bluuebunny/crossref_metadata_2025 huggingface dataset:
A Specific Neuroligin3-αNeurexin1 Code Regulates GABAergic Synaptic Function in Mouse Hippocampus
Authors: Uchigashima Motokazu , Konno Kohtarou , Demchak Emily , Cheung Amy , Watanabe Takuya , Keener David , Abe Manabu , Le Timmy , Sakimura Kenji , Sasaoka Toshikuni , Uemura Takeshi , Kawasawa Yuka Imamura , Watanabe Masahiko , Futai Kensuke
Published: May 2020

Synapse formation and regulation require interactions between pre- and postsynaptic proteins, notably cell adhesion molecules (CAMs). It has been proposed that the functions of neuroligins (Nlgns), postsynaptic CAMs, rely on the formation of trans-synaptic complexes with neurexins (Nrxns), presynaptic CAMs. Nlgn3 is a unique Nlgn isoform that localizes at both excitatory and inhibitory synapses. However, Nlgn3 function mediated via Nrxn interactions is unknown. Here, we demonstrate that Nlgn3 localizes at postsynaptic sites apposing vesicular glutamate transporter 3-expressing (VGT3+) inhibitory terminals and regulates VGT3+ inhibitory interneuron-mediated synaptic transmission in mouse organotypic slice cultures. Gene expression analysis of interneurons revealed that the αNrxn1+AS4 splice isoform is highly expressed in VGT3+ interneurons as compared with other interneurons. Most importantly, postsynaptic Nlgn3 requires presynaptic αNrxn1+AS4 expressed in VGT3+ interneurons to regulate inhibitory synaptic transmission. Our results indicate that specific Nlgn-Nrxn interactions generate distinct functional properties at synapses.
ColTapp, an automated image analysis application for efficient microbial colony growth dynamics quantification
Authors: Bär Julian , Boumasmoud Mathilde , Kouyos Roger , Zinkernagel Annelies S. , Vulin Clément
Published: May 2020

Phenotypic heterogeneity occurs in a population of genetically identical bacteria due to stochastic molecular fluctuations and environmental variations. In extreme cases of phenotypic heterogeneity, a fraction of the bacterial population enters dormancy, and these metabolically inactive or non-dividing bacteria persist through most antibiotic challenges. These subpopulations of persister cells are difficult to study in patient samples. However, the proportion of persisters in a sample can be accessed by physically separating bacteria on a plate measuring the time until colonies become visible as dormant bacteria resume growth later than their active counterparts and form smaller colonies.

Here, we present ColTapp (Colony Time-lapse app), an application dedicated to bacterial colony growth quantification, freely available for download together with its MATLAB source code or as a MacOS/Windows executable. ColTapp’s intuitive graphical user interface allows users without prior coding knowledge to analyze endpoint or time-lapse images of colonies on agar plates. Colonies are detected automatically, and their radius can be tracked over time. Downstream analyses to derive colony lag time and growth rate are implemented.

We demonstrate here the applicability of ColTapp on a dataset ofStaphyloccocus aureuscolony time-lapse images. Colonies on dense plates reached saturation early, biasing lag time estimation from endpoint images. This bias can be reduced by considering the area available to each colony on a plate.

By facilitating the analysis of colony growth dynamics in clinical settings, this application will enable a new type of diagnostics, oriented towards personalized antibiotic therapies.
Seasonal variation in sexual readiness in a facultatively sexual freshwater cnidarian with diapausing eggs
Authors: Tökölyi Jácint , Gergely Réka , Miklós Máté
Published: May 2020

Facultative sexuality combines clonal propagation with sexual reproduction within a single life cycle. Clonal propagation enables quick population growth and the occupancy of favorable habitats. Sex, on the other hand, results in the production of offspring that are more likely to survive adverse conditions (such as the resting eggs of many freshwater invertebrates). In seasonal environments, the timing of sex is often triggered by environmental cues signaling the onset of winter (e.g. temperature drop or changes in photoperiod). Organisms switching to sex to produce resting eggs under these conditions face a trade-off: responding too early to an environmental cue increases the chances of missing out in clonal propagation, while having a delayed response to deteriorating conditions entails the risk of parental mortality before sexual reproduction could be completed. To mitigate these risks, increased sensitivity towards environmental cues with the onset of the winter might be an adaptive strategy. To test this hypothesis, we investigated sexual propensity and time to gonadogenesis in clonal strains derived from spring- and autumn-collected polyps ofHydra oligactis, a facultatively sexual freshwater cnidarian where sex only occurs prior to the onset of winter. We show that autumn-collected individuals and their asexual offspring have a higher propensity for sex and require less time for gonad development compared to strains established from spring-collected individuals that were kept under similar conditions in the laboratory. To see if the above results can be explained by phenotypic plasticity in sexual readiness, we exposed cold-adapted lab strains to different lengths of warm periods. We found that sexual propensity increases with warm exposure. Our results suggest that reciprocal cold and warm periods are required for sex induction inH. oligactis, which would ensure proper timing of sex in this species. Increased sensitivity to environmental deterioration might help maximize fitness in environments that have both a predictable (seasonal) and an unpredictable component.
A Personalized Switched Systems Approach for the Optimal Control of Ventricular Assist Devices based on Atrioventricular Plane Displacement
Authors: Zeile Clemens , Rauwolf Thomas , Schmeisser Alexander , Mizerski Jeremi Kaj , Braun-Dullaeus Rüdiger C. , Sager Sebastian
Published: May 2020

Objective

A promising treatment for congestive heart failure is the implementation of a left ventricular assist device (LVAD) that works as a mechanical pump. Modern LVADs work with adjustable constant rotor speed and provide therefore continuous blood flow; however, recently undertaken efforts try to mimic pulsatile blood flow by oscillating the pump speed. This work proposes an algorithmic framework to construct and evaluate optimal pump speed policies.

Methods

We use a model that captures the atrioventricular plane displacement, which is a physiological indicator for heart failure. We employ mathematical optimization to adapt this model to patient specific data and to find optimal pump speed policies with respect to ventricular unloading and aortic valve opening. To this end, we reformulate the cardiovascular dynamics into a switched system and thereby reduce nonlinearities. We consider system switches that stem from varying the constant pump speed and that are state dependent such as valve opening or closing.

Results

As a proof of concept study, we personalize the model to a selected patient with respect to ventricular pressure. The model fitting results in a root-mean-square deviation of about 6 mmHg. Optimized constant and piecewise constant rotor speed profiles improve the default initialized solution by 31% and 68% respectively.

Conclusion

These in silico findings demon-strate the potential of personalized hemodynamical optimization for the LVAD therapy.

Significance

LVADs and their optimal configuration are active research fields. Mathematical optimization enhances our understanding of how LVADs should provide pulsatility.
Phenotype-dependent habitat choice is too weak to cause assortative mating between Drosophila melanogaster strains differing in light sensitivity
Authors: Peralta-Rincón Juan Ramón , Aoulad Fatima Zohra , Prado Antonio , Edelaar Pim
Published: May 2020

Over the last few years, matching habitat choice has gained attention as a mechanism for maintaining biodiversity and driving speciation. It revolves around the idea that individuals select the habitat in which they perceive to obtain greater fitness after a prior evaluation of their local performance across heterogeneous environments. This results in individuals with similar ecological traits converging to the same patches, and hence could indirectly cause assortative mating when mating occurs in those patches.

White-eyed mutants ofDrosophilafruit flies have a series of disadvantages compared to wild type flies, including a poorer performance under bright light. It has been previously reported that, when given a choice, wild typeDrosophila simulanspreferred a brightly lit habitat while white-eyed mutants occupied a dimly lit one. This spatial segregation allowed the eye color polymorphism to be maintained for several generations, whereas normally it is quickly replaced by the wild type.

Here we compare the habitat choice decisions of white-eyed and wild type flies in another species,D. melanogaster. We released groups of flies in a light gradient and recorded their departure and settlement behavior. Departure depended on sex and phenotype, but not on the light conditions of the release point. Settlement depended on sex, and on the interaction between phenotype and light conditions of the point of settlement. Nonetheless, simulations showed that this differential habitat use by the phenotypes would only cause a minimal degree of assortative mating in this species.
Gap junction mediated feed-forward inhibition ensures ultra precise temporal patterning in vocal behavior
Authors: Chagnaud Boris P. , Perelmuter Jonathan , Forlano Paul , Bass Andrew H.
Published: May 2020

Precise neuronal firing is especially important for behaviors highly dependent on the correct sequencing and timing of muscle activity patterns, such as acoustic signalling. We show that extreme temporal precision in motoneuronal firing within a hindbrain network that directly determines call duration, pulse repetition rate and fundamental frequency in a teleost fish, the Gulf toadfish, depends on gap junction-mediated, feed-forward glycinergic inhibition that generates a period of reduced probability of motoneuron activation. Super-resolution microscopy confirms glycinergic release sites contacting motoneuron somata and dendrites. Synchronous motoneuron activity can also induce action potential firing in pre-motoneurons, a feature that could figure prominently into motor timing. Gap junction-mediated, feed-forward glycinergic inhibition provides a novel means for achieving temporal precision in the millisecond range for rapid modulation of an acoustic signal and perhaps other motor behaviors.
Rationalizing PROTAC-mediated ternary complex formation using Rosetta
Authors: Bai Nan , Kirubakaran Palani , Karanicolas John
Published: May 2020

PROTACs are molecules that combine a target-binding warhead with an E3 ligase-recruiting moiety; by drawing the target protein into a ternary complex with the E3 ligase, PROTACs induce target protein degradation. While PROTACs hold exciting potential as chemical probes and as therapeutic agents, development of a PROTAC typically requires synthesis of numerous analogs to thoroughly explore variations on the chemical linker; without extensive trial and error, it is unclear how to link the two protein-recruiting moieties to promote formation of a productive ternary complex. Here, we describe a structure-based computational method for evaluating suitability of a given linker for ternary complex formation. Our method uses Rosetta to dock the protein components, then builds the PROTAC from its component fragments into each binding mode; complete models of the ternary complex are then refined. We apply this approach to retrospectively evaluate multiple PROTACs from the literature, spanning diverse target proteins. We find that modeling ternary complex formation is sufficient to explain both activity and selectivity reported for these PROTACs, implying that other cellular factors are not key determinants of activity in these cases. We further find that interpreting PROTAC activity is best approached using an ensemble of structures of the ternary complex rather than a single static conformation, and that members of a structurally-conserved protein family can be recruited by the same PROTAC through vastly different binding modes. To encourage adoption of these methods and promote further analyses, we disseminate both the computational methods and the models of ternary complexes.

Significance Statement

Recent years have brought a flood of interest in developing compounds that selectively degrade protein targets in cells, as exemplified by PROTACs. Fully realizing the promise of PROTACs to transform chemical biology by delivering degraders of diverse and undruggable protein targets has been impeded, however, by the fact that designing a suitable chemical linker between the functional moieties requires extensive trial and error. Here, we describe a structure-based computational method to predict PROTAC activity. We envision that this approach will allow design and optimization of PROTACs for efficient target degradation, selection of E3 ligases best suited for pairing with a given target protein, and understanding the basis by which PROTACs can exhibit different target selectivity than their component warheads.
Welcome to the jungle: Algal turf negatively affects recruitment of a Caribbean octocoral
Authors: Wells Christopher D. , Martínez-Quintana Ángela , Tonra Kaitlyn J. , Lasker Howard R.
Published: May 2020

Algal cover has increased and scleractinian coral cover has steadily declined over the past 40 years on Caribbean coral reefs. In contrast, octocoral abundance has increased at those sites where octocoral abundances have been monitored. The effects of algal cover on recruitment may be a key component in these patterns, as upright octocoral recruits have the potential to escape competition with algae by growing above the ubiquitous algal turfs. However, the impacts of algal turf on octocorals have not been tested.

We used laboratory and field recruitment experiments to examine impacts of algal turf on settlement and then survival of newly-settled octocorals. Tiles were preconditioned on a Caribbean reef, allowing algae to settle and grow. Tiles were then partitioned into three treatments: lightly scrubbed (0% turf cover), left alone (19% turf cover), or kept for 15 days in a sea table without fish or large invertebrate herbivores (50% turf cover). Planulae of the common Caribbean octocoralPlexaura homomallawere allowed to settle and metamorphose on the tiles for six days. Tiles were then deployed onto a reef and survival of those recruits was monitored for seven weeks. Settlers that recruited to the tiles after deployment to the reef were also monitored.

Laboratory recruitment rate was significantly higher in lower turf cover treatments. Field survival was significantly reduced by increased turf cover; for every 1% increase in turf cover, polyps died 1.3% faster. In a model parameterized by the observed field survival, polyps exposed to 100% turf cover had a 2% survival rate over 51 days, while polyps exposed to no turf cover had a 32% survival rate over the same time.

Synthesis. We found that high densities of turf algae can significantly inhibit recruitment of octocorals. Octocoral survival rates were similar to those published for scleractinians, but field settlement rates were much higher, which likely contributes to the higher resilience of octocorals to disturbances. The factors that influence recruitment are critical in understanding the dynamics of octocorals on Caribbean reefs as continuing declines in scleractinian cover may lead to more octocoral-dominated communities in the Caribbean.
Neuronal activity remodels the F-actin based submembrane lattice in dendrites but not axons of hippocampal neurons
Authors: Lavoie-Cardinal Flavie , Bilodeau Anthony , Lemieux Mado , Gardner Marc-André , Wiesner Theresa , Laramée Gabrielle , Gagné Christian , De Koninck Paul
Published: May 2020

The nanoscale organization of the F-actin cytoskeleton in neurons comprises membrane-associated periodical rings, bundles, and longitudinal fibers. The F-actin rings have been observed predominantly in axons but only sporadically in dendrites, where fluorescence nanoscopy reveals various patterns of F-actin arranged in mixed patches. These complex dendritic F-actin patterns pose a challenge for investigating quantitatively their regulatory mechanisms. We developed here a weakly supervised deep learning segmentation approach of fluorescence nanoscopy images of F-actin in cultured hippocampal neurons. This approach enabled the quantitative assessment of F-actin remodeling, revealing the disappearance of the rings during neuronal activity in dendrites, but not in axons. The dendritic F-actin cytoskeleton of activated neurons remodeled into longitudinal fibers. We show that this activity-dependent remodeling involves Ca2+and NMDA-dependent mechanisms. This highly dynamic restructuring of dendritic F-actin based submembrane lattice into longitudinal fibers may serve to support activity-dependent membrane remodeling, protein trafficking and neuronal plasticity.
Remnants of the Balbiani body are required for formation of RNA transport granules inXenopusoocytes
Authors: Yang Chao , Wilson Gena M. , Champion Matthew M. , Huber Paul W.
Published: May 2020

Fragmentation of the Balbiani body inXenopusoocytes engenders a region extending from the germinal vesicle (GV) towards the vegetal pole that is enriched in mitochondria. This area is later transversed by RNA that is being localized to the vegetal cortex. Inhibition of mitochondrial ATP synthesis prevents the perinuclear formation of these RNA transport granules that can be reversed by the nonhydrolyzable ATP analog, adenosine 5’-(βγ-imido) triphosphate. The protein composition and sensitivity of the transport granules to hexanediol indicate that they are liquid phase condensates. Mitochondria in the remnants of the Balbiani body produce a region of elevated ATP that appears to act as a hydrotrope to support the perinuclear phase transition leading to granule formation.

Mitochondria in the remnants of the Balbiani body produce elevated levels of ATP required for the formation of liquid phase condensates containing RNA transport granules.
Variability in error-based and reward-based human motor learning is associated with entorhinal volume
Authors: de Brouwer Anouk J. , Rashid Mohammad R. , Flanagan J. Randall , Poppenk Jordan , Gallivan Jason P.
Published: May 2020

Error-based and reward-based processes are critical for motor learning, and are thought to be mediated via distinct neural pathways. However, recent behavioral work in humans suggests that both learning processes are supported by cognitive strategies and that these contribute to individual differences in motor learning ability. While it has been speculated that medial temporal lobe regions may support this strategic component to learning, direct evidence is lacking. Here we first show that faster and more complete learning during error-based visuomotor adaptation is associated with better learning during reward-based shaping of reaching movements. This result suggests that strategic processes, linked to faster and better learning, drive individual differences in both error-based and reward-based motor learning. We then show that right entorhinal cortex volume was larger in good learning individuals—classified across both motor learning tasks—compared to their poorer learning counterparts. This suggests that strategic processes underlying both error- and reward-based learning are linked to neuroanatomical differences in entorhinal cortex.

Significance Statement

While it is widely appreciated that humans vary greatly in their motor learning abilities, little is known about the processes and neuroanatomical bases that underlie these differences. Here, using a data-driven approach, we show that individual variability in error-based and reward-based motor learning is tightly linked, and related to the use of cognitive strategies. We further show that structural differences in entorhinal cortex predict this intersubject variability in motor learning, with larger entorhinal volumes being associated with better overall error-based and reward-based learning. Together, these findings provide support for the notion that the ability to recruit strategic processes underlies intersubject variability in both error-based and reward-based learning, which itself may be linked to structural differences in medial temporal regions.
Competition delays multi-drug resistance evolution during combination therapy
Authors: Berríos-Caro Ernesto , Gifford Danna R. , Galla Tobias
Published: May 2020

Combination therapies have shown remarkable success in preventing the evolution of resistance to multiple drugs, including HIV, tuberculosis, and cancer. Nevertheless, the rise in drug resistance still remains an important challenge. The capability to accurately predict the emergence of resistance, either to one or multiple drugs, may help to improve treatment options. Existing theoretical approaches often focus on exponential growth laws, which may not be realistic when scarce resources and competition limit growth. In this work, we study the emergence of single and double drug resistance in a model of combination therapy of two drugs. The model describes a sensitive strain, two types of single-resistant strains, and a double-resistant strain. We compare the probability that resistance emerges for three growth laws: exponential growth, logistic growth without competition between strains, and logistic growth with competition between strains. Using mathematical estimates and numerical simulations, we show that between-strain competition only affects the emergence of single resistance when resources are scarce. In contrast, the probability of double resistance is affected by between-strain competition over a wider space of resource availability. This indicates that competition between different resistant strains may be pertinent to identifying strategies for suppressing drug resistance, and that exponential models may overestimate the emergence of resistance to multiple drugs. A by-product of our work is an efficient strategy to evaluate probabilities of single and double resistance in models with multiple sequential mutations. This may be useful for a range of other problems in which the probability of resistance is of interest.
Theory and Simulations of condensin mediated loop extrusion in DNA
Authors: Takaki Ryota , Dey Atreya , Shi Guang , Thirumalai D.
Published: May 2020

Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular biological phenomenon. This process is driven by the formation of chromosome loops. The ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE), we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the available experimental data quantitatively, and suggests that condensin must undergo a large conformational change, induced by ATP binding, bringing distant parts of the motor to proximity. Simulations using a simple model confirm that the motor transitions between an open and a closed state in order to extrude loops by a scrunching mechanism, similar to that proposed in DNA bubble formation during bacterial transcription. Changes in the orientation of the motor domains are transmitted over ~ 50 nm, connecting the motor head and the hinge, thus providing an allosteric basis for LE.
The Temporal Relationships between White Matter Hyperintensities, Neurodegeneration, Amyloid β, and Cognition
Authors: Dadar Mahsa , Camicioli Richard , Duchesne Simon , Collins D. Louis ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: May 2020

INTRODUCTION

Cognitive decline in Alzheimer’s disease is associated with amyloid-β accumulation, neurodegeneration and cerebral small vessel disease, but the temporal relationships between these factors is not well established.

METHODS

Data included white matter hyperintensity (WMH) load, grey matter (GM) atrophy and Alzheimer’s Disease Assessment Scale-Cognitive-Plus (ADAS13) scores for 720 participants and cerebrospinal fluid amyloid (Aβ1-42) for 461 participants from the Alzheimer’s Disease Neuroimaging Initiative. Linear regressions were used to assess the relationships between baseline WMH, GM, and Aβ1-42 to changes in WMH, GM, Aβ1-42, and cognition at one-year follow-up.

RESULTS

Baseline WMHs and Aβ1-42 predicted WMH increase and GM atrophy. Baseline WMHs, GM, and Aβ1-42 predicted worsening cognition. Only baseline Aβ1-42 predicted change in Aβ1-42.

DISCUSSION

Baseline WMHs lead to greater future GM atrophy and cognitive decline, suggesting that WM damage precedes neurodegeneration and cognitive decline. Baseline Aβ1-42 predicted WMH increase, suggesting a potential role of amyloid in WM damage.

Research in Context

Systematic Review: Both amyloid β and neurodegeneration are primary pathologies in Alzheimer’s disease. White matter hyperintensities (indicative of presence of cerebrovascular disease) might also be part of the pathological changes in Alzheimer’s. However, the temporal relationship between white matter hyperintensities, amyloid β, neurodegeneration, and cognitive decline is still unclear.

Interpretation: Our results establish a potential temporal order between white matter hyperintensities, amyloid β, neurodegeneration, and cognitive decline, showing that white matter hyperintensities precede neurodegeneration and cognitive decline. The results provide some evidence that amyloid β deposition, in turn, precedes accumulation of white matter hyperintensities.

Future Directions: The current findings reinforce the need for future longitudinal investigations of the mechanisms through which white matter hyperintensities impact the aging population in general and Alzheimer’s disease patients, in particular.
A Study of Coronary Artery Disease in the Left Circumflex Artery via Artificial Vessel Restoration
Authors: Paulraj Akhil , Liu Fei
Published: May 2020

Diagnosis, risk analysis, and treatment of coronary artery disease (CAD) can be improved with a better understanding of cardiovascular flows. Numerical simulations can assist in achieving this understanding. The objective of this study is to compare the dynamics of blood flow in a diseased left circumflex artery (LCX) and its artificially restored counterpart representing its healthy state. This comparison is made to identify flow characteristics in the restored vessel that contribute to the development of CAD. The diseased LCX geometry was derived from computed tomography angiography data. The stenosed region of the diseased LCX was repaired by manually redefining cross-sections of the vessel, creating the restored geometry. To account for inaccuracies, variations of the restored LCX were made by dilating the repaired surface. Numerical simulations were conducted on all geometries and the results were compared. Alongside expected low wall shear stress, a region of high vorticity was present in all of the restored vessels near the location where CAD developed in the diseased vessel. Therefore, this research suggests that flow vorticity is relevant in assessing the risk for CAD, potentially improving the accuracy of non-invasive, computational diagnosis. Such improvements can also help avoid unnecessary invasive diagnosis methods and minimize risk.
Identifying Mangrove-Coral Habitats in the Florida Keys
Authors: Kellogg Christina A. , Moyer Ryan P. , Jacobsen Mary , Yates Kimberly K.
Published: May 2020

Coral reefs are degrading due to many synergistic stressors. Recently there have been a number of global reports of corals occupying mangrove habitats that provide a supportive environment or refugium for corals, sheltering them by reducing stressors such as oxidative light stress and low pH. This study used satellite imagery and manual ground-truthing surveys to search for mangrove-coral habitats in the Florida Keys and then collected basic environmental parameters (temperature, salinity, dissolved oxygen, pHNBS, turbidity) at identified sites using a multi-parameter water quality sonde. Two kinds of mangrove-coral habitats were found in both the Upper and Lower Florida Keys: (1) prop-root corals, where coral colonies were growing directly on (and around) mangrove prop roots, and (2) channel corals, where coral colonies were growing in mangrove channels under the shade of the mangrove canopy, at deeper depths and not in as close proximity to the mangroves. Coral species found growing on and directly adjacent to prop roots includedPorites porites(multiple morphs),Siderastrea radiansandFavia fragum. Channel coral habitats predominantly hostedS. radiansand a fewS. siderea, although single colonies ofSolenastrea bournoniandStephanocoenia interseptawere observed. Circumstantial evidence suggests additional coral communities existed on mangrove shorelines of oceanside and backcountry islands until destroyed, likely by Hurricane Irma. These mangrove-coral habitats may be climate refugia for corals and could be included in ecosystem management plans and considered for their applications in coral restoration, for example, as a source of adapted genetic resources, places to support growth and acclimation of coral outplants, or natural laboratories to test survival of different genotypes.
How good are predictions of the effects of selective sweeps on levels of neutral diversity?
Authors: Charlesworth Brian
Published: May 2020

Selective sweeps are thought to play a significant role in shaping patterns of variability across genomes; accurate predictions of their effects are, therefore, important for understanding these patterns. A commonly used model of selective sweeps assumes that alleles sampled at the end of a sweep, and that fail to recombine with wild-type haplotypes during the sweep, coalesce instantaneously, leading to a simple expression for sweep effects on diversity. It is shown here that there can be a significant probability that a pair of alleles sampled at the end of a sweep coalesce during the sweep before a recombination event can occur, reducing their expected coalescent time below that given by the simple approximation. Expressions are derived for the expected reductions in pairwise neutral diversities caused by both single and recurrent sweeps in the presence of such within-sweep coalescence, although the effects of multiple recombination events during a sweep are only treated heuristically. The accuracies of the resulting expressions were checked against the results of simulations. For even moderate ratios of the recombination rate to the selection coefficient, the simple approximation can be substantially inaccurate. The selection model used here can be applied to favorable mutations with arbitrary dominance coefficients, to sex-linked loci with sex-specific selection coefficients, and to inbreeding populations. Using the results from this model, the expected differences between the levels of variability on X chromosomes and autosomes with selection at linked sites are discussed, and compared with data on a population ofDrosophila melanogaster.
Functional Characterization offer-ts, a Temperature-Sensitive FERONIA Mutant Allele That Alters Root Hair Growth
Authors: Kim Daewon , Yang Jiyuan , Gu Fangwei , Park Sung Jin , Combs Jonathon , Adams Alexander , Mayes Heather B. , Bahk Jeong Dong , Nielsen Erik
Published: May 2020

In plants, root hairs undergo a highly-polarized form of cell expansion called tip-growth, in which cell wall deposition is restricted to the root hair apex. In order to identify essential cellular components that might have been missed in earlier genetic screens we identified conditional temperature sensitive (ts) root hair mutants by EMS mutagenesis. Here we describe one of these mutants,fer-ts(feronia-temperaturesensitive). Mutantfer-tsseedlings grew normally at normal temperatures (20°C), but failed to form root hairs at elevated temperatures (30°C). Map based-cloning and whole genome sequencing revealed thatfer-tsresulted from a G41S substitution in the extracellular domain ofFERONIA(FER). A functional fluorescent fusion of FER containing thefer-tsmutation localized to plasma membranes, but was subject to enhanced protein turnover at elevated temperatures. While tip-growth was rapidly inhibited by addition of RALF1 peptides in both wild-type andfer-tsmutants at normal temperatures, root elongation offer-tsseedlings was resistant to added RALF1 peptide at elevated temperatures. Additionally, at elevated temperaturesfer-tsseedlings displayed altered ROS accumulation upon auxin treatment and phenocopied constitutivefermutant responses to a variety of plant hormone treatments. Molecular modeling and sequence comparison with other CrRLK1L receptor family members revealed that the mutated glycine infer-tsis highly conserved, but is not located in the recently characterized RALF23 and LORELI-LIKE-GLYCOPROTEIN (LLG2) binding domains, perhaps suggesting thatfer-tsphenotypes may not be directly due to loss of binding to RALF1 peptides.
Fast computational optimization of TMS coil placement for individualized electric field targeting
Authors: Gomez Luis J. , Dannhauer Moritz , Peterchev Angel V.
Published: May 2020

Background

During transcranial magnetic stimulation (TMS) a coil placed on the scalp is used to non-invasively modulate activity of targeted brain networks via a magnetically induced electric field (E-field). Ideally, the E-field induced during TMS is concentrated on a targeted cortical region of interest (ROI).

Objective

To improve the accuracy of TMS we have developed a fast computational auxiliary dipole method (ADM) for determining the optimum coil position and orientation. The optimum coil placement maximizes the E-field along a predetermined direction or, alternatively, the overall E-field magnitude in the targeted ROI. Furthermore, ADM can assess E-field uncertainty resulting from precision limitations of TMS coil placement protocols.

Method

ADM leverages the electromagnetic reciprocity principle to compute rapidly the TMS induced E-field in the ROI by using the E-field generated by a virtual constant current source residing in the ROI. The framework starts by solving for the conduction currents resulting from this ROI current source. Then, it rapidly determines the average E-field induced in the ROI for each coil position by using the conduction currents and a fast-multipole method. To further speed-up the computations, the coil is approximated using auxiliary dipoles enabling it to represent all coil orientations for a given coil position with less than 600 dipoles.

Results

Using ADM, the E-fields generated in an MRI-derived head model when the coil is placed at 5,900 different scalp positions and 360 coil orientations per position (over 2.1 million unique configurations) can be determined in under 15 minutes on a standard laptop computer. This enables rapid extraction of the optimum coil position and orientation as well as the E-field variation resulting from coil positioning uncertainty.

Conclusion

ADM enables the rapid determination of coil placement that maximizes E-field delivery to a specific brain target. This method can find the optimum coil placement in under 15 minutes enabling its routine use for TMS. Furthermore, it enables the fast quantification of uncertainty in the induced E-field due to limited precision of TMS coil placement protocols, enabling minimization and statistical analysis of the E-field dose variability.

Highlights

Auxiliary dipole method (ADM) optimizes TMS coil placement in under 8 minutes

Optimum coil position is up to 14 mm away from conventional targeting

Optimum coil orientation is typically near normal to the sulcal wall

TMS induced E-field is less sensitive to orientation than position errors
Odor mixture perception: can molecular complexity be a factor determining elemental or configural perception?
Authors: Hamakawa Masayuki , Ishikawa Hiroya , Kikuchi Yumika , Tamura Kaori , Okamoto Tsuyoshi
Published: May 2020

Odor mixtures can evoke smells that differ from those of their individual odor components. Research has revealed the existence of two perceptual modes, in which a mixture can be perceived as either the original smells of its individual components (elemental) or as a novel smell (configural). However, the factors underlying the perceptual transformation that occurs when smelling a mixture versus its original components remain unclear. Therefore, the present study aimed to identify the properties of odorants that affect olfactory perception of odor mixtures, focusing on the structural complexity of an odorant. We conducted psychophysical experiments in which different groups of participants were instructed to provide olfactory perceptual descriptions of low-, medium-, and high-complexity odor mixtures or components, respectively. To investigate the perceptual modes induced by the mixtures, we compared the participants’ evaluations between mixtures and components via two types of analyses. First, we compared each olfactory description following quantification via principal component analysis. We then compared data based on seven major olfactory perceptual groups. We observed that odor mixtures composed of low-complexity odorants were perceived as relatively novel smells with regard to both minor (olfactory descriptions) and major (perceptual community) odor qualities than medium- and high-complexity mixtures. Such information may further our understanding of the olfactory perceptual modes of odor mixtures.
Human Endogenous Retrovirus K Rec forms a regulatory loop with MITF that opposes the progression of melanoma to an invasive stage
Authors: Singh Manvendra , Cai Huiqiang , Bunse Mario , Feschotte Cédric , Izsvák Zsuzsanna
Published: May 2020

The HML2 subfamily of HERV-K (henceforth HERV-K) represents the most recently endogenized retrovirus in the human genome. While the products of certain HERV-K genomic copies are expressed in normal tissues, they are upregulated in a number of pathological conditions, including various tumours. It remains unclear whether HERV-K(HML2)-encoded products overexpressed in cancer contribute to disease progression or are merely by-products of tumorigenesis. Here, we focus on the regulatory activities of the Long Terminal Repeats (LTR5_Hs) of HERV-K and on the potential role of the HERV-K-encoded Rec in melanoma. Our regulatory genomics analysis of LTR5_Hs loci indicates that Melanocyte Inducing Transcription Factor (MITF) binds to a canonical E-box motif (CA(C/T)GTG) within these elements inproliferativetype of melanoma, and that depletion of MITF results in reduced HERV-K expression. In turn, experimentally depleting Rec in aproliferativemelanoma cell line leads to lower mRNA levels of MITF and its predicted target genes. Furthermore, Rec knockdown leads to an upregulation of epithelial-to-mesenchymal associated genes and to an enhanced invasion phenotype ofproliferativemelanoma cells. Together these results suggest the existence of a regulatory loop between MITF and Rec that may modulate the transition fromproliferativetoinvasivestages of melanoma. Because HERV-K(HML2) elements are restricted to hominoid primates, these findings might explain certain species-specific features of melanoma progression and point to some limitations of animal models in melanoma studies.
One enzyme reverse transcription qPCR using Taq DNA polymerase
Authors: Bhadra Sanchita , Maranhao Andre C. , Ellington Andrew D.
Published: May 2020

Taq DNA polymerase, one of the first thermostable DNA polymerases to be discovered, has been typecast as a DNA-dependent DNA polymerase commonly employed for PCR. However, Taq polymerase belongs to the same DNA polymerase superfamily as the Molony murine leukemia virus reverse transcriptase and has in the past been shown to possess reverse transcriptase activity. We report optimized buffer and salt compositions that promote the reverse transcriptase activity of Taq DNA polymerase, and thereby allow it to be used as the sole enzyme in TaqMan RT-qPCR reactions. We demonstrate the utility of Taq-alone RT-qPCR reactions by executing CDC SARS-CoV-2 N1, N2, and N3 TaqMan RT-qPCR assays that could detect as few as 2 copies/µL of input viral genomic RNA.
Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naïve Mycobacterium tuberculosis clinical strains
Authors: Battaglia S , Spitaleri A , Cabibbe AM , Meehan CJ , Utpatel C , Ismail N , Tahseen S , Skrahina A , Alikhanova N , Mostofa Kamal SM , Barbova A , Niemann S , Groenheit R , Dean AS , Zignol M , Rigouts L , Cirillo DM
Published: May 2020

The role of genetic mutations in genes associated to phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly understood. However, a clear understanding of the role of each genetic variant is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analysed all mutations in candidate genomic regions associated with BDQ- and DLM-resistant phenotypes using a whole genome sequencing (WGS) dataset from a collection of 4795 MTBc clinical isolates from six high-burden countries of tuberculosis (TB). From WGS analysis, we identified 61 and 158 unique mutations in genomic regions potentially involved in BDQ- and DLM-resistant phenotypes, respectively. Importantly, all strains were isolated from patients who likely have never been exposed to the medicines. In order to characterize the role of mutations, we performed an energetic in silico analysis to evaluate their effect in the available protein structures Ddn (DLM), Fgd1 (DLM) and Rv0678 (BDQ), and minimum inhibitory concentration (MIC) assays on a subset of MTBc strains carrying mutations to assess their phenotypic effect. The combination of structural protein information and phenotypic data allowed for cataloging the mutations clearly associated with resistance to BDQ (n= 4) and DLM (n= 35), as well as about a hundred genetic variants without any correlation with resistance. Importantly, these results show that both BDQ and DLM resistance-related mutations are diverse and distributed across the entire region of each gene target, which is of critical importance to the development of comprehensive molecular diagnostic tools.

Importance

Phenotypic drug susceptibility tests (DST) are too slow to provide an early indication of drug susceptibility status at the time of treatment initiation and very demanding in terms of specimens handling and biosafety. The development of molecular assays to detect resistance to bedaquiline (BDQ) and delamanid (DLM) requires accurate categorization of genetic variants according to their association with phenotypic resistance. We have evaluated a large multi-country set of clinical isolates to identify mutations associated with increased minimum inhibitory concentrations (MICs) and used an in silico protein structure analysis to further unravel the potential role of these mutations in drug resistance mechanisms. The results of this study are an important source of information for the development of molecular diagnostic tests to improve the provision of appropriate treatment and care to TB patients.
Exploring the Stony Coral Tissue Loss Disease Bacterial Pathobiome
Authors: Iwanowicz D.D. , Schill W.B. , Woodley C. M. , Bruckner A. , Neely K. , Briggs K.M.
Published: May 2020

A devastating novel coral disease outbreak, referred to as Stony Coral Tissue Loss Disease (SCTLD), was first described in 2014. It is thought to have originated offshore of Miami-Dade County, FL, but has persisted and spread, affecting new reefs along the Florida Reef Tract and reefs of at least 8 other Caribbean jurisdictions. We investigated the microbial communities of clinically normal and diseased specimens of five species of affected corals using targeted 16S ribosomal DNA sequencing (Illumina MiSeq). Fifty-nine bacterial sequences were identified using contrast analysis that had enriched abundance in diseased coral host microbiomes relative to the microbiomes of clinically normal hosts. Several sequences from known bacterial pathogens were identified in this group. Additionally, we identified fifty-three bacterial species that had differentially elevated numbers in clinically normal coral host samples relative to samples from diseased host corals. The bacterial consortia composing the clinically normal and diseased coral microbiomes were clearly distinct taxonomically. Predicted functional profiles based on taxonomy, however, were found to be quite similar. This indicates a high level of functional redundancy among diseased and clinically normal microbiome members. Further examination of the direct sequencing data revealed that while some bacteria were differentially distributed according to disease status, others were not. Fifty-one bacterial species were found in both diseased and clinically normal coral host samples and not differentially abundant in either disease state. These still may be important in explaining the presentation of disease.

IMPORTANCE

Determining causation is a management top priority to guide control and intervention strategies for the SCTLD outbreak. Towards this goal we examined bacterial taxa that were differentially elevated in numbers in diseased corals as compared to clinically normal corals at Looe Key, FL in August 2018. Many of the bacterial species we detected are known to be pathogenic to humans, animals, and (or) plants, and some of these have been found associated with diseased corals in other studies. Microbes that were present (or conspicuous by their absence) in both diseased as well as clinically normal corals were also examined because “healthy” corals from a diseased location such as Looe Key may have been exposed but may not have been showing overt disease at the time of sampling. Although untangling of causation is not possible currently, certain bacterial cliques and excess nutrients appear to be potential risk factors in SCTLD pathology.
Human GBP1 promotes pathogen vacuole rupture and inflammasome activation duringLegionella pneumophilainfection
Authors: Bass Antonia R. , Shin Sunny
Published: May 2020

The inflammasome is an essential component of host defense against intracellular bacterial pathogens, such asLegionella pneumophila, the causative agent of the severe pneumonia Legionnaires’ disease. Inflammasome activation leads to recruitment and activation of caspases, which promote IL-1 family cytokine release and pyroptosis. In mice, interferon (IFN) signaling promotes inflammasome responses againstL. pneumophila, in part through the functions of a family of IFN-inducible GTPases known as guanylate binding proteins (GBPs) (1). Within murine macrophages, IFN signaling promotes rupture of theL. pneumophila-containing vacuole (LCV), whereas GBPs are dispensable for vacuole rupture. Instead, GBPs facilitate the lysis of cytosol-exposedL. pneumophila. In contrast to mouse GBPs, the functions of human GBPs in inflammasome responses toL. pneumophilaare poorly understood. Here, we show that IFN-γ promotes caspase-1, caspase-4, and caspase-5 inflammasome activation duringL. pneumophilainfection and upregulates GBP expression in primary human macrophages. We find that human GBP1 is important for maximal IFN-γ-driven inflammasome responses toL. pneumophila. Furthermore, IFN-γ signaling promotes the rupture of LCVs. Intriguingly, in contrast to murine GBPs, human GBP1 targets the LCV in a T4SS-dependent manner and promotes vacuolar lysis, resulting in increased bacterial access to the host cell cytosol. Our findings show a key role for human GBP1 in targeting and disrupting pathogen-containing vacuoles and reveal mechanistic differences in how mouse and human GBPs promote inflammasome responses toL. pneumophila.