Suppressor Analysis Reveals a Role for SecY in the SecA2-Dependent Protein Export Pathway of Mycobacteria

All bacteria use the conserved Sec pathway to transport proteins across the cytoplasmic membrane, with the SecA ATPase playing a central role in the process. Mycobacteria are part of a small group of bacteria that have two SecA proteins: the canonical SecA (SecA1) and a second, specialized SecA (SecA2). The SecA2-dependent pathway exports a small subset of proteins and is required for Mycobacterium tuberculosis virulence. The mechanism by which SecA2 drives export of proteins across the cytoplasmic membrane remains poorly understood. Here we performed suppressor analysis on a dominant negative secA2 mutant (secA2 K129R) of the model mycobacterium Mycobacterium smegmatis to better understand the pathway used by SecA2 to export proteins. Two extragenic suppressor mutations were identified as mapping to the promoter region of secY, which encodes the central component of the canonical Sec export channel. These suppressor mutations increased secY expression, and this effect was sufficient to alleviate the secA2 K129R phenotype. We also discovered that the level of SecY protein was greatly diminished in the secA2 K129R mutant, but at least partially restored in the suppressors. Furthermore, the level of SecY in a suppressor strongly correlated with the degree of suppression. Our findings reveal a detrimental effect of SecA2 K129R on SecY, arguing for an integrated system in which SecA2 works with SecY and the canonical Sec translocase to export proteins

Localization of bulk matter fields, the hierarchy problem and corrections to Coulomb's law on a pure de Sitter thick braneworld

In this paper we investigate the localization and mass spectra of matter fields with spin 0, 1 and 1/2 on a geometric thick brane generated by pure 4D and 5D positive cosmological constants without bulk scalar fields. This model possesses a 4D cosmological constant that can be made as small as one desires without fine-tuning it with the bulk cosmological constant. The RS model is obtained as an analytic continuation of the flat brane limit of this braneworld configuration when the Hubble parameter disappears. Within this inflating braneworld model it is possible to formulate a mechanism for obtaining TeV mass scales from Planck ones by adding a positive thin brane, where the Standard Model fields are trapped, at a distance y_2 from the origin, where the Planck thick brane resides. The brane separation must be of the same order than the inverse thickness parameter of the model in order for the mechanism to generate the desired hierarchy. This result is obtained by imposing the recovery of both the correct 4D gravitational couplings and the actually observed accelerated expansion of the universe in our de Sitter braneworld. Regarding the localization of matter in the purely geometric thick braneworld, for spin 0 massless and massive scalar fields as well as for spin 1 vector fields, the potentials of the Kaluza--Klein (KK) modes in thecorresponding Schroedinger equations are modified Poeschl-Teller potentials, which lead to the localization of the scalar and vector zero modes on the brane as well as to mass gaps in the mass spectra. We also compute the corrections to Coulomb's law coming from massive KK vector modes. For spin 1/2 fermions, we introduce the bulk mass term MF(z)\bar{\Psi}\Psi in the action and show that localization of the massless left-chiral fermion zero mode is feasible for two mass functions MF(z) with a finite/infinite number of massive KK bound states.Comment: 28 pages in latex, 19 figures, title modified according to substantial additions performed in the text of the manuscript. To appear in Phys Rev

Analytic approximations of scattering effects on beam chromaticity in 21-cm global experiments

Scattering from objects near an antenna produce correlated signals from strong compact radio sources in a manner similar to those used by the Sea Interferometer to measure the radio source positions using the fine frequency structure in the total power spectrum of a single antenna. These fringes or ripples due to correlated signal interference are present at a low level in the spectrum of any single antenna and are a major source of systematics in systems used to measure the global redshifted 21-cm signal from the early universe. In the Sea Interferometer a single antenna on a cliff above the sea is used to add the signal from the direct path to the signal from the path reflected from the sea thereby forming an interferometer. This was used for mapping radio sources with a single antenna by Bolton and Slee in the 1950s. In this paper we derive analytic expressions to determine the level of these ripples and compare these results in a few simple cases with electromagnetic modeling software to verify that the analytic calculations are sufficient to obtain the magnitude of the scattering effects on the measurements of the global 21-cm signal. These analytic calculations are needed to evaluate the magnitude of the effects in cases that are either too complex or take too much time to be modeled using software

A Bayesian approach to modelling spectrometer data chromaticity corrected using beam factors -- I. Mathematical formalism

Accurately accounting for spectral structure in spectrometer data induced by instrumental chromaticity on scales relevant for detection of the 21-cm signal is among the most significant challenges in global 21-cm signal analysis. In the publicly available EDGES low-band data set, this complicating structure is suppressed using beam-factor based chromaticity correction (BFCC), which works by dividing the data by a sky-map-weighted model of the spectral structure of the instrument beam. Several analyses of this data have employed models that start with the assumption that this correction is complete. However, while BFCC mitigates the impact of instrumental chromaticity on the data, given realistic assumptions regarding the spectral structure of the foregrounds, the correction is only partial. This complicates the interpretation of fits to the data with intrinsic sky models (models that assume no instrumental contribution to the spectral structure of the data). In this paper, we derive a BFCC data model from an analytic treatment of BFCC and demonstrate using simulated observations that, in contrast to using an intrinsic sky model for the data, the BFCC data model enables unbiased recovery of a simulated global 21-cm signal from beam-factor chromaticity corrected data in the limit that the data is corrected with an error-free beam-factor model.Comment: 26 pages, 8 figures; accepted for publication in MNRA

LISA:a lightweight stratospheric air sampler

We developed a new lightweight stratospheric air sampler (LISA). The LISA sampler is designed to collect four bag samples in the stratosphere during a balloon flight for CO2, CH4 and CO mole fraction measurements. It consists of four multi-layer foil (MLF) sampling bags, a custom-made manifold, and a diaphragm pump, with a total weight of ∼2.5 kg. A series of laboratory storage tests were performed to assess the stability of CO2, CH4 and CO mole fractions in both MLF and Tedlar bags. The MLF bag was chosen due to its better overall performance than the Tedlar bag for the three species CO2, CH4 and CO. Furthermore, we evaluated the performance of the pump under low pressure conditions to optimize a trade-off between the vertical resolution and the sample size. The LISA sampler was flown on the same balloon flight with an AirCore in Sodankylä, Finland (67.368∘ N, 26.633∘ E, 179 m a.s.l.), on 26 April and 4–7 September 2017. A total of 15 stratospheric air samples were obtained during the ascent of four flights. The sample size ranges between 800 and 180 mL for the altitude between 12 and 25 km, with the corresponding vertical resolution ranging from 0.5 to 1.5 km. The collected air samples were analysed for CO2, CH4 and CO mole fractions, and evaluated against AirCore retrieved profiles, showing mean differences of 0.84 ppm for CO2, 1.8 ppb for CH4 and 6.3 ppb for CO, respectively. High-accuracy stratospheric measurements of greenhouse gas mole fractions are useful to validate remote sensing measurements from ground and from space, which has been performed primarily by comparison with collocated aircraft measurements (0.15–13 km), and more recently with AirCore observations (0–30 km). While AirCore is capable of achieving high-accuracy greenhouse gas mole fraction measurements, it is challenging to obtain accurate altitude registration for AirCore measurements. The LISA sampler provides a viable low-cost tool for retrieving stratospheric air samples for greenhouse gas measurements that is complementary to AirCore. Furthermore, the LISA sampler is advantageous in both the vertical resolution and sample size for performing routine stratospheric measurements of the isotopic composition of trace gases

Adjunct primer for the use of national comprehensive cancer network guidelines for the surgical management of cutaneous malignant melanoma patients

Recently, a Surveillance Epidemiology and End Results (SEER) survey of melanoma patterns of care by the Mayo Clinic, Scottsdale showed remarkable deviations from best practice patterns throughout the country. The study, which analyzed the SEER records of 35,126 stage I to III cutaneous malignant melanoma patients treated from 2004 to 2006, showed that adherence to National Comprehensive Cancer Network (NCCN) therapeutic resection margins occurred in less than 36% of patients. Similarly, considerable variation in the quality of melanoma care in the United States when assessed using 26 quality indicators drawn by a panel of melanoma experts was independently reported. These observations underscore the significant lack of adherence to published best practice patterns reflected by the NCCN guidelines. The untoward effects of these variations in practice pattern can have an inordinate impact on the survival of melanoma patients in whom long term outcomes are affected by the adequacy of surgical management. Thin malignant melanoma is curable; however, thick or node positive melanoma is often incurable. This outcome is determined not only by the stage at presentation but by the use of best practice patterns as reflected in current NCCN cutaneous melanoma practice guidelines

Localization of gravity on a de Sitter thick braneworld without scalar fields

In this work we present a simple thick braneworld model that is generated by an intriguing interplay between a 5D cosmological constant with a de Sitter metric induced in the 3-brane without the inclusion of scalar fields. We show that 4D gravity is localized on this brane, provide analytic expressions for the massive Kaluza-Klein (KK) fluctuation modes and also show that the spectrum of metric excitations displays a mass gap. We finally present the corrections to Newton's law due to these massive modes. This model has no naked singularities along the fifth dimension despite the existence of a mass gap in the graviton spectrum as it happens in thick branes with 4D Poincare symmetry, providing a simple model with very good features: the curvature is completely smooth along the fifth dimension, it localizes 4D gravity and the spectrum of gravity fluctuations presents a mass gap, a fact that rules out the existence of phenomenologically dangerous ultralight KK excitations in the model. We finally present our solution as a limit of scalar thick branes.Comment: 11 pages in latex, no figures, title and abstract changed, a new section and some references adde

Reduced Apaf-1 expression in human cutaneous melanomas

Malignant melanoma is a life-threatening skin cancer due to its highly metastatic character and resistance to radio- and chemotherapy. It is believed that the ability to evade apoptosis is the key mechanism for the rapid growth of cancer cells. However, the exact mechanism for failure in the apoptotic pathway in melanoma cells is unclear. p53, the most frequently mutated tumour suppressor gene in human cancers, is a key apoptosis inducer. However, p53 mutation is only found in 15–20% of melanoma biopsies. Recently, it was found that Apaf-1, a downstream target of p53, is inactivated in metastatic melanoma. Specifically, loss of heterozygosity (LOH) of the Apaf-1 gene was found in 40% of metastatic melanoma. To determine if loss of Apaf-1 expression is indeed involved in melanoma progression, we employed the tissue microarray technology and examined Apaf-1 expression in 70 human primary malignant melanoma biopsies by immunohistochemistry. Our data showed that Apaf-1 expression is significantly reduced in melanoma cells compared with normal nevi (χ2=6.02, P=0.014). Our results also revealed that loss of Apaf-1 was not associated with the tumour thickness, ulceration or subtype, patient's gender, age and 5-year survival. In addition, our in vitro apoptosis assay revealed that overexpression of Apaf-1 can sensitise melanoma cells to anticancer drug treatment. Taken together, our data indicate that Apaf-1 expression is significantly reduced in human melanoma and that Apaf-1 may serve as a therapeutic target in melanoma

Structural basis of outer membrane protein insertion by the BAM complex

All Gram-negative bacteria, mitochondria and chloroplasts have outer membrane proteins (OMPs) that perform many fundamental biological processes. The OMPs in Gram-negative bacteria are inserted and folded into the outer membrane by the β-barrel assembly machinery (BAM). The mechanism involved is poorly understood, owing to the absence of a structure of the entire BAM complex. Here we report two crystal structures of the Escherichia coli BAM complex in two distinct states: an inward-open state and a lateral-open state. Our structures reveal that the five polypeptide transport-associated domains of BamA form a ring architecture with four associated lipoproteins, BamB–BamE, in the periplasm. Our structural, functional studies and molecular dynamics simulations indicate that these subunits rotate with respect to the integral membrane β-barrel of BamA to induce movement of the β-strands of the barrel and promote insertion of the nascent OMP