Gonosomal mosaicism for a novel col5a1 pathogenic variant in classic ehlers-danlos syndrome

(1) Background: Classic Ehlers-Danlos syndrome (cEDS) is a heritable connective tissue disorder characterized by joint hypermobility and skin hyperextensibility with atrophic scarring. Many cEDS individuals carry variants in either the COL5A1 or COL5A2 genes. Mosaicism is relatively common in heritable connective tissue disorders but is rare in EDS. In cEDS, a single example of presumed gonosomal mosaicism for a COL5A1 variant has been published to date. (2) Methods: An 8-year-old girl with cEDS was analyzed by next-generation sequencing (NGS). Segregation was performed by Sanger sequencing in her unaffected parents. In the father, the mosaicism of the variant was further analyzed by targeted NGS and droplet digital PCR (ddPCR) in the blood and by Sanger sequencing in other tissues. (3) Results: The NGS analysis revealed the novel germline heterozygous COL5A1 c.1369G>T, p.(Glu457*) variant in the proband. Sanger chromatogram of the father’s blood specimen suggested the presence of a low-level mosaicism for the COL5A1 variant, which was confirmed by NGS and estimated to be 4.8% by ddPCR. The mosaicism was also confirmed by Sanger sequencing in the father’s saliva, hair bulbs and nails. (4) Conclusions: We described the second case of cEDS caused by paternal gonosomal mosaicism in COL5A1. Parental mosaicism could be an issue in cEDS and, therefore, considered for appropriate genetic counseling

A Direct Comparison between the use of Double Gray and Multiwavelength Radiative Transfer in a General Circulation Model with and without Radiatively Active Clouds

Inhomogeneous cloud formation and wavelength-dependent phenomena are expected to shape hot Jupiter atmospheres. We present a General Circulation Model (GCM) with multiwavelength "picket fence" radiative transfer and radiatively active, temperature dependent clouds, and compare the results to a double gray routine. The double gray method inherently fails to model polychromatic effects in hot Jupiter atmospheres, while picket fence captures these non-gray aspects and performs well compared to fully wavelength-dependent methods. We compare both methods with radiatively active clouds and cloud-free models, assessing the limitations of the double gray method. Although there are broad similarities, the picket fence models have larger day-night side temperature differences, non-isothermal upper atmospheres, and multiwavelength effects in the presence of radiatively active clouds. We model the well-known hot Jupiters HD 189733 b and HD 209458 b. For the hotter HD 209458 b, the picket fence method prevents clouds from thermostating dayside temperatures, resulting in hotter upper atmospheres and the dissipation of dayside clouds. Differences in the temperature structures are then associated with nuanced differences in the circulation patterns and clouds. Models of the cooler HD 189733 b have global cloud coverage, regardless of radiative transfer scheme, whereas there are larger differences in the models of HD 209458 b, particularly in the extent of the partial cloud coverage on its dayside. This results in minor changes to the thermal and reflected light phase curves of HD 189733 b, but more significant differences for the picket fence and double gray versions of HD 209458 b.Comment: Submitted to ApJ, 31 page

AIRR Community Guide to Planning and Performing AIRR-Seq Experiments

The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project

A Lack of Variability Between Repeated Spitzer Phase Curves of WASP-43b

Though the global atmospheres of hot Jupiters have been extensively studied using phase curve observations, the level of time variability in these data is not well constrained. To investigate possible time variability in a planetary phase curve, we observed two full-orbit phase curves of the hot Jupiter WASP-43b at 4.5 microns using the Spitzer Space Telescope, and reanalyzed a previous 4.5 micron phase curve from Stevenson et al. (2017). We find no significant time variability between these three phase curves, which span timescales of weeks to years. The three observations are best fit by a single phase curve with an eclipse depth of 3907 +- 85 ppm, a dayside-integrated brightness temperature of 1479 +- 13 K, a nightside-integrated brightness temperature of 755 +- 46 K, and an eastward-shifted peak of 10.4 +- 1.8 degrees. To model our observations, we performed 3D general circulation model simulations of WASP-43b with simple cloud models of various vertical extents. In comparing these simulations to our observations, we find that WASP-43b likely has a cloudy nightside that transitions to a relatively cloud-free dayside. We estimate that any change in WASP-43bs vertical cloud thickness of more than three pressure scale heights is inconsistent with our observed upper limit on variation. These observations, therefore, indicate that WASP-43bs clouds are stable in their vertical and spatial extent over timescales up to several years. These results strongly suggest that atmospheric properties derived from previous, single Spitzer phase curve observations of hot Jupiters likely show us the equilibrium properties of these atmospheres.Comment: 24 pages, 9 figures, Published in the Astronomical Journal (AJ

Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling

Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community's Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work. Keywords: B-cell Receptor (BCR); IG; T-cell Receptor (TCR); TR; antibody; immunoglobulin; immunology; inflammation; next generation sequencing (NGS)

Illuminating Host-Parasite Interaction at the Cellular and Subcellular Levels with Infrared Microspectroscopy

Toxoplasma gondii (T. gondii) is an opportunistic protozoan that can cause brain infection and other serious health consequences in immuno-compromised individuals. This parasite has a remarkable ability to cross biological barriers and exploit the host cell microenvironment to support its own survival and growth. Recent advances in label-free spectroscopic imaging techniques have made it possible to study biological systems at a high spatial resolution. In this study, we used conventional Fourier-transform infrared (FTIR) microspectroscopy and synchrotron-based FTIR microspectroscopy to analyze the chemical changes that are associated with infection of human brain microvascular endothelial cells (hBMECs) by T. gondii (RH) tachyzoites. Both FTIR microspectroscopic methods showed utility in revealing the chemical alterations in the infected hBMECs. Using a ZnS hemisphere device, to increase the numerical aperture, and the synchrotron source to increase the brightness, we obtained spatially resolved spectra from within a single cell. The spectra extracted from the nucleus and cytosol containing the tachyzoites were clearly distinguished. RNA sequencing analysis of T. gondii-infected and uninfected hBMECs revealed significant changes in the expression of host cell genes and pathways in response to T. gondii infection. These FTIR spectroscopic and transcriptomic findings provide significant insight into the molecular changes that occur in hBMECs during T. gondii infection

A novel Bifidobacterium infantis-mediated TK/GCV suicide gene therapy system exhibits antitumor activity in a rat model of bladder cancer

Bladder cancer is the ninth most common malignancy in the world. Successful clinical management remains a challenge. In order To search for novel targeted and efficacious treatment, we sought to investigate anti-tumor activity of BI-TK suicide gene therapy system in a rat model of bladder tumors. We first constructed and tested an anaerobic Bifidobacterium infantis-mediated thymidine kinase (BI-TK) suicide gene therapy system. To test the in vivo efficacy of this system, we established a rat model of bladder tumors, which was induced by N-methyl-nitrosourea perfusion. Bifidobacterium infantis containing the HSV-TK (i.e., BI-TK) were constructed by transformation of recombinant plasmid pGEX - TK. The engineered BI-TK was injected into tumor-bearing rats via tail vein, followed by intraperitoneal injection of ganciclovir (GCV). Using the rat model of bladder tumors, we found that bladder tumor burdens were significantly lower in the rats treated with BI-TK/GCV group than that treated with normal saline control group (p <0.05). While various degrees of apoptosis of the tumor cells were detected in all groups using in situ TUNEL assay, apoptosis was mostly notable in the BI-TK/GCV treatment group. Immunohistochemical staining further demonstrated that the BI-TK/GCV treatment group had the highest level of caspase3 protein expression than that of the empty plasmid group and normal saline group (p < 0.05). Thus, our results demonstrate that the Bifidobacterium infantis-mediated TK/GCV suicide gene therapy system can effectively inhibit rat bladder tumor growth, possibly through increasing caspase 3 expression and inducing apoptosis