bluuebunny/crossref_metadata_2025 huggingface dataset:
Tacrolimus-Induced Hyponatremia in Lung Transplant Recipients: A Case Series
Authors: Banks Paul N. , Omar Ashraf , Walia Rajat , Bhalla Sarabjit , Chong Yun , Tokman Sofya
Published: March 2018

Background

Lung transplant recipients are treated with a 3-drug immunosuppressive regimen that consists of a calcineurin inhibitor, an antiproliferative agent, and a corticosteroid. Calcineurin inhibitors are the backbone of this regimen, and tacrolimus is used more often than cyclosporine, because tacrolimus is the more potent of the two agents. Tacrolimus-induced hyponatremia has been described among kidney transplant recipients, but not among lung transplant recipients.

Methods

We conducted a retrospective chart review of patients who underwent lung transplant at our institution and went on to develop severe hyponatremia.

Results

We identified 5 lung transplant recipients who developed severe hyponatremia after lung transplantation (median nadir, 117 mEq/L; interquartile range, 116-119 mEq/L). Time to development of hyponatremia ranged from 3 to 85 days posttransplant. Hyponatremia persisted in these patients despite fluid restriction, salt tablets, diuretics, and fludrocortisone therapy. Hyponatremia resolved in 3 patients and significantly improved in 2 patients after they were switched from a tacrolimus-based immunosuppressive regimen to a cyclosporine-based regimen.

Conclusion

Transitioning from a tacrolimus- to a cyclosporine-based immunosuppressive regimen may resolve or improve severe hyponatremia in lung transplant recipients.
Effects of sea ice on Arctic biota: an emerging crisis discipline
Authors: Macias-Fauria Marc , Post Eric
Published: March 2018

The rapid decline in Arctic sea ice (ASI) extent, area and volume during recent decades is occurring before we can understand many of the mechanisms through which ASI interacts with biological processes both at sea and on land. As a consequence, our ability to predict and manage the effects of this enormous environmental change is limited, making this a
crisis discipline
. Here, we propose a framework to study these effects, defining
direct effects
as those acting on life-history events of Arctic biota, and
indirect effects
, where ASI acts upon biological systems through chains of events, normally involving other components of the physical system and/or biotic interactions. Given the breadth and complexity of ASI's effects on Arctic biota, Arctic research requires a truly multidisciplinary approach to address this issue. In the absence of effective global efforts to tackle anthropogenic global warming, ASI will likely continue to decrease, compromising the conservation of many ASI-related taxonomic groups and ecosystems. Mitigation actions will rely heavily on the knowledge acquired on the mechanisms and components involved with the biological effects of ASI.
Collective regulation of cell motility using an accurate density-sensing system
Authors: d'Alessandro Joseph , Mas Lauriane , Aubry Laurence , Rieu Jean-Paul , Rivière Charlotte , Anjard Christophe
Published: March 2018

The capacity of living cells to sense their population density and to migrate accordingly is essential for the regulation of many physiological processes. However, the mechanisms used to achieve such functions are poorly known. Here, based on the analysis of multiple trajectories of vegetativeDictyostelium discoideumcells, we investigate such a system extensively. We show that the cells secrete a high-molecular-weight quorum-sensing factor (QSF) in their medium. This extracellular signal induces, in turn, a reduction of the cell movements, in particular, through the downregulation of a mode of motility with high persistence time. This response appears independent of cAMP and involves a G-protein-dependent pathway. Using a mathematical analysis of the cells' response function, we evidence a negative feedback on the QSF secretion, which unveils a powerful generic mechanism for the cells to detect when they exceed a density threshold. Altogether, our results provide a comprehensive and dynamical view of this system enabling cells in a scattered population to adapt their motion to their neighbours without physical contact.
Cryo-EM structure of the nucleosome containing the
ALB1
enhancer DNA sequence
Authors: Takizawa Yoshimasa , Tanaka Hiroki , Machida Shinichi , Koyama Masako , Maehara Kazumitsu , Ohkawa Yasuyuki , Wade Paul A. , Wolf Matthias , Kurumizaka Hitoshi
Published: March 2018

Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the
ALB1
gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The
ALB1
enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the
ALB1
enhancer (N1) sequence, by cryogenic electron microscopy at 4.0 Å resolution. The nucleosome structure with the
ALB1
enhancer DNA is not significantly different from the previously reported nucleosome structure with the Widom 601 DNA. Interestingly, in the nucleosomes, the
ALB1
enhancer DNA contains local flexible regions, as compared to the Widom 601 DNA. Consistently, DNaseI treatments revealed that, in the nucleosome, the
ALB1
enhancer (N1) DNA is more accessible than the Widom 601 sequence. The histones also associated less strongly with the
ALB1
enhancer (N1) DNA than the Widom 601 DNA in the nucleosome. Therefore, the local histone–DNA contacts may be responsible for the enhanced DNA accessibility in the nucleosome with the
ALB1
enhancer DNA.
Surveillance-ready transcription: nuclear RNA decay as a default fate
Authors: Bresson Stefan , Tollervey David
Published: March 2018

Eukaryotic cells synthesize enormous quantities of RNA from diverse classes, most of which are subject to extensive processing. These processes are inherently error-prone, and cells have evolved robust quality control mechanisms to selectively remove aberrant transcripts. These surveillance pathways monitor all aspects of nuclear RNA biogenesis, and in addition remove nonfunctional transcripts arising from spurious transcription and a host of non-protein-coding RNAs (ncRNAs). Surprisingly, this is largely accomplished with only a handful of RNA decay enzymes. It has, therefore, been unclear how these factors efficiently distinguish between functional RNAs and huge numbers of diverse transcripts that must be degraded. Here we describe how bona fide transcripts are specifically protected, particularly by 5′ and 3′ modifications. Conversely, a plethora of factors associated with the nascent transcripts all act to recruit the RNA quality control, surveillance and degradation machinery. We conclude that initiating RNAPII is ‘surveillance ready’, with degradation being a default fate for all transcripts that lack specific protective features. We further postulate that this promiscuity is a key feature that allowed the proliferation of vast numbers of ncRNAs in eukaryotes, including humans.
A study of laser surface treatment in bonded repair of composite aircraft structures
Authors: Li Shaolong , Sun Ting , Liu Chang , Yang Wenfeng , Tang Qingru
Published: March 2018

Surface pre-treatment is one of the key processes in bonded repair of aircraft carbon fibre reinforced polymer composites. This paper investigates the surface modification of physical and chemical properties by laser ablation and conventional polish treatment techniques. Surface morphology analysed by laser scanning confocal microscopy and scanning electron microscopy showed that a laser-treated surface displayed higher roughness than that of a polish-treated specimen. The laser-treated laminate exhibited more functional groups in the form of O 1 s/C 1 s atomic ratio of 30.89% for laser-treated and 20.14% for polish-treated as evidenced by X-ray photoelectron spectroscopy observation. Contact angle goniometry demonstrated that laser treatment can provide increased surface free energy and wettability. In the light of mechanical interlocking, molecular bonding and thermodynamics theories on adhesion, laser etching process displayed enhanced bonding performance relative to the polishing surface treatment. These properties resulted in an increased single lap shear strength and a cohesive failure mode for laser etching while an adhesive failure mode occurred in polish-treated specimen.
Simplified models of the symmetric single-pass parallel-plate counterflow heat exchanger: a tutorial
Authors: Pickard William F. , Abraham-Shrauner Barbara
Published: March 2018

The heat exchanger is important in practical thermal processes, especially those of (i) the molten-salt storage schemes, (ii) compressed air energy storage schemes and (iii) other load-shifting thermal storage presumed to undergird a Smart Grid. Such devices, although central to the utilization of energy from sustainable (but intermittent) renewable sources, will be unfamiliar to many scientists, who nevertheless need a working knowledge of them. This tutorial paper provides a largely self-contained
conceptual
introduction for such persons. It begins by
modelling
a novel quantized exchanger,
1
impractical as a device, but useful for comprehending the underlying thermophysics. It then reviews the one-dimensional steady-state idealization which demonstrates that effectiveness of heat transfer increases monotonically with (device length)/(device throughput). Next, it presents a two-dimensional steady-state idealization for plug flow and from it derives a novel formula for effectiveness of transfer; this formula is then shown to agree well with a finite-difference time-domain solution of the two-dimensional idealization under Hagen–Poiseuille flow. These results are consistent with a conclusion that effectiveness of heat exchange can approach unity, but may involve unwelcome trade-offs among device cost, size and throughput.
Incorporation of Mn
2+
into CdSe quantum dots by chemical bath co-deposition method for photovoltaic enhancement of quantum dot-sensitized solar cells
Authors: Zhang Chenguang , Liu Shaowen , Liu Xingwei , Deng Fei , Xiong Yan , Tsai Fang-Chang
Published: March 2018

A photoelectric conversion efficiency (PCE) of 4.9% was obtained under 100 mW cm
−2
illumination by quantum-dot-sensitized solar cells (QDSSCs) using a CdS/Mn : CdSe sensitizer. CdS quantum dots (QDs) were deposited on a TiO
2
mesoporous oxide film by successive ionic layer absorption and reaction. Mn
2+
doping into CdSe QDs is an innovative and simple method—chemical bath co-deposition, that is, mixing the Mn ion source with CdSe precursor solution for Mn : CdSe QD deposition. Compared with the CdS/CdSe sensitizer without Mn
2+
incorporation, the PCE was increased from 3.4% to 4.9%. The effects of Mn
2+
doping on the chemical, physical and photovoltaic properties of the QDSSCs were investigated by energy dispersive spectrometry, absorption spectroscopy, photocurrent density–voltage characteristics and electrochemical impedance spectroscopy. Mn-doped CdSe QDs in QDSSCs can obtain superior light absorption, faster electron transport and slower charge recombination than CdSe QDs.
Adopted daughters and adopted daughters-in-law in Taiwan: a mortality analysis
Authors: Mattison Siobhán M. , Seabright Edmond , Reynolds Adam Z. , Cao Jingzhe (Bill) , Brown Melissa J. , Feldman Marcus W.
Published: March 2018

Adoption is sometimes considered paradoxical from an evolutionary perspective because the costs spent supporting an adopted child would be better spent on rearing one's own. Kin selection theory is commonly used to solve this paradox, because the adoption of closely related kin contributes to the inclusive fitness of the adoptive parent. In this paper, we perform a novel test of kin selection theory in the context of adoption by asking whether adopted daughters-in-law, who contribute directly (i.e. genealogically) to the perpetuation of their adoptive families' lineages, experience lower mortality than daughters adopted for other purposes in historical Taiwan. We show that both classes of adopted daughter suffer lower mortality than biological daughters, but that the protective effect of adoption is stronger among daughters who were not adopted with the intention of perpetuating the family lineage. We speculate as to the possible benefits of such a pattern and emphasize the need to move beyond typological definitions of adoption to understand the specific costs and benefits involved in different forms of caring for others' children.
Cleaner fish escape salmon farms and hybridize with local wrasse populations
Authors: Faust Ellika , Halvorsen Kim Tallaksen , Andersen Per , Knutsen Halvor , André Carl
Published: March 2018

The genetic impact of farmed fish escaping aquaculture is a highly debated issue. However, non-target species, such as cleaner fish used to remove sea lice from farmed fish, are rarely considered. Here, we report that wild corkwing wrasse (Symphodus melops), which are transported long distances to be used as cleaner fish in salmon farms, escape and hybridize with local populations. Recently, increasing numbers of corkwing wrasse have been reported in Flatanger in Norway, north of its described distribution range, an area heavily relying on the import of cleaner fish from Skagerrak. Using genetic markers identified with 2bRAD sequencing, we show that, although the Flatanger population largely is a result of a northward range expansion, there is also evidence of considerable gene flow from southern populations in Skagerrak and Kattegat. Of the 40 corkwing wrasses sampled in Flatanger, we discovered two individuals with clear southern genotypes, one first-generation hybrid, and 12 potential second-generation hybrids. In summary, we provide evidence that corkwing wrasse escape from fish farms and hybridize with local populations at the leading edge of an ongoing range expansion. Although the magnitude and significance of escapees warrant further investigation, these results should be taken into consideration in the use of translocated cleaner fish.
Lepidosaurian diversity in the Mesozoic–Palaeogene: the potential roles of sampling biases and environmental drivers
Authors: Cleary Terri J. , Benson Roger B. J. , Evans Susan E. , Barrett Paul M.
Published: March 2018

Lepidosauria is a speciose clade with a long evolutionary history, but there have been few attempts to explore its taxon richness through time. Here we estimate patterns of terrestrial lepidosaur genus diversity for the Triassic–Palaeogene (252–23 Ma), and compare observed and sampling-corrected richness curves generated using Shareholder Quorum Subsampling and classical rarefaction. Generalized least-squares regression (GLS) is used to investigate the relationships between richness, sampling and environmental proxies. We found low levels of richness from the Triassic until the Late Cretaceous (except in the Kimmeridgian–Tithonian of Europe). High richness is recovered for the Late Cretaceous of North America, which declined across the K–Pg boundary but remained relatively high throughout the Palaeogene. Richness decreased following the Eocene–Oligocene Grande Coupure in North America and Europe, but remained high in North America and very high in Europe compared to the Late Cretaceous; elsewhere data are lacking. GLS analyses indicate that sampling biases (particularly, the number of fossil collections per interval) are the best explanation for long-term face-value genus richness trends. The lepidosaur fossil record presents many problems when attempting to reconstruct past diversity, with geographical sampling biases being of particular concern, especially in the Southern Hemisphere.
Sensitive colorimetric assay using insulin G-quadruplex aptamer arrays on DNA nanotubes coupled with magnetic nanoparticles
Authors: Rafati A. , Zarrabi A. , Abediankenari S. , Aarabi M. , Gill P.
Published: March 2018

Described here is a methodology for fabrication of a sensitive colorimetric nanoassay for measurement of insulin using G-quadruplex aptamer arrays on DNA nanotubes (DNTs) coupled with magnetic nanoparticles. The spectroscopic findings (e.g. visible spectra, velocity assay and limit of detection determination) indicated a highly sensitive performance of this new nanoassay in comparison to those results obtained from the insulin assay with non-arrayed aptamers. The clinical performance statistics (i.e. paired sample
t
-test, Bland–Altman plot and scatter diagram) from the newly developed assay and the enzyme-linked immunosorbent assay suggested its reliable precision and its acceptable repeatability for measurement of insulin in human sera. This is, to our knowledge, the first study for the application of magnetic nanoparticle-coupled DNTs for carrying G-quadruplex aptamers for detection of biomolecules (such as insulin) in human serum.
Hypothesized diprotomeric enzyme complex supported by stochastic modelling of palytoxin-induced Na/K pump channels
Authors: Vilallonga Gabriel D. , de Almeida Antônio-Carlos G. , Ribeiro Kelison T. , Campos Sergio V. A. , Rodrigues Antônio M.
Published: March 2018

The sodium–potassium pump (Na
+
/K
+
pump) is crucial for cell physiology. Despite great advances in the understanding of this ionic pumping system, its mechanism is not completely understood. We propose the use of a statistical model checker to investigate palytoxin (PTX)-induced Na
+
/K
+
pump channels. We modelled a system of reactions representing transitions between the conformational substates of the channel with parameters, concentrations of the substates and reaction rates extracted from simulations reported in the literature, based on electrophysiological recordings in a whole-cell configuration. The model was implemented using the UPPAAL-SMC platform. Comparing simulations and probabilistic queries from stochastic system semantics with experimental data, it was possible to propose additional reactions to reproduce the single-channel dynamic. The probabilistic analyses and simulations suggest that the PTX-induced Na
+
/K
+
pump channel functions as a diprotomeric complex in which protein–protein interactions increase the affinity of the Na
+
/K
+
pump for PTX.
How successful are mutants in multiplayer games with fluctuating environments? Sojourn times, fixation and optimal switching
Authors: Baron Joseph W. , Galla Tobias
Published: March 2018

Using a stochastic model, we investigate the probability of fixation, and the average time taken to achieve fixation, of a mutant in a population of wild-types. We do this in a context where the environment in which the competition takes place is subject to stochastic change. Our model takes into account interactions which can involve multiple participants. That is, the participants take part in multiplayer games. We find that under certain circumstances, there are environmental switching dynamics which minimize the time that it takes for the mutants to fixate. To analyse the dynamics more closely, we develop a method by which to calculate the sojourn times for general birth–death processes in fluctuating environments.
Neopterygian phylogeny: the merger assay
Authors: López-Arbarello Adriana , Sferco Emilia
Published: March 2018

The phylogenetic relationships of the recently described genus†Ticinolepisfrom the Middle Triassic of the Monte San Giorgio are explored through cladistic analyses of the so far largest morphological dataset for fossil actinopterygians, including representatives of the crown-neopterygian clades Halecomorphi, Ginglymodi and Teleostei, and merging the characters from previously published systematic studies together with newly proposed characters.†Ticinolepisis retrieved as the most basal Ginglymodi and our results support the monophyly of Teleostei and Holostei, as well as Halecomorphi and Ginglymodi within the latter clade. The patterns of relationships within these clades mostly agree with those of previous studies, although a few important differences require future research. According to our results, ionoscopiforms are not monophyletic, caturids are not amiiforms and leptolepids and luisiellids form a monophyletic clade. Our phylogenetic hypothesis confirms the rapid radiation of the holostean clades Halecomorphi and Ginglymodi during the Early and Middle Triassic and the radiation of pholidophoriform teleosts during the Late Triassic. Crown-group Halecomorphi have an enormous ghost lineage throughout half of the Mesozoic, but ginglymodians and teleosts show a second radiation during the Early Jurassic. The crown-groups of Halecomorphi, Ginglymodi and Teleostei originated within parallel events of radiation during the Late Jurassic.
Small nanoparticles, surface geometry and contact forces
Authors: Takato Yoichi , Benson Michael E. , Sen Surajit
Published: March 2018

In this molecular dynamics study, we examine the local surface geometric effects of the normal impact force between two approximately spherical nanoparticles that collide in a vacuum. Three types of surface geometries—(i) crystal facets, (ii) sharp edges, and (iii) amorphous surfaces of small nanoparticles with radii
R
<10 nm—are considered. The impact forces are compared with their macroscopic counterparts described by nonlinear contact forces based on Hertz contact mechanics. In our simulations, edge and amorphous surface contacts with weak surface energy reveal that the average impact forces are in excellent agreement with the Hertz contact force. On the other hand, facet collisions show a linearly increasing force with increasing compression. Our results suggest that the nearly spherical nanoparticles are likely to enable some nonlinear dynamic phenomena, such as breathers and solitary waves observed in granular materials, both originating from the nonlinear contact force.
Migratory behaviour predicts greater parasite diversity in ungulates
Authors: Teitelbaum Claire S. , Huang Shan , Hall Richard J. , Altizer Sonia
Published: March 2018

Long-distance animal movements can increase exposure to diverse parasites, but can also reduce infection risk through escape from contaminated habitats or culling of infected individuals. These mechanisms have been demonstrated within and between populations in single-host/single-parasite interactions, but how long-distance movement behaviours shape parasite diversity and prevalence across host taxa is largely unknown. Using a comparative approach, we analyse the parasite communities of 93 migratory, nomadic and resident ungulate species. We find that migrants have higher parasite species richness than residents or nomads, even after considering other factors known to influence parasite diversity, such as body size and host geographical range area. Further analyses support a novel ‘environmental tracking' hypothesis, whereby migration allows parasites to experience environments favourable to transmission year-round. In addition, the social aggregation and large group sizes that facilitate migration might increase infection risk for migrants. By contrast, we find little support for previously proposed hypotheses, including migratory escape and culling, in explaining the relationship between host movement and parasitism in mammals at this cross-species scale. Our findings, which support mechanistic links between long-distance movement and increased parasite richness at the species level, could help predict the effects of future environmental change on parasitism in migratory animals.
Patterns of divergence in the morphology of ceratopsian dinosaurs: sympatry is not a driver of ornament evolution
Authors: Knapp Andrew , Knell Robert J. , Farke Andrew A. , Loewen Mark A. , Hone David W. E.
Published: March 2018

Establishing the origin and function of unusual traits in fossil taxa provides a crucial tool in understanding macroevolutionary patterns over long periods of time. Ceratopsian dinosaurs are known for their exaggerated and often elaborate horns and frills, which vary considerably between species. Many explanations have been proposed for the origin and evolution of these ‘ornamental’ traits, from predator defence to socio-sexual dominance signalling and, more recently, species recognition. A key prediction of the species recognition hypothesis is that two or more species possessing divergent ornamental traits should have been at least partially sympatric. For the first time to our knowledge, we test this hypothesis in ceratopsians by conducting a comparison of the morphological characters of 46 species. A total of 350 ceratopsian cladistic characters were categorized as either ‘internal’, ‘display’ (i.e. ornamental) or ‘non display’. Patterns of diversity of these characters were evaluated across 1035 unique species pairs. Display characters were found to diverge rapidly overall, but sympatric species were not found to differ significantly in their ornamental disparity from non-sympatric species, regardless of phylogenetic distance. The prediction of the species recognition hypothesis, and thus the idea that ornamentation evolved as a species recognition mechanism, has no statistical support among known ceratopsians.
Three dimensional two-photon imaging of neuronal activity in freely moving mice using a miniature fiber coupled microscope with active axial-scanning
Authors: Ozbay Baris N. , Futia Gregory L. , Ma Ming , Bright Victor M. , Gopinath Juliet T. , Hughes Ethan G. , Restrepo Diego , Gibson Emily A.
Published: March 2018

We present a miniature head mounted two-photon fiber-coupled microscope (2P-FCM) for neuronal imaging with active axial focusing enabled using a miniature electrowetting lens. Full three-dimensional two-photon imaging of GCaMP6s showing individual neuron activity in multiple focal planes was achieved in a freely-moving mouse. Two-color simultaneous imaging of GFP and tdTomato fluorescence is also demonstrated. Additionally, dynamic control of the axial scanning of the electrowetting lens allows tilting of the focal plane enabling cells in multiple focal planes to be imaged simultaneously. Two-photon imaging allows increased penetration depth in tissue yielding a working distance of 450 μm with an additional 180 μm of active axial focusing. The objective NA is 0.45 with a lateral resolution of 1.8 μm, an axial resolution of 10 μm, and a field-of-view of 240 μm diameter. The 2P-FCM has a weight of only ∼2.5 g and is capable of repeatable and stable head-attachment. The 2P-FCM with dynamic axial scanning provides a new capability to record from functionally distinct neuronal layers, opening new opportunities in neuroscience research.
Qoala-T: A supervised-learning tool for quality control of automatic segmented MRI data
Authors: Klapwijk Eduard T. , van de Kamp Ferdi , van der Meulen Mara , Peters Sabine , Wierenga Lara M.
Published: March 2018

Performing quality control to detect image artifacts and data-processing errors is crucial in structural magnetic resonance imaging, especially in developmental studies. Currently, many studies rely on visual inspection by trained raters for quality control. The subjectivity of these manual procedures lessens comparability between studies, and with growing study sizes quality control is increasingly time consuming. In addition, both inter-rater as well as intra-rater variability of manual quality control is high and may lead to inclusion of poor quality scans and exclusion of scans of usable quality. In the current study we present the Qoala-T tool, which is an easy and free to use supervised-learning model to reduce rater bias and misclassification in manual quality control procedures. First, we manually rated quality of N = 784 FreeSurfer-processed T1-weighted scans. Different supervised-learning models were then compared to predict manual quality ratings. Results show that the Qoala-T tool using random forests is able to predict scan quality with both high sensitivity and specificity (mean area under the curve (AUC) = 0.98). In addition, the Qoala-T tool was also able to adequately predict the quality of a novel unseen dataset (N = 112; mean AUC = 0.95). These outcomes indicate that using Qoala-T in other datasets could greatly reduce the time needed for quality control. More importantly, this procedure could further help to reduce variability related to manual quality control, thereby benefiting the comparability of data quality between studies.
RppH can faithfully replace TAP to allow cloning of 5’-triphosphate carrying small RNAs
Authors: Almeida Miguel Vasconcelos , de Jesus Domingues António Miguel , Lukas Hanna , Mendez-Lago Maria , Ketting René F.
Published: March 2018

RNA interference was first described in the nematode Caenorhabditis elegans. Ever since, several new endogenous small RNA pathways have been described and characterized to different degrees. Much like plants, but unlike Drosophila and mammals, worms have RNA-dependent RNA Polymerases (RdRPs) that directly synthesize small RNAs using other transcripts as a template. The very prominent secondary small interfering RNAs, also called 22G-RNAs, produced by the RdRPs RRF-1 and EGO-1 in C. elegans, maintain the 5’ triphosphate group, stemming from RdRP activity, also after loading into an Argonaute protein. This creates a technical issue, since 5’PPP groups decrease cloning efficiency for small RNA sequencing. To increase cloning efficiency of these small RNA species, a common practice in the field is the treatment of RNA samples, prior to library preparation, with Tobacco Acid pyrophosphatase (TAP). Recently, TAP production and supply was discontinued, so an alternative must be devised. We turned to RNA 5’ pyrophosphohydrolase (RppH), a commercially available pyrophosphatase isolated from E. coli. Here we directly compare TAP and RppH in their use for small RNA library preparation. We show that RppH-treated samples faithfully recapitulate TAP-treated samples. Specifically, there is enrichment for 22G-RNAs and mapped small RNA reads show no small RNA transcriptome-wide differences between RppH and TAP treatment. We propose that RppH can be used as a small RNA pyrophosphatase to enrich for triphosphorylated small RNA species and show that RppH- and TAP-derived datasets can be used in direct comparison.
High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions
Authors: Aprianto Rieza , Slager Jelle , Holsappel Siger , Veening Jan-Willem
Published: March 2018

Streptococcus pneumoniae is an opportunistic human pathogen that typically colonizes the nasopharyngeal passage and causes lethal disease in other host niches such as the lung or the meninges. How pneumococcal genes are expressed and regulated at the different stages of its life cycle, as commensal or as pathogen, has not been entirely described. To chart the transcriptional responses of S. pneumoniae, we quantified the transcriptome under 22 different infection-relevant conditions. The transcriptomic compendium exposed a high level of dynamic expression and, strikingly, all annotated pneumococcal genomic features were expressed in at least one of the studied conditions. By computing the correlation of gene expression of every two genes across all studied conditions, we created a co-expression matrix that provides valuable information on both operon structure and regulatory processes. The co-expression data is highly consistent with well-characterized operons and regulons, such as the PyrR, ComE and ComX regulons, and has allowed us to identify a new member of the competence regulon. Finally, we created an interactive data center named PneumoExpress (www.veeninglab.com/pneumoexpress) that enables users to access the expression data as well as the co-expression matrix in an intuitive and efficient manner, providing a valuable resource to the pneumococcal research community.
Enhancing Simulations With Intra-Subject Variability for Improved Psychophysical Assessments
Authors: Rinderknecht Mike D. , Lambercy Olivier , Gassert Roger
Published: March 2018

Psychometric properties of perceptual assessments, like reliability, depend on the stochastic properties of psychophysical sampling procedures resulting in method variability, as well as inter- and intra-subject variability. Method variability is commonly minimized by optimizing sampling procedures through computer simulations. Inter-subject variability is inherent in the population of interest and cannot be acted upon. In contrast, intra-subject variability introduced by confounds cannot be simply quantified from experimental data, as this data also includes method variability. Therefore, this aspect is generally neglected when developing assessments. Yet, comparing method variability and intra-subject variability could give insights on whether effort should be invested in optimizing the sampling procedure, or in addressing potential confounds instead. We propose a new approach to estimate and model intra-subject variability of psychometric functions by combining computer simulations and behavioral data, and to account for it when simulating experiments. The approach was illustrated in a real-world scenario of proprioceptive difference threshold assessments. The behavioral study revealed a test-retest reliability of 0.212. Computer simulations lacking intra-subject variability predicted a reliability of 0.768, whereas the new approach including an intra-subject variability model lead to a realistic estimate of reliability (0.207). Such a model also allows computing the theoretically maximally attainable reliability (0.552) assuming an ideal sampling procedure. Comparing the reliability estimates when exclusively accounting for method variability versus intra-subject variability reveals that intra-subject variability should be reduced by addressing confounds and that only optimizing the sampling procedure may be insufficient to achieve a high reliability. The new approach also allows accelerating the development of assessments by simulating the converging behavior of the reliability confidence interval with a large number of subjects and retests without requiring additional experiments. Having such a tool of predictive value is especially important for target populations where time is scarce, such as for assessments in clinical settings.
Identification ofciselements for spatio-temporal control of DNA replication
Authors: Sima Jiao , Chakraborty Abhijit , Dileep Vishnu , Michalski Marco , Rivera-Mulia Juan Carlos , Trevilla-Garcia Claudia , Klein Kyle N. , Bartlett Daniel , Washburn Brian K. , Paulsen Michelle T. , Vera Daniel , Nora Elphège P. , Kraft Katerina , Mundlos Stefan , Bruneau Benoit G. , Ljungman Mats , Fraser Peter , Ay Ferhat , Gilbert David M.
Published: March 2018

The temporal order of DNA replication (replication timing, RT) is highly coupled with genome architecture, butcis-elements regulating spatio-temporal control of replication have remained elusive. We performed an extensive series of CRISPR mediated deletions and inversions and high-resolution capture Hi-C of a pluripotency associated domain (DppA2/4) in mouse embryonic stem cells. Whereas CTCF mediated loops and chromatin domain boundaries were dispensable, deletion of three intra-domain prominent CTCF-independent 3D contact sites caused a domain-wide delay in RT, shift in sub-nuclear chromatin compartment and loss of transcriptional activity, These “early replication control elements” (ERCEs) display prominent chromatin features resembling enhancers/promoters and individual and pair-wise deletions of the ERCEs confirmed their partial redundancy and interdependency in controlling domain-wide RT and transcription. Our results demonstrate that discretecis-regulatory elements mediate domain-wide RT, chromatin compartmentalization, and transcription, representing a major advance in dissecting the relationship between genome structure and function.

Highlights

cis-elements (ERCEs) regulate large scale chromosome structure and function

Multiple ERCEs cooperatively control domain-wide replication

ERCEs harbor prominent active chromatin features and form CTCF-independent loops

ERCEs enable genetic dissection of large-scale chromosome structure-function.
A chemoproteomic portrait of the oncometabolite fumarate
Authors: Kulkarni Rhushikesh A. , Bak Daniel W. , Wei Darmood , Bergholtz Sarah E. , Briney Chloe A. , Shrimp Jonathan H. , Thorpe Abigail L. , Bavari Arissa , Alpsoy Aktan , Levy Michaella , Florens Laurence , Washburn Michael P. , Dykhuizen Emily C. , Frizzell Norma , Weerapana Eranthie , Linehan W. Marston , Meier Jordan L.
Published: March 2018

Hereditary cancer disorders often provide an important window into novel mechanisms supporting tumor growth and survival. Understanding these mechanisms and developing biomarkers to identify their presence thus represents a vital goal. Towards this goal, here we report a chemoproteomic map of the covalent targets of fumarate, an oncometabolite whose accumulation marks the genetic cancer predisposition syndrome hereditary leiomyomatosis and renal cell carcinoma (HLRCC). First, we validate the ability of known and novel chemoproteomic probes to report on fumarate reactivity in vitro. Next, we apply these probes in concert with LC-MS/MS to identify cysteine residues sensitive to either fumarate treatment or fumarate hydratase (FH) mutation in untransformed and human HLRCC cell models, respectively. Mining this data to understand the structural determinants of fumarate reactivity reveals an unexpected anti-correlation with nucleophilicity, and the discovery of a novel influence of pH on fumarate-cysteine interactions. Finally, we show that many fumarate-sensitive and FH-regulated cysteines are found in functional protein domains, and perform mechanistic studies of a fumarate-sensitive cysteine in SMARCC1 that lies at a key protein-protein interface in the SWI-SNF tumor suppressor complex. Our studies provide a powerful resource for understanding the influence of fumarate on reactive cysteine residues, and lay the foundation for future efforts to exploit this distinct aspect of oncometabolism for cancer diagnosis and therapy.
Quantitative variation in female sensory structures supports species recognition and intraspecific mate choice functions in damselflies
Authors: Barnard Alexandra A. , Masly John P.
Published: March 2018

Males and females exchange signals prior to mating that convey information such as sex, species identity, or individual condition. Tactile signals relayed during physical contact between males and females before and during mating appear to be important for mate choice and reproductive isolation in some animals. However, compared to our understanding of visual, auditory, and chemical signals, we know little about the importance of tactile signals in mating decisions. Among North American damselflies in the genusEnallagma(Odonata: Coenagrionidae) species-specific tactile stimulation contributes to reproductive isolation between species and may also be important for intraspecific mate choice. We quantified several mechanosensory sensilla phenotypes on the female thorax among multiple sympatric and allopatric populations of twoEnallagmaspecies that occasionally interbreed in nature. Although each species differed in features of sensilla distribution within the thoracic plates, we found no strong evidence of reproductive character displacement among the sensilla traits we measured in regions of sympatry. However, substantial variation of sensilla traits was observed within populations of both species. Our results suggest that species-specific placement of female mechanoreceptors appears sufficient for species recognition, but mechanosensor variation among females within species may be important for mate choice.
Phenotypes associated with genes encoding drug targets are predictive of clinical trial side effects
Authors: Nguyen Phuong A. , Deaton Aimee M. , Nioi Paul , Ward Lucas D.
Published: March 2018

Biomedical scientists face major challenges in developing novel drugs for unmet medical needs. Only a small fraction of early drug programs progress to the market, due to safety and efficacy failures, despite extensive efforts to predict drug and target safety as early as possible using a variety of assays in vitro and in preclinical species. In principle, characterizing the effect of natural variation in the genes encoding drug targets should present a powerful alternate approach to predict not only whether a protein will be an effective drug target, but also whether a protein will be an inherently safe drug target, while avoiding the challenges of translating biology from experiments in non-human species. We have embarked on a retrospective analysis, demonstrating for the first time a statistical link between the organ systems involved in genetic syndromes of drug target genes and the organ systems in which side effects are observed clinically. Across 1,819 drugs and 21 organ system phenotype categories analyzed, drug side effects are more likely to occur in organ systems where there is genetic evidence of a link between the drug target and a phenotype involving that organ system, compared to when there is no such genetic evidence (30.0% vs 19.2%; OR = 1.80). Conversely, we find that having genetic evidence of a Mendelian syndrome involving a drug target in which a certain organ system is unaffected decreases the likelihood that side effects will manifest in that organ system, relative to having no informative syndrome (18.5% vs 20.2%; OR = 0.89). We find a relationship between genetics and side effects even when controlling for known confounders such as drug delivery route and indication. We highlight examples where genetics of drug targets could have anticipated side effects observed during clinical trials. This result suggests that human genetic data should be routinely used to predict potential safety issues associated with novel drug targets. This may lead to selection of better targets, appropriate monitoring of putative side effects early in development, reduction of the use of preclinical animal experiments, and ultimately increased success of molecules. Furthermore, deeply phenotyping human knockouts will be critically important to understand the full spectrum of effects that a new drug may elicit.
Marionette:E. colicontaining 12 highly-optimized small molecule sensors
Authors: Meyer Adam J. , Segall-Shapiro Thomas H. , Voigt Christopher A.
Published: March 2018

Cellular processes are carried out by many interacting genes and their study and optimization requires multiple levers by which they can be independently controlled. The most common method is via a genetically-encoded sensor that responds to a small molecule (an “inducible system”). However, these sensors are often suboptimal, exhibiting high background expression and low dynamic range. Further, using multiple sensors in one cell is limited by cross-talk and the taxing of cellular resources. Here, we have developed a directed evolution strategy to simultaneously select for less background, high dynamic range, increased sensitivity, and low crosstalk. Libraries of the regulatory protein and output promoter are built based on random and rationally-guided mutations. This is applied to generate a set of 12 high-performance sensors, which exhibit >100-fold induction with low background and cross-reactivity. These are combined to build a single “sensor array” and inserted into the genomes ofE. coliMG1655 (wild-type), DH10B (cloning), and BL21 (protein expression). These “Marionette” strains allow for the independent control of gene expression using 2,4-diacetylphophloroglucinol (DAPG), cuminic acid (Cuma), 3-oxohexanoyl-homoserine lactone (OC6), vanillic acid (Van), isopropyl β-D-1-thiogalactopyranoside (IPTG), anhydrotetracycline (aTc), L-arabinose (Ara), choline chloride (Cho), naringenin (Nar), 3,4-dihydroxybenzoic acid (DHBA), sodium salicylate (Sal), and 3-hydroxytetradecanoyl-homoserine lactone (OHC14).
Inferring Disease Risk Genes from Sequencing Data in Multiplex Pedigrees Through Sharing of Rare Variants
Authors: Bureau Alexandre , Begum Ferdouse , Taub Margaret A. , Hetmanski Jacqueline , Parker Margaret M. , Albacha-Hejazi Hasan , Scott Alan F. , Murray Jeffrey C. , Marazita Mary L. , Bailey-Wilson Joan E. , Beaty Terri H. , Ruczinski Ingo
Published: March 2018

We previously demonstrated how sharing of rare variants (RVs) in distant affected relatives can be used to identify variants causing a complex and heterogeneous disease. This approach tested whether single RVs were shared by all sequenced affected family members. However, as with other study designs, joint analysis of several RVs (e.g. within genes) is sometimes required to obtain sufficient statistical power. Further, phenocopies can lead to false negatives for some causal RVs if complete sharing among affecteds is required. Here we extend our methodology (Rare Variant Sharing, RVS) to address these issues. Specifically, we introduce gene-based analyses, refine RV definition based on haplotypes, and introduce a partial sharing test based on RV sharing probabilities for subsets of affected family members. RVS also has the desirable features of not requiring external estimates of variant frequency or control samples, provides functionality to assess and address violations of key assumptions, and is available as open source software for genome-wide analysis. Simulations including phenocopies, based on the families of an oral cleft study, revealed the partial and complete sharing versions of RVS achieved similar statistical power compared to alternative methods (RareIBD and the Gene-Based Segregation Test), and had superior power compared to the pedigree Variant Annotation, Analysis and Search Tool (pVAAST) linkage statistic. In studies of multiplex cleft families, analysis of rare single nucleotide variants in the exome of 151 affected relatives from 54 families revealed no significant excess sharing in any one gene, but highlighted different patterns of sharing revealed by the complete and partial sharing tests.
DNA-Encircled Lipid Bilayers
Authors: Iric Katarina , Subramanian Madhumalar , Oertel Jana , Agarwal Nayan P. , Matthies Michael , Periole Xavier , Sakmar Thomas P. , Huber Thomas , Fahmy Karim , Schmidt Thorsten-Lars
Published: March 2018

Lipid bilayers and lipid-associated proteins play a crucial role in biology. As in vivo studies and manipulation are inherently difficult, several membrane-mimetic systems have been developed to enable investigation of lipidic phases, lipid-protein interactions, membrane protein function and membrane structure in vitro. Controlling the size and shape, or site-specific functionalization is, however, difficult to achieve with established membrane mimetics based on membrane scaffolding proteins, polymers or peptides. In this work, we describe a route to leverage the unique programmability of DNA nanotechnology and create DNA-encircled bilayers (DEBs), which are made of multiple copies of an alkylated oligonucleotide hybridized to a single-stranded minicircle. To stabilize the hydrophobic rim of the lipid bilayer, and to prevent formation of lipid vesicles, we introduced up to 2 alkyl chains per helical that point to the inside of the toroidal DNA ring and interact with the hydrophobic side chains of the encapsulated lipid bilayer. The DEB approach described herein provides unprecedented control of size, and allows the orthogonal functionalizations and arrangement of engineered membrane nanoparticles and will become a valuable tool for biophysical investigation of lipid phases and lipid-associated proteins and complexes including structure determination of membrane proteins and pharmacological screenings of membrane proteins.