Search

Simple Summary: Metagenomics analysis measures microbiome diversity in samples without prior enrichment. Advances in High-Throughput Sequencing (HTS) have expanded its use from identifying known organisms to diagnosing diseases. Reliable results need strong validation with standard samples and databases from real and synthetic controls. We introduce the Metagenomic Standards Generator (MeStanG), a tool for creating HTS Nanopore data sets to test bioinformatics pipelines. MeStanG allows users to design and generate samples with specific numbers of reads for each organism from reference sequences and error profiles. The accuracy was tested by simulating metagenomic samples with known diversities and abundances expressed as number of reads. The analysis showed results that matched the expected organism composition in the samples. MeStanG is a valuable tool for scientists to create mock metagenomic samples useful in diagnostic assay validation studies and assess bioinformatics pipeline performance using simulated samples. Metagenomics analysis has enabled the measurement of the microbiome diversity in environmental samples without prior targeted enrichment. Functional and phylogenetic studies based on microbial diversity retrieved using HTS platforms have advanced from detecting known organisms and discovering unknown species to applications in disease diagnostics. Robust validation processes are essential for test reliability, requiring standard samples and databases deriving from real samples and in silico generated artificial controls. We propose a MeStanG as a resource for generating HTS Nanopore data sets to evaluate present and emerging bioinformatics pipelines. MeStanG allows samples to be designed with user-defined organism abundances expressed as number of reads, reference sequences, and predetermined or custom errors by sequencing profiles. The simulator pipeline was evaluated by analyzing its output mock metagenomic samples containing known read abundances using read mapping, genome assembly, and taxonomic classification on three scenarios: a bacterial community composed of nine different organisms, samples resembling pathogen-infected wheat plants, and a viral pathogen serial dilution sampling. The evaluation was able to report consistently the same organisms, and their read abundances as provided in the mock metagenomic sample design. Based on this performance and its novel capacity of generating exact number of reads, MeStanG can be used by scientists to develop mock metagenomic samples (artificial HTS data sets) to assess the diagnostic performance metrics of bioinformatic pipelines, allowing the user to choose predetermined or customized models for research and training. [ABSTRACT FROM AUTHOR]

Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. To this end, we conducted a comprehensive characterization of exonic variants in the population of Navarre (Spain), utilizing whole genome sequencing data from 358 unrelated individuals of Spanish origin. Our analysis revealed 61,410 biallelic single nucleotide variants (SNV) within the Navarrese cohort, with 35% classified as common (MAF > 1%). By comparing allele frequency data from 1000 Genome Project (excluding the Iberian cohort of Spain, IBS), Genome Aggregation Database, and a Spanish cohort (including IBS individuals and data from Medical Genome Project), we identified 1069 SNVs common in Navarre but rare (MAF ≤ 1%) in all other populations. We further corroborated this observation with a second regional cohort of 239 unrelated exomes, which confirmed 676 of the 1069 SNVs as common in Navarre. In conclusion, this study highlights the importance of population-specific characterization of genetic variation to improve allele frequency filtering in sequencing data analysis to identify disease-causing variants. [ABSTRACT FROM AUTHOR]

Simple Summary: The androgen receptor (AR) is an important protein involved in sensing hormones. The over-activation of a class of AR can lead to cellular dysfunction and diseases such as prostate cancer. This malfunction is connected to abnormal protein clusters known as condensates. To address this, a series of novel small molecules, which can potentially dissolve AR condensates, have been tested for their ability to change the shape of the AR. These molecules interact with disordered regions of the AR and consequently, weak structural signatures are buried in a vast amount of seemingly random shapes of the AR. We use biophysical models and computational approaches to examine the shapes of the AR when it is bound to a therapeutically promising small-molecule modulator. Here, we provide insights on how subtle alterations of the small-molecule modulator can strongly affect their ability to alter AR shapes. Intrinsically disordered regions (IDRs) of transcription factors play an important biological role in liquid condensate formation and gene regulation. It is thus desirable to investigate the druggability of IDRs and how small-molecule binders can alter their conformational stability. For the androgen receptor (AR), certain covalent ligands induce important changes, such as the neutralization of the condensate. To understand the specificity of ligand–IDR interaction and potential implications for the mechanism of neutralizing liquid–liquid phase separation (LLPS), we modeled and performed computer simulations of ligand-bound peptide segments obtained from the human AR. We analyzed how different covalent ligands affect local secondary structure, protein contact map, and protein–ligand contacts for these protein systems. We find that effective neutralizers make specific interactions (such as those between cyanopyrazole and tryptophan) that alter the helical propensity of the peptide segments. These findings on the mechanism of action can be useful for designing molecules that influence IDR structure and condensate of the AR in the future. [ABSTRACT FROM AUTHOR]

Shear-wave seismic reflection velocity-versus-depth models can complement our understanding of seepage pore pressure variations beneath earthen levees at locations between geotechnical sites. The seasonal variations of water level in the Mississippi River create pore pressure changes in the adjacent hydraulically connected aquifer on the protected side of artificial levees. Time-lapse shear-wave velocity analysis or repetition of seismic acquisition over an area is a non-invasive method that can detect seasonal pore pressure variations in shallow (<40 m) aquifers. The seismic reflection patterns during the seasonal pore pressure variations of the river show a distinctive change in the velocity semblance analysis, which is translated as a change in the average stress carried by the grain-to-grain contact, or simply the effective pressure. The seismic data show a greater variation of up to +140/−40 m/s or +700/−150 kPa in the confined aquifer zone, compared with the leaky confined aquifer zone of up to +46/−48 m/s or +140/−80 kPa. These relative effective pressure characteristics allow us to distinguish between confined and leaky aquifers and can be an optional approach for pressure prediction in floodplains along levees without the need to drill borings in the area to measure piezometric data. [ABSTRACT FROM AUTHOR]

The glucagon-like peptide-1 receptor (GLP-1R) plays a key role in metabolism and is an important therapeutic target in diabetes and obesity. Recent studies in experimental animals have shown that certain subsets of T cells express functional GLP-1R, indicating an immune regulatory role of GLP-1. In contrast, less is known about the expression and function of the GLP-1R in human T cells. Here, we provide evidence that activated human T cells express GLP-1R. The expressed GLP-1R was functional, as stimulation with a GLP-1R agonist triggered an increase in intracellular cAMP, which was abrogated by a GLP-1R antagonist. Analysis of CD4+ T cells activated under T helper (Th) 1, Th2, Th17 and regulatory T (Treg) cell differentiation conditions indicated that GLP-1R expression was most pronounced in induced Treg (iTreg) cells. Through multimodal single-cell CITE- and TCR-sequencing, we detected GLP-1R expression in 29–34% of the FoxP3+CD25+CD127- iTreg cells. GLP-1R+ cells showed no difference in their TCR-gene usage nor CDR3 lengths. Finally, we demonstrated the presence of GLP-1R+CD4+ T cells in skin from patients with allergic contact dermatitis. Taken together, the present data demonstrate that T cell activation triggers the expression of functional GLP-1R in human CD4+ T cells. Given the high induction of GLP-1R in human iTreg cells, we hypothesize that GLP-1R+ iTreg cells play a key role in the anti-inflammatory effects ascribed to GLP-1R agonists in humans. [ABSTRACT FROM AUTHOR]

Organic nitrogen plays a significant role in the fermentation performance and production of esters and higher alcohols. This study assessed the use of yeast protein hydrolysate (YPH) as a nitrogen source for grape must fermentation. In this study, we prepared an enzymatic protein hydrolysate using yeasts recovered from a previous fermentation of wine. Three treatments were performed. DAP supplementation was used as a control, while two YPH treatments were used. Low (LDH) and high degrees of hydrolysis (HDH), 3.5% and 10%, respectively, were chosen. Gas chromatography and principal component analysis indicated a significant positive influence of YPH-supplementations on the production of esters and higher alcohols. Significantly high concentrations of 3-methyl-1-penthanol, isoamyl alcohol, isobutanol, and 2-phenylethanol were observed. Significant odorant activity was obtained for 3-methyl-1-pentanol and ethyl-2-hexenoate. The use of YPH as nitrogen supplementation is justified as a recycling yeasts technique by the increase in volatile compounds. [ABSTRACT FROM AUTHOR]

This review aims to point out the importance of the synergic effects of two relevant and appealing polymeric issues: electrospun fibers and shape-memory properties. The attention is focused specifically on the design and processing of electrospun polymeric fibers with shape-memory capabilities and their potential application fields. It is shown that this field needs to be explored more from both scientific and industrial points of view; however, very promising results have been obtained up to now in the biomedical field and also as sensors and actuators and in electronics. [ABSTRACT FROM AUTHOR]

In this work, different poly (lactic acid) (PLA)-based nanocomposite electrospun fibers, reinforced with both organic and inorganic nanoparticles, were obtained. As organic fibers, cellulose nanocrystals, CNC, both neat and functionalized by "grafting from" reaction, chitosan and graphene were used; meanwhile, hydroxyapatite and silver nanoparticles were used as inorganic fibers. All of the nanoparticles were added at 1 wt% with respect to the PLA matrix in order to be able to compare their effect. The main aim of this work was to study the morphological, thermal and mechanical properties of the different systems, looking for differences between the effects of the addition of organic or inorganic nanoparticles. No differences were found in either the glass transition temperature or the melting temperature between the different electrospun systems. However, systems reinforced with both neat and functionalized CNC exhibited an enhanced degree of crystallinity of the electrospun fibers, by up to 12.3%. From a mechanical point of view, both organic and inorganic nanoparticles exhibited a decreased elastic modulus and tensile strength in comparison to neat electrospun PLA fibers, improving their elongation at break. Furthermore, all of the organic and inorganic reinforced systems disintegrated under composting conditions after 35 days. [ABSTRACT FROM AUTHOR]

Simple Summary: Colorectal cancer (CRC) is one of the most preventable yet deadliest cancers, one reason being that it involves very different lesions. Currently, there is a great international effort to improve CRC classification using as many molecular features as possible. A cutting-edge technique, imaging mass spectrometry, is used to enable the visualization of the bidimensional (2D) distribution of molecules across tissues in order to study how the composition of the cell membrane, in particular membrane lipids, changes in tumors. Our previous studies indicate that lipid composition is highly sensitive to cell alterations. Importantly, during the analysis, we are also able to establish changes in charged lipids, observations that can be misinterpreted. A close study of our results alongside information from public databases leads to the identification of gene coding for a potassium channel that could account for our observations and could represent a suitable target for drug development. Even though colorectal cancer (CRC) is one of the most preventable cancers, it is one of the deadliest, and recent data show that the incidence in people <50 years has unexpectedly increased. While new techniques for CRC molecular classification are emerging, no molecular feature is as yet firmly associated with prognosis. Imaging mass spectrometry (IMS) lipidomic analyses have demonstrated the specificity of the lipid fingerprint in differentiating pathological from healthy tissues. During IMS lipidomic analysis, the formation of ionic adducts is common. Of particular interest is the [Na+]/[K+] adduct ratio, which already functions as a biomarker for homeostatic alterations. Herein, we show a drastic shift of the [Na+]/[K+] adduct ratio in adenomatous colon mucosa compared to healthy mucosa, suggesting a robust increase in K+ levels. Interrogating public databases, a strong association was found between poor diagnosis and voltage-gated potassium channel subunit beta-2 (KCNAB2) overexpression. We found this overexpression in three CRC molecular subtypes defined by the CRC Subtyping Consortium, making KCNAB2 an interesting pharmacological target. Consistently, its pharmacological inhibition resulted in a dramatic halt in commercial CRC cell proliferation. Identification of potential pharmacologic targets using lipid adduct information emphasizes the great potential of IMS lipidomic techniques in the clinical field. [ABSTRACT FROM AUTHOR]

The molecular epidemiology of giardiasis in Africa remains unclear. A study was carried out across four hospitals in Algeria. A total of 119 fecal samples from 55 children, 37 adults, and 27 individuals of undetermined age, all scored positive for intestinal parasites by microscopy, and were screened by real-time PCR for Giardia. Molecular characterization of Giardia was performed by assemblage-specific PCR and PCR targeting the triose phosphate isomerase gene (tpi). Of the 119 samples, 80 (67%) were Giardia-positive by real-time PCR. For 48 moderately-highly real-time PCR-positive samples, tpi genotyping assigned 22 samples to Assemblage A and 26 to Assemblage B. Contrary to Assemblage A, Assemblage B exhibited substantial genetic diversity and allelic heterozygosity. Assemblage-specific PCR proved to be specific for discriminating Assemblage A or B but not as sensitive as tpi genotyping. We confirmed that real-time PCR is more sensitive than microscopy for detecting Giardia in stool samples and that robust amplification and sequencing of the tpi gene is feasible when moderate-to-strongly real-time PCR-positive samples are used. This study is one of the few performed in Africa providing genotyping data on Giardia infections in humans. Both assemblages A and B were commonly seen and not associated with specific sociodemographic data. [ABSTRACT FROM AUTHOR]

Integration of the tumor microenvironment as a fundamental part of the tumorigenic process has undoubtedly revolutionized our understanding of cancer biology. Increasing evidence indicates that neoplastic cells establish a dependency relationship with normal resident cells in the affected tissue and, furthermore, develop the ability to recruit new accessory cells that aid tumor development. In addition to normal stromal and tumor cells, this tumor ecosystem includes an infiltrated immune component that establishes complex interactions that have a critical effect during the natural history of the tumor. The process by which immune cells modulate tumor progression is known as immunoediting, a dynamic process that creates a selective pressure that finally leads to the generation of immune-resistant cells and the inability of the immune system to eradicate the tumor. In this context, the cellular and functional characterization of the immune compartment within the tumor microenvironment will help to understand tumor progression and, ultimately, will serve to create novel prognostic tools and improve patient stratification for cancer treatment. Here we review the impact of the immune system on tumor development, focusing particularly on its clinical implications and the current technologies used to analyze immune cell diversity within the tumor. [ABSTRACT FROM AUTHOR]

Colorectal cancer (CRC) is the fourth leading cause of cancer death in the world. Despite the screening programs, its incidence in the population below the 50s is increasing. Therefore, new stratification protocols based on multiparametric approaches are highly needed. In this scenario, the lipidome is emerging as a powerful tool to classify tumors, including CRC, wherein it has proven to be highly sensitive to cell malignization. Hence, the possibility to describe the lipidome at the level of lipid species has renewed the interest to investigate the role of specific lipid species in pathologic mechanisms, being commercial cell lines, a model still heavily used for this purpose. Herein, we characterize the membrane lipidome of five commercial colon cell lines and their extracellular vesicles (EVs). The results demonstrate that both cell and EVs lipidome was able to segregate cells according to their malignancy. Furthermore, all CRC lines shared a specific and strikingly homogenous impact on ether lipid species. Finally, this study also cautions about the need of being aware of the singularities of each cell line at the level of lipid species. Altogether, this study firmly lays the groundwork of using the lipidome as a solid source of tumor biomarkers. [ABSTRACT FROM AUTHOR]

Mitochondrial malfunction is supposed to be involved in the etiology and pathology of major depressive disorder (MDD). Here, we aimed to identify and characterize the molecular pathomechanisms related to mitochondrial dysfunction in adult human skin fibroblasts, which were derived from MDD patients or non-depressive control subjects. We found that MDD fibroblasts showed significantly impaired mitochondrial functioning: basal and maximal respiration, spare respiratory capacity, non-mitochondrial respiration and adenosine triphosphate (ATP)-related oxygen consumption was lower. Moreover, MDD fibroblasts harbor lower ATP levels and showed hyperpolarized mitochondrial membrane potential. To investigate cellular resilience, we challenged both groups of fibroblasts with hormonal (dexamethasone) or metabolic (galactose) stress for one week, and found that both stressors increased oxygen consumption but lowered ATP content in MDD as well as in non-depressive control fibroblasts. Interestingly, the bioenergetic differences between fibroblasts from MDD or non-depressed subjects, which were observed under non-treated conditions, could not be detected after stress. Our findings support the hypothesis that altered mitochondrial function causes a bioenergetic imbalance, which is associated with the molecular pathophysiology of MDD. The observed alterations in the oxidative phosphorylation system (OXPHOS) and other mitochondria-related properties represent a basis for further investigations of pathophysiological mechanisms and might open new ways to gain insight into antidepressant signaling pathways. [ABSTRACT FROM AUTHOR]