Abiotic Gene Transfer: Rare or Rampant?

Phylogenetic studies reveal that horizontal gene transfer (HGT) plays a prominent role in evolution and genetic variability of life. Five biotic mechanisms of HGT among prokaryotic organisms have been extensively characterized: conjugation, competence, transduction, gene transfer agent particles, and transitory fusion with recombination, but it is not known whether they can account for all natural HGT. It is even less clear how HGT could have occurred before any of these mechanisms had developed. Here, we consider contemporary conditions and experiments on microorganisms to estimate possible roles of abiotic HGT—currently and throughout evolution. Candidate mechanisms include freeze-and-thaw, microbeads-agitation, and electroporation-based transformation, and we posit that these laboratory techniques have analogues in nature acting as mechanisms of abiotic HGT: freeze-and-thaw cycles in polar waters, agitation by sand at foreshores and riverbeds, and lightning-triggered electroporation in near-surface aqueous habitats. We derive conservative order-of-magnitude estimates for rates of microorganisms subjected to freeze-and-thaw cycles, sand agitation, and lightning-triggered electroporation, at 1024, 1019, and 1017 per year, respectively. Considering the yield of viable transformants, which is by far the highest in electroporation, we argue this may still favor lightning-triggered transformation over the other two mechanisms. Electroporation-based gene transfer also appears to be the most general of these abiotic candidates, and perhaps even of all known HGT mechanisms. Future studies should provide improved estimates of gene transfer rates and cell viability, currently and in the past, but to assess the importance of abiotic HGT in nature will likely require substantial progress—also in knowledge of biotic HGT.National Institutes of Health (U.S.) (Grant 5RO1GM63857)United States. Air Force Office of Scientific Research. Multidisciplinary University Research Initiativ

Diagnostic accuracy of haemophilia early arthropathy detection with ultrasound (HEAD-US): A comparative magnetic resonance imaging (MRI) study

Background. Repeated haemarthroses affect approximately 90% of patients with severe haemophilia and lead to progressive arthropathy, which is the main cause of morbidity in these patients. Diagnostic imaging can detect even subclinical arthropathy changes and may impact prophylactic treatment. Magnetic resonance imagining (MRI) is generally the gold standard tool for precise evaluation of joints, but it is not easily feasible in regular follow-up of patients with haemophilia. The development of the standardized ultrasound (US) protocol for detection of early changes in haemophilic arthropathy (HEAD-US) opened new perspectives in the use of US in management of these patients. The HEAD-US protocol enables quick evaluation of the six mostly affected joints in a single study. The aim of this prospective study was to determine the diagnostic accuracy of the HEAD-US protocol for the detection and quantification of haemophilic arthropathy in comparison to the MRI. Patients and methods. The study included 30 patients with severe haemophilia. We evaluated their elbows, ankles and knees (overall 168 joints) by US using the HEAD-US protocol and compared the results with the MRI using the International Prophylaxis Study Group (IPSG) MRI score. Results. The results showed that the overall HEAD-US score correlated very highly with the overall IPSG MRI score (r = 0.92). Correlation was very high for the evaluation of the elbows and knees (r 48 0.95), and slightly lower for the ankles (r 48 0.85). Conclusions. HEAD-US protocol proved to be a quick, reliable and accurate method for the detection and quantification of haemophilic arthropathy

Analysis of the circumstellar environment of the B[e] star HD 45677 (FS CMa)

We studied the circumstellar environment of the B[e] star HD 45677 through the analysis of the emission lines from ionized metals. We used the statistical approach of the self absorption curve method (SAC) to derive physical parameters of the line emitting region. The Fe II and Cr II double-peaked emission line structure is explained by the presence of a thin absorption component red shifted by ~3 km/s. This absorption component can be interpreted geometricaly as being due to infalling material perpendicularly to the disk seen nearly pole-on, as indicated by the emission line structure. The Cr II and Fe II emission lines have a complex structure with two (narrow and broad) components, of 45 and 180 km/s FWHM for the permitted lines and 25 and 100 km/s FWHM for the forbidden ones, respectively. We argue that the narrow components are principaly emitted by an optically thin disk seen nearly pole-on, in a region whose minimum radius is estimated to be 4 10^12 cm, while the broad ones are formed in a disk-linked wind.Comment: 14 pages, submitted to Astronomy and Astrophysic

The prolate-to-oblate shape transition of phospholipid vesicles in response to frequency variation of an AC electric field can be explained by the dielectric anisotropy of a phospholipid bilayer

The external electric field deforms flaccid phospholipid vesicles into spheroidal bodies, with the rotational axis aligned with its direction. Deformation is frequency dependent: in the low frequency range (~ 1 kHz), the deformation is typically prolate, while increasing the frequency to the 10 kHz range changes the deformation to oblate. We attempt to explain this behaviour with a theoretical model, based on the minimization of the total free energy of the vesicle. The energy terms taken into account include the membrane bending energy and the energy of the electric field. The latter is calculated from the electric field via the Maxwell stress tensor, where the membrane is modelled as anisotropic lossy dielectric. Vesicle deformation in response to varying frequency is calculated numerically. Using a series expansion, we also derive a simplified expression for the deformation, which retains the frequency dependence of the exact expression and may provide a better substitute for the series expansion used by Winterhalter and Helfrich, which was found to be valid only in the limit of low frequencies. The model with the anisotropic membrane permittivity imposes two constraints on the values of material constants: tangential component of dielectric permittivity tensor of the phospholipid membrane must exceed its radial component by approximately a factor of 3; and the membrane conductivity has to be relatively high, approximately one tenth of the conductivity of the external aqueous medium.Comment: 17 pages, 6 figures; accepted for publication in J. Phys.: Condens. Matte

High-frequency irreversible electroporation (H-FIRE) for non-thermal ablation without muscle contraction

<p>Abstract</p> <p>Background</p> <p>Therapeutic irreversible electroporation (IRE) is an emerging technology for the non-thermal ablation of tumors. The technique involves delivering a series of unipolar electric pulses to permanently destabilize the plasma membrane of cancer cells through an increase in transmembrane potential, which leads to the development of a tissue lesion. Clinically, IRE requires the administration of paralytic agents to prevent muscle contractions during treatment that are associated with the delivery of electric pulses. This study shows that by applying high-frequency, bipolar bursts, muscle contractions can be eliminated during IRE without compromising the non-thermal mechanism of cell death.</p> <p>Methods</p> <p>A combination of analytical, numerical, and experimental techniques were performed to investigate high-frequency irreversible electroporation (H-FIRE). A theoretical model for determining transmembrane potential in response to arbitrary electric fields was used to identify optimal burst frequencies and amplitudes for <it>in vivo </it>treatments. A finite element model for predicting thermal damage based on the electric field distribution was used to design non-thermal protocols for <it>in vivo </it>experiments. H-FIRE was applied to the brain of rats, and muscle contractions were quantified via accelerometers placed at the cervicothoracic junction. MRI and histological evaluation was performed post-operatively to assess ablation.</p> <p>Results</p> <p>No visual or tactile evidence of muscle contraction was seen during H-FIRE at 250 kHz or 500 kHz, while all IRE protocols resulted in detectable muscle contractions at the cervicothoracic junction. H-FIRE produced ablative lesions in brain tissue that were characteristic in cellular morphology of non-thermal IRE treatments. Specifically, there was complete uniformity of tissue death within targeted areas, and a sharp transition zone was present between lesioned and normal brain.</p> <p>Conclusions</p> <p>H-FIRE is a feasible technique for non-thermal tissue ablation that eliminates muscle contractions seen in IRE treatments performed with unipolar electric pulses. Therefore, it has the potential to be performed clinically without the administration of paralytic agents.</p

Physics of the Riemann Hypothesis

Physicists become acquainted with special functions early in their studies. Consider our perennial model, the harmonic oscillator, for which we need Hermite functions, or the Laguerre functions in quantum mechanics. Here we choose a particular number theoretical function, the Riemann zeta function and examine its influence in the realm of physics and also how physics may be suggestive for the resolution of one of mathematics' most famous unconfirmed conjectures, the Riemann Hypothesis. Does physics hold an essential key to the solution for this more than hundred-year-old problem? In this work we examine numerous models from different branches of physics, from classical mechanics to statistical physics, where this function plays an integral role. We also see how this function is related to quantum chaos and how its pole-structure encodes when particles can undergo Bose-Einstein condensation at low temperature. Throughout these examinations we highlight how physics can perhaps shed light on the Riemann Hypothesis. Naturally, our aim could not be to be comprehensive, rather we focus on the major models and aim to give an informed starting point for the interested Reader.Comment: 27 pages, 9 figure

The KELT Follow-Up Network And Transit False-Positive Catalog: Pre-Vetted False Positives For TESS

The Kilodegree Extremely Little Telescope (KELT) project has been conducting a photometric survey of transiting planets orbiting bright stars for over 10 years. The KELT images have a pixel scale of ~23\u27\u27 pixel⁻¹—very similar to that of NASA\u27s Transiting Exoplanet Survey Satellite (TESS)—as well as a large point-spread function, and the KELT reduction pipeline uses a weighted photometric aperture with radius 3\u27. At this angular scale, multiple stars are typically blended in the photometric apertures. In order to identify false positives and confirm transiting exoplanets, we have assembled a follow-up network (KELT-FUN) to conduct imaging with spatial resolution, cadence, and photometric precision higher than the KELT telescopes, as well as spectroscopic observations of the candidate host stars. The KELT-FUN team has followed-up over 1600 planet candidates since 2011, resulting in more than 20 planet discoveries. Excluding ~450 false alarms of non-astrophysical origin (i.e., instrumental noise or systematics), we present an all-sky catalog of the 1128 bright stars (6 \u3c V \u3c 13) that show transit-like features in the KELT light curves, but which were subsequently determined to be astrophysical false positives (FPs) after photometric and/or spectroscopic follow-up observations. The KELT-FUN team continues to pursue KELT and other planet candidates and will eventually follow up certain classes of TESS candidates. The KELT FP catalog will help minimize the duplication of follow-up observations by current and future transit surveys such as TESS

Vascular disrupting action of electroporation and electrochemotherapy with bleomycin in murine sarcoma

Electrochemotherapy has a direct cytotoxic effect on tumour cells, and presumably, a vascular disrupting effect. In this study, on the basis of the prediction of the mathematical model, histological evaluation and physiological measurements of the tumours were carried out to confirm that electroporation and electrochemotherapy of tumours have a vascular disrupting action. In the study, SA-1 solid subcutaneous sarcoma tumours in A/J mice were treated by bleomycin (BLM) given intravenously (1 mg kg−1), application of electric pulses (8 pulses, 1040 V, 100 μs, 1 Hz) or a combination of both – electrochemotherapy. The vascular effect was determined by laser Doppler flowmetry, power Doppler ultrasonographic imaging and Patent blue staining. The extent of tumour hypoxia was determined immunohistochemically by hypoxia marker pimonidazole and partial pressure of oxygen (pO2) in tumours by electron paramagnetic resonance oximetry. Electrochemotherapy with BLM induced good antitumour effect with 22 days, tumour growth delay and 38% tumour cures. The application of electric pulses to the tumours induced instant but transient tumour blood flow reduction (for 70%) that was recovered in 24 h. During this tumour blood flow reduction, we determined an increase in hypoxic tumour area for up to 30%, which was also reflected in reduced tumour oxygenation (for 70%). According to the described mathematical model, endothelial cells lining in tumour blood vessels are exposed to a ∼40% higher electric field than the surrounding tumour cells, and therefore easily electroporated, allowing access of high BLM concentration to the cytosol. Consequently, electrochemotherapy has, besides the immediate vascular disrupting action, also a delayed one (after 24 h), as a consequence of endothelial cell swelling and apoptosis demonstrated by extensive tumour necrosis, tumour hypoxia, prolonged reduction of tumour blood flow and significant tumour growth delay, and tumour cures. Our results demonstrate that in addition to the well-established direct cytotoxic effect on tumour cells, electrochemotherapy also has an indirect vascular disrupting action resulting altogether in extensive tumour cell necrosis leading to complete regression of tumours

Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival

High-grade serous ovarian cancer (HGSC) is the most lethal histotype of ovarian cancer and the majority of cases present with metastasis and late-stage disease. Over the last few decades, the overall survival for patients has not significantly improved, and there are limited targeted treatment options. We aimed to better characterize the distinctions between primary and metastatic tumors based on short- or long-term survival. We characterized 39 matched primary and metastatic tumors by whole exome and RNA sequencing. Of these, 23 were short-term (ST) survivors (overall survival (OS) \u3c 3.5 years) and 16 were long-term (LT) survivors (OS \u3e 5 years). We compared somatic mutations, copy number alterations, mutational burden, differential gene expression, immune cell infiltration, and gene fusion predictions between the primary and metastatic tumors and between ST and LT survivor cohorts. There were few differences in RNA expression between paired primary and metastatic tumors, but significant differences between the transcriptomes of LT and ST survivors in both their primary and metastatic tumors. These findings will improve the understanding of the genetic variation in HGSC that exist between patients with different prognoses and better inform treatments by identifying new targets for drug development