bluuebunny/crossref_metadata_2025 huggingface dataset:
βVPE is involved in tapetal degradation and pollen development by activating proprotease maturation in Arabidopsis thaliana
Authors: Cheng Ziyi , Yin Bin , Zhang Jiaxue , Liu Yadi , Wang Bing , Li Hui , Lu Hai
Published: December 2018

Vacuolar processing enzyme (VPE) is responsible for the maturation and activation of vacuolar proteins in plants. We found that βVPE was involved in tapetal degradation and pollen development by transforming proproteases into mature protease in Arabidopsis thaliana. βVPE was expressed specifically in the tapetum from stages 5–8 of anther development. The βVPE protein first appeared as a proenzyme and transformed into the mature enzyme before stages 7–8. The recombinant βVPE protein self-cleaved and transformed to a 27-kD mature protein at pH 5.2. The mature βVPE protein could induce the maturation of CEP1 in vitro. βvpe mutants exhibited delayed vacuolar degradation and decreased pollen fertility. The maturation of CEP1, RD19A, and RD19C were seriously inhibited in βvpe mutants. Our results indicate that βVPE is a crucial processing enzyme that directly participates in the maturation of cysteine proteases before vacuolar degradation, and is indirectly involved in pollen development and tapetal cell degradation.
Opsin gene evolution in amphibious and terrestrial combtooth blennies (Blenniidae)
Authors: Cortesi Fabio , Cheney Karen M , Cooke Georgina M , Ord Terry
Published: December 2018

Evolutionary adaptations to life on land include changes to the physiology, morphology and behaviour of an animal in response to physical differences between water and air. The visual systems of amphibious species show pronounced morphological adaptations; yet, whether molecular changes also occur remains largely unknown. Here, we investigated the molecular evolution of visual pigment genes (opsins) in amphibious and terrestrial fishes belonging to the Salariini division of blennies (Blenniidae). We hypothesized that when conquering land, blenny opsins adapt, in terms of sequence variation and/or gene expression, to match both higher light intensities as well as the broader light spectrum. Using retinal transcriptomes in six species ranging from fully aquatic to fully terrestrial, we found very little variation in opsin gene sequences or gene expression between species. All blennies expressed a single rod opsin gene as well as two cone opsin genes sensitive to longer-wavelengths of light: RH2A-1 (green-sensitive) and LWS (red-sensitive). They also expressed one or two short-wavelength-sensitive cone opsin genes (SWS2Aα, SWS2Aβ; blue-sensitive) in a phylogenetically inert manner. However, based on amino acid predictions, both SWS2A proteins confer similar peak spectral sensitivities and differential expression is therefore unlikely to be ecologically significant. Red-sensitivity is likely beneficial for feeding on algae and detritus, the main food source of Salariini blennies, and could be co-adapted to perceive visual displays in terrestrial species, which often use red dorsal fins to signal during aggressive disputes and courtship. Our data suggests that on the molecular level, the visual systems that evolved in aquatic blennies have been retained in species that have transitioned onto land.
Maternal psychosocial risk factors and offspring gestational epigenetic age acceleration in a South African birth cohort study
Authors: Koen Nastassja , Jones Meaghan , Nhapi Raymond T. , Donald Kirsten A. , Barnett Whitney , Hoffman Nadia , MacIsaac Julia L. , Morin Alexander M. , Lin David T.S. , Kobor Michael S. , Koenen Karestan C. , Zar Heather J. , Stein Dan J.
Published: December 2018

Epigenetic age (EA) acceleration is associated with higher risk of chronic disease and mortality in adults. However, little is known about whether and how in utero exposures might shape gestational EA acceleration at birth. We aimed to explore associations between maternal psychosocial risk factors and offspring gestational EA acceleration at birth in a South African birth cohort study - the Drakenstein Child Health Study. Maternal psychosocial risk factors included trauma/stressor exposure; posttraumatic stress disorder (PTSD); depression, psychological distress; and alcohol/tobacco use. Offspring gestational EA acceleration at birth was calculated using an epigenetic clock previously devised for neonates. Bivariate linear regression was used to explore unadjusted associations between maternal risk factors and offspring gestational EA acceleration at birth. A stepwise regression method was then used to determine the best multivariable model for adjusted associations. Data from 272 maternal-offspring dyads were included in the current analysis. In the stepwise regression model, maternal trauma exposure (β = 7.92; p<0.01) or PTSD (β = 7.46; p<0.01) were significantly associated with offspring gestational EA acceleration at birth, controlling for ethnicity, offspring sex, head circumference at birth, maternal HIV status, and prenatal tobacco or alcohol use. In site-stratified models, these associations retained statistical significance and direction of effect. Maternal trauma exposure or PTSD may thus be associated with offspring gestational EA acceleration at birth. Given the novelty of this preliminary finding, and its potential translational relevance, further studies to delineate underlying biological pathways and to explore clinical implications of EA acceleration are warranted.
qgg: an R package for large-scale quantitative genetic analyses
Authors: Rohde Palle Duun , Sørensen Izel Fourie , Sørensen Peter
Published: December 2018

Studies of complex traits and diseases are strongly dependent on the availability of user-friendly software designed to handle large-scale genetic and phenotypic data. Here, we present the R package qgg, which provides an environment for large-scale genetic analyses of quantitative traits and disease phenotypes. The qgg package provides an infrastructure for efficient processing of large-scale genetic data and functions for estimating genetic parameters, performing single and multiple marker association analyses, and genomic-based predictions of phenotypes. In particular, we have developed novel predictive models that use information on functional features of the genome that enables more accurate predictions of complex trait phenotypes. We illustrates core facilities of the qgg package by analysing human standing height from the UK Biobank.

Availability and implementation

The R package qgg is freely available. For latest updates, user guides and example scripts, consult the main page http://psoerensen.github.io/qgg/.
A unifying photocycle model for light adaptation and temporal evolution of cation conductance in Channelrhodopsin-2
Authors: Kuhne Jens , Vierock Johannes , Tennigkeit Stefan Alexander , Dreier Max-Aylmer , Wietek Jonas , Petersen Dennis , Gavriljuk Konstantin , El-Mashtoly Samir F. , Hegemann Peter , Gerwert Klaus
Published: December 2018

Although Channelrhodopsin (ChR) is a widely applied light-activated ion channel, important properties such as light-adaptation, photocurrent inactivation, and alteration of the ion selectivity during continuous illumination are not well-understood from a molecular perspective. Herein, we address these open questions using single turn-over electrophysiology, time-resolved step-scan FTIR and Raman spectroscopy of fully dark adapted ChR2. This yields a unifying parallel photocycle model explaining all data: in dark-adapted ChR2, the protonated Schiff base retinal chromophore (RSBH+) adopts an all-trans,C=N-anti conformation only. Upon light activation, a branching reaction into either a 13-cis,C=N-anti or a 13-cis,C=N-syn retinal conformation occurs. The anti-cycle features sequential H+ and Na+ conductance in a late M-like state and an N-like open-channel state. In contrast, the 13-cis,C=N-syn isomer represents a second closed-channel state identical to the long lived P480-state, which has been previously assigned to a late intermediate in a single photocycle model. Light excitation of P480 induces a parallel syn-photocycle with an open channel state of small conductance and high proton selectivity. E90 becomes deprotonated in P480 and stays deprotonated in the C=N-syn-cycle and we show that deprotonation of E90 and successive pore hydration are crucial for late proton conductance following light-adaptation. Parallel anti- and syn-photocycles explain inactivation and ion selectivity changes of ChR2 during continuous illumination, fostering the future rational design of optogenetic tools.

Significance statement

Understanding the mechanisms of photoactivated biological processes facilitates the development of new molecular tools, engineered for specific optogenetic applications, allowing the control of neuronal activity with light. Here, we use a variety of experimental and theoretical techniques to examine the precise nature of the light-activated ion channel in one of the most important molecular species used in optogenetics, channelrhodopsin-2. Existing models for the photochemical and photophysical pathway after light absorption by the molecule fail to explain many aspects of its observed behavior including the inactivation of the photocurrent under continuous illumination. We resolve this by proposing a new branched photocycle explaining electrical and photochemical channel properties and establishing the structure of intermediates during channel turnover.
Impaired reliability and precision of spiking in adults but not juveniles in a mouse model of Fragile X Syndrome
Authors: Dwivedi Deepanjali , Chattarji Sumantra , Bhalla Upinder S.
Published: December 2018

Fragile X Syndrome (FXS) is the most common source of intellectual disability and autism. Extensive studies have been performed on the network and behavioral correlates of the syndrome but our knowledge about intrinsic conductance changes is still limited. In this study we show a differential effect of FMRP Knock Out (KO) in different sub-sections of hippocampus using whole cell patch clamp in mouse hippocampal slices. We observed no significant change in spike numbers in the CA1 region of hippocampus but a significant increase in CA3, in juvenile mice. However, in adult mice we see a reduction in spike number in the CA1 with no significant difference in CA3. In addition, we see increased variability in spike number in CA1 cells following a variety of steady and modulated current step protocols. This effect emerges in adult (8 weeks) but not juvenile (4 weeks) mice. This increased spiking variability was correlated with reduced spike number and with elevated AHP. The increased AHP arose from elevated SK currents (small conductance calcium activated potassium channels) but other currents involved in mAHP, such as Ih and M, were not significantly different. We obtained a partial rescue of the cellular variability phenotype when we blocked SK current using the specific blocker apamin. Our observations provide a single cell correlate of the network observations of response variability and loss of synchronization, and suggest that elevation of SK currents in FXS may provide a partial mechanistic explanation for this difference.

Significance Statement

Fragile-X syndrome leads to a range of intellectual disability effects and autism. We have found differential effect of FMRP KO in different sub sections of hippocampus where it caused an increased spiking in CA3 in juveniles and reduced spiking in CA1, in adults. We have also found that even individual neurons with this mutation exhibit increased variability in their activity patterns. Importantly, this effect emerges after six weeks of age in mice. We showed that a specific ion channel protein, SK channel, was partially responsible, and blockage of these channels led to a partial restoration of cellular activity. This is interesting as it provides a possible molecular link between activity variability in single cells, and reported irregularity in network activity.
Are Zinc oxide nanoparticles safe? A structural study on human serum albumin using in vitro and in silico methods
Authors: Hassanian Marziyeh , Aryapour Hassan , Goudarzi Alireza , Javan Masoud Bezi
Published: December 2018

With due attention to adsorption of proteins on the nanoparticles surface and the formation of nanoparticle-protein corona, investigation of nanoparticles toxicity on the structure of proteins is important. Therefore, this work was done to evaluate toxicity of Zinc oxide nanoparticles (ZnO NPs) on the structure of human serum albumin (HSA) through in vitro and in silico studies. First, ZnO NPs were synthesized using hydrothermal method and their size and morphology were determined by SEM and TEM methods and then to study its toxicity on the HSA structure were used UV-Vis and fluorescence spectroscopy. Also, in order to investigate interaction mechanism of ZnO NP with HSA at the atomistic level was used molecular dynamics (md) simulation. The obtained images from SEM and TEM showed that ZnO NPs were nanosheet with size of less than 40 nm. The results of spectroscopic studies showed ZnO NPs lead to significant conformational changes in the protein’s absorption and emission spectra. Moreover, md results showed the minor structure changes in HSA due to interaction with ZnO NP during the 100 ns simulation and the formation of nanoparticle-protein corona complex that is mainly because of electrostatic interactions between charge groups of HSA and ZnO NP.
Time-resolved succession of epigenetic regulation during early mammalian development
Authors: Chen Hebing , Li Hao , Jiang Shuai , Huang Xin , Li Wanying , Li Ruijiang , Zhang Zhuo , Hong Hao , Zhao Chenghui , Bo Xiaochen
Published: December 2018

During early mammalian embryonic development, different epigenetic mechanisms undergo dramatic changes; yet how these interconnected epigenetic layers function together to coordinate expression of the genetic code in a spatiotemporal manner remains unknown. Here, we describe a time-resolved study of the hierarchy of epigenetic marks and events, which we used to model transcriptional programs that cannot be understood by investigating steady state. We found that, following fertilization, the re-establishment of accessible chromatin together with transcription factors inherited from oocytes initiates transcription at the 2-cell stage, and then the introduction of active histone modification, H3K4me3, facilitates gene up-regulation at the 4-cell stage, then stabilization of higher-order chromatin structures at the 8-cell stage further enhances transcriptional activity. During the first lineage specification at ICM, transcription activity multifaceted regulation of epigenetic marks. Finally, we quantitatively model the stage succession of different epigenetic marks on transcriptional programs during early embryonic development.
Bioorthogonal labeling with tetrazine-dyes for super-resolution microscopy
Authors: Beliu Gerti , Kurz Andreas , Kuhlemann Alexander , Behringer-Pliess Lisa , Wolf Natalia , Seibel Juergen , Shi Zhen-Dan , Schnermann Martin , Grimm Jonathan , Lavis Luke , Doose Soeren , Sauer Markus
Published: December 2018

Genetic code expansion (GCE) technology allows the specific incorporation of functionalized noncanonical amino acids (ncAAs) into proteins. Here, we investigated the Diels-Alder reaction between trans-cyclooct-2-ene (TCO)-modified ncAAs, and 22 known and novel 1,2,4,5-tetrazine-dye conjugates spanning the entire visible wavelength range. A hallmark of this reaction is its fluorogenicity - the tetrazine moiety can elicit substantial quenching of the dye. We discovered that photoinduced electron transfer (PET) from the excited dye to tetrazine as the main quenching mechanism in red-absorbing oxazine and rhodamine derivatives. Upon reaction with dienophiles quenching interactions are reduced resulting in a considerable increase in fluorescence intensity. Efficient and specific labeling of all tetrazine-dyes investigated permits super-resolution microscopy with high signal-to-noise ratio even at the single-molecule level. The different cell permeability of tetrazine-dyes can be used advantageously for specific intra- and extracellular labeling of proteins and highly sensitive fluorescence imaging experiments in fixed and living cells.
Continent-scale phenotype mapping using citizen scientists’ photographs
Authors: Drury Jonathan P. , Barnes Morgan , Finneran Ann E. , Harris Maddie , Grether Gregory F.
Published: December 2018

Field investigations of phenotypic variation in free-living organisms are often limited in scope owing to time and funding constraints. By collaborating with online communities of amateur naturalists, investigators can greatly increase the amount and diversity of phenotypic data in their analyses while simultaneously engaging with a public audience. Here, we present a method for quantifying phenotypes of individual organisms in citizen scientists’ photographs. We then show that our protocol for measuring wing phenotypes from photographs yields accurate measurements in two species of Calopterygid damselflies. Next, we show that, while most observations of our target species were made by members of the large and established community of amateur naturalists at iNaturalist.org, our efforts to increase recruitment through various outreach initiatives were successful. Finally, we present results from two case studies: (1) an analysis of wing pigmentation in male smoky rubyspots (Hetaerina titia) showing previously undocumented geographical variation in a seasonal polyphenism, and (2) an analysis of variation in the relative size of the wing spots of male banded demoiselles (Calopteryx splendens) in Great Britain questioning previously documented evidence for character displacement. Our results demonstrate that our protocol can be used to create high quality phenotypic datasets using citizen scientists’ photographs, and, when combined with metadata (e.g., date and location), can greatly broaden the scope of studies of geographical and temporal variation in phenotypes. Our analyses of the recruitment and engagement process also demonstrate that collaborating with an online community of amateur naturalists can be a powerful way to conduct hypothesis-driven research aiming to elucidate the processes that impact trait evolution at landscape scales.
Transcriptional output, cell types densities and normalization in spatial transcriptomics
Authors: Saiselet Manuel , Rodrigues-Vitória Joël , Tourneur Adrien , Craciun Ligia , Spinette Alex , Larsimont Denis , Andry Guy , Lundeberg Joakim , Maenhaut Carine , Detours Vincent
Published: December 2018

Spatial transcriptomics measures mRNA at hundreds of 100 micrometer-diameter spots evenly spread across 6.5×6.9 mm2 histological slices. Gene expression within each spot is commonly normalized by total read counts. However we show that the transcriptional output of individual spots reflects the number of cells they contain, hence total read counts per spot reflect relevant biology. Although per-spot read-count normalization reveals important enrichment trends, it may heavily distort cell-type-related absolute local expression and conceal important biological information.
1,4-dihydroxy Quininib Attenuates Growth of Colorectal Cancer Cells and Xenografts and Regulates the TIE-2 Signaling Pathway in Patient Tumours
Authors: Butler Clare T , Kennedy Susan , Buckley Amy , Doyle Ronan , Conroy Emer , Gallagher William M , O'Sullivan Jacintha , Kennedy Breandan N
Published: December 2018

Colorectal cancer (CRC) is the second leading cause of cancer associated deaths in developed countries. Cancer progression and metastatic spread is reliant on new blood vasculature, or angiogenesis. Tumour-related angiogenesis is regulated by pro- and anti-angiogenic factors secreted from malignant tissue in a stepwise process. Previously we structurally modified the small anti-angiogenic molecule quininib and discovered a more potent anti-angiogenic compound 1, 4 dihydroxy quininib (Q8), an antagonist of cysteinyl leukotriene receptor-1 with VEGF-independent bioactivity. Here, Q8, quininib (Q1) and five structural analogues were assayed for anti-tumorigenic effects in pre-clinical cancer models. Q8 reduced clone formation of the human colorectal cancer cell line HT29-Luc2. Gene silencing of CysLT1 in HT29-Luc2 cells significantly reduced expression of calpain-2. In human ex vivo colorectal cancer tumour explants, Q8 significantly decreased the secretion of both TIE-2 and VCAM-1 expression. In vivo Q8 was well tolerated up to 50 mg/kg by Balb/C mice and significantly more effective at reducing tumour volume in colorectal tumour xenografts compared to the parent drug quininib. In tumour xenografts, Q8 significantly reduced expression of the angiogenic marker calpain-2 in. In summary, we propose Q8 may act on the TIE-2-Angiopoietin signalling pathway to significantly inhibit the process of tumour angiogenesis in colorectal cancer.
Alopecia areata patients show deficiency of FOXP3+CD39+ T regulatory cells and clonotypic restriction of Treg TCR?-chain, which highlights the immunopathological aspect of the disease
Authors: Åstrand Annika Birgitta Margareta , Hamed Fatma N , Bertolini Marta , Rossi Alfredo , Maleki-Dizaji Afsaneh , Messenger Andrew G , McDonagh Andrew JG , Tazi-Ahnini Rachid
Published: December 2018

Alopecia areata (AA) is a hair loss disorder resulting from an autoimmune reaction against hair follicles. T-helper 1 cells are a major contributor to this disorder, but little is known about the role of T-regulatory cells (Tregs) in AA. Here, we analysed the distribution of circulating Treg subsets in twenty AA patients with active hair loss and fifteen healthy subjects by flow cytometry. The Treg suppressor HLA-DR+ subpopulation was significantly reduced in the patients (P<0.001) and there were significantly fewer cells expressing CD39 among the CD4+CD25+Foxp3+ Treg subpopulation in patients (P=0.001). FOXP3 CD39 Treg cells were also reduced in hair follicles; by 75% in non-lesional skin and 90% in lesional skin, when compared to control healthy skin. To further characterise Treg cells in AA; Tregs (CD4+CD25+FOXP3+) were investigated for their TCR? sequence. PCR products analysed by Next Generation Sequencing techniques, showed that all frequent public clonotypes in AA Tregs were also present in controls at relatively similar frequencies, excepting two public clonotypes: CATSRDEGGLDEKLFF (V15 D1 J1-4) and CASRDGTGPSNYGYTF (V2 D1 J1-2), which were exclusively present in controls. This suggests that these Treg clonotypes may have a protective effect and that they may be an exciting subject for future therapeutic applications.
Aspects of invasiveness of Ludwigia and Nelumbo in shallow temperate fluvial lakes
Authors: Tóth Viktor R. , Villa Paolo , Pinardi Monica , Bresciani Mariano
Published: December 2018

The relationship between invasive plant functional traits and their invasiveness is still the subject of scientific investigation, and the backgrounds of transition from non-native to invasive species in ecosystems are therefore poorly understood. Furthermore, our current knowledge on species invasiveness is heavily biased toward terrestrial species; we know much less about the influence of allochthonous plant traits on their invasiveness in aquatic ecosystems. We studied physiological and ecological traits of two introduced and three native macrophyte species in the Mantua lakes system (northern Italy). We compared their photophysiology, pigment content, leaf reflectance, and phenology in order to assess how the invasive Nelumbo nucifera and Ludwigia hexapetala perform compared to native species, Nuphar lutea, Nymphaea alba, and Trapa natans. We found L. hexapetala to have higher photosynthetic efficiency and able to tolerate higher light intensities than N. nucifera and the native species especially at extreme weather conditions (prolonged exposure to high light and higher temperatures). Chlorophyll a and b, and carotenoid contents of both allochthonous species was substantially higher than that of the native plants suggesting adaptive response to the ecosystem of Mantua lakes system. Higher variability of recorded data in invasive species also was observed. These observations suggest advanced photosynthetic efficiency of the invasive species, especially L. hexapetala, resulting in faster growth rates and higher productivity. This was supported by the evaluation of seasonal dynamics mapped from satellite remote sensing data. This study provides empirical evidence for the relationship between specific plant physiological traits and invasiveness of aquatic plant species, highlighting the importance of trait studies in predicting ecosystem-level impacts of invasive plant species.
Evolutionary implications of the microRNA- and piRNA complement of Lepidodermella squamata (Gastrotricha)
Authors: Fromm Bastian , Tosar Juan Pablo , Aguilera Felipe , Friedlander Marc Riemer , Bachmann Lutz , Hejnol Andreas
Published: December 2018

Gastrotrichs - hairy bellies - are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g. microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a multi-omics approach we here used small-RNA sequencing, available transcriptome and genomic data to unravel the miRNA- and piRNA complements along with the RNAi protein machinery of Lepidodermella squamata (Gastrotricha, Chaetonotida). We identified 52 miRNA genes representing 35 highly conserved miRNA families specific to Eumetazoa, Bilateria, Protostomia, and Spiralia, respectively, with overall high similarities to platyhelminth miRNA complements. In addition, we found four large piRNA clusters that also resemble flatworm piRNAs but not those earlier described for nematodes. Congruently, transcriptomic annotation revealed that the Lepidodermella protein machinery is highly similar to flatworms, too. Taken together, miRNA, piRNA and protein data support a close relationship of gastrotrichs and flatworms.
To integrate or not to integrate: Temporal dynamics of hierarchical Bayesian Causal Inference
Authors: Aller Máté , Noppeney Uta
Published: December 2018

To form a percept of the environment, the brain needs to solve the binding problem – inferring whether signals come from a common cause and be integrated, or come from independent causes and be segregated. Behaviourally, humans solve this problem near-optimally as predicted by Bayesian Causal Inference; but, the neural mechanisms remain unclear. Combining Bayesian modelling, electroencephalography (EEG), and multivariate decoding in an audiovisual spatial localization task, we show that the brain accomplishes Bayesian Causal Inference by dynamically encoding multiple spatial estimates. Initially, auditory and visual signal locations are estimated independently; next, an estimate is formed that combines information from vision and audition. Yet, it is only from 200 ms onwards that the brain integrates audiovisual signals weighted by their bottom-up sensory reliabilities and top-down task-relevance into spatial priority maps that guide behavioural responses. Critically, as predicted by Bayesian Causal Inference, these spatial priority maps take into account the brain’s uncertainty about the world’s causal structure and flexibly arbitrate between sensory integration and segregation. The dynamic evolution of perceptual estimates thus reflects the hierarchical nature of Bayesian Causal Inference, a statistical computation, crucial for effective interactions with the environment.
Extensive recombination suppression and chromosome-wide differentiation of a segregation distorter in Drosophila
Authors: Fuller Zachary L. , Koury Spencer A. , Leonard Christopher J. , Young Randee E. , Ikegami Kobe , Westlake Jonathan , Richards Stephen , Schaeffer Stephen W. , Phadnis Nitin
Published: December 2018

Segregation distorters violate Mendelian Inheritance by over-representing themselves in the progeny of carrier individuals and are commonly associated with chromosomal inversions. When distorting alleles are found on sex chromosomes, the progeny of carrier individuals will exhibit skewed sex ratios, as exemplified by the array ofSex-Ratio(SR) distorting chromosomes found in Drosophila. Because of the strong selective pressures such chromosomes are thought to inflict on genomes, segregation distorters and their associated inversions are expected to experience rapid turn-over. However, theSRX-chromosome ofDrosophila pseudoobscurais found at high frequencies in natural populations, forms stable latitudinal clines, appears to be unsuppressed, and shows evidence of being quite long-lived. Despite being a historically significant and well-studied segregation distortion system, the mechanisms allowing for the long-term persistence of theD.pseudoobscura SRchromosome remain unclear. Here, we perform a comparative genomic analysis betweenSRand uninverted standard X-chromosomes inD.pseudoobscurato study its evolutionary history and dynamics. We find a substantial level of differentiation between theSRand standard chromosome and estimate that the associated inversions have likely existed for the entire lifetime of the species (>2 million generations). Through direct recombination experiments and population genetic analyses, we infer that this high level of differentiation is maintained by a combination of suppressed recombination and epistatic selection. Finally, our data reveal a massive mutational target size for protein and expression level changes specific toSRgenerated by its three non-overlapping inversions. Together our results imply that the entireSRchromosome inD.pseudoobscurabehaves as a single co-adapted gene complex and has been maintained through a combination of suppressed recombination and epistatic selection. This finding highlights the dramatic consequences segregation distorters can have in shaping chromosome-wide patterns of recombination, nucleotide variation, and gene expression.
Diagnostic high-throughput sequencing of 2,390 patients with bleeding, thrombotic and platelet disorders
Authors: Downes Kate , Megy Karyn , Duarte Daniel , Vries Minka , Gebhart Johanna , Hofer Stefanie , Shamardina Olga , Deevil Sri VV , Stephens Jonathan , Mapeta Rutendo , Tuna Salih , Al Hasso Namir , Besser Martin W , Cooper Nichola , Daugherty Louise , Gleadall Nick , Greene Daniel , Haimel Matthias , Martin Howard , Papadia Sofia , Revel-Vilk Shoshana , Sivapalaratnam Suthesh , Symington Emily , Thomas Will , Thys Chantal , Tolios Alexander , Penkett Christopher J ,   NIHR BioResource, Ouwehand Willem H , Abbs Stephen , Laffan Michael A , Turro Ernest , Simeoni Ilenia , Mumford Andrew D , Henskens Yvonne MC , Pabinger Ingrid , Gomez Keith , Freson Kathleen
Published: December 2018

A targeted high-throughput sequencing (HTS) panel test for clinical diagnostics requires careful consideration of the inclusion of appropriate diagnostic-grade genes, the ability to detect multiple types of genomic variation with high levels of analytic sensitivity and reproducibility, and variant interpretation by a multi-disciplinary team (MDT) in the context of the clinical phenotype. We have sequenced 2,390 index patients using the ThromboGenomics HTS panel test of diagnostic-grade genes known to harbour variants associated with rare bleeding, thrombotic or platelet disorders (BPD). The diagnostic rate was determined by the clinical phenotype, with an overall rate of 50.4% for all thrombotic, coagulation, platelet count and function disorder patients and a rate of 6.2% for patients with unexplained bleeding disorders characterized by normal hemostasis test results. The MDT classified 756 unique variants, including copy number and intronic variants, as Pathogenic, Likely Pathogenic or Variants of Uncertain Significance. Almost half (49.7%) of these variants are novel and 41 unique variants were identified in 7 genes recently found to be implicated in BPD. Inspection of canonical hemostasis pathways identified 29 patients with evidence of oligogenic inheritance. A molecular diagnosis has been reported for 897 index patients providing evidence that introducing a HTS genetic test for BPD patients is meeting an important unmet clinical need.
Microglial activation in an amyotrophic lateral sclerosis-like model caused by Ranbp2 loss
and nucleocytoplasmic transport impairment in retinal ganglion neurons
Authors: Cho Kyoung-in , Yoon Dosuk , Yu Minzhong , Peachey Neal S , Ferreira Paulo A
Published: December 2018

Nucleocytoplasmic transport is dysregulated in sporadic and familial amyotrophic lateral sclerosis (ALS) and retinal ganglion neurons (RGNs) are purportedly involved in ALS. The Ran-binding protein 2 (Ranbp2) controls rate-limiting steps of nucleocytoplasmic transport. Mice with Ranbp2 loss in Thy1+-motoneurons develop cardinal ALS-like traits, but the impairments in RGNs and the degree of dysfunctional consonance between RGNs and motoneurons caused by Ranbp2 loss are unknown. This understanding will facilitate to discern the role of nucleocytoplasmic transport in the differential vulnerability of neurons to ALS and to develop therapeutic approaches and biomarkers in ALS. Here, we ascertain Ranbp2 function and endophenotypes in RGNs of an ALS-like mouse model lacking Ranbp2 in motoneurons and RGNs. Thy1+-RGNs lacking Ranbp2 shared with motoneurons the dysregulation of nucleocytoplasmic transport. RGN abnormalities were comprised morphologically by soma hypertrophy and optic nerve axonopathy and physiologically by a delay of the visual pathway evoked potentials. Whole-transcriptome analysis showed restricted transcriptional changes in optic nerves that were distinct from those found in sciatic nerves. Specifically, the level and nucleocytoplasmic partition of the anti-apoptotic and novel substrate of Ranbp2, Pttg1/securin, were dysregulated. Further, acetyl-CoA carboxylase 1, which modulates de novo synthesis of fatty acids and T-cell immunity, showed the highest up-regulation (35-fold). This effect was reflected by the activation of ramified Cd11b+ and CD45+-microglia, increase of F4\80+-microglia and a shift from pseudopodial/lamellipodial to amoeboidal F4\80+-microglia intermingled between RGNs of naive mice. This immunogenic phenotype was accompanied by the intracellular sequestration in RGNs of metalloproteinase-28, which regulates macrophage recruitment and polarization in inflammation. Ranbp2 genetic insults in RGNs and motoneurons trigger distinct paracrine signaling likely by the dysregulation of nucleocytoplasmic transport of neural-type selective substrates. Metabolic and immune-modulators underpinning RGN-to-microglial signaling are regulated by Ranbp2, and this neuroglial system manifests endophenotypes that are likely useful in the prognosis and diagnosis of ALS.
The Bayesian Superorganism: externalised memories facilitate distributed sampling
Authors: Hunt Edmund R. , Franks Nigel R. , Baddeley Roland J.
Published: December 2018

A key challenge for any animal (or sampling technique) is to avoid wasting time by searching for resources (information) in places already found to be unprofitable. In biology, this challenge is particularly strong when the organism is a central place forager – returning to a nest between foraging bouts – because it is destined repeatedly to cover much the same ground. This problem will be particularly acute if many individuals forage from the same central place, as in social insects such as the ants. Foraging (sampling) performance may be greatly enhanced by coordinating movement trajectories such that each ant (‘walker’) visits separate parts of the surrounding (unknown) space. We find experimental evidence for an externalised spatial memory in Temnothorax albipennis ants: chemical markers (either pheromones or cues such as cuticular hydrocarbon footprints) that are used by nestmates to mark explored space. We show these markers could be used by the ants to scout the space surrounding their nest more efficiently through indirect coordination. We also develop a simple model of this marking behaviour that can be applied in the context of Markov chain Monte Carlo methods (Baddeley et al. 2019). This substantially enhances the performance of standard methods like the Metropolis–Hastings algorithm in sampling from sparse probability distributions (such as those confronted by the ants) with little additional computational cost. Our Bayesian framework for superorganismal behaviour motivates the evolution of exploratory mechanisms such as trail marking in terms of enhanced collective information processing.
Amyloid Precursor Protein (APP) controls excitatory/inhibitory synaptic inputs by regulating the transcriptional activator Neuronal PAS Domain Protein 4 (NPAS4)
Authors: Opsomer Rémi , Contino Sabrina , Perrin Florian , Tasiaux Bernadette , Doyen Pierre , Vergouts Maxime , Vrancx Céline , Doshina Anna , Pierrot Nathalie , Octave Jean-Noël , Stanga Serena , Kienlen-Campard Pascal
Published: December 2018

Sequential proteolysis of the amyloid precursor protein (APP) and amyloid-β peptide (Aβ) release is an upstream event in Alzheimer’s disease (AD) pathogenesis. The function of APP in neuronal physiology is still, however, poorly understood. Along with its paralog APP-like Proteins 1 and 2 (APLP1-2), APP is involved in neurite formation and synaptic function by mechanisms that are not elucidated. APP is a single-pass transmembrane protein expressed at high levels in the brain that resembles a cell adhesion molecule or a membrane receptor, suggesting that its function relies on cell interaction processes and/or activation of intracellular pathways of signal transduction. Along this line, the APP intracellular domain (AICD) was reported to act as a transcriptional factor for targeted gene activation that mediates physiological APP functions. Here, we used an unbiased transcriptome-based approach to identify the genes transcriptionally regulated by APP in the rodent embryonic cortex and upon maturation of primary cortical neurons. The transcriptome analysis did not detect any significant differences in expression of previously proposed AICD target genes. The overall transcriptional changes were subtle, but we found that genes clustered in neuronal-activity dependent pathways are dysregulated in the absence of APP. Among these genes, we found the activity-dependent Neuronal PAS domain protein 4 (NPAS4) Immediate Early Gene to be downregulated in the absence of APP. Down-regulation of NPAS4 in APP knock-out (KO) neurons is not related to AICD but to the APP ectodomain. We studied the effect of APP deficiency on GABAergic and glutamatergic transmission, and found an increased production of the inhibitory neurotransmitter GABA in APP KO neurons, along with a reduced expression of the GABA(A) receptors alpha1, suggesting an impaired GABAergic neurotransmission in the absence of APP. CRISPR-Cas-mediated silencing of NPAS4 in neurons led to similar observations. Altogether, our results point out a new role for APP in the regulation of excitatory/inhibitory neurotransmission through the regulation of the activity-dependent NPAS4 gene.
Structural and Biochemical Studies of Dihydrofolate Reductase fromStreptococcus pyogenesas a Target for Antifolate Antibiotics
Authors: Hajian Behnoush , Krucinska Jolanta , Martins Michael , G-Dayanan Narendran , Viswanathan Kishore , Tavakoli Sara , Wright Dennis
Published: December 2018

Streptococcus pyogenes, abeta-hemolytic bacterium, causes a wide spectrum of infections in human including pharyngitis, tonsillitis, scarlet fever, rheumatic fever, and necrotizing fasciitis. Streptococcal infections can also exist as co-infection with methicillin resistantStaphylococcus aureus(MRSA). Trimethoprim-sulfamethoxazole (TMP-SMX) combination has been used for treatment ofS. pyogenesand MRSA co-infection. However, resistance to TMP, an inhibitor of dihydrofolate reductase enzyme (DHFR), has challenged the efficacy of TMP-SMX combination. We explored the activity of a series of novel DHFR inhibitors againstS. pyogenes. This study identified potent inhibitors of DHFR enzyme fromS. pyogeneswith excellent inhibitory activity against the growth of the live bacteria. We determined, for the first time, the crystal structure ofS. pyogenesDHFR which provides structural insights into design and development of antifolate agents against this global pathogen.
Performance evaluation of biosurfactant stabilized microbubbles in enhanced oil recovery
Authors: Dhanarajana Gunaseelan , Perveen Shaheen , Roy Anirban , De Sirshendu , Sen Ramkrishna
Published: December 2018

Microbubble technology is increasingly finding applications in biomedical engineering, soil remediation and wastewater treatment. Recently, the use of surfactant microbubbles has been studied as an alternate to aqueous solution in pollutant remediation since they have the advantage of improving the contact with the contaminant due to their surface properties. In this research endeavor, the application potential of microbubble suspension generated using a lipopeptide biosurfactant produced by a marine strain of Bacillus megaterium in tertiary oil recovery was investigated. The microbubbles were generated using a high speed homogenizer and their properties such as stability and size distribution were studied. The microbubble suspension was used as flooding agent to recover gear oil from an artificially saturated sand packed column. The performance of microbubbles in tertiary oil recovery was compared with that of aqueous biosurfactant solution. It was found that microbubble suspension generated using biosurfactant had higher oil recovery efficiency (46%) than aqueous solution (36%). Moreover, the pressure buildup across the sand packed column was fairly low while using microbubble suspension. The increased oil recovery using microbubbles can be attributed to their effective permeation through the pores of sand packed column and closer contact between biosurfactant molecules and oil. Thus, the results obtained in this study convincingly indicate that biosurfactant stabilized microbubble suspension, due to its higher performance and lower injection pressure requirement, can serve as a potentially efficient flooding agent for tertiary oil recovery.
Design of a Synthetic sRNA-based Feedback Filter Module
Authors: Delalez Nicolas , Sootla Aivar , Wadhams George H. , Papachristodoulou Antonis
Published: December 2018

Filters are widely used in engineering to reduce noise and/or the magnitude of a signal of interest. Feedback filters, or adaptive filters, are preferred if the signal noise distribution is unknown. One of the main challenges in Synthetic Biology remains the design of reliable constructs but these often fail to work as intended due, e.g. to their inherent stochasticity and burden on the host. Here we design, implement and test experimentally a biological feedback filter module based on small non-coding RNAs (sRNAs) and self-cleaving ribozymes. Mathematical modelling demonstrates that it attenuates noise for a large range of parameters due to negative feedback introduced by the use of ribozymes and sRNA. Our module modifies the steady-state response of the filtered signal, and hence can be used for tuning the feedback strength while also reducing noise. We demonstrated these properties theoretically on the TetR autorepressor, enhanced with our sRNA module.
Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries
Authors: Ross Tyler D. , Lee Heun Jin , Qu Zijie , Banks Rachel A. , Phillips Rob , Thomson Matt
Published: December 2018

Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, “active” molecules that create and manipulate non-equilibrium structures and force fields that span up to millimeter length scales [1–3]. Experimental active matter systems of biological or synthetic molecules are capable of spontaneously organizing into structures [4, 5] and generating global flows [6–9]. However, these experimental systems lack the spatiotemporal control found in cells, limiting their utility for studying non-equilibrium phenomena and bioinspired engineering. Here, we uncover non-equilibrium phenomena and principles by optically controlling structures and fluid flow in an engineered system of active biomolecules. Our engineered system consists of purified microtubules and light-activatable motor proteins that crosslink and organize microtubules into distinct structures upon illumination. We develop basic operations, defined as sets of light patterns, to create, move, and merge microtubule structures. By composing these basic operations, we are able to create microtubule networks that span several hundred microns in length and contract at speeds up to an order of magnitude faster than the speed of an individual motor. We manipulate these contractile networks to generate and sculpt persistent fluid flows. The principles of boundary-mediated control we uncover may be used to study emergent cellular structures and forces and to develop programmable active matter devices.
Extended field-of-view ultrathin microendoscopes with built-in aberration correction for high-resolution imaging with minimal invasiveness
Authors: Antonini Andrea , Bovetti Serena , Moretti Claudio , Succol Francesca , Rajamanickam Vijayakumar P , Bertoncini Andrea , Liberale Carlo , Fellin Tommaso
Published: December 2018

We present a novel approach to correct optical aberrations in ultrathin gradient-index rod lens-based endoscopes using microfabricated aspherical lenses. Corrected microendoscopes have up to 9 folds larger field-of-view compared to uncorrected probes. Using extended field-of-view (eFOV) microendoscopes, we report two-photon imaging of GCaMP6 signals in the mouse hippocampus in vivo with unprecedented combination of high spatiotemporal resolution and minimal invasiveness.
Comparison of Two-Talker Attention Decoding from EEG with Nonlinear Neural Networks and Linear Methods
Authors: Ciccarelli Gregory , Nolan Michael , Perricone Joseph , Calamia Paul , Haro Stephanie , O'Sullivan James , Mesgarani Nima , Quatieri Thomas , Smalt Christopher
Published: December 2018

Auditory attention decoding (AAD) through a brain-computer interface has had a flowering of developments since it was first introduced by Mesgarani and Chang (2012) using electrocorticograph recordings. AAD has been pursued for its potential application to hearing-aid design in which an attention-guided algorithm selects, from multiple competing acoustic sources, which should be enhanced for the listener and which should be suppressed. Traditionally, researchers have separated the AAD problem into two stages: reconstruction of a representation of the attended audio from neural signals, followed by determining the similarity between the candidate audio streams and the reconstruction. In this work, we compare the traditional two-stage approach with a novel neural-network architecture that subsumes the explicit similarity step. We compare this new architecture against linear and non-linear (neural-network) baselines using both wet and dry electroencephalogram (EEG) systems. Our results indicate that the wet and dry systems can deliver comparable results despite the latter having one third as many EEG channels as the former, and that the new architecture outperforms the baseline stimulus-reconstruction methods for both EEG modalities. The 14-subject, wet-electrode AAD dataset for two competing, co-located talkers, the 11-subject, dry-electrode AAD dataset, and our software are available to download for further validation, experimentation, and modification.