bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spectral jamming avoidance response does not help bats deal with jamming
Authors: Mazar Omer , Yovel Yossi 
Published: December 2019

AbstractFor decades, researchers have speculated how echolocating bats deal with acoustic interference created by conspecifics when flying in aggregations. It is thus surprising that there has been no attempt to quantify what are the chances of being jammed, or how such jamming would affect a bat’s hunting. To test this, we developed a computer model, simulating numerous bats foraging in proximity. We used a comprehensive sensorimotor model of a hunting bat, taking into consideration the physics of sound propagation and bats’ hearing physiology. We analyzed the instantaneous acoustic signals received by each bat, and were able to tease apart the effects of acoustic interference and of direct resource competition. Specifically, we examined the effectiveness of the spectral Jamming Avoidance Response - a shift in signal frequencies - which has been suggested as a solution for the jamming problem. As expected, we found that hunting performance deteriorates when bats forage near conspecific. However, applying a Jamming Avoidance Response did not improve hunting, and our simulations clearly demonstrate the reason: bats have adequate natural signal variability due to their constant adjustment of echolocation signals to the task. The probability to be jammed is thus small and further shifting the frequencies does not mitigate spectral jamming. Our simulations reveal both negative and positive insight: they show how bats can hunt successfully in a group despite potential sensory interference and they suggest that a Jamming Avoidance Response is not useful.
A novel ribosomal protein S20 variant in a family with unexplained colorectal cancer and polyposis
Authors: Thompson Bryony A. , Snow Angela K. , Koptiuch Cathryn , Kohlmann Wendy K. , Mooney Ryan , Johnson Sara , Huff Chad , Yu Yao , Teerlink Craig C. , Feng Bing-Jian , Neklason Deborah W. , Cannon-Albright Lisa A. , Tavtigian Sean V. 
Published: December 2019

ABSTRACTColorectal cancer (CRC) has a large hereditary component, which is only partially explained by known genetic causes. Recently, variants in ribosomal protein S20 (RPS20, [OMIM: 603682]) were identified in a family with familial CRC type X and in a CRC cancer case-control screen. This study describes a novel splice donor variant inRPS20, NM_001023.3:c.177+1G>A. It segregates with CRC [OMIM: 114500] and polyposis [HP: 0200063] within the proband’s family. Reverse transcription-polymerase chain reaction (RT-PCR) confirms the variant results in two aberrantly-spliced transcripts that are absent in controls. The location of the novelRPS20variant is near two previously-reported truncatingRPS20variants associated with CRC. DNA from colon adenocarcinoma showed no evidence of loss-of-heterozygosity, supporting a haploinsufficiency or dominant negative disease mechanism. These findings support designation ofRPS20as a CRC predisposition gene, and expand the phenotypic spectrum ofRPS20truncating variants to include polyposis.
From zygote to a multicellular soma: body size affects optimal growth strategies under cancer risk
Authors: Erten E. Yagmur , Kokko Hanna 
Published: December 2019

AbstractMulticellularity evolved independently in multiple lineages, yielding organisms with a wide range of adult sizes. Building an intact soma is not a trivial task, when dividing cells accumulate damage. Here, we study ‘ontogenetic management strategies’, i.e. rules of dividing, differentiating and killing somatic cells, to examine two questions. First, do these rules evolve differently for organisms differing in the target mature body size, and second, how well a strategy evolved in small-bodied organisms performs if implemented in a large body – and vice versa (‘large’-evolved strategies in small bodies). We model the growth and mature lifespan of an organism starting from a single cell and optimize, using a genetic algorithm, trait combinations across a range of target sizes, with seven evolving traits: 1) probability of asymmetric division, 2) probability of differentiation (per symmetric cell division), 3) Hayflick limit, 4) damage response threshold, 5) damage response strength, 6) number of differentiation steps, 7) division propensity of cells relative to ‘stemness’. Some, but not all traits, evolve differently depending on body size: large-bodied organisms perform best with a smaller probability of differentiation, a larger number of differentiation steps on the way to form a tissue, and a higher threshold of cellular damage to trigger cell death, than small organisms. Strategies evolved in large organisms are more robust: they maintain high performance across a wide range of body sizes, while those that evolved in smaller organisms fail when attempting to create a large body. This highlights an asymmetry: under various risks of developmental failure and cancer, it is easier for a lineage to become miniaturized (should selection otherwise favour this) than to increase in size.
Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular sensors
Authors: Andreasson Johan O. L. , Gotrik Michael R. , Wu Michelle J. , Wayment-Steele Hannah K. , Kladwang Wipapat , Portela Fernando , Wellington-Oguri Roger , Participants Eterna , Das Rhiju , Greenleaf William J. 
Published: December 2019

AbstractInternet-based scientific communities promise a means to apply distributed, diverse human intelligence towards previously intractable scientific problems. However, current implementations have not allowed communities to propose experiments to test all emerging hypotheses at scale or to modify hypotheses in response to experiments. We report high-throughput methods for molecular characterization of nucleic acids that enable the large-scale videogame-based crowdsourcing of functional RNA sensor design, followed by high-throughput functional characterization. Iterative design testing of thousands of crowdsourced RNA sensor designs produced near-thermodynamically optimal and reversible RNA switches that act as self-contained molecular sensors and couple five distinct small molecule inputs to three distinct protein binding and fluorogenic outputs—results that surpass computational and expert-based design. This work represents a new paradigm for widely distributed experimental bioscience.One Sentence SummaryOnline community discovers standalone RNA sensors.
Delineating the Organization of Projection Neuron Subsets with Multi-fluorescent Rabies Virus Tracing Tool
Authors: Li Liang , Tang Yajie , Sun Leqiang , Yu Jinsong , Gong Hui , Webber Hannah C. , Zhang Xiaoyu , Hu Zhe , Li Xiangning , Rahman Khaista , Fu Zhenfang , Dai Jinxia , Cao Gang 
Published: December 2019

AbstractThe elegant functions of the brain are facilitated by sophisticated connections between neurons, the architecture of which is frequently characterized by one nucleus connecting to multiple targets via projection neurons. Delineating the sub-nucleus fine architecture of projection neurons in a certain nucleus could greatly facilitate its circuit, computational, and functional resolution. Here, we developed multi-fluorescent rabies virus to delineate the fine organization of corticothalamic projection neuron subsets in the primary visual cortex (V1). By simultaneously labeling multiple distinct subsets of corticothalamic projection neurons in V1 from their target nuclei in thalamus (dLGN, LP, LD), we observed that V1-dLGN corticothalamic neurons were densely concentrated in layer VI, except for several sparsely scattered neurons in layer V, while V1-LP and V1-LD corticothalamic neurons were localized to both layers V and VI. Meanwhile, we observed a fraction of V1 corticothalamic neurons targeting multiple thalamic nuclei, which was further confirmed by fMOST whole-brain imaging. We further conceptually proposed an upgraded sub-nucleus tracing system with higher throughput (21 subsets) for more complex architectural tracing. The multi-fluorescent RV tracing tool can be extensively applied to resolve architecture of projection neuron subsets, with a strong potential to delineate the computational and functional organization of these nuclei.
Control of adaptive action selection by secondary motor cortex during flexible visual categorization
Authors: Wang Tian-Yi , Liu Jing , Yao Haishan 
Published: December 2019

AbstractAdaptive action selection during stimulus categorization is an important feature of flexible behavior. To examine neural mechanism underlying this process, we trained mice to categorize the spatial frequencies of visual stimuli according to a boundary that changed between blocks of trials in a session. Using a model with a dynamic decision criterion, we found that sensory history was important for adaptive action selection after the switch of boundary. Bilateral inactivation of the secondary motor cortex (M2) impaired adaptive action selection by reducing the behavioral influence of sensory history. Electrophysiological recordings showed that M2 neurons carried more information about upcoming choice and previous sensory stimuli when sensorimotor association was being remapped than when it was stable. Thus, M2 causally contributes to flexible action selection during stimulus categorization, with the representations of upcoming choice and sensory history regulated by the demand to remap stimulus-action association.
DNA Chisel, a versatile sequence optimizer
Authors: Zulkower Valentin , Rosser Susan 
Published: December 2019

AbstractMotivationAccounting for biological and practical requirements in DNA sequence design often results in challenging optimization problems. Current software solutions are problem-specific and hard to combine.ResultsDNA Chisel is an easy-to-use, easy-to-extend sequence optimization framework allowing to freely define and combine optimization specifications via Python scripts or Genbank annotations.Availabilityas a web application (https://cuba.genomefoundry.org/sculpt_a_sequence) or open-source Python library (code and documentation athttps://github.com/Edinburgh-Genome-Foundry/DNAChisel).Contactvalentin.zulkower@ed.ac.ukSupplementary informationattached.
Fine-scale fronts as hotspots of fish aggregation in the open ocean
Authors: Baudena Alberto , Ser-Giacomi Enrico , d’Onofrio Donatella , Capet Xavier , Cotté Cedric , Cherel Yves , d’Ovidio Francesco 
Published: December 2019

AbstractOceanic Lagrangian Coherent Structures have been shown to deeply influence the distribution of primary producers and, at the other extreme of the trophic chain, top predators. However, the relationship between these structures and intermediate trophic levels is much more obscure. In this paper we address this knowledge gap by comparing acoustic measurements of mesopelagic fish concentrations to satellite-derived fine-scale Lagrangian Coherent Structures in the open ocean. The results demonstrate unambiguously that higher fish concentrations are significantly associated with stronger Lagrangian Coherent Structures, and we observe that these features represent a limiting condition for high fish concentrations. A model, specifically built for mid trophic levels with realistic parameters, provides a possible mechanism of fish aggregation, and is coherent with the observations. These results may help to integrate intermediate trophic levels in trophic models, which can ultimately support management and conservation policies.
Patterns of thermal adaptation in a worldwide plant pathogen: local diversity and plasticity reveal two-tier dynamics
Authors: Boixel Anne-Lise , Chelle Michaël , Suffert Frédéric 
Published: December 2019

SummaryPlant pathogen populations inhabit patchy environments with contrasting, variable thermal conditions. We investigated the diversity of thermal responses in populations sampled over contrasting spatiotemporal scales, to improve our understanding of their dynamics of adaptation to local conditions.Samples of natural populations of the wheat pathogenZymoseptoria triticiwere collected from sites within the Euro-Mediterranean region subject to a broad range of environmental conditions. We tested for local adaptation, by accounting for the diversity of responses at the individual and population levels on the basis of key thermal performance curve parameters and ‘thermotype’ (groups of individuals with similar thermal responses) composition.The characterisation of phenotypic responses and genotypic structure revealed: (i) a high degree of individual plasticity and variation in sensitivity to temperature conditions across spatiotemporal scales and populations; (ii) geographic adaptation to local mean temperature conditions, with major alterations due to seasonal patterns over the wheat-growing season.The seasonal shifts in functional composition suggest that populations are locally structured by selection, contributing to shape adaptation patterns. Further studies combining selection experiments and modelling are required to determine how functional group selection drives population dynamics and adaptive potential in response to thermal heterogeneity.
Phospho-regulation of the Shugoshin - Condensin interaction at the centromere in budding yeast
Authors: Metwaly Galal Yahya , Wu Yehui , Peplowska Karolina , Röhrl Jennifer , Soh Young-Min , Bürmann Frank , Gruber Stephan , Storchova Zuzana 
Published: December 2019

AbstractCorrect bioriented attachment of sister chromatids to mitotic spindle is essential for chromosome segregation. The conserved protein shugoshin (Sgo1) contributes in budding yeast to biorientation by recruiting the protein phosphatase PP2A-Rts1 and the condensin complex to centromeres. Using peptide prints, we identified a Serine-Rich Motif (SRM) of Sgo1 that mediates the interaction with condensin and is essential for centromeric condensin recruitment and the establishment of biorientation. We show that the interaction is regulated via phosphorylation within the SRM and we determined the phospho-sites using mass spectrometry. Analysis of the phosphomimicking and phosphoresistant mutants revealed that SRM phosphorylation disrupts the shugoshin – condensin interaction. We present an evidence that Mps1, a central kinase in the spindle assembly checkpoint, directly phosphorylates Sgo1 within the SRM to regulate the interaction with condensin and thereby condensin localization to centromeres. Our findings identify novel mechanisms that control shugoshin activity at the centromere in budding yeast.Author summaryProper chromosome segregation in eukaryotes is ensured through correct attachment of the spindle microtubules to the centromeric chromosomal regions. The attachment is mediated via the multimolecular proteinaceous complex called kinetochore and precisely regulated. This enables the establishment of so called bioirentation, when each sister chromatid is attached to microtubules emanating from opposite spindle poles. Shugoshin (Sgo1) is a conserved centromeric protein that facilitates biorientation through its interactions with the protein phosphatase PP2A/Rts1, chromosome passanger complex and centromeric condensin. Here, we identified a serin-rich motif that is required for the interaction of shugoshin with the condensin complex. We show that loss of this region impairs condensin enrichment at the centromere, chromosome biorientation, segregation as well as the function of the chromosome passanger complex in the error correction. Moreover, the interaction is phosphoregulated, as phosphorylation of the serin-rich motif on Sgo1 disrupts its interaction with condensin. Finally, we show that the conserved spindle assembly checkpoint kinase Mps1 is responsible for this phosphorylation. Our findings uncover novel regulatory mechanisms that facilitate proper chromosome segregation.
Species and habitat mapping in two dimensions and beyond. Structure-from-Motion Multi-View Stereo photogrammetry for the Conservation Community
Authors: DeBell Leon , Duffy James P. , McKinley Trevelyan J. , Anderson Karen 
Published: December 2019

AbstractStructure-from-Motion Multi View Stereo (SfM-MVS) photogrammetry is a technique by which volumetric data can be derived from overlapping image sets, using changes of an objects position between images to determine its height and spatial structure. Whilst SfM-MVS has fast become a powerful tool for scientific research, its potential lies beyond the scientific setting, since it can aid in delivering information about habitat structure, biomass, landscape topography, spatial distribution of species in both two and three dimensions, and aid in mapping change over time – both actual and predicted. All of which are of strong relevance for the conservation community, whether from a practical management perspective or understanding and presenting data in new and novel ways from a policy perspective.For practitioners outside of academia wanting to use SfM-MVS there are technical barriers to its application. For example, there are many SfM-MVS software options, but knowing which to choose, or how to get the best results from the software can be difficult for the uninitiated. There are also free and open source software options (FOSS) for processing data through a SfM-MVS pipeline that could benefit those in conservation management and policy, especially in instances where there is limited funding (i.e. commonly within grassroots or community-based projects). This paper signposts the way for the conservation community to understand the choices and options for SfM-MVS implementation, its limitations, current best practice guidelines and introduces applicable FOSS options such as OpenDroneMap, MicMac, CloudCompare, QGIS and speciesgeocodeR. It will also highlight why and where this technology has the potential to become an asset for spatial, temporal and volumetric studies of landscape and conservation ecology.
Malaria transmission assisted by interaction betweenPlasmodium α-tubulin-1 andAnophelesFREP1 protein
Authors: Zhang Genwei , Niu Guodong , Perez Laura , Wang Xiaohong , Li Jun 
Published: December 2019

ABSTRACTPassage ofPlasmodiumthrough a mosquito midgut is essential for malaria transmission. FREP1, a peritrophic matrix protein in a mosquito midgut, binds to the parasite and mediatesPlasmodiuminfection inAnopheles. The FREP1-mediatedPlasmodiuminvasion pathway is highly conserved across multiple species ofPlasmodiumandAnopheles. Through pulldown, nineP. bergheiproteins were co-precipitated with FREP1-conjugated beads. After cloning these nine genes fromP. bergheiand expressing them in insect cells, six of them were confirmed to interact with recombinant FREP1 protein. Among them,α-tubulin-1 and heat shock protein 70 (Hsp70) were highly conserved inPlasmodiumspecies with >95% identity. Thus,P. falciparum α-tubulin-1 and Hsp70 were cloned and expressed inE. colito stimulate antibody (Ab) in mice. Our results showed that anti-serum againstP. falciparum α-tubulin-1 significantly inhibitedP. falciparumtransmission toAn. gambiae, while Ab againstP. falciparumHsp70 serum did not. The polyclonal Ab against humanα-tubulin did not interfere formation of ookinetes, however, significantly reduced the number ofP. falciparumoocysts inAn. gambiaemidguts. Moreover, fluorescence microscope assays showed that anti-α-tubulin Ab bound to impermeablePlasmodiumookinete apical invasive apparatus. Therefore, we propose that the interaction betweenAnophelesFREP1 protein andPlasmodium α-tubulin-1 directs the ookinete invasive apparatus towards midgut peritrophic matrix for the efficient passage of the parasite.AnophelesFREP1 andPlasmodiumα-tubulin-1 are potential targets for blocking malaria transmission to the mosquito host.AUTHOR SUMMARYThe molecular mechanisms of malaria transmission to mosquito are not well-understood. FREP1 proteins in mosquito midget PM has been proved to mediate malaria transmission by binding to parasite ookinetes. Here we reported thatPlasmodiumparasite α-tubulin-1 is an FREP1 binding partner. We initially identified the α-tubulin-1 through the FREP1-pulldown assay; Then we clonedP. falciparumα-tubulin-1, and demonstrated that the insect cell expressed recombinantPlasmodiumα-tubulin-1 bound to FREP1in vitro; Next, mouse anti-serum againstP. falciparumα-tubulin-1 was found to inhibitP. falciparumtransmission toAn. gambiae. P. falciparumα-tubulin-1 shares >84% identical amino acid sequence with human α-tubulin, purified Ab against human α-tubulin significantly inhibited malaria transmission. Anti-human α-tubulin Ab did not interfere the gametocyte-to-ookinetes conversion. Final, we found that anti-α-tubulin Ab bound to the apical end of impermeable ookinetes. Structurally, ookinete invasive apparatus locates at the apical opening. Therefore, we propose that the interaction betweenAnophelesmidgut FREP1 protein andPlasmodiumapicalα-tubulin-1 directs the ookinete invasive apparatus towards midgut PM for the efficient parasite invasion.
L-type voltage-gated calcium channel agonists improve hearing loss and modify ribbon synapse morphology in the zebrafish model of Usher Syndrome Type 1
Authors: Koleilat Alaa , Dugdale Joseph A. , Christenson Trace A. , Bellah Jeffrey L. , Lambert Aaron M. , Masino Mark A. , Ekker Stephen C. , Schimmenti Lisa A. 
Published: December 2019

AbstractUsher Syndrome (USH) is the most common cause of human deaf/blindness. The zebrafishmyo7aa-/-mutant, faithfully models USH1; homozygous zebrafish are deaf and exhibit circular swimming. We hypothesized that hair cell morphology would differ inmyo7aa-/-mutants compared to wild type. We also tested the hypothesis that agonists of L-type voltage-gated calcium channels would alter ribbon synapse morphology and behavior of zebrafishmyo7aa-/-mutants. We discovered thatmyo7aa-/-zebrafish have fewer glutamatergic vesicles tethered to hair cell ribbon synapses, yet maintain a comparable ribbon area. We identified thatmyo7aa-/-mutants have fewer total active hair cells, fewer total CTBP2 expressing puncta, and an altered distribution of CTBP2 puncta compared to wildtype. We also identified thatmyo7aa-/-mutants have fewer active post-synaptic cells and fewer total MAGUK puncta, compared to wildtype. Behaviorally,myo7aa-/-mutant fish have abnormal swimming as measured by larger absolute smooth orientations and have little to no acoustic startle. Treatment with L-type voltage-gated calcium channel agonists altered the abnormal cell and behavioral phenotypes toward wildtype. Our data supports that L-type voltage-gated calcium channel agonists induce morphological changes at the ribbon synapse—in both the number of tethered vesicles and the distribution of CTBP2 puncta, shifts swimming behavior towards wildtype swimming and improves acoustic startle response.Summary StatementWe identified that the hair cell biology and behavior of themyo7aa-/-mutant differs from wildtype and this difference can be rescued using L-type voltage-gated calcium channel agonists.