brain oedema and pulmonary congestion and oedema in the early post-mortem period. Conclusion: Ours was the first report on the increase of brain weight with the increase of PMI in the early postmortem period. Further studies on the effects of PMI and the cause of death on organ weight are required to expand our understanding on the mechanisms of death.

Eighteen strains of diatoms isolated from different phytoplankton and microphytobenthic assemblages in the Gulf of Gdańsk (Baltic Sea, Poland) and maintained at the Culture Collection of Baltic Algae (CCBA) were investigated for their species identifications. The latter were tested by phylogenetic analyses of nearly full 18S rDNA sequences as well as through sequence comparisons of 5.8S+ITS2 rDNA fragments for use as DNA barcode. The planktonic species were readily identified as a member of the Cyclotella meneghiniana species complex and Skeletonema marinoi, respectively, by both 18S phylogenies and DNA barcoding. In contrast, for the pennate diatom strains the suitability of DNA sequence comparisons for species identification appeared to be still rather limited. Only one strain could be identified to the species level (Navicula gregaria) using DNA barcodes, and no closest relative barcode sequences were available for the other strains. The 18S rDNA phylogenies supported species identification for only one strain (Bacillaria cf. paxillifera). In all other pennate strains identification was only possible to the genus level. Because for most species identified by morphology no closest neighbouring 18S rDNA sequences were available, the CCBA strains may serve as references to represent certain species which have been well characterized by morphology, 18S rDNA sequence analyses and DNA barcodes. Relatively high 18S rDNA differences between pairs of strains of Fistulifera saprophila and Navicula perminuta indicated that each species may represent a complex of several cryptic species. In contrast, the five isolates of Nitzschia microcephala had identical sequences as well as the two isolates of Nitzschia cf. fonticola. With the addition of new species to the 18S rDNA phylogeny of pennate raphid diatoms, the monophyly of the genera Fistulifera, Haslea and Navicula s.str. were confirmed, while Nitzschia appeared paraphyletic. The traditional family Naviculaceae was paraphyletic, in agreement with previous phylogenetic studies.

Proteomic Signatures: A review on forensic bone proteomics and estimation of post-mortem interval

Forensic entomology has become an indispensable tool for estimating the postmortem interval (PMI), particularly in advanced stages of decomposition where classical forensic methods are limited. Reliable PMI estimation requires accurate and precise identification of insect evidence. Traditional morphological approaches often fail when dealing with immature stages (eggs, larvae, pupae), closely related species, or partially damaged specimens. To overcome these limitations, DNA barcoding has been increasingly integrated into forensic entomology over the past two decades. DNA barcoding typically relies on sequencing a standardized fragment of the mitochondrial cytochrome c oxidase I (COI) gene and comparing the obtained sequence with reference databases such as BOLD and GenBank to assign species identity. In this review, we summarize the theoretical basis of DNA barcoding in forensic entomology, the genetic markers employed, and the main steps of sampling, DNA extraction, PCR amplification, and sequence analysis. We present application examples from Diptera and Coleoptera, and discuss how DNA barcoding contributes to PMI estimation and case reconstruction. Furthermore, we address recent developments such as mini-barcode strategies, Next Generation Sequencing (NGS)/metabarcoding approaches, multi-locus barcoding, and highlight key limitations including database gaps, the barcode gap concept, contamination, and NUMTs. We also evaluate the current situation in Türkiye and propose the establishment of a national barcode reference library for forensically relevant insect taxa. Overall, DNA barcoding emerges as a powerful molecular tool that complements rather than replaces morphology, thereby improving the reliability of species identification and PMI estimations in forensic casework.

DNA barcoding has become a promising tool for rapid species identification using a short fragment of mitochondrial gene. Currently, an increasing number of analytical methods are available to assign DNA barcodes to taxa. The methods can be broadly divided into three main categories: (i) distance-based methods (the classical approach and the automatic barcode gap discovery (ABGD) approach), (ii) coalescent-based methods (the monophyly-based method and the general mixed Yule coalescent (GMYC) model) and (iii) the character-based method (CAOS). This study is set out to evaluate the availability of each method in barcoding Tellinoidea on the cytomchrome c oxidase subunit I (COI) and the 16 small-subunit ribosomal DNA (16S rDNA) genes. As a result, the character-based method was found to be the best in all cases, especially on a genus level. For distance-based methods, the elaborate one gained a success equal or greater than the basic one. The traditional coalescent-based method nicely delimited all of the tellinoideans on a species level. The GMYC model, which is the most radical, clearly inflated the number of species units by 34.6 % for COI gene and by 58.8 % for 16S gene. Thus, we conclude that CAOS better approximates a real barcode, and suggest the use of the ABGD method and the monophyly-based method for primary partitions. Additionally, COI gene may be more suitable as a standard barcode marker than 16S gene, particularly for tree-based methods.

According to the classification system used, 15-60% of stillbirths remain unexplained, despite undergoing recommended autopsy examination, with variable attribution of fetal growth restriction (FGR) as a cause of death. Distinguishing small-for-gestational age (SGA) from pathological FGR is a challenge at postmortem examination. This study uses data from a large, well-characterized series of intrauterine death autopsies to investigate the effects of secondary changes such as fetal maceration, intrauterine retention and postmortem interval on body weight. Autopsy findings from intrauterine death investigations (2005-2013 inclusive, from Great Ormond Street Hospital and St George's Hospital, London) were collated into a research database. Growth charts published by the World Health Organization were used to determine normal expected weight centiles for fetuses born ≥ 24 weeks' gestation, and the effects of intrauterine retention (maceration) and postmortem interval were calculated. There were 1064 intrauterine deaths, including 533 stillbirths ≥ 24 weeks' gestation with a recorded birth weight. Of these, 192 (36%) had an unadjusted birth weight below the 10th centile and were defined as SGA. The majority (86%) of stillborn SGA fetuses demonstrated some degree of maceration, indicating a significant period of intrauterine retention after death. A significantly greater proportion of macerated fetuses were present in the SGA population compared with the non-SGA population (P = 0.01). There was a significant relationship between increasing intrauterine retention interval and both more severe maceration and reduction in birth weight (P < 0.0001 for both), with an average artifactual reduction in birth weight of around -0.8 SD of expected weight. There was an average 12% reduction in fetal weight between delivery and autopsy and, as postmortem interval increased, fetal weight loss increased (P = 0.0001). Based on birth weight alone, 36% of stillbirths are classified as SGA. However, fetuses lose weight in utero with increasing intrauterine retention and continue to lose weight between delivery and autopsy, resulting in erroneous overestimation of FGR. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.

Identification of the exact cause and time of death are important questions that have to be answered by the forensic pathologist. Traumatic cardiac injuries is a leading cause of death. This work aimed at using cardiac troponin C (cTnC) expression to differentiate between different types of cardiac injuries at different postmortem intervals (PMI). This study was performed on 90 forensic autopsies selected in the Medicolegal Department of Ministry of Justice. The cases were divided equally into 5 groups of different causes of death i.e. non-cardiac causes of death (control group), blunt cardiac injury (BCI), civilian cardiac firearm injury, civilian stab injury and sudden cardiac death (SCD). Brown Immunohistochemical expression of TnC was observed in all groups, where the non-cardiac death, blunt injury and firearm injury groups showed less immunohistochemical staining than stab injury and SCD. The density of the cTnC immunohistochemical staining increased by the increase in the PMI. Quantitative morphometric measurement of cTnC immunohistochemical expression was measured. Significant increases in the mean surface area of cTnC immunohistochemical expression were detected in the groups of only stab injury and SCD compared to the other studied groups (p<0.001), while non-significant differences were detected between non-cardiac, BCI and civilian cardiac firearm injury groups. Besides, the mean surface area of cTnC immunohistochemical expression increased significantly by the increase in the postmortem interval. These findings suggest that the mean surface area of cTnC immunohistochemical expression can differentiate between cardiac and non-cardiac deaths, and between the different types of cardiac deaths.

Psocids are serious storage pests, and their control is hampered by the fact that different species respond differently to insecticides used for the control of stored-product insect pests. Additionally, psocids of genus Liposcelis that are commonly associated with stored-products are difficult to identify using morphological characteristics. The goal of this study was to validate molecular identification of stored-product psocids of genus Liposcelis based on 16S rDNA and cytochrome oxidase I (COI) DNA barcoding. Unidentified liposcelids (Liposcelis DK) imported from Denmark to China were compared with 14 population samples of seven common species (L. bostrychophila, L. brunnea, L. corrodens, L. decolor, L. entomophila, L. mendax, and L. paeta). The explored species (DK) liposcelids shared >98% sequence similarity for both the 16S rDNA and COI genes with the reference L. corrodens samples (98.32 and 98.94% for 16S rDNA and COI, respectively). A neighbor-joining tree revealed that the explored DK sample and the reference L. corrodens samples belong to the same clade. These molecular results were verified by morphological identification of DK specimens, facilitated by SEM microphotography. The DNA barcoding method and the neighbor-joining phylogenetic analyses indicated that both the 16S rDNA and COI genes were suitable for Liposcelis species identification. DNA barcoding has great potential for use in fast and accurate liposcelid identification.

Carangidae family has got about 148 species belonging to 32 genera. In Vietnam, Carangidae is of high commercial value and playing an important role in the ecosystem. In the context Vietnam has received yellow card for seafood since Nov. 2017 by the EU, in which one of the main reasons was related to the restriction of traceability. In this study, DNA barcoding technique of mitochondrial cytochrome oxidase I (COI) gene was used to classify 56 specimens of Carangidae from three coastal areas (Northern, Central and Southern) in Vietnam to evaluate the effectiveness compared to the morphological classification method. Results showed that 21 species belonging to 16 genera were determined by the COI barcode while 18 species (16 genera) were determined when using morphological method. Seriola quinqueradiata and Trachinotus anak were newly recorded in Vietnam. From 56 sequences with 660 bp of mtDNA (COI), total 27 haplotypes were detected; haplotype diversity (h) and nucleotide diversity (π) were 0.903 ± 0.00060 and 0.14%, respectively. The DNA barcodes of COI gene of 21 species in Carangidae which were developed in this study could be used as a basis for comparison and traceability of their products. In addition, the results showed the high potentiality in using COI barcode to identify Carangidae fish in Vietnam.

Histological transformations of the dental pulp as possible indicator of post mortem interval: a pilot study

DNA barcoding vs. morphological identification of larval fish and embryos in Lake Huron: Advantages to a molecular approach

Current research involving studies of the effects of drugs on fly’s development has also allowed better estimations of Postmortem Intervals (PMI) or cause of death. Insects’ specimen collected from decomposing or decomposed bodies enable forensic entomologists to estimate the minimum Post-Mortem Interval (PMI) or cause of death. Drugs within a corpse may affect the development rate of insects that feed on them. This study consequently points out the possibilities of analyzing insects, larvae and pupae or empty pupa cases when suitable tissues or other source of information’s are absent. This study investigated the effects of commonly abused drugs on growth rates of insects. These results can be used by the forensic entomologist in forensic entomology for the postmortem interval (PMI) estimation or cause of death of decomposed bodies or tissues in medico criminal investigations.

Determining the time of death by morphological and immunohistochemical evaluation of collagen fibers in postmortem gingival tissues.