bluuebunny/crossref_metadata_2025 huggingface dataset:
Variable branching characteristics of peripheral taste neurons indicates differential convergence
Authors: Huang Tao , Ohman Lisa C. , Clements Anna V. , Whiddon Zachary D. , Krimm Robin F.
Published: August 2020

Taste neurons are functionally and molecularly diverse, but their morphological diversity remains completely unexplored. Using sparse cell genetic labeling, we provide the first reconstructions of peripheral taste neurons. The branching characteristics across 96 taste neurons show surprising diversity in their complexities. Individual neurons had 1 to 17 separate arbors entering between 1 to 7 taste buds, 18 of these neurons also innervated non-taste epithelia. Axon branching characteristics are similar in gustatory neurons from male and female mice. Cluster analysis separated the neurons into four groups according to branch complexity. The primary difference between clusters was the amount of the nerve fiber within the taste bud available to contact taste-transducing cells. Consistently, we found that the maximum number of taste-transducing cells capable of providing convergent input onto individual gustatory neurons varied with a range of 1-22 taste-transducing cells. Differences in branching characteristics across neurons indicate that some neurons likely receive input from a larger number of taste-transducing cells than other neurons (differential convergence). By dividing neurons into two groups based on the type of taste-transducing cell most contacted, we found that neurons contacting primarily sour transducing cells were more heavily branched than those contacting primarily sweet/bitter/umami transducing cells. This suggests that neuron morphologies may differ across functional taste quality. However, the considerable remaining variability within each group also suggests differential convergence within each functional taste quality. Each possibility has functional implications for the system.

Significance statement

Taste neurons are considered relay cells, communicating information from taste-transducing cells to the brain, without variation in morphology. By reconstructing peripheral taste neuron morphologies for the first time, we found that some peripheral gustatory neurons are simply branched, and can receive input from only a few taste-transducing cells. Other taste neurons are heavily branched, contacting many more taste-transducing cells than simply branched neurons. Based on the type of taste-transducing cell contacted, branching characteristics are predicted to differ across (and within) quality types (sweet/bitter/umami vs sour). Therefore, functional differences between neurons likely depends on the number of taste-transducing cells providing input and not just the type of cell providing input.
H-MAGMA, inheriting a shaky statistical foundation, yields excess false positives
Authors: Yurko Ronald , Roeder Kathryn , Devlin Bernie , G’Sell Max
Published: August 2020

The ‘snp-wise mean model’ of Multi-marker Analysis of GenoMic Annotation is often used to perform gene-level testing for association with disease and other phenotypes. This methodology, in turn, forms the foundation for H-MAGMA. Unfortunately, that foundation is unsound, with implications for H-MAGMA results published inNature Neuroscienceregarding genes associated with psychiatric disorders: e.g., only 125 of H-MAGMA’s 275 reported discoveries for autism replicate when the foundation’s flaws are corrected.
Diagnostic performance of the faecal immunochemical test for patients with low-risk symptoms of colorectal cancer in primary care: a service evaluation in the South West of England
Authors: Bailey Sarah ER , Abel Gary A , Atkins Alex , Byford Rachel , Davies Sarah-Jane , Mays Joe , McDonald Timothy J , Miller Jon , Neck Catherine , Renninson John , Thomas Paul , Walter Fiona M , Warren Sarah , Hamilton Willie
Published: August 2020

Objectives

To evaluate the faecal immunochemical test (FIT) for primary care clinicians to triage patients with low-risk symptoms of possible colorectal cancer, and to estimate its diagnostic performance.

Design

Service delivery evaluation.

Setting

All primary and secondary care providers in the South West of England, approximate population 4 million.

Participants

3890 patients aged ≥50 years presenting in primary care with low-risk symptoms of colorectal cancer, following NICE NG12 and DG30, with a FIT (HM-JACKarc assay) analysed from 01/06/2018 to 31/12/2018.

Main outcome measures

Diagnosis of colorectal cancer.

Results

618 (15.9%) patients tested positive at a threshold of 10μg Hb/g faeces (median 36μg Hb/g faeces (IQR 17 to 149)); 458 (74.1%) of these had an urgent referral to specialist lower gastrointestinal (GI) services within three months. 43 were diagnosed with colorectal cancer within 12 months. 3272 patients tested negative; 324 (9.9%) were referred on an urgent lower GI pathway in secondary care within three months. 8 were diagnosed with colorectal cancer within 12 months. The positive predictive value of FIT for colorectal cancer in the low-risk symptomatic population was 7.0% (95% CI 5.1% to 9.3%) and the negative predictive value was 99.8% (CI 99.5% to 99.9%). Sensitivity was 84.3% (CI 71.4% to 93.0%),and specificity 85.0% (CI 83.8% to 86.1%). The area under the ROC curve was 0.92 (CI 0.86 to 0.96). A threshold of 37μg Hb/g faeces would identify patients with an individual 3% risk of cancer.

Conclusions

FIT performs exceptionally well to triage patients with low-risk symptoms of colorectal cancer in primary care. The threshold value of 10μg Hb/g faeces represents a risk of cancer below 3% used in current NICE guidance; however, this lower value may be appropriate to meet the national aspiration of improving cancer diagnostics.
Importance and assessment of quality of life in symptomatic permanent atrial fibrillation: Patient focus groups from the RATE-AF trial
Authors: Jones Jacqueline , Stanbury Mary , Haynes Sandra , Bunting Karina V , Lobban Trudie , Camm A John , Calvert Melanie J. , Kotecha Dipak
Published: August 2020

Aims

To establish the extent and impact of symptoms in patients with atrial fibrillation (AF), the importance of different aspects of quality of life (QoL), and how we should assess wellbeing.

Methods

Focus groups of patients with symptomatic permanent AF in a trial of heart rate control; the RATE-AF trial randomised 160 patients aged ≥60 years with permanent AF and at least NYHA class II dyspnoea to either digoxin or beta-blockers. Patient and public representatives led the focus groups and performed all data acquisition and analysis, using thematic approaches to interpret patient views about QoL and its measurement.

Results

Substantial impairment of health-related QoL was noted in 160 trial patients, with impact on all domains apart from mental health. Eight women and 11 men aged 61–87 years participated in the focus groups. Common themes were a lack of information from healthcare professionals about AF, a lack of focus on QoL in consultations, and a sense of frustration, isolation and reduced confidence. There was marked variability in symptoms in individual patients, with some describing severe impact on activities of daily living, and profound interaction with comorbidities such as arthritis. Day-to-day variation in QoL and difficulty in attributing symptom burden to AF or other comorbidities led to challenges in questionnaire completion. Consensus was reached that collecting both general and AF-specific QoL would be useful in routine practice, along with participation in peer support, which was empowering for the patients.

Conclusions

The impact of comorbidities is poorly appreciated in the context of AF, with considerable variability in QoL that requires both generic and AF-specific assessment. Improvement in QoL should direct the appraisal, and reappraisal, of treatment decisions for patients with permanent AF.
Mass Spectrometric Characterization of Narcolepsy-Associated Pandemic 2009 Influenza Vaccines
Authors: Ambati Aditya , Luo Guo , Pradhan Elora , Louis Jacob , Lin Ling , Lieb Ryan , Ollila Hanna Maria , Poiret Thomas , Adams Christopher , Mignot Emmanuel
Published: August 2020

The onset of narcolepsy, an irreversible sleep disorder, has been associated with 2009 influenza pandemic (pH1N1) infections in China, and with ASO3-adjuvanted pH1N1 vaccinations using Pandemrix in Europe. Intriguingly, however, the increased incidence was only observed following vaccination with Pandemrix but not Arepanrix in Canada. In this study, the mutational burden of actual vaccine lots of Pandemrix (n=6) and Arepanrix (n=5) sourced from Canada, and Northern Europe were characterized by mass spectrometry. The four most abundant influenza proteins across both vaccines were nucleoprotein NP, hemagglutinin HA, matrix protein M1, with the exception that Pandemrix harbored a significantly increased proportion of neuraminidase NA (7.5%) as compared to Arepanrix (2.6%). Most significantly, 17 motifs in HA, NP, and M1 harbored mutations, which significantly differed in Pandemrix versus Arepanrix. Among these, a 6-fold higher deamidation of HA146 (N to D) in Arepanrix was found relative to Pandemrix, while NP257 (T to A) and NP424 (T to I) were increased in Pandemrix. DQ0602 binding and tetramer analysis with mutated epitopes were conducted in Pandemrix-vaccinated cases versus controls but were unremarkable. Pandemrix harbored lower mutational burden than Arepanrix, indicating higher similarity to wild-type 2009 pH1N1, which could explain differences in narcolepsy susceptibility amongst the vaccines.
Serial femtosecond and serial synchrotron crystallography yield data of equivalent quality: a systematic comparison
Authors: Mehrabi P. , Bücker R. , Bourenkov G. , Ginn H.M. , von Stetten D. , Müller-Werkmeister H.M. , Kuo A. , Morizumi T. , Eger B.T. , Ou W.-L. , Oghbaey S. , Sarracini A. , Besaw J.E. , Paré-Labrosse O. , Meier S. , Schikora H. , Tellkamp F. , Marx A. , Sherrell D.A. , Axford D. , Owen R. , Ernst O.P. , Pai E.F. , Schulz E.C. , Miller R.J.D.
Published: August 2020

For the two proteins myoglobin (MB) and fluoroacetate dehalogenase (FAcD), we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of crystals, the same sample delivery device, as well as the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins reasonable data statistics can be obtained with approximately 5000 room temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that diffraction quality is rather linked to the properties of the crystals than to the radiation source. Time-resolved experiments can therefore be conducted at the source that best matches the desired time-resolution.
An ERF transcription factor from Brassica oleracea: a new member of the emerging pathogenicity hub in plant-Xanthomonas interactions
Authors: Zlobin Nikolay , Lebedeva Marina , Monakhova Yuliya , Ustinova Vera , Taranov Vasiliy
Published: August 2020

- TAL effectors (TALEs), which induce the expression of specific plant genes to promote infection, are the main pathogenic determinants of different Xanthomonas bacteria. However, investigation of TALEs fromXanthomonas campestrispv.campestris, which causes black rot disease of crucifers, is in its infancy.

- In this study, we used PCR-based amplification in conjunction with SMRT amplicon sequencing to identify TALE genes in severalXanthomonas campestrispv.campestrisstrains and performed computational prediction in conjunction with RT-PCR-based analysis to identify their target genes inBrassica oleracea.

- Transcription factor from the AP2/ERF family was predicted to be putative target gene for the conserved TALEs present in multipleXanthomonas campestrispv.campestrisstrains. Its expression dramatically increased upon leaf inoculation with strains harbouring such TALEs.

- Several members of the AP2/ERF factor family from different plant species were identified as targets of TALEs from various Xanthomonas species, which suggests that they constitute a new pathogenicity hub in plant-Xanthomonas interactions.
Sphagnumpeat moss thermotolerance is modulated by the microbiome
Authors: Carrell Alyssa A. , Lawrence Travis J. , Cabugao Kristine Grace M. , Carper Dana L. , Pelletier Dale A. , Jawdy Sara , Grimwood Jane , Schmutz Jeremy , Hanson Paul J. , Shaw A. Jonathan , Weston David J.
Published: August 2020

Sphagnumpeat mosses is a major genus that is common to peatland ecosystems, where the species contribute to key biogeochemical processes including the uptake and long-term storage of atmospheric carbon. Warming threatensSphagnummosses and the peatland ecosystems in which they reside, potentially affecting the fate of vast global carbon stores. The competitive success ofSphagnumspecies is attributed in part to their symbiotic interactions with microbial associates. These microbes have the potential to rapidly respond to environmental change, thereby helping their host plants survive under changing environmental conditions. To investigate the importance of microbiome thermal origin on host plant thermotolerance, we mechanically separated the microbiome fromSphagnumplants residing in a whole-ecosystem warming study, transferred the component microbes to germ-free plants, and exposed the new hosts to temperature stress. Although warming decreased plant photosynthesis and growth in germ-free plants, the addition of a microbiome from a thermal origin that matched the experimental temperature completely restored plants to their pre-warming growth rates. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure, including the composition of key cyanobacteria symbionts, in a manner that induced the plant heat shock response, especially the Hsp70 family and jasmonic acid production. The plant heat shock response could be induced even without warming, suggesting that the warming-origin microbiome provided the host plant with thermal preconditioning. Together, our findings show that the microbiome can transmit thermotolerant phenotypes to host plants, providing a valuable strategy for rapidly responding to environmental change.
Forebrain projection neurons target functionally diverse respiratory control areas in the midbrain, pons and medulla oblongata
Authors: Trevizan-Baú Pedro , Dhingra Rishi R. , Furuya Werner I. , Stanić Davor , Mazzone Stuart B. , Dutschmann Mathias
Published: August 2020

Eupnea is generated by neural circuits located in the ponto-medullary brainstem, but can be modulated by higher brain inputs which contribute to volitional control of breathing and the expression of orofacial behaviors, such as vocalization, sniffing, coughing and swallowing. Surprisingly, the anatomical organization of descending inputs that connect the forebrain with the brainstem respiratory network remains poorly defined. We hypothesized that descending forebrain projections target multiple distributed respiratory control nuclei across the neuraxis. To test our hypothesis, we made discrete unilateral microinjections of the retrograde tracer Cholera toxin subunit B (CT-B) in the midbrain periaqueductal gray (PAG), the pontine Kölliker-Fuse nucleus (KFn), the medullary Bötzinger complex (BötC), pre-Bötzinger complex (pre-BötC) or caudal midline raphé nuclei. We quantified the regional distribution of retrogradely-labeled neurons in the forebrain 12-14 days post-injection. Overall, our data reveals that descending inputs from cortical areas predominantly target the PAG and KFn. Differential forebrain regions innervating the PAG (prefrontal, cingulate cortices, and lateral septum) and KFn (rhinal, piriform, and somatosensory cortices) imply that volitional motor commands for vocalization are specifically relayed via the PAG, while the KFn may receive commands to coordinate breathing with other orofacial behaviors (e.g. sniffing, swallowing). Additionally, we observed that the limbic or autonomic (interoceptive) systems are connected to broadly distributed downstream bulbar respiratory networks. Collectively, these data provide a neural substrate to explain how volitional, state-dependent, and emotional modulation of breathing is regulated by the forebrain.
Somatic deficiency causes reproductive parasitism in a fungus
Authors: Grum-Grzhimaylo Alexey A. , Bastiaans Eric , van den Heuvel Joost , Millanes Cristina Berenguer , Debets Alfons J.M. , Aanen Duur K.
Published: August 2020

Some multicellular organisms can fuse because mergers potentially provide mutual benefits. However, experimental evolution in the fungusNeurospora crassahas demonstrated that free fusion of mycelia favours cheater lineages, but the mechanism and evolutionary dynamics of dishonest exploitation are unknown. Here we show, paradoxically, that all convergently evolved cheater lineages have similar fusion deficiencies. These mutants are unable to initiate fusion but retain access to wild-type mycelia that fuse with them. This asymmetry reduces cheater-mutant contributions to somatic substrate-bound hyphal networks, but increases representation of their nuclei in the aerial reproductive hyphae. Cheaters only benefit when relatively rare and likely impose genetic load reminiscent of germline senescence. We show that the consequences of somatic fusion can be unequally distributed among fusion partners, with the passive non-fusing partner profiting more. We discuss how our findings may relate to the extensive variation in fusion frequency of fungi found in nature.
Extrinsic noise acts to lower protein production at higher translation initiation rates
Authors: Sharma Rati
Published: August 2020

Any cellular process at the microscopic level is governed by both extrinsic and intrinsic noise. In this article, we incorporate extrinsic noise in a model of mRNA translation and carry out stochastic simulations of the same. We then evaluate various statistics related to the residence time of the ribosome on the mRNA and subsequent protein production. We also study the effect of slow codons. From our simulations, we show that noise in the translation initiation rate rather than the translation termination rate acts to significantly broaden the distribution of mRNA residence times near the membrane. Further, the presence of slow codons acts to increase the mean residence times. However, this increase also depends on the number and position of the slow codons on the lattice. We also show that the the slow codons act to mask any effect from the extrinsic noise themselves. Our results have implications towards a better understanding of the role the individual components play during the translation process.
Whole-animal connectome and cell-type complement of the three-segmentedPlatynereis dumeriliilarva
Authors: Verasztó Csaba , Jasek Sanja , Gühmann Martin , Shahidi Réza , Ueda Nobuo , Beard James David , Mendes Sara , Heinz Konrad , Bezares-Calderón Luis Alberto , Williams Elizabeth , Jékely Gáspár
Published: August 2020

Nervous systems coordinate effectors across the body during movements. We know little about the cellular-level structure of synaptic circuits for such body-wide control. Here we describe the whole-body synaptic connectome and cell-type complement of a three-segmented larva of the marine annelidPlatynereis dumerilii. We reconstructed and annotated over 1,500 neurons and 6,500 non-neuronal cells in a whole-body serial electron microscopy dataset. The differentiated cells fall into 180 neuronal and 90 non-neuronal cell types. We analyse the modular network architecture of the entire nervous system and describe polysynaptic pathways from 428 sensory neurons to four effector systems – ciliated cells, glands, pigment cells and muscles. The complete somatic musculature and its innervation will be described in a companion paper. We also investigated intersegmental differences in cell-type complement, descending and ascending pathways, and mechanosensory and peptidergic circuits. Our work provides the basis for understanding whole-body coordination in annelids.
T-bet fate mapping identifies a novel ILC1-ILC2 subsetin vivo
Authors: Schroeder J-H , Garrido-Mesa N , Zabinski T , Gallagher AL , Campbell L , Roberts LB , Stolarczyk E , Beattie G , Lo JW , Iseppon A , Heliodoro C Moreira , Reis R , Jenner RG , Lavender P , Howard JK , Grencis RK , Helmby H , Neves J F , Lord GM
Published: August 2020

Innate lymphoid cells (ILC) play a critical role in regulating immune responses at mucosal surfaces. Various subsets exist resembling T cell lineages defined by the expression of specific transcription factors. Thus, T-bet is expressed in ILC1 and Th1 cells. In order to further understand the functional roles of T-bet in ILC, we generated a fate-mapping mouse model that permanently marks cells and their progeny that are expressing, or have ever expressed T-bet. Here we have identified and characterised a novel ILC with characteristics of ILC1 and ILC2 that are “fate-mapped” for T-bet expression and arise early in neonatal life prior to establishment of a mature microbiome. These ILC1-ILC2 cells are critically dependent on T-bet and are able to express type 1 and type 2 cytokines at steady state, but not in the context of inflammation. These findings refine our understanding of ILC lineage regulation and stability and have important implications for the understanding of ILC biology at mucosal surfaces.

Innate lymphoid cells (ILC) play a critical role in regulating immune responses at mucosal surfaces. Three distinct ILC groups have been described according to expression of subset defining transcription factors and other markers. In this study we characterize a novel ILC subset with characteristics of group 1 and group 2 ILCin vivo.
Ectopic histone clipping in the mouse model of progressive myoclonus epilepsy
Authors: Daura Eduard , Tegelberg Saara , Yoshihara Masahito , Jackson Christopher , Simonetti Francesca , Aksentjeff Katri , Ezer Sini , Hakala Paula , Katayama Shintaro , Kere Juha , Lehesjoki Anna-Elina , Joensuu Tarja
Published: August 2020

We establish cystatin B (CSTB) as a regulator of histone H3 tail clipping in murine neural progenitor cells (NPCs) and provide evidence suggesting that epigenetic dysregulation contributes to the early pathogenesis in brain disorders associated with deficient CSTB function. We show that NPCs undergo regulated cleavage of the N-terminal tail of histone H3 at threonine 22 (H3T22) transiently upon induction of differentiation. CSTB-deficient NPCs present premature activation of H3T22 clipping during self-renewal mediated by increased activity of cathepsins L and B. During differentiation, the proportion of immature committed neurons undergoing H3T22 clipping is significantly higher in CSTB-deficient than in wild-type NPCs, with no observable decline within 12 days post-differentiation. CSTB-deficient NPCs exhibit significant transcriptional changes highlighting altered expression of nuclear-encoded mitochondrial genes. These changes are associated with significantly impaired respiratory capacity of differentiating NPCs devoid of CSTB. Our data expand the mechanistic understanding of diseases associated with CSTB deficiency.
Suppression without inhibition: How retinal computation contributes to saccadic suppression
Authors: Idrees Saad , Baumann Matthias-Philipp , Korympidou Maria M. , Schubert Timm , Kling Alexandra , Franke Katrin , Hafed Ziad M. , Franke Felix , Münch Thomas A.
Published: August 2020

Visual perception remains stable across saccadic eye movements, despite the concurrent strongly disruptive visual flow. This stability is partially associated with a reduction in visual sensitivity, known as saccadic suppression, which already starts in the retina with reduced ganglion cell sensitivity. However, the retinal circuit mechanisms giving rise to such suppression remain unknown. Here, we describe these mechanisms using electrophysiology in mouse, pig, and macaque retina, 2-photon calcium imaging, computational modeling, and human psychophysics. We find that sequential stimuli, such as those that naturally occur during saccades, trigger three independent suppressive mechanisms in the retina. The main suppressive mechanism is triggered by contrast-reversing sequential stimuli and originates within the receptive field center of ganglion cells. It does not involve inhibition or other known suppressive mechanisms such as saturation or adaptation. Instead, it relies on temporal filtering of the inherently slow response of cone photoreceptors coupled with downstream nonlinearities. Two further mechanisms of suppression are present predominantly in ON ganglion cells and originate in the receptive field surround, highlighting a novel disparity between ON and OFF ganglion cells. The mechanisms uncovered here likely play a role in shaping the retinal output following eye movements and other natural viewing conditions where sequential stimulation is ubiquitous.
Functional and druggability analysis of the SARS-CoV-2 proteome
Authors: Cavasotto Claudio N. , Sánchez Lamas Maximiliano , Maggini Julián
Published: August 2020

The infectious coronavirus disease (COVID-19) pandemic, caused by the coronavirus SARS-CoV-2, appeared in December 2019 in Wuhan, China, and has spread worldwide. As of today, more than 22 million people have been infected, with almost 800,000 fatalities. With the purpose of contributing to the development of effective therapeutics, this work provides an overview of the viral machinery and functional role of each SARS-CoV-2 protein, and a thorough analysis of the structure and druggability assessment of the viral proteome. All structural, non-structural, and accessory proteins of SARS-CoV-2 have been studied, and whenever experimental structural data of SARS-CoV-2 proteins were not available, homology models were built based on solved SARS-CoV structures. Several potential allosteric or protein-protein interaction druggable sites on different viral targets were identified, knowledge that could be used to expand current drug discovery endeavors beyond the cysteine proteases and the polymerase complex. It is our hope that this study will support the efforts of the scientific community both in understanding the molecular determinants of this disease and in widening the repertoire of viral targets in the quest for repurposed or novel drugs against COVID-19.
Evidence for a role of phenotypic mutations in virus adaptation
Authors: Luzon-Hidalgo Raquel , Risso Valeria A. , Delgado Asuncion , Andrés-Leon Eduardo , Ibarra-Molero Beatriz , Sanchez-Ruiz Jose M.
Published: August 2020

Viruses interact extensively with the host molecular machinery, but the underlying mechanisms are poorly understood. Bacteriophage T7 recruits the small protein thioredoxin of theE. colihost as an essential processivity factor for the viral DNA polymerase. We challenged the phage to propagate in a host in which thioredoxin had been extensively modified to hamper its recruitment. The virus adapted to the engineered host without losing the capability to propagate in the original host, but no genetic mutations were fixed in the thioredoxin binding domain of the viral DNA polymerase. Virus adaptation correlated with mutations in the viral RNA polymerase, supporting that promiscuous thioredoxin recruitment was enabled by phenotypic mutations caused by transcription errors. These results point to a hitherto unknown mechanism of virus adaptation that may play a role in crossspecies transmission. We propose that phenotypic mutations may generally contribute to the capability of viruses to evade antiviral strategies.
Hematopoietic lineages diverge within the stem cell compartment
Authors: Morcos Mina N. F. , Li Congxin , Munz Clara M. , Greco Alessandro , Dressel Nicole , Reinhardt Susanne , Dahl Andreas , Becker Nils B. , Roers Axel , Höfer Thomas , Gerbaulet Alexander
Published: August 2020

Hematopoietic stem cells (HSCs) produce a highly diverse array of cell lineages. To assay hematopoietic differentiation with minimal experimental perturbation, non-invasive methods for heritable labeling1–3or barcoding4–7of HSCsin vivohave recently been developed and used to study lineage fate of HSCs in physiological conditions. However, the differentiation pathways leading from HSCs to mature cells remain controversial8, with suggested models ranging from gradual lineage restriction in a branching cascade of progenitors to HSCs already making ultimate lineage decisions. Here we show, by iterating HSC fate-mapping, mitotic history tracking, single-cell RNA-sequencing and computational inference, that the major differentiation routes to megakaryocytes, erythro-myeloid cells and lymphocytes split within HSCs. We identify the hitherto elusive self-renewing source of physiological hematopoiesis as an HSC subpopulation co-expressing high levels of Sca-1 and CD201. Downstream, HSCs reduce Sca-1 expression and enter into either thrombopoiesis or erythro-myelopoiesis, or retain high Sca-1 levels and the ability to generate lymphocytes. Moreover, we show that a distinct population of CD48−/lomegakaryocyte progenitors links HSCs to megakaryocytes. This direct thrombopoiesis pathway is independent of the classical pathway of megakaryocyte differentiation via multipotent progenitors and becomes the dominant platelet production line upon enhanced thrombopoietin signaling. Our results define a hierarchy of self-renewal and lineage decisions within HSCs in native hematopoiesis. Methodologically, we provide a blueprint for mapping physiological differentiation pathways of stem cells and probing their regulation.
A sort-seq approach to the development of single fluorescent protein biosensors
Authors: Koberstein John N. , Stewart Melissa L. , Mighell Taylor L. , Smith Chadwick B. , Cohen Michael S.
Published: August 2020

The utility of single fluorescent protein biosensors (SFPBs) in biological research is offset by the difficulty in engineering these tools. SFPBs generally consist of three basic components: a circularly permuted fluorescent protein, a ligand-binding domain, and a pair of linkers connecting the two domains. In the absence of predictive methods for biosensor engineering, most designs combining these three components will fail to produce allosteric coupling between ligand binding and fluorescence emission. Methods to construct libraries of biosensor designs with variations in the site of GFP insertion and linker sequences have been developed, however, our ability to construct new variants has exceeded our ability to test them for function. Here, we address this challenge by applying a massively parallel assay termed “sort-seq” to the characterization of biosensor libraries. Sort-seq combines binned fluorescence-activated cell sorting, next-generation sequencing, and maximum likelihood estimation to quantify the dynamic range of many biosensor variants in parallel. We applied this method to two common biosensor optimization tasks: choice of insertion site and optimization of linker sequences. The sort-seq assay applied to a maltose-binding protein domain-insertion library not only identified previously described high-dynamic-range variants but also discovered new functional insertion-sites with diverse properties. A sort-seq assay performed on a pyruvate biosensor linker library expressed in mammalian cell culture identified linker variants with substantially improved dynamic range. Machine learning models trained on the resulting data can predict dynamic range from linker sequence. This high-throughput approach will accelerate the design and optimization of SFPBs, expanding the biosensor toolbox.
Defining the early stages of intestinal colonisation by whipworms
Authors: Duque-Correa María A. , Goulding David , Rodgers Faye H. , Cormie Claire , Rawlinson Kate , Gillis J. Andrew , Bancroft Allison J. , Bennett Hayley M. , Lotkowska Magda , Reid Adam J. , Speak Anneliese , Scott Paul , Redshaw Nicholas , McCarthy Catherine , Brandt Cordelia , Sharpe Catherine , Ridley Caroline , Moya Judit Gali , Carneiro Claudia M. , Starborg Tobias , Hayes Kelly S. , Holroyd Nancy , Sanders Mandy , Thornton David J. , Grencis Richard K. , Berriman Matthew
Published: August 2020

Whipworms are large metazoan parasites that inhabit distinct multi-intracellular epithelial burrows described as syncytial tunnels, in the large intestine of their hosts. How first-stage larvae invade host epithelia and establish infection remains unclear. Here, we investigate early infection events both usingTrichuris murisinfections of mice and murine caecaloids, the firstin-vitrosystem for whipworm infection. We show that larvae degrade the mucus layers to access epithelial cells. In early syncytial tunnels, larvae are completely intracellular but woven through multiple live enterocytes and goblet cells. We also use single cell RNA sequencing for the first time to describe the mouse caecum. From infected caeca, the transcriptome data reveal the progression of infection results in cell damage and an expansion of enterocytes with a type-I interferon (IFN) signature, characterised by the expression ofIsg15, instigating the host immune response to the whipworm and tissue repair. Our results unravel intestinal epithelium invasion by whipworms and reveal new specific interactions between the host and the parasite that allow the whipworm to establish its multi-intracellular niche.
A home and rescue gene drive efficiently spreads and persists in populations
Authors: Kandul Nikolay P. , Liu Junru , Bennett Jared B. , Marshall John M. , Akbari Omar S.
Published: August 2020

Homing based gene drives, engineered using CRISPR/Cas9, have been proposed to spread desirable genes into target populations. However, spread of such drives can be hindered by the accumulation of resistance alleles. To overcome this significant obstacle, we engineer an inherently confinable population modificationHome-and-Rescue (HomeR) drive inDrosophila melanogasterthat, by creative design, limits the accumulation of such alleles. We demonstrate that HomeR can achieve nearly ∼100% transmission enabling it to spread and persist at genotypic fixation in several multi-generational population cage experiments, underscoring its long term stability and drive potential. Finally, we conduct mathematical modeling determining HomeR can outperform contemporary gene drive architectures for population modification over wide ranges of fitness and transmission rates. Given its straightforward design, HomeR could be universally adapted to a wide range of species.
Behavioral assays to study neural development in Xenopus laevis tadpoles
Authors: Khakhalin Arseny S. , Lopez Virgilio , Aizenman Carlos
Published: August 2020

Escape responses, orienting reflexes, and social behaviors in Xenopus laevis tadpoles have been well documented in the literature (Lee et al. 2010; Roberts et al. 2000; Simmons et al. 2004; Katz et al. 1981; Villinger and Waldman 2012). In this article, we describe several behavioral protocols that together allow researchers efficiently (in terms of financial cost and time investment) and effectively assess developmental abnormalities in pre-metamorphic Xenopus tadpoles.
Neuroticism alters the transcriptome of the frontal cortex to contribute to the cognitive decline and onset of Alzheimer’s disease
Authors: De Jager Céline H. , White Charles C. , Bennett David A. , Ma Yiyi
Published: August 2020

Accumulating evidence has suggested that the molecular transcriptional mechanism contributes to Alzheimer’s disease (AD) and its endophenotypes of cognitive decline and neuropathological traits, β-amyloid (Aβ) and phosphorylated tangles (TAU). However, it is unknown what is the impact of the AD risk factors, personality characteristics assessed by the NEO Five-Factor Inventory, on the human brain’s transcriptome. Using postmortem human brain samples from 466 subjects, we found that neuroticism has a significant overall impact on the brain transcriptome (omnibusP=0.005) but not the other 4 personality characteristics. Focused on those cognitive decline related gene co-expressed modules, neuroticism has nominally significant associations (P<0.05) with four neuronal modules, which are more related to PHFtau than Aβ across all eight brain regions. Furthermore, the effect of neuroticism on cognitive decline and AD might be mediated through the expression of module 7 and TAU pathology (P=0.008). To conclude, neuroticism has overall impact on human brains’ transcriptome and its effect on cognitive decline and AD might be mediated through TAU pathology related gene transcription mechanism.
Conserved sex-biased DNA methylation patterns target key developmental genes and non-recombining region of the guppy sex chromosome
Authors: Metzger David C.H. , Mank Judith E.
Published: August 2020

Understanding the regulatory mechanisms that control sexually dimorphic gene expression is a key part of understanding the processes that govern the rate of sex chromosome evolution and phenotypic sex differences. Epigenetic modifications play a major role in tissue-specific gene expression regulation and have been hypothesized to dramatically impact the speed of sex chromosome divergence. The guppy sex chromosomes are an emerging model for studying the initial stages of divergence between the X and Y. In this study, we use comparative epigenomics to identify conserved sex-specific DNA methylation patterns in gonad and muscle tissue between the Trinidadian guppy (Poecilia reticulata) and its sister species, Endler’s guppy (Poecilia wingei). We find that the oldest part of the guppy sex chromosome shows a conserved pattern of male hypomethylation, consistent with a key role in testis-specific gene expression. This pattern provides a potential mechanism for theoretical predictions that sex chromosome divergence can occur remarkably quickly in evolutionary time, and without widespread degradation of the Y chromosome gene content. Our cross-species comparative epigenomic analysis also provides a robust comparative framework to understand constraints of epigenetic programming. We observe conserved, testis-specific hypomethylated regions near key autosomal developmental genes and a potentially imprinted locus. These observations are consistent with DNA methylation in testis from other vertebrates, and suggest broad conservation of DNA methylation patterns in these regions. Our comparative framework reveals conserved DNA methylation differences between males and females across two related species, providing novel insights into the relationship between epigenetic and evolutionary processes.
Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation
Authors: Rosenkrantz Jimi L. , Gaffney Jessica E. , Roberts Victoria HJ. , Carbone Lucia , Chavez Shawn L.
Published: August 2020

Proper placentation, including trophoblast differentiation and function, is essential for the health and well-being of both the mother and baby throughout pregnancy. Placental abnormalities that occur during the early stages of development are thought to contribute to pre-eclampsia and other placenta-related pregnancy complications. However, relatively little is known about these stages in humans due to obvious ethical and technical limitations. Rhesus macaques are considered an ideal surrogate for studying human placentation, but the unclear translatability of known human placental markers and lack of accessible rhesus trophoblast cell lines can impede the use of this animal model. Here, we performed a cross-species transcriptomic comparison of human and rhesus placenta and determined that while the majority of known placental markers were similarly expressed, 952 differentially expressed genes (DEGs) were identified between the two species. Pathway enrichment analysis of the 447 human-upregulated DEGs, includingADAM12,ERVW-1,KISS1,LGALS13,PAPPA2,PGF, andSIGLEC6, revealed over-representation of functional terms associated with pre-eclampsia and other pregnancy disorders. Additionally, to enablein vitrofunctional studies of early placentation, we generated and thoroughly characterized two highly-pure first-trimester telomerase (TERT) immortalized rhesus trophoblast cell lines (iRP-D26 and iRP-D28A) that retained crucial features of isolated primary trophoblasts. Overall, our findings help elucidate the molecular translatability between human and rhesus placenta and reveal notable expression differences in human placental markers and genes associated with pregnancy complications that should be considered when using the rhesus animal model to study normal and pathological human placentation.
Social immunity and chemical communication in the honeybee: immune-challenged bees enter enforced or self-imposed exile
Authors: Conroy Tarli E. , Holman Luke
Published: August 2020

Animals living in large colonies are especially vulnerable to infectious pathogens, and may there-fore have evolved additional defences. Eusocial insects supplement their physiological immune systems with ‘social immunity’, a set of adaptations that impedes the entrance, establishment, and spread of pathogens in the colony. We here find that honey bee workers (Apis mellifera) that had been experimentally immune-challenged with lipopolysaccharide (LPS) often exited the hive and subsequently died; some individuals were dragged out by other workers, while others appeared to leave voluntarily. In a second experiment, we found that healthy workers treated with surface chemicals from LPS-treated bees were evicted from the hive more often than controls, indicating that immune-challenged bees produce chemical cues or signals that elicit their eviction. Thirdly, we observed pairs of bees in the lab, and found that pairs spent more time apart when one member of the pair had received LPS, relative to controls. Our findings suggest that immune-challenged bees altruistically banish themselves, and that workers evict sick individuals which they identify using olfactory cues, putatively because of (kin) selection to limit the spread of pathogens within colonies.
Biological management of fusarium wilt on tomato caused byFusarium oxysporumf. sp.lycospersiciby some plant growth-promoting bacteria
Authors: Hussein Halima Z. , Al-Dulaimi Shaker I.
Published: August 2020

Chemical approaches have been applied to combat Fusarium wilt disease for a long time. Even though pesticides are effective in controlling the disease, they continue to damage the environment. Environmental-friendly approaches to manage plant disease are the goal of many studies recently. This study was conducted to assess the efficacy of some bio-agents in induction of systemic resistance in tomato plants as a management approach of Fusarium wilt disease caused byFusarium oxysporumf.sp.lycopersici(FOL) under condition Plastic house. Results of the plastic house experiments showed that all treatments in decreased Fusarium disease percentage and severity on tomato, two bacterial combinations (Streptomyces sp. (St) andPseudomonas fluorescence(Pf)) decreased the infection percentage and disease severity with 16.6% and 8.3%, respectively. Treatment with St reduced the infection percentage and disease severity with 33.3% and 22.8%, while the Pf treatment showed 41.6% and 31.2% reduction in infection percentage and disease severity, compared to 100% and 91.6% in the control treatment. Results of induced systemic resistance (ISR) biochemical indicators showed significant differences in tomato plants. Peroxidase and Phenylalanine-Ammonia-Lyase (PAL) activity and the Phenol content increased significantly 14 days after treatments compared to the control treatment, which contains only the fungal pathogen FOL.
Alternative splicing of SLAMF6 in human T cells creates a co-stimulatory isoform that counteracts the inhibitory effect of the full-length receptor
Authors: Hajaj Emma , Zisman Elad , Tzaban Shay , Merims Sharon , Cohen Jonathan , Klein Shiri , Frankenburg Shoshana , Sade-Feldman Moshe , Tabach Yuval , Yizhak Keren , Navon Ami , Stepensky Polina , Hacohen Nir , Peretz Tamar , Veillette André , Karni Rotem , Eisenberg Galit , Lotem Michal
Published: August 2020

SLAMF6 is a homotypic receptor of the Ig-superfamily associated with progenitor exhausted T cells. In humans, SLAMF6 has three splice isoforms involving its V-domain. While the canonical 8-exon receptor inhibits T cell activation through SAP recruitment, the short isoform SLAMF6Δ17-65 has a strong agonistic effect. The costimulatory action depends on protein phosphatase SHP-1 and leads to a cytotoxic molecular profile governed by transcription factors Tbet, Runx3, and Tcf7. In T cells from individual patients treated with immune checkpoint blockade, a shift was noted towards SLAMF6Δ17-65. Splice-switching antisense oligonucleotides designed to target the SLAMF6 splice junction, enhanced SLAMF6Δ17-65 in human tumor-infiltrating lymphocytes and improved their capacity to inhibit human melanoma in mice. The possible emergence of two opposing isoforms from the SLAMF6 gene may represent an immune-modulatory mechanism that can be exploited for cancer immunotherapy.
Scaffold-scaffold interactions regulate cell polarity in a bacterium
Authors: Zhao Wei , Duvall Samuel W. , Kowallis Kimberly A. , Zhang Chao , Tomares Dylan T. , Petitjean Haley N. , Childers W. Seth
Published: August 2020

The localization of two biochemically distinct signaling hubs at opposite cell poles provides the foundation for asymmetric cell division inCaulobacter crescentus. Here we identify an interaction between the scaffolds PodJ and PopZ that regulates the assembly of the new cell pole signaling complex. Time-course imaging of a mCherry-sfGFP-PopZ fluorescent timer throughout the cell cycle revealed that existing PopZ resides at the old cell pole while newly translated PopZ accumulates at the new cell pole. Our studies suggest that interactions between PodJ and PopZ promotes the sequestration of older PopZ and robust accumulation of newl PopZ at the new cell pole. Elimination of the PodJ-PopZ interaction impacts PopZ client proteins, leading to chromosome segregation defects in one-third of cells. Additionally, this PopZ-PodJ interaction is crucial for anchoring PodJ and preventing PodJ extracellular loss at the old cell pole through unknown mechanism. Therefore, segregation of PopZ protein at the old pole and recruitment of newly translated PopZ at the new pole via the PodJ scaffold ensures stringent inheritance and maintenance of the polarity axis within dividingC. crescentus cells.