Identifying Planetary Biosignature Impostors: Spectral Features of CO and O4 Resulting from Abiotic O2/O3 Production

O2 and O3 have been long considered the most robust individual biosignature gases in a planetary atmosphere, yet multiple mechanisms that may produce them in the absence of life have been described. However, these abiotic planetary mechanisms modify the environment in potentially identifiable ways. Here we briefly discuss two of the most detectable spectral discriminants for abiotic O2/O3: CO and O4. We produce the first explicit self-consistent simulations of these spectral discriminants as they may be seen by JWST. If JWST-NIRISS and/or NIRSpec observe CO (2.35, 4.6 um) in conjunction with CO2 (1.6, 2.0, 4.3 um) in the transmission spectrum of a terrestrial planet it could indicate robust CO2 photolysis and suggest that a future detection of O2 or O3 might not be biogenic. Strong O4 bands seen in transmission at 1.06 and 1.27 um could be diagnostic of a post-runaway O2-dominated atmosphere from massive H-escape. We find that for these false positive scenarios, CO at 2.35 um, CO2 at 2.0 and 4.3 um, and O4 at 1.27 um are all stronger features in transmission than O2/O3 and could be detected with SNRs $\gtrsim$ 3 for an Earth-size planet orbiting a nearby M dwarf star with as few as 10 transits, assuming photon-limited noise. O4 bands could also be sought in UV/VIS/NIR reflected light (at 0.345, 0.36, 0.38, 0.445, 0.475, 0.53, 0.57, 0.63, 1.06, and 1.27 um) by a next generation direct-imaging telescope such as LUVOIR/HDST or HabEx and would indicate an oxygen atmosphere too massive to be biologically produced.Comment: 7 pages, 4 figures, accepted to the Astrophysical Journal Letter

Sequence Effects on DNA Entropic Elasticity

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by this method is a combination of bend stiffness and intrinsic bend effects reflecting sequence information, just as at zero stretching force. This observation resolves the discrepancy between the value of A measured in these experiments and the larger ``dynamic persistence length'' measured by other means. On the other hand, the twist persistence length deduced from torsionally-constrained stretching experiments suffers no such correction. Our calculation is very simple and analytic; it applies to DNA and other polymers with weak intrinsic disorder.Comment: LaTeX; postscript available at http://dept.physics.upenn.edu/~nelson/index.shtm

Minimally invasive surgery for diabetic plantar foot ulcerations

Complications of diabetes mellitus constitute the most common indications for hospitalization and non-traumatic amputations in the USA. The most important risk factors for the development of diabetic foot ulcerations include the presence of peripheral neuropathy, vasculopathy, limited joint mobility, and pre-existing foot deformities. In our study, 500 diabetic patients treated for plantar forefoot ulcerations were enrolled in a prospective study from 2000 to 2008 at the Federal University of São Paulo, Brazil. Fifty-two patients in the study met the criteria and underwent surgical treatment consisting of percutaneous Achilles tendon lengthening to treat plantar forefoot ulcerations. The postoperative follow-up demonstrated prevention of recurrent foot ulcerations in 92% of these diabetic patients that maintained an improved foot function. In conclusion, our study supports that identification and treatment of ankle equinus in the diabetic population may potentially lead to decreased patient morbidity, including reduced risk for both reulceration, and potential lower extremity amputation

Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites

The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not. Genome-wide maps of nucleosome positions have revealed a salient pattern around transcription start sites, involving a nucleosome-free region (NFR) flanked by a pronounced periodic pattern in the average nucleosome density. While the periodic pattern clearly reflects well-positioned nucleosomes, the positioning mechanism is less clear. A recent experimental study by Mavrich et al. argued that the pattern observed in S. cerevisiae is qualitatively consistent with a `barrier nucleosome model', in which the oscillatory pattern is created by the statistical positioning mechanism of Kornberg and Stryer. On the other hand, there is clear evidence for intrinsic sequence preferences of nucleosomes, and it is unclear to what extent these sequence preferences affect the observed pattern. To test the barrier nucleosome model, we quantitatively analyze yeast nucleosome positioning data both up- and downstream from NFRs. Our analysis is based on the Tonks model of statistical physics which quantifies the interplay between the excluded-volume interaction of nucleosomes and their positional entropy. We find that although the typical patterns on the two sides of the NFR are different, they are both quantitatively described by the same physical model, with the same parameters, but different boundary conditions. The inferred boundary conditions suggest that the first nucleosome downstream from the NFR (the +1 nucleosome) is typically directly positioned while the first nucleosome upstream is statistically positioned via a nucleosome-repelling DNA region. These boundary conditions, which can be locally encoded into the genome sequence, significantly shape the statistical distribution of nucleosomes over a range of up to ~1000 bp to each side.Comment: includes supporting materia

Cross-species genomic and functional analyses identify a combination therapy using a CHK1 inhibitor and a ribonucleotide reductase inhibitor to treat triple-negative breast cancer

INTRODUCTION: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is diagnosed in approximately 15% of all human breast cancer (BrCa) patients. Currently, no targeted therapies exist for this subtype of BrCa and prognosis remains poor. Our laboratory has previously identified a proliferation/DNA repair/cell cycle gene signature (Tag signature) that is characteristic of human TNBC. We hypothesize that targeting the dysregulated biological networks in the Tag gene signature will lead to the identification of improved combination therapies for TNBC. METHODS: Cross-species genomic analysis was used to identify human breast cancer cell lines that express the Tag signature. Knock-down of the up-regulated genes in the Tag signature by siRNA identified several genes that are critical for TNBC cell growth. Small molecule inhibitors to two of these genes were analyzed, alone and in combination, for their effects on cell proliferation, cell cycle, and apoptosis in vitro and tumor growth in vivo. Synergy between the two drugs was analyzed by the Chou-Talalay method. RESULTS: A custom siRNA screen was used to identify targets within the Tag signature that are critical for growth of TNBC cells. Ribonucleotide reductase 1 and 2 (RRM1 and 2) and checkpoint kinase 1 (CHK1) were found to be critical targets for TNBC cell survival. Combination therapy, to simultaneously attenuate cell cycle checkpoint control through inhibition of CHK1 while inducing DNA damage with gemcitabine, improved therapeutic efficacy in vitro and in xenograft models of TNBC. CONCLUSIONS: This combination therapy may have translational value for patients with TNBC and improve therapeutic response for this aggressive form of breast cancer

Inhibition of p38-MAPK signaling pathway attenuates breast cancer induced bone pain and disease progression in a murine model of cancer-induced bone pain

<p>Abstract</p> <p>Background</p> <p>Mechanisms driving cancer-induced bone pain are poorly understood. A central factor implicated to be a key player in the process of tumorigenesis, osteoclastogenesis and nociception is p38 MAPK. We determined the role of p38 MAPK in a mouse model of breast cancer induced bone pain in which mixed osteolytic and osteoblastic remodeling occurs.</p> <p>Results</p> <p>In cancer-treated mice, acute as well as chronic inhibition of p38 MAPK with SB203580 blocked flinching and guarding behaviors in a dose-dependent manner whereas no effect on thresholds to tactile stimuli was observed. Radiographic analyses of bones demonstrated that chronic inhibition of p38 MAPK reduced bone loss and incidence of spontaneous fracture in cancer-treated mice. Histological analysis of bones collected from mice treated with the p38 MAPK inhibitor showed complete absence of osteoblastic growth in the intramedullary space as well as significantly reduced tumor burden.</p> <p>Conclusions</p> <p>Blockade of non-evoked pain behaviors but not hypersensitivity suggests differences in the underlying mechanisms of specific components of the pain syndrome and a possibility to individualize aspects of pain management. While it is not known whether the role of p38 MAPK signaling can be expanded to other cancers, the data suggest a need for understanding molecular mechanisms and cellular events that initiate and maintain cancer-induced bone pain for effective management for both ongoing pain as well as breakthrough pain.</p

A combined transmission spectrum of the Earth-sized exoplanets TRAPPIST-1 b and c

Three Earth-sized exoplanets were recently discovered close to the habitable zone of the nearby ultracool dwarf star TRAPPIST-1. The nature of these planets has yet to be determined, since their masses remain unmeasured and no observational constraint is available for the planetary population surrounding ultracool dwarfs, of which the TRAPPIST-1 planets are the first transiting example. Theoretical predictions span the entire atmospheric range from depleted to extended hydrogen-dominated atmospheres. Here, we report a space-based measurement of the combined transmission spectrum of the two inner planets made possible by a favorable alignment resulting in their simultaneous transits on 04 May 2016. The lack of features in the combined spectrum rules out cloud-free hydrogen-dominated atmospheres for each planet at 10-$\sigma$ levels; TRAPPIST-1 b and c are hence unlikely to harbor an extended gas envelope as they lie in a region of parameter space where high-altitude cloud/haze formation is not expected to be significant for hydrogen-dominated atmospheres. Many denser atmospheres remain consistent with the featureless transmission spectrum---from a cloud-free water vapour atmosphere to a Venus-like atmosphere.Comment: Early release to inform further the upcoming review of HST's Cycle 24 proposal

Tale proteins bind to both active and inactive chromatin

TALE (transcription activator-like effector) proteins can be tailored to bind to any DNA sequence of choice and thus are of immense utility for genome editing and the specific delivery of transcription activators. However, to perform these functions, they need to occupy their sites in chromatin. In the present study, we have systematically assessed TALE binding to chromatin substrates and find that in vitro TALEs bind to their target site on nucleosomes at the more accessible entry/exit sites, but not at the nucleosome dyad. We show further that in vivo TALEs bind to transcriptionally repressed chromatin and that transcription increases binding by only 2-fold. These data therefore imply that TALEs are likely to bind to their target in vivo even at inactive loci

International Consensus Conference on Atopic Dermatitis II (ICCAD II * ): clinical update and current treatment strategies

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74915/1/j.1365-2133.148.s63.1.x.pd