Metabarcoding reveals low prevalence of microsporidian infections in castor bean tick (Ixodes ricinus)

Background Microsporidia is a large group of eukaryotic obligate intracellular spore-forming parasites, of which 17 species can cause microsporidiosis in humans. Most human-infecting microsporidians belong to the genera Enterocytozoon and Encephalitozoon. To date, only five microsporidian species, including Encephalitozoon-like, have been found in hard ticks (Ixodidae) using microscopic methods, but no sequence data are available for them. Furthermore, no widespread screening for microsporidian-infected ticks based on DNA analysis has been carried out to date. Thus, in this study, we applied a recently developed DNA metabarcoding method for efficient microsporidian DNA identification to assess the role of ticks as potential vectors of microsporidian species causing diseases in humans. Methods In total, 1070 (493 juvenile and 577 adult) unfed host-seeking Ixodes ricinus ticks collected at urban parks in the city of Poznan, Poland, and 94 engorged tick females fed on dogs and cats were screened for microsporidian DNA. Microsporidians were detected by PCR amplification and sequencing of the hypervariable V5 region of 18S rRNA gene (18S profiling) using the microsporidian-specific primer set. Tick species were identified morphologically and confirmed by amplification and sequencing of the shortened fragment of cytochrome c oxidase subunit I gene (mini-COI). Results All collected ticks were unambiguously assigned to I. ricinus. Potentially zoonotic Encephalitozoon intestinalis was identified in three fed ticks (3.2%) collected from three different dogs. In eight unfed host-seeking ticks (0.8%), including three males (1.1%), two females (0.7%) and three nymphs (0.7%), the new microsporidian sequence representing a species belonging to the genus Endoreticulatus was identified. Conclusions The lack of zoonotic microsporidians in host-seeking ticks suggests that I. ricinus is not involved in transmission of human-infecting microsporidians. Moreover, a very low occurrence of the other microsporidian species in both fed and host-seeking ticks implies that mechanisms exist to defend ticks against infection with these parasites. Graphical abstract

Nonparametric Path Analysis on Consumer Satisfaction and Consumer Engagement in PT Pertamina

The purpose of this research is to apply nonparametric path analysis on consumer satisfaction and consumer engagement of PT Pertamina. The results of the analysis are expected to be able to provide an estimate of the function in determining consumer satisfaction and consumer engagement of PT Pertamina. This study uses primary data involving five variables, namely Digitalization (X1), Consumer Needs (X2), Consumer Service (X3), Consumer Satisfaction (Y1), Consumer Engagement (Y3). Variable measurement technique is done by calculating the average score on the items. Sampling in this study used a purposive sampling technique with the respondent's criteria being company leaders. The result of this research is the estimation of nonparametric Path function using MARS approach on various interactions. The best estimate of the function of obedient behavior in paying credit is when it involves 3 variables, namely the digitization variable (X1), Consumer Needs (X2), Consumer Service (X3) with a value ofgeneralized cross-validation The smallest (GCV) obtained is 0.2833. The originality of this research is that the variables used are the results of DNA analysis (Discourse Network Analysis), where the analysis extracts information from cyberspace which is then formed as the main issue and becomes a variable. In addition, there is no previous research that examines nonparametric path analysis on PT Pertamina's consumer satisfaction and engagement.The purpose of this research is to apply nonparametric path analysis on consumer satisfaction and consumer engagement of PT Pertamina. The results of the analysis are expected to be able to provide an estimate of the function in determining consumer satisfaction and consumer engagement of PT Pertamina. This study uses primary data involving five variables, namely Digitalization (X1), Consumer Needs (X2), Consumer Service (X3), Consumer Satisfaction (Y1), Consumer Engagement (Y3). Variable measurement technique is done by calculating the average score on the items. Sampling in this study used a purposive sampling technique with the respondent's criteria being company leaders. The result of this research is the estimation of nonparametric Path function using MARS approach on various interactions. The best estimate of the function of obedient behavior in paying credit is when it involves 3 variables, namely the digitization variable (X1), Consumer Needs (X2), Consumer Service (X3) with a value ofgeneralized cross-validation The smallest (GCV) obtained is 0.2833. The originality of this research is that the variables used are the results of DNA analysis (Discourse Network Analysis), where the analysis extracts information from cyberspace which is then formed as the main issue and becomes a variable. In addition, there is no previous research that examines nonparametric path analysis on PT Pertamina's consumer satisfaction and engagement.

Cell-free DNA analysis in current cancer clinical trials: a review

Cell-free DNA (cfDNA) analysis represents a promising method for the diagnosis, treatment selection and clinical follow-up of cancer patients. Although its general methodological feasibility and usefulness has been demonstrated, several issues related to standardisation and technical validation must be addressed for its routine clinical application in cancer. In this regard, most cfDNA clinical applications are still limited to clinical trials, proving its value in several settings. In this paper, we review the current clinical trials involving cfDNA/ctDNA analysis and highlight those where it has been useful for patient stratification, treatment follow-up or development of novel approaches for early diagnosis. Our query included clinical trials, including the terms ‘cfDNA’, ‘ctDNA’, ‘liquid biopsy’ AND ‘cancer OR neoplasm’ in the FDA and EMA public databases. We identified 1370 clinical trials (FDA = 1129, EMA = 241) involving liquid-biopsy analysis in cancer. These clinical trials show promising results for the early detection of cancer and confirm cfDNA as a tool for real-time monitoring of acquired therapy resistance, accurate disease-progression surveillance and improvement of treatment, situations that result in a better quality of life and extended overall survival for cancer patients.

First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First–Third Centuries AD)

This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first–third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops.

Bioaerosols and atmospheric ice nuclei in a Mediterranean dryland: community changes related to rainfall

Certain biological particles are highly efficient ice nuclei (IN), but the actual contribution of bioparticles to the pool of atmospheric IN and their relation to precipitation are not well characterized. We investigated the composition of bioaerosols, ice nucleation activity, and the effect of rainfall by metagenomic sequencing and freezing experiments of aerosol samples collected during the INUIT 2016 campaign in a rural dryland on the eastern Mediterranean island of Cyprus. Taxonomic analysis showed community changes related to rainfall. For the rain-affected samples, we found higher read proportions of fungi, particularly of Agaricomycetes, which are a class of fungi that actively discharge their spores into the atmosphere in response to humidity changes. In contrast, the read proportions of bacteria were reduced, indicating an effective removal of bacteria by precipitation. Freezing experiments showed that the IN population in the investigated samples was influenced by both rainfall and dust events. For example, filtration and heat treatment of the samples collected during and immediately after rainfall yielded enhanced fractions of heat-sensitive IN in the size ranges larger than 5 µm and smaller than 0.1 µm, which were likely of biological origin (entire bioparticles and soluble macromolecular bio-IN). In contrast, samples collected in periods with dust events were dominated by heat-resistant IN active at lower temperatures, most likely mineral dust. The DNA analysis revealed low numbers of reads related to microorganisms that are known to be IN-active. This may reflect unknown sources of atmospheric bio-IN as well as the presence of cell-free IN macromolecules that do not contain DNA, in particular for sizes < 0.1 µm. The observed effects of rainfall on the composition of atmospheric bioaerosols and IN may influence the hydrological cycle (bioprecipitation cycle) as well as the health effects of air particulate matter (pathogens, allergens).

A Disposable DNA Analysis Chip with a Powerless Actuator

A non-instrumented, single-use, affordable, and fully- yet safely-disposable DNA analysis system for Point Of Care (POC) diagnostic process has been proposed by integrating (1) a hydration-reactive mixture for a portable heating element as a powerless actuator, (2) commercially available optical adhesive films as valves, and (3) an exothermic reaction-based recombinant polymerase amplification (RPA) process for non-instrumented DNA amplification. The operational error tolerance of the adhesive valves was evaluated by gas production and long-lasting ability, and the amplification performance of the RPA device was validated by gel electrophoresis. Finally, a DNA analysis device was fabricated and tested based on a hydration reaction with a DNA extraction microfluidic channel and an exothermic reaction-based RPA device. In the DNA extraction process, dimethyl adipimidate (DMA) solution was used to eliminate some required injection steps from the extraction process. The integrated system's functionality was successfully demonstrated, and the suggested system could become a foundation for the ultimate total solution for POC DNA analysis.

Acanthosaura meridiona sp. nov. (Squamata: Agamidae), a new short-horned lizard from southern Thailand

A new short – horned lizard species of the genus Acanthosaura from southern Thailand, is described herein. The species was previously recognised as Acanthosaura crucigera and has been reported to present a wide distribution across mainland south-east Asia. The combination of modern morphological studies of Acanthosaura meridiona sp. nov. allows its separation from closely related species A. crucigera, on the basis of presenting more nuchal scales, more scales between diastema, more scales bordering rostral scales and more midline ventral scales. Mitochondrial DNA analysis also indicated a sister relationship between A. meridiona sp. nov. and A. crucigera with a 100 % probability according to Bayesian and maximum – likelihood analyses. The pairwise distance between A. meridiona sp. nov. and A. crucigera ranges from 9.9 – 11.1 %, while the distance between A. meridiona populations ranges from 0 – 0.9 %. This new discovery contributes to the redescription of the distribution of A. crucigera under Kra Isthmus and its replacement by A. meridiona sp. nov.

Genetic Profile Evaluation of Human Cell Lines Treated with Anastatica hierochuntica Using Forensic DNA Fingerprinting Markers

Cell line authentication using Short Tandem Repeats (STRs) is necessary to ensure the integrity of the cell for its continuous culture and to identify misidentification and cross-contamination issues. This study investigates the changes in the genetic profile of MCF-7 and HepG2 cell lines caused by the methanolic leaf extract of Anastatica hierochuntica (AH) using human identification based STR markers. MCF-7 and HepG2 cell lines were treated with various concentrations of AH extracts for three different periods. The treated and control cells' DNA was extracted using a QIAamp® DNA Micro Kit, quantified using a Quantifiler Duo DNA Quantification Kit, and amplified using an AmpFlSTR Identifiler plus PCR Amplification Kit. The concentrations of the DNA extracted from control and MCF-7 and HepG2 cell lines treated with AH extract at 300 to 2400 µg/ml for 24hr and 150 to 2400 µg/ml for 48 and 72hrs were statistically significant (p<0.05). Microsatellite instability (MSI), loss of heterozygosity (LOH), insertion/deletions changes in the STRs profile were observed in treated cell lines at 1200 and 2400 µg/ml in MCF-7 cells for 48 and 72hrs and HepG2 cells for 24, 48, and 72hrs. We conclude that the highest concentration of AH extracts affected the genotype of the cell lines leading to misidentification. Therefore, cell line authentication by forensic DNA analysis techniques plays a decisive role for cells tested with a high concentration of chemical compounds and gives the forensic investigator an insight into these changes in the STR genotype of a victim/suspect who has been been under long term chemotherapeutic treatment.

Nanotechnology: A Powerful Tool in Forensic Science for Solving Criminal Cases

Nanotechnology has emerged as a phoenix in the field of forensic science and proved to be of great importance in solving criminal cases where other techniques failed to provide conclusive results. This field of science possess humongous potential in the field of forensic science and assist in crime detection. It holds huge amount of value in making a positive contribution in assisting forensic experts and scientists in nabbing the criminals and most importantly prevent any wrongful conviction. In the past decade, many researchers have reported the satisfactory application of Nano technique in Forensic Science for the analysis of latent fingerprints, drugs in alleged drug-facilitated crimes, warfare agent detection, DNA analysis, counter terrorism, GSR detection, post-blast residue analysis, security measures, etc. It has been proved to be a robust approach for the detection of crime with greater selectivity, sensitivity, reliability and results are produced in a timely appropriate manner. The constant development of nanotechnology and its application in the field of Forensic Science over the past decade has been highlighted in this review article.