skip to main content

Search for: All records

Creators/Authors contains: "Mika, ��."

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Free, publicly-accessible full text available June 1, 2023
  2. Despite renewed interest, development of chemical biology methods to study peptidoglycan metabolism has lagged in comparison to the glycobiology field in general. To address this, a panel of diamides were screened against the Gram-positive bacterium Streptococcus pneumoniae to identify inhibitors of bacterial growth. The screen identified the diamide masarimycin as a bacteriostatic inhibitor of S. pneumoniae growth with an MIC of 8 µM. The diamide inhibited detergent-induced autolysis in a concentration-dependent manner, indicating perturbation of peptidoglycan degradation as the mode-of-action. Cell based screening of masarimycin against a panel of autolysin mutants, identified a higher MIC against a Δ lytB strain lackingmore »an endo-N-acetylglucosaminidase involved in cell division. Subsequent biochemical and phenotypic analyses suggested that the higher MIC was due to an indirect interaction with LytB. Further analysis of changes to the cell surface in masarimycin treated cells identified the overexpression of several moonlighting proteins, including elongation factor Tu which is implicated in regulating cell shape. Checkerboard assays using masarimycin in concert with additional antibiotics identified an antagonistic relationship with the cell wall targeting antibiotic fosfomycin, which further supports a cell wall mode-of-action.« less
    Free, publicly-accessible full text available April 25, 2023
  3. Free, publicly-accessible full text available January 1, 2023
  4. Abstract Spectral lines of ammonia, NH 3 , are useful probes of the physical conditions in dense molecular cloud cores. In addition to advantages in spectroscopy, ammonia has also been suggested to be resistant to freezing onto grain surfaces, which should make it a superior tool for studying the interior parts of cold, dense cores. Here we present high-resolution NH 3 observations with the Very Large Array and Green Bank Telescope toward a prestellar core. These observations show an outer region with a fractional NH 3 abundance of X (NH 3 ) = (1.975 ± 0.005) × 10 −8 (±10%more »systematic), but it also reveals that, after all, the X (NH 3 ) starts to decrease above a H 2 column density of ≈2.6 × 10 22 cm −2 . We derive a density model for the core and find that the break point in the fractional abundance occurs at the density n (H 2 ) ∼ 2 × 10 5 cm −3 , and beyond this point the fractional abundance decreases with increasing density, following the power law n −1.1 . This power-law behavior is well reproduced by chemical models where adsorption onto grains dominates the removal of ammonia and related species from the gas at high densities. We suggest that the break-point density changes from core to core depending on the temperature and the grain properties, but that the depletion power law is anyway likely to be close to n −1 owing to the dominance of accretion in the central parts of starless cores.« less
    Free, publicly-accessible full text available May 27, 2023
  5. Free, publicly-accessible full text available December 29, 2022
  6. Abstract Background

    Microbial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as many evolutionarily important clades remain unexamined. There is currently no data on the microbiota associated with any Chondrichthyan species during embryonic development, despite the global distribution, ecological importance, and phylogenetic position of this clade. In this study, we take the first steps towards filling this gap by investigating the microbiota associated with embryonic development in the little skate,Leucoraja erinacea,a common North Atlantic species and popular system for chondrichthyan biology.

    Methods

    To assess the potential for bacterial transmission in an oviparousmore »chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate,at six points during ontogeny. Community composition was analyzed using the QIIME2 pipeline and microbial continuity between stages was tracked using FEAST.

    Results

    We identify site-specific and stage-specific microbiota dominated by the bacterial phylaProteobacteriaandBacteroidetes. This composition is similar to, but distinct from, that of previously published data on the adult microbiota of other chondrichthyan species. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop.

    Conclusions

    Our study is the first exploration of the chondrichthyan microbiota throughout ontogeny and provides the first evidence of vertical transmission in this group.

    « less
  7. Abstract Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, themore »resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract« less
    Free, publicly-accessible full text available December 1, 2022
  8. Carriers of heterozygous germline BAP1 mutations ( BAP1 +/− ) are affected by the “BAP1 cancer syndrome.” Although they can develop almost any cancer type, they are unusually susceptible to asbestos carcinogenesis and mesothelioma. Here we investigate why among all carcinogens, BAP1 mutations cooperate with asbestos. Asbestos carcinogenesis and mesothelioma have been linked to a chronic inflammatory process promoted by the extracellular release of the high-mobility group box 1 protein (HMGB1). We report that BAP1 +/− cells secrete increased amounts of HMGB1, and that BAP1 +/− carriers have detectable serum levels of acetylated HMGB1 that further increase when they developmore »mesothelioma. We linked these findings to our discovery that BAP1 forms a trimeric protein complex with HMGB1 and with histone deacetylase 1 (HDAC1) that modulates HMGB1 acetylation and its release. Reduced BAP1 levels caused increased ubiquitylation and degradation of HDAC1, leading to increased acetylation of HMGB1 and its active secretion that in turn promoted mesothelial cell transformation.« less
    Free, publicly-accessible full text available November 30, 2022
  9. Abstract. In the global methane budget, the largest natural sourceis attributed to wetlands, which encompass all ecosystems composed ofwaterlogged or inundated ground, capable of methane production. Among them,northern peatlands that store large amounts of soil organic carbon have beenfunctioning, since the end of the last glaciation period, as long-termsources of methane (CH4) and are one of the most significant methanesources among wetlands. To reduce uncertainty of quantifying methane flux in theglobal methane budget, it is of significance to understand the underlyingprocesses for methane production and fluxes in northern peatlands. A methanemodel that features methane production and transport by plants, ebullitionprocessmore »and diffusion in soil, oxidation to CO2, and CH4 fluxes tothe atmosphere has been embedded in the ORCHIDEE-PEAT land surface modelthat includes an explicit representation of northern peatlands.ORCHIDEE-PCH4 was calibrated and evaluated on 14 peatland sites distributedon both the Eurasian and American continents in the northern boreal andtemperate regions. Data assimilation approaches were employed to optimizedparameters at each site and at all sites simultaneously. Results show thatmethanogenesis is sensitive to temperature and substrate availability overthe top 75 cm of soil depth. Methane emissions estimated using single siteoptimization (SSO) of model parameters are underestimated by 9 g CH4 m−2 yr−1 on average (i.e., 50 % higher than the site average ofyearly methane emissions). While using the multi-site optimization (MSO),methane emissions are overestimated by 5 g CH4 m−2 yr−1 onaverage across all investigated sites (i.e., 37 % lower than the siteaverage of yearly methane emissions).« less
    Free, publicly-accessible full text available January 1, 2023
  10. Suppose Alice and Bob each start with private randomness and no other input, and they wish to engage in a protocol in which Alice ends up with a set x ⊆ [ n ] and Bob ends up with a set y ⊆ [ n ], such that ( x , y ) is uniformly distributed over all pairs of disjoint sets. We prove that for some constant β < 1, this requires Ω ( n ) communication even to get within statistical distance 1− β n of the target distribution. Previously, Ambainis, Schulman, Ta-Shma, Vazirani, and Wigderson (FOCS 1998)more »proved that Ω (√ n ) communication is required to get within some constant statistical distance ɛ > 0 of the uniform distribution over all pairs of disjoint sets of size √ n .« less