On the second homology group of the Torelli subgroup of Aut(F_n)

Let IA_n be the Torelli subgroup of Aut(F_n). We give an explicit finite set of generators for H_2(IA_n) as a GL_n(Z)-module. Corollaries include a version of surjective representation stability for H_2(IA_n), the vanishing of the GL_n(Z)-coinvariants of H_2(IA_n), and the vanishing of the second rational homology group of the level l congruence subgroup of Aut(F_n). Our generating set is derived from a new group presentation for IA_n which is infinite but which has a simple recursive form.Comment: 39 pages; minor revision; to appear in Geom. Topo

A Birman exact sequence for the Torelli subgroup of Aut(F_n)

We develop an analogue of the Birman exact sequence for the Torelli subgroup of Aut(F_n). This builds on earlier work of the authors who studied an analogue of the Birman exact sequence for the entire group Aut(F_n). These results play an important role in the authors' recent work on the second homology group of the Torelli group.Comment: 31 pages, minor revision; to appear in Int. J. Algebr. Compu

Picoradian deflection measurement with an interferometric quasi-autocollimator using weak value amplification

We present an "interferometric quasi-autocollimator" that employs weak value amplification to measure angular deflections of a target mirror. The device has been designed to be insensitive to all translations of the target. We present a conceptual explanation of the amplification effect used by the device. An implementation of the device demonstrates sensitivities better than 10 picoradians per root hertz between 10 and 200 hertz.Comment: To be published in Optics Letter

Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D. Y., Hoehler, T., Cardace, D., & Schrenk, M. O. . Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer. mSystems, 5(2), (2020): e00607-00619, doi: 10.1128/mSystems.00607-19.Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.We thank McLaughlin Reserve, in particular Paul Aigner and Cathy Koehler, for hosting sampling at CROMO and providing access to the wells, A. Daniel Jones and Anthony Schilmiller for their advice regarding metabolite extraction and mass spectrometry, Elizabeth Kujawinski for her guidance in metabolomics data analysis and interpretation, and Julia McGonigle, Christopher Thornton, and Katrina Twing for assistance with metagenomic and computational analyses

Duchamp: a 3D source finder for spectral-line data

This paper describes the Duchamp source finder, a piece of software designed to find and describe sources in 3-dimensional, spectral-line data cubes. Duchamp has been developed with HI (neutral hydrogen) observations in mind, but is widely applicable to many types of astronomical images. It features efficient source detection and handling methods, noise suppression via smoothing or multi-resolution wavelet reconstruction, and a range of graphical and text-based outputs to allow the user to understand the detections. This paper details some of the key algorithms used, and illustrates the effectiveness of the finder on different data sets.Comment: MNRAS, in press. 17 pages, 8 figure

Beyond Tryptophan Synthase: Identification of Genes That Contribute to Chlamydia trachomatis Survival during Gamma Interferon-Induced Persistence and Reactivation

Chlamydia trachomatis can enter a viable but nonculturable state in vitro termed persistence. A common feature of C. trachomatis persistence models is that reticulate bodies fail to divide and make few infectious progeny until the persistence-inducing stressor is removed. One model of persistence that has relevance to human disease involves tryptophan limitation mediated by the host enzyme indoleamine 2,3-dioxygenase, which converts l-tryptophan to N-formylkynurenine. Genital C. trachomatis strains can counter tryptophan limitation because they encode a tryptophan-synthesizing enzyme. Tryptophan synthase is the only enzyme that has been confirmed to play a role in interferon gamma (IFN-γ)-induced persistence, although profound changes in chlamydial physiology and gene expression occur in the presence of persistence-inducing stressors. Thus, we screened a population of mutagenized C. trachomatis strains for mutants that failed to reactivate from IFN-γ-induced persistence. Six mutants were identified, and the mutations linked to the persistence phenotype in three of these were successfully mapped. One mutant had a missense mutation in tryptophan synthase; however, this mutant behaved differently from previously described synthase null mutants. Two hypothetical genes of unknown function, ctl0225 and ctl0694, were also identified and may be involved in amino acid transport and DNA damage repair, respectively. Our results indicate that C. trachomatis utilizes functionally diverse genes to mediate survival during and reactivation from persistence in HeLa cells

Defining graphenic crystallites in disordered carbon: moving beyond the platelet model

We develop a picture of graphenic crystallites within disordered carbons that goes beyond the traditional model of graphitic platelets at random orientation. Using large atomistic models containing one million atoms, we redefine the meaning of the quantity La extracted from X-ray diffraction (XRD) patterns. Two complementary approaches are used to measure the size of graphenic crystallites, which are defined as regions of regularly arranged hexagons. Firstly, we calculate the X-ray diffraction pattern directly from the atomistic coordinates of the structure and analyse them following a typical experimental process. Second, the graphenic crystallites are identified from a direct geometrical approach. By mapping the structure directly, we replace the idealised picture of the crystallite with a more realistic representation of the material and provide a well-defined interpretation for $L_a$ measurements of disordered carbon. A key insight is that the size distribution is skewed heavily towards small fragments, with more than 75% of crystallites smaller than half of $L_a$

Accretion of the Magellanic system onto the Galaxy

Our Galaxy is surrounded by a large family of dwarf galaxies of which the most massive are the Large and Small Magellanic Clouds (LMC and SMC). Recent evidence suggests that systems with the mass of the Local Group accrete galaxies in smaller groups rather than individually. If so, at least some of the Galaxy's dwarfs may have fallen in with the LMC and SMC, and were formed as part of the Magellanic system in the nearby universe. We use the latest measurements of the proper motions of the LMC and SMC and a multicomponent model of the Galactic potential to explore the evolution of these galaxy configurations under the assumption that the Magellanic system may once have contained a number of bound dwarf galaxies. We compare our results to the available kinematic data for the local dwarf galaxies, and examine whether this model can account for recently discovered stellar streams and the planar distribution of Milky Way satellites. We find that in situations where the LMC and SMC are bound to the Milky Way, the kinematics of Draco, Sculptor, Sextans, Ursa Minor and the Sagittarius Stream are consistent with having fallen in along with the Magellanic system. These dwarfs, if so associated, will likely have been close to the tidal radius of the LMC originally and are unlikely to have affected each other throughout the orbit. However there are clear cases, such as Carina and Leo I, that cannot be explained this wayComment: 13 pages, 7 figure, ApJ accepte

Interrogating Genes That Mediate Chlamydia trachomatis Survival in Cell Culture Using Conditional Mutants and Recombination

Intracellular bacterial pathogens in the family Chlamydiaceae are causes of human blindness, sexually transmitted disease, and pneumonia. Genetic dissection of the mechanisms of chlamydial pathogenicity has been hindered by multiple limitations, including the inability to inactivate genes that would prevent the production of elementary bodies. Many genes are also Chlamydia-specific genes, and chlamydial genomes have undergone extensive reductive evolution, so functions often cannot be inferred from homologs in other organisms. Conditional mutants have been used to study essential genes of many microorganisms, so we screened a library of 4,184 ethyl methanesulfonate-mutagenized Chlamydia trachomatis isolates for temperature-sensitive (TS) mutants that developed normally at physiological temperature (37°C) but not at nonphysiological temperatures. Heat-sensitive TS mutants were identified at a high frequency, while cold-sensitive mutants were less common. Twelve TS mutants were mapped using a novel markerless recombination approach, PCR, and genome sequencing. TS alleles of genes that play essential roles in other bacteria and chlamydia-specific open reading frames (ORFs) of unknown function were identified. Temperature-shift assays determined that phenotypes of the mutants manifested at distinct points in the developmental cycle. Genome sequencing of a larger population of TS mutants also revealed that the screen had not reached saturation. In summary, we describe the first approach for studying essential chlamydial genes and broadly applicable strategies for genetic mapping in Chlamydia spp. and mutants that both define checkpoints and provide insights into the biology of the chlamydial developmental cycle. IMPORTANCE: Study of the pathogenesis of Chlamydia spp. has historically been hampered by a lack of genetic tools. Although there has been recent progress in chlamydial genetics, the existing approaches have limitations for the study of the genes that mediate growth of these organisms in cell culture. We used a genetic screen to identify conditional Chlamydia mutants and then mapped these alleles using a broadly applicable recombination strategy. Phenotypes of the mutants provide fundamental insights into unexplored areas of chlamydial pathogenesis and intracellular biology. Finally, the reagents and approaches we describe are powerful resources for the investigation of these organisms