Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.

Enhancers are important genomic regulatory elements directing cell type-specific transcription. They assume a key role during development and disease, and their identification and functional characterization have long been the focus of scientific interest. The advent of next-generation sequencing and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based genome editing has revolutionized the means by which we study enhancer biology. In this review, we cover recent developments in the prediction of enhancers based on chromatin characteristics and their identification by functional reporter assays and endogenous DNA perturbations. We discuss that the two latter approaches provide different and complementary insights, especially in assessing enhancer sufficiency and necessity for transcription activation. Furthermore, we discuss recent insights into mechanistic aspects of enhancer function, including findings about cofactor requirements and the role of post-translational histone modifications such as monomethylation of histone H3 Lys4 (H3K4me1). Finally, we survey how these approaches advance our understanding of transcription regulation with respect to promoter specificity and transcriptional bursting and provide an outlook covering open questions and promising developments.

Resolving systematic errors in widely used enhancer activity assays in human cells.

The identification of transcriptional enhancers in the human genome is a prime goal in biology. Enhancers are typically predicted via chromatin marks, yet their function is primarily assessed with plasmid-based reporter assays. Here, we show that such assays are rendered unreliable by two previously reported phenomena relating to plasmid transfection into human cells: (i) the bacterial plasmid origin of replication (ORI) functions as a conflicting core promoter and (ii) a type I interferon (IFN-I) response is activated. These cause confounding false positives and negatives in luciferase assays and STARR-seq screens. We overcome both problems by employing the ORI as core promoter and by inhibiting two IFN-I-inducing kinases, enabling genome-wide STARR-seq screens in human cells. In HeLa-S3 cells, we uncover strong enhancers, IFN-I-induced enhancers, and enhancers endogenously silenced at the chromatin level. Our findings apply to all episomal enhancer activity assays in mammalian cells and are key to the characterization of human enhancers.

Individual differences in frontolimbic circuitry and anxiety emerge with adolescent changes in endocannabinoid signaling across species.

Anxiety disorders peak in incidence during adolescence, a developmental window that is marked by dynamic changes in gene expression, endocannabinoid signaling, and frontolimbic circuitry. We tested whether genetic alterations in endocannabinoid signaling related to a common polymorphism in fatty acid amide hydrolase (FAAH), which alters endocannabinoid anandamide (AEA) levels, would impact the development of frontolimbic circuitry implicated in anxiety disorders. In a pediatric imaging sample of over 1,000 3- to 21-y-olds, we show effects of the FAAH genotype specific to frontolimbic connectivity that emerge by ∼12 y of age and are paralleled by changes in anxiety-related behavior. Using a knock-in mouse model of the FAAH polymorphism that controls for genetic and environmental backgrounds, we confirm phenotypic differences in frontoamygdala circuitry and anxiety-related behavior by postnatal day 45 (P45), when AEA levels begin to decrease, and also, at P75 but not before. These results, which converge across species and level of analysis, highlight the importance of underlying developmental neurobiology in the emergence of genetic effects on brain circuitry and function. Moreover, the results have important implications for the identification of risk for disease and precise targeting of treatments to the biological state of the developing brain as a function of developmental changes in gene expression and neural circuit maturation.

Tuning the Stiffness of Surfaces by Assembling Genetically Engineered Polypeptides with Tailored Amino Acid Sequence.

We introduce elastin-like recombinamers (ELRs) as polypeptides with precise amino acid positioning to generate polypeptide coatings with tunable rigidity. Two ELRs are used: V84-ELR, a hydrophobic monoblock, and EI-ELR, an amphiphilic diblock. Both were modified with the amine-reactive tetrakis (hydroxymethyl) phosphonium chloride compound. We evaluated the affinity, conformation, and dissipative behavior of ELRs assembled on alkanethiol self-assembled coatings by quartz crystal microbalance with dissipation monitoring, multiparametric surface plasmon resonance, and atomic force microscopy. The thickness of the polypeptide coatings showcases the preferential affinity of ELRs to NH2- and CH3-terminated surfaces. We demonstrate that V84-ELR strongly bonded to the substrate and reorganizes into an extended and more hydrated layer as the adsorbed amount increases, whereas EI-ELR has a less dissipative behavior. The results suggest that ELR adsorption depends on the amino acid sequence and the substrate chemistry, ultimately influencing the stiffness of the polypeptide coatings.

In vitro quality control analysis after processing and during storage of feline packed red blood cells units.

BACKGROUND: During the storage of packed red blood cells (pRBC), packed cell volume (PCV), bacterial contamination and percentage of haemolysis [percentage of free haemoglobin (HGB) in relation to the total HGB] are important quality parameters. Both PCV and haemolysis are indicators of the cellular integrity of stored units. There are no published experimental studies that evaluated these parameters during storage of feline pRBC using SAGM (adenine, dextrose, mannitol and sodium chloride) as the additive solution. The present study aims to (1) evaluate the quality of feline pRBCs stored in SAGM; (2) test for the semi-closed system's suitability for use and risk of bacterial contamination; (3) establish the maximum storage time that may be appropriate to meet the criteria established by the United States Food and Drug Administration (US-FDA) guidelines for human blood banking; and (4) evaluate the need to calculate the percentage of haemolysis prior to the administration of units stored for more than 4 weeks. Four hundred eighty nine feline pRBC units were analyzed. Bacterial culture, PCV and percentage of haemolysis were determined within 6 h after processing (t0). One hundred and eighty units were re-tested for haemolysis and PCV after 29-35 days of storage (t1) and 118 units after 36-42 days (t2). RESULTS: Bacterial contamination was not detected in any pRBC unit. Mean PCV at t0 was 52.25% (SD: ±5.27) and decreased significantly (p < 0.001) during storage to 48.15% (SD: ±3.79) at t1 and to 49.34% (SD: ±4.45) at t2. Mean percentage of haemolysis at t0 was 0.07% (SD: ±0.06) and increased significantly (p < 0.001) to 0.69% (SD: ±0.40) at t1 and to 0.81% (SD: ±0.47) at t2. In addition, 13.88% and 19.49% of pRBC units exceeded 1% haemolysis at t1 and t2, respectively. CONCLUSIONS: According to the US-FDA guidelines for human blood banking that recommend a maximum of 1% haemolysis, the results of this study show that all feline pRBC units with less than 24 h of shelf life have low levels of haemolysis. However, units preserved up to 28 days can only be administered if tested for haemolysis before use, since 13.88% units exceeded the 1% limit. The semi-closed system was considered safe for use as bacterial contamination was not detected in any pRBC unit.

Polo-like kinase 1 inhibition results in misaligned chromosomes and aberrant spindles in porcine oocytes during the first meiotic division.

Polo-like kinase 1 (Plk1), a type of serine/threonine protein kinase, has been implicated in various functions in the regulation of mitotic processes. However, these kinase's roles in meiotic division are not fully understood, particularly in the meiotic maturation of porcine oocytes. In this study, the expression and spatiotemporal localization of Plk1 were initially assessed in the meiotic process of pig oocytes by utilizing Western blotting with immunofluorescent staining combined with confocal microscopy imaging technique. The results showed that Plk1 was expressed and exhibited a dynamic subcellular localization throughout the meiotic process. After germinal vesicle breakdown (GVBD), Plk1 was detected prominently around the condensed chromosomes and subsequently exhibited a similar subcellular localization to α-tubulin throughout subsequent meiotic phases, with particular enrichment being observed near spindle poles at MI and MII. Inhibition of Plk1 via a highly selective inhibitor, GSK461364, led to the failure of first polar body extrusion in porcine oocytes, with the majority of the treated oocytes being arrested in GVBD. Further subcellular structure examination results indicated that Plk1 inhibition caused the great majority of oocytes with spindle abnormalities and chromosome misalignment during the first meiotic division. The results of this study illustrate that Plk1 is critical for the first meiotic division in porcine oocytes through its influence on spindle organization and chromosome alignment, which further affects the ensuing meiotic cell cycle progression.

[Relationship between Myofibril Fragmentation Index and Postmortem Interval].

OBJECTIVES: To study the relationship between myofibril fragmentation index （MFI） of human skeletal muscle and postmortem interval （PMI）. METHODS: The protein concentrations of human right biceps brachii muscle and right quadriceps femoris muscle were obtained at different PMI, and detected at room temperature by biuret method. The MFI of skeletal muscle at 540 nm was measured by ultraviolet spectrophotometer. Regression analysis was performed with time of death as independent variable （x） and MFI as dependent variable （y）. RESULTS: In early PMI, the MFI of human skeletal muscle increased obviously according to the prolongation of PMI, and peaking by 12 h and then tended to steady. Within 12 h after death, the regression equations of right biceps brachii muscle and right quadriceps femoris muscle were y=32.660+3.227 x（r=0.987 9） and y=32.380+3.495 x（r=0.983 9）, respectively. CONCLUSIONS: There's high correlation between MFI and PMI. Combining with forensic practice, MFI can be used for the estimation of early PMI （especially in 12 h）.

Enzymatic Degradation of Polysaccharide-Based Layer-by-Layer Structures.

The lack of knowledge on the degradation of layer-by-layer structures is one of the causes hindering its translation to preclinical assays. The enzymatic degradation of chitosan/hyaluronic acid films in the form of ultrathin films, freestanding membranes, and microcapsules was studied resorting to hyaluronidase. The reduction of the thickness of ultrathin films was dependent on the hyaluronidase concentration, leading to thickness and topography variations. Freestanding membranes exhibited accelerated weight loss up to 120 h in the presence of the enzyme, achieving complete degradation. Microcapsules with around 5 µm loaded simultaneously with FITC-BSA and hyaluronidase showed that the coencapsulation of such enzyme and protein mixture led to a FITC-BSA release four times higher than in the absence of hyaluronidase. The results suggest that the degradation of LbL devices may be tuned via embedded enzymes, namely, in the controlled release of active agents in biomedical applications.

Chitosan/Chondroitin Sulfate Membranes Produced by Polyelectrolyte Complexation for Cartilage Engineering.

Membranes made of chitosan (CHT) and chondroitin sulfate (CS) are herein presented using a polyelectrolyte complexation sedimentation/evaporation method. The membranes present high roughness and heterogeneous morphology induced by salt crystals. Exposing the membranes to different salt concentrations induces saloplastic behavior, as shown by an increasing water absorption and decreasing stiffness while exposed to increasing concentrations of salt. Establishing contact between two parts of a cut membrane leads to their self-adhesion and maintenance of their stretching ability. The membranes sustain the adhesion of ATDC5 prechondrocyte cells, inducing their rearrangement in cellular aggregates typical of chondrogenesis, and the expression of cartilage markers. Impregnated TGF-ß3 remains loaded after 14 days of incubation, releasing only 1.2% of its total loaded mass. CHT/CS polyelectrolyte membranes are here shown as suitable candidates for the biomedical field, namely, for cartilage regeneration.

Marine Origin Polysaccharides in Drug Delivery Systems.

Oceans are a vast source of natural substances. In them, we find various compounds with wide biotechnological and biomedical applicabilities. The exploitation of the sea as a renewable source of biocompounds can have a positive impact on the development of new systems and devices for biomedical applications. Marine polysaccharides are among the most abundant materials in the seas, which contributes to a decrease of the extraction costs, besides their solubility behavior in aqueous solvents and extraction media, and their interaction with other biocompounds. Polysaccharides such as alginate, carrageenan and fucoidan can be extracted from algae, whereas chitosan and hyaluronan can be obtained from animal sources. Most marine polysaccharides have important biological properties such as biocompatibility, biodegradability, and anti-inflammatory activity, as well as adhesive and antimicrobial actions. Moreover, they can be modified in order to allow processing them into various shapes and sizes and may exhibit response dependence to external stimuli, such as pH and temperature. Due to these properties, these biomaterials have been studied as raw material for the construction of carrier devices for drugs, including particles, capsules and hydrogels. The devices are designed to achieve a controlled release of therapeutic agents in an attempt to fight against serious diseases, and to be used in advanced therapies, such as gene delivery or regenerative medicine.

Early-life stress has persistent effects on amygdala function and development in mice and humans.

Relatively little is known about neurobiological changes attributable to early-life stressors (e.g., orphanage rearing), even though they have been associated with a heightened risk for later psychopathology. Human neuroimaging and animal studies provide complementary insights into the neural basis of problem behaviors following stress, but too often are limited by dissimilar experimental designs. The current mouse study manipulates the type and timing of a stressor to parallel the early-life stress experience of orphanage rearing, controlling for genetic and environmental confounds inherent in human studies. The results provide evidence of both early and persistent alterations in amygdala circuitry and function following early-life stress. These effects are not reversed when the stressor is removed nor diminished with the development of prefrontal regulation regions. These neural and behavioral findings are similar to our human findings in children adopted from orphanages abroad in that even following removal from the orphanage, the ability to suppress attention toward potentially threatening information in favor of goal-directed behavior was diminished relative to never-institutionalized children. Together, these findings highlight how early-life stress can lead to altered brain circuitry and emotion dysregulation that may increase the risk for psychopathology.

pH Responsiveness of Multilayered Films and Membranes Made of Polysaccharides.

We investigated the pH-dependent properties of multilayered films made of chitosan (CHI) and alginate (ALG) and focused on their postassembly response to different pH environments using a quartz crystal microbalance with dissipation monitoring (QCM-D), swelling studies, ζ potential measurements, and dynamic mechanical analysis (DMA). In an acidic environment, the multilayers presented lower dissipation values and, consequently, higher moduli when compared with the values obtained for the pH used during the assembly (5.5). When the multilayers were exposed to alkaline environments, the opposite behavior occurred. These results were further corroborated by the ability of this multilayered system to exhibit a reversible swelling-deswelling behavior within the pH range from 3 to 9. The changes in the physicochemical properties of the multilayer system were gradual and different from those of individual solubilized polyelectrolytes. This behavior is related to electrostatic interactions between the ionizable groups combined with hydrogen bonding and hydrophobic interactions. Beyond the pH range of 3-9, the multilayers were stabilized by genipin cross-linking. The multilayered films also became more rigid while the pH responsiveness conferred by the ionizable moieties of the polyelectrolytes was preserved. This work demonstrates the versatility and feasibility of LbL methodology to generate inherently pH stimulus-responsive nanostructured films. Surface functionalization using pH responsiveness endows several biomedical applications with abilities such as drug delivery, diagnostics, microfluidics, biosensing, and biomimetic implantable membranes.

Altered fear learning across development in both mouse and human.

The only evidence-based behavioral treatment for anxiety and stress-related disorders involves desensitization techniques that rely on principles of extinction learning. However, 40% of patients do not respond to this treatment. Efforts have focused on individual differences in treatment response, but have not examined when, during development, such treatments may be most effective. We examined fear-extinction learning across development in mice and humans. Parallel behavioral studies revealed attenuated extinction learning during adolescence. Probing neural circuitry in mice revealed altered synaptic plasticity of prefrontal cortical regions implicated in suppression of fear responses across development. The results suggest a lack of synaptic plasticity in the prefrontal regions, during adolescence, is associated with blunted regulation of fear extinction. These findings provide insight into optimizing treatment outcomes for when, during development, exposure therapies may be most effective.

Volume-dependent hemodynamic effects of blood collection in canine donors - evaluation of 13% and 15% of total blood volume depletion.

BACKGROUND: There is no consensus regarding the blood volume that could be safely donated by dogs, ranging from 11 to 25% of its total blood volume (TBV). No previous studies evaluated sedated donors. AIM: To evaluate the hemodynamic effects of blood collection from sedated and non-sedated dogs and to understand if such effects were volume-dependent. MATERIALS AND METHODS: Fifty three donations of 13% of TBV and 20 donations of 15% TBV were performed in dogs sedated with diazepam and ketamine. Additionally, a total of 30 collections of 13% TBV and 20 collections of 15% TBV were performed in non-sedated dogs. Non-invasive arterial blood pressures and pulse rates were registered before and 15 min after donation. RESULTS: Post-donation pulse rates increased significantly in both sedated groups, with higher differences in the 15% TBV collections. Systolic arterial pressures decreased significantly in these groups, while diastolic pressures increased significantly in 13% TBV donations. Non-sedated groups revealed a slight, but significant, SBP decrease. No clinical signs related to donations were registered. CONCLUSION: These results suggest that the collection of 15% TBV in sedated donors induces hemodynamic variations that may compromise the harmlessness of the procedure, while it seems to be a safe procedure in non-sedated dogs.

Polyelectrolyte multilayered assemblies in biomedical technologies.

Layer-by-layer (LbL) was first introduced as a surface modification technique based on the sequential spontaneous adsorption of at least two distinct materials onto planar substrates. In the last two decades, this technique has been expanded to the coating of more convoluted geometries with high levels of tailored functionalization or with structural purposes. In this review, the potential uses of LbL films in biomedical engineering based mainly on the assembly of polyelectrolytes are reviewed. Examples of recent developments are provided, from the modification of substrates to improve their biointegration or to add specialized properties, to the three-dimensional extrapolation of this technique to more complex structures for cell seeding, drug delivery devices, biosensors and customizable microreactors. Future strategies and opportunities are compared with current medical and laboratorial methodologies. Through them, it is expected that LbL will contribute greatly to the development of new functional devices with high perspectives of return for the administration of active agents, supports for cells in regenerative medicine and tissue engineering, biosensing and construction of microtissues and disease models in the laboratory.

Personal exposure levels of PAHs in the general population in northern rural area of Jiangsu Province, China.

Polycyclic aromatic hydrocarbons (PAHs) are a group of compounds that are produced by incomplete combustion of organic matters. Studies in humans have shown associations between PAHs exposure and development of cancers. Urinary monohydroxy polycyclic aromatic hydrocarbons (OH-PAHs) are a class of PAH metabolites used as biomarkers for estimating human exposure to PAHs. We collected 332 urinary samples from a nonoccupational population in northern rural area of Jiangsu. Levels of 2-hydroxynathalene (2-OHN), 2-hydroxyfluorene (2-OHF) and 1-hydroxypyrene (1-OHP) were measured as biomarkers to assess body PAHs burdens. Three PAH metabolites were detected in more than 80% of urinary samples. After being adjusted with urinary creatinine concentration, the urinary concentrations were determined as 2-OHF > 1-OHP > 2-OHN in terms. The medians of 2-OHN, 2-OHF, 1-OHP for the general population were 1.74, 30.01, 25.24 µmoL/moL creatinine, respectively. The results demonstrated that nonoccupational populations in northern rural area of Jiangsu were exposed to extremely high PAHs. The urinary concentration (median and geometric mean) of 2-OHN,2-OHF,1-OHP in males (1.90, 0.37 ± 0.46; 34.90, 1.53 ± 0.41; 27.84, 1.52 ± 0.29 µmoL/moL creatinine, respectively) was slightly higher than in females (1.56, 0.32 ± 0.42; 29.60, 1.48 ± 0.40; 23.13, 1.49 ± 0.32 µmoL/moL creatinine, respectively). However, only 2-OHN was different significantly between males and females.

Multifunctional compartmentalized capsules with a hierarchical organization from the nano to the macro scales.

Inspired by the cells' structure, we present compartmentalized capsules with temperature and magnetic-based responsiveness and hierarchical organization ranging from the nano- to the visible scales. Liquefied alginate macroscopic beads coated with a layer-by-layer (LbL) chitosan/alginate shell served as containers both for model fluorophores and microcapsules, which in their turn encapsulated either another fluorophore or magnetic nanoparticles (MNPs). The microcapsules were coated with a temperature-responsive chitosan/elastin-like recombinamer (ELR) nanostructured shell. By varying the temperature from 25 to 37 °C, the two-hour release of rhodamine encapsulated within the microcapsules and its diffusion through the external compartment decreased from 84% and 71%. The devices could withstand handling and centrifugal stress, with 50% remaining intact at a rotation speed of 2000g. MNPs attributed magnetic responsiveness toward external magnetic fields. Such a customizable system can be envisaged to transport bioactive agents and cells in tissue engineering applications.

Nanostructured and thermoresponsive recombinant biopolymer-based microcapsules for the delivery of active molecules.

Multilayer capsules conceived at the nano- and microscales are receiving increasing interest due to their potential role as carriers of biomolecules for drug delivery and tissue engineering. Herein we report the construction of microcapsules by the sequential adsorption of chitosan and a biomimetic elastin-like recombinamer into nanostructured layers on inorganic microparticle templates. The release profile of bovine serum albumin, which was studied at 25 and 37 °C, shows higher retention and Fickian diffusion at physiological temperature. The self-assembled multilayers act as a barrier and allowed for sustained release over 14 days. The capsules studied are non-cytotoxic towards L929 cells, thereby suggesting multiple applications in the fields of biotechnology and bioengineering, where high control of the delivery of therapeutics and growth/differentiation factors is required. FROM THE CLINICAL EDITOR: In this paper, the construction of microcapsules by sequential adsorption of chitosan and a biomimetic, elastin-like recombinamer into nanostructured layers on inorganic microparticle templates is reported. The layers demonstrated sustained drug release over 14 days. These microcapsules are non-cytotoxic toward L929 cells, suggesting multiple applications where high control of drug or growth factor delivery is required.

Layer-by-layer coated calcium carbonate nanoparticles for targeting breast cancer cells.

Breast cancer is resistant to conventional treatments due to the specific tumour microenvironment, the associated acidic pH and the overexpression of receptors that enhance cells tumorigenicity. Herein, we optimized the synthesis of acidic resorbable calcium carbonate (CaCO3) nanoparticles and the encapsulation of a low molecular weight model molecule (Rhodamine). The addition of ethylene glycol during the synthetic process resulted in a particle size decrease: we obtained homogeneous CaCO3 particles with an average size of 564 nm. Their negative charge enabled the assembly of layer-by-layer (LbL) coatings with surface-exposed hyaluronic acid (HA), a ligand of tumour-associated receptor CD44. The coating decreased Rhodamine release by two-fold compared to uncoated nanoparticles. We demonstrated the effect of nanoparticles on two breast cancer cell lines with different aggressiveness - SK-BR-3 and the more aggressive MDA-MB-231 - and compared them with the normal breast cell line MCF10A. CaCO3 nanoparticles (coated and uncoated) significantly decreased the metabolic activity of the breast cancer cells. The interactions between LbL-coated nanoparticles and cells depended on HA expression on the cell surface: more particles were observed on the surface of MDA-MB-231 cells, which had the thickest endogenous HA coating. We concluded that CaCO3 nanoparticles are potential candidates to carry low molecular weight chemotherapeutics and deliver them to aggressive breast cancer sites with an HA-abundant pericellular matrix.

Evaluation of bacterial growth, effects on albumin, and coagulation factors in canine fresh frozen plasma administered as continuous rate infusion exposed to room temperature for 12 hours.

OBJECTIVES: To determine the risk of bacterial growth and to analyze the stability of albumin and coagulation factors in canine fresh frozen plasma (FFP) units exposed to room temperature (24°C) administered as a continuous rate infusion (CRI) for 12 hours. DESIGN: Ex vivo study. SETTING: University teaching hospital and pet blood bank. ANIMALS: None. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: An FFP CRI was simulated to replicate the standard routine procedure used in dogs. Plasma samples were collected before starting the CRI (H0), after 4 hours (H4), and after 12 hours (H12). Bacterial culture of FFP was performed and albumin concentration and specific activity levels for factors V, VII, VIII, and IX were measured and compared. All plasma culture results were negative. There were no statistically significant differences at any time point in the factor VIII activity (median 105.5% [range, 75.6%-142.0%] at H0; median 107.8% [range, 75.0%-172.7%] at H4; and median 112.1% [range, 81.7%-171.0%] at H12); factor IX activity (median 119.3% [range, 89.1%-175.9%] at H0; median 123.1% [range, 72.5%-172.7%] at H4; and median 118.3% [range, 86.6%-177.5%] at H12); or albumin concentration (median 21.0 g/L [range, 17.0-23.0 g/L] at H0 and median 20.0 g/L [range, 17.0-24.0 g/L] at H12). A slight but significant increase in factor V activity was observed when comparing H0 (median 107.0% [range, 71.0%-159.0%]) to H4 (median 117.7% [range, 71.0%-176.7%]) (P = 0.002) or H12 (median 116.2% [range, 71.0%-191.6%]) (P = 0.001). A slight but significant increase in factor VII activity was observed when comparing H0 (median 115.4% [range, 70.6%-183.7%]) to H4 (median 118.2% [range, 82.7%-194.6%]) (P = 0.005); H0 to H12 (median 128.7% [range, 86.4%-200.0%]) (P < 0.001); and H4 to H12 (P = 0.002). CONCLUSIONS: FFP CRI at room temperature for 12 hours could be considered safe with regard to risk for bacterial growth and also effective by providing albumin and clotting factors.