Carbon Black and Titanium Dioxide Nanoparticles Differentially Activate Oxidative Stress and Apoptosis in A549 Human Alveolar Epithelial Cells

Recent studies have demonstrated that variation between particulate matter compositions have universally adverse effects on cells and living tissues. Carbon black and titanium dioxide are two such particulates that we are continuously exposed to, yet there is limited research to examine the potential deleterious effects on living tissue. The objective of this study is to characterize the effect of carbon black (CB) and titanium dioxide (TiO2) particulates on A549 human alveolar epithelial lung cells. CB and TiO2 powders were dispersed throughout a solution of water and bovine serum albumin by high-powered sonication. The effects of these particulates on A549 cells were analyzed through fluorescent microscope imaging, DAPI nuclear fluorescent staining, western blotting, H2DCFDA fluorescent staining. Death assays with DAPI revealed that both particulate types exhibit toxicity to cells and induce apoptosis. Live cell imaging showed perinuclear localization of both CB and TiO2 particulates. The human A549 cells were tested for reactive oxygen species (ROS) levels, which revealed a significant increase in ROS production induced by CB, but lowered ROS induction by TiO2. Interplay between ROS and intracellular calcium was examined; 2-APB, a calcium blocker was added to cells treated with CB. Results indicated that 50uM 2-APB provided notable protection to cells by decreasing ROS induction levels. Further research is required to determine through which apoptotic signaling pathway CB causes cell death and to definitively identify the signaling pathways involved in TiO2 associated toxicity. Further investigation of the explicit involvement of the ER in particulate induced apoptosis is a promising direction for future research

The High-Energy Radiation Environment Around a 10 Gyr M Dwarf: Habitable at Last?

High levels of X-ray and UV activity on young M dwarfs may drive rapid atmospheric escape on temperate, terrestrial planets orbiting within the liquid water habitable zone. However, secondary atmospheres on planets orbiting older, less active M dwarfs may be stable and present more promising candidates for biomarker searches. We present new HST and Chandra observations of Barnard's Star (GJ 699), a 10 Gyr old M3.5 dwarf, acquired as part of the Mega-MUSCLES program. Despite the old age and long rotation period of Barnard's star, we observe two FUV ($\delta_{130}$ $\approx$ 5000s; $E_{130}$ $\approx$ 10$^{29.5}$ erg each) and one X-ray ($E_{X}$ $\approx$ 10$^{29.2}$ erg) flares, and estimate a high-energy flare duty cycle (defined here as the fraction of the time the star is in a flare state) of $\sim$ 25\%. A 5 A - 10 $\mu$m SED of GJ 699 is created and used to evaluate the atmospheric stability of a hypothetical, unmagnetized terrestrial planet in the habitable zone ($r_{HZ}$ $\sim$ 0.1 AU). Both thermal and non-thermal escape modeling indicate (1) the $quiescent$ stellar XUV flux does not lead to strong atmospheric escape: atmospheric heating rates are comparable to periods of high solar activity on modern Earth, and (2) the $flare$ environment could drive the atmosphere into a hydrodynamic loss regime at the observed flare duty cycle: sustained exposure to the flare environment of GJ 699 results in the loss of $\approx$ 87 Earth atmospheres Gyr$^{-1}$ through thermal processes and $\approx$ 3 Earth atmospheres Gyr$^{-1}$ through ion loss processes, respectively. These results suggest that if rocky planet atmospheres can survive the initial $\sim$ 5 Gyr of high stellar activity, or if a second generation atmosphere can be formed or acquired, the flare duty cycle may be the controlling stellar parameter for the stability of Earth-like atmospheres around old M stars.Comment: Accepted to A

The unusual M-dwarf Warm Jupiter TOI-1899~b: Refinement of orbital and planetary parameters

TOI-1899~b is a rare exoplanet, a temperate Warm Jupiter orbiting an M-dwarf, first discovered by \citet{Canas2020_toi1899} from a TESS single-transit event. Using new radial velocities (RVs) from the precision RV spectrographs HPF and NEID, along with additional TESS photometry and ground-based transit follow-up, we are able to derive a much more precise orbital period of $P = 29.090312_{-0.000035}^{+0.000036}$~d, along with a radius of $R_p = 0.99\pm0.03$~\unit{R_{J}}. We have also improved the constraints on planet mass, $M_p = 0.67\pm{0.04}$~\unit{M_{J}}, and eccentricity, which is consistent with a circular orbit at 2$\sigma$ ($e = 0.044_{-0.027}^{+0.029}$). TOI-1899~b occupies a unique region of parameter space as the coolest known ($T_{eq} \approx$ 380~K) Jovian-sized transiting planet around an M-dwarf; we show that it has great potential to provide clues regarding the formation and migration mechanisms of these rare gas giants through transmission spectroscopy with JWST as well as studies of tidal evolution.Comment: 19 pages, 7 figures, 3 tables, submitted to AJ (comments welcome

The Bioinformatics Virtual Coordination Network: An open-source and interactive learning environment

Lockdowns and “stay-at-home” orders, starting in March 2020, shuttered bench and field dependent research across the world as a consequence of the global COVID-19 pandemic. The pandemic continues to have an impact on research progress and career development, especially for graduate students and early career researchers, as strict social distance limitations stifle ongoing research and impede in-person educational programs. The goal of the Bioinformatics Virtual Coordination Network (BVCN) was to reduce some of these impacts by helping research biologists learn new skills and initiate computational projects as alternative ways to carry out their research. The BVCN was founded in April 2020, at the peak of initial shutdowns, by an international group of early-career microbiology researchers with expertise in bioinformatics and computational biology. The BVCN instructors identified several foundational bioinformatic topics and organized hands-on tutorials through cloud-based platforms that had minimal hardware requirements (in order to maximize accessibility) such as RStudio Cloud and MyBinder. The major topics included the Unix terminal interface, R and Python programming languages, amplicon analysis, metagenomics, functional protein annotation, transcriptome analysis, network science, and population genetics and comparative genomics. The BVCN was structured as an open-access resource with a central hub providing access to all lesson content and hands-on tutorials (https://biovcnet.github.io/). As laboratories reopened and participants returned to previous commitments, the BVCN evolved: while the platform continues to enable “a la carte” lessons for learning computational skills, new and ongoing collaborative projects were initiated among instructors and participants, including a virtual, open-access bioinformatics conference in June 2021. In this manuscript we discuss the history, successes, and challenges of the BVCN initiative, highlighting how the lessons learned and strategies implemented may be applicable to the development and planning of future courses, workshops, and training programs

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery

Cinema-going trajectories in the digital age

The activity of cinema-going constantly evolves and gradually integrates the use of digital data and platforms to become more engaging for the audiences. Combining methods from the fields of Human Computer Interaction and Film Studies, we conducted two workshops seeking to understand cinema audiences’ digital practices and explore how the contemporary cinema-going experience is shaped in the digital age. Our findings suggest that going to the movies constitutes a trajectory during which cinemagoers interact with multiple digital platforms. At the same time, depending on their choices, they construct unique digital identities that represent a set of online behaviours and rituals that cinemagoers adopt before, while and after cinema-going. To inform the design of new, engaging cinemagoing experiences, this research establishes a preliminary map of contemporary cinema-going including digital data and platforms. We then discuss how audiences perceive the potential improvement of the experience and how that would lead to the construction of digital identities

Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies

Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different Francisella subspecies (subsp.): the F. tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public Francisella sequences, including the rare F. tularensis subsp. mediasiatica FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the holarctica subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic F. tularensis subsp. mediasiatica FSC147 strain, including modulator of drug activity B (mdaB) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in Francisella subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Trophic Ecology of Atlantic Bluefin Tuna (Thunnus thynnus) Larvae from the Gulf of Mexico and NW Mediterranean Spawning Grounds: A Comparative Stable Isotope Study

The present study uses stable isotopes of nitrogen and carbon (δ15Nandδ13C) as trophic indicators for Atlantic bluefin tuna larvae (BFT) (6–10mm standard length) in the highly contrasting environmental conditions of the Gulf of Mexico (GOM) and the Balearic Sea (MED). These regions are differentiated by their temperature regime and relative productivity, with the GOM being significantly warmer and more productive. MED BFT larvae showed the highest δ15N signatures, implying an elevated trophic position above the underlyingmicrozooplankton baseline. Ontogenetic dietary shifts were observed in the BFT larvae from the GOM and MED which indicates early life trophodynamics differences between these spawning habitats. Significant trophic differences between the GOM and MED larvae were observed in relation to δ15N signatures in favour of the MED larvae, which may have important implications in their growth during their early life stages. These low δ15N levels in the zooplankton from the GOM may be an indication of a shifting isotopic baseline in pelagic food webs due to diatrophic inputs by cyanobacteria. Lack of enrichment for δ15N in BFT larvae compared to zooplankton implies an alternative grazing pathway from the traditional food chain of phytoplankton— zooplankton—larval fish. Results provide insight for a comparative characterization of the trophic pathways variability of the two main spawning grounds for BFT larvaeVersión del editor4,411

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University