bluuebunny/crossref_metadata_2025 huggingface dataset:
Benthic communities under anthropogenic pressure show resilience across the Quaternary
Authors: Martinelli Julieta C. , Soto Luis P. , González Jorge , Rivadeneira Marcelo M.
Published: September 2017

The Southeast Pacific is characterized by rich upwelling systems that have sustained and been impacted by human groups for at least 12 ka. Recent fishing and aquaculture practices have put a strain on productive coastal ecosystems from Tongoy Bay, in north-central Chile. We use a temporal baseline to determine whether potential changes to community structure and composition over time are due to anthropogenic factors, natural climatic variations or both. We compiled a database (n = 33 194) with mollusc species abundances from the Mid-Pleistocene, Late Pleistocene, Holocene, dead shell assemblages and live-sampled communities. Species richness was not significantly different, neither were diversity and evenness indices nor rank abundance distributions. There is, however, an increase in relative abundance for the cultured scallopArgopecten, while the previously dominant clamMuliniais locally very rare. Results suggest that impacts from both natural and anthropogenic stressors need to be better understood if benthic resources are to be preserved. These findings provide the first Pleistocene temporal baseline for the south Pacific that shows that this highly productive system has had the ability to recover from past alterations, suggesting that if monitoring and management practices continue to be implemented, moderately exploited communities from today have hopes for recovery.
On the Keller–Rubinow model for Liesegang ring formation
Authors: Duley J. M. , Fowler A. C. , Moyles I. R. , O'Brien S. B. G.
Published: September 2017

We study the model of Keller & Rubinow (Keller & Rubinow 1981J. Chem. Phys74, 5000–5007. (doi:10.1063/1.441752)) describing the formation of Liesegang rings due to Ostwald's supersaturation mechanism. Keller and Rubinow provided an approximate solution both for the growth and equilibration of the first band, and also for the formation of secondary bands, based on a presumed asymptotic limit. However, they did not provide a parametric basis for the assumptions in their solution, nor did they provide any numerical corroboration, particularly of the secondary band formation. Here, we provide a different asymptotic solution, based on a specific parametric limit, and we show that the growth and subsequent cessation of the first band can be explained. We also show that the model is unable to explain the formation of finite width secondary bands, and we confirm this result by numerical computation. We conclude that the model is not fully posed, lacking a transition variable which can describe the hysteretic switch across the nucleation threshold.
Irreversible particle motion in surfactant-laden interfaces due to pressure-dependent surface viscosity
Authors: Manikantan Harishankar , Squires Todd M.
Published: September 2017

The surface shear viscosity of an insoluble surfactant monolayer often depends strongly on its surface pressure. Here, we show that a particle moving within a bounded monolayer breaks the kinematic reversibility of low-Reynolds-number flows. The Lorentz reciprocal theorem allows such irreversibilities to be computed without solving the full nonlinear equations, giving the leading-order contribution of surface pressure-dependent surface viscosity. In particular, we show that a disc translating or rotating near an interfacial boundary experiences a force in the direction perpendicular to that boundary. In unbounded monolayers, coupled modes of motion can also lead to non-intuitive trajectories, which we illustrate using an interfacial analogue of the Magnus effect. This perturbative approach can be extended to more complex geometries, and to two-dimensional suspensions more generally.
Uncertainties in the 2004 Sumatra–Andaman source through nonlinear stochastic inversion of tsunami waves
Authors: Gopinathan D. , Venugopal M. , Roy D. , Rajendran K. , Guillas S. , Dias F.
Published: September 2017

Numerical inversions for earthquake source parameters from tsunami wave data usually incorporate subjective elements to stabilize the search. In addition, noisy and possibly insufficient data result in instability and non-uniqueness in most deterministic inversions, which are barely acknowledged. Here, we employ the satellite altimetry data for the 2004 Sumatra–Andaman tsunami event to invert the source parameters. We also include kinematic parameters that improve the description of tsunami generation and propagation, especially near the source. Using a finite fault model that represents the extent of rupture and the geometry of the trench, we perform a new type of nonlinear joint inversion of the slips, rupture velocities and rise times with minimala prioriconstraints. Despite persistently good waveform fits, large uncertainties in the joint parameter distribution constitute a remarkable feature of the inversion. These uncertainties suggest that objective inversion strategies should incorporate more sophisticated physical models of seabed deformation in order to significantly improve the performance of early warning systems.
On the topology of the Lorenz system
Authors: Pinsky Tali
Published: September 2017

We present a new paradigm for three-dimensional chaos, and specifically for the Lorenz equations. The main difficulty in these equations and for a generic flow in dimension 3 is the existence of singularities. We show how to use knot theory as a way to remove the singularities. Specifically, we claim: (i) for certain parameters, the Lorenz system has an invariant one-dimensional curve, which is a trefoil knot. The knot is a union of invariant manifolds of the singular points. (ii) The flow is topologically equivalent to an Anosov flow on the complement of this curve, and moreover to a geodesic flow. (iii) When varying the parameters, the system exhibits topological phase transitions, i.e. for special parameter values, it will be topologically equivalent to an Anosov flow on a knot complement. Different knots appear for different parameter values and each knot controls the dynamics at nearby parameters.
Toroidal drop under electric field: arbitrary drop-to-ambient fluid viscosity ratio
Authors: Zabarankin Michael
Published: September 2017

In the absence of external forces, a liquid toroidal drop freely suspended in another fluid shrinks towards its centre. It is shown that if the two phases are slightly conducting viscous incompressible fluids with the drop-to-ambient fluid ratios of electric conductivities, dielectric constants and viscosities to be 1/
R
,
Q
and
λ
, respectively, then the toroidal drop with volume 4
π
/3 and having major radius
ρ
can become almost stationary when subjected to a uniform electric field aligned with the drop’s axis of symmetry. In this case,
Q
and electric capillary number
Ca

E

that defines the ratio of electric stress to surface tension, are functions of
R
,
ρ
and
λ
and are found analytically. Those functions are relatively insensitive to
λ
, and for
ρ
≥3, they admit simple approximations, which coincide with those obtained recently for
λ
=1. Streamlines inside and outside the toroidal drop for the same
R
and
ρ
but different
λ
are qualitatively similar.
Stochastic partial differential fluid equations as a diffusive limit of deterministic Lagrangian multi-time dynamics
Authors: Cotter C. J. , Gottwald G. A. , Holm D. D.
Published: September 2017

In Holm (Holm 2015Proc. R. Soc. A471, 20140963. (doi:10.1098/rspa.2014.0963)), stochastic fluid equations were derived by employing a variational principle with an assumed stochastic Lagrangian particle dynamics. Here we show that the same stochastic Lagrangian dynamics naturally arises in a multi-scale decomposition of the deterministic Lagrangian flow map into a slow large-scale mean and a rapidly fluctuating small-scale map. We employ homogenization theory to derive effective slow stochastic particle dynamics for the resolved mean part, thereby obtaining stochastic fluid partial equations in the Eulerian formulation. To justify the application of rigorous homogenization theory, we assume mildly chaotic fast small-scale dynamics, as well as a centring condition. The latter requires that the mean of the fluctuating deviations is small, when pulled back to the mean flow.
Cautionary tales on air-quality improvement in Beijing
Authors: Zhang Shuyi , Guo Bin , Dong Anlan , He Jing , Xu Ziping , Chen Song Xi
Published: September 2017

The official air-quality statistic reported that Beijing had a 9.9% decline in the annual concentration of PM
2.5
in 2016. While this statistic offered some relief for the inhabitants of the capital, we present several analyses based on Beijing's PM
2.5
data of the past 4 years at 36 monitoring sites along with meteorological data of the past 7 years. The analyses reveal the air pollution situation in 2016 was not as rosy as the 9.9% decline would convey, and improvement if any was rather uncertain. The paper also provides an assessment on the city's PM
2.5
situation in the past 4 years.
Elastodynamic image forces on screw dislocations in the presence of phase boundaries
Authors: Gurrutxaga-Lerma Beñat
Published: September 2017

The elastodynamic image forces acting on straight screw dislocations in the presence of planar phase boundaries are derived. Two separate dislocations are studied: (i) the injected, non-moving screw dislocation and (ii) the injected (or pre-existing), generally non-uniformly moving screw dislocation. The image forces are derived for both the case of a rigid surface and of a planar interface between two homogeneous, isotropic phases. The case of a rigid interface is shown to be solvable employing Head's image dislocation construction. The case of the elastodynamic image force due to an interface is solved by deriving the reflected wave's contribution to the global solution across the interface. This entails obtaining the fundamental solution (Green's function) for a point unit force via Cagniard's method, and then applying the convolution theorem for a screw dislocation modelled as a force distribution. Complete, explicit formulae are provided when available. It is shown that the elastodynamic image forces are generally affected by retardation effects, and that those acting on the moving dislocations display a dynamic magnification that exceed the attraction (or repulsion) predicted in classical elastostatic calculations.
Evolution of cross-resistance to medical triazoles inAspergillus fumigatusthrough selection pressure of environmental fungicides
Authors: Zhang Jianhua , van den Heuvel Joost , Debets Alfons J. M. , Verweij Paul E. , Melchers Willem J. G. , Zwaan Bas J. , Schoustra Sijmen E.
Published: September 2017

Resistance to medical triazoles inAspergillus fumigatusis an emerging problem for patients at risk of aspergillus diseases. There are currently two presumed routes for medical triazole-resistance selection: (i) through selection pressure of medical triazoles when treating patients and (ii) through selection pressure from non-medical sterol-biosynthesis-inhibiting (SI) triazole fungicides which are used in the environment. Previous studies have suggested that SI fungicides can induce cross-resistance to medical triazoles. Therefore, to assess the potential of selection of resistance to medical triazoles in the environment, we assessed cross-resistance to three medical triazoles in lineages ofA. fumigatusfrom previous work where we applied an experimental evolution approach with one of five different SI fungicides to select for resistance. In our evolved lines we found widespread cross-resistance indicating that resistance to medical triazoles rapidly arises through selection pressure of SI fungicides. All evolved lineages showed similar evolutionary dynamics to SI fungicides and medical triazoles, which suggests that the mutations inducing resistance to both SI fungicides and medical triazoles are likely to be the same. Whole-genome sequencing revealed that a variety of mutations were putatively involved in the resistance mechanism, some of which are in known target genes.
Extending the durability of cultivar resistance by limiting epidemic growth rates
Authors: Carolan Kevin , Helps Joe , van den Berg Femke , Bain Ruairidh , Paveley Neil , van den Bosch Frank
Published: September 2017

Cultivar resistance is an essential part of disease control programmes in many agricultural systems. The use of resistant cultivars applies a selection pressure on pathogen populations for the evolution of virulence, resulting in loss of disease control. Various techniques for the deployment of host resistance genes have been proposed to reduce the selection for virulence, but these are often difficult to apply in practice. We present a general technique to maintain the effectiveness of cultivar resistance. Derived from classical population genetics theory; any factor that reduces the population growth rates of both the virulent and avirulent strains will reduce selection. We model the specific example of fungicide application to reduce the growth rates of virulent and avirulent strains of a pathogen, demonstrating that appropriate use of fungicides reduces selection for virulence, prolonging cultivar resistance. This specific example of chemical control illustrates a general principle for the development of techniques to manage the evolution of virulence by slowing epidemic growth rates.
Cross-taxa generalities in the relationship between population abundance and ambient temperatures
Authors: Bowler Diana E. , Haase Peter , Hof Christian , Kröncke Ingrid , Baert Léon , Dekoninck Wouter , Domisch Sami , Hendrickx Frederik , Hickler Thomas , Neumann Hermann , O'Hara Robert B. , Sell Anne F. , Sonnewald Moritz , Stoll Stefan , Türkay Michael , van Klink Roel , Schweiger Oliver , Vermeulen Rikjan , Böhning-Gaese Katrin
Published: September 2017

Identifying patterns in the effects of temperature on species' population abundances could help develop a general framework for predicting the consequences of climate change across different communities and realms. We used long-term population time series data from terrestrial, freshwater, and marine species communities within central Europe to compare the effects of temperature on abundance across a broad range of taxonomic groups. We asked whether there was an average relationship between temperatures in different seasons and annual abundances of species in a community, and whether species attributes (temperature range of distribution, range size, habitat breadth, dispersal ability, body size, and lifespan) explained interspecific variation in the relationship between temperature and abundance. We found that, on average, warmer winter temperatures were associated with greater abundances in terrestrial communities (ground beetles, spiders, and birds) but not always in aquatic communities (freshwater and marine invertebrates and fish). The abundances of species with large geographical ranges, larger body sizes, and longer lifespans tended to be less related to temperature. Our results suggest that climate change may have, in general, positive effects on species’ abundances within many terrestrial communities in central Europe while the effects are less predictable in aquatic communities.
Ecosystem engineering strengthens bottom-up and weakens top-down effects via trait-mediated indirect interactions
Authors: Zhong Zhiwei , Li Xiaofei , Pearson Dean , Wang Deli , Sanders Dirk , Zhu Yu , Wang Ling
Published: September 2017

Trophic interactions and ecosystem engineering are ubiquitous and powerful forces structuring ecosystems, yet how these processes interact to shape natural systems is poorly understood. Moreover, trophic effects can be driven by both density- and trait-mediated interactions. Microcosm studies demonstrate that trait-mediated interactions may be as strong as density-mediated interactions, but the relative importance of these pathways at natural spatial and temporal scales is underexplored. Here, we integrate large-scale field experiments and microcosms to examine the effects of ecosystem engineering on trophic interactions while also exploring how ecological scale influences density- and trait-mediated interaction pathways. We demonstrate that (i) ecosystem engineering can shift the balance between top-down and bottom-up interactions, (ii) such effects can be driven by cryptic trait-mediated interactions, and (iii) the relative importance of density- versus trait-mediated interaction pathways can be scale dependent. Our findings reveal the complex interplay between ecosystem engineering, trophic interactions, and ecological scale in structuring natural systems.
DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade
Authors: de Boer Hugo J. , Ghorbani Abdolbaset , Manzanilla Vincent , Raclariu Ancuta-Cristina , Kreziou Anna , Ounjai Sarawut , Osathanunkul Maslin , Gravendeel Barbara
Published: September 2017

In eastern Mediterranean countries orchids continue to be collected from the wild for the production of salep, a beverage made of dried orchid tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to identify orchid and other plant species present in 55 commercial salep products purchased in Iran, Turkey, Greece and Germany. Thirty samples yielded a total of 161 plant taxa, and 13 products (43%) contained orchid species and these belonged to 10 terrestrial species with tuberous roots. Another 70% contained the substitute ingredient
Cyamopsis tetraganoloba
(Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2 shows the potential of these markers and approach for identification of species used in salep products. The analysis of interspecific genetic distances between sequences of these markers for the most common salep orchid genera shows that species level identifications can be made with a high level of confidence. Understanding the species diversity and provenance of salep orchid tubers will enable the chain of commercialization of endangered species to be traced back to the harvesters and their natural habitats, and thus allow for targeted efforts to protect or sustainably use wild populations of these orchids.
Single-sperm sequencing reveals the accelerated mitochondrial mutation rate in male
Daphnia pulex
(Crustacea, Cladocera)
Authors: Xu Sen , Van Tran Kenny , Neupane Swatantra , Snyman Marelize , Huynh Trung Viet , Sung Way
Published: September 2017

Mutation rate in the nuclear genome differs between sexes, with males contributing more mutations than females to their offspring. The male-biased mutation rates in the nuclear genome is most likely to be driven by a higher number of cell divisions in spermatogenesis than in oogenesis, generating more opportunities for DNA replication errors. However, it remains unknown whether male-biased mutation rates are present in mitochondrial DNA (mtDNA). Although mtDNA is maternally inherited and male mtDNA mutation typically does not contribute to genetic variation in offspring, male mtDNA mutations are critical for male reproductive health. In this study, we measured male mtDNA mutation rate using publicly available whole-genome sequences of single sperm of the freshwater microcrustacean
Daphnia pulex
. Using a stringent mutation detection pipeline, we found that the male mtDNA mutation rate is 3.32 × 10
−6
per site per generation. All the detected mutations are heteroplasmic base substitutions, with 57% of mutations converting G/C to A/T nucleotides. Consistent with the male-biased mutation in the nuclear genome, the male mtDNA mutation rate in
D. pulex
is approximately 20 times higher than the female rate per generation. We propose that the elevated mutation rate per generation in male mtDNA is consistent with an increased number of cell divisions during male gametogenesis.
The language of cooperation: shared intentionality drives variation in helping as a function of group membership
Authors: McClung Jennifer Susan , Placì Sarah , Bangerter Adrian , Clément Fabrice , Bshary Redouan
Published: September 2017

While we know that the degree to which humans are able to cooperate is unrivalled by other species, the variation humans actually display in their cooperative behaviour has yet to be fully explained. This may be because research based on experimental game-theoretical studies neglects fundamental aspects of human sociality and psychology, namely social interaction and language. Using a new optimal foraging game loosely modelled on the prisoner's dilemma, the egg hunt, we categorized players as either in-group or out-group to each other and studied their spontaneous language usage while they made interactive, potentially cooperative decisions. Both shared group membership and the possibility to talk led to increased cooperation and overall success in the hunt. Notably, analysis of players' conversations showed that in-group members engaged more in shared intentionality, the human ability to both mentally represent and then adopt another's goal, whereas out-group members discussed individual goals more. Females also helped more and displayed more shared intentionality in discussions than males. Crucially, we show that shared intentionality was the mechanism driving the increase in helping between in-group players over out-group players at a cost to themselves. By studying spontaneous language during social interactions and isolating shared intentionality as the mechanism underlying successful cooperation, the current results point to a probable psychological source of the variation in cooperation humans display.
Integration of anatomy ontologies and evo-devo using structured Markov models suggests a new framework for modeling discrete phenotypic traits
Authors: Tarasov Sergei
Published: September 2017

Abstract

Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes – hierarchical and hidden – which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of structured Markov models with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of gene regulatory networks and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing tail color problem (that aims at coding tail when it is absent) and presents a previously unknown issue called the “two-scientist paradox”. The latter issue refers to the confounding nature of the coding of a trait and the hidden processes driving the trait’s evolution; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This paper gives practical examples of using the new framework for phylogenetic inference and comparative analysis.
Regulator of calcineurin-2 is a centriolar protein with a role in cilia length control
Authors: Stevenson Nicola L. , Bergen Dylan J.M. , Xu Amadeus , Wyatt Emily , Henry Freya , McCaughey Janine , Vuolo Laura , Hammond Chrissy L. , Stephens David J.
Published: September 2017

Almost every cell in the human body extends a primary cilium. Defective cilia function leads to a set of disorders known as ciliopathies characterised by debilitating developmental defects affecting many tissues. Here we report a new role for regulator of calcineurin 2, RCAN2, in primary cilia function. It localises to centrioles and the basal body and is required to maintain normal cilia length. RCAN2 was identified as the most strongly upregulated gene from a comparative RNAseq analysis of cells in which expression of the Golgi matrix protein giantin had been abolished by gene editing. In contrast to previous work where we showed that depletion of giantin by RNAi results in defects in ciliogenesis and in cilia length control, giantin knockout cells generate normal cilia on serum withdrawal. Furthermore, giantin knockout zebrafish show increased expression of RCAN2. Importantly, suppression of RCAN2 expression in giantin knockout cells results in the same defects in cilia length control seen on RNAi of giantin itself. Together these data define RCAN2 as a regulator of cilia function that can compensate for loss of giantin function.
A blood-based signature of cerebrospinal fluid Aβ1–42status
Authors: Goudey Benjamin , Fung Bowen J , Schieber Christine ,   for the Alzheimer’s Disease Metabolomics Consortium,   for the Alzheimer’s Disease Neuroimaging Initiative, Faux Noel G
Published: September 2017

It is increasingly recognized that Alzheimer’s disease (AD) exists before dementia is present and that shifts in amyloid beta occur long before clinical symptoms can be detected. Early detection of these molecular changes is a key aspect for the success of interventions aimed at slowing down rates of cognitive decline. Recent evidence indicates that of the two established methods for measuring amyloid, a decrease in cerebrospinal fluid (CSF) amyloidβ1–42(Aβ1–42) may be an earlier indicator of Alzheimer’s disease risk than measures of amyloid obtained from Positron Emission Tomography (PET). However, CSF collection is highly invasive and expensive. In contrast, blood collection is routinely performed, minimally invasive and cheap. In this work, we develop a blood-based signature that can provide a cheap and minimally invasive estimation of an individual’s CSF amyloid status using a machine learning approach. We show that a Random Forest model derived from plasma analytes can accurately predict subjects as having abnormal (low) CSF Aβ1–42levels indicative of AD risk (0.84 AUC, 0.78 sensitivity, and 0.73 specificity). Refinement of the modeling indicates that onlyAPOEε4carrier status and four plasma analytes (CGA, Aβ1–42, Eotaxin 3, APOE) are required to achieve a high level of accuracy. Furthermore, we show across an independent validation cohort that individuals with predicted abnormal CSF Aβ1–42levels transitioned to an AD diagnosis over 120 months significantly faster than those with predicted normal CSF Aβ1–42levels and that the resulting model also validates reasonably across PET Aβ1-42status (0.78 AUC).

This is the first study to show that a machine learning approach, using plasma protein levels, age andAPOEε4carrier status, is able to predict CSF Aβ1–42status, the earliest risk indicator for AD, with high accuracy.
Diminished dynamic cerebral autoregulatory capacity with forced oscillations in mean arterial pressure with elevated cardiorespiratory fitness
Authors: Labrecque Lawrence , Rahimaly Kevan , Imhoff Sarah , Paquette Myriam , Le Blanc Olivier , Malenfant Simon , Lucas Samuel JE , Bailey Damian M. , Smirl Jonathan D. , Brassard Patrice
Published: September 2017

The effect that cardiorespiratory fitness has on the dynamic cerebral autoregulatory capacity during changes in mean arterial pressure (MAP) remains equivocal. Using a multiple-metrics approach, challenging MAP across the spectrum of physiological extremes (i.e. spontaneous through forced MAP oscillations), we characterized dynamic cerebral autoregulatory capacity in 19 male endurance athletes and 8 controls via three methods: [1] onset of regulation (i.e., time delay before an increase in middle cerebral artery (MCA) conductance [MCA flow velocity (MCAv)/mean arterial pressure (MAP)] and rate of regulation, after transient hypotension induced by sit-to-stand, and transfer function analysis (TFA) of MAP and MCAv responses during [2] spontaneous and [3] forced oscillations (5-min of squat-stand maneuvers performed at 0.05 and 0.10 Hz). Reductions in MAP and mean MCAv (MCAVmean) during initial orthostatic stress (0-30 s after sit-to-stand) and the prevalence of orthostatic hypotension were also determined. Onset of regulation was delayed after sit-to-stand in athletes (3.1±1.7 vs. 1.5±1.0 s; p=0.03), but rate of regulation was not different between groups (0.24±0.05 vs. 0.21±0.09 s-1; p=0.82). While both groups had comparable TFA metrics during spontaneous oscillations, athletes had higher TFA gain during 0.10 Hz squat-stand vs. recreational controls (p=0.01). Reductions in MAP (p=0.15) and MCAVmean(p=0.11) during orthostatic stress and the prevalence of initial orthostatic hypotension (p=0.65) were comparable between groups. These results indicate an intact ability of the cerebral vasculature to react to spontaneous oscillations but an attenuated capability to counter rapid and large changes in MAP in individuals with elevated cardiorespiratory fitness.

New findings

What is the central question of this study?

What is the impact of cardiorespiratory fitness on dynamic cerebral autoregulatory capacity?

What is the main finding and its importance?

Our results indicate an intact ability of the cerebral vasculature to react to spontaneous oscillations but an attenuated capability to counter rapid and large changes in mean arterial pressure in individuals with elevated cardiorespiratory fitness.
Limitations of compensatory plasticity: the organization of the primary sensorimotor cortex in foot-using bilateral upper limb dysplasics
Authors: Striem-Amit Ella , Vannuscorps Gilles , Caramazza Alfonso
Published: September 2017

What forces direct brain organization and its plasticity? When a brain region is deprived of its input would this region reorganize based on compensation for the disability and experience, or would strong limitations of brain structure limit its plasticity? People born without hands activate their sensorimotor hand region while moving body parts used to compensate for this ability (e.g. their feet). This has been taken to suggest a neural organization based on functions, such as performing manual-like dexterous actions, rather than on body parts. Here we test the selectivity for functionally-compensatory body parts in the sensorimotor cortex of people born without hands. Despite clear compensatory foot use, the sensorimotor hand area in the dysplasic subjects showed preference for body parts whose cortical territory is close to the hand area, but which are not compensatorily used as effectors. This suggests that function-based organization, originally proposed for congenital blindness and deafness, does not apply to cases of the primary sensorimotor cortex deprivation in dysplasia. This is consistent with the idea that experience-independent functional specialization occurs at relatively high levels of representation. Indeed, increased and selective foot movement preference in the dysplasics was found in the association cortex, in the inferior parietal lobule. Furthermore, it stresses the roles of neuroanatomical constraints such as topographical proximity and connectivity in determining the functional development of brain regions. These findings reveal limitations to brain plasticity and to the role of experience in shaping the functional organization of the brain.

Significance Statement

What determines the role of brain regions, and their plasticity when typical inputs or experience is not provided? To what extent can extreme compensatory use affect brain organization? We tested the functional reorganization of the primary sensorimotor cortex hand area in people born without hands, who use their feet for every-day tasks. We found that it is preferentially activated by close-by body-parts which cannot serve as effectors, and not by the feet. In contrast, foot-selective compensatory plasticity was found in the association cortex, in an area involved in tool use. This shows limitations of compensatory plasticity and experience in modifying brain organization of early topographical cortex, as compared to association cortices where function-based organization is the driving factor.

Classification

Biological Sciences\Neuroscience
Cdk9 regulates a promoter-proximal checkpoint to modulate RNA Polymerase II elongation rate
Authors: Booth Gregory T. , Parua Pabitra K. , Sansó Miriam , Fisher Robert P. , Lis John T.
Published: September 2017

Multiple kinases modify RNA Polymerase II (Pol II) and its associated pausing and elongation factors to regulate Pol II transcription and transcription-coupled mRNA processing1,2. The conserved Cdk9 kinase is essential for regulated eukaryotic transcription3, but its mechanistic role remains incompletely understood. Here, we use altered-specificity kinase mutations and highly-specific inhibitors in fission yeast,Schizosaccharomyces pombeto examine the role of Cdk9, and related Cdk7 and Cdk12 kinases, on transcription at base-pair resolution using Precision Run-On sequencing (PRO-seq). Within a minute, Cdk9 inhibition causes a dramatic reduction in the phosphorylation of Pol II-associated factor, Spt5. The effects of Cdk9 inhibition on transcription are the more severe than inhibition of Cdk7 and Cdk12 and result in a shift of Pol II towards the transcription start site (TSS). A kinetic time course of Cdk9 inhibition reveals that early transcribing Pol II is the most compromised, with a measured rate of only ~400 bp/min, while Pol II that is already well into the gene continues rapidly to the end of genes with a rate > 1 kb/min. Our results indicate that while Pol II inS. pombecan escape promoter-proximal pausing in the absence of Cdk9 activity, it is impaired in elongation, suggesting the existence of a conserved global regulatory checkpoint that requires Cdk9 kinase activity.
Big trouble with little inserts: boundaries in metagenomic screenings usinglacZα based vectors
Authors: Alves Luana de Fátima , Borelli Tiago Cabral , Westmann Cauã Antunes , Silva-Rocha Rafael , Guazzaroni María-Eugenia
Published: September 2017

The vast biochemical repertoire found in microbial communities from a wide-range of environments allows screening and isolation of novel enzymes with improved catalytic features. In this sense, metagenomics approaches have been of high relevance for providing enzymes used in diverse industrial applications. For instance, glycosyl hydrolases, which catalyze the hydrolysis of carbohydrates to sugars, are essential for bioethanol production from renewable resources. In the current study, we have focused on the prospection of protease and glycosyl hydrolase activities from microbial communities inhabiting a soil sample by using thelacZα-based plasmid pSEVA232 in the generation of a screenable metagenomic library. For this, we used a functional screen based on skimmed milk agar and a pH indicator dye as previously reported in literature. Although we effectively identified nine positive clones in the screenings, subsequent experiments revealed that this phenotype was not because of the hydrolytic activity encoded in the metagenomic fragments, but rather due to the insertion of small metagenomic DNA fragmentsin framewithin the coding region of thelacZαalpha gene present in the original vector. We concluded that the current method has a higher tendency for false positive recovery of clones, when used in combination with alacZα-based vector. Finally, we discuss the molecular explanation for positive phenotype recovering and highlight the importance of reporting boundaries in metagenomic screenings methodologies.
Functional genomics of lipid metabolism in the oleaginous yeastRhodosporidium toruloides
Authors: Coradetti Samuel T , Pinel Dominic , Geiselman Gina , Ito Masakazu , Mondo Stephen , Reilly Morgann C , Cheng Ya-Fang , Bauer Stefan , Grigoriev Igor V , Gladden John M , Simmons Blake A , Brem Rachel B , Arkin Adam P , Skerker Jeffrey M
Published: September 2017

The basidomycete yeastRhodosporidium toruloides(a.k.a.Rhodotorula toruloides)accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcodedAgrobacterium tumefaciensT-DNA insertions into theR. toruloidesgenome. We identified 1337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We found that both mitochondrial and peroxisomal enzymes were required for growth on fatty acids, with different peroxisomal enzymes required on different fatty acids. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, as well as genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species, identify key biological processes to be further explored and optimized for production of lipid-based bioproducts, and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.
Simultaneously measuring image features and resolution in live-cell STED images
Authors: Barentine Andrew E. S. , Schroeder Lena K. , Graff Michael , Baddeley David , Bewersdorf Joerg
Published: September 2017

Reliable interpretation and quantification of cellular features in fluorescence microscopy requires an accurate estimate of microscope resolution. This is typically obtained by measuring the image of a non-biological proxy for a point-like object, such as a fluorescent bead. While appropriate for confocal microscopy, bead-based measurements are problematic for Stimulated Emission Depletion (STED) and similar techniques where the resolution depends critically on the choice of fluorophore and acquisition parameters. We demonstrate that for a known geometry, e.g. tubules, the resolution can be accurately measured by fitting a model that accounts for both the Point Spread Function (PSF) and the fluorophore distribution. To address the problem of coupling between tubule diameter and PSF width, we developed a technique, Nested-loop Ensemble PSF (NEP) fitting. NEP fitting enables extraction of the size of cellular features and the PSF in fixed-cell and live-cell images without relying on beads or pre-calibration. We validate our technique using fixed microtubules and apply it to measure the diameter of endoplasmic reticulum tubules in live COS-7 cells. NEP fitting has been implemented as a plugin for the PYthon Microscopy Environment (PYME), a freely available and open source software.
Brain-behavior patterns define a dimensional biotype in medication-naïve adults with attention-deficit hyperactivity disorder
Authors: Lin Hsiang-Yuan , Cocchi Luca , Zalesky Andrew , Lv Jinglei , Perry Alistair , Tseng Wen-Yih Isaac , Kundu Prantik , Breakspear Michael , Gau Susan Shur-Fen
Published: September 2017

Background

Childhood-onset attention-deficit hyperactivity disorder (ADHD) in adults is clinically heterogeneous and commonly presents with different patterns of cognitive deficits. It is unclear if this clinical heterogeneity expresses a dimensional or categorical difference in ADHD.

Methods

We first studied differences in functional connectivity in multi-echo resting-state functional magnetic resonance imaging (rs-fMRI) acquired from 80 medication-naïve adults with ADHD and 123 matched healthy controls. We then used canonical correlation analysis (CCA) to identify latent relationships between symptoms and patterns of altered functional connectivity (dimensional biotype) in patients. Clustering methods were implemented to test if the individual associations between resting-state brain connectivity and symptoms reflected a non-overlapping categorical biotype.

Results

Adults with ADHD showed stronger functional connectivity compared to healthy controls, predominantly between the default-mode, cingulo-opercular and subcortical networks. CCA identified a single mode of brain-symptom co-variation, corresponding to an ADHD dimensional biotype. This dimensional biotype is characterized by a unique combination of altered connectivity correlating with symptoms of hyperactivity-impulsivity, inattention, and intelligence. Clustering analyses did not support the existence of distinct categorical biotypes of adult ADHD.

Conclusions

Overall, our data advance a novel finding that the reduced functional segregation between default-mode and cognitive control networks supports a clinically important dimensional biotype of childhood-onset adult ADHD. Despite the heterogeneity of its presentation, our work suggests that childhood-onset adult ADHD is a single disorder characterized by dimensional brain-symptom mediators.
Untangling Sequences: Behavior vs. External Causes
Authors: Ahmad Subutai , Hawkins Jeff
Published: September 2017

There are two fundamental reasons why sensory inputs to the brain change over time. Sensory inputs can change due to external factors or they can change due to our own behavior. Interpreting behavior-generated changes requires knowledge of how the body is moving, whereas interpreting externally-generated changes relies solely on the temporal sequence of input patterns. The sensory signals entering the neocortex change due to a mixture of both behavior and external factors. The neocortex must disentangle them but the mechanisms are unknown. In this paper, we show that a single neural mechanism can learn and recognize both types of sequences. In the model, cells are driven by feedforward sensory input and are modulated by contextual input. If the contextual input includes information derived from efference motor copies, the cells learn sensorimotor sequences. If the contextual input consists of nearby cellular activity, the cells learn temporal sequences. Through simulation we show that a network containing both types of contextual input automatically separates and learns both types of input patterns. We review experimental data that suggests the upper layers of cortical regions contain the anatomical structure required to support this mechanism.
Superiorab initioIdentification, Annotation and Characterisation of TEs and Segmental Duplications from Genome Assemblies
Authors: Zeng Lu , Kortschak R. Daniel , Raison Joy M. , Bertozzi Terry , Adelson David L.
Published: September 2017

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotateab initiobecause of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensiveab initioRepeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods forab initiorepeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared ourab initiorepeat annotations for 7 genome assemblies (1 unpublished) to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.

Author summary

Transposable elements (TEs) are interspersed repetitive DNA sequences, also known as ‘jumping genes’, because of their ability to replicate in to new genomic locations. TEs account for a significant proportion of all eukaryotic genomes. Previous studies have found that TE insertions have contributed to new genes, coding sequences and regulatory regions. They also play an important role in genome evolution. Therefore, we developed a novel,ab initioapproach for identifying and annotating repetitive elements. The idea is simple: define a “repeat” as any sequence that occurs at least twice in the genome. Ourab initiomethod is able to identify species-specific TEs with high sensitivity and accuracy including both TEs and segmental duplications. Because of the high degree of sequence identity used in our method, the TEs we find are less diverged and may still be active. We also retain all the information that links identified repeat consensus sequences to their genome intervals, permiting direct evolutionary analysis of the TE families we identify.
The partial duplication of an E3-ligase gene inTriticeaespecies mediates resistance to powdery mildew fungi
Authors: Rajaraman Jeyaraman , Douchkov Dimitar , Lück Stefanie , Hensel Götz , Nowara Daniela , Pogoda Maria , Rutten Twan , Meitzel Tobias , Höfle Caroline , Hückelhoven Ralph , Klinkenberg Jörn , Trujillo Marco , Bauer Eva , Schmutzer Thomas , Himmelbach Axel , Mascher Martin , Lazzari Barbara , Stein Nils , Kumlehn Jochen , Schweizer Patrick
Published: September 2017

In plant-pathogen interactions, components of the plant ubiquitination machinery are preferred targets of pathogen-encoded effectors suppressing defense responses or co-opting host cellular functions for accommodation. Here, we employed transient and stable gene silencing-and over-expression systems inHordeum vulgare(barley) to study the function ofHvARM1(forH. vulgare Armadillo 1), a partial gene duplicate of the U-box/armadillo-repeat E3 ligase HvPUB15(forH. vulgare Plant U-Box 15). The partialARM1gene was derived from an ancient gene-duplication event in a common ancestor of theTriticeaetribe of grasses comprising the major crop speciesH. vulgare,Triticum aestivumandSecale cereale. The barley geneHvARM1contributed to quantitative host as well as nonhost resistance to the biotrophic powdery mildew fungusBlumeria graminis, and allelic variants were found to be associated with powdery mildew-disease severity. Both HvPUB15 and HvARM1 proteins interacted in yeast and plant cells with the susceptibility-related, plastid-localized barley homologs of THF1 (for Thylakoid formation 1) and of ClpS1 (for Clp-protease adaptor S1) ofArabidopsis thaliana. The results suggest a neo-functionalizationHvARM1to increase resistance against powdery mildew and provide a link to plastid function in susceptibility to biotrophic pathogen attack.