bluuebunny/crossref_metadata_2025 huggingface dataset:
Heimdallarchaea encodes profilin with eukaryotic-like actin regulation and polyproline binding
Authors: Survery Sabeen , Hurtig Fredrik , Haq Syed Razaul , Lindås Ann-Christin , Chi Celestine N.
Published: April 2020

The evolutionary events which led to the first eukaryotic cell are still controversial1-4. The Asgard genome encodes a variety of eukaryotic signature proteins previously unseen in prokaryotes. Functional and structural characterization of these proteins is beginning to shed light on the complexity and pedigree of the ancestral eukaryotic cell5,6. In eukaryotes, the key cytoskeletal protein actin is important for diverse cellular processes such as membrane remodeling and cell motility7. Dynamic polymerization of actin provides both structure and generates the force which drives motility and membrane remodeling. These processes demand rapid filament assembly and disassembly on microsecond timescales. In eukaryotes, a variety of highly adapted proteins including gelsolin, profilin, VASP, ARP2/3 and signaling molecules (Phosphatidylinositol-4,5-bisphosphate (PIP2)) are crucial for organizing cellular cytoskeleton dynamics. Amongst others, the Asgard genomes encode predicted putative profilin homologues that regulate eukaryotic actin polymerizationin vitro5,8. Interestingly, Asgard profilins appear to be regulated by PIP2, but not by polyproline rich motifs which are important for recruitment of actin:profilin complexes in eukaryotes5,9. These findings indicate that the Asgard archaea may have possessed analogous membrane organization to present-day eukaryotes, but that polyproline-mediated profilin regulation may have emerge later in the eukaryotic lineage5. Here, we show that Heimdallarchaeota, a candidate phylum within the Asgard superphylum, encodes a putative profilin (heimProfilin) that interacts with PIP2and is regulated by polyproline motifs, implicative of an origin predating the rise of the eukaryotes. Additionally, we provide evidence for a novel regulatory mechanism whereby an extended N-terminal loop abolishes PIP2and polyproline interactions. Lastly, we provide the first evidence for actin polymerization of an Asgard actin homologue. In context, these findings provide further evidence for the existence of a complex cytoskeleton already in Last eukaryotic common ancestor (LECA).
Physiological diversity enhanced by recurrent divergence and secondary gene flow within a grass species
Authors: Bianconi Matheus E. , Dunning Luke T. , Curran Emma V. , Hidalgo Oriane , Powell Robyn F. , Mian Sahr , Leitch Ilia J. , Lundgren Marjorie R. , Manzi Sophie , Vorontsova Maria S. , Besnard Guillaume , Osborne Colin P. , Olofsson Jill K. , Christin Pascal-Antoine
Published: April 2020

C4photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grassAlloteropsis semialatais an exception, as this single species encompasses C4and non-C4populations.

Using phylogenomics and population genomics, we infer the history of dispersal and secondary exchanges before, during, and after photosynthetic divergence inA. semialata. We further establish the genetic origins of polyploids in this species.

Organelle phylogenies indicate limited seed dispersal within the Central Zambezian region of Africa, where the species originated ∼ 2–3 Ma. Outside this region, the species spread rapidly across the paleotropics to Australia. Comparison of nuclear and organelle phylogenies and analyses of whole genomes reveal extensive secondary gene flow. In particular, the genomic group corresponding to the C4trait was swept into seeds from distinct geographic regions. Multiple segmental allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types.

Limited dispersal and isolation allowed lineage divergence, while episodic secondary exchanges led to the pollen-mediated, rapid spread of the derived C4physiology. Overall, our study suggests that local adaptation followed by recurrent secondary gene flow promoted physiological diversification in this grass species.
Neural correlates of state transitions elicited by a chemosensory danger cue
Authors: Jesuthasan Suresh , Krishnan Seetha , Cheng Ruey-Kuang , Mathuru Ajay
Published: April 2020

Background

Detection of predator cues changes the brain state in prey species and helps them avoid danger. Dysfunctionality in changing the central state appropriately in stressful situations is proposed to be an underlying cause of multiple psychiatric disorders in humans.

Methods

Here, we investigate the dynamics of neural circuits mediating response to a threat, to characterize these states and to identify potential control networks. We use resonant scanning 2-photon microscopy forin vivobrain-wide imaging and custom designed behavioral assays for the study.

Results

We first show that 5-7 day old zebrafish larvae react to an alarm pheromone (Schreckstoff) with reduced mobility. They subsequently display heightened vigilance, as evidenced by increased dark avoidance. Calcium imaging indicates that exposure toSchreckstoffelicits stimulus-locked activity in olfactory sensory neurons innervating a lateral glomerulus and in telencephalic regions including the putative medial amygdala and entopeduncular nucleus. Sustained activity outlasting the stimulus delivery was detected in regions regulating neuromodulator release, including the lateral habenula, posterior tuberculum, superior raphe, and locus coeruleus.

Conclusion

We propose that these latter regions contribute to the network that defines the “threatened” state, while neurons with transient activity serve as the trigger. Our study highlights the utility of the zebrafish larval alarm response system to examine neural circuits during stress dependent brain state transitions and to discover potential therapeutic agents when such transitions are disrupted.
Symbiotic and non-symbiotic members of the genusEnsifer(syn.Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping
Authors: Fagorzi Camilla , Ilie Alexandru , Decorosi Francesca , Cangioli Lisa , Viti Carlo , Mengoni Alessio , diCenzo George C
Published: April 2020

Rhizobium – legume symbioses serve as a paradigmatic example for the study of mutualism evolution. The genusEnsifer(syn.Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and inter-kingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genusEnsifer. The data suggest that SNF emerged several times within the genusEnsifer, likely through independent horizontal gene transfer events. Yet, the majority (105 of 106) of theEnsiferstrains with thenodABCandnifHDKnodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “non-symbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the non-symbiotic clade. Characterizing a subset of tenEnsiferstrains identified several phenotypic differences between the clades. Strains of the non-symbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genusEnsiferinto two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.
FaDA: A Shiny web application to accelerate common lab data analyses
Authors: Feseha Yodit , Moiteaux Quentin , Geffard Estelle , Ramstein Gérard , Brouard Sophie , Danger Richard
Published: April 2020

Background

Web-based data analysis and visualization tools are mostly designed for specific purposes, such as data from whole transcriptome RNA sequencing or single-cell RNA sequencing. However, limited efforts have been made to develop tools designed for data of common laboratory data for non-computational scientists. The importance of such web-based tool is stressed by the current increased samples capacity of conventional laboratory tools such as quantitative PCR, flow cytometry or ELISA.

Results

We provide a web-based application FaDA, developed with the R Shiny package providing users to perform statistical group comparisons, including parametric and non-parametric tests, with multiple testing corrections suitable for most of the standard wet-lab analyses. FaDA provides data visualization such as heatmap, principal component analysis (PCA) and receiver operating curve (ROC). Calculations are performed through the R language.

Conclusions

FaDA application provides a free and intuitive interface allowing biologists without bioinformatic skills to easily and quickly perform common lab data analyses. The application is freely accessible athttps://shiny-bird.univ-nantes.fr/app/Fada

Abbreviations

AUC: Area Under the Curve; FaDA: Fast Data Analysis; GEO: Gene Expression Omnibus; ELISA: enzyme-linked immunosorbent assay; PCA: Principal Component Analysis; qPCR: quantitative PCR; ROC: Receiver Operating Curve.
Maturation of lateral habenula and early-life experience-dependent alteration with behavioral disorders in adulthood
Authors: Nakamura Tomoya , Kurosaki Kohei , Kanemoto Munenori , Sasahara Masakiyo , Ichijo Hiroyuki
Published: April 2020

The lateral habenula (LHb) inhibits midbrain monoaminergic neurons, thereby regulating emotion/cognition. Abnormally high activity in the LHb causes behavioral disorders, but how stressful experiences affect neuronal circuits underlying emotion remains poorly understood. Here, we report the effects of chronic stress on the LHb in postnatal day (P)1-9, P10-20, and P36-45 mice in the pre-, early, and late stages of LHb maturation. At P60, only mice exposed during P10-20 exhibited LHb-specific changes: abnormally high-stress reactivity shown by the expression of the immediate-early gene product (Zif268/Egr1) with insufficient number of parvalbumin (PV) neurons containing GABA. Furthermore, these mice showed anxiety/depression-like behaviors in the light-dark box test/forced swim test. Thus, experiences in early-life are essential for the maturation of neuronal circuits underlying emotion. Early-life stress is thought to have caused anxiety/depression in adulthood by disrupting the maturation of inhibitory PV neurons in the LHb in a period-specific manner.
SARS-CoV-2 Isolation and Propagation from Turkish COVID-19 patients
Authors: Tastan Cihan , Yurtsever Bulut , Sir Gozde , Kancagi Derya Dilek , Demir Sevda , Abanuz Selen , Seyis Utku , Yildirim Mulazim , Kuzay Recai , Elibol Omer , Arbak Serap , Elmas Merve Acikel , Birdogan Selcuk , Sahin Eray , Ozcan Orhan , Sezerman Ugur , Ovali Ercument
Published: April 2020

The novel coronavirus pneumonia, which was named later as Coronavirus Disease 2019 (COVID-19), is caused by the Severe Acute Respiratory Syndrome Coronavirus 2, namely SARS-CoV-2. It is a positive-strand RNA virus that is the seventh coronavirus known to infect humans. The COVID-19 outbreak presents enormous challenges for global health behind the pandemic outbreak. The first diagnosed patient in Turkey has been reported by the Republic of Turkey Ministry of Health on March 11, 2020. Today, over ninety thousand cases in Turkey, and two million cases around the world have been declared. Due to the urgent need for vaccine and anti-viral drug, isolation of the virus is crucial. Here, we report one of the first isolation and characterization studies of SARS-CoV-2 from nasopharyngeal and oropharyngeal specimens of diagnosed patients in Turkey. This study provides an isolation and replication methodology, and cell culture tropism of the virus that will be available to the research communities.

Article Summary

Scientists have isolated virus from Turkish COVID-19 patients. The isolation, propagation, and plaque and immune response assays of the virus described here will serve in following drug discovery and vaccine testing.
Single-cell transcriptomic analysis identifies neocortical developmental differences between human and mouse
Authors: Zhou Ziheng , Wang Shuguang , Zhang Dengwei , Jiang Xiaosen , Li Jie , Gu Ying , Sun Hai-Xi
Published: April 2020

Background

The specification and differentiation of neocortical projection neurons is a complex process under precise molecular regulation; however, little is known about the similarities and differences in cerebral cortex development between human and mouse at single-cell resolution.

Results

Here, using single-cell RNA-seq (scRNA-seq) data we explore the divergence and conservation of human and mouse cerebral cortex development using 18,446 and 7,610 neocortical cells. Systematic cross-species comparison reveals that the overall transcriptome profile in human cerebral cortex is similar to that in mouse such as cell types and their markers genes. By single-cell trajectories analysis we find human and mouse excitatory neurons have different developmental trajectories of neocortical projection neurons, ligand-receptor interactions and gene expression patterns. Further analysis reveals a refinement of neuron differentiation that occurred in human but not in mouse, suggesting that excitatory neurons in human undergo refined transcriptional states in later development stage. By contrast, for glial cells and inhibitory neurons we detected conserved developmental trajectories in human and mouse.

Conclusions

Taken together, our study integrates scRNA-seq data of cerebral cortex development in human and mouse, and uncovers distinct developing models in neocortical projection neurons. The earlier activation of cognition -related genes in human may explain the differences in behavior, learning or memory abilities between the two species.
Multi-day rTMS exerts site-specific effects on functional connectivity but does not influence associative memory performance
Authors: Hendrikse Joshua , Coxon James , Thompson Sarah , Suo Chao , Fornito Alex , Yücel Murat , Rogasch Nigel C
Published: April 2020

Transcranial magnetic stimulation (TMS) is a non-invasive brain stimulation technique with the capacity to modulate brain network connectivity and cognitive function. Recent studies have demonstrated long-lasting improvements in associative memory and resting-state connectivity following multi-day repetitive TMS (rTMS) to individualised parietal-hippocampal networks. We aimed to assess the reproducibility and network- and cognitive-specificity of these effects following multi-day rTMS. Participants received four days of 20 Hz rTMS to a subject-specific region of left lateral parietal cortex exhibiting peak functional connectivity to the left hippocampus. In a separate week, the same stimulation protocol was applied to a subject-specific region of pre-supplementary motor area (pre-SMA) exhibiting peak functional connectivity to the left putamen. We assessed changes to associative memory before and after each week of stimulation (N = 39), and changes to resting-state functional connectivity before and after stimulation in week one (N = 36). We found no evidence of long-lasting enhancement of associative memory or increased parieto-hippocampal connectivity following multi-day rTMS to the parietal cortex, nor increased pre-SMA-putamen connectivity following multi-day rTMS to pre-SMA. Instead, we observed some evidence of site-specific modulations of functional connectivity lasting ∼24 hours, with reduced connectivity within targeted networks and increased connectivity across distinct non-targeted networks. Our findings suggest a complex interplay between multi-day rTMS and network connectivity. Further work is required to develop reliable rTMS paradigms for driving changes in functional connectivity between cortical and subcortical regions.
Wharton’s Jelly-derived mesenchymal stromal cells retain their immunophenotype and immunomodulating characteristics after transfection with polyethylenimine
Authors: Ramos-Murillo Ana Isabel , Rodríguez Elizabeth , Ricaurte Cristian , Beltrán Karl , Camacho Bernardo , Salguero Gustavo A. , Godoy-Silva Rubén Darío
Published: April 2020

Background

Wharton’s Jelly-derived mesenchymal stromal cells (WJ-MSCs) present several advantages over other sources of multipotent stem cells, not only because they are obtained from neonatal umbilical cord, which is considered a biological waste, but also display higher proliferation rate and low senescence at later passages compared to stromal cells obtained from other sources. In the field of tissue engineering, WJ-MSCs have a wide therapeutic potential, due to their multipotential capacity, which can be reinforced if cells are genetically modified to direct their differentiation towards a specific lineage; unfortunately, as primary cells, WJ-MSC are difficult to transfect. Therefore, the objective of the present work was to standardize a protocol for the transfection of WJ-MSCs using a cationic polymer. Such protocol is important for future developments that contemplate the genetic modification of WJ-MSCs for therapeutic purposes.

Methods

In this work, WJ-MSCs were genetically modified using polyethylenimine (PEI) and a lentiviral plasmid that encodes for green fluorescent protein (pGFP). To achieve WJ-MSCs transfection, complexes between PEI and pGFP, varying its composition (N/P ratio), were evaluated and characterized by size, zeta potential and cytotoxicity. At the N/P ratio condition where the highest transfection efficiencies were obtained, immunophenotype, immunomodulation properties and multipotential capacity of WJ-MSCs were evaluated.

Results

Here, we present the standardization of the transfection conditions of the WJ-MSCs in a monolayer culture with PEI. The concentrations of plasmid and PEI that have the best transfection efficiencies were established

Conclusions

Transfection with PEI doesn’t affect immunophenotype, immunomodulatory properties and differentiation capacity of WJ-MSCs.
Freely chosen cadence during cycling attenuates intracortical inhibition and increases intracortical facilitation compared to a similar fixed cadence
Authors: Sidhu Simranjit , Lauber Benedikt
Published: April 2020

In contrast to other rhythmic tasks such as running, the preferred movement rate in cycling does not minimize energy consumption. It is possible that neurophysiological mechanisms contribute to the choice of cadence, however this phenomenon is not well understood. Eleven participants cycled at a fixed workload of 125 W and different cadences including a freely chosen cadence (FCC, ∼72), and fixed cadences of 70, 80, 90 and 100 revolutions per minute (rpm) during which transcranial magnetic stimulation (TMS) was used to measure short interval intracortical inhibition (SICI) and intracortical facilitation (ICF). There was significant increase in SICI at 70 (P= 0.004), 80 (P= 0.008) and 100 rpm (P= 0.041) compared to FCC. ICF was significantly reduced at 70 rpm compared to FCC (P= 0.04). Inhibition-excitation ratio (SICI divided by ICF) declined (P= 0.014) with an increase in cadence. The results demonstrate that SICI is attenuated during FCC compared to fixed cadences. The outcomes suggest that the attenuation of intracortical inhibition and augmentation of ICF may be a contributing factor for FCC.
Structural and functional complexity of vocalizations in a cooperatively breeding passerine, Jungle Babbler
Authors: Yambem Soniya Devi , Chorol Sonam , Jain Manjari
Published: April 2020

Animal vocal communication ranges from simple to complex based on repertoire size, structure, and composition of calls and the information encoded in them. According to the social complexity hypothesis, communication complexity tends to increase with an increase in social complexity. While several studies on mammalian systems exist supporting this, evidence from avian systems is comparatively limited. Towards this, we present evidence for complex acoustic communication in a cooperatively breeding passerine, Jungle Babbler, based on three aspects of complexity: an extensive repertoire of acoustically-distinct calls, within-call structural complexity and the diverse behavioural contexts in which these calls are used. Jungle Babblers were found to possess a structurally and functionally diverse vocal repertoire comprising 15 different calls. Detailed acoustic analyses of multisyllabic calls revealed that these calls are composed of different notes. Further, despite a large number of notes present in the repertoire, the number of calls were limited to 15. This implies that there may be underlying rules that determine call composition to give rise to functional calls to which receivers respond. We also found that these calls were produced in a variety of affiliative and agonistic contexts and were employed towards coordination of diverse social behaviours including group movement, foraging, brood care, aggression and vigilance. Yet, 7 out of 15 vocalizations were produced in the context of vigilance. This disproportionate investment of vocalizations towards co-ordinated acoustic vigilance is characteristic of many cooperatively breeding birds. Our study extends support for the social complexity hypothesis and also lays the foundation for future investigations on combinatorial and syntactical rules underlying call structure and function in bird vocalizations.

Significance statement

Studies on vocal complexity in birds have focussed mainly on repertoire size, structure and function. However, fine temporal and spectral features of elements that constitute a call/song are rarely examined to evaluate vocal complexity. We examined complex communication in a cooperatively breeding social passerine, Jungle Babbler for which we assessed repertoire size, function, acoustic features of calls and of their constituent elements. Jungle Babblers were found to possess a structurally and functionally diverse vocal repertoire comprising of 15 calls, 46% of which were in the context of vigilance, thereby extending support to the social complexity hypothesis. We also found that several calls were composed of multiple, acoustically distinct notes. These findings will be foundational in understanding the interrelations between sociality and communicative complexity and underlying combinatorial rules that determine call structure and function.
Italian Odonates in the Pandora’s Box: A Comprehensive DNA Barcoding Inventory Shows Taxonomic Warnings at the Holarctic Scale
Authors: Galimberti Andrea , Assandri Giacomo , Maggioni Davide , Ramazzotti Fausto , Baroni Daniele , Bazzi Gaia , Chiandetti Ivan , Corso Andrea , Ferri Vincenzo , Galuppi Mirko , Ilahiane Luca , La Porta Gianandrea , Laddaga Lorenzo , Landi Federico , Mastropasqua Fabio , Ramellini Samuele , Santinelli Roberto , Soldato Giovanni , Surdo Salvatore , Casiraghi Maurizio
Published: April 2020

The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference datasets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658 bp 5’ end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the dataset to 1294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC, bGMYC) methods were used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct Molecular Operational Units, whereas the remaining ones were classified as ‘warnings’ (i.e., showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped in three categories depending on if they showed low, high, or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic, and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.
Poly-dispersed-acid-functionalized-single-walled carbon nanotubes (AF-SWCNTs) are potent inhibitor of BCG induced inflammatory response in macrophage cell lines
Authors: Bhardwaj Deepika , Saxena Rajiv K.
Published: April 2020

Present study is focussed on the modulation ofMycobacterium bovisBCG induced inflammatory response by poly-dispersed acid-functionalized single-walled carbon nanotubes (AF-SWCNTs) in macrophages. Flow cytometric and confocal microscopy studies indicated that both BCG and AF-SWCNTs were efficiently internalized by RAW 264.7 and MH-S macrophage cell lines and were essentially localized in the cytoplasmic area. The results indicated strong antioxidant activity of AF-SWCNTs in mitigating BCG induced oxidative and nitrosative stress. We also found a marked decline in expression of BCG induced pro-inflammatory genes like COX-2, iNOS, TNF-α, IL-6 and IL-1β on treatment with AF-SWCNTs at transcriptional level. Decline in expression of BCG induced COX-2 by AF-SWCNTs was also confirmed at protein level using Western blotting. Anti-inflammatory activity of AF-SWCNTs was further validated by our results showing that AF-SWCNTs treatment induced a precipitous decline in BCG induced release of Matrix Metalloproteinases MMP-2 and MMP-9 by macrophage cell lines, by using Gelatin zymography. Taken together, our results demonstrate potent anti-inflammatory role of AF-SWCNTs in alleviating BCG induced inflammation.
Structural landscape of the complete genomes of Dengue serotypes and other viral hemorrhagic fevers
Authors: Delli-Ponti Riccardo , Mutwil Marek
Published: April 2020

Background

With more than 300 million potentially infected people every year, and with the expanded habitat of mosquitoes due to climate change, dengue cannot be considered anymore only a tropical disease. The RNA secondary structure is a functional characteristic of RNA viruses, and together with the accumulated high-throughput sequencing data could provide general insights towards understanding virus biology. Here, we profiled the RNA secondary structure of >7500 complete viral genomes from 11 different species of viral hemorrhagic fevers, including dengue serotypes, ebola, and yellow fever.

Results

We achieved hig prediction scores (AUC up to 0.85 with experimental data), and computed consensus secondary structure profiles using hundreds of structuralin silicomodels. We observed that virulent viruses such as DENV-2 and ebola tend to be less structured than the other viruses. Furthermore, we observed virus-specific correlations between secondary structure and the number of interaction sites with human proteins, reaching a correlation of 0.89 in the case of zika. We demonstrate that the secondary structure and presence of protein-binding domains in the genomes can be used as intrinsic signature to further classify the viruses. We also used structural data to study the geographical distribution of dengue, finding a significant difference between DENV-3 from Asia and South-America, which could imply different evolutionary routes of this subtype.

Conclusions

Our massive computational analysis provided novel results regarding the secondary structure and the interaction with human proteins, not only for Dengue serotypes, but also for other viral hemorrhagic fevers. We also provided a new approach to classify viruses according ot their structure, which could be useful for future cassifications. We envision that these approaches can be used by the scientific community to further classify and characterise these complex viruses.
Development of a SYBR Green quantitative PCR assay for detection ofLates calcarifer herpesvirus(LCHV) in farmed barramundi
Authors: Meemetta Watcharachai , Domingos Jose A. , Dong Ha Thanh , Senapin Saengchan
Published: April 2020

Lates calcariferherpes virus (LCHV) is a new virus of farmed barramundi in Southeast Asia. However, a rapid detection method is yet to be available for LCHV. This study, therefore, aimed to develop a rapid quantitative PCR (qPCR) detection method for LCHV and made it timely available to public for disease diagnostics and surveillance in barramundi farming countries. A newly designed primer set targeting a 93-bp fragment of the LCHV putative major envelope protein encoding gene (MEP) was used for developing and optimizing a SYBR Green based qPCR assay. The established protocol could detect as low as 10 viral copies per µl of DNA template in a reaction containing spiked host DNA. No cross-amplification with genomic DNA extracted from host as well as common aquatic pathogens (12 bacteria and 3 viruses) were observed. Validation test of the method with clinical samples revealed that the virus was detected in multiple organs of the clinically sick fish but not in the healthy fish. We thus recommend that barramundi farming countries should promptly initiate active surveillance for LCHV in order to understand their circulation for preventing possibly negative impact to the industry.

Highlights

This study reported a new SYBR Green qPCR method for detection of LCHV

The qPCR method had detection limit of 10 copies per µl plasmid DNA template when spiked with genomic DNA from the host

The aforementioned method is highly specific to LCHV

Validation with clinical samples revealed that LCHV could be detected from multiple organs with fin and brain the best organs for qPCR detection
G protein-regulated endocytic trafficking of adenylyl cyclase type 9
Authors: Lazar André M. , Irannejad Roshanak , Baldwin Tanya A. , Sundaram Aparna A. , Gutkind J. Silvio , lnoue Asuka , Dessauer Carmen W. , von Zastrow Mark
Published: April 2020

GPCRs are increasingly recognized to initiate signaling via heterotrimeric G proteins as they move through the endocytic network, but little is known about how relevant G protein effectors are localized. Here we report dynamic trafficking of adenylyl cyclase type 9 (AC9) from the plasma membrane to endosomes, while adenylyl cyclase type 1 (AC1) remains in the plasma membrane, and stimulation of AC9 trafficking by ligand-induced activation of Gs-coupled GPCRs or Gs. AC9 transits a similar dynamin-dependent early endocytic pathway as activated GPCRs but, in contrast to GPCR trafficking which is regulated by β-arrestin but not Gs, AC9 trafficking is regulated by Gs but not β-arrestin. We also show that AC9, but not AC1, contributes to cAMP production from endosomes. These results reveal dynamic and isoform-specific trafficking of adenylyl cyclase in the endocytic network, and a discrete role of a heterotrimeric G protein in controlling subcellular location of a relevant effector.
ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from anin silicostudy
Authors: Calcagnile Matteo , Forgez Patricia , Iannelli Antonio , Bucci Cecilia , Alifano Marco , Alifano Pietro
Published: April 2020

The current SARS covid-19 epidemic spread appears to be influenced by ethnical, geographical and sex-related factors that may involve genetic susceptibility to diseases. Similar to SARS-CoV, SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells, notably type II alveolar epithelial cells. Importantly, ACE2 gene is highly polymorphic. Here we have usedin silicotools to analyze the possible impact of ACE2 single-nucleotide polymorphisms (SNPs) on the interaction with SARS-CoV-2 spike glycoprotein. We found that S19P (common in African people) and K26R (common in European people) were, among the most diffused SNPs worldwide, the only two SNPs that were able to potentially affect the interaction of ACE2 with SARS-CoV-2 spike. FireDock simulations demonstrated that while S19P may decrease, K26R might increase the ACE2 affinity for SARS-CoV-2 Spike. This finding suggests that the S19P may genetically protect, and K26R may predispose to more severe SARS-CoV-2 disease.
SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o
Authors: Puente-Sánchez Fernando , García-García Natalia , Tamames Javier
Published: April 2020

Background

The dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches.

Results

Here we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvi’o analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment.

Conclusions

Altogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.
Fat1 regulates astrocyte maturation and angiogenesis in the retina
Authors: Helmbacher Françoise
Published: April 2020

Angiogenesis is a stepwise process leading to blood vessel formation. In the vertebrate retina, endothelial cells are guided by astrocytes migrating along the inner surface, and the two processes are coupled by a tightly regulated cross-talk between the two cell types. Here, we investigated how the FAT1 Cadherin, a regulator of tissue morphogenesis governing tissue cross-talks, influences retinal vascular development. Through late-onset inactivation in the neural lineage in mice, we bypassed an early contribution of Fat1 to eye development, and assessed its requirement for postnatal retina angiogenesis. We found that neural Fat1 expression, by controlling the polarity of astrocyte progenitor migration, regulates astrocyte maturation. By interfering with astrocyte migration and maturation, neural Fat1 deletion deregulates the astrocyte/endothelial cell coupling, and delays retinal angiogenesis. Mice with neural-Fat1 ablation exhibit persistent abnormalities of the retinal vascular architecture, such as an increased vascular density in deep layers. Altogether, this study identifies Fat1 as a regulator of neurovascular communication, essential for retinal vascular development and integrity.
Detecting rare copy number variants (CNVs) from Illumina genotyping arrays with the CamCNV pipeline: segmentation of z-scores improves detection and reliability
Authors: Dennis Joe , Walker Logan , Tyrer Jonathan , Michailidou Kyriaki , Easton Douglas F.
Published: April 2020

Background

The intensities from genotyping array data can be used to detect CNVs but a high level of noise in the data and overlap between different copy-number intensity distributions produces unreliable calls, particularly when only a few probes are covered by the CNV.

Results

We present a novel pipeline (CamCNV) with a series of steps to reduce noise and detect more reliably rare CNVs covering as few as three probes. The method uses the information from all samples to convert intensities to z-scores, thus adjusting for variance between probes. We tested the sensitivity of our pipeline by looking for known CNVs from the 1000 Genomes project in our genotyping of 1000 Genomes samples. We also compared the CNV calls for 1,661 pairs of genotyped replicate samples. At the chosen mean z-score cut-off, sensitivity to detect the 1000 Genomes CNVs was approximately 85% for deletions and 65% for duplications. From the replicates we estimate the false discovery rate is controlled at ∼10% for deletions (falling to below 3% with more than five probes) and ∼28% for duplications. The pipeline demonstrates improved sensitivity when compared to calling with PennCNV, particularly for short deletions covering only a few probes

Conclusion

The CamCNV pipeline provides a reliable method of detecting rare CNVs from Illumina array data and can be used for CNVs that only cover a few probes. For each called CNV the mean z-score is a useful metric for controlling the false discovery rate.
Respiration modulates oscillatory neural network activity at rest
Authors: Kluger Daniel S. , Gross Joachim
Published: April 2020

Despite recent advances in understanding how respiration affects neural signalling to influence perception, cognition, and behaviour, it is yet unclear to what extent breathing modulates brain oscillations at rest. We acquired respiration and resting state magnetoencephalography (MEG) data from human participants to investigate if, where, and how respiration cyclically modulates oscillatory amplitudes (2 – 150 Hz). Using measures of phase-amplitude coupling, we show respiration-modulated brain oscillations (RMBOs) across all major frequency bands. Sources of these modulations spanned a widespread network of cortical and subcortical brain areas with distinct spectro-temporal modulation profiles. Globally, high-frequency gamma modulation increased with distance to the head centre, whereas delta and theta modulation decreased with height in the sagittal plane. Overall, we provide the first comprehensive mapping of RMBOs across the entire brain, highlighting respiration-brain coupling as a fundamental mechanism to shape neural processing within canonical resting-state and respiratory control networks.
A polyetic modelling framework for plant disease emergence
Authors: Willocquet Laetitia , Savary S. , McDonald B.A. , Mikaberidze A.
Published: April 2020

Plant disease emergences have dramatically increased recently as a result of global changes, especially with respect to trade, host genetic uniformity, and climate change. A better understanding of the conditions and processes determining epidemic outbreaks caused by the emergence of a new pathogen, or pathogen strain, is needed to develop strategies and inform decisions to manage emerging diseases. A polyetic process-based model is developed to analyse conditions of disease emergence. This model simulates polycyclic epidemics during successive growing seasons, the yield losses they cause, and the pathogen survival between growing seasons. This framework considers an immigrant strain coming into a system where a resident strain is already established. Outcomes are formulated in terms of probability of emergence, time to emergence, and yield loss, resulting from deterministic and stochastic simulations. An analytical solution to determine a threshold for emergence is also derived. Analyses focus on the effects of two fitness parameters on emergence: the relative rate of reproduction (speed of epidemics), and the relative rate of mortality (decay of population between seasons). Analyses revealed that stochasticity is a critical feature of disease emergence. The simulations suggests that: (1) emergence may require a series of independent immigration events before a successful invasion takes place; (2) an explosion in the population size of the new pathogen (or strain) may be preceded by many successive growing seasons of cryptic presence following an immigration event, and; (3) survival between growing seasons is as important as reproduction during the growing season in determining disease emergence.
Shared neuronal bases of inhibition and economic choice in orbitofrontal cortex
Authors: Balasubramani Pragathi Priyadharsini , Hayden Benjamin Y.
Published: April 2020

Economic choice and inhibition are two important elements of our cognitive repertoires that may be closely related. We and others have noted that during economic choice, options are typically considered serially; this fact provides important constraints on our understanding of choice. Notably, asynchronous contemplation means that each individual option is subject to an accept-reject decision. We have proposed that these component accept-reject decisions may have some kinship with stopping decisions. One prediction of this idea is that stopping and choice may reflect similar neural processes occurring in overlapping brain circuits. To test the idea, we recorded neuronal activity in orbitofrontal cortex (OFC) Area 13 while macaques performed a stop signal task interleaved with a structurally matched choice task. Using neural network decoders, we find that OFC ensembles have overlapping codes for stopping and choice: the decoder that was only trained to identify accept vs. reject trials performed with higher efficiency even when tested on the stop trials. These results provide tentative support for the idea that mechanisms underlying inhibitory control and choice selection may be subject to theoretical unification.
Degradation of Alzheimer’s amyloid-β by a catalytically inactive insulin-degrading enzyme
Authors: Sahoo Bikash R. , Panda Pritam Kumar , Liang Wenguang , Tang Wei-Jen , Ahuja Rajeev , Ramamoorthy Ayyalusamy
Published: April 2020

It is known that insulin-degrading-enzyme (IDE) plays a crucial role in the clearance of Alzheimer’s amyloid-β (Aβ). The cysteine-free IDE mutant (cf-E111Q-IDE) is catalytically inactive against insulin, but its effect on Aβ degradation is unknown that would help in the allosteric modulation of the enzyme activity. Herein, the degradation of Aβ(1-40) by cf-E111Q-IDE via a non-chaperone mechanism is demonstrated by NMR and LC-MS, and the aggregation of fragmented peptides is characterized using fluorescence and electron microscopy. cf-E111Q-IDE presented a reduced effect on the aggregation kinetics of Aβ(1-40) when compared with the wild-type IDE. Whereas LC-MS and diffusion ordered NMR spectroscopy revealed the generation of Aβ fragments by both wild-type and cf-E111Q-IDE. The aggregation propensities and the difference in the morphological phenotype of the full-length Aβ(1-40) and its fragments are explained using multi-microseconds molecular dynamics simulations. Notably, our results reveal that zinc binding to Aβ(1-40) inactivates cf-E111Q-IDE’s catalytic function, whereas zinc removal restores its function as evidenced from high-speed AFM, electron microscopy, chromatography, and NMR results. These findings emphasize the catalytic role of cf-E111Q-IDE on Aβ degradation and urge the development of zinc chelators as an alternative therapeutic strategy that switches on/off IDE’s function.
Tracking crystallophore nucleating properties: setting-up a database for statistical analysis
Authors: Jiang Tao , Roux Amandine , Engilberge Sylvain , Alsalman Zaynab , Di Pietro Sebastiano , Franzetti Bruno , Riobé François , Maury Olivier , Girard Eric
Published: April 2020

In this article, the principle of a database aimed at facilitating the understanding of the unique protein nucleating properties of the Crystallophore is presented. A first analysis allows us to compare the efficiency of Tb-Xo4 with the new Lu-Xo4 variant, featuring improved phasing properties. Then, the concept ofsubset-of-interestis introduced to reveal potential antagonistic/synergistic effects between Tb-Xo4 and physico-chemical parameters of the crystallisation kits such as pH. The overall approach may be of interest for any studies working on solutions dedicated to improve the nucleating step in protein crystallization.

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Synopsis

A database and associated representation tools are highlighted to understand nucleating properties of the crystallophore.
Cassava common mosaic viruscauses photosynthetic alterations associated with changes in chloroplast ultrastructure and carbohydrate metabolism of cassava plants
Authors: Zanini Andrea A. , Di Feo Liliana , Luna Dario F. , Paccioretti Pablo , Collavino Agostina , Rodriguez Marianela S.
Published: April 2020

Cassava common mosaic virus(CsCMV) is a potexvirus that causes systemic infections in cassava plants, leading to chlorotic mosaic and producing significant yield losses. To date, the physiological alterations and the mechanism underlying biotic stress during the cassava-CsCMV compatible interaction remains unknown. In this study, we found that CsCMV infection adversely modified chloroplast structure and had functional effects on chloroplasts in source leaves during the course of viral infection. Extrusion of the chloroplast membrane with amoeboid-shaped appearance was observed in infected mesophyll cells. These alterations were associated with lower relative chlorophyll content, and reduced PSII efficiency and CO2fixation. Moreover, an oxidative stress process was observed in CsCMV-infected plants. Strong declines in the maximum quantum yield of primary photochemistry (Fv/Fm) were observed in infected plants. Furthermore, the analysis of Chlorophyll-a fluorescence (ChlF) evidenced a progressive loss of both oxygen evolving complex activity and “connectivity” within the tripartite system (core antenna-LHCII-Reaction Centre). Other effects of the pathogen included reduction of starch and maltose content in source leaves, and a significant increase of the sucrose/starch ratio, which indicates alteration pattern of carbon. Our results suggest that CsCMV induces chloroplast distortion associated with progressive chloroplast function loss and diversion of carbon flux in source leaf tissue, which should be key in inducing yield losses of infected crops.

Main conclusion

CsCMV infection adversely modified chloroplast structure and had functional effects on chloroplasts during the course of viral infection, associated with metabolic adjustment in cassava source leaves, which would partly explain cassava root yield losses.
The coronavirus proofreading exoribonuclease mediates extensive viral recombination
Authors: Gribble Jennifer , Pruijssers Andrea J. , Agostini Maria L. , Anderson-Daniels Jordan , Chappell James D. , Lu Xiaotao , Stevens Laura J. , Routh Andrew L. , Denison Mark R.
Published: April 2020

Coronaviruses (CoVs) emerge as zoonoses and cause severe disease in humans, demonstrated by the SARS-CoV-2 (COVID-19) pandemic. RNA recombination is required during normal CoV replication for subgenomic mRNA (sgmRNA) synthesis and generates defective viral genomes (DVGs) of unknown function. However, the determinants and patterns of CoV recombination are unknown. Here, we show that divergent β-CoVs SARS-CoV-2, MERS-CoV, and murine hepatitis virus (MHV) perform extensive RNA recombination in culture, generating similar patterns of recombination junctions and diverse populations of DVGs and sgmRNAs. We demonstrate that the CoV proofreading nonstructural protein (nsp14) 3’-to-5’ exoribonuclease (nsp14-ExoN) is required for normal CoV recombination and that its genetic inactivation causes significantly decreased frequency and altered patterns of recombination in both infected cells and released virions. Thus, nsp14-ExoN is a key determinant of both high fidelity CoV replication and recombination, and thereby represents a highly-conserved and vulnerable target for virus inhibition and attenuation.