Fragment Profiles Research Articles

Crystal structure analysis and fragmentation profile of lorcaserin hydrochloride hemihydrate

Lorcaserin, a 2,3,4,5-tetrahydro-3-benzazepine possessing a methyl and chloro groups in C-4 and C-9, respectively, is a drug currently used to treat obesity. Considering the role of the crystalline state to the understanding of the drug properties, allied to inexistence of solid state structural data in the worldwide accessible literature and database such as Crystallographic Cambridge Data Centre (CCDC), here we report the crystal structure of lorcaserin hydrochloride hemihydrate, inspecting in full detail its intra and intermolecular features for the first time, together with NMR data and fragmentation profile by ESI(+)-MS/MS.

Modeling cell-free DNA fragment size densities for non-invasive detection of cancer.

3058 Background: Circulating cell-free DNA (cfDNA) is largely nucleosomal in origin with typical fragment lengths of 167 base-pairs reflecting the length of DNA wrapped around-the histone and H1 linker. Given the nucleosomal origin of cfDNA, we have previously used low coverage whole genome sequencing to evaluate DNA fragmentation profiles to sensitively and specifically detect tumor-derived DNA with altered fragment lengths or coverage. Methods: Here we evaluate the use of Bayesian finite mixtures to model the fragment length distribution and demonstrate how the parameters from these models can be useful to distinguish between individuals with and without cancer. We examined the number of cfDNA fragments by size ranging from 100-220bp and approximated the mixture component location, scale, and weight using Markov Chain Monte Carlo. The performance of the method was determined using a ten-fold, ten repeat cross-validation of Gradient Boosted Machine model using 1) our previously described genome-wide fragmentation profile approach, 2) the parameters from the mixture model and 3) a combination of approaches 1) and 2) as features. Results: In this study of 215 cancer patients and 208 cancer-free individuals, we observed cross-validated AUCs of 1) 0.94, 2) 0.95, and 3) 0.97 among the three approaches. Conclusions: Our findings indicate that parsimonious mixture models may improve detection of cancer in conjunction with fragmentation profile analyses across the genome.

Early detection of lung cancer using cfDNA fragmentation.

8519 Background: Lung cancer incidence and mortality are increasing worldwide despite more effective treatments. This is primarily due to the late stage of diagnosis when treatments are less effective. Although large randomized trials have demonstrated a significant decrease in lung cancer mortality through screening of high-risk individuals with chest low dose computed tomography (LDCT), LDCT has made little impact in the community, mainly due to lack of accessibility. There is therefore an unmet clinical need for development of cost-effective and easily implemented tests for early lung cancer detection. Methods: We have previously shown that altered genome-wide fragmentation of cell free DNA (cfDNA) is a common characteristic of many cancers. In this study, we leverage this knowledge to increase the sensitivity of lung cancer detection by interrogating characteristics of the size distribution of cfDNA fragments across the genome using machine learning methods. The approach we present, called DELFI (DNA evaluation of fragments for early interception) generates a score that reflects the presence of tumor-derived DNA in plasma based on a multi-feature genomic analysis that assesses millions of cfDNA fragments for tumor-derived genomic and epigenomic changes in a small amount of blood (2-4 mls) via inexpensive low coverage (1-2x) whole genome sequencing. We applied this methodology in a prospectively collected cohort of 365 individuals under investigation for lung cancer and we prospectively validated it in a separate case-control cohort of patients with newly diagnosed early stage lung cancer as well as individuals without cancer (n=427). Results: These analyses revealed high performance for detection of early and late stage disease (Table). When DELFI was used as a prescreen for LDCT it increased specificity from 58% with CT imaging alone to 80% using the combined approach. The DELFI score was significantly associated with T and N stage in lung cancer cases (p<0.0001) as well as with overall survival (p=0.003). In a multivariable analysis including age, histology and stage, DELFI score was an independent prognostic factor of overall survival (HR=2.53; p=0.0003). Finally, we determined that genome-wide fragmentation profiles can be used to distinguish small cell lung cancer from non-small cell lung cancer with high accuracy (AUC 0.98). Conclusions: These findings provide key insights into cfDNA fragmentation in patients with cancer and a new and easily accessible avenue for non-invasive diagnosis and molecular profiling of lung cancer.[Table: see text]

Role of microscopic temperature-dependent binding energies in the decay of Si*32 formed in the O20+C12 reaction

The investigation of fusion reactions involving light neutron-rich exotic nuclei is of paramount significance to understand nucleosynthesis in astrophysical scenarios. It is also estimated as a possible heat source to ignite $^{12}\mathrm{C}+^{12}\mathrm{C}$ reaction and production of x-ray superbursts from accreting neutron star. Recently, the fusion of neutron-rich $^{20}\mathrm{O}$ with $^{12}\mathrm{C}$ target has been studied with measurement of fusion cross-section $({\ensuremath{\sigma}}_{\text{fus}})$. Bass model under predicts the ${\ensuremath{\sigma}}_{\text{fus}}$ and time-dependent Hartree-Fock model also fails to explain the experimental data. To explicate the same, the investigation of $^{20}\mathrm{O}+^{12}\mathrm{C}$ reaction at near barrier energies has been made within quantum mechanical fragmentation-based dynamical cluster-decay model (DCM). Within DCM, the fragmentation potential comprises temperature-dependent Coulomb, nuclear and centrifugal potentials, along with temperature-dependent binding energies (T.B.E.) calculated within the macroscopic approach of Davidson mass formula. Recently, we have explored the temperature-dependence of different nuclear properties and nuclear symmetry energy within microscopic relativistic mean-field (RMF) theory [M. Kaur et al., Nucl. Phys. A 1000, 121871 (2020)]. In the present work, we inculcate the microscopic T.B.E. from RMF theory within DCM and investigate the structure of fragmentation potential for $^{32}\mathrm{Si}^{*}$ formed in $^{20}\mathrm{O}+^{12}\mathrm{C}$ reaction, comparatively for macroscopic (mac) and microscopic (mic) T.B.E. obtained from Davidson mass formula and RMF theory, respectively. The structure and magnitude of fragmentation potential are found to change drastically/notably along with a change in energetically favored/minimized fragments for both choices of T.B.E. The $\ensuremath{\alpha}$ particles $(^{4}\mathrm{He}$, $^{5}\mathrm{He})$ are favored at lower angular momenta in fragmentation profile for mic T.B.E. case only, which is in the agreement with predictions of statistical model results. This change in the nuclear structure embodied via fragmentation potential energy carries its imprints in the preformation probability ${P}_{0}$ of different fragments and affects the contribution of individual light-charged particle (LCP) channel in the ${\ensuremath{\sigma}}_{\text{fus}}$. A comparison of the relative cross-section of different LCP channels toward ${\ensuremath{\sigma}}_{\text{fus}}$ is quite different for both cases of T.B.E. The cross-section of $^{2}\mathrm{H}$ and $^{4}\mathrm{He}$ LCP channels is relatively enhanced for mic T.B.E. compared to mac T.B.E. Among different LCP channels, the $^{5}\mathrm{He}$ channel is the major contributor in ${\ensuremath{\sigma}}_{\text{fus}}$, which is in line with the results of the statistical EVAPOR model. The DCM-calculated ${\ensuremath{\sigma}}_{\text{fus}}$ is in agreement with the experimental data.

Enhancing liquid biopsies

Medicine Liquid biopsies, analyses of cell-free DNA that circulates in the blood, can be used in prenatal testing, oncology, and to monitor organ transplant recipients. Lo et al. review the nongenetic information that can be gleaned from analyses of cell-free DNA, which offers additional promise for the applications of this procedure. These analyses include DNA methylation patterns, fragmentation profiles, and topology, which can be informative about the health and origin of the tissue from which they are derived. Science , this issue p. [eaaw3616][1] [1]: /lookup/doi/10.1126/science.aaw3616

Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies.

Liquid biopsies that analyze cell-free DNA in blood plasma are used for noninvasive prenatal testing, oncology, and monitoring of organ transplant recipients. DNA molecules are released into the plasma from various bodily tissues. Physical and molecular features of cell-free DNA fragments and their distribution over the genome bear information about their tissues of origin. Moreover, patterns of DNA methylation of these molecules reflect those of their tissue sources. The nucleosomal organization and nuclease content of the tissue of origin affect the fragmentation profile of plasma DNA molecules, such as fragment size and end motifs. Besides double-stranded linear fragments, other topological forms of cell-free DNA also exist-namely circular and single-stranded molecules. Enhanced by these features, liquid biopsies hold promise for the noninvasive detection of tissue-specific pathologies with a range of clinical applications.

Expression Profiles of tRNA-Derived Fragments and Their Potential Roles in Multiple Myeloma.

BackgroundMultiple myeloma is an incurable hematologic malignancy. The discovery of mechanisms may help to find new therapeutic targets and prolong survival. tRNA-related fragments (tRF) and tRNA halves (tiRNA) are small RNA derived from tRNAs and implicated in a wide variety of pathological processes, including cancer initiation and progression. However, there are almost no research reporting the role of these tRNA derived fragments in myeloma as far as we know.MethodsIn this study, we proposed the expression profiles of tRFs/tiRNAs in myeloma through RNA-sequencing in new diagnosed myeloma and healthy donors. The expression of selected tRFs/tiRNAs was further validated in clinical specimens by qPCR. Bioinformatic analysis was performed to predict their potential roles in multiple myeloma.ResultsA total of 33 upregulated tRFs/tiRNAs and 22 downregulated tRFs/tiRNAs were identified. GO enrichment and KEGG pathway analysis were performed to analyze the functions of one significantly up-regulated and one significantly down-regulated tRNA-derived fragments. tRFs/tiRNAs may be involved in MM initiation and progression.ConclusionWe concluded that tRFs/tiRNAs were dysregulated and could be potential biomarkers for multiple myeloma.

Characterization of stress degradation products of nintedanib by UPLC, UHPLC-Q-TOF/MS/MS and NMR: Evidence of a degradation product with a structure alert for mutagenicity

Nintedanib is an anti-cancer drug used for the treatment of idiopathic pulmonary fibrosis and non-small cell lung cancer. The purpose of this study was to explore its degradation chemistry under various stress conditions recommended in ICH guidelines Q1A R(2). The drug was subjected to hydrolytic, photolytic, thermal and oxidative (H2O2, AIBN, FeCl3 and FeSO4) stress conditions. The degradation products formed in stressed solutions were successfully separated on an ACQUITY UPLC CSH C18 (2.1 × 100 mm, 1.7 μm) column, using a gradient UPLC-PDA method, developed with acetonitrile:methanol (90:10) and 0.1 % formic acid (pH 3.0) as the mobile phase. The drug proved to be labile to acidic, neutral and alkaline hydrolytic, and H2O2/AIBN oxidative conditions. It was stable to photolytic and thermal stress conditions, and even in oxidative reaction solutions containing FeCl3 or FeSO4. Additionally, the drug exhibited instability when its powder with added sodium bicarbonate was stored at 40 °C/75 % RH for 3 months. In total, nine degradation products (DPs 1–9) were formed. To characterize them, a comprehensive mass fragmentation pathway of the drug was first established using UHPLC-Q-TOF/MS/MS data. Similarly, the mass studies were then carried out on the stressed samples using the developed UPLC method. All the degradation products were primarily characterized through comparison of their mass fragmentation profiles with that of the drug. To confirm the structure in one case (DP 3), additional nuclear magnetic resonance (NMR) studies were carried out on the isolated product. Subsequently, mechanisms for their formation were laid down. A significant finding was the formation of a degradation product upon acid hydrolysis having a free aromatic amine moiety, which is considered as a structural alert for mutagenicity. Furthermore, the physicochemical and ADMET properties of the drug and its degradation products were predicted using ADMET predictor™ software.

A Metabolomics and Molecular Networking Approach to Elucidate the Structures of Secondary Metabolites Produced by Serratia marcescens Strains.

An integrated approach that combines reverse-phase high-performance liquid chromatography (RP-HPLC), electrospray ionization mass spectrometry, untargeted ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MSE) and molecular networking (using the Global Natural Products Social molecular network platform) was used to elucidate the metabolic profiles and chemical structures of the secondary metabolites produced by pigmented (P1) and non-pigmented (NP1) Serratia marcescens (S. marcescens) strains. Tandem mass spectrometry-based molecular networking guided the structural elucidation of 18 compounds for the P1 strain (including 6 serratamolides, 10 glucosamine derivatives, prodigiosin and serratiochelin A) and 15 compounds for the NP1 strain (including 8 serratamolides, 6 glucosamine derivatives and serratiochelin A) using the MSE fragmentation profiles. The serratamolide homologues were comprised of a peptide moiety of two L-serine residues (cyclic or open-ring) linked to two fatty acid chains (lengths of C10, C12, or C12:1). Moreover, the putative structure of a novel open-ring serratamolide homologue was described. The glucosamine derivative homologues (i.e., N-butylglucosamine ester derivatives) consisted of four residues, including glucose/hexose, valine, a fatty acid chain (lengths of C13 – C17 and varying from saturated to unsaturated) and butyric acid. The putative structures of seven novel glucosamine derivative homologues and one glucosamine derivative congener (containing an oxo-hexanoic acid residue instead of a butyric acid residue) were described. Moreover, seven fractions collected during RP-HPLC, with major molecular ions corresponding to prodigiosin, serratamolides (A, B, and C), and glucosamine derivatives (A, C, and E), displayed antimicrobial activity against a clinical Enterococcus faecalis S1 strain using the disc diffusion assay. The minimum inhibitory and bactericidal concentration assays however, revealed that prodigiosin exhibited the greatest antimicrobial potency, followed by glucosamine derivative A and then the serratamolides (A, B, and C). These results provide crucial insight into the secondary metabolic profiles of pigmented and non-pigmented S. marcescens strains and confirms that S. marcescens strains are a promising natural source of novel antimicrobial metabolites.

A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea.

Simple SummaryIn recent years, a growing interest has been devoted to the bacterial characterization of marine plastic debris. So far, a few publications have explored the composition of microbial communities on polyethylene (PE) waste items and the occurrence of antibiotic-resistant bacteria (ARB). The occurrence of ARB in natural matrices can contribute to the spread of antibiotic resistance genes (ARGs) among environmental bacteria. In this study, we compared the microbial composition and the presence of ARGs in water and PE fragments collected from a stream and the seawater in a coastal area of Northwestern Sicily. Our findings showed more ARGs on PE fragments than the corresponding water samples, confirming that PE can act as a carrier of antibiotic-resistance genes causing high damage to the marine environment and living organisms.In this study, we evaluated the microbiome and the resistome profile of water and fragments of polyethylene (PE) waste collected at the same time from a stream and the seawater in a coastal area of Northwestern Sicily. Although a core microbiome was determined by sequencing of the V3–V4 region of the bacterial 16S rDNA gene, quantitative differences were found among the microbial communities on PE waste and the corresponding water samples. Our findings indicated that PE waste contains a more abundant and increased core microbiome diversity than the corresponding water samples. Moreover, PCR analysis of specific antibiotic resistance genes (ARGs) showed that PE waste harbors more ARGs than the water samples. Thus, PE waste could act as a carrier of antibiotic-resistant microbiota, representing an increased danger for the marine environment and living organisms, as well.

Analysis of Vannamei shrimp DNA fragment resistant to White Spot Virus Syndrome

The attack of WSSV in Vannamei shrimp cultivation is still common. Shrimp quality improvement can be made through selection with the help of markers (marker-assisted choice). This study aimed to evaluate the DNA fragment profile of white shrimp that was resistant to WSSV disease. The analysis was performed using the PCR-RAPD method. WSSV challenged four groups of 100 Vannamei shrimp, then DNA was extracted from live and dead shrimp. The results showed that 2 of the 17 primers tested had high potential as markers, namely OP-09 and OPD-2. PCR products with OPC-09 primers had specific DNA bands measuring about 1.2 kb in all post-challenge WSSV resistant shrimp individuals. The amplification results using OPD-02 primers showed a particular band of DNA with a length of about 1.0 kb, with 60 % of the appearance in WSSV-resistant shrimp. In contrast, the WSSV-susceptible shrimp group did not have specific DNA fragments. Thus, the two RAPD primers had a high chance of being used in the selection with the help of markers to produce WSSV resistant shrimp.

Mechanism of biochar-gas-tar-soot formation during pyrolysis of different biomass feedstocks: Effect of inherent metal species

The thermal behavior and evolution profiles of major volatile fragments from each biomass pyrolysis (i.e., rice husk, sawdust, cornstalk) have been discussed in depth, while paying close attention to the impact and contributions of inherent metal species on the raw material pyrolysis. It is found that high temperature would promote the conversion of tar to soot. The insertion of O atoms increases the size of microcrystalline structure of soot. The formation of soot mainly comes from the polymerization reaction between the cracked products of macromolecular precursors produced by devolatilization. And inherent metal species can inhibit the formation of soot. Before 500 °C, the pyrolysis of biomass has basically been completed. The inherent metal species would promote the biomass pyrolysis reaction, according to the kinetic results. The inherent metal species decrease the O atoms of tar component, increase its complexity and reduce the degree of polymerization. In homogeneous transformation, the inherent metal species would promote the cracking of tar precursors into gases, and inhibit the polymerization of aromatic compounds. In heterogeneous transformation, the inherent metal species could promote the production of small molecular gases. This research could lay the foundation for further analysis of the homogeneous/heterogeneous conversion of biomass pyrolysis and provide theoretical support for the process optimization of biomass utilization technology.

Genetic Identification of all Four Mangrove Mud Crab Species (genus Scylla) Using Multiple Molecular Markers.

Misleading identification and subsequent publications on biological, molecular, and aquaculture data of mangrove mud crab (genus Scylla de Hann 1833) is a major concern in many countries. In this study, multiple molecular markers were used for genetic identification of all four known mud crab species under genus Scylla collected from India, Philippines, Myanmar, Malaysia and Indonesia. Internal Transcribed Spacer (ITS-1), Polymerase chain reaction (PCR)-Restriction Fragment Length Polymorphism (PCR-RFLP) and PCR-based species-specific markers were used to resolve taxonomic ambiguity. PCR-RFLP techniques using NlaIV and BsaJI restriction endonucleases were efficient to differentiate four different mud crab species under genus Scylla with specific fragment profile. The results also justified the use of ITS-1 and PCR-based species-specific markers to identify mud crab species available in many countries quite rapidly and effectively. Several new molecular markers generated during the study are reported here to resolve the taxonomic ambiguity of Scylla species and the results reconfirmed that India is only having two commonly available mud crab species which was reported by the authors earlier.

Enhanced Detection of Genitourinary Cancers Using Fragmentation and Copy Number Profiles Obtained from Urinary Cell-Free DNA.

Recent studies have reported that examining the fragmentation profiles (FP) of plasma cell-free DNA (cfDNA) further improves the clinical sensitivity of tumor detection. We hypothesized that considering the differences of the FP of urinary cfDNA would increase the clinical sensitivity of genitourinary (GU) cancer detection. 177 patients with GU cancer and 94 individuals without tumors were enrolled in the discovery cohort. An independent validation dataset comprising 30 patients without tumors and 66 patients with GU cancer was also collected. We constructed an ensemble classifier, GUIDER, to detect and localize GU cancers using fragmentation and copy number profiles obtained from shallow whole-genome sequencing of urinary cfDNA. Urinary cfDNA of patients with GU cancer had a higher proportion of long fragments (209-280 bp) and a lower proportion of short fragments (140-208 bp) compared to controls. The overall mean classification accuracy of the FP was 74.62%-85.39% for different algorithms, and integration of the FP and copy number alteration (CNA) features further enhanced the classification of samples from patients with GU cancer. The mean diagnostic accuracy was further improved by the ensemble classifier GUIDER, which integrated the FP and CNA profiles and resulted in a higher mean accuracy (87.52%) compared to the analysis performed without FP features (74.62%). GUIDER performed well in an independent validation dataset. The lengthening and shortening of urinary cfDNA within specific size ranges were identified in patients with GU cancer. Integration of the FP should further enhance the ability to use urinary cfDNA as a molecular diagnostic tool.

Dose quantification in carbon ion therapy using in-beam positron emission tomography

This work presents an iterative method for the estimation of the absolute dose distribution in patients undergoing carbon ion therapy, via analysis of the distribution of positron annihilations resulting from the decay of positron-emitting fragments created in the target volume. The proposed method relies on the decomposition of the total positron-annihilation distributions into profiles of the three principal positron-emitting fragment species - 11C, 10C and 15O. A library of basis functions is constructed by simulating a range of monoenergetic 12C ion irradiations of a homogeneous polymethyl methacrylate phantom and measuring the resulting one-dimensional positron-emitting fragment profiles and dose distributions. To estimate the dose delivered during an arbitrary polyenergetic irradiation, a linear combination of factors from the fragment profile library is iteratively fitted to the decomposed positron annihilation profile acquired during the irradiation, and the resulting weights combined with the corresponding monoenergetic dose profiles to estimate the total dose distribution. A total variation regularisation term is incorporated into the fitting process to suppress high-frequency noise. The method was evaluated with 14 different polyenergetic 12C dose profiles in a polymethyl methacrylate target: one which produces a flat biological dose, 10 with randomised energy weighting factors, and three with distinct dose maxima or minima within the spread-out Bragg peak region. The proposed method is able to calculate the dose profile with mean relative errors of 0.8%, 1.0% and 1.6% from the 11C, 10C, 15O fragment profiles, respectively, and estimate the position of the distal edge of the SOBP to within an average of 0.7 mm, 1.9 mm and 1.2 mm of its true location.

Genome-wide and size-based cell-free DNA indices as predictive biomarkers for locally advanced esophageal squamous cell carcinoma treated with preoperative or definitive chemoradiotherapy

For locally advanced esophageal cancer, concurrent chemoradiotherapy (CRT) followed by surgery has been a standard treatment, while clinical studies showed comparable survival outcomes between definitive CRT and neoadjuvant CRT followed by surgery in patients responding to CRT. Thus, biomarkers are required to predict treatment outcomes and benefit of adding surgery after CRT. This prospective biomarker study examined the role of cell-free DNA (cfDNA) fragmentation profiles and genomic copy number variations (CNVs) in predicting treatment outcomes in esophageal squamous cell carcinoma patients treated with neoadjuvant or definitive CRT. The clinical response was evaluated after induction chemotherapy and after CRT. Fragment Ratio (FR)-score and I-score were calculated from plasma cfDNA reflecting fragment lengths and CNV of cfDNA, respectively. The association between indices of cfDNA (cfDNA concentration, FR-score, and I-score) and treatment outcomes (clinical response, time to progression [TTP], and overall survival [OS]) were evaluated. Sixty-one patients were included. Thirty patients received neoadjuvant CRT followed by surgery, whereas 31 received definitive CRT. Low baseline, post-induction chemotherapy, and post-CRT FR-scores and low post-induction I-score were significantly associated with improved treatment response (P < 0.05). Additionally, patients with surgery after CRT showed significantly longer survival than patients without surgery in the FR-score-high group (median TTP, 12.7 vs 3.4 months; P = 0.011; OS, not reached vs 12.9 months; P = 0.02), while there was no survival benefit with surgery in the FR-score-low group. FR-score may be a new biomarker to predict treatment response, residual tumor burden after CRT, and consequently, survival benefit of adding morbid surgery after CRT. FR-score has strength in a relatively simple and inexpensive methodology compared to deep sequencing, resulting in high availability and accessibility, despite limited sensitivity.

Effect of spray drying on the polyphenolic compounds present in purple sweet potato roots: Identification of new cinnamoylquinic acids

The effect of spray drying on the different polyphenolic compounds present in the root of a purple-fleshed sweet potato variety of Ipomoea batatas native from Peru was performed by HPLC-QTOF-MSMS. Nine anthocyanins, including four peonidin, three cyanidin and two pelargonidin derivatives glycosylated with sophorose and/or glucose and acylated with caffeic, ferulic and p-hydroxybenzoic acid were identified. Twenty nine cinnamoylquinic acids (CiQA), including eight mono-CiQA, fourteen di-CiQA, and five tri-CiQA, were identified on the base of their MS fragmentation profile. Relevant amounts of feruloylquinic acid derivatives were identified. Among them, some di and tri-CiQAs containing feruloyl and caffeoyl moieties in their structures, and di-feruloylquinic acids were reported here, for the first time, in Ipomoea. Spray drying process negatively affected the different phenolic groups, with polyphenol losses representing around 90% of the initial amounts. Mono-CiQAs presenting feruloyl moieties and mono acylated peonidin derivatives with p-hydroxybenzoic acid were the less affected compounds.

Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes.

Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.

Facile Synthesis and Nano-Silver Encapsulation of Paeonia emodi for Cardioprotective and Antihyperlipidemic Nursing Care Potentials

Paeonia emodi is a medicinal plant that is a vital family group of Paeoniaceae and traditionally utilized for treating cardiovascular diseases, such as hypertension, heart failure, atherosclerosis, epilepsy, and palpitations. In this work, we have constructed P. emodi (Pemodi. EA) ethyl acetate subsegment of which was exposed to gain fractions via column chromatography. These subsegments were confirmed by various electroscopic methods. Further, the subsegments were examined for their cardioprotective property on induced isoproterenol hydrochloride (ISO) myocardial infractions (MIs) in nude mice. Pemodi-EA-40 was utilized with maximum segment for synthesis of silver nanoparticles (Pemodi.EA-40@AgNPs). The extreme active segments Pe-EA-40 were examined for antihyperlipidemic, cardioprotective, and histopathological examinations. The body weights of Pemodi.EA-40 (100 mg/kg) remarkably reduced the blood levels of Alanine Aminotransferase (ALT), Aspartate Aminotransferase (AST), Lactic Acid Dehydrogenase (LDH), and Creatine Phosphokinase (CPK) associated with induced ISO treated groups. Pemodi.EA-40@AgNPs also reduced the ALT, AST, LDH, and CPK connected to the Pemodi.EA-40, respectively. The biochemical parameters and histological results reduced the changes as compared to induced ISO treated groups. The outcomes of our examinations proposed that the Pemodi.EA-40@AgNPs medicinal plant improves beneficial profiles of medicinal plant extract fragments for treatments and nursing care of myocardial infractions and atherosclerosis.

Tumor microenvironment and Oral Squamous Cell Carcinoma: A crosstalk between the inflammatory state and tumor cell migration

To analyze the inflammatory millieu in oral squamous cell carcinoma (OSCC) tumors and the influence of macrophages related-cytokines on the tumor cell migration. Inflammatory protein profile and macrophage population (M2/M1 ratio) of human OSCC fragments were analyzed by proteomic analysis and flow cytometry assay respectively. To evaluate the effects of inflammation on OSCC behavior, we analyzed the role of polarized macrophages and cytokines (IL-6, IL-1β and TNF-α) on OSCC cell lines (SCC25 and Cal27) responsiveness by western blotting (cell signaling) and time-lapse (cell migration). Also, it was addressed the crosstalk of IL-6-STAT3 axis with cell migration signaling using a STAT3 inhibitor (Stattic®) and a pull down assay for the RhoGTPase Rac1 activity. It was observed a ~2 fold predominance of M2 over M1 macrophages and a pro-inflammatory state in OSCC fragments. The M2 conditioned media increased migration speed and directionality of highly invasive OSCC cells (SCC25). OSCC cell lines were responsive to cytokine stimuli (IL6, IL-1β and TNF-α), but only IL-6 increased migration properties of OSCC cells. This effect was dependent on STAT3-phosphorylation levels, which interfered with Rac1 activation levels. Our results suggest that the inflammatory milieu might favor invasion and metastasis of OSCC by the direct effect of macrophage-related cytokines on tumor migration.