Search

Abstract A hallmark of cancer is a tumor cell’s ability to evade immune destruction. Somatic mutations in tumor cells that prevent immune destruction have been extensively studied. However, somatic mutations in tumor infiltrating immune (TII) cells, to our knowledge, have not been previously studied. Understandably so since normal hematopoiesis prevents the accumulation of somatic mutations in immune cells. However, clonal hematopoiesis does result in the accumulation of somatic mutations in immune cells. These mutations cannot “drive” tumor growth, however, they may “facilitate” it by inhibiting an effective anti-tumor immune response. To identify potential immunosuppressive clonal hematopoietic (CH) mutations in TII cells, we analyzed exome and RNA sequencing data from matched tumor and normal blood samples, and single-cell RNA sequencing data, from breast cancer patients. We selected mutations that were somatic, present in TII cells, clonally expanded, potentially pathogenic, expressed in TII cells, unlikely to be a passenger mutation, and in immune response associated genes. We identified eight potential immunosuppressive CH mutations in TII cells. This work is a first step towards determining if immunosuppressive CH mutations in TII cells can affect the progression of solid tumors. Subsequent experimental confirmation could represent a new paradigm in the etiology of cancer.

Fibro-adipogenic progenitors (FAPs) are essential in supporting regeneration in skeletal muscle, but in muscle pathologies FAPs the are main source of excess extracellular matrix (ECM) resulting in fibrosis. Fibrotic ECM has altered mechanical and architectural properties, but the feedback onto FAPs of stiffness or ECM properties is largely unknown. In this study, FAPs' sensitivity to their ECM substrate was assessed using collagen coated polyacrylamide to control substrate stiffness and collagen hydrogels to engineer concentration, crosslinking, fibril size, and alignment. FAPs on substrates of fibrotic stiffnesses had increased myofibroblast activation, depicted by αSMA expression, compared to substrates mimicking healthy muscle, which correlated strongly YAP nuclear localization. Surprisingly, fibrosis associated collagen crosslinking and larger fibril size inhibited myofibroblast activation, which was independent of YAP localization. Additionally, collagen crosslinking and larger fibril diameters were associated with decreased remodeling of the collagenous substrate as measured by second harmonic generation imaging. Inhibition of YAP activity through verteporfin reduced myofibroblast activation on stiff substrates but not substrates with altered architecture. This study is the first to demonstrate that fibrotic muscle stiffness can elicit FAP activation to myofibroblasts through YAP signaling. However, fibrotic collagen architecture actually inhibits myofibroblast activation through a YAP independent mechanism. These data expand knowledge of FAPs sensitivity to ECM and illuminate targets to block FAP's from driving progression of muscle fibrosis.

The extracellular matrix (ECM) is a complex mixture composed of fibrillar collagens as well as additional protein and carbohydrate components. Proteoglycans (PGs) contribute to the heterogeneity of the ECM and play an important role in its structure and function. While the small leucine rich proteoglycans (SLRPs), including decorin and lumican, have been studied extensively as mediators of collagen fibrillogenesis and organization, the function of large matrix PGs in collagen matrices is less well known. In this study, we showed that different matrix PGs have distinct roles in regulating collagen behaviors. We found that versican, a large chondroitin sulfate PG, promotes collagen fibrillogenesis in a turbidity assay and upregulates cell-mediated collagen compaction and reorganization, whereas aggrecan, a structurally-similar large PG, has different and often opposing effects on collagen. Compared to versican, decorin and lumican also have distinct functions in regulating collagen behaviors. The different ways in which matrix PGs interact with collagen have important implications for understanding the role of the ECM in diseases such as fibrosis and cancer, and suggest that matrix PGs are potential therapeutic targets.

Abstract We previously demonstrated that P. aeruginosa isolates that persisted in children with cystic fibrosis (CF) despite inhaled tobramycin treatment had increased anti-Psl antibody binding in vitro compared to those successfully eradicated. We aimed to validate these findings by directly visualizing P. aeruginosa in CF sputum. This was a prospective observational study of children with CF with new-onset P. aeruginosa infection who underwent inhaled tobramycin eradication treatment. Using microbial identification passive clarity technique (MiPACT), P. aeruginosa was visualized in sputum samples obtained before treatment and classified as persistent or eradicated based on outcomes. Pre-treatment isolates were also grown as biofilms in vitro. Of 11 patients enrolled, 4 developed persistent infection and 7 eradicated infection. P. aeruginosa biovolume and the number as well as size of P. aeruginosa aggregates were greater in the sputum of those with persistent compared with eradicated infections (p

Abstract Recently, ocular biometrics in unconstrained environments using images obtained at visible wavelength have gained the researchers’ attention, especially with images captured by mobile devices. Periocular recognition has been demonstrated to be an alternative when the iris trait is not available due to occlusions or low image resolution. However, the periocular trait does not have the high uniqueness presented in the iris trait. Thus, the use of datasets containing many subjects is essential to assess biometric systems’ capacity to extract discriminating information from the periocular region. Also, to address the within-class variability caused by lighting and attributes in the periocular region, it is of paramount importance to use datasets with images of the same subject captured in distinct sessions. As the datasets available in the literature do not present all these factors, in this work, we present a new periocular dataset containing samples from 1122 subjects, acquired in 3 sessions by 196 different mobile devices. The images were captured under unconstrained environments with just a single instruction to the participants: to place their eyes on a region of interest. We also performed an extensive benchmark with several Convolutional Neural Network (CNN) architectures and models that have been employed in state-of-the-art approaches based on Multi-class Classification, Multi-task Learning, Pairwise Filters Network, and Siamese Network. The results achieved in the closed- and open-world protocol, considering the identification and verification tasks, show that this area still needs research and development.

Abstract The main effectors in the innate immune system of Bombyx mori L. are antimicrobial peptides (AMPs). Here, we infected B. mori with varied inoculum sizes of Pseudomonas aeruginosa ATCC 25668 cells to investigate changes in morpho-anatomical responses, physiological processes and AMP production. Ultraviolet–visible spectra revealed a sharp change in λmax from 278 to 285 nm (bathochromic shift) in the hemolymph of infected B. mori incubated for 24 h. Further, Fourier Transform InfraRed studies on the hemolymph extracted from the infected B. mori showed a peak at 1550 cm−1, indicating the presence of α-helical peptides. The peptide fraction was obtained through methanol, acetic acid and water mixture (90:1:9) extraction, followed by peptide purification using Reverse Phase High Performance Liquid Chromatography. The fraction exhibiting antibacterial properties was collected and characterized by Matrix-Assisted Laser Desorption/Ionization-Time of Flight. A linear α-helical peptide with flexible termini (LLKELWTKMKGAGKAVLGKIKGLL) was found, corresponding to a previously described peptide from ant venom and here denominated as Bm-ponericin-L1. The antibacterial activity of Bm-ponericin-L1 was determined against ESKAPE pathogens. Scanning electron microscopy confirmed the membrane disruption potential of Bm-ponericin-L1. Moreover, this peptide also showed promising antibiofilm activity. Finally, cell viability and hemolytic assays revealed that Bm-ponericin-L1 is non-toxic toward primary fibroblasts cell lines and red blood cells, respectively. This study opens up new perspectives toward an alternative approach to overcoming multiple-antibiotic-resistance by means of AMPs through invertebrates’ infection with human pathogenic bacteria.

Abstract Fibro-adipogenic progenitors (FAPs) are essential in supporting regeneration in skeletal muscle, but in muscle pathologies FAPs the are main source of excess extracellular matrix (ECM) resulting in fibrosis. Fibrotic ECM has altered mechanical and architectural properties, but the feedback onto FAPs of stiffness or ECM properties is largely unknown. In this study, FAPs’ sensitivity to their ECM substrate was assessed using collagen coated polyacrylamide to control substrate stiffness and collagen hydrogels to engineer concentration, crosslinking, fibril size, and alignment. FAPs on substrates of fibrotic stiffnesses had increased myofibroblast activation, depicted by αSMA expression, compared to substrates mimicking healthy muscle, which correlated strongly YAP nuclear localization. Surprisingly, fibrosis associated collagen crosslinking and larger fibril size inhibited myofibroblast activation, which was independent of YAP localization. Additionally, collagen crosslinking and larger fibril diameters were associated with decreased remodeling of the collagenous substrate as measured by second harmonic generation imaging. Inhibition of YAP activity through verteporfin reduced myofibroblast activation on stiff substrates but not substrates with altered architecture. This study is the first to demonstrate that fibrotic muscle stiffness can elicit FAP activation to myofibroblasts through YAP signaling. However, fibrotic collagen architecture actually inhibits myofibroblast activation through a YAP independent mechanism. These data expand knowledge of FAPs sensitivity to ECM and illuminate targets to block FAP’s from driving progression of muscle fibrosis.

Abstract Sow mortality attributable to pelvic organ prolapse (POP) has increased in the U.S. swine industry and continues to worsen. Two main objectives of this study were, (1) to develop a perineal scoring system that can be correlated with POP risk, and (2) identify POP risk-associated biological factors. To assess POP risk during late gestation, sows (n = 213) were scored using a newly developed perineal scoring (PS) system. Sows scored as PS1 (low), PS2 (moderate), or PS3 (high) based on POP risk. Subsequently, 1.5, 0.8, and 23.1% of sows scored PS1, PS2, or PS3, respectively, experienced POP. To identify biomarkers, serum and vaginal swabs were collected from late gestation sows differing in PS. Using GC–MS, 82 serum metabolite differences between PS1 and PS3 animals (P

Abstract Dispersion and deformation of cratonic fragments within orogens require weakening of the craton margins in a process of decratonization. The orogenic Borborema Province, in NE Brazil, is one of several Brasiliano/Pan-African late Neoproterozoic orogens that led to the amalgamation of Gondwana. A common feature of these orogens is that a period of extension and opening of narrow oceans preceded inversion and collision. For the case of the Borborema Province, the São Francisco Craton was pulled away from its other half, the Benino-Nigerian Shield, during an intermittent extension event between 1.0–0.92 and 0.9–0.82 Ga. This was followed by inversion of an embryonic and confined oceanic basin at ca. 0.60 Ga and transpressional orogeny from ca. 0.59 Ga onwards. Here we investigate the boundary region between the north São Francisco Craton and the Borborema Province and demonstrate how cratonic blocks became physically involved in the orogeny. We combine these results with a wide compilation of U–Pb and Nd-isotopic model ages to show that the Borborema Province consists of up to 65% of strongly sheared ancient rocks affiliated with the São Francisco/Benino-Nigerian Craton, separated by major transcurrent shear zones, with only ≈ 15% addition of juvenile material during the Neoproterozoic orogeny. This evolution is repeated across a number of Brasiliano/Pan-African orogens, with significant local variations, and indicate that extension weakened cratonic regions in a process of decratonization that prepared them for involvement in the orogenies, that led to the amalgamation of Gondwana.

Abstract Plants may contain beneficial or potentially dangerous substances to humans. This study aimed to prepare and evaluate a new drug delivery system based on a glass-ionomer-Brazilian pepper extract composite, to check for its activity against pathogenic microorganisms of the oral cavity, along with its in vitro biocompatibility. The ethanolic Brazilian pepper extract (BPE), the glass-ionomer cement (GIC) and the composite GIC-BPE were characterized by scanning electron microscopy, attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), and thermal analysis. The BPE compounds were identified by UPLC–QTOF–MS/MS. The release profile of flavonoids and the mechanical properties of the GIC-BPE composite were assessed. The flavonoids were released through a linear mechanism governing the diffusion for the first 48 h, as evidenced by the Mt/M∞ relatively to $$\sqrt t$$ t , at a diffusion coefficient of 1.406 × 10–6 cm2 s−1. The ATR-FTIR analysis indicated that a chemical bond between the GIC and BPE components may have occurred, but the compressive strength of GIC-BPE does not differ significantly from that of this glass-ionomer. The GIC-BPE sample revealed an ample bacterial activity at non-cytotoxic concentrations for the human fibroblast MRC-5 cells. These results suggest that the prepared composite may represent an alternative agent for endodontic treatment.

Mangrove forests provide many ecosystem services but are among the world's most threatened ecosystems. Mangroves vary substantially according to their geomorphic and sedimentary setting; while several conceptual frameworks describe these settings, their spatial distribution has not been quantified. Here, we present a new global mangrove biophysical typology and show that, based on their 2016 extent, 40.5% (54,972 km 2 ) of mangrove systems were deltaic, 27.5% (37,411 km 2 ) were estuarine and 21.0% (28,493 km 2 ) were open coast, with lagoonal mangroves the least abundant (11.0%, 14,993 km 2 ). Mangroves were also classified based on their sedimentary setting, with carbonate mangroves being less abundant than terrigenous, representing just 9.6% of global coverage. Our typology provides a basis for future research to incorporate geomorphic and sedimentary setting in analyses. We present two examples of such applications. Firstly, based on change in extent between 1996 and 2016, we show while all types exhibited considerable declines in area, losses of lagoonal mangroves (- 6.9%) were nearly twice that of other types. Secondly, we quantify differences in aboveground biomass between mangroves of different types, with it being significantly lower in lagoonal mangroves. Overall, our biophysical typology provides a baseline for assessing restoration potential and for quantifying mangrove ecosystem service provision.

Peropsin or retinal pigment epithelium-derived rhodopsin homolog, found in many animals, belongs to the opsin family. Most opsins bind to 11-cis-retinal as a chromophore and act as light-activated G protein-coupled receptors. Some peropsins, however, bind all-trans-retinal and isomerise it into 11-cis form by light, and peropsin has been suggested to supply other visual opsins with 11-cis-retinal. Additionally, peropsin has some amino acid sequence motifs that are highly conserved among G protein-coupled opsins. Here, using chimeric mutant peropsins, we found that peropsin potentially generates an "active form" that drives G-protein signalling in the dark by binding to all-trans-retinal and that the active form photo-converts to an inactive form containing 11-cis-retinal. Comparative spectroscopic analysis demonstrated that spider peropsin exhibited catalytic efficiency for retinal photoisomerisation that was much lower than a retinal photoisomerase, squid retinochrome. The chimeric peropsins, constructed by replacing the third intracellular loop region with that of Gs- or Gi-coupled opsin, were active and drove Gs- or Gi-mediated signalling in the dark, respectively, and were inactivated upon illumination in mammalian cultured cells. These results suggest that peropsin acts as a dark-active, light-inactivated G protein-coupled receptor and is useful as a novel optogenetic tool.

Qualitative similarities between hip fracture trends in different countries suggests variations of the same epidemic. We tested a single statistical shape to describe time trends in Europe, while allowing for country-level variability. Using data from 14 countries, we modelled incidence rates over time using linear mixed-effects models, including the fixed effects of calendar year and age. Random effects were tested to quantify country-level variability in background rates, timing of trend reversal and tempo of reversal. Mixture models were applied to identify clusters of countries defined by common behavioural features. A quadratic function of time, with random effects for background rates and timing of trend reversal, adjusted well to the observed data. Predicted trend reversal occurred on average in 1999 in women (peak incidence about 600 per 100 000) and 2000 in men (about 300 per 100 000). Mixture modelling of country-level effects suggested three clusters for women and two for men. In both sexes, Scandinavia showed higher rates but earlier trend reversals, whereas later trend reversals but lower peak incidences were found in Southern Europe and most of Central Europe. Our finding of a similar overall reversal pattern suggests that different countries show variations of a shared hip fracture epidemic.