bluuebunny/crossref_metadata_2025 huggingface dataset:
Mental health and health behaviours before and during the initial phase of the COVID-19 lockdown: Longitudinal analyses of the UK Household Longitudinal Study
Authors: Niedzwiedz Claire L , Green Michael J , Benzeval Michaela , Campbell Desmond D , Craig Peter , Demou Evangelia , Leyland Alastair H , Pearce Anna , Thomson Rachel M , Whitley Elise , Katikireddi S Vittal
Published: June 2020

Background

There are concerns that COVID-19 mitigation measures, including the “lockdown”, may have unintended health consequences. We examined trends in mental health and health behaviours in the UK before and during the initial phase of the COVID-19 lockdown and differences across population subgroups.

Methods

Repeated cross-sectional and longitudinal analysis of the UK Household Longitudinal Study, including representative samples of adults (aged 18+) interviewed in four survey waves between 2015 and 2020 (n=48,426). 9,748 adults had complete data for longitudinal analyses. Outcomes included psychological distress (General Health Questionnaire-12 (GHQ)), loneliness, current cigarette smoking, use of e-cigarettes and alcohol consumption. Cross-sectional prevalence estimates were calculated and multilevel Poisson regression assessed associations between time period and the outcomes of interest, as well as differential associations by age, gender, education level and ethnicity.

Results

Psychological distress increased one month into lockdown with the prevalence rising from 19.4% (95% CI 18.7%-20.0%) in 2017-19 to 30.3% (95% CI 29.1%-31.6%) in April 2020 (RR=1.3, 95% CI: 1.1,1.4). Groups most adversely affected included women, young adults, people from an Asian background and those who were degree educated. Loneliness remained stable overall (RR=0.9, 95% CI: 0.6,1.5). Smoking declined (RR=0.9, 95% CI=0.8,1.0) and the proportion of people drinking four or more times per week increased (RR=1.4, 95% CI: 1.3,1.5), as did binge drinking (RR=1.5, 95% CI: 1.3,1.7).

Conclusions

Psychological distress increased one month into lockdown, particularly among women and young adults. Smoking declined, but adverse alcohol use generally increased. Effective measures are required to mitigate adverse impacts on health.

What is already known on this topic

Countries around the world have implemented radical COVID-19 lockdown measures, with concerns that these may have unintended consequences for a broad range of health outcomes.

Evidence on the impact of lockdown measures on mental health and health-related behaviours remains limited.

What this study adds

In the UK, psychological distress markedly increased during lockdown, with women particularly adversely affected.

Cigarette smoking fell, but adverse drinking behaviour generally increased.
Design of a Companion Bioinformatic Tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants
Authors: Massacci Alice , Sperandio Eleonora , D’Ambrosio Lorenzo , Maffei Mariano , Palombo Fabio , Aurisicchio Luigi , Ciliberto Gennaro , Pallocca Matteo
Published: June 2020

Background

Tracking the genetic variability of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is a crucial challenge. Mainly to identify target sequences in order to generate robust vaccines and neutralizing monoclonal antibodies, but also to track viral genetic temporal and geographic evolution and to mine for variants associated with reduced or increased disease severity. Several online tools and bioinformatic phylogenetic analyses have been released, but the main interest lies in the Spike protein, which is the pivotal element of current vaccine design, and in the Receptor Binding Domain, that accounts for most of the neutralizing the antibody activity.

Methods

Here, we present an open-source bioinformatic protocol, and a web portal focused on SARS-CoV-2 single mutations and minimal consensus sequence building as a companion vaccine design tool. Furthermore, we provide immunogenomic analyses to understand the impact of the most frequent RBD variations.

Results

Results on the whole GISAID sequence dataset at the time of the writing (October 2020) reveals an emerging mutation, S477N, located on the central part of the Spike protein Receptor Binding Domain, the Receptor Binding Motif. Immunogenomic analyses revealed some variation in mutated epitope MHC compatibility, T-cell recognition, and B-cell epitope probability for most frequent human HLAs.

Conclusions

This work provides a framework able to track down SARS-CoV-2 genomic variability.
Individual Differences in the Connectivity of Left and Right Anterior Temporal Lobes Relate to Modality and Category Effects in Semantic Categorisation
Authors: Alam Tirso RJ Gonzalez , Krieger-Redwood Katya , Evans Megan , Rice Grace E , Smallwood Jonathan , Jefferies Elizabeth
Published: June 2020

Contemporary neuroscientific accounts suggest that ventral anterior temporal lobe (ATL) regions act as a bilateral heteromodal semantic hub. However, research also shows graded functional differences between the hemispheres relating to linguistic versus non-linguistic semantic tasks and to knowledge of objects versus people. Individual differences in connectivity from bilateral ATL and between left and right ATL might therefore give rise to differences in function within this system. We investigated whether the relative strength of intrinsic connectivity from left and right ATL would relate to differences in performance on semantic tasks. We examined resting-state fMRI in 74 individuals and, in a separate session, examined semantic categorisation, manipulating stimulus type (famous faces versus landmarks) and modality of presentation (visual versus verbal). We found that people with greater connectivity between left and right ATL were more efficient at categorising landmarks, especially when these were presented visually. In addition, participants who showed stronger connectivity from right than left ATL to medial occipital cortex showed more efficient semantic categorisation of landmarks regardless of modality of presentation. These findings show that individual differences in the intrinsic connectivity of left and right ATL are associated with effects of category and modality in semantic categorisation. The results can be interpreted in terms of graded differences in the strengths of inputs from ‘spoke’ regions, such as regions of visual cortex, to a bilateral yet partially segregated semantic ‘hub’, encompassing left and right ATL.
Dot1L interacts with Zc3h10 to activate UCP1 and other thermogenic genes
Authors: Yi Danielle , Nguyen Hai P. , Dinh Jennie , Viscarra Jose A. , Xie Ying , Dempersmier Jon M. , Wang Yuhui , Sul Hei Sook
Published: June 2020

Brown adipose tissue is a metabolically beneficial organ capable of dissipating chemical energy into heat, thereby increasing energy expenditure. Here, we identify Dot1L, the only known H3K79 methyltransferase, as an interacting partner of Zc3h10 that transcriptionally activates the UCP1 promoter and other BAT genes. Through a direct interaction, Dot1L is recruited by Zc3h10 to the promoter regions of thermogenic genes to function as a coactivator by methylating H3K79. We also show that Dot1L is induced during brown fat cell differentiation and by cold exposure and that Dot1L and its H3K79 methyltransferase activity is required for thermogenic gene program. Furthermore, we demonstrate that Dot1L ablation in mice using UCP1-Cre prevents activation of UCP1 and other target genes to reduce thermogenic capacity and energy expenditure, promoting adiposity. Hence, Dot1L plays a critical role in the thermogenic program and may present as a future target for obesity therapeutics.
Life history scaling and the division of energy in forests
Authors: Grady John M. , Read Quentin D. , Record Sydne , Rüger Nadja , Zarnetske Phoebe L. , Dell Anthony I. , Hubbell Stephen P. , Michaletz Sean T. , Shenkin Alexander , Enquist Brian J.
Published: June 2020

The competition for light has long been regarded as a key axis of niche partitioning that promotes forest diversity, but available evidence is contradictory. Despite strong tradeoffs between growth and survival with light, field tests suggest neutral forces govern tree composition across forest gaps and resource use across size classes. Here we integrate scaling and niche theory, and use data from >114,000 woody plants in a tropical, old growth forest to test and predict patterns of niche partitioning with size and light. Consistent with predictions, the relative abundance, production, light capture, and richness of species in life histories with fast growth follow a power law relationship, increasing 1–2 orders of magnitude along a solar and size gradient. Competitive neutrality between size classes emerges above the sapling layer, where increasing access to light is counterbalanced by stronger self-shading. Convergent power law patterns of resource partitioning across taxa and spatial scale suggest general life history tradeoffs drive the organization of diverse communities.
A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus) (Hottuyn, 1782) provides insights into its osmoregulation and sex reversal
Authors: Zhu Kecheng , Zhang Nan , Liu Bao-Suo , Guo Liang , Guo Hua-Yang , Jiang Shi-Gui , Zhang Dianchang
Published: June 2020

The yellowfin seabreamAcanthopagrus latusis the economically most important Sparidae fish species in the northern South China Sea. As euryhaline fish, they are perfect model for investigating osmoregulatory mechanisms in teleosts. Moreover, the reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. To elucidate genetic mechanisms of osmoregulation and sex reversal in this fish, a high-quality reference genome of the yellowfin seabream was generated by a combination of Illumina and PacBio technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23% universal single-copy orthologues based on benchmarking universal single-copy orthologs (BUSCO) analysis. Moreover, among the 19,631 protein-coding genes, we found that theARRDC3andGSTAgene families related to osmoregulation underwent an extensive expansion in two euryhaline Sparidae fish genomes compared to other teleost genomes. Moreover, integrating sex-specific transcriptome analyses, several genes related to the transforming growth factor beta (TGF-β) signalling pathway involved in sex differentiation and development. This genomic resource will not only be valuable for studying the osmoregulatory mechanisms in estuarine fish and sex determination in hermaphrodite vertebrate species, but also provide useful genomic tools for facilitating breeding of the yellowfin seabream.
The regulatory genome of the malaria vectorAnopheles gambiae: integrating chromatin accessibility and gene expression
Authors: Ruiz José L. , Ranford-Cartwright Lisa C. , Gómez-Díaz Elena
Published: June 2020

Anopheles gambiaemosquitoes are primary human malaria vectors, but we know very little about mechanisms of transcriptional regulation. We profiled chromatin accessibility by ATAC-seq in laboratory-rearedAn. gambiaemosquitoes experimentally infected with the human malaria parasitePlasmodium falciparum. By integrating ATAC-seq, RNA-seq and ChIP-seq data we showed a positive correlation between accessibility at promoters and introns, gene expression and active histone marks. By comparing expression and chromatin structure patterns in different tissues, we were able to infer cis-regulatory elements controlling tissue specific gene expression and to predict the in vivo binding sites of relevant transcription factors. The ATAC-seq assay also allowed the precise mapping of active regulatory regions, including novel transcription start sites and enhancers that annotate to mosquito immune-response genes. This study is important not only for advancing our understanding of mechanisms of transcriptional regulation in the mosquito vector of human malaria, but the information is of great potential for developing new mosquito-control and anti-malaria strategies.
Long-range neural coherence encodes stimulus information in primate visual cortex
Authors: Kermani Mojtaba , Zavitz Elizabeth , Oakley Brian , Price Nicholas S.C. , Hagan Maureen A. , Wong Yan T.
Published: June 2020

In the primary visual cortex, neurons with similar receptive field properties are bound together through widespread networks of horizontal connections that span orientation columns. How connectivity across the cortical surface relates to stimulus information is not fully understood. We recorded spiking activity and the local field potential (LFP) from the primary visual cortex of marmoset monkeys and examined how connectivity between distant orientation columns affect the encoding of visual orientation.

Regardless of their spatial separation, recording sites with similar orientation preferences have higher coherence between spiking activity and the local field potential than sites with different preferred orientation. Using information theoretic methods, we measured the amount of stimulus information that is shared between pairs of sites. More stimulus information can be decoded from pairs with the same preferred stimulus orientation than the pairs with a different preferred orientation, and the amount of information is significantly correlated with the magnitude of beta-band spike-LFP coherence. These effects remained after controlling for firing rate differences.

Our results thus show that spike-LFP synchronization in the beta-band is associated with the encoding of stimulus information within the primary visual cortex of marmoset monkeys.

Significance Statement

A fundamental step in processing images in the visual cortex is coordinating the neural activity across distributed populations of neurons. Here, we demonstrate that populations of neurons in the primary visual cortex of marmoset monkeys with the same stimulus orientation preference temporally coordinate their activity patterns when presented with a visual stimulus. We find maximum synchronization in the beta range depends on the similarity of orientation preference at each pair of the neural population.
Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins
Authors: Li Xiaobing , Xiao Kangpeng , Chen Xiaoyuan , Liang Xianghui , Zhang Xu , Zhang Zhipeng , Zhai Junqiong , Wang Ruichen , Zhou Niu , Chen Zu-Jin , Su Renwei , Zhou Fuqing , Holmes Edward C. , Irwin David M. , Chen Rui-Ai , He Qian , Wu Ya-Jiang , Wang Chen , Du Xue-Qing , Peng Shi-Ming , Xie Wei-Jun , Shan Fen , Li Wan-Ping , Dai Jun-Wei , Shen Xuejuan , Feng Yaoyu , Xiao Lihua , Chen Wu , Shen Yongyi
Published: June 2020

SARS-CoV-2 is having severe impact on public health at a global scale. Malayan pangolin SARS-CoV-2-related coronavirus (SARSr-CoV-2) is closely related to SARS-CoV-2. We show that CT scans of virus-positive pangolins reveal bilateral ground-glass opacities in lungs in similar manner to COVID-19 patients. The virus infected multiple organs in pangolins, with the lungs being the major target. Histological expression showed that ACE2 and TMPRSS2 are co-expressed with viral RNA. Transcriptome analysis revealed an inadequate interferon response, with different dysregulated chemokines and cytokines responses in pregnant and non-pregnant adults and fetuses. Viral RNA and protein were detected in three fetuses providing evidence for vertical virus transmission. In sum, our study identifies the biological framework of SARSr-CoV-2 in pangolins, revealing striking similarities to COVID-19 in humans.
Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals: Streptomyces strains and phages for antibiotic discovery
Authors: Montaño Elizabeth T. , Nideffer Jason F. , Brumage Lauren , Erb Marcella , Derman Alan I. , Davis John Paul , Estrada Elena , Fu Sharon , Le Danielle , Vuppala Aishwarya , Tran Cassidy , Luterstein Elaine , Lakkaraju Shivani , Panchagnula Sriya , Ren Caroline , Doan Jennifer , Tran Sharon , Soriano Jamielyn , Fujita Yuya , Gutala Pranathi , Fujii Quinn , Lee Minda , Bui Anthony , Villarreal Carleen , Shing Samuel R. , Kim Sean , Freeman Danielle , Racha Vipula , Ho Alicia , Kumar Prianka , Falah Kian , Dawson Thomas , Enustun Eray , Prichard Amy , Gomez Ana , Khanna Kanika , Trigg Shelly , Pogliano Kit , Pogliano Joe
Published: June 2020

The threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcare’s most potent antibiotics are becoming obsolete. Approximately two-thirds of the world’s antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, in order to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 101 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistantStaphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) againstS. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.
Fecal microbiota transplantation reconstructs the gut microbiota of septic mice and protects the intestinal mucosal barrier
Authors: Gai Xiaowei , Wang Huawei , Li Yaqing , Zhao Haotian , He Cong , Wang Zihui , Zhao Heling
Published: June 2020

The gastrointestinal (GI) tract has long been hypothesized to play an integral role in the pathophysiology of sepsis, and gut microbiota (GM) dysbiosis may be the key factor. Previous studies has confirmed that microbiome is markedly altered in critical illness. We aimed to confirm the existence of gut microbiota imbalance in the early stage of sepsis, observe the effect of fecal microbiota transplantation (FMT) on sepsis, and explore whether FMT can reconstruct the GM of septic mice and restore its protective function on the intestinal mucosal barrier. Through the study of flora, mucus layer, tight junction, immune barrier, and short-chain fatty acid changes in septic mice and fecal microbiota transplanted mice, we found that GM imbalance exists early in sepsis. FMT can improve morbidity and effectively reduce mortality in septic mice. After the fecal bacteria were transplanted, the abundance and diversity of the gut flora were restored, and the microbial characteristics of the donors changed. FMT can effectively reduce epithelial cell apoptosis, improve the composition of the mucus layer, upregulate the expression of tight junction proteins, and reduce intestinal permeability and the inflammatory response, thus protecting the intestinal barrier function. After FMT, Lachnospiraceae contributes the most to intestinal protection through enhancement of the L-lysine fermentation pathway, resulting in the production of acetate and butanoate, and may be the key bacteria for short-chain fatty acid metabolism and FMT success.
Structural details of amyloid beta oligomers in complex with human prion protein as revealed by solid-state MAS NMR spectroscopy
Authors: König Anna S. , Rösener Nadine S. , Gremer Lothar , Flender Daniel , Hoyer Wolfgang , Neudecker Philipp , Willbold Dieter , Heise Henrike
Published: June 2020

Human PrP (huPrP) is a high-affinity receptor for oligomeric Aβ. Synthetic oligomeric Aβ species are known to be heterogeneous, dynamic and transient, rendering their structural investigation particularly challenging. Here, we used huPrP to preserve Aβ oligomers by co-precipitating them into large hetero-assemblies to investigate the conformation of Aβ(1-42) oligomers and huPrP in the complex by solid-state MAS NMR spectroscopy. The disordered N-terminal region of huPrP becomes immobilized in the complex and therefore visible in dipolar spectra without adopting chemical shifts characteristic of a regular secondary structure. Most of the well-defined C-terminal part of huPrP is part of the rigid complex, and solid-state NMR spectra suggest a loss in regular secondary structure in the last two α-helices. For Aβ(1-42) oligomers in complex with huPrP, secondary chemical shifts reveal a substantial β-strand content. Importantly, not all Aβ(1-42) molecules within the complex have identical conformations. Comparison with the chemical shifts of synthetic Aβ fibrils suggests that the Aβ oligomer preparation represents a heterogeneous mixture of β-strand-rich assemblies, of which some have the potential to evolve and elongate into different fibril polymorphs, reflecting a general propensity of Aβ to adopt variable β-structure conformers.
Organization of DNA replication origin firing inXenopusegg extracts : the role of intra-S checkpoint
Authors: Ciardo Diletta , Haccard Olivier , Narassimprakash Hemalatha , Arbona Jean-Michel , Hyrien Olivier , Audit Benjamin , Marheineke Kathrin , Goldar Arach
Published: June 2020

During cell division, the duplication of the genome starts at multiple positions called replication origins. Origin firing requires the interaction of rate-limiting factors with potential origins during the S(ynthesis)-phase of the cell cycle. Origins fire as synchronous clusters which is proposed to be regulated by the intra-S checkpoint. By modelling the unchallenged, the checkpoint-inhibited and the checkpoint protein Chk1 over-expressed replication pattern of single DNA molecules fromXenopussperm chromatin replicated in egg extracts, we demonstrate that the quantitative modelling of data requires: 1) a segmentation of the genome into regions of low and high probability of origin firing; 2) that regions with high probability of origin firing escape intra-S checkpoint regulation and 3) the variability of the rate of DNA synthesis close to replication forks is a necessary ingredient that should be taken in to account in order to describe the dynamic of replication origin firing. This model implies that the observed origin clustering emerges from the apparent synchrony of origin firing in regions with high probability of origin firing and challenge the assumption that the intra-S checkpoint is the main regulator of origin clustering.

Author summary

DNA replication is one of the fundamental cell functions. The genome of eukaryotic organisms is duplicated from multiple positions named replication origins. Single molecule experiments allow to visualise the dynamics of spatio-temporal patterns created during replication process. The dynamic of replication process is regulated by checkpoints. However, the influence and the role of checkpoint regulation in the dynamics of spatio-temporal patterns of DNA replication is not understood. In this work we build a minimal, process-based and data rooted numerical model that allows to decipher the impact of checkpoint regulation on the dynamics of spatio-temporal pattern of DNA replication.
Dissection-independent production of a protective whole-sporozoite malaria vaccine
Authors: Blight Joshua , Sala Katarzyna A. , Atcheson Erwan , Kramer Holger , El-Turabi Aadil , Real Eliana , Dahalan Farah A. , Bettencourt Paulo , Dickinson Emma , Alves Eduardo , Salman Ahmed M. , Janse Chris J. , Ashcroft Frances , Hill Adrian V. S. , Reyes-Sandoval Arturo , Blagborough Andrew M. , Baum Jake
Published: June 2020

Complete protection against human malaria challenge has been achieved using infected mosquitoes as the delivery route for immunization withPlasmodiumparasites. Strategies seeking to replicate this efficacy with either a manufactured whole-parasite or subunit vaccine, however, have shown only limited success. A major roadblock to whole parasite vaccine progress and understanding of the human infective sporozoite form in general, is reliance on manual dissection for parasite isolation from infected mosquitoes. We report here the development of a four-step process based on whole mosquito homogenization, slurry and density-gradient filtration, combined with free-flow electrophoresis that is able to rapidly produce a pure, aseptic sporozoite inoculum from hundreds of mosquitoes. MurineP. bergheior human-infectiveP. falciparumsporozoites produced in this way are 2-3-fold more infective within vitrohepatocytes and can confer sterile protection when immunized intravenously with subsequent challenge using a mouse malaria model. Critically, we can also demonstrate for the first time 60-70% protection when the same parasites are administered via intramuscular (i.m.) route. In developing a process amenable to industrialisation and demonstrating efficacy by i.m. route these data represent a major advancement in capacity to produce a whole parasite malaria vaccine at scale.

One-Sentence Summary

A four-step process for isolating pure infective malaria parasite sporozoites at scale from homogenized whole mosquitoes, independent of manual dissection, is able to produce a whole parasite vaccine inoculum that confers sterilizing protection.
BEHAVIOURAL AND MOLECULAR EFFECTS OF CANNABIDIOLIC ACID IN MICE
Authors: Alegre-Zurano Laia , Martín-Sánchez Ana , Valverde Olga
Published: June 2020

Aims

Cannabidiolic acid (CBDA) is one of the most abundant phytocannabinoid acids in theCannabis Sativaplant. It has been shown it is able to exert some therapeutic effects such as antiemetic, anti-inflammatory, anxiolytic or antidepressant, although some of them remain under debate. In the present study we aim to assess the potential effects of CBDA on different behaviours and on the modulation of neuroinflammatory markers in the prefrontal cortex (PFC).

Main methods

the effects of acute and/or chronic CBDA (0.001-1 mg/kg i.p.) treatment were evaluated on cognitive, emotional, motivational and nociceptive behaviours in male CD1 mice. For this, Y-maze and elevated plus maze paradigms, spontaneous locomotor activity, social interaction, hot-plate, formalin and tail suspension tests were used. We also studied the effects of CBDA on the rewarding responses of cocaine in the conditioned place preference (CPP) paradigm. PFC was dissected after acute and chronic CBDA treatments to evaluate inflammatory markers.

Key findings

acute CBDA treatment induced antinociceptive responses in the hot-plate test. A 10-day chronic CBDA treatment reduced despair-like behaviour in the tail suspension test. CBDA did not alter the remaining behavioural tests assayed, including cocaine-induced reward in the CPP. Regarding the biochemical analysis, chronic CBDA treatment diminished peroxisome proliferator-activated receptor gamma (PPAR-γ) and increased interleukin-6 (IL-6) protein levels in PFC.

Significance

these results show that CBDA has limitedin vivoeffects modulating mice behaviour, highlighting the current disagreement regarding its therapeutic potential.
High-throughput 5’P sequencing enables the study of degradation-associated ribosome stalls
Authors: Zhang Yujie , Pelechano Vicent
Published: June 2020

RNA degradation is critical for gene expression and mRNA quality control. mRNA degradation is connected to the translation process up to the degree that 5’-3’ mRNA degradation follows the las translating ribosome. Here we present an improved high-throughput 5’P degradome RNA sequencing method (HT-5Pseq). HT-5Pseq is easy, scalable and uses affordable duplex-specific nuclease based rRNA depletion. We investigatein vivoribosome stalls focusing on translation termination. By comparing ribosome stalls identified by ribosome profiling, disome-seq and HT-5PSeq we identify that degradation-associated ribosome stalls are often enriched in Arg preceding the stop codon. On the contrary, mRNAs depleted for those stalls use more frequently TAA stop codon preceded by hydrophobic amino acids. Finally, we shown that termination stalls identified by HT-5Pseq, and not by other approaches, are associated to decreased mRNA stability. Our work suggests that ribosome stalls associated to mRNA decay can be easily captured by investigating the 5’P degradome.
Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence
Authors: Vattepu Ravi , Klausmeyer Rachel A. , Ayella Allan , Yadav Rahul , Dille Joseph T. , Saiz Stan V. , Beck Moriah R.
Published: June 2020

Immunoglobulin (Ig) domains are the most prevalent protein domain structure and share a highly conserved folding pattern; however, this structural family of proteins is also the most diverse in terms of biological roles and tissue expression. Ig domains vary significantly in amino acid sequence but share a highly conserved tryptophan in the hydrophobic core of this beta-stranded protein. Palladin is an actin binding and bundling protein that has five Ig domains and plays an important role in normal cell adhesion and motility. Mutation of the core tryptophan in one Ig domain of palladin has been identified in a pancreatic cancer cell line, suggesting a crucial role for this sole tryptophan in palladin Ig domain structure, stability, and function. We found that actin binding and bundling was not completely abolished with removal of this tryptophan despite a partially unfolded structure and significantly reduced stability of the mutant Ig domain as shown by circular dichroism investigations. In addition, this mutant palladin domain displays a tryptophan-like fluorescence attributed to an anomalous tyrosine emission at 345 nm. Our results indicate that this emission originates from a tyrosinate that may be formed in the excited ground state by proton transfer to a nearby glutamyl residue. Furthermore, this study emphasizes the importance of tryptophan in protein structural stability and illustrates how tyrosinate emission contributions may be overlooked during the interpretation of the fluorescence properties of proteins.

SHORT ABSTRACT

This study explores the functional and structural consequences of a point mutation in palladin, an Ig domain protein first identified in a pancreatic tumor cancer cell line. While exploring the consequences of mutating this conserved tryptophan in the hydrophobic core of the most prevalent domain structure found in proteins, an anomalous tyrosine fluorescence phenomenon was exposed.
In vivoantiviral host response to SARS-CoV-2 by viral load, sex, and age
Authors: Lieberman Nicole A. P. , Peddu Vikas , Xie Hong , Shrestha Lasata , Huang Meei-Li , Mears Megan C. , Cajimat Maria N. , Bente Dennis A. , Shi Pei-Yong , Bovier Francesca , Roychoudhury Pavitra , Jerome Keith R. , Moscona Anne , Porotto Matteo , Greninger Alexander L.
Published: June 2020

Despite limited genomic diversity, SARS-CoV-2 has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA-sequencing profiles of nasopharyngeal swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with upregulation of antiviral factors such asOAS1-3 and IFIT1-3, and Th1 chemokinesCXCL9/10/11, as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial cultures replicated thein vivoantiviral host response. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, includingACE2, increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of Th1 chemokinesCXCL9/10/11and their cognate receptor,CXCR3, as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B and NK cell-specific transcripts and an increase in inhibitors of NF-κB signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.
Human brain function during pattern separation follows hippocampal and neocortical connectivity gradients
Authors: Li Qiongling , Tavakol Shahin , Royer Jessica , Larivière Sara , Vos De Wael Reinder , Park Bo-yong , Paquola Casey , Zeng Debin , Caldairou Benoit , Bassett Danielle S. , Bernasconi Andrea , Bernasconi Neda , Frauscher Birgit , Smallwood Jonathan , Caciagli Lorenzo , Li Shuyu , Bernhardt Boris C.
Published: June 2020

Abstract

Episodic memory is our ability to remember past events accurately. Pattern separation, the process of of orthogonalizing similar aspects of external information into nonoverlapping representations, is one of its mechanisms. Converging evidence suggests a pivotal role of the hippocampus, in concert with neocortical areas, in this process. The current study aimed to identify principal dimensions of functional activation associated with pattern separation in hippocampal and neocortical areas, in both healthy individuals and patients with lesions to the hippocampus. Administering a pattern separation fMRI paradigm to a group of healthy adults, we detected task-related activation in bilateral hippocampal and distributed neocortical areas. Capitalizing on manifold learning techniques applied to parallel resting-state fMRI data, we could identify that hippocampal and neocortical activity patterns were efficiently captured by their principal gradients of intrinsic functional connectivity, which follows the hippocampal long axis and sensory-fugal cortical organization. Functional activation patterns and their alignment with these principal dimensions were altered in patients. Notably, inter-individual differences in the concordance between task-related activity and intrinsic functional gradients were correlated with pattern separation performance in both patients and controls. Our work outlines a parsimonious approach to capture the functional underpinnings of episodic memory processes at the systems level, and to decode functional reorganization in clinical populations.
b3galt6knock-out zebrafish recapitulate β3GalT6-deficiency disorders in human and reveal a trisaccharide proteoglycan linkage region
Authors: Delbaere Sarah , De Clercq Adelbert , Mizumoto Shuji , Noborn Fredrik , Bek Jan Willem , Alluyn Lien , Gistelinck Charlotte , Syx Delfien , Salmon Phil L. , Coucke Paul J. , Larson Göran , Yamada Shuhei , Willaert Andy , Malfait Fransiska
Published: June 2020

Proteoglycans are structurally and functionally diverse biomacromolecules found abundantly on cell membranes and in the extracellular matrix. They consist of a core protein linked to glycosaminoglycan chains via a tetrasaccharide linkage region. Here, we show that CRISPR/Cas9-mediatedb3galt6knock-out zebrafish, lacking galactosyltransferase II, which adds the third sugar in the linkage region, largely recapitulate the phenotypic abnormalities seen in human β3GalT6-deficiency disorders. These comprise craniofacial dysmorphism, generalized skeletal dysplasia, skin involvement and indications for muscle hypotonia. In-depth TEM analysis revealed disturbed collagen fibril organization as the most consistent ultrastructural characteristic throughout different affected tissues. Strikingly, despite a strong reduction in glycosaminoglycan content, as demonstrated by anion-exchange HPLC, subsequent LC-MS/MS analysis revealed a small amount of proteoglycans containing a unique linkage region consisting of only three sugars. This implies that formation of glycosaminoglycans with an immature linkage region is possible in a pathogenic context. Our study therefore unveils a novel rescue mechanism for proteoglycan production in the absence of galactosyltransferase II, hereby opening new avenues for therapeutic intervention.
Tissue-specific dynamic codon redefinition in Drosophila
Authors: Hudson Andrew M. , Loughran Gary , Szabo Nicholas L. , Wills Norma M. , Atkins John F. , Cooley Lynn
Published: June 2020

Stop codon readthrough during translation occurs in many eukaryotes, including Drosophila, yeast, and humans. Recoding of UGA, UAG or UAA to specify an amino acid allows the ribosome to synthesize C-terminally extended proteins. We previously found evidence for tissue-specific regulation of stop codon readthrough in decoding the Drosophilakelchgene, whose first open reading frame (ORF1) encodes a subunit of a Cullin3-RING ubiquitin ligase. Here, we show that the efficiency ofkelchreadthrough varies markedly by tissue. Immunoblotting for Kelch ORF1 protein revealed high levels of the readthrough product in lysates of larval and adult central nervous system (CNS) tissue and larval imaginal discs. A sensitive reporter ofkelchreadthrough inserted after the secondkelchopen reading frame (ORF2) directly detected synthesis of Kelch readthrough product in these tissues. To analyze the role of cis-acting sequences in regulatingkelchreadthrough, we used cDNA reporters to measure readthrough in both transfected human cells and transgenic Drosophila. Results from a truncation series suggest that a predicted mRNA stem-loop 3’ of the ORF1 stop codon stimulates high-efficiency readthrough. Expression of cDNA reporters using cell type-specific Gal4 drivers revealed that CNS readthrough is restricted to neurons. Finally, we show that high-effficiency readthrough in the CNS is common in Drosophila, raising the possibility that the neuronal proteome includes many proteins with conserved C-terminal extensions. This work provides new evidence for a remarkable degree of tissue- and cell-specific dynamic stop codon redefinition in Drosophila.
Advancing science or advancing careers? Researchers’ opinions on success indicators
Authors: Bonn Noémie Aubert , Pinxten Wim
Published: June 2020

The way in which we assess researchers has been under the radar in the past few years. Critics argue that current research assessments focus on productivity and that they increase unhealthy pressures on scientists. Yet, the precise ways in which assessments should change is still open for debate. We circulated a survey with Flemish researchers to understand how they work, and how they would rate the relevance of specific indicators used in research assessments. We found that most researchers worked far beyond their expected working schedule. We also found that, although they spent most of their time doing research, respondents wished they could dedicate more time to it and spend less time writing grants and performing other activities such as administrative duties and meetings. When looking at success indicators, we found that indicators related to openness, transparency, quality, and innovation were perceived as highly important in advancing science, but as relatively overlooked in career advancement. Conversely, indicators which denoted of prestige and competition were generally rated as important to career advancement, but irrelevant or even detrimental in advancing science. Open comments from respondents further revealed that, although indicators which indicate openness, transparency, and quality (e.g., publishing open access, publishing negative findings, sharing data, etc.) should ultimately be valued more in research assessments, the resources and support currently in place were insufficient to allow researchers to endorse such practices. In other words, current research assessments are inadequate and ignore practices which are essential in contributing to the advancement of science. Yet, before we change the way in which researchers are being assessed, supporting infrastructures must be put in place to ensure that researchers are able to commit to the activities that may benefit the advancement of science.

Submission history

The first version of this manuscript was submitted to PLOS ONE on 27th June 2020. Revisions after peer-review were submitted on 4th October 2020 and 20th November 2020.
Snf1p/Hxk2p/Mig1p pathway regulates exponential growth, mitochondrial respiration, and hexose transporters transcription inSaccharomyces cerevisiae
Authors: Carrillo-Garmendia Andres , Martinez-Ortiz Cecilia , Martinez-Garfias Jairo Getzemani , González-Hernández Juan Carlos , Nava Gerardo M. , Ramos-Gomez Minerva , Dufoo-Hurtado Miguel David , Madrigal-Perez Luis Alberto
Published: June 2020

The Crabtree effect occurs under high-glucose concentrations and is characterized by the increase of the growth and a decrease in mitochondrial respiration of yeasts. Regulation of the Crabtree effect could enhance ethanol production with biotechnological purposes and a better understanding of the etiology of cancer due to its similitude with the Warburg effect. Nonetheless, the conclusive molecular mechanism of the Crabtree effect is still on debate. The pathway Snf1p/Hxk2p/Mig1p has been linked with the transcriptional regulation of the hexose transporters and has also been identified in the modulation of phenotypes related to the Crabtree effect. Nevertheless, it has not been directly identified the genetic regulation of the hexose transporters with modulation of the Crabtree effect phenotypes by Snf1p/Hxk2p/Mig1p pathway. In this sense, we provide evidence that the deletion of theSNF1andHXK2genes affects the exponential growth, mitochondrial respiration, and the transcription of hexose transporters in a glucose-dependent manner inSaccharomyces cerevisiae. TheVmaxof the main hexose transporters transcribed showed a positive correlation with the exponential growth and a negative correlation with the mitochondrial respiration. Transcription of the geneHXT2was the most affected by the deletion of the pathwaySNF1/HXK2/MIG1. Deletion of the orthologous genesSNF1andHXK2in the Crabtree negative yeast,K. marxianus,has a differential effect in exponential growth and mitochondrial respiration in comparison withS. cerevisiae. Overall, these results indicate that theSNF1/HXK2/MIG1pathway transcriptionally regulates the hexose transporters having an influence in the exponential growth and mitochondrial respiration in a glucose-dependent manner.
Online Transcranial Random Noise stimulation improves perception at high levels of visual white noise
Authors: Melnick Michael D. , Park Woon Ju , Croom Sholei , Chen Shuyi , Batelli Lorella , Busza Ania , Huxlin Krystel R. , Tadin Duje
Published: June 2020

Transcranial random noise stimulation (tRNS), a relatively recent addition to the field of non-invasive, electrical brain stimulation, has been shown to improve perceptual and cognitive functions across a wide variety of tasks. However, the underlying mechanisms of visual improvements caused by tRNS remain unclear. To study this question, we employed a well-established, equivalent-noise approach, which measures perceptual performance at various levels of external noise and is formalized by the Perceptual Template Model (PTM). This approach has been used extensively to infer the underlying mechanisms behind changes in visual processing, including those from perceptual training, adaptation and attention. Here, we used tRNS during an orientation discrimination task in the presence of increasing quantities of external visual white noise and fit the PTM to gain insights into the effects of tRNS on visual processing. Our results show that tRNS improves visual processing when stimulation is applied during task performance, but only at high levels of external visual white noise—a signature of improved external noise filtering. There were no significant effects of tRNS on task performance after the stimulation period. Of interest, the reported effects of tRNS on visual processing mimic those previously reported for endogenous spatial attention, offering a potential area of investigation for future work.
Organisms causing secondary pneumonias in COVID-19 patients at 5 UK ICUs as detected with the FilmArray test
Authors: Dhesi Zaneeta , Enne Virve I , Brealey David , Livermore David M , High Juliet , Russell Charlotte , Colles Antony , Kandil Hala , Mack Damien , Martin Daniel , Page Valerie , Parker Robert , Roulston Kerry , Singh Suveer , Wey Emmanuel , Swart Ann Marie , Stirling Susan , Barber Julie A , O’Grady Justin , Gant Vanya
Published: June 2020

Introduction

Several viral respiratory infections - notably influenza - are associated with secondary bacterial infection and additional pathology. The extent to which this applies for COVID-19 is unknown. Accordingly, we aimed to define the bacteria causing secondary pneumonias in COVID-19 ICU patients using the FilmArray Pneumonia Panel, and to determine this test’s potential in COVID-19 management.

Methods

COVID-19 ICU patients with clinically-suspected secondary infection at 5 UK hospitals were tested with the FilmArray at point of care. We collected patient demographic data and compared FilmArray results with routine culture.

Results

We report results of 110 FilmArray tests on 94 patients (16 had 2 tests): 69 patients (73%) were male, the median age was 59 yrs; 92 were ventilated. Median hospital stay before testing was 14 days (range 1-38). Fifty-nine (54%) tests were positive, with 141 bacteria detected. Most were Enterobacterales (n=55, includingKlebsiellaspp. [n= 35]) orStaphylococcus aureus(n=13), as is typical of hospital and ventilator pneumonia. Community pathogens, includingHaemophilus influenzae(n=8) andStreptococcus pneumoniae(n=1), were rarer. FilmArray detected one additional virus (Rhinovirus/Enterovirus) and no atypical bacteria. Fewer samples (28 % vs. 54%) were positive by routine culture, and fewer species were reported per sample;Klebsiellaspecies remained the most prevalent pathogens.

Conclusion

FilmArray had a higher diagnostic yield than culture for ICU COVID-19 patients with suspected secondary pneumonias. The bacteria found mostly were Enterobacterales,S. aureusandP. aeruginosa, as in typical HAP/VAP, but withKlebsiellaspp. more prominent. We found almost no viral co-infection. Turnaround from sample to results is around 1h 15 min compared with the usual 72h for culture, giving prescribers earlier data to inform antimicrobial decisions.