Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells

While distinct stem cell phenotypes follow global changes in chromatin marks, single-cell chromatin technologies are unable to resolve or predict stem cell fates. We propose the first such use of optical high content nanoscopy of histone epigenetic marks (epi-marks) in stem cells to classify emergent cell states. By combining nanoscopy with epi-mark textural image informatics, we developed a novel approach, termed EDICTS (Epi-mark Descriptor Imaging of Cell Transitional States), to discern chromatin organizational changes, demarcate lineage gradations across a range of stem cell types and robustly track lineage restriction kinetics. We demonstrate the utility of EDICTS by predicting the lineage progression of stem cells cultured on biomaterial substrates with graded nanotopographies and mechanical stiffness, thus parsing the role of specific biophysical cues as sensitive epigenetic drivers. We also demonstrate the unique power of EDICTS to resolve cellular states based on epi-marks that cannot be detected via mass spectrometry based methods for quantifying the abundance of histone posttranslational modifications. Overall, EDICTS represents a powerful new methodology to predict single cell lineage decisions by integrating high content super-resolution nanoscopy and imaging informatics of the nuclear organization of epi-marks.National Institutes of Health (U.S.) (Grant GM110174

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

Genome of the Asian Longhorned Beetle (\u3cem\u3eAnoplophora glabripennis\u3c/em\u3e), a Globally Significant Invasive Species, Reveals Key Functional and Evolutionary Innovations at the Beetle-Plant Interface

Background: Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle. Results: The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates. Conclusions: Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants

Isolation and characterization of canine perivascular stem/stromal cells for bone tissue engineering

For over 15 years, human subcutaneous adipose tissue has been recognized as a rich source of tissue resident mesenchymal stem/stromal cells (MSC). The isolation of perivascular progenitor cells from human adipose tissue by a cell sorting strategy was first published in 2008. Since this time, the interest in using pericytes and related perivascular stem/stromal cell (PSC) populations for tissue engineering has significantly increased. Here, we describe a set of experiments identifying, isolating and characterizing PSC from canine tissue (N = 12 canine adipose tissue samples). Results showed that the same antibodies used for human PSC identification and isolation are cross-reactive with canine tissue (CD45, CD146, CD34). Like their human correlate, canine PSC demonstrate characteristics of MSC including cell surface marker expression, colony forming unit-fibroblast (CFU-F) inclusion, and osteogenic differentiation potential. As well, canine PSC respond to osteoinductive signals in a similar fashion as do human PSC, such as the secreted differentiation factor NEL-Like Molecule-1 (NELL-1). Nevertheless, important differences exist between human and canine PSC, including differences in baseline osteogenic potential. In summary, canine PSC represent a multipotent mesenchymogenic cell source for future translational efforts in tissue engineering

3D Printing of Resorbable Poly(Propylene Fumarate) Tissue Engineering Scaffolds

Efficient, reproducible, and precise methodologies for fabricating tissue engineering (TE) scaffolds using three-dimensional (3D) printing techniques are evaluated. Fusion deposition modeling, laser sintering, and photo printing each have limitations, including the materials that can be used with each printing system. However, new and promising resorbable materials are surfacing as alternatives to previously studied resorbable TE materials for 3D printing. One such resorbable polymer is poly(propylene fumarate) (PPF), which can be printed using photocross-linking 3D printing. The ability to print new materials opens up TE to a wide range of possibilities not previously available. The ability to control precise geometries, porosity, degradation, and functionalities present on 3D printable polymers such as PPF shows a new layer of complexity available for the design and fabrication of TE scaffolds

l‑Leucine-Based Poly(ester urea)s for Vascular Tissue Engineering

Poly­(ester urea)­s (PEUs) derived from α-amino acids are promising for vascular tissue engineering applications. The objective of this work was to synthesize and characterize l-leucine-based PEUs and evaluate their suitability for vascular tissue engineering. Four different PEUs were prepared from di-<i>p</i>-toluenesulfonic acid salts of bis-l-leucine esters and triphosgene using interfacial condensation polymerizations. Mechanical testing indicated that the elastic moduli of the respective polymers were strongly dependent on the chain length of diols in the monomers. Three of the resulting PEUs showed elastic moduli that fall within the range of native blood vessels (0.16 to 12 MPa). The in vitro degradation assays over 6 months indicated that the polymers are surface eroding and no significant pH drop was observed during the degradation process. Human umbilical vein endothelial cells (HUVECs) and A-10 smooth muscle cells (A-10 SMCs) were cultured on PEU thin films. Protein adsorption studies showed the PEUs did not led to significant platelet adsorption in platelet rich plasma (PRP) after pretreatment with fibrinogen. Taken together, our data suggest that the l-leucine-based PEUs are viable candidate materials for use in vascular tissue engineering applications

The USDA-ARS Ag100pest initiative: High-quality genome assemblies for agricultural pest arthropod research

The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale

Differences in Outcomes Based on Sex for Pediatric Patients Undergoing Pyloromyotomy

BackgroundMales and females are known to have varied responses to medical interventions. Our study aimed to determine the effect of sex on surgical outcomes after pyloromyotomy.Materials and methodsUsing the Kids' Inpatient Database for the years 2003-2012, we performed a serial, cross-sectional analysis of a nationally representative sample of all patients aged &lt;1&nbsp;y who underwent pyloromyotomy for hypertrophic pyloric stenosis. The primary predictor of interest was sex. Outcomes included mortality, in-hospital complications, cost, and length of stay. Regression models were adjusted by race, age group, comorbidity, complications, and whether operation was performed on the day of admission with region and year fixed effects.ResultsOf 48,834 weighted operations, 81.8% were in males and 18.2% were in females. The most common reported race was white (47.3%) and most of the patients were ≥29&nbsp;days old (72.5%). There was no difference in the odds of postoperative complications, but females had a significantly longer length of stay (incidence rate ratio, 1.28; 95% confidence interval [95% CI], 1.18-1.39; P&nbsp;≤&nbsp;0.01), higher cost (5%, 95% CI, 1.02-1.08; P&nbsp;≤&nbsp;0.01), and higher odds of mortality (odds ratio, 3.26; 95% CI, 1.52-6.98; P&nbsp;≤&nbsp;0.01).ConclusionsOur study demonstrated that females had worse outcomes after pyloromyotomy compared with males. These findings are striking and are important to consider when treating either sex to help set physician and family expectations perioperatively. Further studies are needed to determine why such differences exist and to develop targeted treatment strategies for both females and males with pyloric stenosis

The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale