A data-driven, high-throughput methodology to determine tissue-specific differentially methylated regions able to discriminate body fluids.

Tissue-specific differentially methylated regions (tDMRs) are regions of the genome with methylation patterns that modulate gene expression in those tissue types. The detection of tDMRs in forensic evidence can permit the identification of body fluids at trace levels. In this report, we have performed a bioinformatic analysis of an existing array dataset to determine if new tDMRs could be identified for use in body fluid identification from forensic evidence. Once these sites were identified, primers were designed and bisulfite modification was performed. The relative methylation level for each body fluid at a given locus was then determined using qPCR with high-resolution melt analysis (HRM). After screening 127 tDMR's in multiple body fluids, we were able to identify four new markers able to discriminate blood (2 markers), vaginal epithelia (1 marker) and buccal cells (1 marker). One marker for each target body fluid was also tested with pyrosequencing showing results consistent with those obtained by HRM. This work successfully demonstrates the ability of in silico analysis to develop a novel set of tDMRs capable of being differentiated by real time PCR/HRM. The method can rapidly determine the body fluids left at crime scenes, assisting the triers of fact in forensic casework.

Bioactivity of Chitosan-Based Particles Loaded with Plant-Derived Extracts for Biomedical Applications: Emphasis on Antimicrobial Fiber-Based Systems.

Marine-derived chitosan (CS) is a cationic polysaccharide widely studied for its bioactivity, which is mostly attached to its primary amine groups. CS is able to neutralize reactive oxygen species (ROS) from the microenvironments in which it is integrated, consequently reducing cell-induced oxidative stress. It also acts as a bacterial peripheral layer hindering nutrient intake and interacting with negatively charged outer cellular components, which lead to an increase in the cell permeability or to its lysis. Its biocompatibility, biodegradability, ease of processability (particularly in mild conditions), and chemical versatility has fueled CS study as a valuable matrix component of bioactive small-scaled organic drug-delivery systems, with current research also showcasing CS's potential within tridimensional sponges, hydrogels and sutures, blended films, nanofiber sheets and fabric coatings. On the other hand, renewable plant-derived extracts are here emphasized, given their potential as eco-friendly radical scavengers, microbicidal agents, or alternatives to antibiotics, considering that most of the latter have induced bacterial resistance because of excessive and/or inappropriate use. Loading them into small-scaled particles potentiates a strong and sustained bioactivity, and a controlled release, using lower doses of bioactive compounds. A pH-triggered release, dependent on CS's protonation/deprotonation of its amine groups, has been the most explored stimulus for that control. However, the use of CS derivatives, crosslinking agents, and/or additional stabilization processes is enabling slower release rates, following extract diffusion from the particle matrix, which can find major applicability in fiber-based systems within ROS-enriched microenvironments and/or spiked with microbes. Research on this is still in its infancy. Yet, the few published studies have already revealed that the composition, along with an adequate drug release rate, has an important role in controlling an existing infection, forming new tissue, and successfully closing a wound. A bioactive finishing of textiles has also been promoting high particle infiltration, superior washing durability, and biological response.

Functionalization of Crosslinked Sodium Alginate/Gelatin Wet-Spun Porous Fibers with Nisin Z for the Inhibition of Staphylococcus aureus-Induced Infections.

Nisin Z, an amphipathic peptide, with a significant antibacterial activity against Gram-positive bacteria and low toxicity in humans, has been studied for food preservation applications. Thus far, very little research has been done to explore its potential in biomedicine. Here, we report the modification of sodium alginate (SA) and gelatin (GN) blended microfibers, produced via the wet-spinning technique, with Nisin Z, with the purpose of eradicating Staphylococcus aureus-induced infections. Wet-spun SAGN microfibers were successfully produced at a 70/30% v/v of SA (2 wt%)/GN (1 wt%) polymer ratio by extrusion within a calcium chloride (CaCl2) coagulation bath. Modifications to the biodegradable fibers' chemical stability and structure were then introduced via crosslinking with CaCl2 and glutaraldehyde (SAGNCL). Regardless of the chemical modification employed, all microfibers were labelled as homogeneous both in size (≈246.79 µm) and shape (cylindrical and defect-free). SA-free microfibers, with an increased surface area for peptide immobilization, originated from the action of phosphate buffer saline solution on SAGN fibers, were also produced (GNCL). Their durability in physiological conditions (simulated body fluid) was, however, compromised very early in the experiment (day 1 and 3, with and without Nisin Z, respectively). Only the crosslinked SAGNCL fibers remained intact for the 28 day-testing period. Their thermal resilience in comparison with the unmodified and SA-free fibers was also demonstrated. Nisin Z was functionalized onto the unmodified and chemically altered fibers at an average concentration of 178 µg/mL. Nisin Z did not impact on the fiber's morphology nor on their chemical/thermal stability. However, the peptide improved the SA fibers (control) structural integrity, guaranteeing its stability for longer, in physiological conditions. Its main effect was detected on the time-kill kinetics of the bacteria S. aureus. SAGNCL and GNCL loaded with Nisin Z were capable of progressively eliminating the bacteria, reaching an inhibition superior to 99% after 24 h of culture. The peptide-modified SA and SAGN were not as effective, losing their antimicrobial action after 6 h of incubation. Bacteria elimination was consistent with the release kinetics of Nisin Z from the fibers. In general, data revealed the increased potential and durable effect of Nisin Z (significantly superior to its free, unloaded form) against S. aureus-induced infections, while loaded onto prospective biomedical wet-spun scaffolds.

Poly(γ-glutamic acid) and poly(γ-glutamic acid)-based nanocomplexes enhance type II collagen production in intervertebral disc.

Intervertebral disc (IVD) degeneration often leads to low back pain, which is one of the major causes of disability worldwide, affecting more than 80% of the population. Although available treatments for degenerated IVD decrease symptoms' progression, they fail to address the underlying causes and to restore native IVD properties. Poly(γ-glutamic acid) (γ-PGA) has recently been shown to support the production of chondrogenic matrix by mesenchymal stem/stromal cells. γ-PGA/chitosan (Ch) nanocomplexes (NCs) have been proposed for several biomedical applications, showing advantages compared with either polymer alone. Hence, this study explores the potential of γ-PGA and γ-PGA/Ch NCs for IVD regeneration. Nucleotomised bovine IVDs were cultured ex vivo upon injection of γ-PGA (pH 7.4) and γ-PGA/Ch NCs (pH 5.0 and pH 7.4). Tissue metabolic activity and nucleus pulposus DNA content were significantly reduced when NCs were injected in acidic-buffered solution (pH 5.0). However, at pH 7.4, both γ-PGA and NCs promoted sulphated glycosaminoglycan production and significant type II collagen synthesis, as determined at the protein level. This study is a first proof of concept that γ-PGA and γ-PGA/Ch NCs promote recovery of IVD native matrix, opening new perspectives on the development of alternative therapeutic approaches for IVD degeneration.

Forensic discrimination of vaginal epithelia by DNA methylation analysis through pyrosequencing.

The accurate identification of body fluids from crime scenes can aid in the discrimination between criminal and innocent intent. This research aimed to determine if the levels of DNA methylation in the locus PFN3A could be used to discriminate vaginal epithelia from other body fluids. In this work we bisulfite-modified and amplified DNA samples from blood, saliva, semen, and vaginal epithelia using primers for PFN3A. Through pyrosequencing we were able to show that vaginal epithelia present distinct methylation levels when compared to other body fluids. Mixtures of different body fluids present methylation values that correlate with single-source body fluid samples and the primers for PFN3A are specific for primates. This report successfully demonstrated that the analysis of methylation in the PFN3A locus can be used for vaginal epithelia discrimination in forensic samples.

A collaborative exercise on DNA methylation based body fluid typing.

A collaborative exercise on DNA methylation based body fluid identification was conducted by seven laboratories. For this project, a multiplex methylation SNaPshot reaction composed of seven CpG markers was used for the identification of four body fluids, including blood, saliva, semen, and vaginal fluid. A total of 30 specimens were prepared and distributed to participating laboratories after thorough testing. The required experiments included four increasingly complex tasks: (1) CE of a purified single-base extension reaction product, (2) multiplex PCR and multiplex single-base extension reaction of bisulfite-modified DNA, (3) bisulfite conversion of genomic DNA, and (4) extraction of genomic DNA from body fluid samples. In tasks 2, 3 and 4, one or more mixtures were analyzed, and specimens containing both known and unknown body fluid sources were used. Six of the laboratories generated consistent body fluid typing results for specimens of bisulfite-converted DNA and genomic DNA. One laboratory failed to set up appropriate conditions for capillary analysis of reference single-base extension products. In general, variation in the values obtained for DNA methylation analysis between laboratories increased with the complexity of the required experiments. However, all laboratories concurred on the interpretation of the DNA methylation profiles produced. Although the establishment of interpretational guidelines on DNA methylation based body fluid identification has yet to be performed, this study supports the addition of DNA methylation profiling to forensic body fluid typing.

High-resolution melt analysis of DNA methylation to discriminate semen in biological stains.

The goal of this study was to develop a method for the detection of semen in biological stains using high-resolution melt (HRM) analysis and DNA methylation. To perform this task, we used an epigenetic locus that targets a tissue-specific differentially methylated region for semen. This specific locus, ZC3H12D, contains methylated CpG sites that are hypomethylated in semen and hypermethylated in blood and saliva. Using this procedure, DNA from forensic stains can be isolated, processed using bisulfite-modified polymerase chain reaction (PCR), and detected by real-time PCR with HRM capability. The method described in this article is robust; we were able to obtain results from samples with as little as 1 ng of genomic DNA. Samples inhibited by humic acid still produced reliable results. Furthermore, the procedure is specific and will not amplify non-bisulfite-modified DNA. Because this process can be performed using real-time PCR and is quantitative, it fits nicely within the workflow of current forensic DNA laboratories. As a result, it should prove to be a useful technique for processing trace evidence samples for serological analysis.

Evaluation of DNA methylation markers and their potential to predict human aging.

We present epigenetic methylation data for two genetic loci, GRIA2, and NPTX2, which were tested for prediction of age from different donors of biofluids. We analyzed 44 saliva samples and 23 blood samples from volunteers with ages ranging from 5 to 72 years. DNA was extracted and bisulfite modified using commercial kits. Specific primers were used for amplification and methylation profiles were determined by pyrosequencing. Methylation data from both markers and their relationship with age were determined using linear regression analysis, which indicates a positive correlation between methylation and age. Older individuals tend to have increased methylation in both markers compared to younger individuals and this trend was more pronounced in the GRIA2 locus when compared to NPTX2. The epigenetic predicted age, calculated using a GRIA2 regression analysis model, was strongly correlated to chronological age (R(2) = 0.801), with an average difference of 6.9 years between estimated and observed ages. When using a NPTX2 regression model, we observed a lower correlation between predicted and chronological age (R(2) = 0.654), with an average difference of 9.2 years. These data indicate these loci can be used as a novel tool for age prediction with potential applications in many areas, including clinical and forensic investigations.

Fibrous Structures: An Overview of Their Responsiveness to External Stimuli towards Intended Application.

In recent decades, the interest in responsive fibrous structures has surged, propelling them into diverse applications: from wearable textiles that adapt to their surroundings, to filtration membranes dynamically altering selectivity, these structures showcase remarkable versatility. Various stimuli, including temperature, light, pH, electricity, and chemical compounds, can serve as triggers to unleash physical or chemical changes in response. Processing methodologies such as weaving or knitting using responsive yarns, electrospinning, as well as coating procedures, enable the integration of responsive materials into fibrous structures. They can respond to these stimuli, and comprise shape memory materials, temperature-responsive polymers, chromic materials, phase change materials, photothermal materials, among others. The resulting effects can manifest in a variety of ways, from pore adjustments and altered permeability to shape changing, color changing, and thermal regulation. This review aims to explore the realm of fibrous structures, delving into their responsiveness to external stimuli, with a focus on temperature, light, and pH.

Utility of realistic microscopy-based cell models in simulation studies of nanoparticle-enhanced photon radiotherapy.

To enhance the effect of radiation on the tumor without increasing the dose to the patient, the combination of high-Z nanoparticles with radiotherapy has been proposed. In this work, we investigate the effects of the physical parameters of nanoparticles (NPs) on the Dose Enhancement Factor (DEF), and on the Sensitive Enhancement Ratio (SER) by applying a version of the Linear Quadratic Model. A method for constructing voxelized realistic cell geometries in Monte Carlo simulations from confocal microscopy images was developed and applied to Gliobastoma Multiforme cell lines (U87 and U373). The comparison of simulations with realistic geometry and spherical geometry shows that there is significant impact on the survival curves obtained for the same irradiation conditions. Using this model, the DEF and the SER are determined as a function of the concentration, size and distribution of gold nanoparticles within the cell. For small NPs,dAuNP= 10 nm, no clear trend in the DEF and SER was observed when the number of NPs within the cell increases. Experimentally, the variable number of NPs measured inside the U373 cells (ranging between 1.48 × 105and 1.19 × 106) also did not influence much the observed cell survival upon irradiation of the cells with a Co-60 source. The same lack of trend is obtained when the Au content in the cell is kept constant, 0.897 mg/g, but the size of the NPs is changed. However, if the number of NPs is kept constant (7.91 × 105) and the size changes, there is a critical diameter above which the dose effect increases significantly. Using the realistic geometries, it was verified that the key parameter for the DEF and the SER enhancement is the volume fraction of Au in the cell, with NP size being a more important parameter than the number of NPs.

Microplastics in beach sediments of the Azores archipelago, NE Atlantic.

Oceanic islands are exposed to plastic debris that has accumulated in the open ocean, particularly in the subtropical gyres. This study investigates the abundance and typology of microplastics (from 0.1 to 5 mm) on 19 sandy beaches spread across 8 oceanic islands of the Azores archipelago. Between January and April 2016, a total of 341 particles retrieved from all beaches, were identified as microplastics. The highest concentration (50.19 ± 21.93 particles kg-1 dw) was found in Terceira Island. Beach morphology and grain size were important factors explaining microplastic concentration. Fibres were the most dominant morphology recovered (80.9 %), followed by fragments (12.3 %). Fourier transform infrared spectroscopy (FTIR) revealed that 41 % of the fibres consisted of polyester and 60 % of the fragments were polyethylene. This research underlines the widespread contamination of microplastics in oceanic islands of the Atlantic Ocean.

Pathological Complete Response After Neoadjuvant Imatinib in a Recurrent Duodenal Gastrointestinal Stromal Tumor (GIST).

Gastrointestinal stromal tumors (GISTs) are the most frequent mesenchymal neoplasms of the gastrointestinal (GI) tract. Although surgery is the treatment of choice in resectable disease, neoadjuvant therapy is indicated in advanced, metastatic, and recurrent tumors. Decreasing tumor burden may facilitate resection and reduce surgical morbidity. We describe a case of a 66-year-old male with a recurrent duodenal GIST, after surgery and adjuvant imatinib five years before. Following neoadjuvant therapy with imatinib for 12 months, the patient underwent a cephalic pancreaticoduodenectomy, without complications. The final histopathology showed a pathological complete response (pCR) with no residual neoplasm. A pathological complete response to imatinib in a recurrent disease is extremely rare. Molecular testing should be performed before neoadjuvant therapy to identify response-predictive mutations. In recurrent/metastatic disease, systemic therapy is the standard treatment for all patients. Surgery should be considered in a tailored approach in patients with good responses to systemic therapy before developing therapeutic resistance.

Developmental validation of the ForenSeq® Kintelligence kit, MiSeq FGx® sequencing system and ForenSeq Universal Analysis Software.

Forensic Investigative Genetic Genealogy, a recent sub discipline of forensic genomics, leverages the high throughput and sensitivity of detection of next generation sequencing and established genetic and genealogical approaches to support the identification of human remains from missing persons investigations and investigative lead generation in violent crimes. To facilitate forensic DNA evidence analysis, the ForenSeq® Kintelligence multiplex, consisting of 10,230 SNPs, was developed. Design of the ForenSeq Kintelligence Kit, the MiSeq FGx® Sequencing System and the ForenSeq Universal Analysis Software is described. Developmental validation in accordance with SWGDAM guidelines and forensic quality assurance standards, using single source samples, is reported for the end-to-end workflow from library preparation to data interpretation. Performance metrics support the conclusion that more genetic information can be obtained from challenging samples compared to other commercially available forensic targeted DNA assays developed for capillary electrophoresis (CE) or other current next generation sequencing (NGS) kits due to the higher number of markers, the overall shorter amplicon sizes (97.8% <150 bp), and kit design. Data indicate that the multiplex is robust and fit for purpose for a wide range of quantity and quality samples. The ForenSeq Kintelligence Kit and the Universal Analysis Software allow transfer of the genetic component of forensic investigative genetic genealogy to the operational forensic laboratory.

Clinical course and disease burden of patients with generalized pustular psoriasis in Portugal: a multicenter retrospective cohort study.

OBJECTIVES: Generalized pustular psoriasis (GPP) is a rare, life-threatening skin inflammatory disorder. This study aimed to describe the disease course, treatment strategies, and healthcare utilization among patients with GPP in Portugal. METHODS: This multicentric, observational, retrospective study included consecutive adult patients with GPP undergoing a dermatology evaluation in different reporting institutions by experienced dermatologists between 2002 and 2023. RESULTS: A total of 59 patients were assessed. Most of the cohort had a previous history of plaque psoriasis (71%) and 83% presented at least one comorbidity. At the initial encounter, 64% of the cohort needed hospitalization. Systemic involvement was common, including fever (37%), and elevated white blood cell count and erythrocyte sedimentation rate/C-reactive protein (49%). Nearly, 73% of patients initiated systemic drugs, and 70% had to discontinue the first treatment. During the study, 98% of patients experienced at least one flare. At the last visit, 3.4% of patients had died, and 71.2% exhibited signs of active disease despite undergoing treatment. CONCLUSIONS: Our study demonstrates that GPP is a chronic, debilitating condition associated with systemic involvement, frequent flares, and hospitalizations, despite receiving multiple systemic treatments. Improved disease awareness and new treatments are needed to improve patient care and decrease the burden of the disease.