Simple detection of bacterioplankton using a loop-mediated isothermal amplification (LAMP) assay: First practical approach to 72 cases of suspected drowning

Stepping towards pollen DNA metabarcoding: A breakthrough in forensic sciences

This review is engaged in determining the capability of plant pollen as a significant source of evidence for the linkage between suspects and crime location in forensic sciences. Research and review articles were collected from Google Scholar, the Web of Science, and PubMed. Articles were searched using specific keywords such as "Forensic Palynology," "Pollen metabarcoding," "Plant forensics," and "Pollen" AND "criminal investigation." Boolean logic was also utilized to narrow the articles to be included in this review article. Through the literature and exploratory research, it has been observed in the current study that with advancements in technology, forensic palynology has found its application in creating an association between the crime scene and suspected individuals to have a link to it, as pollen DNA is a long-lasting investigative tool that can effectively help forensic investigations. Moreover, the literature shows that the DNA of pollen and spores has helped forensic scientists link suspects to crime scenes, and the introduction of pollen DNA metabarcoding tools has eased the efforts of palynologists to analyze pollen DNA. The introduction of DNA metabarcoding techniques to analyze pollen from plants has helped identify the geological locations of the plants and ultimately identify the culprit.

Conventional diatom testing using strong acid: Notable false-positive results caused by an underestimated contamination source (blind spot)

Low rates of diatom positivity in the closed organs of drowning victims present challenges for diatom testing. High positivity rates in closed organs of non-drowning victims also raise an important issue. These contradictory findings were common in diatom testing studies undertaken during the 1960-80 s, but the reasons remained unclear. In the present study, we identified one of the most important factors associated with false-positive results in diatom testing using strong acid. One to 290 false-positive diatoms were found in reused Kjeldahl flasks that were thoroughly washed after the first diatom testing and kept free of tissue before the second testing. False-positive results occurred in 11 of 20 cases when more than approximately 10,000 diatoms were present in digested tissue or water samples. Reused flasks were found to contain many common diatoms (<30 µm), including Cocconeis, Cymbella, Diatoma, Gomphonema, Navicula, and Nitzschia, in agreement with reports of diatoms identified in closed organs. Surprisingly, such false-positive results occurred even at the sixth diatom testing using the same flasks kept free of tissues in each analysis. In contrast, no diatoms were detected in any reagent or associated with other glassware. Thus, reuse of Kjeldahl flasks can readily cause false-positive results that cannot be completely prevented by cleaning the flasks using alkali detergents, as evidenced by detection of diatoms even after six tests. We assume that diatoms causing false-positive results are partially melted by heating and fixed onto the flask's inner surface glass, as the diatom frustule consists primarily of SiO₂, similar to glass. Adherent diatoms are then released from the glass by re-heating at the next diatom testing. These results also suggest that the number of diatoms remaining in a flask can increase steadily as a result of repeated reuse for analysis of lung or water samples. In contrast, in analyses using only new flasks, only one or two diatoms were found in 4 of 20 kidney, 2 of 12 liver, and 2 of 8 blood samples from 20 drowning victims. It is difficult to determine whether such diatoms are actually carried via the blood circulation, as contamination with a few diatoms can occur during autopsy procedures and diatom testing. In conclusion, only new (unused) Kjeldahl flasks should be used for diatom testing with strong acid digestion. Moreover, these data suggest that the number and frequency of diatoms present in closed organs of drowning victims may be much lower than previously thought.

Determination of a criminal suspect using environmental plant DNA metabarcoding technology

There are criminal cases that no frequently used evidence, for example, human DNAs from the criminal, is available. Such cases usually are unresolvable. With the advent of DNA metabarcoding, evidences are mined from environmental DNA and such cases become resolvable. This study reports how a criminal suspect was determined by environmental plant DNA metabarcoding technology. A girl was killed in a rural wet area in China without a witness or video record. Pants with dried mud was found from one of her classmate's house. The mud was removed from the pants and 11 more mud or soil samples surrounding murder scene were collected. DNA was extracted from the soil. Chloroplast rbcL gene were amplified and sequenced on a next generation sequencing platform. After bioinformatics analysis, ZOTU composition of 12 samples demonstrated that the mud on the suspect's pants was from the criminal scene. The suspect finally made a clean breast of his crime. This case implies that plant DNA in the environment soil is a new source of evidence in determination of suspects using DNA metabarcoding technology and has high potentials of extensive applications in criminal cases.

Development of 18S rRNA gene arrays for forensic detection of diatoms

Diatom test is the most commonly used method to diagnose drowning in forensic laboratories. However, microscopic examination and identification of diatom frustules is time-consuming and requires taxonomic expertise. At present, the identification of drowning is still a challenge in forensic casework. In this study, we developed a novel diatom microarray based on the detection of specific 18S rRNA gene fragments of diatom species. The array covers 169 diatom species which were documented as commonly found in a wide range of fresh waters in China. Diatom arrays were prepared from species specific oligonucleotide probes targeting to variable regions of the 18S rRNA gene. We also developed an auxiliary sample preparation method for isolation of diatom DNA from tissues, which enabled detection of diatom species in real forensic samples as well as environmental waters. We applied the diatom arrays to analyze six drowned cases and eight environmental samples. The diatom arrays showed much better sensitivity and more consistent results than those of the conventional SEM methods. We discovered major discrepancies between results generated by the diatom arrays and the routinely used SEM based diatom tests. We verified the results of our diatom arrays by species specific PCR and Sanger sequencing and found that the currently used SEM diatom test method has a serious deficiency in sensitivity due to high loss rate of frustules in the sample preparation procedure. We anticipate that the application of diatom arrays will transform current forensic practice of diagnosing drowning deaths.

Simple Visualized Detection Method of Virulence-Associated Genes of Vibrio cholerae by Loop-Mediated Isothermal Amplification

Vibrio cholerae is a leading waterborne pathogenic bacterium worldwide. It can cause human cholera that is still pandemic in developing nations. Detection of V. cholerae contamination in drinking water and aquatic products is imperative for assuring food safety. In this study, a simple, sensitive, specific, and visualized method was developed based on loop-mediated isothermal amplification (LAMP) (designated sssvLAMP) to detect virulence-associated (ctxA, tcpA, hapA, mshA, pilA, and tlh) and species-specific (lolB) genes of V. cholerae. Three pairs of oligonucleotide primers (inner, outer, and loop primers) were designed and or synthesized to target each of these genes. The optimal conditions of the sssvLAMP method was determined, and one-step sssvLAMP reaction was performed at 65°C for 40 min. Positive results were simply read by the naked eye via color change (from orange to light green) under the visible light, or by the production of green fluorescence under the UV light (260 nm). The sssvLAMP method was more efficient in detecting 6.50 × 101-6.45 × 104-fold low number of V. cholerae cells, and more sensitive in V. cholerae genomic DNA (1.36 × 10-2-4.42 × 10-6 ng/reaction) than polymerase chain reaction (PCR) method. Among 52 strains of V. cholerae and 50 strains of non-target species (e.g., other Vibrios and common pathogens) examined, the sensitivity and specificity of the sssvLAMP method were 100% for all the target genes. Similar high efficiency of the method was observed when tested with spiked samples of water and aquatic products, as well as human stool specimens. Water from various sources and commonly consumed fish samples were promptly screened by this simple and efficient visualized method and diversified variation in the occurrence of the target genes was observed. V. cholerae strains could be mostly detected by the presence of hapA and tlh alone or in combination with other genes, indicating a variable risk of potentially pathogenic non-O1/O139 strains in edible food products. This novel LAMP method can be a promising tool to address the increasing need of food safety control of aquatic products.