bluuebunny/crossref_metadata_2025 huggingface dataset:
Repeated gain and loss of a single gene modulates the evolution of vascular pathogen lifestyles
Authors: Gluck-Thaler Emile , Cerutti Aude , Perez-Quintero Alvaro , Butchacas Jules , Roman-Reyna Verónica , Madhaven Vishnu Narayanan , Shantharaj Deepak , Merfa Marcus V. , Pesce Céline , Jauneau Alain , Vancheva Taca , Lang Jillian M. , Allen Caitilyn , Verdier Valerie , Gagnevin Lionel , Szurek Boris , Cunnac Sébastien , Beckham Gregg , de la Fuente Leonardo , Patel Hitendra Kumar , Sonti Ramesh V , Bragard Claude , Leach Jan E. , Noël Laurent D. , Slot Jason C. , Koebnik Ralf , Jacobs Jonathan M.
Published: April 2020

Vascular pathogens travel long distances through host veins leading to life-threatening, systemic infections. In contrast, non-vascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and non-vascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and non-vascular plant pathogenesis.cbsAwas enriched in genomes of vascular phytopathogenic bacteria in the Xanthomonadaceae family and absent in most non-vascular species. CbsA expression allowed non-vascularXanthomonasto cause vascular blight whilecbsAmutagenesis resulted in reduction of vascular or enhanced non-vascular symptom development. Phylogenetic hypothesis testing further revealed thatcbsAwas lost in multiple non-vascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.
Establishment of a Replicon System for Bourbon Virus and Identification of Small Molecules that Efficiently Inhibit Virus Replication
Authors: Hao Siyuan , Ning Kang , Wang Xiaomei , Wang Jianke , Cheng Fang , Ganaie Safder S. , Tavis John E. , Qiu Jianming
Published: April 2020

Bourbon virus (BRBV) was first isolated from a patient hospitalized at the University of Kansas Hospital in 2014. Since then, several deaths have been reported to be caused by BRBV infection in the Midwest and Southern United States. BRBV is a tick-borne virus that is widely carried by lone star ticks. It belongs to genusThogotovirusof theOrthomyxoviridaefamily. Currently, there are no treatments or vaccines available for BRBV or thogotovirus infection caused diseases. In this study, we reconstituted a replicon reporter system, composed of plasmids expressing the RNA-dependent RNA polymerase (RdRP) complex (PA, PB1 and PB2), nucleocapsid (NP) protein, and a reporter gene flanked by the 3’ and 5’ UTR of the envelope glycoprotein (GP) genome segment. By using the luciferase reporter, we screened a few small molecule compounds of anti-endonuclease that inhibited the nicking activity by parvovirus B19 (B19V) NS1, as well as FDA-approved drugs targeting the RdRP of influenza virus. Our results demonstrated that myricetin, and an anti-B19V NS1 nicking inhibitor, efficiently inhibited the RdRP activity of BRBV and virus replication. The IC50and EC50of myricetin are 2.22 μM and 4.6 μM, respectively, in cells. Myricetin had minimal cytotoxicity in cells, and therefore the therapeutic index of the compound is high. In conclusion, the BRBV replicon system is a useful tool to study viral RNA replication and to develop antivirals, and myricetin may hold promise in treatment of BRBV infected patients.
How Fishing CatsPrionailurus viverrinusfish: Describing a felid’s strategy to hunt aquatic prey
Authors: Ganguly Divyajyoti , Adhya Tiasa
Published: April 2020

Hunting strategies are key to carnivore survival (Krebs and Davies 2009;Kamil et al. 2012;Michalko and Pekar 2016). Fishing Cat’s(Prionailurus viverrinus)persistence in the ‘semi-aquatic niche’ (Kitchener et al. 2010) despite felids being terrestrial carnivores in general (>95%) (Hunter 2019) suggests the evolution of a successful hunting strategy. Its further suggest selection for hunting in wetlands. What energy conserving strategies did the Fishing Cat borrow from its family and how were these adapted to optimize energy gained from hunting fish, its primary prey? We attempt to answer this by analyzing 197 video footages collected opportunistically from a participatory science initiative conducted over 2.5 years. We found that the felid switches between stationary and active modes of searching for prey depending on the depth of water and the corresponding loss of body heat/energy. For example, diving in deeper waters requires the submergence of the upper portions of the body and loss of more body heat/energy. Our analysis shows that the cat spent much of its time (~52%) sitting and waiting for prey (fish) to come nearer and then took limited attempts to dive into deeper water (2.78%). We suggest that this is a strategy to optimize the net energy gain. In shallow waters where the cat could forage without submerging the upper body it adopted a predominantly active mode of hunting (~96%) to flush out prey. Thus, prominent hunting strategies in the small cat lineage like ‘sit-and-wait’ and ‘active foraging’ is adapted to hunt in the water. We recorded a 60% hunting success in deeper waters but did not detect a successful hunt in shallow waters due to the low sample size of data from shallow water hunting. The major caveat in our study is the post-hoc analysis of opportunistically collected data as opposed to data derived from a structured design with predefined objectives. With more sampling from various seasons and landscapes, finer details can be explored which would have conservation implications. For example, we would expect variations in ‘attempts to hunt’ during cold seasons because heat loss might be less of a challenge in the latter. Quantifying ‘attempts to hunt’ and ‘successful hunts’ across seasons could help focus management interventions to minimize negative interactions between fish cultivators and Fishing Cat. The strictly nocturnal activity of fishing cat as demonstrated in our study could be a strategy taken by the cat to avoid humans. Our approach of using participatory-science is relevant for conducting research on mammal behavior in human dominated landscapes.
Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins
Authors: Bai Yunmeng , Jiang Dawei , Lon Jerome R , Chen Xiaoshi , Hu Meiling , Lin Shudai , Chen Zixi , Wang Xiaoning , Meng Yuhuan , Du Hongli
Published: April 2020

Objectives

To reveal epidemic trend and possible origins of SARS-CoV-2 by exploring its evolution and molecular characteristics based on a large number of genomes since it has infected millions of people and spread quickly all over the world.

Methods

Various evolution analysis methods were employed.

Results

The estimated Ka/Ks ratio of SARS-CoV-2 is 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes, and the time to the most recent common ancestor (tMRCA) was inferred in late September 2019. Further 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The Ka/Ks, detected population size and development trends of each major haplotype showed H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating H3 and H4 might have existed for a long time, while H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time. Notably the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37).

Conclusions

In this study, the evolution and molecular characteristics of more than 16000 genomic sequences provided a new perspective for revealing epidemiology of SARS-CoV-2.
Latent defense response to non-pathogenic microbial factors impairs plant-rhizobacteria mutualism
Authors: Yang Yu , Chen Shenglan , Peng Li , Liu Xiaomin , Kaushal Richa , Yuan Fengtong , Singh Sunil K. , He Danxia , Lv Suhui , Vílchez Juan I. , Morcillo Rafael J. L. , Wang Wei , Huang Weichang , Lei Mingguang , Song Chun-Peng , Zhu Jian-Kang , Paré Paul W. , Zhang Huiming
Published: April 2020

Unlike pathogens that trigger plant defense responses, commensal or beneficial microbes are compatible with plants and do not elicit a defense response. An assumption underlying the compatibility is that plants are inert in mounting a defense response to non-pathogenic microbial factors. However, the mechanisms underlying this inertness in defense are unknown. Here a forward genetic screen led to the isolation of an Arabidopsis mutant displaying a new type of immunity which we named as latent defense response (LDR) to a beneficial rhizobacterium. The mutant, known asgp1forGrowth-Promotion 1, is impaired in rhizobacteria-induced plant growth-promotion due to disrupted oleic acid homeostasis and consequent activation of defense responses. Several bacterial volatile compounds trigger LDR ingp1but not wild type plants. GP1 dysfunction strongly represses colonization of the beneficial rhizobacterium and alters root-associated microbiota. Our findings reveal a hidden layer of plant defense, LDR, which is suppressed by GP1 to allow mutualistic association between plants and beneficial rhizobacteria.

One Sentence Summary

A hidden layer of host immunity against non-pathogenic microbes leads to plant incompatibility with beneficial rhizobacteria.
SIRT1 ameliorates premature senescence-induced defenestration in hepatic sinusoidal endothelial cell
Authors: Luo Xiaoying , Bai Yangqiu , He Shuli , Jiang Xiaoke , Yang Zhiyu , Sun Suofeng , Lu Di , Wei Peiru , Liang Yuan , Peng Cong , Wang Yaru , Sheng Ruli , Han Shuangyin , Li Xiuling , Zhang Bingyong
Published: April 2020

Premature senescence, linked to progerin, involves in endothelial dysfunction and liver diseases. Activating sirtuin 1 (SIRT1) ameliorates liver fibrosis. However, the potential mechanisms of premature senescence in defenestration in hepatic sinusoidal endothelial cells (HSECs) and how SIRT1 affects fenestrae remains elusive. Our study showed thatin vivo, premature senescence occurred, with decrease of SIRT1, during CCl4-induced defenestration in HSECs and liver fibrogenesis; whereas overexpressing SIRT1 with adenovirus vector lessened progerin-associated premature senescence to relieve CCl4-induced defenestration and liver fibrosis.In vitro, fenestrae in HSECs disappeared, with progerin-associated premature senescence; these effects aggravated by H2O2-induced oxidative damage. Nevertheless, knockdown of NOX2 or overexpression of SIRT1 with adenovirus vector reduced progerin-associated premature senescence to maintain fenestrae through deacetylating p53. Furthermore, more Ac p53 K381 and progerin co-localized with accumulation of actin filament (F-actin) in the nuclear envelope of H2O2-treated HSECs; in contrast, these effects were rescued by overexpressing SIRT1. In conclusion, NOX2-dependent oxidative damage aggravates defenestration in HSECs via progerin-associated premature senescence; SIRT1-mediated deacetylation of p53 maintains fenestrae and attenuates liver fibrogenesis through inhibiting premature senescence.
Identification and characterization of the hypoxia response regulatory elements in the accessible genome
Authors: Lu Xi , Chen Xingqi
Published: April 2020

Hypoxia is commonly observed in the solid tumor and contributes to the drug resistance in cancer therapy. Deciphering the epigenetic feature under the hypoxia condition in the solid tumor is critical for us to understand the tumorigenesis and design the precision therapy. Using the time series of ATAC-seq data under the hypoxia treatment from the epithelia cells, we identified the hypoxia response regulatory elements (HRREs) in the accessible genome. We found that these different HRREs have unique genomic features and are enriched with different transcriptional factors (TFs). Our study provides insights into the chromatin structure response to the hypoxia treatment and identifies useful genomic features for a better understanding of the hypoxia biology in the solid tumor.
Biochemical, structural insights of newly isolated AA16 family of Lytic Polysaccharide Monooxygenase (LPMO) fromAspergillus fumigatusand investigation of its synergistic effect using biomass
Authors: Hossain Musaddique , Dodda Subba Reddy , Kapoor Bishwajit Singh , Aikat Kaustav , Mukhopadhyay Sudit S.
Published: April 2020

The efficient conversion of lignocellulosic biomass into fermentable sugar is a bottleneck for the cheap production of bio-ethanol. The recently identified enzyme Lytic Polysaccharide Monooxygenase (LPMO) family has brought new hope because of its boosting capabilities of cellulose hydrolysis. In this report, we have identified and characterized a new class of auxiliary (AA16) oxidative enzyme LPMO from the genome of a locally isolated thermophilic fungusAspergillus fumigatus(NITDGPKA3) and evaluated its boosting capacity of biomass hydrolysis. TheAfLPMO16 is an intronless gene and encodes the 29kDa protein. While Sequence-wise, it is close to the C1 type ofAaAA16 and cellulose-active AA10 family of LPMOs, but the predicted three-dimensional structure shows the resemblance with the AA11 family of LPMO (PDB Id: 4MAH). The gene was expressed under an inducible promoter (AOX1) with C-terminal His tag in thePichia pastoris. The protein was purified using Ni-NTA affinity chromatography, and we studied the enzyme kinetics with 2,6-dimethoxyphenol. We observed polysaccharides depolymerization activity with Carboxymethyl cellulose (CMC) and Phosphoric acid swollen cellulose (PASC). Moreover, the simultaneous use of cellulase cocktail (commercial) andAfLPMO16 enhances lignocellulosic biomass hydrolysis by 2-fold, which is highest so far reported in the LPMO family.

Importance

The auxiliary enzymes, such as LPMOs, have industrial importance. These enzymes are used in cellulolytic enzyme cocktail due to their synergistic effect along with cellulases. In our study, we have biochemically and functionally characterized the new AA16 family of LPMO fromAspergillus fumigatus(NITDGPKA3). The biochemical characterization is the fundamental scientific elucidation of the newly isolated enzyme. The functional characterization, biomass degradation activity ofAfLPMO16, and cellulase cocktail (commercial) combination enhancing the activity by 2-fold. This enhancement is the highest reported so far, which gives the enzymeAfLPMO16 enormous potential for industrial use.
Inhibitory effect of eslicarbazepine acetate and S-licarbazepine on Nav1.5 channels
Authors: Leslie Theresa K. , Brückner Lotte , Chawla Sangeeta , Brackenbury William J.
Published: April 2020

Eslicarbazepine acetate (ESL) is a dibenzazepine anticonvulsant approved as adjunctive treatment for partial-onset epileptic seizures. Following first pass hydrolysis of ESL, S-licarbazepine (S-Lic) represents around 95 % of circulating active metabolites. S-Lic is the main enantiomer responsible for anticonvulsant activity and this is proposed to be through the blockade of voltage-gated Na+channels (VGSCs). ESL and S-Lic both have a voltage-dependent inhibitory effect on the Na+current in N1E-115 neuroblastoma cells expressing neuronal VGSC subtypes including Nav1.1, Nav1.2, Nav1.3, Nav1.6 and Nav1.7. ESL has not been associated with cardiotoxicity in healthy volunteers, although a prolongation of the electrocardiographic PR interval has been observed, suggesting that ESL may also inhibit cardiac Nav1.5 isoform. However, this has not previously been studied. Here, we investigated the electrophysiological effects of ESL and S-Lic on Nav1.5 using whole-cell patch clamp recording. We interrogated two model systems: (1) MDA-MB-231 metastatic breast carcinoma cells, which endogenously express the ‘neonatal’ Nav1.5 splice variant, and (2) HEK-293 cells stably over-expressing the ‘adult’ Nav1.5 splice variant. We show that both ESL and S-Lic inhibit transient and persistent Na+current, hyperpolarise the voltage-dependence of fast inactivation, and slow the recovery from channel inactivation. These findings highlight, for the first time, the potent inhibitory effects of ESL and S-Lic on the Nav1.5 isoform, suggesting a possible explanation for the prolonged PR interval observed in patients on ESL treatment. Given that numerous cancer cells have also been shown to express Nav1.5, and that VGSCs potentiate invasion and metastasis, this study also paves the way for future investigations into ESL and S-Lic as potential invasion inhibitors.
eCovSens-Ultrasensitive Novel In-House Built Printed Circuit Board Based Electrochemical Device for Rapid Detection of nCovid-19 antigen, a spike protein domain 1 of SARS-CoV-2
Authors: Mahari Subhasis , Roberts Akanksha , Shahdeo Deepshikha , Gandhi Sonu
Published: April 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or nCovid-19) outbreak has become a huge public health issue due to its rapid transmission and global pandemic. Currently, there are no vaccines or drugs available for nCovid-19, hence early detection is crucial to help and manage the outbreak. Here, we report an in-house built biosensor device (eCovSens) and compare it with a commercial potentiostat for the detection of nCovid-19 spike antigen (nCovid-19Ag) in spiked saliva samples. A potentiostat based sensor was fabricated using fluorine doped tin oxide electrode (FTO) with gold nanoparticle (AuNPs) and immobilized with nCovid-19 monoclonal antibody (nCovid-19Ab) to measure change in the electrical conductivity. Similarly, eCovSens was used to measure change in electrical conductivity by immobilizing nCovid-19 Ab on screen printed carbon electrode (SPCE). The performances of both sensors were recorded upon interaction of nCovid-19Ab with its specific nCovid-19Ag. Under optimum conditions, the FTO based immunosensor and eCovSens displayed high sensitivity for detection of nCovid-19Ag, ranging from 1 fM to 1 μM. Our in-house developed device can successfully detect nCovid-19Ag at 10 fM concentration in standard buffer that is in close agreement with FTO/AuNPs sensor. The limit of detection (LOD) was found to be 90 fM with eCovSens and 120 fM with potentiostst in case of spiked saliva samples. The proposed portable eCovSens device can be used as a diagnostic tool for the rapid (within 10-30 s) detection of nCovid-19Ag traces directly in patient saliva in a non-invasive manner.
Zika virus-based immunotherapy enhances long-term survival of rodents with brain tumors through upregulation of memory T-cells
Authors: Crane Andrew T. , Chrostek Matthew R. , Krishna Venkatramana D. , Shiao Maple , Toman Nikolas G. , Pearce Clairice , Tran Sarah K. , Sipe Christopher J. , Guo Winston , Voth Joseph P. , Vaid Shivanshi , Xie Hui , Lu Wei-Cheng , Swanson Will , Grande Andrew W. , Schleiss Mark R. , Bierle Craig J. , Cheeran Maxim C-J. , Low Walter C.
Published: April 2020

Zika virus (ZIKV) exhibits a tropism for brain tumor cells and has been used as an oncolytic virus to target brain tumors in mice with modest effects on extending median survival. Recent studies have highlighted the potential for combining virotherapy and immunotherapy to target cancer. We postulated that ZIKV could be used as an adjuvant to enhance the long-term survival of mice with malignant glioblastoma and generate memory T-cells capable of providing long-term immunity against cancer remission. To test this hypothesis mice bearing malignant intracranial GL261 tumors were subcutaneously vaccinated with irradiated GL261 cells previously infected with the ZIKV. Mice also received intracranial injections of live ZIKV, irradiated ZIKV, or irradiated GL261 cells previously infected with ZIKV. Long-term survivors were rechallenged with a second intracranial tumor to examine their immune response and look for the establishment of protective memory T-cells. Mice with subcutaneous vaccination plus intracranial irradiated ZIKV or intracranial irradiated GL261 cells previously infected with ZIKV exhibited the greatest extensions to overall survival. Flow cytometry analysis of immune cells within the brains of long-term surviving mice after tumor rechallenge revealed an upregulation in the levels of T-cells, including CD4+and tissue-resident memory CD4+T-cells, in comparison to long-term survivors that were mock-rechallenged, and in comparison to naïve untreated mice challenged with intracranial gliomas. These results suggest that ZIKV can serve as an adjuvant to subcutaneous tumor vaccines that enhance long-term survival and generate protective tissue-resident memory CD4+T-cells.
High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains
Authors: Flament-Simon Saskia-Camille , de Toro María , Chuprikova Liubov , Blanco Miguel , Moreno-González Juan , Salas Margarita , Blanco Jorge , Redrejo-Rodríguez Modesto
Published: April 2020

Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus-host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB).

We have now surveyed the presence of pipolins in a collection of 2238 human and animal pathogenicEscherichia colistrains and found that, although detected in only 25 new isolates (1.1%), they are present inE. colistrains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belongs to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring strains from GenBank further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons.

In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulatingE. coliand possibly also among other pathogenic bacteria.
Analyzing Genomic Data Using Tensor-Based Orthogonal Polynomials with Application to Synthetic RNAs
Authors: Nafees Saba , Rice Sean H. , Wakeman Catherine A.
Published: April 2020

An important goal in molecular biology is to quantify both the patterns across a genomic sequence and the relationship between phenotype and underlying sequence. We propose a multivariate tensor-based orthogonal polynomial approach to characterize nucleotides or amino acids in a given sequence and map corresponding phenotypes onto the sequence space. We have applied this method to a previously published case of small transcription activating RNAs (STARs). Covariance patterns along the sequence showcased strong correlations between nucleotides at the ends of the sequence. However, when the phenotype is projected onto the sequence space, this pattern doesn’t emerge. When doing second order analysis and quantifying the functional relationship between the phenotype and pairs of sites along the sequence, we identified sites with high regressions spread across the sequence, indicating potential intramolecular binding. In addition to quantifying interactions between different parts of a sequence, the method quantifies sequence-phenotype interactions at first and higher order levels. We discuss the strengths and constraints of the method and compare it to computational methods such as machine learning approaches. An accompanying command line tool to compute these polynomials is provided. We show proof of concept of this approach and demonstrate its potential application to other biological systems.
Validation and standardization of a new radial-arm water maze protocol using a murine model of mild closed head traumatic brain injury
Authors: Macheda Teresa , Roberts Kelly N. , Bachstetter Adam D.
Published: April 2020

Cognitive impairments can be a significant problem after a traumatic brain injury (TBI), which affects millions worldwide each year. There is a need for establish reproducible cognitive assays in rodents to better understand disease mechanisms and to develop therapeutic interventions towards treating TBI-induced impairments. Our goal was to validate and standardize the radial arm water maze (RAWM) test as an assay to screen for cognitive impairments caused by TBI. RAWM is a visuo-spatial learning test, originally designed for use with rats, and later adapted for mice. The present study investigates whether test procedures, such us the presence of extra-maze cues influences learning and memory performance. C57BL/6 mice were tested in an 8-arm RAWM using a four-day protocol. We demonstrated that two days of training, exposing the mice to extra-maze cues and a visible platform, influenced learning and memory performance. Mice that did not receive training performed poorer compared to mice trained. To further validate our RAWM protocol, we used scopolamine. We, also, demonstrated that a single mild closed head injury (CHI) caused deficits in this task at two weeks post-CHI. Our data supported the use of 7 trials per day and a spaced training protocol as key factor to unmask memory impairment following CHI. Here, we provide a detailed standard operating procedure for RAWM test, which can be applied to a variety of mouse models including neurodegenerative diseases and pathology, as well as when pharmacological approaches are used.
Greenhouse conditions in lower Eocene coastal wetlands? – Lessons from Schöningen, Northern Germany
Authors: Lenz Olaf K. , Riegel Walter , Wilde Volker
Published: April 2020

The Paleogene succession of the Helmstedt Lignite Mining District in Northern Germany includes coastal peat mire records from the latest Paleocene to the middle Eocene at the southern edge of the Proto-North Sea. Therefore, it covers the different long- and short-term climate perturbations of the Paleogene greenhouse. 56 samples from three individual sections of a lower Eocene seam in the record capture the typical succession of the vegetation in a coastal wetland during a period that was not affected by climate perturbation. This allows facies-dependent vegetational changes to be distinguished from those that were climate induced. Cluster analyses and NMDS of well-preserved palynomorph assemblages reveal four successional stages in the vegetation during peat accumulation: (1) a coastal vegetation, (2) an initial mire, (3) a transitional mire, and (4) a terminal mire. Biodiversity measures show that plant diversity decreased significantly in the successive stages. The highly diverse vegetation at the coast and in the adjacent initial mire was replaced by low diversity communities adapted to wet acidic environments and nutrient deficiency. The palynomorph assemblages are dominated by elements such asAlnus(Betulaceae) orSphagnum(Sphagnaceae). Typical tropical elements which are characteristic for the middle Eocene part of the succession are missing. This indicates that a more warm-temperate climate prevailed in northwestern Germany during the early lower Eocene.
LINCS gene expression signatures analysis revealed bosutinib as a radiosensitizer of breast cancer cells by targetingeIF4G1
Authors: Hu Sai , Zhou Pingkun , Liu Xiaodan , Yin Xiaoyao , Xie Dafei , Huang Bo , Guan Hua
Published: April 2020

Radioresistance represents the predominant cause for radiotherapy failure and disease progression, resulting in increased breast cancer mortality. Through gene expression signatures analyses of Library of Integrated Network-Based Cellular Signatures (LINCS) and Gene Expression Omnibus (GEO), the present study aimed to identify potential candidate radiosensitizers from known drugs systematically. The similarity of integrated gene expression signatures between irradiatedeIF4G1-silenced breast cancer cells and known drugs was measured by enrichment scores. Drugs with positive enrichment scores were selected as potential radiosensitizers. The radiosensitizing effects of the candidate radiosensitizers were analyzed in breast cancer cells (MCF-7, MX-1, and MDA-MB-231) by CCK-8 assays and colony-forming capability after exposure to ionizing radiation. Cell apoptosis was detected by flow cytometry. Expressions ofeIF4G1and a series of DNA damage response proteins were analyzed by Western blot assays. Bosutinib was proposed to be a promising radiosensitizer as its administration markedly reduced the dosages of both the drug and ionizing radiation and was associated with fewer adverse drug reactions. The combined treatment with ionizing radiation and bosutinib significantly increased the cells killing potency in all three cell lines as compared to ionizing radiation or bosutinib alone. MX-1 cells were revealed to be the most sensitive to both ionizing radiation and bosutinib among the three cell lines. Bosutinib noticeably downregulated the expression ofeIF4G1in a dose-dependent manner and also reduced the expression of DNA damage response proteins (includingATM,XRCC4,ATRIP, andGADD45a). Moreover,eIF4G1could be a key target of bosutinib through which it regulates DNA damage induced by ionizing radiation. Thus, taken together, bosutinib may serve as a potential candidate radiosensitizer for breast cancer therapy.
The DMCdrive: practical 3D-printable micro-drive system for reliable chronic multi-tetrode recording and optogenetic application in freely behaving rodents
Authors: Kim Hoseok , Brünner Hans Sperup , Carlén Marie
Published: April 2020

Electrophysiological recording and optogenetic control of neuronal activity in behaving animals have been integral to the elucidation of how neurons and circuits modulate network activity in the encoding and causation of behavior. However, most current electrophysiological methods require substantial economical investments and prior expertise. Further, the inclusion of optogenetics with electrophysiological recordings in freely moving animals remains a general challenge. Expansion of the technological repertoire across laboratories, research institutes, and countries, demands open access to high-quality devices that can be built with little or no prior expertise from easily accessible parts of low cost. We here present a very affordable, truly easy-to-assemble micro-drive for electrophysiology in combination with optogenetics in freely moving mice and rats. The DMCdrive is particularly suited for reliable long-term recordings of neurons and network activities, and simplify optical tagging and manipulation of neurons in the recorded brain region. The highly functional and practical drive design has been optimized for accurate tetrode movement in brain tissue, and remarkably reduced build time. We provide a complete overview of the drive design, its assembly and use, and proof-of-principle demonstration of long-term recordings paired with cell-type-specific optogenetic manipulations in the prefrontal cortex (PFC) of freely moving transgenic mice and rats.
Tapestry: validate and edit small eukaryotic genome assemblies with long reads
Authors: Davey John W. , Davis Seth J. , Mottram Jeremy C. , Ashton Peter D.
Published: April 2020

Small eukaryotic genome assemblies based on long reads are often close to complete, but still require validation and editing. Tapestry produces an interactive report which can be used to validate, sort and filter the contigs in a raw genome assembly, taking into account GC content, telomeres, read depths, contig alignments and read alignments. The report can be shared with collaborators and included as supplemental material in publications.

Availability

Source code is freely available athttps://github.com/johnomics/tapestry. Package is freely available in Bioconda (https://anaconda.org/bioconda/tapestry).

Contact

john.davey@york.ac.uk
Use of a highly specific kinase inhibitor for rapid, simple and precise synchronization ofPlasmodium falciparumandPlasmodium knowlesiasexual stage parasites
Authors: Ressurreição Margarida , Thomas James A. , Nofal Stephanie D. , Flueck Christian , Moon Robert W. , Baker David A. , van Ooij Christiaan
Published: April 2020

During the course of the asexual erythrocytic stage of development,Plasmodiumspp. parasites undergo a series of morphological changes and induce alterations in the host cell. At the end of this stage, the parasites exit the host cell, after which the progeny invade a new host cell. These processes are rapid and occur in a time-dependent manner. Of particular importance, egress and invasion of erythrocytes by the parasite are difficult to capture in an unsynchronized culture, or even a culture that has been synchronized to within hours. Therefore, precise synchronization of parasite cultures is of paramount importance for the investigation of these processes. Here we describe a method for synchronizingPlasmodium falciparumandPlasmodium knowlesiasexual blood stage parasites with ML10, a highly specific inhibitor of the cGMP-dependent protein kinase (PKG) that arrests parasite growth approximately 15 minutes prior to egress. This inhibitor allows parasite cultures to be synchronized to within minutes, with a simple wash step. Furthermore, we show that parasites remain viable for several hours after becoming arrested by the compound and that ML10 has advantages over the previously used PKG inhibitor Compound 2. Here, we demonstrate that ML10 is an invaluable tool for the study ofPlasmodium spp. asexual blood stage biology and for the routine synchronization ofP. falciparumandP. knowlesicultures.
Consensus transcriptional regulatory networks of coronavirus-infected human cells
Authors: Ochsner Scott A , Pillich Rudolf T , McKenna Neil J
Published: April 2020

Establishing consensus around the transcriptional interface between coronavirus (CoV) infection and human cellular signaling pathways can catalyze the development of novel anti-CoV therapeutics. Here, we used publicly archived transcriptomic datasets to compute consensus regulatory signatures, or consensomes, that rank human genes based on their rates of differential expression in MERS-CoV (MERS), SARS-CoV-1 (SARS1) and SARS-CoV-2 (SARS2)-infected cells. Validating the CoV consensomes, we show that high confidence transcriptional targets (HCTs) of CoV infection intersect with HCTs of signaling pathway nodes with known roles in CoV infection. Among a series of novel use cases, we gather evidence for hypotheses that SARS2 infection efficiently represses E2F family target genes encoding key drivers of DNA replication and the cell cycle; that progesterone receptor signaling antagonizes SARS2-induced inflammatory signaling in the airway epithelium; and that SARS2 HCTs are enriched for genes involved in epithelial to mesenchymal transition. The CoV infection consensomes and HCT intersection analyses are freely accessible through the Signaling Pathways Project knowledgebase, and as Cytoscape-style networks in the Network Data Exchange repository.
Zika viral proteome analysis reveals an epitope cluster within NS3 helicase as a potential vaccine candidate: anin silicostudy
Authors: Haque Md Tangigul , Shah Md Nur Ahad , Paul Shatabdi , Khan Md Kawsar , Barua Payal
Published: April 2020

Zika virus (ZIKV), a mosquito-borne flavivirus, is now an emerging global public health concern. Currently, the pathogenicity, genetic diversity and the consequences of ZIKV infection are little known but a protective vaccine against ZIKV is an urgency. In this study, we have taken an immunoinformatics based approach to predict epitope cluster region in the whole proteome (3423 amino acids) of ZIKV. We have operated a range of bioinformatics algorithms to determine the epitopes of CD8+ cytotoxic T-cell (CTL), CD4+ helper T-cell (THL) and B cell. We have predicted an epitope cluster of 23 contiguous amino acids (region 1989-2011, WLEARMLLDNIYLQDGLIASLYR) residing on the protein NS3 helicase in ZIKV proteome. This epitope cluster contains fourteen CD4+ (THL) epitopes and six CD8+ (CTL) epitopes. The cluster region predicted to provide 93.86% population coverage worldwide. Finally, we have validated the epitopes by analysing their binding efficiency (binding energy within −4.7 to −6.9 kcal/mol) with specific HLA alleles. Based on our immunoinformatics analysis, we propose the peptide WLEARMLLDNIYLQDGLIASLYR as a new peptide vaccine candidate against Zika virus for further validation.
Introductions and early spread of SARS-CoV-2 in France
Authors: Gámbaro Fabiana , Behillil Sylvie , Baidaliuk Artem , Donati Flora , Albert Mélanie , Alexandru Andreea , Vanpeene Maud , Bizard Méline , Brisebarre Angela , Barbet Marion , Derrar Fawzi , van der Werf Sylvie , Enouf Vincent , Simon-Loriere Etienne
Published: April 2020

Following the emergence of coronavirus disease (COVID-19) in Wuhan, China in December 2019, specific COVID-19 surveillance was launched in France on January 10, 2020. Two weeks later, the first three imported cases of COVID-19 into Europe were diagnosed in France. We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France. Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases. This study emphasizes the importance of continuous and geographically broad genomic sequencing and calls for further efforts with inclusion of asymptomatic infections.
TAPBPR Promotes Antigen Loading on MHC-I Molecules Using a Peptide Trap
Authors: McShan Andrew C. , Devlin Christine A. , Morozov Giora I. , Overall Sarah A. , Moschidi Danai , Akella Neha , Procko Erik , Sgourakis Nikolaos G.
Published: April 2020

Chaperones tapasin and TAP-binding protein related (TAPBPR) perform the important functions of stabilizing nascent MHC-I molecules (chaperoning) and selecting high affinity peptides in the MHC-I groove (editing). While X-ray and cryo-EM snapshots of MHC-I in complex with TAPBPR and tapasin, respectively, have provided important insights into the peptide-deficient MHC-I groove structure, the molecular mechanism through which these chaperones influence the selection of specific amino acid sequences remains incompletely characterized. Of particular importance is a 16 residue loop in TAPBPR (corresponding to 11 residues in tapasin), which has been proposed to actively compete with incoming peptides by forming direct contacts in the F-pocket of the empty MHC-I groove. Using a deep mutational scanning functional analysis of TAPBPR, we find that important residues for the chaperoning activity are located on the major interaction surfaces with nascent MHC-I molecules, excluding the loop. However, interactions with properly conformed molecules toward peptide editing are influenced by loop mutations, in an MHC-I allele- and peptide-dependent manner. Detailed biophysical characterization by ITC, FP and NMR reveals that the loop does not interact with the peptide-deficient MHC-I groove to compete with incoming peptides, but instead promotes peptide loading by acting as a kinetic trap. Our results suggest that the longer loop of TAPBPR lowers the affinity threshold for peptide selection, to promote loading within subcellular compartments of reduced peptide concentration and to prevent disassembly of high affinity peptide-MHC-I complexes that are transiently interrogated by TAPBPR during editing.
Homeostatic control of meiotic G2/prophase checkpoint function by Pch2 and Hop1
Authors: Raina Vivek B. , Vader Gerben
Published: April 2020

Checkpoints cascades coordinate cell cycle progression with essential chromosomal processes. During meiotic G2/prophase, recombination and chromosome synapsis are monitored by what are considered distinct checkpoints [1–3]. In budding yeast, the AAA+ ATPase Pch2 is thought to specifically promote cell cycle delay in response to synapsis defects [4–6]. However, unperturbedpch2Δcells are delayed in meiotic G2/prophase [6], suggesting paradoxical roles for Pch2 in cell cycle progression. Here, we provide insight into the checkpoint roles of Pch2 and its connection to Hop1, a HORMA domain-containing client protein. Contrary to current understanding, we find that the Pch2-Hop1 module is crucial for checkpoint function in response to both recombination and synapsis defects, thus revealing a shared meiotic checkpoint cascade. Meiotic checkpoint responses are transduced by DNA break-dependent phosphorylation of Hop1 [7, 8]. Based on our data and on the effect of Pch2 on HORMA topology [9–11], we propose that Pch2 promotes checkpoint proficiency by catalyzing the availability of signaling-competent Hop1. Conversely, we demonstrate that Pch2 can act as a checkpoint silencer, also in the face of persistent DNA repair defects. We establish a framework in which Pch2 and Hop1 form a homeostatic module that governs general meiotic checkpoint function. We show that this module can - depending on the cellular context - fuel or extinguish meiotic checkpoint function, which explains the contradictory roles of Pch2 in cell cycle control. Within the meiotic checkpoint, the Pch2-Hop1 module thus operates analogous to the Pch2/TRIP13-Mad2 module in the spindle assembly checkpoint that monitors chromosome segregation [12–16].
Identification and Characterization of Fbxl22, a novel skeletal muscle atrophy-promoting E3 ubiquitin ligase
Authors: Hughes David C. , Baehr Leslie M. , Driscoll Julia R. , Lynch Sarah A. , Waddell David S. , Bodine Sue C.
Published: April 2020

Muscle-specific E3 ubiquitin ligases have been identified in muscle atrophy-inducing conditions. The purpose of the current study was to explore the functional role of Fbxl22, and a newly identified splice variant (Fbxl22-193), in skeletal muscle homeostasis and neurogenic muscle atrophy. In mouse C2C12muscle cells, promoter fragments of the Fbxl22 gene were cloned and fused with the secreted alkaline phosphatase reporter gene to assess the transcriptional regulation of Fbxl22. The tibialis anterior muscles of male C57/BL6 mice (12-16 weeks old) were electroporated with expression plasmids containing the cDNA of two Fbxl22 splice variants and tissues collected after 7, 14 and 28 days. Gastrocnemius muscles of wild type and MuRF1 knockout mice were electroporated with an Fbxl22 RNAi or empty plasmid, denervated three days post-transfection, and tissues collected 7 days post-denervation. The full-length gene and novel splice variant are transcriptionally induced early (after 3 days) during neurogenic muscle atrophy. In vivo overexpression of Fbxl22 isoforms in mouse skeletal muscle lead to evidence of myopathy/atrophy suggesting that both are involved in the process of neurogenic muscle atrophy. Knockdown of Fbxl22 in MuRF1 KO muscles resulted in significant additive muscle sparing at 7 days of denervation. Targeting two E3 ubiquitin ligases appears to have a strong additive effect on protecting muscle mass loss with denervation and these findings have important implications in the development of therapeutic strategies to treat muscle atrophy.
Transient and layer-specific reduction in neocortical PV inhibition during sensory association learning
Authors: Kuljis Dika A. , Park Eunsol , Myal Stephanie E. , Clopath Claudia , Barth Alison L.
Published: April 2020

Sensory and motor learning reorganizes neocortical circuitry, particularly manifested in the strength of excitatory synapses. Prior studies suggest reduced inhibition can facilitate glutamatergic synapse plasticity during learning, but the role of specific inhibitory neurons in this process has not been well-documented. Here we investigate whether inhibition from parvalbumin (PV)-expressing neurons is altered in primary somatosensory cortex in mice trained in a whisker-based reward-association task. Anatomical and electrophysiological analyses show PV input to L2/3, but not L5, pyramidal (Pyr) neurons is rapidly suppressed during early stages of sensory training, effects that are reversed after longer training periods. Importantly, sensory stimulation without reward does not alter PV-mediated inhibition. Computational modeling indicates that reduced PV inhibition in L2/3 selectively enables an increase in translaminar recurrent activity, also observed during SAT. PV disinhibition in superficial layers of the neocortex may be one of the earliest changes in learning-dependent rewiring of the cortical column.

Impact statement

Tactile learning is associated with reduced PV inhibition in superficial layers of somatosensory cortex. Modeling studies suggest that PV disinhibition can support prolonged recurrent activity initiated by thalamic input.
Cell autonomous requirement of Neurofibromin (Nf1) for postnatal muscle hypertrophic growth and metabolic homeostasis
Authors: Wei Xiaoyan , Franke Julia , Ost Mario , Wardelmann Kristina , Börno Stefan , Timmermann Bernd , Meierhofer David , Kleinridders Andre , Klaus Susanne , Stricker Sigmar
Published: April 2020

Background

Neurofibromatosis type 1 (NF1) is a multi-organ disease caused by mutations in Neurofibromin(NF1).Amongst other features, NF1 patients frequently show reduced muscle mass and strength, impairing patients’ mobility and increasing the risk of fall. The role of Nf1 in muscle and the cause for the NF1-associated myopathy is mostly unknown.

Methods

To dissect the function of Nf1 in muscle, we created muscle-specific knockout mouse models for Nf1, inactivating Nf1 in the prenatal myogenic lineage either under the Lbx1 promoter or under the Myf5 promoter. Mice were analyzed during pre-and postnatal myogenesis and muscle growth.

Results

Nf1Lbx1and Nf1Myf5animals showed only mild defects in prenatal myogenesis. Nf1Lbx1animals were perinatally lethal, while Nf1Myf5animals survived only up to approx. 25 weeks. A comprehensive phenotypic characterization of Nf1Myf5animals showed decreased postnatal growth, reduced muscle size, and fast fiber atrophy. Proteome and transcriptome analysis of muscle tissue indicated decreased protein synthesis and increased proteasomal degradation, and decreased glycolytic and increased oxidative activity in muscle tissue. High-resolution respirometry confirmed enhanced oxidative metabolism in Nf1Myf5muscles, which was concomitant to a fiber type shift from type 2B to type 2A and type 1. Moreover, Nf1Myf5muscles showed hallmarks of decreased activation of mTORC1 and increased expression of atrogenes. Remarkably, loss of Nf1 promoted a robust activation of AMPK with a gene expression profile indicative of increased fatty acid catabolism. Additionally, we observed a strong induction of genes encoding catabolic cytokines in muscle Nf1Myf5animals, in line with a drastic reduction of white, but not brown adipose tissue.

Conclusions

Our results demonstrate a cell-autonomous role for Nf1 in myogenic cells during postnatal muscle growth required for metabolic and proteostatic homeostasis. Furthermore, Nf1 deficiency in muscle drives cross-tissue communication and mobilization of lipid reserves.