Heavy water reduces GFP expression in prokaryotic cell-free assays at the translation level while stimulating its transcription

Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17

The influence of a single 2H/1H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an 2H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had. It was revealed that a single deuterium substitution for protium has an influence on the frequency generation of DNA bubbles, which also depends on their size and is always higher for the smaller bubbles under the largest number of the studied energies. Wherein, compared to the natural condition under the same critical value of energy, the bigger raises of the bubble frequency occurrence (maximums) were found for 11-30 base pair (bp) bubbles (higher by 319%), 2-4 bp bubbles (higher by 300%), and 31 bp and over ones (higher by 220%); whereas the most significant reductions of the indicators (minimums) were observed for 11-30 bp bubbles (lower by 43%) and bubbles size over 30 bp (lower by 82%). In this study, we also analyzed the impact of several circumstances on the AT/GC ratio in the formation of DNA bubbles, both under natural conditions and after a single hydrogen isotope exchange. Moreover, based on the obtained data, substantial positive and inverse correlations were revealed between the AT/GC ratio and some factors (energy values, size of DNA bubbles). So, this modeling and variant of the modified algorithm, adapted for researching DNA bubbles, can be useful to study the regulation of replication and transcription in the genes under different isotopic substitutions in the nucleobases.

Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range

The effect of single substitutions of protium for deuterium in hydrogen bonds between pairs of nitrogenous bases on the open states occurrence probability at high critical breaking energies of these bonds has been studied. The study was carried out using numerical methods based on the angular mathematical model of DNA. The IFNA17 gene was divided into three approximately equal parts. A comparison of the open states occurrence probability in these parts of the gene was done. To improve the accuracy of the results, a special data processing algorithm was developed. The developed methods have shown their suitability for taking into account the occurrence of open states in the entire range of high critical energies. It has been established that single ²H/¹H substitutions in certain nitrogenous bases can be a mechanism for maintaining the vital activity of IFNA17 under critical conditions. In general, the developed method of the mathematical modeling provide unprecedented insight into the DNA behavior under the highest critical energy range, which greatly expands scientific understanding of nucleobases interaction.

Cells in Slow Motion: Apparent Undercooling Increases Glassy Behavior at Physiological Temperatures

Solvent conditions are unexpectedly sufficient to drastically and reversibly slow down cells. In vitro on the molecular level, protein-solvent interactions drastically change in the presence of heavy water (D2 O) and its stronger hydrogen bonds. Adding D2 O to the cell medium of living cells increases the molecular intracellular viscosity. While cell morphology and phenotype remain unchanged, cellular dynamics transform into slow motion in a changeable manner. This is exemplified in the slowdown of cell proliferation and migration, which is caused by a reversible gelation of the cytoplasm. In analogy to the time-temperature superposition principle, where temperature is replaced by D2 O, an increase in viscosity slows down the effective time. Actin networks, crucial structures in the cytoplasm, switch from a power-law-like viscoelastic to a more rubber-like elastic behavior. The resulting intracellular resistance and dissipation impair cell movement. Since cells are highly adaptive non-equilibrium systems, they usually respond irreversibly from a thermodynamic perspective. D2 O induced changes, however, are fully reversible and their effects are independent of signaling as well as expression. The stronger hydrogen bonds lead to glass-like, drawn-out intramolecular dynamics, which may facilitate longer storage times of biological matter, for instance, during transport of organ transplants.

An Animal Able To Tolerate D2 O

It is possible to gain a deeper insight into the role of water in biology by using physicochemical variant molecules, such as deuterium oxide (D₂ O); however, D₂ O is toxic to multicellular organisms in high concentrations. By using a unique desiccation-rehydration process, we demonstrate that the anhydrobiotic nematode Panagrolaimus superbus is able to tolerate and proliferate in 99 % D₂ O. Moreover, we analysed P. superbus' water-channel protein (aquaporin; AQP), which is associated with dehydration/rehydration, by comparing its primary structure and modelling its tertiary structure in silico. Our data evidence that P. superbus' AQP is an aquaglyceroporin, a class of water channel known to display a wider pore; this helps to explain the rapid and successful organismal influx of D₂ O into this species. This is the first demonstration of an animal able to withstand high D₂ O levels, thus paving a way for the investigation of the effects D₂ O on higher levels of biological organization.

Understanding the influence of heavy water stress on the physiology of Salmonella Typhimurium

The heavy isotope of water is used in understanding the physiology of bacteria. Deuterium (D₂O) reduces chemical reaction kinetics. In the present study, the survivability of the food-borne pathogen Salmonella Typhimurium grown in D₂O supplemented medium is studied under various stress conditions. The growth of S, Typhimurium was studied in rich (Luria Broth-LB) and minimal medium (M9) prepared in D₂O. The reduced growth rate of S. tTyphimurium in M9 (2.4 fold) as compared to that in LB (1.6 fold) was observed. S. tTyphimurium grown in D₂O supplemented medium was significantly more tolerant to heat and gamma radiation (1.2 fold), but was sensitive to extreme pH (both alkaline and acidic) and osmotic stress (10 fold). These results suggest that the change in the biological reaction kinetics in the cell due to D₂O may modify the stress tolerance of S. tTyphimurium. This is the first study carried out to understand how a bacterial system (S. Typhimurium) in D₂O responds to different stresses. This study suggests that investigations on bacterial physiology in D₂O supplemented medium helps in understanding the underlying mechanisms of stress tolerance.

X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-ångström resolutions

Hydrogen atoms are critical to the nature and properties of proteins, and thus deuteration has the potential to influence protein function. In fact, it has been reported that some deuterated proteins show different physical and chemical properties to their protiated counterparts. Consequently, it is important to investigate protonation states around the active site when using deuterated proteins. Here, hydrogen isotope effects on the S65T/F99S/M153T/V163A variant of green fluorescent protein (GFP), in which the deprotonated B form is dominant at pH 8.5, were investigated. The pH/pD dependence of the absorption and fluorescence spectra indicates that the protonation state of the chromophore is the same in protiated GFP in H₂O and protiated GFP in D₂O at pH/pD 8.5, while the pK_a of the chromophore became higher in D₂O. Indeed, X-ray crystallographic analyses at sub-ångström resolution revealed no apparent changes in the protonation state of the chromophore between the two samples. However, detailed comparisons of the hydrogen OMIT maps revealed that the protonation state of His148 in the vicinity of the chromophore differed between the two samples. This indicates that protonation states around the active site should be carefully adjusted to be the same as those of the protiated protein when neutron crystallographic analyses of proteins are performed.

Characterization of perdeuterated high-potential iron-sulfur protein with high-resolution X-ray crystallography

Perdeuteration in neutron crystallography is an effective method for determining the positions of hydrogen atoms in proteins. However, there is shortage of evidence that the high-resolution details of perdeuterated proteins are consistent with those of the nondeuterated proteins. In this study, we determined the X-ray structure of perdeuterated high-potential iron-sulfur protein (HiPIP) at a high resolution of 0.85 å resolution. The comparison of the nondeuterated and perdeuterated structures of HiPIP revealed slight differences between the two structures. The spectroscopic and spectroelectrochemical studies also showed that perdeuterated HiPIP has approximately the same characteristics as nondeuterated HiPIP. These results further emphasize the suitability of using perdeuterated proteins in the high-resolution neutron crystallography.

Antibiotic susceptibility of Propionibacterium acnes isolated from patients with acne in a public hospital in Southwest China: prospective cross-sectional study

OBJECTIVE

Antibiotics have been routinely used for several decades against Propionibacterium acnes (P. acnes), but antibiotic resistance of P. acnes is becoming a global problem. Only one related Chinese study is available. The aim of this study was to assess the antibiotic susceptibility of P. acnes obtained from patients with acne in Southwest China.

DESIGN

This was a prospective cross-sectional study. Cutaneous samples were obtained from acne lesions on the face of 375 patients. Samples were cultured in anaerobic medium to identify the presence of P. acnes. Susceptibility tests of isolated P. acnes were performed for tetracycline, doxycycline, clindamycin, erythromycin, azithromycin and clarithromycin using the Epsilometer test.

RESULTS

P. acnes was isolated from 227 patients; 224 isolates (98.7%) were susceptible to doxycycline and 220 (96.9%) were susceptible to tetracycline, followed by clindamycin and clarithromycin in 101 (44.5%) and 102 (44.93%) isolates, respectively. Susceptibility of P. acnes was detected for erythromycin in 96 (42.3%) patients, followed by azithromycin in 94 (41.4%). Subjects who received antibiotics (topical and oral) had higher frequencies of antibiotic-resistant P. acnes as well as increased antibiotic minimum inhibitory concentrations compared with patients without antibiotic treatment.

CONCLUSIONS

P. acnes was highly sensitive to cyclines (doxycycline and tetracycline). P. acnes showed higher resistance rates to macrolides-lincosamides-streptogramins antibiotics (such as erythromycin, azithromycin, clarithromycin and clindamycin). The irrational use of antibiotics for acne treatment is probably a problem in China and elsewhere. These results suggest that dermatologists should be more prudent in prescribing antibiotics for acne.

Deuterium induces a distinctive Escherichia coli proteome that correlates with the reduction in growth rate

Substitution of protium (H) for deuterium (D) strongly affects biological systems. Whereas higher eukaryotes such as plants and mammals hardly survive a deuterium content of >30%, many microorganisms can grow on fully deuterated media, albeit at reduced rates. Very little is known about how the H/D replacement influences life at the systems level. Here, we used MS-based analysis to follow the adaptation of a large part of the Escherichia coli proteome from growth on a protonated full medium, over a protonated minimal medium, to a completely deuterated minimal medium. We could quantify >1800 proteins under all conditions, several 100 of which exhibited strong regulation during both adaptation processes. The adaptation to minimal medium strongly up-regulated amino acid synthesis and sugar metabolism and down-regulated translational proteins on average by 9%, concomitant with a reduction in growth rate from 1.8 to 0.67 h-1 In contrast, deuteration caused a very wide proteomic response over many cell functional categories, together with an additional down-regulation of the translational proteins by 5%. The latter coincided with a further reduction in growth rate to 0.37 h-1, revealing a clear linear correlation between growth rate and abundance of translational proteins. No significant morphological effects are observed under light and electron microscopies. Across all protein categories, about 80% of the proteins up-regulated under deuteration are enzymes with hydrogen transfer functions. Thus, the H/D kinetic isotope effect appears as the major limiting factor of cellular functions under deuteration.

Effectiveness of intravenous albumin therapy to prevent spontaneous bacterial peritonitis, renal dysfunction and death in adults with cirrhosis: a protocol for a systematic review

INTRODUCTION

Use of albumin therapy is recommended for management of disease complications in cirrhosis. The effectiveness of albumin to prevent specific disease complications and death, however, is less clear.

METHODS AND ANALYSIS

We will search Medline (Ovid), Embase (Ovid), Cochrane Hepato-Biliary Controlled Trials Register and Cochrane Central Register of Controlled Trials for published reports on randomised controlled trials and observational studies on the effectiveness of intravenous albumin therapy to prevent spontaneous bacterial peritonitis, renal dysfunction and death in cirrhotic patients. Two independent reviewers will screen the studies for eligibility, extract data and assess risk of bias and quality of evidence using Grading of Recommendations Assessment, Development and Evaluation system. Random effects meta-analyses will be performed when appropriate.

ETHICS AND DISSEMINATION

As no primary data will be collected, a formal ethical approval is not required. We plan to publish the results of this study in a relevant peer-reviewed journal or journals. The study results may also be presented at relevant conferences and meetings.

PROSPERO REGISTRATION NUMBER

CRD42018100798.

Increased optical pathlength through aqueous media for the infrared microanalysis of live cells

The study of live cells using Fourier transform infrared spectroscopy (FTIR) and FTIR microspectroscopy (FT-IRMS) intrinsically yields more information about cell metabolism than comparable experiments using dried or chemically fixed samples. There are, however, a number of barriers to obtaining high-quality vibrational spectra of live cells, including correction for the significant contributions of water bands to the spectra, and the physical stresses placed upon cells by compression in short pathlength sample holders. In this study, we present a water correction method that is able to result in good-quality cell spectra from water layers of 10 and 12 μm and demonstrate that sufficient biological detail is retained to separate spectra of live cells based upon their exposure to different novel anti-cancer agents. The IR brilliance of a synchrotron radiation (SR) source overcomes the problem of the strong water absorption and provides cell spectra with good signal-to-noise ratio for further analysis. Supervised multivariate analysis (MVA) and investigation of average spectra have shown significant separation between control cells and cells treated with the DNA cross-linker PL63 on the basis of phosphate and DNA-related signatures. Meanwhile, the same control cells can be significantly distinguished from cells treated with the protein kinase inhibitor YA1 based on changes in the amide II region. Each of these separations can be linked directly to the known biochemical mode of action of each agent.

Funaria hygrometrica Hedw. elevated tolerance to D2O: its use for the production of highly deuterated metabolites

The method introduced here to grow F. hygrometrica in high concentrations of D ₂ O is an excellent alternative to produce highly deuterated metabolites with broad applications in metabolic studies. Our mass spectrometry experiments strongly indicate the successful incorporation of deuterium into organic compounds. Deuterated metabolites are useful tracers for metabolic studies, yet their wide utilization in research is limited by the multi-step total synthesis required to produce them in the laboratory. Alternatively, deuterated metabolites can be obtained from organisms grown in D₂O or deuterated nutrients. This approach also has limitations as D₂O in high concentrations negatively affects the survival of most organisms. Here we report the moss Funaria hygrometrica as an unusual high tolerant to D₂O in liquid culture. We found that this moss is able to grow in up to 90% D₂O, a condition lethal for many eukaryotes. Mass spectrometric analyses of F. hygrometrica extracts showed a strong deuteration pattern. The ability to tolerate high concentrations of D₂O together with the development of a rich molecular toolbox makes F. hygrometrica an ideal system for the production of valuable deuterated metabolites.

Characterization of Protein Structural Changes in Living Cells Using Time-Lapsed FTIR Imaging

Fourier-transform infrared (FTIR) spectroscopic imaging is a widely used method for studying the chemistry of proteins, lipids, and DNA in biological systems without the need for additional tagging or labeling. This technique can be especially powerful for spatially resolved, temporal studies of dynamic changes such as in vivo protein folding in cell culture models. However, FTIR imaging experiments have typically been limited to dry samples as a result of the significant spectral overlap between water and the protein Amide I band centered at 1650 cm(-1). Here, we demonstrate a method to rapidly obtain high quality FTIR spectral images at submicron pixel resolution in vivo over a duration of 18 h and longer through the development and use of a custom-built, demountable, microfluidic-incubator and a FTIR microscope coupled to a focal plane array (FPA) detector and a synchrotron light source. The combined system maximizes ease of use by allowing a user to perform standard cell culture techniques and experimental manipulation outside of the microfluidic-incubator, where assembly can be done just before the start of experimentation. The microfluidic-incubator provides an optimal path length of 6-8 μm and a submillimeter working distance in order to obtain FTIR images with 0.54-0.77 μm pixel resolution. In addition, we demonstrate a novel method for the correction of spectral distortions caused by varying concentrations of water over a subconfluent field of cells. Lastly, we use the microfluidic-incubator and time-lapsed FTIR imaging to determine the misfolding pathway of mutant copper-zinc superoxide dismutase (SOD1), the protein known to be a cause of familial amyotrophic lateral sclerosis (FALS).