bluuebunny/crossref_metadata_2025 huggingface dataset:
Survey of Anisoptera diversity in flood prone areas in Tirurangadi taluk of Kerala, India
Authors: Kalliyil Arshad , Jasna Sherin MK , Ashiba Amal K , Noushad Nimna , Shibitha P , Hency CT , Fathimath Sahla P , Mathew Bini
Published: June 2020

Biodiversity forms the foundation of the vast array of ecosystem that critically contribute to human well being. Biodiversity is important in human managed as well as natural ecosystems. The changing status of insects and other invertebrates is the key indicator of biodiversity and environment that shapes it. The order Odonata comes under the class insecta. Odonata are divided into two suborders; Zygoptera (damselflies) and Anisoptera (dragonflies). Natural calamities can alter the ecosystem and thereby biodiversity drastically. This study was conducted in Tirurangadi taluk of kerala, India which is a flood prone taluk due to the over flow of the Kadalundi river during monsoon season. We reported a total of 12 species belonging to 10 genera and 2 families during the entire study. Sub-order Anisoptera was represented by the families, Libellulidae and Aeshnidae, comprising 11 species of Libellulidae and one species of Aeshnidae. On a long term, we aim at studying the impacts on insect biodiversity caused by floods.
Müller Glia regenerative potential is maintained throughout life despite neurodegeneration and gliosis in the ageing zebrafish retina
Authors: Martins Raquel R. , Zamzam Mazen , Moosajee Mariya , Thummel Ryan , Henriques Catarina M. , MacDonald Ryan B.
Published: June 2020

Ageing is a significant risk factor for degeneration of the retina. Harnessing the regenerative potential of Müller glia cells (MG) in the retina offers great promise for the treatment of blinding conditions. Yet, the impact of ageing on MG regenerative capacity has not yet been considered. Here we show that the zebrafish retina undergoes telomerase-independent age-related neurodegeneration. Yet, this progressive neuronal loss in the ageing retina is insufficient to stimulate the MG regenerative response. Instead, age-related neurodegeneration leads to MG gliosis and loss of vision, similarly to humans. Nevertheless, gliotic MG cells retain Yap expression and the ability to regenerate neurons after acute light damage. Therefore, we identify key differences in the MG response to acute versus chronic damage in the zebrafish retina and show that aged gliotic MG can be stimulated to repair damaged neurons in old age.

Our data suggest there are key differences between mechanisms driving regeneration in response to acute damage versus age-related chronic damage. It may be that either the number of cells dying in natural ageing is not enough to stimulate MG to proliferate, or the low number of microglia and respective signals released are not sufficient to trigger MG proliferation. Importantly, we show that gliotic MG cells can be stimulated to repair damaged neurons in old zebrafish retina.
Evidence of recent increased pathogenicity within the AustralianAscochyta rabieipopulation
Authors: Sambasivam P , Mehmood Y , Bar I , Davidson J , Hobson K , Moore K , Ford R
Published: June 2020

Ascochyta Blight (AB), caused byAscochyta rabiei(synPhoma rabiei), is the major endemic foliar fungal disease affecting the Australian chickpea industry, resulting with potential crop loss and management costs. This study was conducted to better understand the risk posed by the AustralianA. rabieipopulation to current resistance sources and to provide informed decision support for chemical control strategies. Recent changes in the pathogenicity of the population were proposed based on disease severity and histopathological observations on a host set. Controlled environment disease screening of 201 isolates on the host set revealed distinct pathogenicity groups, with 41% of all isolates assessed as highly aggressive and a significant increase in the proportion of isolates able to cause severe damage on resistant and moderately resistant cultivars since 2013. In particular, the frequency of highly aggressive isolates on the widely adopted PBA HatTrick cultivar rose from 18% in 2013 to 68% in 2017. In addition, isolates collected since 2016 caused severe disease on Genesis 090, another widely adopted moderately resistant cultivar and on ICC3996, a commonly used resistance source. Of immediate concern was the 10% of highly aggressive isolates able to severely damage the recently released resistant cultivar PBA Seamer (2016). Histopathology studies revealed that the most aggressive isolates were able to germinate, develop appressoria and invade directly through the epidermis faster than lower aggressive isolates on all hosts assessed, including ICC3996. The fungal invasion triggered a common reactive oxygen species (ROS) and hypersensitive response (HR) on all assessed resistant genotypes with initial biochemical and subsequent structural defence responses initiated within 24 hours of inoculation by the most highly aggressive isolates. These responses were much faster on the less resistant and fastest on the susceptible check host, indicating that speed of recognition was correlated with resistance rating. This will inform fungicide application timing so that infected crops are sprayed with prophylactic chemistries prior to invasion and with systemic chemistries after the pathogen has invaded.
Three-dimensional Multi-site Random Access Photostimulation (3D-MAP)
Authors: Xue Yi , Waller Laura , Adesnik Hillel , Pégard Nicolas
Published: June 2020

Optical control of neural ensemble activity is crucial for understanding brain function and disease, yet no technology can achieve optogenetic control of very large numbers of neurons at extremely fast rate over a large volume. State-of-the-art multiphoton holographic optogenetics requires high power illumination that only addresses relatively small populations of neurons in parallel. Conversely, one-photon holographic techniques can stimulate more neurons with 2-3 orders lower power, but with a trade-off between resolution and addressable volume. Perhaps most problematically, two-photon holographic optogenetic systems are extremely expensive and sophisticated which has precluded their broader adoption in the neuroscience community. To address this technical gap, we introduce a new one-photon light sculpting technique, Three- Dimensional Multi-site random Access Photostimulation (3D-MAP), that overcomes these limitations by modulating light dynamically, both in the spatial and in the angular domain at multi-kHz rates. We use 3D-MAP to interrogate neural circuits in 3D and demonstrate simultaneous photostimulation and imaging of dozens of user-selected neurons in the intact mouse brainin vivowith high spatiotemporal resolution. 3D-MAP could be broadly adopted for high-throughput all-optical interrogation of brain circuits owing to its powerful combination of scale, speed, simplicity, and cost.
Involuntary shifts of spatial attention contribute to distraction - Evidence from oscillatory alpha power and reaction time data
Authors: Weise Annekathrin , Hartmann Thomas , Parmentier Fabrice , Weisz Nathan , Ruhnau Philipp
Published: June 2020

Imagine you are focusing on the traffic on a busy street to ride your bike safely when suddenly you hear the siren of an ambulance. This unexpected sound involuntarily captures your attention and interferes with ongoing performance. We tested whether this type of distraction involves a spatial shift of attention. We measured behavioral data and magnetoencephalographic alpha power during a crossmodal paradigm that combined an exogenous cueing task and a distraction task. In each trial, a task-irrelevant sound preceded a visual target (left or right). The sound was usually the same animal sound (i.e., standard sound). Rarely, it was replaced by an unexpected environmental sound (i.e., deviant sound). Fifty percent of the deviants occurred on the same side as the target, and 50% occurred on the opposite side. Participants responded to the location of the target. As expected, responses were slower to targets that followed a deviant compared to a standard. Crucially, this distraction effect was mitigated by the spatial relationship between the targets and the deviants: responses were faster when targets followed deviants on the same versus different side, indexing aspatialshift of attention. This was further corroborated by a posterior alpha power modulation that was higher in the hemisphere ipsilateral (vs. contralateral) to the location of the attention-capturing deviant. We suggest that this alpha power lateralization reflects a spatial attention bias. Overall, our data support the contention that spatial shifts of attention contribute to deviant distraction.
FUNGAL DYSBIOSIS CORRELATES WITH THE DEVELOPMENT OF TUMOUR-INDUCED CACHEXIA IN MICE
Authors: Jabes D.L. , de Maria Y.N.L.F. , Aciole Barbosa D. , Santos K.B.N.H. , Carvalho L.M. , Humberto A.C. , Alencar V.C. , Costa de Oliveira R. , Batista M.L. , Menegidio F.B. , Nunes L.R.
Published: June 2020

Cachexia (CC) is a devastating metabolic syndrome associated with a series of underlying diseases that greatly affects life quality and expectancy among cancer patients. Studies involving mouse models, in which CC was induced through inoculation with tumor cells, originally suggested the existence of a direct correlation between the development of this syndrome and changes in the relative proportions of several bacterial groups present in the digestive tract. However, these analyses have focus solely on the characterization of bacterial dysbiosis, ignoring the possible existence of changes in the relative populations of fungi, during the development of CC. Thus, the present study sought to expand such analyses, by characterizing changes that occur in the gut fungal population (mycobiota) of mice, during the development of cancer-induced cachexia. Our results confirm that cachectic animals display significant differences in their gutmycobiota, when compared to healthy controls. Moreover, identification of dysbiotic fungi showed remarkable consistency across successive levels of taxonomic hierarchy. Many of these fungi have also been associated with dysbioses observed in a series of gut inflammatory diseases, such as obesity, Colorectal Cancer (CRC), Myalgic Encephalomyelitis (ME) and Inflammatory Bowel Disease (IBD). Nonetheless, the CC-associated dysbiosis seems to be unique, presenting features observed in both obesity (reduced proportion ofMucoromycota) and CRC/ME/IBD (increased proportions ofSordariomycetes, SaccharomycetaceaeandMalassezia). One species ofMucoromycota(Rhyzopus oryzae) stands out as a promising probiotic candidate in adjuvant therapies, aimed at treating and/or preventing the development of CC.
Personalization of mathematical models of human atrial action potential
Authors: Pikunov Andrey V. , Syunyaev Roman A. , Steckmeister Vanessa , Kutschka Ingo , Voigt Niels , Efimov Igor R.
Published: June 2020

Atrial cardiomyocytes demonstrate a wide spectrum of patient-specific, tissue-specific, and pathology-specific action potential (AP) phenotypes due to differences in protein expression and posttranslational modifications. Accurate simulation of the AP excitation and propagation in healthy or diseased atria requires a mathematical model capable of reproducing all the differences by parameter rescaling. In the present study, we have benchmarked two widely used electrophysiological models of the human atrium: the Maleckar and the Grandi models. In particular, patch-clamp AP recordings from human atrial myocytes were fitted by the genetic algorithm (GA) to test the models' versatility. We have shown that the Maleckar model results in a more accurate fitting of heart rate dependence of action potential duration (APD) and resting potential (RP). On the other hand, both models demonstrate the poor fitting of the plateau phase and spike-and-dome morphologies. We propose that modifications to L-type calcium current-voltage relationships are required to improve atrial models' fidelity.
SARS-CoV-2 Spike protein binds to bacterial lipopolysaccharide and boosts proinflammatory activity
Authors: Petruk Ganna , Puthia Manoj , Petrlova Jitka , Strömdahl Ann-Charlotte , Kjellström Sven , Schmidtchen Artur
Published: June 2020

There is a well-known and established link between high lipopolysaccharide (LPS) levels in blood and the metabolic syndrome (MS). MS is a risk factor for developing severe COVID-19 and acute respiratory distress syndrome (ARDS). Here we define an interaction between SARS-CoV-2 Spike (S) protein and LPS and its link to aggravated inflammation in vitro and in vivo. Electrophoresis under native conditions demonstrated that SARS-CoV-2 S protein binds toEscherichia coliLPS, forming high molecular weight aggregates. Microscale thermophoresis analysis further defined the interaction, having a KDof ~47 nM, similar to the observed affinity between LPS and the human receptor CD14. Moreover, S protein, when combined with low levels of LPS, boosted nuclear factor-kappa B (NF-κB) and cytokine responses in monocytic THP-1 cells and human blood, respectively. In an experimental model of localized inflammation, employing NF-κB reporter mice and in vivo bioimaging, S protein in conjunction with LPS significantly increased the inflammatory response when compared with S protein and LPS alone. Apart from providing information on LPS as a ligand for S protein, our results are of relevance for studies on comorbidities involving bacterial endotoxins, such as the MS, or co-existing acute and chronic infections in COVID-19 patients.
CoExp Web, a web tool for the exploitation of co-expression networks
Authors: García-Ruiz Sonia , Gil-Martínez Ana L. , Cisterna Alejandro , Jurado-Ruiz Federico , Reynolds Regina R. ,   NABEC (North America Brain Expression Consortium), Cookson Mark R. , Hardy John , Ryten Mina , Botía Juan A.
Published: June 2020

This paper presents the CoExp Web tool. CoExp is a software tool and a Web resource that fosters research on co-expression network models by providing a highly usable means to exploit and share multiple network models.

Availability and Implementation

the Web resource is accessible athttps://snca.atica.um.es/coexp/. The software at the front and back-ends is accessible athttps://github.com/SoniaRuiz/CoExp_Web.

Contact

skgtsg0@ucl.ac.uk(Sonia García-Ruíz)
Unique Proteomes Implicate Functional Specialization across Heterocysts, Akinetes, and Vegetative Cells inAnabaena cylindrica
Authors: Qiu Yeyan , Gu Liping , Brözel Volker , Whitten Douglas , Hildreth Michael , Zhou Ruanbao
Published: June 2020

In response to environmental changes, vegetative cells ofAnabaena cylindricacan differentiate into two other cell types: a heterocyst for oxic N2-fixation, and an enlarged spore called akinete for stress survival. Akinetes normally differentiate from vegetative cells adjacent to heterocysts. Heterocysts inhibit nearby cells from differentiating into heterocysts but can induce adjacent cells to become akinetes, a rare embryogenetic induction in prokaryotes. The mechanism for a patterned differentiation inA. cylindricahas been little studied. Here, we isolated three types of cells fromA. cylindricato identify their proteomes using LC-MS/MS.

A total of 1395 proteins were identified, including 664 proteins from akinetes, 751 proteins from heterocysts, and 1236 proteins from vegetative cells. There were 45 proteins (33 novel proteins) found exclusive to akinetes, 57 heterocyst-specific proteins (33 novel proteins), includingnifgene products, and 485 proteins exclusively in vegetative cells. Our proteomic data suggest that akinetes, unlike the typical spores of bacteria, perform unique biochemical functions that collaborate with both heterocysts and vegetative cells. A HAVe model for collaboration among heterocysts, akinetes and vegetative cells is proposed to illustrate the metabolic network of cyanophycin and carbohydrates based on the distribution of their biosynthesis related proteins in three types of cells. Interestingly, cell division proteins, DNA replication proteins, some carboxysomal proteins including RuBisCO and proteins in photosystems I, II were found abundant in heterocysts, the non-dividing cells dedicated exclusively to oxic N2-fixation. The identification of the akinete and heterocyst proteomes enables the pursuit of genetic studies into the patterned differentiation of akinetes and heterocysts.
Bursting out: linking changes in nano-topography and biomechanical properties of biofilm-forming Escherichia coli to T4 lytic cycle
Authors: Abraham Shiju , Kaufman Yair , Perreault François , Young Ry , Bar-Zeev Edo
Published: June 2020

Bacteriophage infection cycle has been extensively studied, yet little is known on the structural and mechanical changes that lead to bacterial lysis. Here, bio-atomic force microscopy was used to study in real-time andin-situthe impact of the canonical phage T4 on the nano-topography and biomechanics of irreversibly attached, biofilm-formingE. colicells. The results show that in contrast to the lytic cycle in planktonic cells, which ends explosively, anchored cells that are in the process of forming biofilms undergo gradual lysis, developing distinct sub-micron lesions (∼300 nm in diameter) within the cell envelope. Furthermore, it is shown that the envelope rigidity and cell elasticity decrease (>50% and >40%, respectively) following T4 infection. These new insights show that the well-established lytic pathway of planktonic cells may be significantly different from that of biofilm-forming cells. Elucidating the lysis paradigm of these cells may advance biofilm removal and phage therapeutic.

There is no conflict of interest and all co-authors have seen and approved the current version for submission.
Cellular logics bringing the symmetry breaking in spiral nucleation revealed by trans-scale imaging
Authors: Kakizuka Taishi , Hara Yusuke , Ohta Yusaku , Mukai Asuka , Ichiraku Aya , Arai Yoshiyuki , Ichimura Taro , Nagai Takeharu , Horikawa Kazuki
Published: June 2020

The spiral wave is a commonly observed spatio-temporal order in diverse signal relaying systems. Although properties of generated spirals have been well studied, the mechanisms for their spontaneous generation in living systems remain elusive. By the newly developed imaging system for trans-scale observation of the intercellular communication among ∼130,000 cells of social amoeba, we investigated the onset dynamics of cAMP signaling and identified mechanisms for the self-organization of the spiral wave at three distinct scalings: At the population-level, the structured heterogeneity of excitability fragments traveling waves at its high/low boundary, that becomes the generic source of the spiral wave. At the cell-level, both the pacemaking leaders and pulse-amplifying followers regulate the heterogeneous growth of the excitability. At the intermediate-scale, the essence of the spontaneous wave fragmentation is the asymmetric positioning of the pacemakers in the high-excitability territories, whose critical controls are operated by a small number of cells, pulse counts, and pulse amounts.
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacteriumEscherichia coli
Authors: Hör Jens , Di Giorgio Silvia , Gerovac Milan , Venturini Elisa , Förstner Konrad U. , Vogel Jörg
Published: June 2020

Stable protein complexes, including those formed with RNA, are major building blocks of every living cell.Escherichia colihas been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ~85% of allE. colitranscripts and ~49% of the proteins. These include the majority of small noncoding RNAs (sRNAs) detectable in this bacterium as well as the general sRNA-binding proteins, CsrA, Hfq and ProQ. In presenting use cases for utilization of these RNA and protein maps, we show that a stable association of RyeG with 30S ribosomes gives this seemingly noncoding RNA of prophage origin away as an mRNA of a toxic small protein. Similarly, we show that the broadly conserved uncharacterized protein YggL is a 50S subunit factor in assembled 70S ribosomes. Overall, this study crucially extends our knowledge about the cellular interactome of the primary model bacteriumE. colithrough providing global RNA/protein complexome information and should facilitate functional discovery in this and related species.
Decoding herbal materials of representative TCM preparations with the multi-barcoding approach
Authors: Yao Qi , Zhu Xue , Han Maozhen , Chen Chaoyun , Li Wei , Bai Hong , Ning Kang
Published: June 2020

With the rapid development of high-throughput sequencing (HTS) technology, the techniques for the assessment of biological ingredients in Traditional Chinese Medicine (TCM) preparations have also advanced. By using HTS together with the multi-barcoding approach, all biological ingredients could be identified from TCM preparations in theory, as long as their DNA is present. The biological ingredients of a handful of classical TCM preparations were analyzed successfully based on this approach in previous studies. However, the universality, sensitivity and reliability of this approach used on TCM preparations remain unclear. Here, four representative TCM preparations, namely Bazhen Yimu Wan, Da Huoluo Wan, Niuhuang Jiangya Wan and You Gui Wan, were selected for concrete assessment of this approach. We have successfully detected from 77.8% to 100% prescribed herbal materials based on both ITS2 andtrnLbiomarkers. The results based on ITS2 have also shown a higher level of reliability than those oftrnLat species level, and the integration of both biomarkers could provide higher sensitivity and reliability. In the omics big-data era, this study has undoubtedly made one step forward for the multi-barcoding approach for prescribed herbal materials analysis of TCM preparation, towards better digitization and modernization of drug quality control.
Visuomotor temporal adaptation is tuned to gamma brain oscillatory coherence
Authors: Cámara Clara , de la Malla Cristina , Marco-Pallarés Josep , López-Moliner Joan
Published: June 2020

Every time we use our smartphone, tablet, or other electronic devices we are exposed to temporal delays between our actions and the sensory feedback. We can compensate for such delays by adjusting our motor commands and doing so likely requires establishing new temporal mappings between motor areas and sensory predictions. However, little is known about the neural underpinnings that would support building new temporal correspondences between different brain areas. We here address the possibility that communication through coherence, which is thought to support neural interareal communication, lies behind the neural processes accounting for how humans cope with additional delays between motor and sensory areas. We recorded EEG activity while participants intercepted moving targets while seeing a cursor that followed their hand with a delay rather than their own hand. Participants adjusted their movements to the delayed visual feedback and intercepted the target with the cursor. The EEG data shows a significant increase in coherence of beta and gamma bands between visual and motor areas during the hand on-going movement towards interception. However, when looking at differences between participants depending on the level of adaptation, only the increase in gamma band correlated with the level of temporal adaptation. We are able to describe the time course of the coherence using coupled oscillators showing that the times at which high coherence is achieved are within useful ranges to solve the task. Altogether, these results evidence the functional relevance of brain coherence in a complex task where adapting to new delays is crucial.

AUTHOR SUMMARY

Humans are often exposed to delays between their actions and the incoming sensory feedback caused by actions. While there have been advances in the understanding of the conditions at which temporal adaptation can occur, little is known about the neural mechanisms enabling temporal adaptation. In the present study we measure brain activity (EEG) to investigate whether communication through coherence between motor and sensory areas might be responsible for one’s ability to cope with externally imposed delays in an interception task. We show evidence that neural coherence at gamma band between visual and motor areas is related to the degree of adaptation to temporal delays.
Domain Binding and Isotype Dictate the Activity of Anti-human OX40 Antibodies
Authors: Griffiths Jordana , Hussain Khiyam , Smith Hannah L , Sanders Theodore , Cox Kerry , Semmrich Monika , Martensson Linda , Kim Jinny , Inzhelevskaya Tatyana , Penfold Chris , Tutt Alison L , Mockridge Ian M , Chan Claude HT , English Vikki , French Ruth R , Teige Ingrid , Al-Shamkhani Aymen , Glennie Martin J , Frendeus Bjorn , Willoughby Jane E , Cragg Mark S
Published: June 2020

Previous data suggests that anti-OX40 mAb can elicit anti-tumour effects in mice through deletion of Tregs. However, OX40 also has powerful costimulatory effects on T cells which could evoke therapeutic responses. The contributions of these different effector mechanisms has not previously been systematically evaluated, particularly for mAb directed to human OX40. Therefore, we generated a novel human OX40 knock-in (KI) mouse to evaluate a panel of anti-hOX40 mAb and show that their activities relate directly to two key properties: 1) isotype – with mIgG1 mAb evoking receptor agonism and CD8+ T cell expansion and mIgG2a mAb evoking deletion of Treg and; 2) epitope - with membrane-proximal mAb delivering more powerful agonism. Intriguingly, both isotypes acted therapeutically in tumour models by engaging these different mechanisms. These findings highlight the significant impact of isotype and epitope on the modulation of anti-hOX40 mAb therapy, and indicate that CD8+ T cell expansion or Treg depletion might be preferable according to the composition of different tumours.

Human trials with anti-OX40 antibodies have been disappointing indicating that optimal reagents have not yet been developed. Here, using a new panel of antibodies, we show that isotype and epitope combine to determine agonistic and therapeutic activity.
Shear flow-driven actin re-organization induces ICAM-1 nanoclustering on endothelial cells that impact T-cell migration
Authors: Piechocka Izabela K. , Keary Sarah , Sosa-Costa Alberto , Lau Lukas , Mohan Nitin , Stanisavljevic Jelena , Borgman Kyra J. E. , Lakadamyali Melike , Manzo Carlo , Garcia-Parajo Maria F.
Published: June 2020

The leukocyte specific β2-integrin LFA-1, and its ligand ICAM-1 expressed on endothelial cells (ECs), are involved in the arrest, adhesion and transendothelial migration of leukocytes. Although the role of mechanical forces on LFA-1 activation is well established, the impact of forces on its major ligand ICAM-1, has received less attention. Using a parallel-plate flow chamber combined with confocal and super-resolution microscopy, we show that prolonged shear-flow induces a global translocation of ICAM-1 on ECs upstream of flow direction. Interestingly, shear-forces promoted ICAM-1 nanoclustering prior to LFA-1 engagement. This spatial nanoscale organization was driven by actin cytoskeleton re-arrangements induced by shear-force. We further assessed the impact of prolonged shear-stress EC stimulation on T cell migration. T cells adhered to mechanically pre-stimulated ECs developed a more pro-migratory phenotype, migrated faster and exhibited shorter EC interactions than when adhered to non-mechanically stimulated ECs. Together, our results indicate that shear-forces increase the number of ICAM-1/LFA-1 bonds due to ICAM-1 nanoclustering, strengthening adhesion and thereby reducing actin retrograde flow of T-cells, leading to their increased migration speed. Our data also underscores the importance of mechanical forces regulating the spatial organization of cell membrane receptors and their contribution to adhesion regulation, regardless of integrin activation.

Summary statement

We show that shear forces promote ICAM-1 spatial re-arrangement and actin-dependent nanoclustering on ECs prior to integrin engagement. This mechanism might be important for firm leukocyte adhesion and migration during the immune response.
Rethinking root-shoot growth dynamics
Authors: Robinson David
Published: June 2020

Using a simple plant growth model based on the logistic equation I re-evaluate how biomass allocation between roots and shoots articulates dynamically with the rate of whole-plant biomass production. Defined by parameters reflecting lumped physiological properties, the model constrains roots and shoots to grow sigmoidally over time. From those temporal patterns detailed trajectories of allocation and growth rate are reconstructed. Sigmoid growth trajectories of roots and shoots are incompatible with the dominant ‘functional equilibrium’ model of adaptive allocation and growth often used to explain plants’ responses to nutrient shortage and defoliation. Anything that changes the differential rates of growth between roots and shoots will automatically change allocation and, unavoidably, change whole-plant growth rate. Biomass allocation and whole-plant growth rate are not independent traits. Allocation and growth rate have no unique relationship to one another but can vary across a wide spectrum of possible relationships. When root-shoot allocation seems to respond to the environment it is likely to be a secondary illusory consequence of other primary responses such as localised root proliferation in soil or leaf expansion within canopy gaps. Changes in root-shoot allocation cannot themselves compensate directly for an impairment of growth rate caused by an external factor such as nutrient shortage or defoliation; therefore, such changes cannot be ‘adaptive’.

‘The reasons are so simple they often escape notice.’ (James 2012, p. 6).
Grooming interventions in female rhesus macaques as social niche construction
Authors: Mielke Alexander , Bruchmann Carina , Schülke Oliver , Ostner Julia
Published: June 2020

Social animals invest time and resources into building and adapting their social environment, which emerges not only from their own but also from the decisions of other group members. Thus, individuals have to monitor interactions between others and potentially decide when and how to interfere to prevent damage to their own investment. These interventions can be subtle, as in the case of affiliative interactions such as grooming, but they can inform us about how animals structure their world and influence other group members. Here, we used interventions into grooming bouts in 29 female rhesus macaques (Macaca mulatta) to determine who intervened into which grooming bouts, why, and what determined intervention outcomes, based on kinship, dominance rank, and affiliative relationships between groomers and (potential) interveners. Using 1132 grooming bouts and 521 interventions, we show that high dominance rank of groomers reduced the risk of intervention. Bystanders, particularly when high-ranking, intervened in grooming of their kin, close affiliates, and close-ranked competitors. Interveners gained access to their close affiliates for subsequent grooming. Affiliative relationship and rank determined intervention outcomes, with reduced aggression risk facilitating grooming involving three individuals. Thus, interventions in this species involved the monitoring of grooming interactions, decision-making based on several individual and dyadic characteristics, and potentially allowed individuals to broaden their access to grooming partners, protect their own relationships, and influence their social niche.
BREC: An R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes
Authors: Mansour Yasmine , Chateau Annie , Fiston-Lavier Anna-Sophie
Published: June 2020

Motivation

Meiotic recombination is a vital biological process playing an essential role in genomes structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated with several chromatin states. However, eu-heterochromatin boundaries are not available nor easily provided for non-model organisms, especially for newly sequenced ones. Hence, we miss accurate local recombination rates, necessary to address evolutionary questions.

Results

Here, we propose an automated computational tool, based on the Marey maps method, allowing to identify heterochromatin boundaries along chromosomes and estimating local recombination rates. Our method, calledBREC(heterochromatinBoundaries andRECombination rate estimates) is non-genome-specific, running even on non-model genomes as long as genetic and physical maps are available. BREC is based on pure statistics and is data-driven, implying that good input data quality remains a strong requirement. Therefore, a data pre-processing module (data quality control and cleaning) is provided. Experiments show that BREC handles different markers density and distribution issues. BREC’s heterochromatin boundaries have been validated with cytological equivalents experimentally generated on the fruit flyDrosophila melanogastergenome, for which BREC returns congruent corresponding values. Also, BREC’s recombination rates have been compared with previously reported estimates. Based on the promising results, we believe our tool has the potential to help bring data science into the service of genome biology and evolution. We introduce BREC within an R-package and a Shiny web-based user-friendly application yielding a fast, easy-to-use, and broadly accessible resource.

Availability

BREC R-package is available at the GitHub repositoryhttps://github.com/ymansour21/BREC.
Unique actions of GABA arising from cytoplasmic chloride microdomains
Authors: Rahmati Negah , Normoyle Kieran P. , Glykys Joseph , Dzhala Volodymyr I. , Lillis Kyle P. , Kahle Kristopher T. , Raiyyani Rehan , Jacob Theju , Staley Kevin J.
Published: June 2020

Developmental, cellular, and subcellular variations in the direction of neuronal Cl−currents elicited by GABAAreceptor activation have been frequently reported, and we found a corresponding variance in the reversal potential (EGABA) for individual interneurons synapsing on a single pyramidal cell. These findings suggest a corresponding variance in the cytoplasmic concentration of Cl−([Cl−i]). We determined [Cl−]iby: 1) two-photon imaging of the Cl−sensitive, ratiometric fluorescent protein SuperClomeleon (sCLM); 2) Fluorescence Lifetime IMaging (FLIM) of the Cl−sensitive fluorophore MEQ; and 3) electrophysiological measurements of EGABA. These methods collectively demonstrated stable [Cl−]imicrodomains in individual neuronsin vivo. Fluorometric and electrophysiological estimates of local [Cl−]iwere highly correlated. [Cl−]imicrodomains persisted after pharmacological inhibition of cation-chloride cotransporters (CCCs) but steadily decreased after inhibiting the polymerization of the anionic macromolecule actin. These studies highlight the existence of functionally significant neuronal Cl−microdomains that modify the impact of GABAergic inputs.
The eyes reflect an internal cognitive state hidden in the population activity of cortical neurons
Authors: Johnston Richard , Snyder Adam C. , Khanna Sanjeev B. , Issar Deepa , Smith Matthew A.
Published: June 2020

Decades of research have shown that global brain states such as arousal can be indexed by measuring the properties of the eyes. Neural signals from individual neurons, populations of neurons, and field potentials measured throughout much of the brain have been associated with the size of the pupil, small fixational eye movements, and vigor in saccadic eye movements. However, precisely because the eyes have been associated with modulation of neural activity across the brain, and many different kinds of measurements of the eyes have been made across studies, it has been difficult to clearly isolate how internal states affect the behavior of the eyes, and vice versa. Recent work in our laboratory identified a latent dimension of neural activity in macaque visual cortex on the timescale of minutes to tens of minutes. This ‘slow drift’ was associated with perceptual performance on an orientation-change detection task, as well as neural activity in visual and prefrontal cortex (PFC), suggesting it might reflect a shift in a global brain state. This motivated us to ask if the neural signature of this internal state is correlated with the action of the eyes in different behavioral tasks. We recorded from visual cortex (V4) while monkeys performed a change detection task, and the prefrontal cortex, while they performed a memory-guided saccade task. On both tasks, slow drift was associated with a pattern that is indicative of changes in arousal level over time. When pupil size was large, and the subjects were in a heighted state of arousal, microsaccade rate and reaction time decreased while saccade velocity increased. These results show that the action of the eyes is associated with a dominant mode of neural activity that is pervasive and task-independent, and can be accessed in the population activity of neurons across the cortex.
Adolescent sleep is critical for the developmental shaping of social novelty preference
Authors: Bian Wen-Jie , de Lecea Luis
Published: June 2020

Sleep takes one-third of our lives, yet its functions remain largely unknown. A large proportion of young patients with neurodevelopmental disorders such as autism spectrum disorders (ASDs) and schizophrenia have sleep problems, including delayed sleep onset, shortened sleep duration and sleep fragmentation, which have been linked to social interaction deficit, a shared symptom of these disorders. However, the causal relationship between sleep disruption and social defects as well as the underlying mechanisms have not yet been established despite its importance in understanding the etiology of these disorders and developing potential therapeutic means. Here using the three-chamber social interaction test, we found that developmental sleep disruption (SD) in adolescent mice caused significant and long-lasting impairment in the preference towards social novelty during adult social interactions without affecting the overall sociality. Interestingly, SD performed in the adulthood did not induce any social defect, indicating a critical period within adolescence during which sleep shapes social novelty preference. Furthermore, by analyzing the adolescent sleep and adult social behavior in a mouse model of Shank3 mutation that mimics a genetic aberrance in ASDs, we found that the development of sociality is correlated with adolescent NREM sleep while social novelty preference is correlated with adolescent REM sleep. Collectively, these results demonstrate a critical role of adolescent sleep in the forming of social novelty preference and the developmental shaping of social behavior.
Limited evidence for parallel evolution among desert adaptedPeromyscusdeer mice
Authors: Colella Jocelyn P. , Tigano Anna , Dudchenko Olga , Omer Arina D. , Khan Ruqayya , Bochkov Ivan D. , Aiden Erez L. , MacManes Matthew D.
Published: June 2020

Phenotypic plasticity enables an immediate response to changing conditions, but for most species, evolutionary change through adaptation will be more important for long-term survival. Warming climate and increasing desertification urges the identification of genes involved in heat-and dehydration-tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another desert specialist deer mouse (P. eremicus) and a widely-distributed habitat generalist (P. maniculatus), that may locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in theP. crinitusgenome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic regulation (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important to accommodating hot and dry environmental conditions.
Modeling the hemodynamic response function using EEG-fMRI data during eyes-open resting-state conditions and motor task execution
Authors: Prokopiou Prokopis C. , Xifra-Porxas Alba , Kassinopoulos Michalis , Boudrias Marie-Hélène , Mitsis Georgios D.
Published: June 2020

In this work, we investigated the regional characteristics of the dynamic interactions between oscillatory sources of ongoing neural activity obtained using electrophysiological recordings and the corresponding changes in the BOLD signal using simultaneous EEG-fMRI measurements acquired during a motor task, as well as under resting conditions. We casted this problem within a system-theoretic framework, where we initially performed distributed EEG source space reconstruction and subsequently employed block-structured linear and non-linear models to predict the BOLD signal from the instantaneous power in narrow frequency bands of the source local field potential (LFP) spectrum (<100 Hz). Our results suggest that the dynamics of the BOLD signal can be sufficiently described as the convolution between a linear combination of the power profile within individual frequency bands with a hemodynamic response function (HRF). During the motor task, BOLD signal variance was mainly explained by the EEG oscillations in the beta band. On the other hand, during resting-state all frequency bands of EEG exhibited significant contributions to BOLD signal variance. Moreover, the contribution of each band was found to be region specific. Our results also revealed considerable variability of the HRF across different brain regions. Specifically, sensory-motor cortices exhibited positive HRF shapes, whereas parietal and occipital cortices exhibited negative HRF shapes under both experimental conditions.
Accounting for imperfect detection reveals role of host traits in structuring viral diversity of a wild bat community
Authors: Sjodin Anna R. , Anthony Simon J. , Willig Michael R. , Tingley Morgan W.
Published: June 2020

Understanding how multi-scale host heterogeneity affects viral community assembly can illuminate ecological drivers of infection and host-switching. Yet, such studies are hindered by imperfect viral detection. To address this issue, we used a community occupancy model – refashioned for the hierarchical nature of molecular-detection methods – to account for failed detection when examining how individual-level host traits affect herpesvirus richness in eight species of wild bats. We then used model predictions to examine the role of host sex and species identity on viral diversity at the levels of host individual, population, and community. Results demonstrate that cPCR and viral sequencing failed to perfectly detect viral presence. Nevertheless, model estimates correcting for imperfect detection show that reproductively active bats, especially reproductively active females, have significantly higher viral richness, and host sex and species identity interact to affect viral richness. Further, host sex significantly affects viral turnover across host populations, as females host more heterogeneous viral communities than do males. Results suggest models of viral ecology benefit from integration of multi-scale host factors, with implications for bat conservation and epidemiology. Furthermore, by accounting for imperfect detection in laboratory assays, we demonstrate how statistical models developed for other purposes hold promising possibilities for molecular and epidemiological applications.
Data-driven estimation of change points reveals correlation between face mask use and accelerated curtailing of the COVID-19 epidemic in Italy
Authors: Pedersen Morten Gram , Meneghini Matteo
Published: June 2020

Italy was the first Western country to be seriously affected by COVID-19, and the first to implement drastic measures, which have successfully curtailed the epidemic. To understand which containment measures altered disease dynamics, we estimate change points in COVID-19 dynamics from official Italian data. We find excellent correlation between nationwide lockdown and the epidemic peak in late March 2020. Surprisingly, we find a change point in mid April, which does not correspond to national measures, but may be explained by regional interventions. Change points in regional COVID-19 dynamics correlate well with local distribution of free face masks and regional orders requiring their mandatory use. Regions with no specific interventions showed no change point during April. We speculate that widespread use of face masks and other protective means has contributed substantially to keeping the number of new Italian COVID-19 cases under control in spite of society turning towards a new normality.
Warming temperatures could expose more than 1.3 billion new people to Zika virus risk by 2050
Authors: Ryan Sadie J. , Carlson Colin J. , Tesla Blanka , Bonds Matthew H. , Ngonghala Calistus N. , Mordecai Erin A. , Johnson Leah R. , Murdock Courtney C.
Published: June 2020

In the aftermath of the 2015 pandemic of Zika virus, concerns over links between climate change and emerging arboviruses have become more pressing. Given the potential that much of the world might remain at risk from the virus, we use a model of thermal bounds on Zika virus (ZIKV) transmission to project climate change impacts on transmission suitability risk by mid-century (a generation into the future). In the worst-case scenario, over 1.3 billion new people could face suitable transmission temperatures for ZIKV by 2050. Given these suitability risk projections, we suggest an increased priority on research establishing the immune history of vulnerable populations, modeling when and where the next ZIKV outbreak might occur, evaluating the efficacy of conventional and novel intervention measures, and increasing surveillance efforts to prevent further expansion of ZIKV.

Author Summary

First discovered in Uganda in the 1950s, Zika virus (ZIKV) is a new threat to global health security. The virus is spread primarily by female Aedes mosquitoes, with occasional sexual transmission in humans, and can cause Zika congenital syndrome (which includes fetal abnormalities like microcephaly) when women are infected during pregnancy. Our study is the first to quantify how many people may be exposed to temperatures suitable for ZIKV transmission in a changing climate. In the worst-case scenario, by 2050, climate change could expose more than 1.3 billion people worldwide to temperatures suitable for transmission - for the first time. The next generation will face substantially increased ZIKV transmission temperature suitability in North America and Europe, where naïve populations might be particularly vulnerable. Mitigating climate change even to moderate emissions scenarios could significantly reduce global expansion of climates suitable for ZIKV transmission, potentially protecting around 200 million people.