bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suspensor-derived somatic embryogenesis in Arabidopsis
Authors: Radoeva Tatyana , Albrecht Catherine , Piepers Marcel , de Vries Sacco , Weijers Dolf 
Published: January 2020

AbstractIn many flowering plants, includingArabidopsis thaliana, asymmetric division of the zygote generates apical and basal cells with different fates. The apical cell continues to produce the embryo while the basal cell undergoes a restricted number of anticlinal divisions leading to a suspensor of 6-9 quiescent cells that remain extra-embryonic and eventually senesce. In some genetic backgrounds, or upon ablation of the embryo, suspensor cells can however undergo periclinal cell divisions and eventually form a second, twin seedling. Likewise, embryogenesis can be induced from somatic cells by various genes, but the relation to suspensor-derived embryos is unclear. Here, we addressed the nature of the suspensor to embryo fate transformation, and its genetic triggers. We expressed most known embryogenesis-inducing transcriptional regulators and receptor-like kinases specifically in suspensor cells. Among these, only RKD1 and WUS could induce a heritable twin seedling phenotype. We next analyzed morphology and fate marker expression in embryos in which suspensor division were activated by different triggers to address the developmental paths towards reprogramming. Our results show that reprogramming of Arabidopsis suspensor cells towards embryonic identity is a specific cellular response that is triggered by defined regulators, follows a conserved developmental trajectory and shares similarity to the process of somatic embryogenesis from post-embryonic tissues.
Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors
Authors: Kult Shiri , Olender Tsviya , Osterwalder Marco , Krief Sharon , Blecher-Gonen Ronnie , Ben-Moshe Shani , Farack Lydia , Keren-Shaul Hadas , Leshkowitz Dena , Salame Tomer Meir , Capellini Terence D. , Itzkovitz Shalev , Amit Ido , Visel Axel , Zelzer Elazar 
Published: January 2020

AbstractThe connection between different tissues is vital for the development and function of any organs and systems. In the musculoskeletal system, the attachment of elastic tendons to stiff bones poses a mechanical challenge that is solved by the formation of a transitional tissue, which allows the transfer of muscle forces to the skeleton without tearing. Here, we show that tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte transcriptomes, which is regulated by sharing regulatory elements with these cells and by Krüppel-like factors transcription factors (KLF).To uncover the molecular identity of attachment cells, we first applied high-throughput RNA sequencing to murine humeral attachment cells. The results, which were validated byin situhybridization and single-moleculein situhybridization, reveal that attachment cells express hundreds of chondrogenic and tenogenic genes. In search for the underlying mechanism allowing these cells to express these genes, we performed ATAC sequencing and found that attachment cells share a significant fraction of accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis further revealed transcriptional enhancer signatures for the majority of these regions. We then examined a subset of these regions using transgenic mouse enhancer reporter. Results verified the shared activity of some of these enhancers, supporting the possibility that the transcriptome of attachment cells is regulated by enhancers with shared activities in tenocytes or chondrocytes. Finally, integrative chromatin and motif analyses, as well as the transcriptome data, indicated that KLFs are regulators of attachment cells. Indeed, blocking the expression ofKlf2andKlf4in the developing limb mesenchyme led to abnormal differentiation of attachment cells, establishing these factors as key regulators of the fate of these cells.In summary, our findings show how the molecular identity of bi-fated attachment cells enables the formation of the unique transitional tissue that connect tendon to bone. More broadly, we show how mixing the transcriptomes of two cell types through shared enhancers and a dedicated set of transcription factors can lead to the formation of a new cell fate that connects them.
Symbiosis between river and dry lands: phycobiont dynamics on river gravel bars
Authors: Vančurová Lucie , Kalníková Veronika , Peksa Ondřej , Škvorová Zuzana , Malíček Jiří , Moya Patricia , Chytrý Kryštof , Černajová Ivana , Škaloud Pavel 
Published: January 2020

AbstractRiver gravel bars are dynamic and heterogeneous habitats standing on transition between aquatic and terrestrial environment. Periodical flooding, low nutrient content, frost, missing safe sites, drought, and heat on the ground surface significantly influence life in these habitats. Mutualistic symbiosis may be a successful strategy for organisms to survive and to proliferate under harsh conditions. The lichen genusStereocaulonwas selected as a model symbiotic system among the organisms living on river gravel bars. The aim of our work was to determine effect of this dynamic environment on a phycobiont (i.e., green eukaryotic photobiont) community structure. We analysed 147Stereocaulonspecimens collected in the Swiss Alps using Sanger sequencing (fungal ITS rDNA, algal ITS rDNA, algal actin type I gene) and 8 selected thalli and 12 soil samples using Illumina metabarcoding (ITS2 rDNA). We performed phytosociological sampling on each study plot (n=13). Our analyses of communities of phycobionts, lichens, bryophytes, and vascular plants indicated an ongoing colonisation by phycobionts and gradual change of phycobiont community along to the successional gradient. We recovered great phycobiont diversity associated withStereocaulonmycobionts including algae reported as phycobionts for the first time. Each of twoStereocaulonmycobiont OTUs has distinct pool of predominant phycobionts in the study area. Finally, all thalli selected for Illumina metabarcoding contained a wide range of additional intrathalline algae, i.e., showed algal plurality. In general, succession process on newly emerged or recently disturbed localities also takes place within a community of microscopic symbiotic organisms, such as phycobionts.
Bistability of prefrontal states gates access to consciousness
Authors: Dwarakanath Abhilash , Kapoor Vishal , Werner Joachim , Safavi Shervin , Fedorov Leonid A. , Logothetis Nikos K. , Panagiotaropoulos Theofanis I. 
Published: January 2020

SummaryAccess of sensory information to consciousness is thought to be mediated through ignition of neural activity in the prefrontal cortex (PFC). Ignition occurs once activity elicited by sensory input crosses a threshold, which has been shown to depend on brain state fluctuations. However, the neural correlates of fluctuations and their interaction with the neural representations of conscious contents within the PFC remain largely unknown. To understand the role of prefrontal state fluctuations in conscious access, we combined multielectrode intracortical recordings with a no-report binocular rivalry (BR) paradigm that induces spontaneously-driven changes in conscious perception. During BR, antagonistic coupling of two prefrontal states, characterised by dominance of low frequency (1-9Hz) or beta (20-40Hz) local field potentials (LFP), reflect competition between two states of visual consciousness; perceptual update and stability, respectively. Low frequency perisynaptic bursts precede spontaneous transitions in conscious perception, signalling upcoming perceptual update of conscious content. We therefore show that it is a global cortical state that seems to drive internal switches, rather than the spiking activity of selective neuronal ensembles, which subsequently, only report the active percept. Beta band bursts were found to be correlated with periods of stable conscious perception, and selectively synchronised the neural ensemble coding for the consciously perceived stimulus. Similar ongoing fluctuations in the LFPs, with dynamics resembling the distribution of perceptual dominance periods during BR, dominated the prefrontal cortex during resting-state, thus pointing to their default, endogenous nature. Our results suggest that the two modes of conscious perception: perceptual update, and stability, can be associated with distinct prefrontal cortical states.
Neurovascular Function in a Novel Model of Experimental Atherosclerosis
Authors: Shabir Osman , Pendry Ben , Heath Paul R , Rebollar Monica A , Howarth Clare , Wharton Stephen B , Berwick Jason , Francis Sheila E 
Published: January 2020

AbstractObjectiveAtherosclerosis is a major risk factor for dementia. The aims of this study were to determine if experimental atherosclerosis leads to altered neurovascular function and causes neurovascular damage.Approach and ResultsWe analysed cerebral blood volume in male C57BL6/J mice injected with an adeno-associated virus (AAV) vector for mutated proprotein convertase subtilisin/kexin type 9 (PCSK9D377Y) fed a Western diet for 35 weeks to induce atherosclerosis (ATH) and 9-12m male wild-type (WT) C57BL/6J. We imaged blood volume responses to sensory stimulation and vascular reactivity gas challenges in the cortex of the brain through a thinned cranial window using 2D-optical imaging spectroscopy (2D-OIS). Neural activity was also recorded with multi-channel electrodes. Stimulation-evoked cortical haemodynamics, in terms of cerebral blood volume, were significantly reduced in ATH mice compared to WT and evoked neural activity was also significantly lower. However, vascular reactivity as assessed by 10% hypercapnia, remained intact in ATH mice. Immunohistochemistry in ATH mice revealed a reduced number of cortical neurons and pericytes in the cortex, but increased astrogliosis. qRT-PCR revealed significantly enhanced TNFα & IL1β in ATH mice compared to WT as well as significant upregulation of eNOS.ConclusionSystemic atherosclerosis causes significant neurovascular decline by 9m in atherosclerotic mice characterised by reduced neural activity, associated with loss of neurons and subsequent reduced cortical haemodynamics in response to physiological stimulations. The altered neurovascular function in ATH mice is chiefly mediated by TNFα.HighlightsSystemic atherosclerosis leads to significantly reduced stimulus-evoked hemodynamic responses in the cortex by 9m of age in the rAAV8-mPCSK9-D377Y mouse model of atherosclerosis compared to wild-type controls.Reduced cerebral haemodynamics are related to reduced neural activity in the cortex that could be due to a loss of cortical neurons potentially caused by significant TNFa-mediated neuroinflammation.
Wide-vergence, multi-spectral adaptive optics scanning laser ophthalmoscope with diffraction-limited illumination and collection
Authors: Mozaffari Sanam , Larocca Francesco , Jaedicke Volker , Tiruveedhula Pavan , Roorda Austin 
Published: January 2020

AbstractVisualizing and assessing the function of microscopic retinal structures in the human eye is a challenging task that has been greatly facilitated by ophthalmic adaptive optics (AO). Yet, as AO imaging systems advance in functionality by employing multiple spectral channels and larger vergence ranges, achieving optimal resolution and signal-to-noise ratios (SNR) becomes difficult and is often compromised. While current-generation AO retinal imaging systems have demonstrated excellent, near diffraction-limited imaging performance over wide vergence and spectral ranges, a full theoretical and experimental analysis of an AOSLO that includes both the light delivery and collection optics has not been done, and neither has the effects of extending wavefront correction from one wavelength to imaging performance in different spectral channels. Here, we report a methodology and system design for simultaneously achieving diffraction-limited performance in both the illumination and collection paths for a wide-vergence, multi-spectral AO scanning laser ophthalmoscope (SLO) over a 1.2 diopter vergence range while correcting the wavefront in a separate wavelength. To validate the design, an AOSLO was constructed to have three imaging channels spanning different wavelength ranges (543 ± 11 nm, 680 ± 11 nm, and 840 ± 6 nm, respectively) and one near-infrared wavefront sensing channel (940 ± 5 nm). The AOSLO optics and their alignment were determined via simulations in optical and optomechanical design software and then experimentally verified by measuring the AOSLO’s illumination and collection point spread functions (PSF) for each channel using a phase retrieval technique. The collection efficiency was then measured for each channel as a function of confocal pinhole size when imaging a model eye achieving near-theoretical performance. Imaging results from healthy human adult volunteers demonstrate the system’s ability to resolve the foveal cone mosaic in all three imaging channels despite a wide spectral separation between the wavefront sensing and imaging channels.OCIS codes(110.1080) Active or adaptive optics; (170.4460) Ophthalmic optics and devices; (170.4470) Ophthalmology
Taking population stratification into account by local permutations in rare-variant association studies on small samples
Authors: Mullaert J. , Bouaziz M. , Seeleuthner Y. , Bigio B. , Casanova J-L. , Alcais A. , Abel L. , Cobat A. 
Published: January 2020

AbstractMany methods for rare variant association studies require permutations to assess the significance of tests. Standard permutations assume that all individuals are exchangeable and do not take population stratification (PS), a known confounding factor in genetic studies, into account. We propose a novel strategy,LocPerm, in which individuals are permuted only with their closest ancestry-based neighbors. We performed a simulation study, focusing on small samples, to evaluate and compareLocPermwith standard permutations and classical adjustment on first principal components. Under the null hypothesis,LocPermwas the only method providing an acceptable type I error, regardless of sample size and level of stratification. The power ofLocPermwas similar to that of standard permutation in the absence of PS, and remained stable in different PS scenarios. We conclude thatLocPermis a method of choice for taking PS and/or small sample size into account in rare variant association studies.
The role of group I p21-activated kinases in contraction-stimulated skeletal muscle glucose transport
Authors: Møller Lisbeth L. V. , Nielsen Ida L. , Knudsen Jonas R. , Andersen Nicoline R. , Jensen Thomas E. , Sylow Lykke , Richter Erik A. 
Published: January 2020

AbstractAimMuscle contraction stimulates skeletal muscle glucose transport. Since it occurs independently of insulin, it is an important alternative pathway to increase glucose uptake in insulin-resistant states, but the intracellular signalling mechanisms are not fully understood. Muscle contraction activates group I p21-activated kinases (PAKs) in mouse and human skeletal muscle. PAK1 and PAK2 are downstream targets of Rac1, which is a key regulator of contraction-stimulated glucose transport. Thus, PAK1 and PAK2 could be downstream effectors of Rac1 in contraction-stimulated glucose transport. The current study aimed to test the hypothesis that PAK1 and/or PAK2 regulate contraction-induced glucose transport.MethodsGlucose transport was measured in isolated soleus and extensor digitorum longus (EDL) mouse skeletal muscle incubated either in the presence or absence of a pharmacological inhibitor (IPA-3) of group I PAKs or originating from whole-body PAK1 knockout (KO), muscle-specific PAK2 (m)KO or double whole-body PAK1 and muscle-specific PAK2 knockout mice.ResultsIPA-3 attenuated (−22%) the increase in muscle glucose transport in response to electrically-stimulated contraction. PAK1 was dispensable for contraction-stimulated glucose uptake in both soleus and EDL muscle. Lack of PAK2, either alone (−13%) or in combination with PAK1 (−14%), reduced contraction-stimulated glucose transport compared to control littermates in EDL, but not soleus muscle.ConclusionContraction-stimulated glucose transport in isolated glycolytic mouse EDL muscle is partly dependent on PAK2, but not PAK1.
Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix
Authors: Iuliano James N. , Collado Jinnette Tolentino , Gil Agnieszka A. , Ravindran Pavithran T. , Lukacs Andras , Shin SeungYoun , Woroniecka Helena A. , Adamczyk Katrin , Aramini James M. , Edupuganti Uthama R. , Hall Christopher R. , Greetham Gregory M. , Sazanovich Igor V. , Clark Ian P. , Daryaee Taraneh , Toettcher Jared E. , French Jarrod B. , Gardner Kevin H. , Simmerling Carlos L. , Meech Stephen R. , Tonge Peter J. 
Published: January 2020

AbstractLight-activated protein domains provide a convenient, modular, and genetically encodable sensor for optogenetics and optobiology. Although these domains have now been deployed in numerous systems, the precise mechanism of photoactivation and the accompanying structural dynamics that modulate output domain activity remain to be fully elucidated. In the C-terminal light, oxygen, voltage (LOV) domain of plant phototropins (LOV2), blue light activation leads to formation of an adduct between a conserved Cys residue and the embedded FMN chromophore, rotation of a conserved Gln (Q513), and unfolding of a helix (Jα-helix) which is coupled to the output partner. In the present work, we focus on the allosteric pathways leading to Jα helix unfolding inAvena sativaLOV2 (AsLOV2) using an interdisciplinary approach involving molecular dynamics simulations extending to 7 μs, time-resolved infrared spectroscopy, solution NMR spectroscopy, and in-cell optogenetic experiments. In the dark state, the side chain of N414 is hydrogen bonded to the backbone N-H of Q513. The simulations predict a lever-like motion of Q513 after Cys adduct formation resulting in loss of the interaction between the side chain of N414 and the backbone C=O of Q513, and formation of a transient hydrogen bond between the Q513 and N414 side chains. The central role of N414 in signal transduction was evaluated by site-directed mutagenesis supporting a direct link between Jα helix unfolding dynamics and the cellular function of the Zdk2-AsLOV2 optogenetic construct. Through this multifaceted approach, we show that Q513 and N414 are critical mediators of protein structural dynamics, linking the ultrafast (sub-ps) excitation of the FMN chromophore to the microsecond conformational changes that result in photoreceptor activation and biological function.
A rapidly evolved shift in life history timing during ecological speciation is driven by the transition between developmental phases
Authors: Powell Thomas H. Q. , Nguyen Andrew , Xia Qinwen , Feder Jeffrey L. , Ragland Gregory J. , Hahn Daniel A. 
Published: January 2020

AbstractFor insect species in temperate environments, seasonal timing is often governed by the regulation of diapause, a complex developmental program that allows insects to weather unfavorable conditions and synchronize their lifecycles with available resources. Diapause consists of a series of phases that govern initiation, maintenance, and termination of this developmental pathway. The evolution of insect seasonal timing depends in part on how these phases of diapause development and post-diapause development interact to affect variation in phenology. Here, we dissect the physiological basis of a recently evolved phenological shift inRhagoletis pomonella(Diptera: Tephritidae), a model system for ecological divergence. A recently derived population ofR. pomonellashifted from specializing on native hawthorn fruit to earlier fruiting introduced apples, resulting in a 3-4 week shift in adult emergence timing. We tracked metabolic rates of individual flies across post-winter development to test which phases of development may act either independently or in combination to contribute to this recently evolved divergence in timing. Apple and hawthorn flies differed in a number of facets of their post-winter developmental trajectories. However, divergent adaptation in adult emergence phenology in these flies was due almost entirely to the end of the pupal diapause maintenance phase, with post-diapause development having a very small effect. The relatively simple underpinnings of variation in adult emergence phenology suggest that further adaptation to seasonal change in these flies for this trait might be largely due to the timing of diapause termination unhindered by strong covariance among different components of post-diapause development.Data accessibilityAll data (in the form of tables of all metabolic rate measurements for all individual flies in the study) will be available on DRYAD when the manuscript is published.
A Tug of War Between Condensate Phases in a Minimal Macromolecular System
Authors: Ghosh Archishman , Zhang Xiaojia , Zhou Huan-Xiang 
Published: January 2020

AbstractMembraneless organelles formed via liquid-liquid phase separation (LLPS) contain a multitude of macromolecular species. A few of these species drive LLPS while most serve as regulators. The LLPS of SH35(S) and PRM5(P), two oppositely charged protein constructs, was promoted by a polyanion heparin (H) but suppressed by a cationic protein lysozyme (L). Here, using these four components alone, we demonstrate complex phase behaviors associated with membraneless organelles and uncover the underlying physical rules. The S:P, S:L, and P:H binaries form droplets, but the H:L binary forms precipitates, therefore setting off a tug of water between different phases within the S:P:H:L quaternary. We observe dissolution of precipitates upon compositional change, transformation from precipitates to droplet-like condensates over time, and segregation of S:L-rich and P:H-rich foci inside droplet-like condensates. A minimal macromolecular system can thus recapitulate membraneless organelles in essential ways and provide crucial physical understanding.