Evaluation of Bacteriophage ϕ11 host recognition protein and its host-binding peptides for diagnosing/targeting of Saphylococcus aureus infections.

Evaluating the potential of using both synthetic and biological products as targeting agents for the diagnosis, imaging, and treatment of infections due to particularly antibiotic-resistant pathogens is important for controlling infections. We examined the interaction between Gp45, a receptor-binding protein of the ϕ11 lysogenic phage, and its host S. aureus, a common cause of nosocomial infections. Using molecular dynamics and docking simulations, we identified the peptides that bind to S. aureus wall teichoic acids via Gp45. We compared the binding affinity of Gp45 and the two highest-scoring peptide sequences (P1 and P3) and their scrambled forms using microscopy, spectroscopy, and ELISA. Our results revealed that rGp45 (recombinant Gp45) and chemically synthesized P1 had a higher binding affinity for S. aureus compared with all other peptides, with the exception of E. coli. Furthermore, rGp45 had a capture efficiency of over 86%; P1 had a capture efficiency of over 64%. Overall, our findings suggest that receptor-binding proteins such as rGp45, which provide a critical initiation of the phage life cycle for host adsorption, might play an important role in the diagnosis, imaging, and targeting of bacterial infections. Studying such proteins could accordingly enable the development of effective strategies for controlling infections.

Time-dependent change in the microbiota structure of seminal stains exposed to indoor environmental.

Seminal stains acquired from fabric surfaces stand as pivotal biological evidence of utmost significance for elucidating sexual assault cases. The ability to determine the temporal aspect of a forensic incident via the analysis of a biological specimen found at the crime scene is crucial in resolving most cases. This study aimed to investigate the time-dependent change in the microbiota structure of human seminal stains exposed to indoor environmental conditions. Stains on polyester fabric generated using semen samples from five male volunteers were kept indoors for varying durations of up to 20 days, followed by sequencing of the V1-V9 regions of the 16S rRNA gene of the microbial DNA extracted from the stains. The acquired data provided the taxonomic composition, and microbial alterations across different days were examined. The most abundantly detected phyla in all samples were Firmicutes, Proteobacteria, and Bacteroidetes, and the relative abundances of bacteria were observed to change over time. Statistically significant changes at the species level were found for Treponema medium, Corynebacterium tuberculostearicum, Faecalibacterium prausnitzii, and Anaerostipes hadrus. Alterations observed in the samples between the analyzed time periods were investigated. The changes during the specified time periods were examined, identifying rare bacterial species that were initially present on certain days but later ceased to exist in the environment. Conversely, bacterial species that were absent before exposure but emerged at a later stage were also identified. The findings of this study demonstrate that species-level evaluations, in particular, can provide crucial insights into semen stain age.

The uselessness of using salivary microbiota in forensic identification purposes of a person with recent antibiotic use.

The detection of microbial flora changes in saliva samples because of antibiotic use through advanced molecular genetic analysis is important for forensic and clinical applications. This study aims to reveal the variability in the microbial structure of human saliva after antibiotic use with metagenomic analysis techniques from a forensic point of view. Within the scope of the study, saliva samples were collected from patients who were under the effect of regional anesthesia to be administered a standardized course of antibiotic therapy that lasted for a week. The analysis was conducted on 56 saliva samples from 14 individuals over four different time intervals. Isolation of the 16S rRNA region and PCR analysis were performed prior to sequence analysis to determine the microbiome structure of the samples at phylum, genus, and species levels. As expected, changes were observed in bacterial species found in saliva samples after administration of antibiotics and this was linked to the specific type of antibiotics that were administered. This change was statistically significant for Firmicutes, Spirochetes, and Verrucomicrobiota. Furthermore, although the oral microbiome tends to return to its former state at the phylum and genus level within a 4-week period after the start of antibiotic use, it is observed that the change, especially in some bacterial species, still continues. The findings of this study show that because of the inability of stabilization at species-level in a period of 4 weeks from the start of antibiotic use, it is not suitable to assess saliva samples at species-level for forensic identification.

Evaluation of the detectability of different ages of bloodstains on fabrics in different washing conditions and at various wavelengths.

PURPOSE: The detection of bloodstains at crime scenes is extremely useful in forensic investigations. This study aimed to investigate the effects of washing temperature, fabric type, fabric color, and stain age (time from staining to laundering) on the detection and identification of bloodstains on fabrics after washing. MATERIAL AND METHOD: A total of 240 fabrics (4 different colors and 5 different types) were stained with blood and washed in 4 different washing temperatures with 3 different lag times. The evaluations of fabric images were performed using the FLS system (Forenscope-Mobile Multispectral UV-VIS-IR Imaging Systems®) on a total of 1200 images using 5 different wavelengths and filter options. The bloodstained areas of the fabric pieces were then excised, and the hemoglobin presence was analyzed using the SERATEC® HemDirect hemoglobin test. RESULTS: The analyses of laundered samples using the FLS system revealed that the best images were obtained from velvet, cotton fleece, denim, and polyester fabrics, in that order. Except for polyester fabrics, the SERATEC® HemDirect hemoglobin screening test, which was used to detect bloodstains on fabrics, showed positive results after washing at low temperatures (approximately 15 °C and 30 °C). At higher temperatures (60 °C and 90 °C), the SERATEC® HemDirect hemoglobin test yielded negative results. CONCLUSION: The fabric type and color played a crucial role in stain detection using the FLS system on the laundered fabrics. The FLS system and the SERATEC® HemDirect hemoglobin test revealed that stain age had a limited effect on the stain's detectability.

Investigating changes in salivary microbiota due to dental treatment: A metagenomic analysis study for forensic purposes.

The advent of next generation sequencing techniques as well as the existing traditional culture methods has enabled metagenomic studies on the usability of microbiomes for the forensic identification of individuals to gain momentum. However, before the utilization of microbiomes as a potential technique for real forensic case resolutions, it is necessary to understand the stability of the microbiota compositions in an individual's biological samples and the factors responsible for their variations. In the present study, we compared the microbiota compositions present in the saliva of individuals with active dental caries before and after treatment from a forensic and clinical perspective using an approach based on the sequencing of all the variable regions (V1-V9) of the bacterial 16 S rRNA gene. For this purpose, 10 individuals were included in the study comprising of 8 individuals between the ages of 18-50 years with at least 3 deep dentin caries as patients and 2 healthy individuals without any dental or gingival diseases as controls. Saliva samples were collected from the patients at two timepoints, before and after treatment, as well as from the healthy individuals (before and after control) at an interval of 1 month. The collected 20 saliva samples were subjected to metagenomic analysis using the MinION device, which was developed by Oxford Nanopore Technologies (ONT Oxford, UK). Bioinformatic analyses were performed on the obtained data and the results were evaluated using statistical comparison methods and alpha/beta diversity analyses within the scope of the study objective. On evaluation using the distance metrics, it was observed that the microbial compositions in the saliva of individuals with active caries remained relatively stable after treatment. However, the relative abundance levels of bacteria of 28 genera and species showed statistically significant differences before and after treatment (p < 0.05). As a result, although the composition of salivary microbiome remained relatively stable after caries treatment, there were significant changes in many types of bacteria, especially at the species level, between the BT and AT samples. Our results provide a framework for further forensic and clinical investigations regarding the factors that affect human salivary microbiome diversity.

Assessment of the link between evidence and crime scene through soil bacterial and fungal microbiome: A mock case in forensic study.

In forensic studies, soil traces can be used to find clues to the origin of an unknown sample or the relationship between a crime scene and a suspect and can provide invaluable evidence as they frequently adhere to objects, with high persistence. In this study, it was aimed to investigate the potential of the bacterial and fungal microbiome diversity of the soil to be used as legitimate evidence in the resolution of homicide cases. Within the scope of a mock homicide case scenario, a total of 12 soil samples were collected, including two evidence samples, three crime scene samples and seven non-crime scene related control samples. Both bacterial and fungal microbiome profiles of these samples were analysed using Illumina NovaSeq platform. The resulting sequences were analysed using QIIME 2 microbiome bioinformatics platform. Beta diversity analysis was performed to determine the difference between samples. In bacterial community analyses, it has been observed that it is difficult to distinguish evidence samples and crime scene samples from control samples at phylum and class level, whereas differentiation could be made at genus and species level. Fungal community analyses allowed to distinguish evidence samples and crime scene samples from control samples at both phylum and class and genus and species level. Principal coordinate analysis (PCoA) results showed that distance between evidence samples and crime scene reference samples was closer to each other than non-crime scene related control samples. The results of this study showed that bacterial and especially fungal DNA in soil has the potential to contribute effectively to the resolution of forensic cases. Thus, it has been understood that it is possible to establish a relationship between the case and the crime scene with the help of microbiome analyses on soil samples obtained in homicide cases.

Publication rates of abstracts presented at the annual scientific meetings held by the American Academy of Forensic Sciences in 2011 and 2016.

Prior research evaluating the papers presented in forensic sciences in international meetings is scant. This study determines the possible predictions concerning publications by comparing the publication rates, publication years, and presentation types, time until publication, participating countries, and criteria of the published journals in the American Academy of Forensic Sciences (AAFS). The publication rates of abstracts presented at scientific meetings of AAFS, a prestigious forensic science organization, along with the aforementioned components and the extent of their contribution in 2011 and 2016 were investigated. The abstracts presented at the AAFS meetings in 2011 and 2016 were reviewed retrospectively within the scope of this study. The Web of Science, PubMed, Scopus, Science Direct, and Google Scholar databases were searched using a specified process that included the title, first and last author surnames, and keywords. Results revealed that approximately 21% and 24% of the papers presented at the 2011 and 2016 AAFS meetings, respectively, were published. Considering the publication rates of abstracts according to sections, the publication rates for the 2011 AAFS meeting ranged from 4% (questioned documents) to 31% (anthropology) and from 5% (questioned documents) to 32% (pathology/biology), on average, for the 2016 AAFS meeting. It was determined that the papers were largely published in the Journal of Forensic Sciences for both annual scientific meetings. Future studies should concentrate on the obstacles to the publication of papers presented at such prestigious organizations and strategies to facilitate the publication process such that they do not lose their value over time.

Assessment of the exclusion potential of suspects by using microbial signature in sexual assault cases: A scenario-based experimental study.

Sexual assault offences are one of the most serious crimes committed against a person, typically rank only second to homicide, and represent one of the major challenges in forensic sciences. In some cases of sexual assault, there may be more than one suspect and the analysis of the biological evidence with currently available methods such as human DNA analysis may not yield results. In this study using the designed experimental model (with different experimental scenarios that can be designed), it was aimed to investigate the effectiveness of the microbiome profile for the identification of the offender by comparing the microbiome structures of the suspects' saliva samples with the mixed samples on the victim (saliva transmitted on breast skin) within the first 48 h after a sexual assault. For this purpose, a total of 44 samples was collected from four healthy females and four healthy males aged 20-50 years. Microbiome profiles of 44 samples in four groups containing saliva, breast skin and mixed samples were determined with the IIlumina HiSeq platform. Differentiation between samples were calculated by beta-diversity analysis methods by using QIIME software (v1.80). To compare the differentiation among samples and groups, unweighted UniFrac distance values were applied. Eight dominant microbial genera accounted for 86.15% of the total bacterial population in male saliva samples and were composed of Fusobacterium, Haemophilus, Neisseria, Porphyromonas, Prevotella, Rothia, Streptococcus and Veillonella. These genera constituted 76.72% of the bacterial population in mixed samples, whereas they constituted 34.40% of the bacterial population in the breast skin samples. Results of this study show that bacterial DNA in saliva can be recovered from saliva transmitted breast skin within at least 48 h. In conclusion, it has been found that examination of the microbiota of the saliva transmitted to breast skin of a sexual assault victim as a forensic tool may have the potential to determine the offender of the incident among the suspects or to reduce the number of suspects. Supporting the results of this study with further studies using parameters such as different case models, different body regions, larger time periods and a higher number of participants will be beneficial to draw accurate conclusion of the judicial case.

Evaluation of the relationship between the detectability of seminal stains on laundered fabric and stain age.

In some cases of sexual assault that are not reported to judicial authorities within a certain time, it is important to detect and identify seminal stains on laundered fabrics. In this study, we aimed to reveal the effect of the time from staining to laundering on the detectability and identification of seminal stains on laundered clothes. A total of 180 pieces of fabric (four different colours and five different types) were stained with seminal fluids, and three different lag times (12 hours, 1 week and 1 month) from staining to laundering were used. Three different laundering protocols were applied to these fabrics after staining. The built-in camera of the Mobile Multispectral UV-VIS-IR Imaging System® was used to take photos (1260 in total) of the stains with seven different wavelength and filter options, and the obtained images were evaluated. The Seratec® PSA Semiquant test was used to analyse the presence of prostate-specific antigen (PSA) in the seminal stains laundered after different lag times. We observed that in examining with the forensic light source (FLS) system, the time from staining to laundering affected the detectability of seminal stains on pieces of cloth. The best fluorescence was obtained in the examination of semen-stained fabric with FLS, particularly when the fabric was not laundered for one month after staining. On the other hand, the time from staining to laundering had a more limited effect on PSA test positivity than on the results of the examination with FLS.

Development of dental charts according to tooth development and eruption for Turkish children and young adults.

PURPOSE: In this study, we aimed to develop dental charts for Turkish children and young adults of both genders within the age group of 4.5-22.5 years according to tooth mineralization and eruption in a format similar to that proposed by AlQahtani et al. MATERIALS AND METHODS: In total, 753 digital panoramic radiographs from 350 males and 403 females were assessed. The permanent teeth were evaluated according to the classification system described by Demirjian et al. The eruption stage was assessed with Bengston's system, which was modified by AlQahtani et al at four points. RESULTS: Teeth generally developed earlier in females than in males. This was particularly notable in the age group of 5-14 years. However, this difference was usually visible in only one stage, not in all teeth. It has been determined that the mixed dentition period ended with the shedding of the second deciduous molars in both genders. CONCLUSION: The dental charts presented here included information that could be beneficial to dental clinicians in making appropriate diagnosis and planning orthodontic and surgical procedures. These charts also provided datasets for preliminary dental age estimation in Turkish children and young adults.

Radiological age estimation: based on third molar mineralization and eruption in Turkish children and young adults.

Radiographic evaluation of mineralization and eruption stages of third molars using dental panoramic radiographies can be an efficient tool for chronological age estimation in both forensic sciences and legal medicine. The third molar tooth is utilized for dental age estimation about the age span of 15-23 years because it represents the only tooth still in development. The aim of this study is to obtain and analyze data regarding third molar development and eruption in Turkish population for dental age estimation. A total of 744 dental panoramic radiographies of 394 female and 350 male subjects aged between 8 and 22 years were examined. Third molar development was determined according to the Nolla classification system, and eruption was assessed relative to the alveolar bone level. Mandibular and maxillary third molars were generally found at similar stages of development on both sides. Nolla stage 6 (completed crown calcification) was reached at around the age of 15 in both maxillary and mandibular third molars in both sexes. Alveolar emergence was at around the age of 16 in males and around age of 17 in females. Although third molars' eruption shows greater variability than development of third molars, data which were obtained from this study about eruption of these teeth can be supportive to development data for age estimation.