Search Results (15)

Dairy-borne Pseudomonas spp., known for causing spoilage, may also exhibit antibiotic resistance and form biofilms, enhancing their persistence in dairy environments and contaminating final products. This study examined biofilm formation and antibiotic resistance in 106 Pseudomonas spp. strains isolated from milk, whey, and spoiled dairy products. Phylogenetic analysis (based on partial ileS sequences) grouped most strains within the P. fluorescens group, clustering into the P. fluorescens, P. gessardii, P. koorensis, and P. fragi subgroups. Biofilm formation in polystyrene microplates was assessed at 6 °C and 25 °C by crystal violet staining. After 48 h, 72% and 65% of Pseudomonas strains formed biofilms at 6 °C and 25 °C, respectively, with higher biomass production at 6 °C. High biofilm producers included most P. fluorescens, P. shahriarae, P. salmasensis, P. atacamensis, P. gessardii, P. koreensis, and P. lundensis strains. The adnA gene, associated with biofilm formation, was detected in 60% of the biofilm producers, but was absent in P. fragi, P. lundensis, P. weihenstephanensis, and P. putida. Antibiotic susceptibility was tested using the disk diffusion method. All strains were susceptible to amikacin and tobramycin; however, 73% of the strains were resistant to aztreonam, 28% to imipenem and doripenem, 19% to ceftazidime, 13% to meropenem, and 7% to cefepime. A multiple antibiotic resistance index (MARI) > 0.2 was found in 30% of the strains, including multidrug-resistant (n = 15) and extensively drug-resistant (n = 3) strains. These findings highlight Pseudomonas spp. as persistent contaminants and antibiotic resistance reservoirs in dairy environments and products, posing public health risks and economic implications for the dairy industry. Full article

Ancient human viruses have been detected in ancient DNA (aDNA) samples of both Anatomically Modern Humans and Neanderthals. Reconstructing genomes from aDNA using reference mapping presents numerous problems due to the unique nature of ancient samples, their degraded state, smaller read sizes and the limitations of current methodologies. The spurious alignments of reads to reference sequences (mapping) are a main source of false positives in aDNA assemblies and the assessment of signal-to-noise ratios is essential to differentiate bona fide reconstructions from random, noisy assemblies. Here, we analyzed the statistical distributions of viral genome assemblies, ancient and modern, and their respective random “mock” controls used to evaluate the signal-to-noise ratio. We tested if differences between real and random assemblies could be detected from their statistical distributions. Our analysis shows that the coverage distributions of (1) real viral aDNA assemblies of adenovirus (ADV), herpesvirus (HSV) and papillomavirus (HPV) do not follow power laws nor log-normal laws, (2) (ADV) and control aDNA assemblies are well approximated by log-normal laws, (3) negative control parvovirus B19 (real and random) follow a power law with infinite variance and (4) the mapDamage negative control with non-ancient DNA (modern ADV) and the mapDamage positive control (human mtDNA) are well approximated by the negative binomial distribution, consistent with the Lander–Waterman model. Our results show that the tails of the distributions of aDNA and their controls reveal the weight of random effects and can differentiate spurious assemblies, or false positives, from bona fide assemblies. Full article

Regarding the development of new antineoplastic agents, with a view to assess the selective antitumoral potential which aims at causing irreversible damage to cancer cells while preserving the integrity of their healthy counterparts, it is essential to evaluate the cytotoxic effects in both healthy and malignant human cell lines. In this study, a complex with two Pd(II) centers linked by the biogenic polyamine spermine (Pd₂Spm) was tested on healthy (PNT-2) and cancer (LNCaP and PC-3) prostate human cell lines, using cisplatin as a reference. To understand the mechanisms of action of both cisplatin and Pd₂Spm at a molecular level, Fourier Transform Infrared (FTIR) and Raman microspectroscopies were used. Principal component analysis was applied to the vibrational data, revealing the major metabolic changes caused by each drug, which were found to rely on DNA, lipids, and proteins, acting as biomarkers of drug impact. The main changes were observed between the B-DNA native conformation and either Z-DNA or A-DNA, with a higher effect on lipids having been detected in the presence of cisplatin as compared to Pd₂Spm. In turn, the Pd-agent showed a more significant impact on proteins. Full article

Circulating tumor cells (CTCs) crosstalk with different blood cells before a few of them settle down as disseminated tumor cells (DTCs). We evaluated the correlation between CTC subtypes, DTCs and the neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR) and monocyte to lymphocyte ratio (MLR) for better prognostication of 171 early staged diagnosed breast cancer (BC) patients. —Clinical data and blood values before treatment were retrospectively recorded, representing the 75% percentile, resulting in 3.13 for NLR, 222.3 for PLR and 0.39 for MLR, respectively. DTCs were analyzed by immunocytochemistry using the pan-cytokeratin antibodyA45-B/B3. CTCs were determined applying the AdnaTests BreastCancerDetect and EMT (Epithelial Mesenchymal Transition) Detect. —Reduced lymphocyte (p = 0.007) and monocyte counts (p = 0.012), an elevated NLR (p = 0.003) and PLR (p = 0.001) significantly correlated with the presence of epithelial CTCs while a reduced MLR was related to EMT-CTCs (p = 0.045). PLR (p = 0.029) and MLR (p = 0.041) significantly related to lymph node involvement and monocyte counts significantly correlated with OS (p = 0.034). No correlations were found for NLR, PLR and MLR with DTCs, however, DTC-positive patients, harboring a lower PLR, had a significant shorter OS (p = 0.043). —Pro-inflammatory markers are closely related to different CTC subsets. This knowledge might improve risk prognostication of these patients. Full article

Liquid biopsy is emerging as a potential diagnostic tool for prostate cancer (PC) prognosis and diagnosis. Unfortunately, most circulating tumor cells (CTC) technologies, such as AdnaTest or Cellsearch^®, critically rely on the epithelial cell adhesion molecule (EpCAM) marker, limiting the possibility of detecting cancer stem-like cells (CSCs) and mesenchymal-like cells (EMT-CTCs) that are present during PC progression. In this context, dielectrophoresis (DEP) is an epCAM independent, label-free enrichment system that separates rare cells simply on the basis of their specific electrical properties. As compared to other technologies, DEP may represent a superior technique in terms of running costs, cell yield and specificity. However, because of its higher complexity, it still requires further technical as well as clinical development. DEP can be improved by the use of microfluid, nanostructured materials and fluoro-imaging to increase its potential applications. In the context of cancer, the usefulness of DEP lies in its capacity to detect CTCs in the bloodstream in their epithelial, mesenchymal, or epithelial–mesenchymal phenotype forms, which should be taken into account when choosing CTC enrichment and analysis methods for PC prognosis and diagnosis. Full article

HER2-dependent signaling may support the development of metastatic castration-resistant prostate cancer (mCRPC) by activating androgen receptor signaling through ligand-independent mechanisms. From 41 mCRPC patients (including 31 treated with Androgen Receptor Signaling Inhibitors [ARSI]), Circulating Tumor Cells (CTCs) were prospectively enriched with AdnaTest platform and analyzed with a multiplexed assay for HER2 and AR-V7 mRNA expression. Then, we evaluated the impact of HER2 expression on PSA-response, Progression Free Survival (PFS) and Overall Survival (OS). HER2 expression was detected in CTCs of 26 patients (63%). Although PSA response was similar regardless of HER2 status, patients with HER2 positive CTCs had shorter PSA-PFS (median: 6.2 months versus 13.0 months, p = 0.034) and radiological-PFS (6.8 months versus 25.6 months, p = 0.022) than patients without HER2 expression. HER2 expression was also associated with a shorter OS (22.7 months versus not reached, p = 0.05). In patients treated with ARSI, multivariate analyses revealed that the prognostic impact of HER2 status on PSA-PFS was independent of AR-V7 expression and of the detection of CTCs by an AdnaTest. We showed for the first time the poor prognostic value of HER2 expression in CTCs from patients with mCRPC. The therapeutic interest of targeting this actionable pathway remains to be explored. Full article

We aimed to extract DNA and amplify PCR fragments at the mitochondrial DNA Nad7.1 locus and 11 nuclear microsatellite loci in nine circa 11,000-year-old individuals of Scots pine found at the bottom of the Baltic sea and test the genetic associations with the present-day gene pool of Scots pine in Lithuania. We followed a strict anticontamination protocol in the lab and, simultaneously with the aDNA specimens, tested DNA-free controls. The DNA was extracted by an ATMAB protocol from the ancient wood specimens sampled underwater from Scots pine stumps located circa 20–30 m deep and circa 12 km ashore in western Lithuania. As the references, we used 30 present-day Lithuanian populations of Scots pine with 25–50 individuals each. The aDNA yield was 11–41 ng/μL. The PCR amplification for the mtDNA Nad7.1 locus and the nDNA loci yielded reliable aDNA fragments for three and seven out of nine ancient pines, respectively. The electrophoresis profiles of all the PCR tested DNA-free controls contained the sizing standard only, indicating low likelihood for contamination. At the mtDNA Nad7.1 locus, all three ancient Scots pine individuals had the type A (300 bp) allele, indicating postglacial migration from the refugia in Balkan peninsula. The GENECLASS Bayesian assignment tests revealed relatively stringer and consistent genetic associations between the ancient Scots pine trees and the present-day southern Lithuanian populations (assignment probability 0.37–0.55) and several wetlands in Lithuania. Our study shows that salty sea water efficiently preserves ancient DNA in wood at the quality levels suitable for genetic testing of trees dated back as far as 11,000 years before present. Full article

Circulating tumor cells (CTCs) are important biomarkers for the diagnosis, prognosis, and treatment of cancer. However, because of their extreme rarity, a more precise technique for isolating CTCs is required to gain deeper insight into the characteristics of cancer. This study compares the performance of a lateral magnetophoretic microseparator (“CTC-μChip”), as a representative microfluidic device, and AdnaTest ProstateCancer (Qiagen), as a commercially available specialized method, for isolating CTCs from the blood of patients with prostate cancer. The enumeration and genetic analysis results of CTCs isolated via the two methods were compared under identical conditions. In the CTC enumeration experiment, the number of CTCs isolated by the CTC-μChip averaged 17.67 CTCs/mL, compared to 1.56 CTCs/mL by the AdnaTest. The number of contaminating white blood cells (WBCs) and the CTC purity with the CTC-μChip averaged 772.22 WBCs/mL and 3.91%, respectively, whereas those with the AdnaTest averaged 67.34 WBCs/mL and 1.98%, respectively. Through genetic analysis, using a cancer-specific gene panel (AR (androgen receptor), AR-V7 (A\androgen receptor variant-7), PSMA (prostate specific membrane antigen), KRT19 (cytokeratin-19), CD45 (PTPRC, Protein tyrosine phosphatase, receptor type, C)) with reverse transcription droplet digital PCR, three genes (AR, AR-V7, and PSMA) were more highly expressed in cells isolated by the CTC-μChip, while KRT19 and CD45 were similarly detected using both methods. Consequently, this study showed that the CTC-μChip can be used to isolate CTCs more reliably than AdnaTest ProstateCancer, as a specialized method for gene analysis of prostate CTCs, as well as more sensitively obtain cancer-associated gene expressions. Full article

A historical crypt offers us a particular view of the conditions of some buried materials (in this case textiles) and the various biogenic phenomena to which they were subjected over the centuries. In addition, significant knowledge can come by studying the DNA of buried objects which allows the recognition of materials, but also to reveal some practice of the funeral ceremony. In this study, the deteriorating microbial communities colonizing various funeral textile items were identified and characterized using microscopic observation, cultivation, polymerase chain reaction (PCR) and sequencing, hydrolytic tests; and culture-independent analysis (high-throughput sequencing, MinION platform). Different PCR assays and consequent sequencing of amplicons were employed to recognize the animal origin of bodice reinforcements and the type of plant used to embellish the young girl. The analysis of ancient DNA (aDNA from animal and plant) was also completed by the application of high-throughput sequencing through Illumina platform. The combination of all these techniques permitted the identification of a complex microbiota composed by dangerous degradative microorganisms able to hydrolyze various organic substrates such as fibroin, keratin, and cellulose. Bacteria responsible for metal corrosion and bio-mineralization, and entomopathogenic and phytopathogenic fungi. The analysis of aDNA identified the animal component used in bodice manufacturing, the plant utilized as ornament and probably the season of this fatal event. Full article

The purpose of this Milankovitch review is to explain the significance of Quaternary DNA studies and the importance of the recent methodological advances that have enabled the study of late Quaternary remains in more detail, and the testing of new assumptions in evolutionary biology and phylogeography to reconstruct the past. The topic is wide, and this review is not intended to be an exhaustive account of all the aDNA work performed in the last three decades on late-Quaternary remains. Instead, it is a selection of relevant studies aimed at illustrating how aDNA has been used to reconstruct not only environments of the past, but also the history of many species including our own. Full article

Background: Circulating tumor cells (CTC), androgen receptor full-length (AR-FL), and androgen receptor splice variant 7 (AR-V7) are prognostic in patients (pts) with metastatic castration-resistant prostate cancer (mCRPC). AR-V7 seems to predict resistance to androgen-receptor signaling inhibitors (ARSi). Methods: We assessed the association of CTC, AR-FL, and AR-V7 with prostate-specific antigen (PSA) response and overall survival (OS). We used a modified AdnaTest CTC-based AR-FL and AR-V7 mRNA assay. Chi-square test, Fisher Exact test, Kaplan–Meier method, log-rank test, Cox proportional hazards models were used as appropriate. Results: We enrolled 39 mCRPC pts, of those 24 started a first-line treatment for mCRPC (1L subgroup) and 15 had received at least two lines for mCRPC (>2L subgroup). CTC, AR-FL, and AR-V7 were enriched in >2L compared to 1L subgroup. Detection of these biomarkers was associated with a lower percentage of biochemical responses. Only 1/7 AR-V7+ pts had a PSA response and received cabazitaxel. Median OS was 4.7 months (95% CI 0.6–8.9) in AR-V7+ pts and not reached in AR-V7− pts. AR-V7 was the only variable with prognostic significance in the Cox model. Conclusion: AR-V7, CTC, and AR-FL are associated with advanced mCRPC and AR-V7+ predicts for shorter OS. Full article

Liquid biopsy analytes such as cell-free DNA (cfDNA) and circulating tumor cells (CTCs) exhibit great potential for personalized treatment. Since cfDNA and CTCs are considered to give additive information and blood specimens are limited, isolation of cfDNA and CTC in an “all from one tube” format is desired. We investigated whether cfDNA variant sequencing from CTC-depleted blood (CTC-depl. B; obtained after positive immunomagnetic isolation of CTCs (AdnaTest EMT-2/Stem Cell Select, QIAGEN)) impacts the results compared to cfDNA variant sequencing from matched whole blood (WB). Cell-free DNA was isolated using matched WB and CTC-depl. B from 17 hormone receptor positive/human epidermal growth factor receptor 2 negative (HR+/HER2−) metastatic breast cancer patients (QIAamp MinElute ccfDNA Kit, QIAGEN). Cell-free DNA libraries were constructed (customized QIAseq Targeted DNA Panel for Illumina, QIAGEN) with integrated unique molecular indices. Sequencing (on the NextSeq 550 platform, Illumina) and data analysis (Ingenuity Variant Analysis) were performed. RNA expression in CTCs was analyzed by multimarker quantitative PCR. Cell-free DNA concentration and size distribution in the matched plasma samples were not significantly different. Seventy percent of all variants were identical in matched WB and CTC-depl. B, but 115/125 variants were exclusively found in WB/CTC-depl. B. The number of detected variants per patient and the number of exclusively detected variants per patient in only one cfDNA source did not differ between the two matched cfDNA sources. Even the characteristics of the exclusively detected cfDNA variants in either WB or CTC-depl. B were comparable. Thus, cfDNA variants from matched WB and CTC-depl. B exhibited no relevant differences, and parallel isolation of cfDNA and CTCs from only 10 mL of blood in an “all from one tube” format was feasible. Matched cfDNA mutational and CTC transcriptional analyses might empower a comprehensive liquid biopsy analysis to enhance the identification of actionable targets for individual therapy strategies. Full article

The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, however, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA. Further the high missingness rates in ancient—and oftentimes haploid—DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories. Full article

The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna. Full article

The analysis of mitochondrial DNA (mtDNA) has proven useful in forensic genetics and ancient DNA (aDNA) studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR) is commonly sequenced using established Sanger-type Sequencing (STS) protocols involving fragment sizes down to approximately 150 base pairs (bp). Recent developments include Massively Parallel Sequencing (MPS) of (multiplex) PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC) methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less), and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples), and tested challenging forensic samples (n = 2) as well as compromised solid tissue samples (n = 15) up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS method for final implementation in forensic genetic laboratories. Full article