Wafer-level uniformity of atomic-layer-deposited niobium nitride thin films for quantum devices

Superconducting niobium nitride thin films are used for a variety of photon detectors, quantum devices, and superconducting electronics. Most of these applications require highly uniform films, for instance, when moving from single-pixel detectors to arrays with a large active area. Plasma-enhanced atomic layer deposition (ALD) of superconducting niobium nitride is a feasible option to produce high-quality, conformal thin films and has been demonstrated as a film deposition method to fabricate superconducting nanowire single-photon detectors before. Here, we explore the property spread of ALD-NbN across a 6-in. wafer area. Over the equivalent area of a 2-in. wafer, we measure a maximum deviation of 1% in critical temperature and 12% in switching current. Toward larger areas, structural characterizations indicate that changes in the crystal structure seem to be the limiting factor rather than film composition or impurities. The results show that ALD is suited to fabricate NbN thin films as a material for large-area detector arrays and for new detector designs and devices requiring uniform superconducting thin films with precise thickness control

An expansive human regulatory lexicon encoded in transcription factor footprints.

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency

The accessible chromatin landscape of the human genome

DNaseI hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers, and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ~2.9 million DHSs that encompass virtually all known experimentally-validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation, and regulatory factor occupancy patterns. We connect ~580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is choreographed with dozens to hundreds of co-activated elements, and the trans-cellular DNaseI sensitivity pattern at a given region can predict cell type-specific functional behaviors. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation

Mammalian Target of Rapamycin Is a Therapeutic Target for Murine Ovarian Endometrioid Adenocarcinomas with Dysregulated Wnt/β-Catenin and PTEN

Despite the fact that epithelial ovarian cancers are the leading cause of death from gynecological cancer, very little is known about the pathophysiology of the disease. Mutations in the WNT and PI3K pathways are frequently observed in the human ovarian endometrioid adenocarcinomas (OEAs). However, the role of WNT/β-catenin and PTEN/AKT signaling in the etiology and/or progression of this disease is currently unclear. In this report we show that mice with a gain-of-function mutation in β-catenin that leads to dysregulated nuclear accumulation of β-catenin expression in the ovarian surface epithelium (OSE) cells develop indolent, undifferentiated tumors with both mesenchymal and epithelial characteristics. Combining dysregulated β-catenin with homozygous deletion of PTEN in the OSE resulted in development of significantly more aggressive tumors, which was correlated with inhibition of p53 expression and cellular senescence. Induced expression of both mTOR kinase, a master regulator of proliferation, and phosphorylation of its downstream target, S6Kinase was also observed in both the indolent and aggressive mouse tumors, as well as in human OEA with nuclear β-catenin accumulation. Ectopic allotransplants of the mouse ovarian tumor cells with a gain-of-function mutation in β-catenin and PTEN deletion developed into tumors with OEA histology, the growth of which were significantly inhibited by oral rapamycin treatment. These studies demonstrate that rapamycin might be an effective therapeutic for human ovarian endometrioid patients with dysregulated Wnt/β-catenin and Pten/PI3K signaling

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

MS

thesisThe lymphokines (interieukins) IL-4 and IL-5 are important regulatory elements of the immune system and are able to synergize with each other in regulating B cell maturation and differentiation. Thus, many studies have proposed a common in vivo and in vitro regulation of IL~4 and IL-5 production by mitogen or antigen activated T cells. Results reported here indicate a similar distribution of IL-4 and IL-5 production by T cells isolated from a variety of lymphoid organs in both aged and young mice. IL-4 and IL-5 production by activated T ceUs is similarly enhanced in aged mice (74 weeks old) within the mucosal lymph node (MLN), peripheral lymph node (PLN) and spleen compared to adult mice (15 weeks old). Our laboratory has observed that selected endogenous steroids are capable of altering the lymphokine-producing potential of activated T cells; the effect of some of these steroids is to elicit a lymphokine profile similar to that produced by T cells isolated from different lymphoid tissues. To further address the apparent coordinated regulation of IL-4 and IL-5 production, T cells were pulsed with either dehydroepiandrosterone (DHEA), dihydrotestosterone (DHT), glucocorticosterone (GCS), or 1,25 dihydroxyvitamin D3 (l,25(OH)2D3). Murine activated T cells and T cell clones exposed to the active form of Vitamin D3, l,25(OH)2D3, upregulated secretion of IL-4 and IL-5. However DHT, the active form of the androgen testosterone, reduced IL-4 and IL-5 production by anti-CD3 activated T ceUs. DHEA, which has been shown to upregulate IL-2 secretion by murine activated T cells, had no effect on IL-4 or 11-5 production. Similar regulation of IL-4 and 11-5 has important implications for augmenting the humoral arm of the immune response. The results presented herein indicate that naturally produced steroids have regulatory influences on these lymphokines and that steroids may also be important controlling elements of immune regulation. The murine BCL1 lymphoma has been described as the murine correlative to human chronic lymphocytic leukemia. It may be an important tumor model for understanding tumor growth and how transformation occurs. This tumor cell line has been well recognized as responsive, at least in the short term, to the lymphokines IL-4 and IL-5 in vitro. These lymphokines are T cell products which have been shown to contribute to regulation of humoral immunity and may also be important to maintenance and growth of BCL1 in vivo. To investigate this hypothesis, three approaches were used to obtain a T cell deficient experimental system: Nude mice, thymectimized/gamma irradiated mice (ATXBM), and in vivo antibody-mediated CD4 and CDS depletions. The last model was most effective where Balb/c mice were depleted of CD4+ and CDS+ T cells by injection of monoclonal antibody before and after injection of BCLi tumor. Tumor growth was examined by ability to palpate the spleen, spleen weight, splenic gross examination, histochemical staining, and flow cytometry. Results indicated that neither CD4+ or CDS+ cells contributed significantly to the transplantability or tumorigenicity of murine BCL1i lymphoma. BCL1 apparently proliferated with increased rate of growth, as evaluated by tumor mass, in the absence of T cells

Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy.

The vaginal microbiome (VMB) is a complex microbial community that is closely tied to reproductive health. Optimal VMB communities have compositions that are commonly defined by the dominance of certain Lactobacillus spp. and can remain stable over time or transition to non-optimal states dominated by anaerobic bacteria and associated with bacterial vaginosis (BV). The ability to remain stable or undergo transitions suggests a system with either single (mono-stable) or multiple (multi-stable) equilibrium states, though factors that contribute to stability have been difficult to determine due to heterogeneity in microbial growth characteristics and inter-species interactions. Here, we use a computational model to determine whether differences in microbial growth and interaction parameters could alter equilibrium state accessibility and account for variability in community composition after menses and antibiotic therapies. Using a global uncertainty and sensitivity analysis that captures parameter sets sampled from a physiologically relevant range, model simulations predicted that 79.7% of microbial communities were mono-stable (gravitate to one composition type) and 20.3% were predicted to be multi-stable (can gravitate to more than one composition type, given external perturbations), which was not significantly different from observations in two clinical cohorts (HMP cohort, 75.2% and 24.8%; Gajer cohort, 78.1% and 21.9%, respectively). The model identified key microbial parameters that governed equilibrium state accessibility, such as the importance of non-optimal anaerobic bacteria interactions with Lactobacillus spp., which is largely understudied. Model predictions for composition changes after menses and antibiotics were not significantly different from those observed in clinical cohorts. Lastly, simulations were performed to illustrate how this quantitative framework can be used to gain insight into the development of new combinatorial therapies involving altered prebiotic and antibiotic dosing strategies. Altogether, dynamical models could guide development of more precise therapeutic strategies to manage BV