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

Transport and Boundary Scattering in Confined Geometries: Analytical Results

We utilize a geometric argument to determine the effects of boundary scattering on the carrier mean-free path in samples of various cross sections. Analytic expressions for samples with rectangular and circular cross sections are obtained. We also outline a method for incorporating these results into calculations of the thermal conductivity.Comment: 35 pages, Late

Ursinus College Bulletin Vol. 9, No. 9, June 1893

A digitized copy of the June 1893 Ursinus College Bulletin.https://digitalcommons.ursinus.edu/ucbulletin/1087/thumbnail.jp

Expression of inhibitor of apoptosis protein Livin in renal cell carcinoma and non-tumorous adult kidney

The antiapoptotic Livin/ML-IAP gene has recently gained much attention as a potential new target for cancer therapy. Reports indicating that livin is expressed almost exclusively in tumours, but not in the corresponding normal tissue, suggested that the targeted inhibition of livin may present a novel tumour-specific therapeutic strategy. Here, we compared the expression of livin in renal cell carcinoma and in non-tumorous adult kidney tissue by quantitative real-time reverse transcription-PCR, immunoblotting, and immunohistochemistry. We found that livin expression was significantly increased in tumours (P=0.0077), but was also clearly detectable in non-tumorous adult kidney. Transcripts encoding Livin isoforms α and β were found in both renal cell carcinoma and normal tissue, without obvious qualitative differences. Livin protein in renal cell carcinoma samples exhibited cytoplasmic and/or nuclear staining. In non-tumorous kidney tissue, Livin protein expression was only detectable in specific cell types and restricted to the cytoplasm. Thus, whereas the relative overexpression of livin in renal cell carcinoma indicates that it may still represent a therapeutic target to increase the apoptotic sensitivity of kidney cancer cells, this strategy is likely to be not tumour-specific

A Single Nucleotide Change Affects Fur-Dependent Regulation of sodB in H. pylori

Helicobacter pylori is a significant human pathogen that has adapted to survive the many stresses found within the gastric environment. Superoxide Dismutase (SodB) is an important factor that helps H. pylori combat oxidative stress. sodB was previously shown to be repressed by the Ferric Uptake Regulator (Fur) in the absence of iron (apo-Fur regulation) [1]. Herein, we show that apo regulation is not fully conserved among all strains of H. pylori. apo-Fur dependent changes in sodB expression are not observed under iron deplete conditions in H. pylori strains G27, HPAG1, or J99. However, Fur regulation of pfr and amiE occurs as expected. Comparative analysis of the Fur coding sequence between G27 and 26695 revealed a single amino acid difference, which was not responsible for the altered sodB regulation. Comparison of the sodB promoters from G27 and 26695 also revealed a single nucleotide difference within the predicted Fur binding site. Alteration of this nucleotide in G27 to that of 26695 restored apo-Fur dependent sodB regulation, indicating that a single base difference is at least partially responsible for the difference in sodB regulation observed among these H. pylori strains. Fur binding studies revealed that alteration of this single nucleotide in G27 increased the affinity of Fur for the sodB promoter. Additionally, the single base change in G27 enabled the sodB promoter to bind to apo-Fur with affinities similar to the 26695 sodB promoter. Taken together these data indicate that this nucleotide residue is important for direct apo-Fur binding to the sodB promoter

MAX-DOAS measurements of HONO slant column densities during the MAD-CAT campaign: Inter-comparison, sensitivity studies on spectral analysis settings, and error budget

In order to promote the development of the passive DOAS technique the Multi Axis DOAS – Comparison campaign for Aerosols and Trace gases (MAD-CAT) was held at the Max Planck Institute for Chemistry in Mainz, Germany, from June to October 2013. Here, we systematically compare the differential slant column densities (dSCDs) of nitrous acid (HONO) derived from measurements of seven different instruments. We also compare the tropospheric difference of SCDs (delta SCD) of HONO, namely the difference of the SCDs for the non-zenith observations and the zenith observation of the same elevation sequence. Different research groups analysed the spectra from their own instruments using their individual fit software. All the fit errors of HONO dSCDs from the instruments with cooled large-size detectors are mostly in the range of 0.1 to 0.3  ×  1015 molecules cm−2 for an integration time of 1 min. The fit error for the mini MAX-DOAS is around 0.7  ×  1015 molecules cm−2. Although the HONO delta SCDs are normally smaller than 6  ×  1015 molecules cm−2, consistent time series of HONO delta SCDs are retrieved from the measurements of different instruments. Both fits with a sequential Fraunhofer reference spectrum (FRS) and a daily noon FRS lead to similar consistency. Apart from the mini-MAX-DOAS, the systematic absolute differences of HONO delta SCDs between the instruments are smaller than 0.63  ×  1015 molecules cm−2. The correlation coefficients are higher than 0.7 and the slopes of linear regressions deviate from unity by less than 16 % for the elevation angle of 1°. The correlations decrease with an increase in elevation angle. All the participants also analysed synthetic spectra using the same baseline DOAS settings to evaluate the systematic errors of HONO results from their respective fit programs. In general the errors are smaller than 0.3  ×  1015 molecules cm−2, which is about half of the systematic difference between the real measurements. The differences of HONO delta SCDs retrieved in the selected three spectral ranges 335–361, 335–373 and 335–390 nm are considerable (up to 0.57  ×  1015 molecules cm−2) for both real measurements and synthetic spectra. We performed sensitivity studies to quantify the dominant systematic error sources and to find a recommended DOAS setting in the three spectral ranges. The results show that water vapour absorption, temperature and wavelength dependence of O4 absorption, temperature dependence of Ring spectrum, and polynomial and intensity offset correction all together dominate the systematic errors. We recommend a fit range of 335–373 nm for HONO retrievals. In such fit range the overall systematic uncertainty is about 0.87  ×  1015 molecules cm−2, much smaller than those in the other two ranges. The typical random uncertainty is estimated to be about 0.16  ×  1015 molecules cm−2, which is only 25 % of the total systematic uncertainty for most of the instruments in the MAD-CAT campaign. In summary for most of the MAX-DOAS instruments for elevation angle below 5°, half daytime measurements (usually in the morning) of HONO delta SCD can be over the detection limit of 0.2  ×  1015 molecules cm−2 with an uncertainty of  ∼  0.9  ×  1015 molecules cm−2

High-intensity mechanical therapy for loss of knee extension for worker's compensation and non-compensation patients

<p>Abstract</p> <p>Background</p> <p>Knee flexion contractures have been associated with increased pain and a reduced ability to perform activities of daily living. Contractures can be treated either surgically or conservatively, but these treatment options may not be as successful with worker's compensation patients. The purposes of retrospective review were to 1) determine the efficacy of using adjunctive high-intensity stretch (HIS) mechanical therapy to treat flexion contractures, and 2) compare the results between groups of worker's compensation and non-compensation patients.</p> <p>Methods</p> <p>Fifty-six patients (19 women, 37 men, age = 51.5 ± 17.0 years) with flexion contractures were treated with HIS mechanical therapy as an adjunct to outpatient physical therapy. Mechanical therapy was only prescribed for those patients whose motion had reached a plateau when treated with physical therapy alone. Patients were asked to perform six, 10-minute bouts of end-range stretching per day with the ERMI Knee Extensionater^(r)(ERMI, Inc., Atlanta, GA). Passive knee extension was recorded during the postoperative visit that mechanical therapy was prescribed, 3 months after beginning mechanical therapy, and at the most recent follow-up. We used a mixed-model 2 × 3 ANOVA (group × time) to evaluate the change in passive knee extension between groups over time.</p> <p>Results</p> <p>Regardless of group, the use of adjunctive HIS mechanical therapy resulted in passive knee extension deficits that significantly improved from 10.5° ± 5.2° at the initial visit to 2.6° ± 3.5° at the 3 month visit (p < 0.001). The degree of extension was maintained at the most recent follow-up (2.0° ± 2.9°), which was significantly greater than the initial visit (p < 0.001), but did not differ from the 3 month visit (p = 0.23). The gains in knee extension did not differ between worker's compensation and non-compensation patients (p = 0.56).</p> <p>Conclusions</p> <p>We conclude that the adjunctive use of HIS mechanical therapy is an effective treatment option for patients with knee flexion contractures, regardless of whether the patient is being treated as part of a worker's compensation claim or not.</p

EZH2 Depletion Blocks the Proliferation of Colon Cancer Cells

The Enhancer of Zeste 2 (EZH2) protein has been reported to stimulate cell growth in some cancers and is therefore considered to represent an interesting new target for therapeutic intervention. Here, we investigated a possible role of EZH2 for the growth control of colon cancer cells. RNA interference (RNAi)-mediated intracellular EZH2 depletion led to cell cycle arrest of colon carcinoma cells at the G1/S transition. This was associated with a reduction of cell numbers upon transient transfection of synthetic EZH2-targeting siRNAs and with inhibition of their colony formation capacity upon stable expression of vector-borne siRNAs. We furthermore tested whether EZH2 may repress the growth-inhibitory p27 gene, as reported for pancreatic cancer. However, expression analyses of colon cancer cell lines and colon cancer biopsies did not reveal a consistent correlation between EZH2 and p27 levels. Moreover, EZH2 depletion did not re-induce p27 expression in colon cancer cells, indicating that p27 repression by EZH2 may be cell- or tissue-specific. Whole genome transcriptome analyses identified cellular genes affected by EZH2 depletion in colon cancer cell lines. They included several cancer-associated genes linked to cellular proliferation or invasion, such as Dag1, MageD1, SDC1, Timp2, and Tob1. In conclusion, our results demonstrate that EZH2 depletion blocks the growth of colon cancer cells. These findings might provide benefits for the treatment of colon cancer