bluuebunny/crossref_metadata_2025 huggingface dataset:
High prevalence of SARS-CoV-2 antibodies in care homes affected by COVID-19; prospective cohort study, England
Authors: Ladhani Shamez N , Jeffery-Smith Anna , Patel Monika , Janarthanan Roshni , Fok Jonathan , Crawley-Boevey Emma , Vusirikala Amoolya , Fernandez Elena , Perez Marina Sanchez , Tang Suzanne , Dun-Campbell Kate , Wynne-Evans Edward , Bell Anita , Patel Bharat , Amin-Chowdhury Zahin , Aiano Felicity , Paranthaman Karthik , Ma Thomas , Saavedra-Campos Maria , Ellis Joanna , Chand Meera , Brown Kevin , Ramsay Mary E , Hopkins Susan , Shetty Nandini , Chow J. Yimmy , Gopal Robin , Zambon Maria
Published: August 2020

Background

We investigated six London care homes experiencing a COVID-19 outbreak and found very high rates of SARS-CoV-2 infection among residents and staff. Here we report follow-up serological analysis in these care homes five weeks later.

Methods

Residents and staff had a convalescent blood sample for SARS-CoV-2 antibody levels and neutralising antibodies by SARS-COV-2 RT-PCR five weeks after the primary COVID-19 outbreak investigation.

Results

Of the 518 residents and staff in the initial investigation, 208/241 (86.3%) surviving residents and 186/254 (73.2%) staff underwent serological testing. Almost all SARS-CoV-2 RT-PCR positive residents and staff were antibody positive five weeks later, whether symptomatic (residents 35/35, 100%; staff, 22/22, 100%) or asymptomatic (residents 32/33, 97.0%; staff 21/22, 95.1%). Symptomatic but SARS-CoV-2 RT-PCR negative residents and staff also had high seropositivity rates (residents 23/27, 85.2%; staff 18/21, 85.7%), as did asymptomatic RT-PCR negative individuals (residents 62/92, 67.3%; staff 95/143, 66.4%). Neutralising antibody was present in 118/132 (89.4%) seropositive individuals and was not associated with age or symptoms. Ten residents (10/108, 9.3%) remained RT-PCR positive, but with lower RT-PCR cycle threshold values; all 7 tested were seropositive. New infections were detected in three residents and one staff member.

Conclusions

RT-PCR testing for SARS-CoV-2 significantly underestimates the true extent of an outbreak in institutional settings. Elderly frail residents and younger healthier staff were equally able to mount robust and neutralizing antibody responses to SARS-CoV-2. More than two-thirds of residents and staff members had detectable antibodies against SARS-CoV-2 irrespective of their nasal swab RT-PCR positivity or symptoms status.
Extended SEIQR type model for COVID-19 epidemic and data analysis
Authors: Sharma Swarnali , Volpert Vitaly , Banerjee Malay
Published: August 2020

An extended SEIQR type model is considered in order to model the COVID-19 epidemic. It contains the classes of susceptible individuals, exposed, infected symptomatic and asymptomatic, quarantined, hospitalized and recovered. The basic reproduction number and the final size of epidemic are determined. The model is used to fit available data for some European countries. A more detailed model with two different subclasses of susceptible individuals is introduced in order to study the influence of social interaction on the disease progression. The coefficient of social interaction K characterizes the level of social contacts in comparison with complete lockdown (K = 0) and the absence of lockdown (K = 1). The fitting of data shows that the actual level of this coefficient in some European countries is about 0.1, characterizing a slow disease progression. A slight increase of this value in the autumn can lead to a strong epidemic burst.
A simple stochastic theory of extinction shows rapid elimination of a Sars-like pandemic
Authors: Khatri Bhavin S.
Published: August 2020

The SARS-Cov-2 pandemic has seen the challenge of controlling novel zoonotic diseases that have high infection fatality rates, including a natural capacity for the evolution of variants that transmit more easily and evade immunity. In dealing with current and future similar pandemics, the question arises: what is the optimum strategy to control infections. Although a complex question, a key neglected component to appraise the elimination strategy is simple theory predicting the expected timescales of elimination. We use simple random walk and branching process theory to provide new insights on the process of elimination using non-pharmaceutical interventions. Our central achievement is a full theory of the distribution of extinction times — which we find is an extreme value Gumbel distribution — for any value of the reproductive number including some degree of population immunity. Overall, for the original SARS-Cov-2 variant our results predict rapid extinction — of order months — of an epidemic or pandemic if the reproductive number is kept toRe<0.5; in a counterfactual scenario with global adoption of an elimination strategy in June 2020, SARS-Cov-2 could have been eliminated world-wide by early January 2021. Looking to the future, our results would suggest that elimination using NPIs is a more optimal strategy to control — and potentially eradicate — a Sars-like pandemic, in its early stages before the evolution of variants with greater transmissibility.
Low awareness of past SARS-CoV-2 infection in healthy adults
Authors: van den Hurk Katja , Merz Eva-Maria , Prinsze Femmeke J. , Spekman Marloes L.C. , Quee Franke A. , Ramondt Steven , Slot Ed , Vrielink Hans , Huis in ’t Veld Elisabeth M.J. , Zaaijer Hans L. , Hogema Boris M.
Published: August 2020

Background

The coronavirus disease 2019 (COVID-19) pandemic challenges governments worldwide to balance appropriate virus control measures and their societal and economic consequences. These control measures include the identification, isolation and testing of potentially infected individuals. As this relies on an individual’s awareness of infection, we investigated the extent to which healthy adults suspected having had COVID-19, and how COVID-19 suspicion and symptoms relate to antibodies indicative of a past infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Methods and findings

For this cross-sectional study, individuals donating plasma anywhere in the Netherlands between May 11th and 18th were screened for total SARS-CoV-2 antibodies using ELISA and invited to participate in an online questionnaire about COVID-19-related symptoms and awareness. Antibody and questionnaire data were complete for 3,676 individuals, including 239 (6.5%) that tested positive for SARS-CoV-2 antibodies. Here, we show that a 38% of the individuals that tested positive for SARS-CoV-2 antibodies reported having had no or only very mild symptoms at any time during the peak of the epidemic. The loss of taste and/or smell in particular was significantly associated with seropositivity, independent of age and sex. Forty-eight percent of antibody-positive persons did not suspect having had COVID-19, in spite of most of them reporting symptoms.

Conclusions

Awareness of infection was low among individuals that tested positive for SARS-CoV-2 antibodies, even at the peak of the epidemic. Improved awareness and recognition of COVID-19 symptoms and tracing of asymptomatic contacts is crucial to halting SARS-CoV-2 transmission.
On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: emergence and geotemporal spread of a highly prevalent variant in Portugal
Authors: Borges Vítor , Isidro Joana , Cortes-Martins Helena , Duarte Sílvia , Vieira Luís , Leite Ricardo , Gordo Isabel , Caetano Constantino P. , Nunes Baltazar , Sá Regina , Oliveira Ana , Guiomar Raquel , Gomes João Paulo ,   Portuguese network for SARS-CoV-2 genomics
Published: August 2020

Mutations in the Spike motif predicted to correspond to the fusion peptide are considered of interest as this domain is a potential target for anti-viral drug development that plays a pivotal role in inserting SARS-CoV-2 into human cell membranes. We tracked the temporal and geographical spread of a SARS-CoV-2 variant with the Spike D839Y mutation in the fusion peptide, which was detected early during the COVID-19 epidemic in Portugal. We show that this variant was most likely imported from Italy in mid-late February 2020, becoming prevalent in the Northern and Central regions of Portugal, where represented 22% and 59% of the sampled genomes, respectively, until the end of April 2020. Based on our high sequencing sampling during the early epidemics [15,5% (1275/8251) and 6,0% (1500/24987) of all confirmed cases until the end of March and April, respectively)], we estimate that, between March 14th and April 9th (covering the exponential phase of the epidemic), the relative frequency of Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) at every three days, being potentially associated with one in each four (20.8-29.7%, CI 95%) COVID-19 cases in Portugal during the same period. This observation places the Spike Y839 variant in the origin of the largest SARS-CoV-2 transmission chain during the first month of the COVID-19 epidemic in Portugal. We hypothesize that population/epidemiological effects (founder effects) and enhanced selective advantage might have concomitantly contributed to the increasing frequency trajectory of the Spike Y839 variant. Screening of the D839Y mutation globally confirmed its detection in 12 additional countries, even though the huge differences in genome sampling between countries hampers any accurate estimate of D839Y global frequency. In summary, our data points out that SARS-CoV-2 Spike Y839 variants, namely the descendent variant of the globally spread G614 variant detected in Portugal, need continuous and close surveillance.
Novel effector genes revealed by the genomic analysis of the phytopathogenic fungusFusarium oxysporumf. sp.physali(Foph) that infects cape gooseberry plants
Authors: Simbaqueba Jaime , Rodriguez Edwin A. , Burbano-David Diana , Gonzalez Carolina , Caro-Quintero Alejandro
Published: August 2020

The vascular wilt disease caused by the fungusFusarium oxysporumf. sp.physali(Foph) is one of the most limiting factors for the production and export of cape gooseberry (Physalis peruviana) in Colombia. A previous study of the transcriptomic profile of a highly virulent strain ofF. oxysporumin cape gooseberry plants, from a collection of 136 fungal isolates obtained from wilted cape gooseberry plants, revealed the presence of secreted in the xylem (SIX) effector genes, known to be involved in the pathogenicity of otherF. oxysporum formae speciales(ff. spp.). This pathogenic strain was namedFoph, due to its specificity for cape gooseberry hosts. Here, we sequenced the genome ofFoph, using the Illumina MiSeq platform. We analyzed the assembled genome, focusing on the confirmation of the presence of homologues of SIX effectors and the identification of novel candidates of effector genes unique ofFoph.By comparative and phylogenomic analyses based on single-copy orthologues, we identified thatFophis closely related toF. oxysporumff. spp., associated with solanaceous hosts. We confirmed the presence of highly identical homologous genomic regions betweenFophandFol, that contain effector genes and identified seven new effector gene candidates, specific toFophstrains. We also conducted a molecular characterization of a panel of 29F. oxysporumadditional stains associated to cape gooseberry crops isolated from different regions of Colombia. These results suggest the polyphyletic origin ofFophand the putative independent acquisition of new candidate effectors in different clades of related strains. The novel effector candidates identified by sequencing and analyzing the genome ofFoph, represent new sources involved in the interaction betweenFophand cape gooseberry. These resources could be implemented to develop appropriate management strategies of the wilt disease caused byFophin the cape gooseberry crop.
Induced drought strongly affects richness and composition of ground-dwelling ants in the eastern Amazon
Authors: Almeida Rony P.S. , Silva Rogério R. , da Costa Antonio C.L. , Ferreira Leandro V. , Meir Patrick , Ellison Aaron M.
Published: August 2020

Environmental change scenarios caused by low precipitation forecast species loss in tropical regions. We use one year of data from a long-term rainwater exclusion experiment in primary Amazonian rainforest to test whether induced water stress and covarying changes in soil moisture, soil respiration, tree species richness, diversity, size, and total biomass affected species richness and composition (relative abundance) of ground-dwelling ants. Induced drought reduced ant richness, whereas increased soil moisture and variability in tree biomass increased it. Species composition differed between control and rainfall-excluded plots. Occurrence of many ant species was strongly reduced by induced drought, but some generalist groups of ants were favored by it. The expected loss of ant species and changes in ant species composition in tropical forests likely will lead to cascading effects on ecosystem processes and the services they mediate.
A Proteome-scale Analysis of Vertebrate Protein Amino Acid Occurrence: Thermoadaptation shows a Correlation with Protein Solvation but less so with Dynamics
Authors: Li Z.L. , Buck M
Published: August 2020

Despite differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins, often with subtle differences in amino acid sequence. Here, we present a simple way to analyze the difference in amino acid occurrence by comparing highly homologous proteins on a sub-proteome level between several vertebrate model organisms. Specifically, we use this method to identify a pattern of amino acid conservation as well as a shift in amino acid occurrence between homeotherms (warm-blooded species) and poikilotherms (cold-blooded species). Importantly, this general analysis and a specific example further establish a correlation, if not likely connection between the thermoadaptation of protein sequences and two of their physical features: a possible change in their protein dynamics and, even more strongly, in their solvation. For poikilotherms, such as frog and fish, the lower body temperature is expected to increase the association of proteins due to a decrease in protein internal dynamics. In order to prevent overly-sticky protein association at low temperatures, the use of amino acids suggests that poikilotherms enhance the solvation of their proteins by favoring polar groups on their protein’s surface. This feature appears to dominate over possible changes in dynamics. The results suggest that a general trend for amino acid choice is part of the mechanism for thermoadaptation of vertebrate organisms at the molecular level.
Location, location, location: Feeding site affects aphid performance by altering access and quality of nutrients
Authors: Nalam Vamsi J. , Han Jinlong , Pitt William Jacob , Acharya Shailesh Raj , Nachappa Punya
Published: August 2020

Feeding location on a plant can affect aphid reproduction and survival, however little is known about factors that influence aphid performance on specific plant parts. We determined performance and feeding behavior of soybean aphid (Aphis glycines) on stem, adaxial (upper) and abaxial (lower) leaf surfaces during early vegetative growth of soybean plants and analyzed the associated phloem sap composition. Stems harbored greater aphid populations and aphids had shorter development time on stems compared to adaxial and abaxial leaf surfaces. While aphids feeding on the stem took the longest time to begin probing, potentially due to higher density and length of trichomes, this did not impact aphid population growth. Once aphids began probing, the sieve elements were more conducive to feeding as evidenced by less salivation from the stem as compared to either leaf surface. Moreover, vascular sap-enriched exudates from stems had higher sugars and amino acids, which supported higher aphid populations in artificial diet feeding assays. The high quality of stems as a food source may in part explain the shorter development time and overall greater population of aphids observed on stems. In summary, our findings suggest that the choice of feeding location and performance of aphids on a specific plant is driven largely by accessibility to and the quality of nutrients rather than morphological factors.
Meta-matching: a simple framework to translate phenotypic predictive models from big to small data
Authors: He Tong , An Lijun , Feng Jiashi , Bzdok Danilo , Holmes Avram J , Eickhoff Simon B. , Yeo B.T. Thomas
Published: August 2020

There is significant interest in using brain imaging data to predict non-brain-imaging phenotypes in individual participants. However, most prediction studies are underpowered, relying on less than a few hundred participants, leading to low reliability and inflated prediction performance. Yet, small sample sizes are unavoidable when studying clinical populations or addressing focused neuroscience questions. Here, we propose a simple framework – “meta-matching” – to translate predictive models from large-scale datasets tonew unseennon-brain-imaging phenotypes in boutique studies. The key observation is that many large-scale datasets collect a wide range inter-correlated phenotypic measures. Therefore, a unique phenotype from a boutique study likely correlates with (but is not the same as) some phenotypes in some large-scale datasets. Meta-matching exploits these correlations to boost prediction in the boutique study. We applied meta-matching to the problem of predicting non-brain-imaging phenotypes using resting-state functional connectivity (RSFC). Using the UK Biobank (N = 36,848), we demonstrated that meta-matching can boost the prediction of new phenotypes in small independent datasets by 100% to 400% in many scenarios. When considering relative prediction performance, meta-matching significantly improved phenotypic prediction even in samples with 10 participants. When considering absolute prediction performance, meta-matching significantly improved phenotypic prediction when there were least 50 participants. With a growing number of large-scale population-level datasets collecting an increasing number of phenotypic measures, our results represent a lower bound on the potential of meta-matching to elevate small-scale boutique studies.
Reelin deficiency contributes to long-term behavioral abnormalities induced by chronic adolescent exposure to Δ9-tetrahydrocannabinol in mice
Authors: Iemolo Attilio , Nur Aisha , Montilla-Perez Patricia , Risbrough Victoria B , Telese Francesca
Published: August 2020

Heavy and frequent use of cannabis during adolescence increases the risk of developing psychiatric disorders. However, the neurobiological mechanisms underlying this vulnerability remain largely unknown. Here, we explore whether adolescent vulnerability to long-term behavioral effects of cannabis is modulated byReelin, a gene implicated in the development of the brain and of psychiatric disorders. To this aim, heterozygous Reeler (HR) mice, that express reduced level ofReelin, were chronically exposed during adolescence to high doses (10mg/kg) of Δ9-tetrahydrocannabinol (THC), a major psychoactive component of cannabis. Mice were tested in early adulthood with multiple behavioral assays, including working memory, social interaction, locomotor activity, anxiety-like responses, stress reactivity, and pre-pulse inhibition. Compared to wild-type (WT), HR mice treated with THC showed impaired social behaviors, elevated disinhibitory phenotypes and increased responsiveness to aversive situations, in a sex-specific manner. Independent of THC exposure, HR mice also spent more time exploring unfamiliar objects, indicating that Reelin modulates novelty seeking behavior. To identify the neuronal ensemble underlying this elevated novelty seeking in HR mice, we mapped the regional brain expression of the immediate early gene,Fos, in mice exposed to novel objects. HR mice exhibited reduced neuronal activation in the lateral septum, a subcortical brain structure implicated in emotions, cognition and reward processes. Overall, these findings show that (1)Reelindeficiency influences behavioral abnormalities caused by heavy consumption of THC during adolescence, and (2) that Reelin plays a role in the neurobiological mechanisms underlying disinhibitory behaviors, such as novelty seeking.

Significant Statement

The link between cannabis abuse and the development psychiatric disorders, especially in adolescents, makes understanding the neurobiological mechanisms underlying cannabis effects on the brain a significant biomedical problem. Reelin is a key signaling molecule in the development of the adolescent brain and of psychiatric disorders, but its role in modulating the behavioral changes induced by cannabis remain unknown. Here, we report an interaction betweenReelindeficiency and chronic adolescent exposure to THC, a major psychoactive component of cannabis. This interaction led to cognitive deficits, disinhibitory behaviors and altered emotional reactivity in mice, in a sex-specific manner. These experiments are the first to establish a link between Reelin signaling and the endocannabinoid system targeted by THC.
Redefining De Novo Gammaherpesvirus Infection Through High-Dimensional, Single-Cell Analysis of Virus and Host
Authors: Berger Jennifer N. , Sanford Bridget , Kimball Abigail K. , Oko Lauren M. , Kaspar Rachael E. , Niemeyer Brian F. , Jones Kenneth L. , Clambey Eric T. , van Dyk Linda F.
Published: August 2020

Virus infection is frequently characterized using bulk cell populations. How these findings correspond to infection in individual cells remains unclear. Here, we integrate high-dimensional single-cell approaches to quantify viral and host RNA and protein expression signatures using de novo infection with a well-characterized model gammaherpesvirus. While infected cells demonstrated genome-wide transcription, individual cells revealed pronounced variation in gene expression, with only 9 of 80 annotated viral open reading frames uniformly expressed in all cells, and a 1000-fold variation in viral RNA expression between cells. Single-cell analysis further revealed positive and negative gene correlations, many uniquely present in a subset of cells. Beyond variation in viral gene expression, individual cells demonstrated a pronounced, dichotomous signature in host gene expression, revealed by measuring host RNA abundance and post-translational protein modifications. These studies provide a resource for the high-dimensional analysis of virus infection, and a conceptual framework to define virus infection as the sum of virus and host responses at the single-cell level.

HIGHLIGHTS

CyTOF and scRNA-seq identify wide variation in gene expression between infected cells.

Host RNA expression and post-translational modifications stratify virus infection.

Single cell RNA analysis reveals new relationships in viral gene expression.

Simultaneous measurement of virus and host defines distinct infection states.
Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms
Authors: Grobas Iago , Polin Marco , Asally Munehiro
Published: August 2020

Self-organized multi-cellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here we address this question usingBacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multi-layer formation, emerging from a biophysical mechanism reminiscent to motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a promising strategy of antibiotic treatment to effectively inhibit the transition from swarms to biofilms by targeting the localized phase transition.
The luteinizing hormone receptor knock-out mouse as a tool to probe thein vivoactions of gonadotropic hormones/receptors in females
Authors: Jonas Kim Carol , Rivero Müller Adolfo , Oduwole Olayiwola , Peltoketo Hellevi , Huhtaniemi Ilpo
Published: August 2020

Mouse models with altered gonadotropin functions have provided invaluable insight into the functions of these hormones/receptors. Here we describe the repurposing of the infertile and hypogonadal LHR knockout mouse model (LuRKO), to address outstanding questions in reproductive physiology. Using crossbreeding strategies and physiological and histological analyses, we first addressed the physiological relevance of forced LHR homomerization in female mice using BAC expression of two mutant LHR, that have previously shown to undergo functional complementation and rescue the hypogonadal phenotype of male LuRKO mice. In female LuRKO mice, co-expression of signal and binding deficient LHR mutants failed to rescue the hypogonadal and anovulatory phenotype. This was apparently due to the low-level expression of the two mutant LHR and potential lack of LH/LHR-dependent pleiotropic signaling that has previously been shown to be essential for ovulation. Next, we utilized a mouse model overexpressing human chorionic gonadotropin (hCG) with increased circulating ‘LH/hCG’-like bioactivity to ~40 fold higher than WT females, to determine if high circulating hCG could reveal putative LHR-independent actions. No effects were found, thus, suggesting that LH/hCG mediate their gonadal and non-gonadal effects solely via LHR. Finally, targeted expression of a constitutively active FSHR progressed antral follicles to pre-ovulatory follicles and displayed phenotypic markers of enhanced estrogenic activity but failed to induce ovulation in LuRKO mice. This study highlights the critical importance and precise control of LHR and FSHR for mediating ovarian functions and of the potential re-purposing existing genetically modified mouse models in answering outstanding physiological questions.
Anti-pausing activity of region 4 of the RNA polymerase σ subunit and its regulation by σ-remodeling factors
Authors: Brodolin Konstantin , Morichaud Zakia
Published: August 2020

The basal transcription factors of cellular RNA polymerases (RNAPs) stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor σ in promoter-independent initial transcription. We found that the RNAP holoenzyme lacking the promoter-binding domain σ4 is ineffective inde novotranscription initiation and displays high propensity to pausing upon extension of RNAs 3 to 7 nucleotides in length. The σ4 domain stabilizes short RNA:DNA hybrids and suppresses pausing by stimulating RNAP active-center translocation. The anti-pausing activity of σ4 is modulated by its interaction with the β subunit flap domain and by the σ remodeling factors AsiA and RbpA. Our results suggest that the presence of σ4 within the RNA exit channel compensates for the intrinsic instability of short RNA:DNA hybrids by increasing RNAP processivity, thus favoring productive transcription initiation. This “RNAP boosting” activity of the initiation factor is shaped by the the thermodynamics of RNA:DNA interactions and thus, should be relevant for any factor-dependent RNAP.
Shiga toxin remodels the intestinal epithelial transcriptional response to Enterohemorrhagic Escherichia coli
Authors: Warr Alyson R. , Kuehl Carole J. , Waldor Matthew K.
Published: August 2020

EnterohemorrhagicEscherichia coli(EHEC) is a food-borne pathogen that causes diarrheal disease and the potentially lethal hemolytic uremic syndrome. We used an infant rabbit model of EHEC infection that recapitulates many aspects of human intestinal disease to comprehensively assess colonic transcriptional responses to this pathogen. Cellular compartment-specific RNA-sequencing of intestinal tissue from animals infected with EHEC strains containing or lacking Shiga toxins (Stx) revealed that EHEC infection elicits a robust response that is dramatically shaped by Stx, particularly in epithelial cells. Many of the differences in the transcriptional responses elicited by these strains were in genes involved in immune signaling pathways, such asIL23A,and coagulation, includingF3, the gene encoding Tissue Factor. RNA FISH confirmed that these elevated transcripts were found almost exclusively in epithelial cells. Collectively, these findings suggest that within the intestine, Stx primarily targets epithelial cells, and that the potent Stx-mediated modulation of innate immune signaling skews the host response to EHEC towards type 3 immunity.

Significance Statement

EnterohemorrhagicEscherichia coli(EHEC) is a potentially lethal foodborne pathogen. During infection, EHEC releases a potent toxin, Shiga toxin (Stx), into the intestine, but there is limited knowledge of how this toxin shapes the host response to infection. We used an infant rabbit model of infection that closely mimics human disease to profile intestinal transcriptomic responses to EHEC infection. Comparisons of the transcriptional responses to infection by strains containing or lacking Stx revealed that this toxin markedly remodels how the epithelial cell compartment responds to infection. Our findings suggest that Stx biases the intestinal innate immune response to EHEC and provide insight into the complex host-pathogen dialogue that underlies disease.
Production of common carp donor-derived offspring from goldfish surrogate broodstock
Authors: Franěk Roman , Kašpar Vojtěch , Gela David , Pšenička Martin
Published: August 2020

Background

Common carp is the fourth most-produced species in worldwide aquaculture. Significant efforts are invested in breeding and preservation of genetic integrity of this important species. However, maintaining carp gene bankin situcan be considered as demanding due to its big body size. Recent progress in reproductive biotechnologies in fish allows improving some unfavourable characteristics of a target species using surrogate reproduction. Germ stem cells (gamete precursors) from one species are transplanted into different surrogate species with small body size. After maturation, surrogates are producing donor-derived progeny. Efficient protocols for cryopreservation of carp male and female germ stem cells have been developed lately. Thus, the next logical goal was to assess the potential of goldfish surrogate to produce donor-derived gametes of common carp after intraperitoneal transplantation of testicular cells.

Results

High transplantation success was achieved when 44% of the surviving goldfish produced pure donor-derived gametes of common carp. More importantly, both viable eggs and sperm giving rise to pure common carp progeny were produced, witnessing sustainability of the presented method. Donor-derived identity of the offspring was confirmed by genotyping and typical phenotype corresponding to the donor species. Reproductive performance of chimeras was similar to goldfish controls. Assessment of gamete characteristics showed that the size of donor-derived eggs is between control carp and goldfish eggs. Interestingly, flagellum length in donor-derived spermatozoa was comparable to common carp flagellum and significantly shorter than goldfish flagellum.

Conclusions

In this study, we succeeded in the production of pure common carp progeny from surrogate goldfish recipients transplanted intraperitoneally by testicular germ cells. Here we reported production of viable eggs between most distant species up to date. Good reproductive performance of goldfish germline chimeras gives a promising prospect for further analysis about the long-term reproductive performance of surrogates, recovery of cryopreserved germ cells or production of monosex stocks. Presented technology is ready to ease needs for carp breeds preservation and their recovery using many times smaller goldfish surrogates.
Carbamazepine and GABA have distinct effects on seizure onset dynamics in mouse brain slices
Authors: Crisp Dakota N. , Parent Rachel , Nakatani Mitsuyoshi , Murphy Geoffrey G. , Stacey William C.
Published: August 2020

Optimizing antiepileptic drug therapy is very challenging due to the absence of a reliable method to assess how brain activity changes between seizures. This work uses the Taxonomy of Seizure Dynamics (Saggioet al., 2020) to investigate how anticonvulsants influence seizure onset dynamotypes. The no Mg2+/high K+mouse brain-slice seizure model (N = 92) was used to generate consistent epileptiform onsets. We compared the onset bifurcations of controls with slices treated with either GABA or carbamazepine. Each anticonvulsant uniquely changed the types of bifurcations in the slices. This experiment provides proof-of-concept evidence that brain states exist on a “map” of seizure dynamics, and that antiepileptic drugs with different mechanisms can change the positioning of the brain states on the map.

Impact statement

Antiepileptic drugs modify underlying brain states and influence the pathway into seizure onset in brain slices.
Evaluation of Fecal Immunoassays for CanineEchinococcusInfection in China
Authors: Wang Liying , Wang Qian , Cai Huixia , Wang Hu , Huang Yan , Feng Yu , Bai Xuefei , Qin Min , Manguin Sylvie , Gavotte Laurent , Wu Weiping , Frutos Roger
Published: August 2020

Human echinococcosis is present worldwide but it is in China that prevalence is the highest. Western China and in particular the Tibetan plateau is the region where the burden of echinococcosis is the most important. Dogs are a major carrier of echinococcosis and monitoring the presence ofEchinococcusworms in dogs is therefore essential for efficiently controlling the disease. Detection kits based on three different technologies, i.e. sandwich ELISA, ELISA and gold immunodiffusion are currently marketed and used in China. The objective of this work was to assess the efficacy of these kits, in particular with respect to sensitivity and specificity. Four fecal antigen detection kits for canine echinococcosis covering the three technologies were obtained from companies and tested in parallel on 220 fecal samples. The results indicate that the performance is lower than expected, in particular in terms of sensitivity. The best results were obtained with the sandwich ELISA technology. The gold immunofiltration yielded the poorest results. In all cases, further development is needed to improve the performance of these kits, which represent a key element for the control of echinococcosis.

Author summary

Although present worldwide, human echinococcosis is at its highest prevalence in Western China and particularly on the Tibetan plateau. Controlling echinococcosis is a national priority and routine monitoring must be established. Dogs are the main carriers of echinococcosis and surveyingEchinococcusworms in dogs is therefore a key issue. Commercial detection kits are currently in use in China for monitoring the presence of Echinococcosis in dogs. These kits are based on three different technologies, i.e. sandwich ELISA with two monoclonal antibodies, ELISA, and gold immunodiffusion. National survey programs are essential for the control of echinococcosis and it is thus very important to assess the efficacy of these kits, planned to be used for the national survey programs. The work was thus undertaken to assess this efficacy, in particular with respect to sensitivity and specificity. Four fecal antigen detection kits for canine echinococcosis covering the three technologies were obtained from companies and tested in parallel on 220 fecal samples. The performance was lower than expected, in particular for their sensitivity, which ranged from 51.5% to 83.9% with only two samples displaying a worm burden lower than 100. Three out of four kits showed non-specific cross-reactions with other parasites. The best results were obtained with the sandwich ELISA technology, whereas gold immunofiltration yielded the poorest results. However, in all cases, further development is strongly needed to improve the performance of these kits, which represent a key element for the control of echinococcosis.
Effect of cutting depth during sugarcane harvest on root characteristics and yield
Authors: Zhang Yue-bin , Yang Shao-lin , Deng Jun , Li Ru-dan , Fan Xian , Dao Jing-mei , Quan Yi-ji , Bukhari Syed Asad Hussain , Zeng Zhao-hai
Published: August 2020

Ratooning is an important cultivation practice in sugarcane production around the world, with underground buds on the remaining stalk acting as the source for establishment of a subsequent ratoon crop. However, the optimal depth of cutting during harvest in terms of yield and root growth remains unknown. We carried out a two-year field study to determine the effects of three cutting depths (0, 5 and 10 cm below the surface) ratoon cane root and yield. Results showed that cutting to a depth of 5 cm increased the root fresh weight and root volume by 32-40% and 49-85%, respectively, compared to cutting depths of 0 and 10 cm. Remarkably, cutting to a depth of 5 cm also had a significant effect on the development of fine roots, which is closely linked to cane yield. The effect was particularly noticeable in terms of two root traits, root volume and the surface area of roots with a diameter of 1.0-2.0mm, and root length and the number of root tips in roots with a diameter of 0-0.5mm. As a result, a cutting depth of 5 cm below the surface increased cane yield by 35 and 25% compared to depths of 0 and 10 cm below the surface, respectively. Overall, these findings suggest that a cutting depth of 5 cm is optimal in terms of sugarcane yield, largely due to the enhanced effect on root traits, especially the development of fine roots. These findings will help optimize sugarcane ratoon management and improve the ratoon cycle.
Scaling laws of graphs of 3D protein structures
Authors: Pražnikar Jure
Published: August 2020

The application of graph theory in structural biology offers an alternative means of studying 3D models of large macromolecules, such as proteins. However, basic structural parameters still play an important role in the description of macromolecules. For example, the radius of gyration, which scales with exponent ~0.4, provides quantitative information about the compactness of the protein structure. In this study, we combine two proven methods, the graph-theoretical and the fundamental scaling laws, to study 3D protein models.

This study shows that the mean node degree of the protein graphs, which scales with exponent 0.038, is scale-invariant. In addition, proteins that differ in size have a highly similar node degree distribution, which peaks at node degree 7, and additionally conforms to the same statistical properties at any scale. Linear regression analysis showed that the graph parameters (radius, diameter and mean eccentricity) can explain up to 90% of the total radius of gyration variance. Thus, the graph parameters of radius, diameter and mean eccentricity scale with the same exponent as the radius of gyration. The main advantage of graph eccentricity compared to the radius of gyration is that it can be used to analyse the distribution of the central and peripheral amino acids/nodes of the macromolecular structure. The central nodes are hydrophobic amino acids (Val, Leu, Ile, Phe), which tend to be buried, while the peripheral nodes are more hydrophilic residues (Asp, Glu, Lys). Furthermore, it has been shown that the number of central and peripheral nodes is more related to the fold of the protein than to the protein length.
The RAD51 recombinase protects mitotic chromatin in human cells
Authors: Wassing Isabel E. , Saayman Xanita , Rampazzo Lucia , Ralf Christine , Bassett Andrew , Esashi Fumiko
Published: August 2020

The RAD51 recombinase plays critical roles in safeguarding genome integrity, which is fundamentally important for all living cells. While interphase functions of RAD51 in repairing broken DNA and protecting stalled replication forks are well characterised, its role in mitosis remains contentious. In this study, we show that RAD51 protects under-replicated DNA in mitotic human cells and, in this way, promotes mitotic DNA synthesis (MiDAS) and successful chromosome segregation. MiDAS was globally detectable irrespective of DNA damage and was promoted byde novoRAD51 recruitment, RAD51-mediated fork protection, and RAD51 phosphorylation by the key mitotic regulator Polo-like kinase 1. Importantly, acute inhibition of RAD51-promoted MiDAS led to mitotic DNA damage, delayed anaphase onset and induced centromere fragility, revealing a mechanism that prevents the satisfaction of the spindle assembly checkpoint when chromosomal replication remains incomplete. This study hence identifies an unexpected function of RAD51 in promoting the stability of mitotic chromatin.
A new rat model of creatine transporter deficiency reveals behavioral disorder and altered brain metabolism
Authors: Duran-Trio Lara , Fernandes-Pires Gabriella , Simicic Dunja , Grosse Jocelyn , Roux Clothilde , Binz Pierre-Alain , Sandi Carmen , Cudalbu Cristina , Braissant Olivier
Published: August 2020

Creatine is an organic compound used as fast phosphate energy buffer to recycle ATP, important in tissues with high energy demand such as muscle or brain. Creatine is taken from the diet or endogenously synthetized by the enzymes AGAT and GAMT, and specifically taken up by the transporter SLC6A8. Deficit in the endogenous synthesis or in the transport leads to Cerebral Creatine Deficiency Syndromes (CCDS). CCDS are characterized by brain creatine deficiency, intellectual disability with severe speech delay, behavioral troubles such as attention deficits and/or autistic features, and epilepsy. Among CCDS, the X-linked creatine transporter deficiency (CTD) is the most prevalent with no efficient treatment so far. Different mouse models of CTD were generated by doing long deletions in theSlc6a8gene showing reduced brain creatine and cognitive deficiencies or impaired motor function. We present a new knock-in (KI) rat model of CTD holding an identical point mutation found in patients with reported lack of transporter activity. KI males showed brain creatine deficiency, increased urinary creatine/creatinine ratio, cognitive deficiency and autistic features.Slc6a8xY389CKI rat fairly enriches the spectrum of CTD models and provides new data about the pathology, being the first animal model of CTD carrying a point mutation.
The phase of Theta oscillations modulates successful memory formation at encoding
Authors: Cruzat Josephine , Torralba Mireia , Ruzzoli Manuela , Fernández Alba , Deco Gustavo , Soto-Faraco Salvador
Published: August 2020

Several past studies have shown that attention and perception can depend upon the phase of ongoing neural oscillations at stimulus onset. Here, we extend this idea to the memory domain. We tested the hypothesis that ongoing fluctuations in neural activity have an impact on memory encoding using a picture paired-associates task to gauge episodic memory performance. Experiment 1 capitalized on the principle of phase reset. We tested if subsequent memory performance fluctuates rhythmically, time-locked to a reset cue presented before the to-be-remembered pairs. We found indication that behavioral performance was periodically and selectively modulated at theta frequency (∼4 Hz). In Experiment 2 we focused on prestimulus ongoing activity using scalp EEG recorded while participants performed the pair-associate task. We analyzed subsequent memory performance as a function of theta and alpha activity around the presentation of the to-be-remembered pairs. The results of the pre-registered analyses, using large electrode clusters and generic spectral ranges, returned null results of prestimulus phase-behavior correlation. However, we found that post-stimulus theta-power modulations in left frontal scalp predicted subsequent memory performance. This post-stimulus effect in theta power was used to guide a post-hoc prestimulus phase analysis, narrowed down to more precise scalp location and frequency. This analysis returned a correlation between prestimulus theta phase and subsequent memory. Altogether, these results suggest that the prestimulus theta activity at encoding has an impact on later memory performance.
dCas9 regulator to neutralize competition in CRISPRi circuits
Authors: Huang Hsin-Ho , Bellato Massimo , Qian Yili , Cárdenas Pablo , Pasotti Lorenzo , Magni Paolo , Del Vecchio Domitilla
Published: August 2020

CRISPRi-mediated gene repression allows simultaneous control of many genes. However, despite highly specific sgRNA-promoter binding, multiple sgRNAs still interfere with one another by competing for dCas9. We created a dCas9 regulator that adjusts dCas9 concentration based on sgRNAs’ demand, mitigating competition in CRISPRi-based logic gates. The regulator’s performance is demonstrated on both single-stage and layered CRISPRi logic gates and in two commonE. colistrains. When a competitor sgRNA causes between two and ~25 fold-change in a logic gate’s input/output response without dCas9 regulator, the response is essentially unchanged when the regulator is used. The dCas9 regulator thus enables concurrent and independent operation of multiple sgRNAs, thereby supporting independent control of multiple genes.
Variants inRABL2Acausing male infertility and ciliopathy
Authors: Ding Xinbao , Fragoza Robert , Singh Priti , Zhang Shu , Yu Haiyuan , Schimenti John C
Published: August 2020

Purpose

Approximately 7% of men suffer from infertility worldwide and sperm abnormalities are the major cause. Though genetic defects are thought to underlie a substantial fraction of all male infertility cases, the actual molecular bases are usually undetermined. Because the consequences of most genetic variants in populations are unknown, this complicates genetic diagnosis even after genome sequencing of patients. Some patients with ciliopathies, including primary ciliary dyskinesia (PCD) and Bardet-Biedl syndrome (BBS), also suffer from infertility because sperm flagella, which share several characteristics with cilia, are also affected in these patients.

Methods

To identify infertility-causing genetic variants in human populations, we usedin silicopredictions to identify potentially deleterious SNP (single nucleotide polymorphism) alleles ofRABL2A, a gene essential for normal cilia and flagella function. Candidate variants were assayed for protein stabilityin vitro, and the destabilizing variants were modeled in mice using CRISPR/Cas9-mediated genome editing. The resulting mice were characterized phenotypically for reproductive and developmental defects.

Results

Two of the SNP alleles,Rabl2L119F(rs80006029) andRabl2V158F(rs200121688), destabilized the protein. Mice bearing these alleles exhibited PCD- and BBS-associated disorders including male infertility, early growth retardation, excessive weight gain in adulthood, heterotaxia, pre-axial polydactyly, neural tube defects (NTD) and hydrocephalus.

Conclusion

Our study identified and validated pathogenicity of two variants causing ciliopathies and male infertility in human populations, and identified phenotypes not previously described for null alleles ofRabl2.
Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons
Authors: Ipsaro Jonathan J. , O’Brien Paul A. , Bhattacharya Shibani , Palmer Arthur G. , Joshua-Tor Leemor
Published: August 2020

The piRNA pathway safeguards genomic integrity by silencing transposable elements in the germline. While Piwi is the central piRNA factor, others including Asterix/Gtsf1 have also been demonstrated to be critical for effective silencing. Here, using eCLIP with a custom informatic pipeline, we show that Asterix/Gtsf1 specifically binds tRNAs in cellular contexts. We determined the structure of mouse Gtsf1 by NMR spectroscopy and identified the RNA binding interface on the protein’s first zinc finger, which was corroborated by biochemical analysis as well as cryo-EM structures of Gtsf1 in complex with co-purifying tRNA. We further show that LTR retrotransposons are preferentially de-repressed in Asterix mutants. Given the role of tRNAs as LTR retrotransposon primers, our work implicates Asterix/Gtsf1 as exploiting tRNA dependence to identify transposon transcripts and promote piRNA silencing.