Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome.

Mutation in the germline is the ultimate source of genetic variation, but little is known about the influence of germline chromatin structure on mutational processes. Using ATAC-seq, we profile the open chromatin landscape of human spermatogonia, the most proliferative cell type of the germline, identifying transcription factor binding sites (TFBSs) and PRDM9 binding sites, a subset of which will initiate meiotic recombination. We observe an increase in rare structural variant (SV) breakpoints at PRDM9-bound sites, implicating meiotic recombination in the generation of structural variation. Many germline TFBSs, such as NRF1, are also associated with increased rates of SV breakpoints, apparently independent of recombination. Singleton short insertions (≥5 bp) are highly enriched at TFBSs, particularly at sites bound by testis active TFs, and their rates correlate with those of structural variant breakpoints. Short insertions often duplicate the TFBS motif, leading to clustering of motif sites near regulatory regions in this male-driven evolutionary process. Increased mutation loads at germline TFBSs disproportionately affect neural enhancers with activity in spermatogonia, potentially altering neurodevelopmental regulatory architecture. Local chromatin structure in spermatogonia is thus pervasive in shaping both evolution and disease.

Ceramide-2 nanovesicles for effective transdermal delivery: development, characterization and pharmacokinetic evaluation.

UNLABELLED: Abstract Context: The vesicles based on skin lipid have a drug localization effect and its main lipid, ceramide provides protective and regenerative effects while oleic acid (OA) is a penetration enhancer, however, it causes slight irritation, so we have formulated formulation incorporating both of these to develop a transdermal formulation for better permeation. OBJECTIVE: Present study investigated the preparation and characterization of physicochemical properties and permeation of nanovesicles of ceramide-2 containing OA and palmitic acid (PA) respectively and a commercial gel. MATERIALS AND METHODS: The vesicles were made using ceramide 2, cholesterol (Chol), cholesteryl sulfate (CS) and OA or PA, respectively, using film hydration method. The vesicles were characterized for physicochemical properties, ex vivo permeation using human skin and pharmacokinetic parameters and anti-inflammatory activity in rats. RESULTS: The vesicles showed size at 102-125 nm while PDI was 0.11-0.13 and negative zeta potential. OV-3 showed highest entrapment efficiency. The drug fluxes were 92.02 and 8.920 µg/cm(2)/h, respectively, for OV-3 and PV-1. The Cmax were 7.91 and 4.01 µg/ml at 4 and 6 h for OV-3 (2.5 mg) and PV-1 (10 mg), respectively. OV-3 and PV-1 showed 98.8% and 77.36% edema inhibition, respectively, at 3 h. DISCUSSION: Both formulations showed similar physical parameters and different permeation since OA get incorporated in vesicles and increases its permeability and ceramide makes sure that vesicles can rapidly traverse the stratum corneum. CONCLUSION: OV-3 containing 3% OA showed optimum physical parameters and good permeation with maximum anti-inflammatory activity.

Preparation, characterization and permeation studies of a nanovesicular system containing diclofenac for transdermal delivery.

CONTEXT: Transdermal formulations contain permeation enhancer which causes skin damage. Ceramide 2 is natural lipid found in stratum corneum (SC). OBJECTIVE: Drug-loaded nanovesicles of ceramide-2, cholesterol, palmitic acid, cholesteryl sulfate were formulated and analyzed for physical and biological properties. Diclofenac was used as a model drug. MATERIALS AND METHOD: The vesicles were prepared using the film hydration method and characterized for physical parameters, in vitro drug release, accelerated stability studies and formulated into gel. Respective gels were compared with a commercial formulation (CEG) and plain carbopol gel (CG) containing drug for ex vivo, in vivo drug permeation and anti-inflammatory activity. RESULTS: The vesicles were stable with optimum physical parameters. DCG-1 showed 92.89% in vitro drug release. Ceramide vesicles showed drug release between 18 and 25 µg/cm(2) whereas CG and CEG released 0.33 and 1.35 µg/cm(2) drug, respectively. DCG-1 and CEG showed corresponding Cmax at 6 and 4 h, respectively. DCG-1 showed six times AUC than CEG. DCG-1 inhibited edema by 86.37% by 4th hour of application. DISCUSSION: The presence of ceramide 2 specifically promotes the drug permeation through SC and dermis and also contribute towards stability and non-irritancy. CONCLUSION: The composition of the nanovesicle played an important role in physical properties and drug permeation.

Clinical Performance of I-gel® and BlockBuster™ Laryngeal Mask Airway in Adult Patients during General Anesthesia: A Randomized Comparison.

Background: Supraglottic devices have revolutionized the current practice of airway management. We compared the clinical performance of a recently introduced BlockBuster™ Laryngeal mask airway with i-gel® in adult patients under general anesthesia. Methods: Following Institutional ethical clearance, the present study was conducted on 62 patients belonging to American Society of Anesthesiologists physical status 1 and 2 of either sex in the age group of 20-60 years under general anesthesia. Patients were randomly assigned to i-gel® (I) and BlockBuster™ (B) groups (31 per group). Time for successful insertion, insertion success rate, ease of insertion, oropharyngeal leak pressures (OLPs), and complications were assessed. Results: Mean insertion time of device was less in Group I (13.52 ± 2.58 s) than that of Group B (14.10 ± 2.04 s), which was neither clinically nor statistically significant (P = 0.330). OLP in Group B (24.52 ± 2.77 cm of H2O) was found to be significantly higher compared to Group I (20.81 ± 2.56 cm of H2O) with P < 0.001. Overall insertion and first attempt success was similar (i-gel® 31/31 [100%] and 29/31 [93.5%] and BlockBuster™ 31/31 [100%] and 29/31 [93.5%], respectively). Ease of insertion (P = 0.684) and complications (P = 0.782) of both the devices were comparable. Conclusions: Both the devices are useful and effective for airway management in adult under general anesthesia. Having a high OLP and comparable insertion time, risk of aspiration may be further reduced with the use of BlockBuster™ in comparison to i-gel®.

A unique nucleosome arrangement, maintained actively by chromatin remodelers facilitates transcription of yeast tRNA genes.

BACKGROUND: RNA polymerase (pol) III transcribes a unique class of genes with intra-genic promoters and high transcriptional activity. The major contributors to the pol III transcriptome, tRNAs genes are found scattered on all chromosomes of yeast. A prototype tDNA of <150 bp length, is generally considered nucleosome-free while some pol III-transcribed genes have been shown to have nucleosome-positioning properties. RESULTS: Using high resolution ChIP-chip and ChIP-seq methods, we found several unique features associated with nucleosome profiles on all tRNA genes of budding yeast, not seen on nucleosome-dense counterparts in fission yeast and resting human CD4+ T cells. The nucleosome-free region (NFR) on all but three yeast tDNAs is found bordered by an upstream (US) nucleosome strongly positioned at -140 bp position and a downstream (DS) nucleosome at variable positions with respect to the gene terminator. Perturbation in this nucleosomal arrangement interferes with the tRNA production. Three different chromatin remodelers generate and maintain the NFR by targeting different gene regions. Isw1 localizes to the gene body and makes it nucleosome-depleted, Isw2 maintains periodicity in the upstream nucleosomal array, while RSC targets the downstream nucleosome. Direct communication of pol III with RSC serves as a stress-sensory mechanism for these genes. In its absence, the downstream nucleosome moves towards the gene terminator. Levels of tRNAs from different families are found to vary considerably as different pol III levels are seen even on isogenes within a family. Pol III levels show negative correlation with the nucleosome occupancies on different genes. CONCLUSIONS: Budding yeast tRNA genes maintain an open chromatin structure, which is not due to sequence-directed nucleosome positioning or high transcription activity of genes. Unlike 5' NFR on pol II-transcribed genes, the tDNA NFR, which facilitates tDNA transcription, results from action of chromatin remodeler Isw1, aided by Isw2 and RSC. The RSC-regulated nucleosome dynamics at the 3' gene-end serves as a novel regulatory mechanism for pol III transcription in vivo, probably by controlling terminator-dependent facilitated recycling of pol III. Salient features of yeast tDNA chromatin structure reported in this study can explain the basis of the novel non-transcriptional roles ascribed to tDNAs.

Expansion of ventral foregut is linked to changes in the enhancer landscape for organ-specific differentiation.

Cell proliferation is fundamental for almost all stages of development and differentiation that require an increase in cell number. Although cell cycle phase has been associated with differentiation, the actual process of proliferation has not been considered as having a specific role. Here we exploit human embryonic stem cell-derived endodermal progenitors that we find are an in vitro model for the ventral foregut. These cells exhibit expansion-dependent increases in differentiation efficiency to pancreatic progenitors that are linked to organ-specific enhancer priming at the level of chromatin accessibility and the decommissioning of lineage-inappropriate enhancers. Our findings suggest that cell proliferation in embryonic development is about more than tissue expansion; it is required to ensure equilibration of gene regulatory networks allowing cells to become primed for future differentiation. Expansion of lineage-specific intermediates may therefore be an important step in achieving high-fidelity in vitro differentiation.

Mena regulates nesprin-2 to control actin-nuclear lamina associations, trans-nuclear membrane signalling and gene expression.

Interactions between cells and the extracellular matrix, mediated by integrin adhesion complexes, play key roles in fundamental cellular processes, including the sensing and transduction of mechanical cues. Here, we investigate systems-level changes in the integrin adhesome in patient-derived cutaneous squamous cell carcinoma cells and identify the actin regulatory protein Mena as a key node in the adhesion complex network. Mena is connected within a subnetwork of actin-binding proteins to the LINC complex component nesprin-2, with which it interacts and co-localises at the nuclear envelope. Moreover, Mena potentiates the interactions of nesprin-2 with the actin cytoskeleton and the nuclear lamina. CRISPR-mediated Mena depletion causes altered nuclear morphology, reduces tyrosine phosphorylation of the nuclear membrane protein emerin and downregulates expression of the immunomodulatory gene PTX3 via the recruitment of its enhancer to the nuclear periphery. We uncover an unexpected role for Mena at the nuclear membrane, where it controls nuclear architecture, chromatin repositioning and gene expression. Our findings identify an adhesion protein that regulates gene transcription via direct signalling across the nuclear envelope.

Cohesin is required for long-range enhancer action at the Shh locus.

The regulatory landscapes of developmental genes in mammals can be complex, with enhancers spread over many hundreds of kilobases. It has been suggested that three-dimensional genome organization, particularly topologically associating domains formed by cohesin-mediated loop extrusion, is important for enhancers to act over such large genomic distances. By coupling acute protein degradation with synthetic activation by targeted transcription factor recruitment, here we show that cohesin, but not CTCF, is required for activation of the target gene Shh by distant enhancers in mouse embryonic stem cells. Cohesin is not required for activation directly at the promoter or by an enhancer located closer to the Shh gene. Our findings support the hypothesis that chromatin compaction via cohesin-mediated loop extrusion allows for genes to be activated by enhancers that are located many hundreds of kilobases away in the linear genome and suggests that cohesin is dispensable for enhancers located more proximally.

Therapeutic Potential of Antileukotriene Drug-Camellia sinensis Extract Co-Formulation on Histamine Induced Asthma in Guinea Pigs.

BACKGROUND/OBJECTIVE: To study the therapeutic potential of Antileukotriene drug- Camellia sinensis extract co-formulation on histamine induced asthma in guinea pigs. METHODS: SRSD of Montelukast sodium was prepared by the solvent evaporation method. Lyophilized aqueous extract of Camellia sinensis leaves and SRSD mixture was filled in capsule and the capsule shell was coated to achieve initial release lag time. In vitro and pharmacokinetic study of capsules was performed and compared with commercial tablets. A further role of green tea, as an antioxidant adjunct for asthma management, has been analyzed by lung histology, mast cell count and oxidative stress assay in the serum of control and experimental animals. RESULTS: The drug release from the commercial tablet was immediate and rapid, but capsule has shown an initial 3.5 hr lag time followed by sustained action up to 8 hr. Pharmacokinetic results show that studied formulations are bioequivalent with respect to Cmax and AUC, while rest parameters showed asignificant difference. Mast cells count in lung tissue were increased (p<0.001) in the experimental group along with glycoprotein deposition in asthmatic bronchioles. Levels of SOD and GPX were decreased (p<0.05) while CAT was increased (p<0.04) in the asthma group in comparison to control. CONCLUSION: In the experimental animal model, co-formulation was effective in modulating allergic inflammation and contributing to better control of the inflammatory response. Our findings suggest that Camellia sinensis leaves extract may be used as an adjunct for future improvements in asthma treatment and prevention.

Recent advances in the spatial organization of the mammalian genome.

The mammalian genome is complex and presents a dynamic structural organization that reflects function. Organization of the genome inside the mammalian nucleus impacts all nuclear processes including but not limited to transcription, replication and repair, and in many biological contexts such as early development, differentiation and physiological adaptations. However, there is limited understating of how 3D organization of the mammalian genome regulates different nuclear processes. Recent advances in microscopy and a myriad of genomics methods -- ropelled by next-generation sequencing -- have advanced our knowledge of genome organization to a great extent. In this review, we discuss nuclear compartments in general and recent advances in the understanding of how mammalian genome is organized in these compartments with an emphasis on dynamics at the nuclear periphery.