bluuebunny/crossref_metadata_2025 huggingface dataset:
A new perspective of the 2014/15 failed El Niño as seen from ocean salinity
Authors: Chi J. , Du Y. , Zhang Y. , Nie X. , Shi P. , Qu T.
Published: February 2019

This study investigates the 2014/15 failed El Niño using salinity from an ocean general circulation model. The results indicate that subsurface processes were especially strong in the summer of 2014 and they led to positive sea surface salinity anomalies in the central equatorial Pacific. The positive sea surface salinity anomalies induced a westward displacement of the sea surface salinity front that represents the eastern boundary of the western Pacific warm pool, preventing the warm surface water from shifting eastward as seen in a typical El Niño event. In the meantime, more salty water was transported equatorward by a strengthening subtropical cell in the South Pacific. The enhanced subsurface processes in the central equatorial Pacific conveyed the salinity anomalies of subtropical origin to the sea surface and were largely responsible for the sea surface salinity variability but had less impacts on sea surface temperature during the 2014/15 failed El Niño, suggesting some potential advantage of ocean salinity in the El Niño-Southern Oscillation prediction.
Structure of amyloid β25–35 in lipid environment and cholesterol-dependent membrane pore formation
Authors: Kandel Nabin , Matos Jason O. , Tatulian Suren A.
Published: February 2019

The amyloid β (Aβ) peptide and its shorter variants, including a highly cytotoxic Aβ25–35 peptide, exert their neurotoxic effect during Alzheimer’s disease by various mechanisms, including cellular membrane permeabilization. The intrinsic polymorphism of Aβ has prevented the identification of the molecular basis of Aβ pore formation by direct structural methods, and computational studies have led to highly divergent pore models. Here, we have employed a set of biophysical techniques to directly monitor Ca2+-transporting Aβ25–35 pores in lipid membranes, to quantitatively characterize pore formation, and to identify the key structural features of the pore. Moreover, the effect of membrane cholesterol on pore formation and the structure of Aβ25–35 has been elucidated. The data suggest that the membrane-embedded peptide forms 6- or 8-stranded β-barrel like structures. The 8-stranded barrels may conduct Ca2+ ions through an inner cavity, whereas the tightly packed 6-stranded barrels need to assemble into supramolecular structures to form a central pore. Cholesterol affects Aβ25–35 pore formation by a dual mechanism, i.e., by direct interaction with the peptide and by affecting membrane structure. Collectively, our data illuminate the molecular basis of Aβ membrane pore formation, which should advance both basic and clinical research on Alzheimer’s disease and membrane-associated pathologies in general.
Sex affects N-homocysteinylation at lysine residue 212 of albumin in mice
Authors: Sikora Marta , Marczak Łukasz , Perła-Kajan Joanna , Jakubowski Hieronim
Published: February 2019

The modification of protein lysine residues by the thioester homocysteine (Hcy)-thiolactone has been implicated in cardiovascular and neurodegenerative diseases. However, only a handful of proteins carrying Hcy on specific lysine residues have been identified and quantified in humans or animals. In the present work, we developed a liquid chromatography/mass spectrometry targeted assay, based on multiple reaction monitoring, for quantification of N-Hcy-Lys212 (K212Hcy) and N-Hcy-Lys525 (K525Hcy) sites in serum albumin in mice. Using this assay, we found that female (n = 20) and male (n = 13) Cbs−/− mice had significantly elevated levels of K212Hcy and K525Hcy modifications in serum albumin relative to their female (n = 19) and male (n = 17) Cbs+/− littermates. There was significantly more K212Hcy modification in Cbs−/− males than in Cbs−/− females (5.78 ± 4.21 vs. 3.15 ± 1.38 units, P = 0.023). Higher K212Hcy levels in males than in females were observed also in Cbs+/− mice (2.72 ± 0.81 vs. 1.89 ± 1.07 units, P = 0.008). In contrast, levels of the K525Hcy albumin modification were similar between males and females, both in Cbs−/− and Cbs+/− mice. These findings suggest that the sex-specific K212Hcy modification in albumin might have an important biological function in mice that is not affected by the Cbs genotype.
How peptide/MHC presence affects the dynamics of the LC13 T-cell receptor
Authors: Dominguez Jose Luis , Knapp Bernhard
Published: February 2019

The interaction between T-cell receptors (TCRs) of T-cells and potentially immunogenic peptides presented by MHCs of antigen presenting cells is one of the most important mechanisms of the adaptive human immune system. A large number of structural simulations of the TCR/peptide/MHC system have been carried out. However, to date no study has investigated the differences of the dynamics between free TCRs and pMHC bound TCRs on a large scale. Here we present a study totalling 37 100 ns investigating the LC13 TCR in its free form as well as in complex with HLA-B*08:01 and different peptides. Our results show that the dynamics of the bound and unbound LC13 TCR differ significantly. This is reflected in (a) expected results such as an increased flexibility and increased solvent accessible surface of the CDRs of unbound TCR simulations but also in (b) less expected results such as lower CDR distances and compactness as well as alteration in the hydrogen bond network around CDR3α of unbound TCR simulations. Our study further emphasises the structural flexibility of TCRs and confirms the importance of the CDR3 loops for the adoption to MHC.
Amino acid content in rice grains is affected by high temperature during the early grain-filling period
Authors: Huang Min , Zhang Hengdong , Zhao Chunrong , Chen Guanghui , Zou Yingbin
Published: February 2019

Amino acid content in grains is an important nutritional quality trait in rice. High temperature can affect rice quality by accelerating grain filling. However, there is limited information available on the influence of high temperature on amino acid content in rice grains, especially under natural conditions. In this study, grain-filling traits and amino acid content in the grain of two rice cultivars (Luliangyou 996 and Lingliangyou 268) were compared between two years (2016 and 2017) with contrasting temperatures during the early grain-filling period under field conditions. Average daily mean temperature during the period of 0–5 days after full heading in 2016 (30.1 °C) was 5.4 °C higher than that in 2017. Initial, maximum, and mean grain-filling rates were 42–307% higher in 2016 than in 2017 for Luliangyou 996 and Lingliangyou 268. The time taken to reach the maximum grain-filling rate and active grain-filling duration were 6.3–10.7 d shorter in 2016 compared to 2017 for Luliangyou 996 and Lingliangyou 268. Grain weight was equal to or significantly higher in 2016 than in 2017 for Luliangyou 996 and Lingliangyou 268. N accumulation and N content in the grain were significantly lower in 2016 than in 2017 for both cultivars. The grain contents of all detected amino acids, except for methionine in Luliangyou 996, were significantly lower in 2016 than in 2017. Our study suggests that high temperature during the early grain-filling period can result in an accelerated grain-filling process, reduced N accumulation and content in rice grains, and consequently reduced amino acid content in the grain.
Validation of Size Estimation of Nanoparticle Tracking Analysis on Polydisperse Macromolecule Assembly
Authors: Kim Ahram , Ng Wei Beng , Bernt William , Cho Nam-Joon
Published: February 2019

As the physicochemical properties of drug delivery systems are governed not only by the material properties which they are compose of but by their size that they conform, it is crucial to determine the size and distribution of such systems with nanometer-scale precision. The standard technique used to measure the size distribution of nanometer-sized particles in suspension is dynamic light scattering (DLS). Recently, nanoparticle tracking analysis (NTA) has been introduced to measure the diffusion coefficient of particles in a sample to determine their size distribution in relation to DLS results. Because DLS and NTA use identical physical characteristics to determine particle size but differ in the weighting of the distribution, NTA can be a good verification tool for DLS and vice versa. In this study, we evaluated two NTA data analysis methods based on maximum-likelihood estimation, namely finite track length adjustment (FTLA) and an iterative method, on monodisperse polystyrene beads and polydisperse vesicles by comparing the results with DLS. The NTA results from both methods agreed well with the mean size and relative variance values from DLS for monodisperse polystyrene standards. However, for the lipid vesicles prepared in various polydispersity conditions, the iterative method resulted in a better match with DLS than the FTLA method. Further, it was found that it is better to compare the native number-weighted NTA distribution with DLS, rather than its converted distribution weighted by intensity, as the variance of the converted NTA distribution deviates significantly from the DLS results.
Angiotensin-converting enzyme inhibitors or angiotensin receptor blocker monotherapy retard deterioration of renal function in Taiwanese chronic kidney disease population
Authors: Zheng Cai-Mei , Wang Jia-Yi , Chen Tzu-Ting , Wu Yun-Chun , Wu Yi-Lien , Lin Hsin-Ting , Chiu Sheng-Po , Chang Tian-Jong , Zheng Jing-Quan , Chu Nain-Feng , Lin Yu-Me , Su Sui-Lung , Lu Kuo-Cheng , Chen Jin-Shuen , Sung Fung-Chang , Lee Chien-Te , Yang Yu , Hwang Shang-Jyh , Wang Ming-Cheng , Hsu Yung-Ho , Chiou Hung-Yi , Kao Senyeong , Wu Mei-Yi , Lin Yuh-Feng
Published: February 2019

It remains unclear how different uses of angiotensin-converting inhibitors (ACEIs) or angiotensin receptor blockers (ARBs) influence the progression of chronic kidney disease (CKD). This study explored CKD progression in a multicentre, longitudinal cohort study that included 2639 patients with CKD stage 1–5 and hypertension. Patients treated with ACEI or ARB for ≥90 days during a 6-mo period comprised the study group, or no treatment, comprised the control group. The study group was subdivided on the basis of treatment: ACEI monotherapy or ARB monotherapy. Progression of renal deterioration was defined by an average eGFR decline of more than 5 mL/min/1.73 m2/yr or the commencement of dialysis. With at least 1-year follow up, a progression of renal deterioration was demonstrated in 29.70% of the control group and 25.09% of the study group. Patients in the study group had significantly reduced progression of CKD with adjusted odds ratio 0.79 (95% confidence interval: 0.63–0.99). However, when ACEI monotherapy and ARB monotherapy were analyzed separately, none of their associations with CKD progression was statistically significant. In conclusion, ACEI or ARB monotherapy may retard the deterioration of renal function among patients with CKD and hypertension.
Quantitative impacts of incubation phase transmission of foot-and-mouth disease virus
Authors: Arzt Jonathan , Branan Matthew A. , Delgado Amy H. , Yadav Shankar , Moreno-Torres Karla I. , Tildesley Michael J. , Stenfeldt Carolina
Published: February 2019

The current investigation applied a Bayesian modeling approach to a unique experimental transmission study to estimate the occurrence of transmission of foot-and-mouth disease (FMD) during the incubation phase amongst group-housed pigs. The primary outcome was that transmission occurred approximately one day prior to development of visible signs of disease (posterior median 21 hours, 95% CI: 1.1–45.0). Updated disease state durations were incorporated into a simulation model to examine the importance of addressing preclinical transmission in the face of robust response measures. Simulation of FMD outbreaks in the US pig production sector demonstrated that including a preclinical infectious period of one day would result in a 40% increase in the median number of farms affected (166 additional farms and 664,912 pigs euthanized) compared to the scenario of no preclinical transmission, assuming suboptimal outbreak response. These findings emphasize the importance of considering transmission of FMD during the incubation phase in modeling and response planning.
Molecular mechanism of lysophosphatidic acid-induced hypertensive response
Authors: Kano Kuniyuki , Matsumoto Hirotaka , Inoue Asuka , Yukiura Hiroshi , Kanai Motomu , Chun Jerold , Ishii Satoshi , Shimizu Takao , Aoki Junken
Published: February 2019

Lysophosphatidic acid (LPA) is a blood-derived bioactive lipid with numerous biological activities exerted mainly through six defined G protein-coupled receptors (LPA1-LPA6). LPA was first identified as a vasoactive compound because it induced transient hypertension when injected intravenously in rodents. Here, we examined the molecular mechanism underlying the LPA-induced hypertensive response. The LPA-induced hypertensive response was significantly attenuated by pretreatment with a Rho kinase inhibitor, which blocks Gα12/13 signaling. Consistent with this, the response was weakened in KO mice of LPA4, a Gα12/13-coupling LPA receptor. KO mice of another Gα12/13-coupling LPA receptor, LPA6, also showed an attenuated LPA-induced hypertensive response. However, LPA6 KO mice also displayed attenuated pressor responses to an adrenergic agent and abnormal blood vessel formation. Using several LPA analogs with varied affinity for each LPA receptor, we found a good correlation between the hypertensive and LPA4 agonistic activities. Incubated mouse plasma, which contained abundant LPA, also induced a hypertensive response. Interestingly the response was completely abolished when the plasma was incubated in the presence of an ATX inhibitor. Together, these results indicate that circulating LPA produced by ATX contributes to the elevation of blood pressure through multiple LPA receptors, mainly LPA4.
Long-duration spaceflight adversely affects post-landing operator proficiency
Authors: Moore Steven T. , Dilda Valentina , Morris Tiffany R. , Yungher Don A. , MacDougall Hamish G. , Wood Scott J.
Published: February 2019

Performance of astronaut pilots during space shuttle landing was degraded after a few weeks of microgravity exposure, and longer-term exposure has the potential to impact operator proficiency during critical landing and post-landing operations for exploration-class missions. Full-motion simulations of operationally-relevant tasks were utilized to assess the impact of long-duration spaceflight on operator proficiency in a group of 8 astronauts assigned to the International Space Station, as well as a battery of cognitive/sensorimotor tests to determine the underlying cause of any post-flight performance decrements. A ground control group (N = 12) and a sleep restriction cohort (N = 9) were also tested to control for non-spaceflight factors such as lack of practice between pre- and post-flight testing and fatigue. On the day of return after 6 months aboard the space station, astronauts exhibited significant deficits in manual dexterity, dual-tasking and motion perception, and a striking degradation in the ability to operate a vehicle. These deficits were not primarily due to fatigue; performance on the same tasks was unaffected after a 30-h period of sleep restriction. Astronauts experienced a general post-flight malaise in motor function and motion perception, and a lack of cognitive reserve apparent only when faced with dual tasks, which had recovered to baseline by four days after landing.
Pancreatic acinar differentiation is guided by differential laminin deposition
Authors: Heymans Charlotte , Degosserie Jonathan , Spourquet Catherine , Pierreux Christophe E.
Published: February 2019

Endothelial cells play multiple roles during pancreas organogenesis. First, they are required to instruct endoderm-derived pancreatic progenitor cells to initiate branching morphogenesis. Later, blood vessels promote β-cell differentiation but also limit acinar development. In this work, we show how endothelial cells might signal to pancreatic progenitors and spatially regulate acinar differentiation. Using an ex vivo culture system of undifferentiated E12.5 pancreata, we demonstrate that embryonic endothelial progenitor cells and their conditioned medium prevent the expression of two members of the pro-acinar transcriptional PTF1L-complex. This effect is not mediated by SPARC, a protein abundantly released in the medium conditioned by endothelial progenitors. On the contrary, heterotrimeric laminin-α1β1γ1, also produced by endothelial progenitor cells, can repress acinar differentiation when used on its own on pancreatic explants. Lastly, we found that laminin-α1 is predominantly found in vivo around the pancreatic trunk cells, as compared to the tip cells, at E14.5. In conclusion, we propose that expression or deposition of laminin-α1β1γ1 around the trunk cells, where blood vessels are predominantly localized, prevent acinar differentiation of these cells. On the contrary, transient decreased expression or deposition of laminin-α1β1γ1 around the tip cells would allow PTF1L-complex formation and acinar differentiation.
Triplet superconductivity in coupled odd-gon rings
Authors: Reja Sahinur , Nishimoto Satoshi
Published: February 2019

Shedding light on the nature of spin-triplet superconductivity has been a long-standing quest in condensed matter physics since the discovery of superfluidity in liquid 3He. Nevertheless, the mechanism of spin-triplet pairing is much less understood than that of spin-singlet pairing explained by the Bardeen-Cooper-Schrieffer theory or even observed in high-temperature superconductors. Here we propose a versatile mechanism for spin-triplet superconductivity which emerges through a melting of macroscopic spin polarization stabilized in weakly coupled odd-gon (e.g., triangle, pentagon, etc) systems. We demonstrate the feasibility of sustaining spin-triplet superconductivity with this mechanism by considering a new class of quasi-one-dimensional superconductors A2Cr3As3 (A = K, Rb, and Cs). Furthermore, we suggest a simple effective model to easily illustrate the adaptability of the mechanism to general systems consisting of odd-gon units. This mechanism provides a rare example of superconductivity from on-site Coulomb repulsion.
The Impact of Future Fuel Consumption on Regional Air Quality in Southeast Asia
Authors: Lee Hsiang-He , Iraqui Oussama , Wang Chien
Published: February 2019

Aerosols emitted from fossil fuel burning can cause air quality and human health issues. In this sensitivity study, we examine the impact of fossil fuel aerosols on air quality in Southeast Asia under five different hypothetical fuel consumption scenarios. These scenarios reflect air pollutant outcomes of implementations of certain idealized policies in the power generation, industry, and residential sectors. Analyses based on comparison among the modeling results from these scenarios reveal the sectors that should be targeted by air pollution mitigation policy. The results reveal that in Southeast Asia, sulfate could be decreased by 25% if coal were to be replaced by natural gas in the power generation and industry sectors. Black carbon concentration would reduce 42% overall if biofuel were replaced by natural gas in the residential sector. Shipping emissions are especially critical for the urban air quality in Singapore: fine particular matters (PM2.5) could be dramatically cut by 69% in Singapore by merely eliminating shipping emissions.
Flocculation of kaolin particles with cationic lignin polymers
Authors: Hasan Agha , Fatehi Pedram
Published: February 2019

Currently, lignin of black liquor is incinerated to generate energy in pulp mills; but it has potential to be valorized through different modification methods. In this work, kraft lignin (KL) was polymerized with 2-[(methacryloyloxy) ethyl] trimethylammonium chloride (DMC) to produce cationic water soluble polymers. After producing five polymers with different molecular weights and charge densities, their flocculation efficiency in kaolin suspensions was investigated. The adsorption, zeta potential and flocculation results confirmed that the polymer with the highest charge density and molecular weight (KLD5) was a more effective flocculant than other polymers. The structure and size of flocs formed from the interaction of kaolin with KLD were determined by a focused beam reflectance measurement (FBRM). The sedimentation studies, conducted under gravitational (by vertical scan analyzer) and centrifugal force (by Lumisizer analytical centrifuge), revealed that KLD5 was very effective in flocculating kaolin particles.
Ovalbumin Epitope SIINFEKL Self-Assembles into a Supramolecular Hydrogel
Authors: Kamalov Meder , Kählig Hanspeter , Rentenberger Christian , Müllner Alexander R.M. , Peterlik Herwig , Becker Christian F. W.
Published: February 2019

Here we show that the well-known ovalbumin epitope SIINFEKL that is routinely used to stimulate ovalbumin-specific T cells and to test new vaccine adjuvants can form a stable hydrogel. We investigate properties of this hydrogel by a range of spectroscopic and imaging techniques demonstrating that the hydrogel is stabilized by self-assembly of the peptide into nanofibres via stacking of β-sheets. As peptide hydrogels are known to stimulate an immune response as adjuvants, the immunoactive properties of the SIINFEKL peptide may also originate from its propensity to self-assemble into a hydrogel. This finding requires a re-evaluation of this epitope in adjuvant testing.
Conversion of a soluble protein into a potent chaperone in vivo
Authors: Kwon Soon Bin , Ryu Kisun , Son Ahyun , Jeong Hotcherl , Lim Keo-Heun , Kim Kyun-Hwan , Seong Baik L. , Choi Seong Il
Published: February 2019

Molecular chaperones play an important role in cellular protein-folding assistance and aggregation inhibition. As a different but complementary model, we previously proposed that, in general, soluble cellular macromolecules with large excluded volume and surface charges exhibit intrinsic chaperone activity to prevent aggregation of their connected polypeptides irrespective of the connection type, thereby contributing to efficient protein folding. As a proof of concept, we here demonstrated that a model recombinant protein with a specific sequence-binding domain robustly exerted chaperone activity toward various proteins harbouring a short recognition tag of 7 residues in Escherichia coli. The chaperone activity of this protein was comparable to that of representative E. coli chaperones in vivo. Furthermore, in vitro refolding experiments confirmed the in vivo results. Our findings reveal that a soluble protein exhibits the intrinsic chaperone activity to prevent off-pathway aggregation of its interacting proteins, leading to more productive folding while allowing them to fold according to their intrinsic folding pathways. This study gives new insights into the plausible chaperoning role of soluble cellular macromolecules in terms of aggregation inhibition and indirect folding assistance.
Bautin bifurcations in a forest-grassland ecosystem with human-environment interactions
Authors: Russo Lucia , Spiliotis Konstantinos , Giannino Francesco , Mazzoleni Stefano , Siettos Constantinos
Published: February 2019

Ecosystems may be characterized by a complex dynamical behaviour where external disturbances and/or internal perturbations may trigger sudden/irreversible changes, called catastrophic shifts. Simple mathematical models in the form of ordinary and/or partial differential equations have been proposed to approximate in a qualitatively manner the observed complex phenomena, where catastrophic shifts are determined by bifurcation points. In this work, we show that in ecosystems, gradual/smooth changes may be transformed in sudden/catastrophic shifts as a consequence of codimension-2 bifurcations. We stress the importance of using the full arsenal of numerical bifurcation theory to systematically identify and characterize criticalities in ecological models in the 2D parameter space. For our demonstrations, we revisit the analysis of a simple model of a forest-grassland mosaic ecosystem constructing the 2D bifurcation diagram with respect to the impact of human influence and that of natural causes. Our numerical analysis reveals that this simple model is able to approximate both abrupt (catastrophic) and smooth transitions as the system undergoes Bautin bifurcations.
A 3D Model of the Effect of Tortuosity and Constrictivity on the Diffusion in Mineralized Collagen Fibril
Authors: Bini Fabiano , Pica Andrada , Marinozzi Andrea , Marinozzi Franco
Published: February 2019

Bone tissue is a hierarchically structured material composed at the nanoscale by an organic matrix of collagen type I, apatite mineral and water. We considered an idealized 3D geometrical model of the mineralized collagen fibril in order to analyze the influence of structural factors, i.e. tortuosity, constrictivity, on the water effective diffusivity. The average values of the factors investigated in the diffusivity are computed on 5000 iterations by means of the Montecarlo method. The input parameters of the numerical model are the geometrical dimensions of the apatite mineral, collagen fibrils and their spatial orientation obtained with random extractions from Gaussian probability distribution functions. We analyzed the diffusion phenomenon for concentration gradients parallel to three orthogonal directions (Length, Width and Thickness) and for different scenarios, namely low, intermediate and high apatite volume fraction. For each degree of volume fraction, in the thickness direction, the tortuosity assumes greater values, up to two orders of magnitude, in comparison with the tortuous factors computed in the other directions, highlighting the anisotropy of the nanostructure. Furthermore, it was found that the tortuosity is the dominant parameter which control the effective transport properties within the mineralized collagen fibrils.
Risk factors for delayed bleeding by onset time after endoscopic submucosal dissection for gastric neoplasm
Authors: Nam Hyeong Seok , Choi Cheol Woong , Kim Su Jin , Kim Hyung Wook , Kang Dae Hwan , Park Su Bum , Ryu Dae Gon
Published: February 2019

Post-endoscopic submucosal dissection bleeding (PEB) is one of the important complications after endoscopic submucosal dissection (ESD), but still difficult to predict. The present study aimed to identify significant risk factors for PEB according to onset time. Between November 2008 and January 2016, a total of 1864 lesions resected via ESD were analyzed. PEB was classified as either early or late according to onset time (within or after 24 hours post-ESD, respectively). During second-look endoscopy, the artificial ulcer bed was subjected to Forrest classification. A high risk of stigma was defined as active spurting bleeding, oozing bleeding, and a non-bleeding visible vessel in the ulcer. The endoscopic factors and medications associated with PEB were analyzed. PEB occurred in 77 lesions (4.1%): early only in 46 (2.4%), late only in 22 (1.1%), and early and late in 9 (0.4%). Among 55 early PEB events, 25 were asymptomatic and diagnosed during second-look endoscopy. Age ≤65 years, resection size ≥30 mm, procedure time ≥20 min, lower third of the stomach, erosion, and clopidogrel use were significantly associated with early PEB. If the number of risk factors were ≤1, the risk of early PEB was 0.6%. For late PEB, the mid to upper third of the stomach, undifferentiated carcinoma, erosion, high risk of stigma during second-look endoscopy, history of early PEB, and clopidogrel use were significant risk factors. If risk factors were absent, the risk of late PEB was 0.1%. For patients at high risk of early PEB, selective second-look endoscopy might be a useful. For patients at high risk of late PEB, careful monitoring of bleeding should be considered.
Functionality of membrane proteins overexpressed and purified from E. coli is highly dependent upon the strain
Authors: Mathieu Khadija , Javed Waqas , Vallet Sylvain , Lesterlin Christian , Candusso Marie-Pierre , Ding Feng , Xu Xiaohong Nancy , Ebel Christine , Jault Jean-Michel , Orelle Cédric
Published: February 2019

Overexpression of correctly folded membrane proteins is a fundamental prerequisite for functional and structural studies. One of the most commonly used expression systems for the production of membrane proteins is Escherichia coli. While misfolded proteins typically aggregate and form inclusions bodies, membrane proteins that are addressed to the membrane and extractable by detergents are generally assumed to be properly folded. Accordingly, GFP fusion strategy is often used as a fluorescent proxy to monitor their expression and folding quality. Here we investigated the functionality of two different multidrug ABC transporters, the homodimer BmrA from Bacillus subtilis and the heterodimer PatA/PatB from Streptococcus pneumoniae, when produced in several E. coli strains with T7 expression system. Strikingly, while strong expression in the membrane of several strains could be achieved, we observed drastic differences in the functionality of these proteins. Moreover, we observed a general trend in which mild detergents mainly extract the population of active transporters, whereas a harsher detergent like Fos-choline 12 could solubilize transporters irrespective of their functionality. Our results suggest that the amount of T7 RNA polymerase transcripts may indirectly but notably impact the structure and activity of overexpressed membrane proteins, and advise caution when using GFP fusion strategy.
Sub-seasonal Levee Deformation Observed Using Satellite Radar Interferometry to Enhance Flood Protection
Authors: Özer Işıl E. , Rikkert Stephan J. H. , van Leijen Freek J. , Jonkman Sebastiaan N. , Hanssen Ramon F.
Published: February 2019

Levees are critical in providing protection against catastrophic flood events, and thus require continuous monitoring. Current levee inspection methods rely on limited information obtained by visual inspection, resulting in infrequent, localized, mostly qualitative and subjective assessments. This hampers the timely detection of problematic locations and the assessment of levee safety in general. Satellite radar interferometry yields weekly observations of levee conditions with high precision which complement current inspection methods. Here we show that levees are susceptible to short-term swelling and shrinkage associated with meteorological conditions, and assess how deformations can be related to the geohydrological properties and the safety of the levee. Our findings allow to understand the sub-seasonal behaviour of the levee in greater detail and to predict swelling and shrinkage due to variation of the loading conditions. This will improve the detection of anomalous levee responses which contributes to the development of reliable early warning methods using continuous deformation monitoring.
Extracellular matrix remodelling induced by alternating electrical and mechanical stimulations increases the contraction of engineered skeletal muscle tissues
Authors: Kim Hyeonyu , Kim Min-Cheol , Asada H. Harry
Published: February 2019

Engineered skeletal muscles are inferior to natural muscles in terms of contractile force, hampering their potential use in practical applications. One major limitation is that the extracellular matrix (ECM) not only impedes the contraction but also ineffectively transmits the forces generated by myotubes to the load. In the present study, ECM remodelling improves contractile force in a short time, and a coordinated, combined electrical and mechanical stimulation induces the desired ECM remodelling. Notably, the application of single and combined stimulations to the engineered muscles remodels the structure of their ECM networks, which determines the mechanical properties of the ECM. Myotubes in the tissues are connected in parallel and in series to the ECM. The stiffness of the parallel ECM must be low not to impede contraction, while the stiffness of the serial ECM must be high to transmit the forces to the load. Both the experimental results and the mechanistic model suggest that the combined stimulation through coordination reorients the ECM fibres in such a way that the parallel ECM stiffness is reduced, while the serial ECM stiffness is increased. In particular, 3 and 20 minutes of alternating electrical and mechanical stimulations increase the force by 18% and 31%, respectively.
[18F]BODIPY-triglyceride-containing chylomicron-like particles as an imaging agent for brown adipose tissue in vivo
Authors: Paulus Andreas , Drude Natascha , Nascimento Emmani B. M. , Buhl Eva M. , Berbée Jimmy F. P. , Rensen Patrick C. N. , van Marken Lichtenbelt Wouter D. , Mottaghy Felix M. , Bauwens Matthias
Published: February 2019

Brown adipose tissue (BAT) is present in human adults and the current gold standard to visualize and quantify BAT is [18F]FDG PET-CT. However, this method fails to detect BAT under insulin-resistant conditions associated with ageing and weight gain, such as type 2 diabetes. The aim of this study was to develop a novel triglyceride-based tracer for BAT. For this purpose we designed a dual-modal fluorescent/PET fatty acid tracer based on commercially available BODIPY-FL-C16, which can be esterified to its correspondent triglyceride, radiolabeled and incorporated into pre-synthesized chylomicron-like particles. BODIPY-FL-C16 was coupled to 1,2-diolein with a subsequent radiolabeling step resulting in [18F]BODIPY-C16-triglyceride that was incorporated into chylomicron-like particles. Various quality control steps using fluorescent and radioactive methods were conducted before BAT visualization was tested in mice. Triglyceride synthesis, radiolabeling and subsequent incorporation into chylomicron-like particles was carried out in decent yields. This radiotracer appeared able to visualize BAT in vivo, and the uptake of the radiotracer was stimulated by cold exposure. The here reported method can be used to incorporate radiolabeled triglycerides into pre-synthesized chylomicron-like particles. Our approach is feasible to visualize and quantify the uptake of triglyceride-derived fatty acids by BAT.
The effects of a single session of chiropractic care on strength, cortical drive, and spinal excitability in stroke patients
Authors: Holt Kelly , Niazi Imran Khan , Nedergaard Rasmus Wiberg , Duehr Jens , Amjad Imran , Shafique Muhammad , Anwar Muhammad Nabeel , Ndetan Harrison , Turker Kemal S. , Haavik Heidi
Published: February 2019

The objective of this study was to investigate whether a single session of chiropractic care could increase strength in weak plantar flexor muscles in chronic stroke patients. Maximum voluntary contractions (strength) of the plantar flexors, soleus evoked V-waves (cortical drive), and H-reflexes were recorded in 12 chronic stroke patients, with plantar flexor muscle weakness, using a randomized controlled crossover design. Outcomes were assessed pre and post a chiropractic care intervention and a passive movement control. Repeated measures ANOVA was used to asses within and between group differences. Significance was set at p < 0.05. Following the chiropractic care intervention there was a significant increase in strength (F (1,11) = 14.49, p = 0.002; avg 64.2 ± 77.7%) and V-wave/Mmax ratio (F(1,11) = 9.67, p = 0.009; avg 54.0 ± 65.2%) compared to the control intervention. There was a significant strength decrease of 26.4 ± 15.5% (p = 0.001) after the control intervention. There were no other significant differences. Plantar flexor muscle strength increased in chronic stroke patients after a single session of chiropractic care. An increase in V-wave amplitude combined with no significant changes in H-reflex parameters suggests this increased strength is likely modulated at a supraspinal level. Further research is required to investigate the longer term and potential functional effects of chiropractic care in stroke recovery.
Altered splicing and cytoplasmic levels of tRNA synthetases in SF3B1-mutant myelodysplastic syndromes as a therapeutic vulnerability
Authors: Liberante Fabio Giuseppe , Lappin Katrina , Barros Eliana M. , Vohhodina Jekaterina , Grebien Florian , Savage Kienan I. , Mills Kenneth Ian
Published: February 2019

Myelodysplastic syndromes (MDS) are haematopoietic malignancies that are characterised by a heterogeneous clinical course. In recent years, sequencing efforts have uncovered recurrent somatic mutations within RNA splicing factors, including SF3B1, SRSF2, U2AF1 and ZRSR2. The most frequently mutated gene is SF3B1, mutated in 17% of MDS patients. While SF3B1 mutations and their effects on splicing have been well characterised, much remains to be explored about their more far-reaching effects on cellular homeostasis. Given that mRNA splicing and nuclear export are coordinated processes, we hypothesised that SF3B1 mutation might also affect export of certain mRNAs and that this may represent a targetable pathway for the treatment of SF3B1-mutant MDS. We used CRISPR/Cas9-genome editing to create isogenic cellular models. Comprehensive transcriptome and proteome profiling of these cells identified alterations in the splicing and export of components of the translational machinery, primarily tRNA synthetases, in response to the SF3B1 K700E mutation. While steady-state protein synthesis was unaffected, SF3B1 mutant cells were more sensitive to the clinically-relevant purine analogue, 8-azaguanine. In this study, we also demonstrated that 8-azaguanine affects splicing. Our results suggest that the simultaneous targeting of RNA metabolism and splicing by 8-azaguanine represents a therapeutic opportunity for SF3B1-mutant myelodysplastic syndromes.
CALHM1/CALHM3 channel is intrinsically sorted to the basolateral membrane of epithelial cells including taste cells
Authors: Kashio Makiko , Wei-qi Gao , Ohsaki Yasuyoshi , Kido Mizuho A. , Taruno Akiyuki
Published: February 2019

The CALHM1/CALHM3 channel in the basolateral membrane of polarized taste cells mediates neurotransmitter release. However, mechanisms regulating its localization remain unexplored. Here, we identified CALHM1/CALHM3 in the basolateral membrane of type II taste cells in discrete puncta localized close to afferent nerve fibers. As in taste cells, CALHM1/CALHM3 was present in the basolateral membrane of model epithelia, although it was distributed throughout the membrane and did not show accumulation in puncta. We identified canonical basolateral sorting signals in CALHM1 and CALHM3: tyrosine-based and dileucine motifs. However, basolateral sorting remained intact in mutated channels lacking those signals, suggesting that non-canonical signals reside elsewhere. Our study demonstrates intrinsic basolateral sorting of CALHM channels in polarized cells, and provides mechanistic insights.
Paneth cell granule dynamics on secretory responses to bacterial stimuli in enteroids
Authors: Yokoi Yuki , Nakamura Kiminori , Yoneda Tsukasa , Kikuchi Mani , Sugimoto Rina , Shimizu Yu , Ayabe Tokiyoshi
Published: February 2019

Paneth cells at the base of small intestinal crypts secrete granules containing α-defensins in response to bacteria and maintain the intestinal environment by clearing enteric pathogens and regulating the composition of the intestinal microbiota. However, Paneth cell secretory responses remain debatable and the mechanisms that regulate the secretion are not well understood. Although enteroids, three-dimensional cultures of small intestinal epithelial cells, have proven useful for analyzing intestinal epithelial cell functions including ion transport, their closed structures have imposed limitations to investigating interactions between Paneth cells and the intestinal microbiota. Here, we report that microinjection of bacteria or lipopolysaccharide (LPS) into the enteroid lumen provides an ex vivo system for studying Paneth cell secretion in real-time. The results show that Paneth cells released granules immediately when the apical surfaces of enteroid epithelial cells were exposed to LPS or live bacteria by microinjection. However, Paneth cells did not respond to LPS delivered in culture media to enteroid exterior basolateral surface, although they responded to basolateral carbamyl choline. In addition, Paneth cells replenished their granules after secretion, enabling responses to second stimulation. These findings provide new insight for apically-induced Paneth cell secretory responses in regulating the intestinal environment.
Gut microbiota of the European Brown Hare (Lepus europaeus)
Authors: Stalder G. L. , Pinior B. , Zwirzitz B. , Loncaric I. , Jakupović D. , Vetter S. G. , Smith S. , Posautz A. , Hoelzl F. , Wagner M. , Hoffmann D. , Kübber-Heiss A. , Mann E.
Published: February 2019

Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA:P = 0.002 andP = 0.031, respectively), but in both sample typesFirmicutesandBacteroidetesdominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment ofProteobacteriacompared with faecal samples (15.71-fold change,P < 0.001). At OTU level, a significant enrichment with best BLAST hits to theEscherichia-Shigellagroup,Eubacterium limosum,Sphingomonas kyeonggiensis,Flintibacter butyricusandBlautia faeciswere detected in intestinal samples (P < 0.05). In our statistical model, geographic location and possibly associated environmental factors had a greater impact on the microbiota composition than host factors. Population had a significant effect on the composition of abundant intestinal and faecal OTUs, and on the abundance of potential pathogenic bacteria of the familyEnterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.
How to predict seasonal weather and monsoons with radionuclide monitoring
Authors: Terzi Lucrezia , Kalinowski Martin , Schoeppner Michael , Wotawa Gerhard
Published: February 2019

Monsoon in India is of particular importance for the $2 trillion economy, highly dependent on agriculture. Monsoon rains water two-thirds of India’s harvest. However, the monsoon season also causes large-scale flooding, resulting in loss of human life and economic damage estimated around $7 billion annually. Beryllium-7 is a tracer that can be used to monitor the intensity of stratosphere-troposphere exchange, which varies in accordance with the annual cycle of the global atmospheric circulation (Hadley, Ferrel and Polar cells). Based on the beryllium-7 data collected globally as part of the monitoring of the Comprehensive Nuclear-Test-Ban Treaty, the presented empirical method demonstrates the possibility to predict the start, withdrawal and intensity of the Indian monsoon season. Onset can be forecasted with an unprecedented accuracy of ±3 days, 2 months in advance compared to 1–3 weeks in advance by traditional methods. Applying this new method will enable better preparation for economic and natural hazard impacts of the monsoon season in India. This method can also be extended to other regions where the movement of Hadley cells governs monsoon onset and withdrawal.
Circadian regulation in human white adipose tissue revealed by transcriptome and metabolic network analysis
Authors: Christou Skevoulla , Wehrens Sophie M. T. , Isherwood Cheryl , Möller-Levet Carla S. , Wu Huihai , Revell Victoria L. , Bucca Giselda , Skene Debra J. , Laing Emma E. , Archer Simon N. , Johnston Jonathan D.
Published: February 2019

Studying circadian rhythms in most human tissues is hampered by difficulty in collecting serial samples. Here we reveal circadian rhythms in the transcriptome and metabolic pathways of human white adipose tissue. Subcutaneous adipose tissue was taken from seven healthy males under highly controlled ‘constant routine’ conditions. Five biopsies per participant were taken at six-hourly intervals for microarray analysis and in silico integrative metabolic modelling. We identified 837 transcripts exhibiting circadian expression profiles (2% of 41619 transcript targeting probes on the array), with clear separation of transcripts peaking in the morning (258 probes) and evening (579 probes). There was only partial overlap of our rhythmic transcripts with published animal adipose and human blood transcriptome data. Morning-peaking transcripts associated with regulation of gene expression, nitrogen compound metabolism, and nucleic acid biology; evening-peaking transcripts associated with organic acid metabolism, cofactor metabolism and redox activity. In silico pathway analysis further indicated circadian regulation of lipid and nucleic acid metabolism; it also predicted circadian variation in key metabolic pathways such as the citric acid cycle and branched chain amino acid degradation. In summary, in vivo circadian rhythms exist in multiple adipose metabolic pathways, including those involved in lipid metabolism, and core aspects of cellular biochemistry.
Males have more aggressive and less sociable personalities than females in semi-captive Asian elephants
Authors: Seltmann Martin W. , Helle Samuli , Htut Win , Lahdenperä Mirkka
Published: February 2019

Personality, i.e. consistent between-individual differences in behaviour, has been documented in many species. Yet little is known about how males and females of long-lived, highly social species differ in their measures of personality structure. We investigated sex differences in the mean, variance, and covariance of three previously reported personality traits (Attentiveness, Sociability, Aggressiveness) in 150 female and 107 male Asian elephants (Elephas maximus) from a semi-captive population in Myanmar. These three personality traits were obtained by performing exploratory factor analysis on 28 behavioural items that had been rated by experienced elephant handlers. We found that males scored significantly higher on Aggressiveness and tended to score lower on Sociability than females. However, no sex difference was found in the mean scores of Attentiveness. Variances for the three personality traits did not differ between the sexes, suggesting that male and female elephants share the same range of personality variation. Likewise, trait covariances were similar between the sexes. While both sexes show complex sociality in the wild, female Asian elephants typically live in highly social family units, whereas male elephants’ social bonds are weaker. Males usually form dominance ranks by aggressive interactions, especially during musth. Our results on a large sample of individuals living in their natural environment are thus in agreement with elephant life-histories and parallel the findings of sex differences in other long-lived highly social species with similar life-histories.