Asynchronous Transcriptional Silencing of Individual Retroviral Genomes in Embryonic Cells

Background Retroviral DNAs are profoundly silenced at the transcriptional level in embryonic cell types. The transcriptional profile of pluripotent stem cells has been demonstrated to be extremely heterogeneous from cell to cell, and how the silencing of retroviral DNAs is achieved is not yet well characterized. Results In the current study, we investigated the transcriptional silencing dynamics in stem cells by independently monitoring the expression of two Moloney murine leukemia virus (MMLV) retroviral vectors newly introduced into embryonic carcinoma (EC) cells. Although MMLV is efficiently silenced by epigenetic mechanisms in most such cells, a small number of the doubly-transduced EC cells transiently show double-positive proviral expression. These cells were sorted and their expression patterns were studied over time as silencing is established. Conclusions Our data suggest that retroviral silencing occurs stochastically, in an individual locus-specific fashion, and often without synchronous silencing of both viruses in the same cells. Surprisingly, the chromatin modifications that mark the silenced proviruses are unchanged even in cells that temporarily escape silencing. This local silencing effect is a feature of stem cell epigenomic regulation that has not previously been revealed

A Novel Role for Stat1 in Phagosome Acidification and Natural Host Resistance to Intracellular Infection by Leishmania major

Intracellular parasites of the genus Leishmania generate severe diseases in humans, which are associated with a failure of the infected host to induce a protective interferon γ (IFNγ)-mediated immune response. We tested the role of the JAK/STAT1 signaling pathway in Leishmania pathogenesis by utilizing knockout mice lacking the signal transducer and activator of transcription 1 (Stat1) and derived macrophages. Unexpectedly, infection of Stat1-deficient macrophages in vitro with promastigotes from Leishmania major and attenuated LPG1 knockout mutants (lpg−) specifically lacking lipophosphoglycan (LPG) resulted in a twofold increased intracellular growth, which was independent of IFNγ and associated with a substantial increase in phagosomal pH. Phagosomes in Stat1−/− macrophages showed normal maturation as judged by the accumulation of the lysosomal marker protein rab7, and provided normal vATPase activity, but were defective in the anion conductive pathway required for full vesicular acidification. Our results suggest a role of acidic pH in the control of intracellular Leishmania growth early during infection and identify for the first time an unexpected role of Stat1 in natural anti-microbial resistance independent from its function as IFNγ-induced signal transducer. This novel Stat1 function may have important implications to studies of other pathogens, as the acidic phagolysosomal pH plays an important role in antigen processing and the uncoating process of many viruses

Evaluation of Noninvasive Respiratory Volume Monitoring in the PACU of a Low Resource Kenyan Hospital

This research aims to evaluate the use of the noninvasive respiratory volume monitor (RVM) compared to the standard of care (SOC) in the Post-Anesthesia Care Unit (PACU) of Kijabe Hospital, Kenya. The RVM provides real-time measurements for quantitative monitoring of non-intubated patients. Our evaluation was focused on the incidence of postoperative opioid-induced respiratory depression (OIRD). The RVM cohort (N = 50) received quantitative OIRD assessment via the RVM, which included respiratory rate, minute ventilation, and tidal volume. The SOC cohort (N = 46) received qualitative OIRD assessment via patient monitoring with oxygenation measurements (SpO2) and physical examination. All diagnosed cases of OIRD were in the RVM cohort (9/50). In the RVM cohort, participants stayed longer in the PACU and required more frequent airway maneuvers and supplemental oxygen, compared to SOC (all p \u3c 0.05). The SOC cohort may have had fewer diagnoses of OIRD due to the challenging task of distinguishing hypoventilation versus OIRD in the absence of quantitative data. To account for the higher OIRD risk with general anesthesia (GA), a subgroup analysis was performed for only participants who underwent GA, which showed similar results. The use of RVM for respiratory monitoring of OIRD may allow for more proactive care

Players in the silencing of retroviral DNAs in embryonic stem cells

Embryonic stem (ES) cells potently repress retroviral infection through transcriptional silencing of the newly established proviral DNAs. We have characterized two distinct types of silencing in embryonic mouse cells infected by the Moloney murine leukemia virus (MLV): a highly efficient one targeted to the proline tRNA primer binding site (PBSpro) on the MLV genome, and a less efficient one occurring independently of the PBS. We determined that the PBS-specific silencing is mediated by TRIM28 (Kap-1), a known transcriptional silencer, tethered to the DNA by ZFP809, one of the dozens of zinc finger proteins encoded in the mammalian genome. At least two more components, HP1gamma and EBP1, are implicated in this silencing. We have also begun characterizing a non-PBS directed silencing complex acting more broadly on incoming viral DNAs in ES cells. We suggest that a major player in this process is Yin Yang1 (YY1), a GLI-Kruppel zinc finger protein, ubiquitously expressed and highly conserved between species. We show by ChIP that YY1 binds the LTR of both exogenous and endogenous retroviruses in ES cells. Deletion of the YY1 binding site from the MLV-LTR increased expression of the provirus at least four fold over that of the wild-type virus. Moreover, in YY1 KD cells the expression of the IAP (class II) endogenous retroviruses was remarkably upregulated

Determination of a lower bound on Earth’s climate sensitivity

Transient and equilibrium sensitivity of Earth's climate has been calculated using global temperature, forcing and heating rate data for the period 1970–2010. We have assumed increased long-wave radiative forcing in the period due to the increase of the long-lived greenhouse gases. By assuming the change in aerosol forcing in the period to be zero, we calculate what we consider to be lower bounds to these sensitivities, as the magnitude of the negative aerosol forcing is unlikely to have diminished in this period. The radiation imbalance necessary to calculate equilibrium sensitivity is estimated from the rate of ocean heat accumulation as 0.37±0.03W m^−2 (all uncertainty estimates are 1−σ). With these data, we obtain best estimates for transient climate sensitivity 0.39±0.07K (W m^−2)^−1 and equilibrium climate sensitivity 0.54±0.14K (W m^−2)^−1, equivalent to 1.5±0.3 and 2.0±0.5K (3.7W m^−2)^−1, respectively. The latter quantity is equal to the lower bound of the ‘likely’ range for this quantity given by the 2007 IPCC Assessment Report. The uncertainty attached to the lower-bound equilibrium sensitivity permits us to state, within the assumptions of this analysis, that the equilibrium sensitivity is greater than 0.31K (W m^−2)^−1, equivalent to 1.16K(3.7W m^−2)^−1, at the 95% confidence level

Natural climate solutions

Our thanks for inputs by L. Almond, A. Baccini, A. Bowman, S. CookPatton, J. Evans, K. Holl, R. Lalasz, A. Nassikas, M. Spalding, M. Wolosin, and expert elicitation respondents. Our thanks for datasets developed by the Hansen lab and the NESCent grasslands working group (C. Lehmann, D. Griffith, T. M. Anderson, D. J. Beerling, W. Bond, E. Denton, E. Edwards, E. Forrestel, D. Fox, W. Hoffmann, R. Hyde, T. Kluyver, L. Mucina, B. Passey, S. Pau, J. Ratnam, N. Salamin, B. Santini, K. Simpson, M. Smith, B. Spriggs, C. Still, C. Strömberg, and C. P. Osborne). This study was made possible by funding from the Doris Duke Charitable Foundation. Woodbury was supported in part by USDA-NIFA Project 2011-67003-30205 Data deposition: A global spatial dataset of reforestation opportunities has been deposited on Zenodo (https://zenodo.org/record/883444). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1710465114/-/DCSupplemental.Peer reviewedPublisher PD

Biochar has no effect on soil respiration across Chinese agricultural soils

This work was supported by NSFC (41371298 and 41371300), Ministry of Science and Technology (2013GB23600666 and 2013BAD11B00), and Ministry of Education of China (20120097130003). The international cooperation was funded under a “111” project by the State Agency of Foreign Expert Affairs of China and jointly supported under a grant for Priority Disciplines in Higher Education by the Department of Education, Jiangsu Province, China; The work was also a contribution to the cooperation project of “Estimates of Future Agricultural GHG Emissions and Mitigation in China” under the UK-China Sustainable Agriculture Innovation Network (SAIN). Pete Smith contributed to this work under a UK BBSRC China Partnership Award. The authors are grateful to Yuming Liu, Bin Zhang, Xiao Li, Gang Wu, Jinjin Qu and Yinxin Ye and Dongqi Liu for their contribution to field experiments, and to Rongjun Bian and Qaiser Hussain for their participation in discussions of the data analysis and interpretation, and to Xinyan Yu and Jiafang Wang for their assistance in lab works.Peer reviewedPostprin

Evidence for carbon sequestration by agricultural liming

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95356/1/gbc1382.pd