bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA polymerases as moving barriers to condensin loop extrusion
Authors: Brandão Hugo B. , Paul Payel , van den Berg Aafke A. , Rudner David Z. , Wang Xindan , Mirny Leonid A.
Published: September 2019

To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop-extrusion process is largely unexplored, but recent experiments have shown that sites of high transcription may directionally affect condensin loop extrusion. We quantitatively investigate different mechanisms of interaction between condensin and elongating RNA polymerases (RNAPs) and find that RNAPs are likely steric barriers that can push and interact with condensins. Supported by chromosome conformation capture and chromatin immunoprecipitation for cells after transcription inhibition and RNAP degradation, we argue that translocating condensins must bypass transcribing RNAPs within ∼1 to 2 s of an encounter at rRNA genes and within ∼10 s at protein-coding genes. Thus, while individual RNAPs have little effect on the progress of loop extrusion, long, highly transcribed operons can significantly impede the extrusion process. Our data and quantitative models further suggest that bacterial condensin loop extrusion occurs by 2 independent, uncoupled motor activities; the motors translocate on DNA in opposing directions and function together to enlarge chromosomal loops, each independently bypassing steric barriers in their path. Our study provides a quantitative link between transcription and 3D genome organization and proposes a mechanism of interactions between SMC complexes and elongating transcription machinery relevant from bacteria to higher eukaryotes.
Crystal growth kinetics as an architectural constraint on the evolution of molluscan shells
Authors: Schoeppler Vanessa , Lemanis Robert , Reich Elke , Pusztai Tamás , Gránásy László , Zlotnikov Igor
Published: September 2019

Significance

Using notions from classic materials science, we expand our understanding of the macroscopic morphospace of possible molluscan shell shapes to the level of possible ultrastructures that comprise them. This provides us with a unique opportunity to explore this morphospace using well-developed analytical, theoretical, and numerical tools and to test the effects of a discrete number of parameters on shell biomineralization. The physical model presented here sheds a new light on the evolutionary aspect of molluscan shell ultrastructural fabrication and suggests that the repeated “discovery” of some mineral morphologies partially reflects a series of architectural constraints provided by biomineral growth kinetics.
A
Tmc1
mutation reduces calcium permeability and expression of mechanoelectrical transduction channels in cochlear hair cells
Authors: Beurg Maryline , Barlow Amanda , Furness David N. , Fettiplace Robert
Published: September 2019

Significance

Cochlear hair cells transduce sound into electrical signals by activation of mechanically sensitive ion channels thought to be formed by TMC1. We generated a single aspartate/asparagine substitution in mouse TMC1 which is homologous to a human genetic deafness mutation. The main consequence was reduction in the Ca
2+
permeability of the mechanically sensitive channel with little change in its unitary conductance. Nevertheless, there was a much reduced expression of the ion channel, which led within 4 wk to death of the outer hair cells culminating in deafness. The mouse mutant accounts for the human deafness and implies that TMC1, in addition to forming the mechanically sensitive ion channel, regulates its own expression.
The making of natural iron sulfide nanoparticles in a hot vent snail
Authors: Okada Satoshi , Chen Chong , Watsuji Tomo-o , Nishizawa Manabu , Suzuki Yohey , Sano Yuji , Bissessur Dass , Deguchi Shigeru , Takai Ken
Published: September 2019

Significance

Highly adapted to deep-sea hot vents, the scaly-foot gastropod
Chrysomallon squamiferum
is unique among living and extinct animals in possessing an imbricating scale-armor reinforced by iron sulfide nanoparticles. Mechanisms behind its biogenic sulfide synthesis are expected to revolutionize industrial production of metal chalcogenide nanoparticles, but how the gastropod manages such processes remains entirely unknown. Here, using state-of-art microscopy and elemental analyses, we show that the living animal mediates biomineralization of iron sulfide nanoparticles via a channel-like columnar organic matrix that transports sulfur, which then reacts with iron ions diffusing in from the surrounding vent fluid. This allows the snail to make iron sulfide nanoparticles in a dynamic low-temperature environment, opening the potential to significantly reduce the industrial production costs of such particles.
SDS22 selectively recognizes and traps metal-deficient inactive PP1
Authors: Choy Meng S. , Moon Thomas M. , Ravindran Rini , Bray Johnny A. , Robinson Lucy C. , Archuleta Tara L. , Shi Wuxian , Peti Wolfgang , Tatchell Kelly , Page Rebecca
Published: September 2019

The metalloenzyme protein phosphatase 1 (PP1), which is responsible for ≥50% of all dephosphorylation reactions, is regulated by scores of regulatory proteins, including the highly conserved SDS22 protein. SDS22 has numerous diverse functions, surprisingly acting as both a PP1 inhibitor and as an activator. Here, we integrate cellular, biophysical, and crystallographic studies to address this conundrum. We discovered that SDS22 selectively binds a unique conformation of PP1 that contains a single metal (M2) at its active site, i.e., SDS22 traps metal-deficient inactive PP1. Furthermore, we showed that SDS22 dissociation is accompanied by a second metal (M1) being loaded into PP1, as free metal cannot dissociate the complex and M1-deficient mutants remain constitutively trapped by SDS22. Together, our findings reveal that M1 metal loading and loss are essential for PP1 regulation in cells, which has broad implications for PP1 maturation, activity, and holoenzyme subunit exchange.
The NMDA receptor activation by
d
-serine and glycine is controlled by an astrocytic Phgdh-dependent serine shuttle
Authors: Neame Samah , Safory Hazem , Radzishevsky Inna , Touitou Ayelet , Marchesani Francesco , Marchetti Marialaura , Kellner Shai , Berlin Shai , Foltyn Veronika N. , Engelender Simone , Billard Jean-Marie , Wolosker Herman
Published: September 2019

Significance

Phgdh is a crucial enzyme in the astrocytic synthesis of
l
-serine from glucose. Our study uncovers the role of glial-neuronal cross-talk in regulating NMDAR synaptic activation through the astrocytic export of Phgdh-derived
l
-serine to generate the coagonists
d
-serine and glycine. We clarify the relative roles of
d
-serine and glycine by showing that like
d
-serine, Phgdh-derived glycine mediates NMDAR synaptic activation in the mature hippocampus. We show that glycine is a significant regulator of
d
-serine synthesis and release, revealing a cross-talk between glycine and
d
-serine metabolism that fine tunes NMDAR activation. Our data reveal a multifaceted mechanism regulating NMDAR activity, which ultimately depends on a Phgdh-dependent serine shuttle.
Ignition characteristics of pre-combustion plasma jet igniter*
Authors: Wang Si-Bo , Yu Jin-Lu , Ye Jing-Feng , Li Guo-Hua , Chen Zhao , Jiang Lu-Yun , Gu Chen-Li
Published: September 2019

At present, aero-engines face a major need to widen the ignition envelope. In order to provide a technical support to expand the high altitude ignition envelope of aero-engines, in this article we propose a novel ignition technology, i.e., “pre-combustion plasma jet ignition technology”. In this paper, we also design a pre-combustion plasma jet igniter. Its discharge characteristics, jet characteristics, and ignition effects are studied. The results show that increasing the equivalent ratio of jet gas can enhance the discharge stability and increase the duty cycle. At the same time, it can reduce working power and energy consumption. The increase of equivalent ratio in jet gas can enhance the length and ignition area of plasma jet. In the process of ignition, the pre-combustion plasma jet igniter has obvious advantages, suchn as shortening the ignition delay time and enlarging the ignition boundary. When the airflow velocity is 39.11 m/s and the inlet air temperature is 80 °C, compared with the spark igniter and the air plasma jet igniter, the pre-combustion plasma jet igniter has an ignition boundary that is expanded by 319.8% and 55.7% respectively.
Scalar current limit from the beta-neutrino correlation: the WISArD experiment
Authors: Araujo-Escalona V. , Alfaurt P. , Ascher P. , Atanasov D. , Blank B. , Daudin L. , Fléchard X. , Gerbaux M. , Giovinazzo J. , Grévy S. , Kurtukian Nieto T. , Liénard E. , Nies L. , Quéméner G. , Roche M. , Severijns N. , Vanlangendonck S. , Versteegen M. , Wagenknecht P. , Zakoucky D.
Published: September 2019

Beta - neutrino correlation measurements are key in the research of physics beyond the Standard Model. In pure Fermi beta transitions, the beta-neutrino correlation coefficient, a
βν, is sensitive to the presence of scalar currents. The present limits were established by experimental studies of various nuclear systems with allowed Fermi transitions. A new experiment to improve the constraints on scalar currents is being developed, by the WISArD collaboration at ISOLDE/CERN, where the aim is to measure the energy shift of the β-delayed protons emitted from the isobaric analogue state of the 32Ar ground state. To enhance the sensitivity, protons and positrons are guided by a strong magnetic field and measured in coincidence between the two detection configurations located on both sides of a catcher foil in which the radioactive samples are implanted. Kinematic energy shifts of the protons in coincidence with positrons, in the same or opposite hemisphere of the catcher foil, will be more or less pronounced as a function of the possible scalar current component of the weak interaction. Details of the apparatus and preliminary results of the experiment are presented.
Study of the 32S(3He,d)33Cl one-proton transfer reaction with a new generation hodoscope
Authors: Cinausero M , Dell’Aquila D , Lombardo I , Vigilante M , Barlini S , Bolzonella R , Bruno M , Buccola A , Cartuan S , Casini G , Cicerchia M , D’Andrea M , Degerlier M , Fabris D , Gasques L , Gramegna F , Lepine-Szily A , Mantovani G , Marchi T , Piantelli S , Rigato V , Scomparin L , Valdrè S
Published: September 2019

The 32S(3He,d)33Cl one-proton transfer reaction is a powerful tool to investigate the spectroscopy of low-lying states in the proton-rich 33Cl nucleus. However, the extraction of firm differential cross-section data at various angles, against which benchmarking theoretical models to correctly constrain the spectroscopy of 33Cl, is made challenging by the presence of competitive reaction products contaminating the detected energy spectra. We have recently measured the 32S(3He,d)33Cl reaction at 9.8 MeV incident energy by using a new generation hodoscope of silicon detectors, capable to detect and identify emitted deuterons down to energies of the order of 2 MeV. The high angular segmentation of our hodoscope allowed to unambiguously disentangle the contribution of one-proton transfer reactions in the ground state of 33Cl and in its 0.810 MeV, 2.352 MeV, 2.685 MeV, 2.846 MeV excited states from contaminant deuteron-emitting reactions. These data will be crucial to help to constrain Jπ
and spectroscopic factor C
2
Sp
values of low-lying 33Cl states, still ambiguous in the literature. The present status of the analysis is discussed in the paper.
THM applied to the investigation of explosive astrophysical scenarios
Authors: La Cognata M. , Cherubini S. , Gulino M. , Lamia L. , Pizzone R.G. , Romano S. , Spitaleri C. , Tumino A.
Published: September 2019

The Trojan Horse Method (THM) makes use of quasi-free reactions to deduce the cross section of nuclear reactions relevant for astrophysics at the energies of interest. Thanks to the suppression of the Coulomb barrier, the THM cross section does not exponentially vanishes at astrophysical energies. Here we will briefly summarise the fundamentals of the method, then we will discuss two applications of the method to reactions that have a pivotal role in the latest stages of stellar evolution, leading to explosive scenarios. In particular, we will focus on the indirect investigation of the 18F(p,α)15O reaction, which is the most important 18F destruction channel in novae, and the 12C + 12C reaction, which plays a critical role in astrophysics to understand stellar burning scenarios in carbon-rich environments, including supernovae.
19F(p, α)16O and 19F(α,p)22Ne Reaction Rate Measured via THM and Fluorine Nucleosynthesis in AGB stars
Authors: Palmerini S. , D’Agata G. , La Cognata M. , Indelicato I. , Pizzone R. G. , Trippella O. , Vescovi D.
Published: September 2019

Asymptotic Giant Branch (AGB) stars have been proven to be sites of F production through spectroscopy observations by several authors, but it is not clear whether these stars might account for the total fluorine abundance of the Galaxy. Recently the two main channels for 19F destruction in AGB stars, namely the 19F(α,p)22Ne and 19F(p,α)16O reactions, have been studied via the Trojan Horse Method in the energy range of interest for astrophysics. In both cases experimental results have shown the presence of resonant structures below 500 keV, hinting to an enhancements in efficiency of fluorine destruction by stellar H- and He- burning. In particular the 19F(p, α)16O reaction rate at T
9
≤ 0.2K turns out to be increased up to a factor of 1.7 while the 19F(p, α)16O is enhanced more than a factor of 4 at 0.1 ≤ T
9
≤ 0.25. We present here a re-analysis of the role of AGB stars as fluorine galactic source by comparing stellar observations with predictions of AGB nucleosynthesis (for stellar masses from 1.5 to 5M⊙) computed by employing in state-of-the-art models the THM reaction rates for 19F destruction.
First measurements of capture reactions for the γ-process using HECTOR
Authors: Simon A , Kelmar R , Olivas-Gomez O , Churchman E , Millican P , Reingold C S , Anderson T , Clark A M , Cooper N , Dombos A C , Frentz B , Henderson S L , Kelly S , Robertson D , Skulski M , Stech E , Strauss S Y , Tan W P , Vande Kolk B
Published: September 2019

The first measurements of the capture reactions for the astrophysical γ-process using HECTOR, a total absorption spectrometer are presented. Two reactions: 102Pd(p,γ)103Ag and 90Zr(α,γ)94Mo were measured using the γ-summing technique. The results are compared with the previous measurements found in the literature and with the NON-SMOKER predictions. The results from the current work are in a good agreement with the data found in the literature and serve as a test of the newly developed detector.
Mathematical simulation of stability of steady-state conditions for a road train
Authors: Sakno O , Moisia D , Kolesnikova T , Ollo V
Published: September 2019

The article is devoted to the application of the parameter continuation method for solving the problem of maneuverability of a three-trailer road train. The mathematical model of a three-trailer road train with a wheelless intermediate link is worked out. The analysis of the equilibrium conditions of the system is performed. The structural instability of the model of the road train in the neighbourhood of the linear motion is presented. The presence of stable circular steady-state conditions is proved when moving along circles of a sufficiently small radius. It is established that for a given longitudinal velocity there is a certain range of changes in the rotation angle of the steering wheels of the tractor unit, within which stable steady-state conditions may be. The analysis of the stability of the steady-state conditions at θ = 0.38 rad. For the steady-state conditions, the configuration of the road train is drawn, where it can be seen that the without bearing link can only be oriented to the outer side of the turn. Also in the process of numerical integration, it is found that the resulting steady-state conditions are asymptotically stable.
Modeling and investigation of a diesel engine with ethanol additives
Authors: Iliev S , Mitev E
Published: September 2019

Ethanol is a promising alternative fuel, due to its renewable origin based on biomass. Also, it has a lower carbon content than the diesel fuel, which contains oxygen. For this reason, ethanol provides a remarkable potential for particulate reduction in diesel engines. One-dimensional simulation of a single-cylinder diesel engine with the help of the GT-Power software has been done. The simulation is designed to test the characteristics of the ethanol-filled diesel engine at full load. The obtained results were compared with pure diesel fuel.
Flue Gas Desulfurization by Using Calcined Dolomite
Authors: Baslayici S , Bugdayci M , Turan A , Oncel L , Acma E
Published: September 2019

SO2 emissions has begun to cause serious problems in industrialized countries. Today, various methods are used for removal of SO2 gas. SO2 gas is an important raw material for production of sulfuric acid. However, SO2 content of flue gas must be over 6% to produce sulfuric acid commercially. Flue gases, which don’t have enough amount of SO2 to produce sulfuric acid commercially are harmful to the environment and human health and they must be filtered. In this study, calcined dolomite was used to remove SO2 in flue gas which doesn’t have enough SO2 to produce sulfuric acid but have high emission values. Pyrite was used as SO2 source and SO2 removal efficiency of dolomite was determined for different experimental parameters. SO2 capturing system was thermodynamically modeled and SO2 capturing efficiency was determined as 77.81% in the experiments.
Low-energy optical phonons induce glassy-like vibrational and thermal anomalies in ordered crystals
Authors: Baggioli Matteo , Zaccone Alessio
Published: September 2019

It is widely accepted that structural glasses and disordered crystals exhibit anomalies in their thermal, mechanical and acoustic properties as manifestations of the breakdown of the long-wavelength approximation in a disordered dissipative environment. However, the same type of glassy-like anomalies (i.e. boson peak in the vibrational density of states (VDOS) above the Debye level, peak in the normalized specific heat at T ≃ 10 K etc) have been recently observed also in perfectly ordered crystals, including thermoelectric compounds. Here we present a theory that predicts these surprising effects in perfectly ordered crystals as a result of low-lying (soft) optical phonons. In particular, it is seen that a strong boson peak anomaly (low-energy excess of modes) in the VDOS can be due almost entirely to the presence of low-energy optical phonons, provided that their energy is comparable to that of the acoustic modes at the Brillouin zone boundary. The boson peak is predicted also to occur in the heat capacity at low T. In presence of strong damping (which might be due to anharmonicities in the ordered crystals), these optical phonons contribute to the low-T deviation from Debye’s T
3 law, producing a linear-in-T behavior which is typical of glasses, even though no assumptions of disorder whatsoever are made in the model. These findings are relevant for understanding and tuning thermal transport properties of thermoelectric compounds, and possibly for the enhancement of electron–phonon superconductivity.
Left anterior descending coronary artery compressed by a giant coronary fistula aneurysm: a case report
Authors: Bertolín Boronat Javier , Faga Valentina , Aguar Carrascosa Pablo , Mora Llabata Vicente
Published: September 2019

Background

Ischaemic chest pain can be originated by different causes. Among all, coronary fistulas are rarely the reason. Such entities are usually asymptomatic and can be diagnosed by echocardiography or coronary angiography. In an even rarer scenario, coronary fistulas might dilate and form an aneurysm.

Case summary

We report the case of a 62-year-old patient who was initially referred to the emergency department for stable angina. Coronary angiography and computed tomography scan showed a giant aneurysm relating to a coronary fistula with a course from the circumflex coronary artery to the superior vena cava. The aneurysm was critically compressing the left anterior descending coronary artery. It was confirmed and resolved by surgery.

Discussion

Giant aneurysms of a coronary fistula are very uncommon entities. We describe a rare case of angina caused by extrinsic compression of the left anterior descending artery from a giant aneurysm of a coronary fistula.
Procalcitonin and C-Reactive Protein for Bacterial Infection Diagnosis in Elderly Patients After Traumatic Orthopedic Surgery
Authors: Villain Cédric , Chenevier-Gobeaux Camille , Cohen-Bittan Judith , Ray Patrick , Epelboin Loïc , Verny Marc , Riou Bruno , Khiami Frédéric , Vallet Hélène , Boddaert Jacques
Published: September 2019

Background

Biomarkers prove valuable for diagnosing postoperative bacterial infection, but data in elderly patients are scarce. Here we analyze how procalcitonin and C-reactive protein (CRP) perform for bacterial infection diagnosis after traumatic orthopedic surgery in elderly patients.

Methods

We included all patients admitted to our perioperative geriatrics unit after traumatic orthopedic surgery. Patients on antibiotics, presenting preoperative bacterial infection, or without procalcitonin measurement were excluded. Clinical and biological data were collected prospectively. Medical charts were reviewed by three experts blinded to biomarker results to assess bacterial infection diagnosis. Areas under the curve and 90%-specificity thresholds were analyzed for baseline procalcitonin and CRP levels and relative variations.

Results

Analysis included 229 patients (median age 86 years, hip fracture 83%), of which 40 had bacterial infection (pneumonia [n = 23], urinary tract infection [n = 8]; median delay to onset: 2 days post-admission). For bacterial infection diagnosis, the computed areas under the curve were not significantly different (procalcitonin–baseline 0.64 [95% confidence interval: 0.57–0.70]; procalcitonin–relative variation 0.65 [0.59–0.71]; CRP–baseline 0.68 [0.61–0.74]; CRP–relative variation 0.70 [0.64–0.76]). The 90%-specificity thresholds were 0.75 µg/L for procalcitonin–baseline, +62% for procalcitonin–variation, 222 mg/L for CRP–baseline, +111% for CRP–variation.

Conclusions

Diagnostic performances of procalcitonin and CRP were not significantly different. Baseline levels and relative variations of these biomarkers showed little diagnostic value after traumatic orthopedic surgery in elderly patients.
Volcanic earthquake foreshocks during the 2018 collapse of Kīlauea Caldera
Authors: Butler Rhett
Published: September 2019

The summit collapse of the Kīlauea Caldera—due to magma chamber drainage being directed to the Volcano's lower east rift zone—was accompanied by 50 large, nearly identical magnitude Mw 5 earthquakes between 29 May and 2 August 2 2018. I have examined the seismicity associated with these 50 primary earthquakes, and find that the typical pattern of earthquake aftershocks decaying in number and magnitude is not evident. Rather, immediately after the primary shock there is a hiatus of one-to-several hours before the associated earthquakes grow in number and magnitude up to the next primary shock. In essence, the associated seismicity consists of thousands of foreshocks. The magnitude of completeness is estimated at ML = 2.5. The trend of foreshocks does not fit an Omori power-law model. Rather, the pattern of foreshocks (number per hour) is fit well by a semi-Gaussian curve, which initially grows rapidly and slows hours prior to the primary earthquakes. The Gaussian fits (${r^2} > 0.98$) for three different magnitude thresholds are self-similar with a common half-width, $\sigma \sim 13$ hr. The pattern of foreshock seismic moments aligned with and stacked for the 50 primary events is fit by an exponential trend, growing at the mean (stacked intervals) rate of 17 per cent per hour. The power of foreshocks measured within each interval also grows with time—the total foreshock power per interval (J hr–1) increases by a factor of 18 through the first half of the sequence (May 29 through June 26), and then declines by half through to the end.
Quinine Enhances Photo-Inactivation of Gram-Negative Bacteria
Authors: Leanse Leon G , Dong Pu-Ting , Goh Xueping S , Lu Min , Cheng Ji-Xin , Hooper David C , Dai Tianhong
Published: September 2019

Background

Antimicrobial resistance is a significant concern to public health, and there is a pressing need to develop novel antimicrobial therapeutic modalities.

Methods

In this study, we investigated the capacity for quinine hydrochloride (Q-HCL) to enhance the antimicrobial effects of antimicrobial blue light ([aBL] 405 nm wavelength) against multidrug-resistant (MDR) Gram-negative bacteria in vitro and in vivo.

Results

Our findings demonstrated the significant improvement in the inactivation of MDR Pseudomonas aeruginosa and Acinetobacter baumannii (planktonic cells and biofilms) when aBL was illuminated during Q-HCL exposure. Furthermore, the addition of Q-HCL significantly potentiated the antimicrobial effects of aBL in a mouse skin abrasion infection model. In addition, combined exposure of aBL and Q-HCL did not result in any significant apoptosis when exposed to uninfected mouse skin.

Conclusions

In conclusion, aBL in combination with Q-HCL may offer a novel approach for the treatment of infections caused by MDR bacteria.
Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics
Authors: Zhang Y Miles , Williams Jason L , Lucky Andrea
Published: September 2019

Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and biogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCEs in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.
Overwintering of West Nile Virus in the United States
Authors: Reisen William K , Wheeler Sarah S
Published: September 2019

The establishment of a tropical virus such as West Nile (WNV; Flaviviridae: Flavivirus) within the temperate latitudes of the continental United States was unexpected and perhaps contingent, in part, upon the ability of this invasive virus to persist during winter when temperatures become too cold for replication and vector mosquito gonotrophic activity. Our Forum article reviews research examining possible overwintering mechanisms that include consistent reintroduction and local persistence in vector mosquitoes and avian hosts, mostly using examples from research conducted in California. We conclude that the transmission of WNV involves so many vectors and hosts within different landscapes that multiple overwintering pathways are possible and collectively may be necessary to allow this virus to overwinter consistently within the United States.
Galaxies and clusters of galaxies as peak patches of the density field
Authors: Fukugita Masataka , Böhringer Hans
Published: September 2019

The mass function of galaxies and clusters of galaxies can be derived observationally based on different types of observations. In this study we test if these observations can be combined to a consistent picture which is also in accord with structure formation theory. The galaxy data comprise the optical galaxy luminosity function and the gravitational lensing signature of the galaxies, while the galaxy cluster mass function is derived from the X-ray luminosity distribution of the clusters. We show the results of the comparison in the form of the mass density fraction that is contained in collapsed objects relative to the mean matter density in the Universe. The mass density fraction in groups and clusters of galaxies extrapolated to low masses agrees very well with that of the galaxies: both converge at the low mass limit to a mass fraction of about 28 per cent if the outer radii of the objects are taken to be r200. Most of the matter contained in collapsed objects is found in the mass range $M_{200} \sim 10^{12}\!-\!10^{14}\, h^{-1}_{70} \, \mathrm{M}_\odot$, while a larger amount of the cosmic matter resides outside of r200 of collapsed objects.
Ultrastructure and intercellular contact-mediated communication in cultured human early stage follicles exposed to mTORC1 inhibitor
Authors: Grosbois J , Vermeersch M , Devos M , Clarke H J , Demeestere I
Published: September 2019

The reproductive lifespan of a woman is determined by the gradual recruitment of quiescent follicles into the growing pool. In humans, ovarian tissue removal from its in vivo environment induces spontaneous activation of resting follicles. Similarly, pharmacological activation of the PI3K/Akt pathway leads to accelerated follicle recruitment, but has been associated with follicular damage. Recent findings demonstrate that everolimus (EVE), an mTORC1 inhibitor, limits primordial follicle activation. However, its potential benefit regarding growing follicle integrity remains unexplored. Ovarian cortical fragments were exposed to ± EVE for 24 h and cultured for an additional 5 days. After 0, 1 and 6 days of culture, fragments were either processed for ultrastructural analysis or subjected to follicular isolation for gene expression and immunofluorescence assessments. Data from transmission electron microscopy showed that growing follicles displayed similar ultrastructural features irrespective of the conditions and maintained close contacts between germinal and stromal compartments. Establishment of intra-follicular communication was confirmed by detection of a gap junction component, Cx43, in both groups throughout culture, whereas transzonal projections, which physically link granulosa cells to oocyte, formed later in EVE-treated follicles. Importantly, levels of GJA1 mRNA, encoding for the Cx43 protein, significantly increased from Day 0 to Day 1 in the EVE group, but not in the control group. Given that EVE-treated follicles were smaller than controls, these findings suggest that EVE might facilitate the establishment of appropriate intercellular communications without impairing follicle ultrastructure. Therefore, mTORC1 inhibitors might represent an attractive tool to delay the culture-induced primordial follicle activation while maintaining follicles in a functionally integrated state.
Early Postnatal Manganese Exposure Reduces Rat Cortical and Striatal Biogenic Amine Activity in Adulthood
Authors: Lasley Stephen M , Fornal Casimir A , Mandal Shyamali , Strupp Barbara J , Beaudin Stephane A , Smith Donald R
Published: September 2019

Growing evidence from studies with children and animal models suggests that elevated levels of manganese during early development lead to lasting cognitive and fine motor deficits. This study was performed to assess presynaptic biogenic amine function in forebrain of adult Long-Evans rats exposed orally to 0, 25, or 50 mg Mn/kg/day over postnatal day 1–21 or continuously from birth to the end of the study (approximately postnatal day 500). Intracerebral microdialysis in awake rats quantified evoked outflow of biogenic amines in the right medial prefrontal cortex and left striatum. Results indicated that brain manganese levels in the early life exposed groups (postnatal day 24) largely returned to control levels by postnatal day 66, whereas levels in the lifelong exposed groups remained elevated 10%–20% compared with controls at the same ages. Manganese exposure restricted to the early postnatal period caused lasting reductions in cortical potassium-stimulated extracellular norepinephrine, dopamine, and serotonin, and reductions in striatal extracellular dopamine. Lifelong manganese exposure produced similar effects with the addition of significant decreases in cortical dopamine that were not evident in the early postnatal exposed groups. These results indicate that early postnatal manganese exposure produces persistent deficits in cortical and striatal biogenic amine function. Given that these same animals exhibited lasting impairments in attention and fine motor function, these findings suggest that reductions in catecholaminergic activity are a primary factor underlying the behavioral effects caused by manganese, and indicate that children exposed to elevated levels of manganese during early development are at the greatest risk for neuronal deficiencies that persist into adulthood.
Benefits of Activity-Based Interventions Among Female Adolescents Who Are Overweight and Obese
Authors: Bonney Emmanuel , Ferguson Gillian , Burgess Theresa , Smits-Engelsman Bouwien
Published: September 2019

Purpose:

The purpose of this study was to compare the effects of 2 activity-based motor interventions among female adolescents who are overweight and obese.

Methods:

This study was conducted in a low-income community of Cape Town, South Africa. The study involved 52 participants classified as overweight and obese. Participants were randomly assigned to task-oriented functional training or Wii Fit intervention. Both interventions were 45 minutes of active training once a week for 14 weeks. Outcome measures included aerobic fitness, motor coordination, and self-efficacy. Data were collected before and after the interventions.

Results:

Participants in both groups demonstrated significant improvement in aerobic fitness and motor coordination but not self-efficacy. However, no between-group differences were observed on any of the outcomes.

Conclusions:

Activity-based interventions may improve aerobic fitness and motor coordination in female adolescents who are overweight and obese and may also help prevent declines in physical fitness and coordination in this population.
Complete genome dynamics of a dominant-lineage strain of Xanthomonas oryzae pv. oryzae harbouring a novel plasmid encoding a type IV secretion system
Authors: Kaur Amandeep , Bansal Kanika , Kumar Sanjeet , Sonti Ramesh V. , Patil Prabhu B.
Published: September 2019

Xanthomonas oryzae

pv. oryzae (Xoo) is a serious pathogen causing bacterial blight disease in rice. Population genomic studies have revealed that rampant inter-strain rather than inter-lineage differences are contributing to the evolutionary success of this pathogen. Here, we report the complete genome sequence of BXO1, a strain of Xoo belonging to a dominant lineage from India. A complete genome-based investigation revealed the presence of two plasmids, pBXO1-1 (66.7 kb) and pBXO1-2 (25.6 kb). The pBXO1-1 plasmid encodes 71 genes, 38 of which encode hypothetical proteins of unknown function. However, these hypothetical genes possess atypical GC content, pointing towards their acquisition and movement through horizontal gene transfer. Interestingly, pBXO1-2 encodes a type IV secretion system (T4SS), which is known to play an important role in the conjugative transfer of genetic material, and also provides fitness to pathogenic bacteria for their enhanced survival. Neither plasmid has been reported previously in any other complete Xoo genome published to date. Our analysis also revealed that the pBXO1-2 plasmid is present in

Xanthomonas albilineans

str. GPE PC73, which is known to cause leaf scald, a lethal disease in sugarcane. Our complete genome sequence analysis of BXO1 has provided us with detailed insights into the two novel strain-specific plasmids, in addition to decoding their functional capabilities, which were not assessable when using the draft genome sequence of the strain. Overall, our study has revealed the mobility of a novel T4SS in two pathogenic species of

Xanthomonas

that infect the vascular tissues of two economically important monocot plants, i.e. rice and sugarcane.
Interneuron-specific plasticity at parvalbumin and somatostatin inhibitory synapses onto CA1 pyramidal neurons shapes hippocampal output
Authors: Udakis Matt , Pedrosa Victor , Chamberlain Sophie E.L. , Clopath Claudia , Mellor Jack R
Published: September 2019

The formation and maintenance of spatial representations within hippocampal cell assemblies is strongly dictated by patterns of inhibition from diverse interneuron populations. Although it is known that inhibitory synaptic strength is malleable, induction of long-term plasticity at distinct inhibitory synapses and its regulation of hippocampal network activity is not well understood. Here, we show that inhibitory synapses from parvalbumin and somatostatin expressing interneurons undergo long-term depression and potentiation respectively (PV-iLTD and SST-iLTP) during physiological activity patterns. Both forms of plasticity rely on T-type calcium channel activation to confer synapse specificity but otherwise employ distinct mechanisms. Since parvalbumin and somatostatin interneurons preferentially target perisomatic and distal dendritic regions respectively of CA1 pyramidal cells, PV-iLTD and SST-iLTP coordinate a reprioritisation of excitatory inputs from entorhinal cortex and CA3. Furthermore, circuit-level modelling reveals that PV-iLTD and SST-iLTP cooperate to stabilise place cells while facilitating representation of multiple unique environments within the hippocampal network.
A viral ring nuclease anti-CRISPR subverts type III CRISPR immunity
Authors: Athukoralage Januka S , McMahon Stephen , Zhang Changyi , Grüschow Sabine , Graham Shirley , Krupovic Mart , Whitaker Rachel J , Gloster Tracey , White Malcolm F
Published: September 2019

The CRISPR system provides adaptive immunity against mobile genetic elements in bacteria and archaea. On detection of viral RNA, type III CRISPR systems generate a cyclic oligoadenylate (cOA) second messenger1–3, activating defence enzymes and sculpting a powerful antiviral response that can drive viruses to extinction4,5. Cyclic nucleotides are increasingly implicated as playing an important role in host-pathogen interactions6,7. Here, we identify a widespread new family of viral anti-CRISPR (Acr) enzymes that rapidly degrade cyclic tetra-adenylate (cA4). The viral ring nuclease (AcrIII-1) is the first Acr described for type III CRISPR systems and is widely distributed in archaeal and bacterial viruses, and proviruses. The enzyme uses a novel fold to bind cA4specifically and utilizes a conserved active site to rapidly cleave the signalling molecule, allowing viruses to neutralise the type III CRISPR defence system. The AcrIII-1 family has a broad host range as it targets cA4signalling molecules rather than specific CRISPR effector proteins. This study highlights the crucial role of cyclic nucleotide signalling in the conflict between viruses and their hosts.
CNVmap: a method and software to detect and map copy number variants from segregation data
Authors: Falque Matthieu , Jebreen Kamel , Paux Etienne , Knaak Carsten , Mezmouk Sofiane , Martin Olivier C.
Published: September 2019

Single nucleotide polymorphisms (SNPs) are widely used for detecting quantitative trait loci or for searching for causal variants of diseases. Nevertheless,structuralvariations such as copy-number variants (CNVs) represent a large part of natural genetic diversity and contribute significantly to trait variation. Over the past decade, numerous methods and softwares have been developed to detect CNVs. Such approaches are based on exploiting sequencing data or SNP arrays, but they bypass a wealth of information such as genotyping data from segregating populations, producede.g.for QTL mapping. Here we propose an original method to both detect andgenetically mapCNVs using mapping panels. Specifically, we exploit the apparent heterozygous state of duplicated loci: peaks in appropriately defined genome-wide allelic profiles provide highly specific signatures that identify the nature and position of the CNVs. Our original method and software can detect and map automatically up to 33 different predefined types of CNVs based on segregation data only. We validate this approach on simulated and experimental bi-parental mapping panels in two maize and one wheat populations. Most of the events found correspond to having just one extra copy in one of the parental lines but the corresponding allelic value can be that of either parent. We also find cases with two or more additional copies, especially in wheat where these copies locate to homeologues. More generally, our computational tool can be used to give additional value, at no cost, to many datasets produced over the past decade from genetic mapping panels.
Bacterial genes outnumber archaeal genes in eukaryotic genomes
Authors: Brückner Julia , Martin William F.
Published: September 2019

The origin of eukaryotes is one of evolution’s most important transitions, yet it is still poorly understood. Evidence for how it occurred should be preserved in eukaryotic genomes. Based on phylogenetic trees from ribosomal RNA and ribosomal proteins, eukaryotes are typically depicted as branching together with or within archaea. This ribosomal affiliation is widely interpreted as evidence for an archaeal origin of eukaryotes. However, the extent to which the archaeal ancestry of genes for the cytosolic ribosomes of eukaryotic cells is representative for the rest of the eukaryotic genome is unknown. Here we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups to identify genes that link eukaryotes exclusively to bacteria and archaea respectively. By downsampling the bacterial sample we obtain estimates for the bacterial and archaeal proportions of genes among 150 eukaryotic genomes. Eukaryotic genomes possess a bacterial majority of genes. On average, eukaryotic genes are 56% bacterial in origin. The majority drops to 53% in eukaryotes that never possessed plastids, and increases to 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic genome, reaching 67% in higher plants. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. In the current sample, this process of adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.
Resegmentation is an ancestral feature of the gnathostome vertebral skeleton
Authors: Criswell Katharine E. , Gillis J. Andrew
Published: September 2019

The vertebral skeleton is a defining feature of vertebrate animals. However, the mode of vertebral segmentation varies considerably between major lineages. In tetrapods, adjacent somite halves recombine to form a single vertebra through the process of “resegmentation”. However, in teleost fishes, there is considerable mixing between cells of the anterior and posterior somite halves, without clear resegmentation. To determine whether resegmentation is a tetrapod novelty, or an ancestral feature of jawed vertebrates, we tested the relationship between somites and vertebrae in a cartilaginous fish, the skate (Leucoraja erinacea). Using cell lineage tracing, we show that skate trunk vertebrae arise through tetrapod-like resegmentation, with anterior and posterior halves of each vertebra deriving from adjacent somites. We further show that tail vertebrae also arise through resegmentation, despite a duplication of the number of vertebrae per body segment. These findings resolve axial resegmentation as an ancestral feature of the jawed vertebrate body plan.
Thalamocortical network connectivity controls spatiotemporal dynamics of cortical and thalamic traveling waves
Authors: Bhattacharya Sayak , Le Cauchois Matthieu B. , Iglesias Pablo A. , Chen Zhe S.
Published: September 2019

Propagation of neural activity in spatially structured neuronal networks has been observed in awake, anesthetized and sleeping brains. However, it remains unclear how traveling waves are coordinated temporally across recurrently connected brain structures, and how network connectivity affects spatiotemporal neural activity. Here we develop a computational model of a two-dimensional thalamocortical network that enables us to investigate traveling wave characteristics in space-time. We show that thalamocortical and intracortical network connectivity, excitation/inhibition balance, thalamocortical/corticothalamic delay can independently or jointly change the spatiotemporal patterns (radial, planar and rotating waves) and characteristics (speed, direction and frequency) of cortical and thalamic traveling waves. Simulations of our model further predict that increased thalamic inhibition induces slower cortical wave frequency, and enhanced cortical excitation increases cortical wave speed and oscillation frequencies. Overall, the model study provides not only theoretical insight into the basis for spatiotemporal wave patterns, but also experimental predictions that potentially control these dynamics.

Author Summary

Cognition or sensorimotor control requires the coordination of neural activity across widespread brain circuits. Propagating waves of oscillatory neural activities have been observed at both macroscopic and mesoscopic levels, with various frequencies, spatial coverage, and modalities. However, a complete understanding how thalamocortical traveling waves are originated and temporally coordinated in the thalamus and cortex are still unclear. Furthermore, it remains unknown how the network connectivity, excitation/inhibition balance, thalamocortical or corticothalamic delay determine the spatiotemporal wave patterns and characteristics of cortical and thalamic traveling waves. Here we develop a computational model of a two-dimensional thalamocortical network to investigate the thalamic and neocortical traveling wave characteristics in space-time, which allows us to quantitatively assess the impact of thalamocortical network properties on the formation and maintenance of complex traveling wave patterns. Our computational model provides strong theoretical insight into the basis of spatiotemporal wave propagation, as well as experimental predictions that control these wave dynamics.