bluuebunny/crossref_metadata_2025 huggingface dataset:
α-lipoic acid has the potential to normalize copper metabolism, which is dysregulated in Alzheimer’s disease
Authors: Metsla Kristel , Kirss Sigrid , Laks Katrina , Sildnik Gertrud , Palgi Mari , Palumaa Teele , Tõugu Vello , Palumaa Peep
Published: March 2021

Alzheimer’s disease (AD) is an age-dependent progressive neurodegenerative disorder and the most common cause of dementia. The treatment and prevention of AD present immense yet unmet needs. One of the hallmarks of AD is the formation of extracellular amyloid plaques in the brain, composed of amyloid-beta (Aβ) peptides. Multiple amyloid-targeting drug candidates have recently failed in clinical trials, which creates the necessity to focus also on alternative therapeutic strategies. One factor contributing to the development of AD is dysregulated copper metabolism, reflected in the intracellular copper deficit and excess extracellular copper levels. In the current study, we follow the widely accepted hypothesis that the normalization of copper metabolism leads to the prevention or slowing of the disease and searched for new copper-regulating ligands. We demonstrate that the natural intracellular copper chelator, α-lipoic acid (LA) translocates copper from extracellular to intracellular space in a SH-SY5Y-based neuronal cell model, and is thus suitable to alleviate the intracellular copper deficit characteristic of AD neurons. Furthermore, we show that supplementation with LA protects theDrosophila melanogastermodel of AD from developing AD phenotype, reflecting in decreased locomotor activity. Collectively, these results provide evidence that LA has the potential to normalize copper metabolism in AD and supports the hypothesis that LA supplementation may serve as a promising cost-effective method for the prevention and/or treatment of AD.

Significance statement

Alzheimer’s disease (AD) is a major biomedical concern that requires novel effective prevention and treatment approaches. An early determinant of AD pathology is dysregulated copper metabolism, which initiates the amyloid cascade, induces oxidative stress and impairs the functioning of cellular copper proteins, all contributing to the development of neurodegeneration. We suggest that the natural copper chelator α-lipoic acid (LA) can normalize impaired copper metabolism in AD. We demonstrate that LA promotes the influx of copper into SH-SY5Y cells in a dose-dependent manner. Moreover, we show that LA alleviates the disease phenotype in a Drosophila melanogaster model of AD. Together with previously published data, these results support the hypothesis that LA has the potential for the prevention and treatment of AD.
Tissue environment, not ontogeny, defines intestinal intraepithelial T lymphocytes
Authors: Brenes Alejandro , Vandereyken Maud , James Olivia J. , Hukelmann Jens , Spinelli Laura , Lamond Angus I. , Swamy Mahima
Published: March 2021

Tissue-resident intestinal intraepithelial T lymphocytes (T-IEL) patrol the gut and have important roles in regulating intestinal homeostasis. T-IEL include both induced T-IEL, derived from systemic antigen-experienced lymphocytes, and natural IEL, which are developmentally targeted to the intestine. While the processes driving T-IEL development have been elucidated, the precise roles of the different subsets and the processes driving activation and regulation of these cells remain unclear. To gain functional insights into these enigmatic cells, we used high-resolution, quantitative mass spectrometry to investigate the proteomic landscape of the main T-IEL populations in the gut. Comparing the proteomes of induced T-IEL and natural T-IEL subsets, with naive CD8+T cells from lymph nodes exposes the dominant effect of the gut environment over ontogeny on T-IEL phenotypes. Analyses of protein copy numbers of >7000 proteins in T-IEL reveal skewing of the cell surface repertoire towards epithelial interactions and checkpoint receptors; strong suppression of the metabolic machinery indicating a high energy barrier to functional activation; and changes in T cell antigen receptor signalling pathways reminiscent of chronically activated T cells. These novel findings illustrate how multiple input signals need to be integrated to regulate T-IEL function.
Identity and compatibility of reference genome resources
Authors: Stolarczyk Michał , Xue Bingjie , Sheffield Nathan C.
Published: March 2021

Genome analysis relies on reference data like sequences, feature annotations, and aligner indexes. These data can be found in many versions from many sources, making it challenging to identify and assess compatibility among them. For example, how can you determine which indexes are derived from identical raw sequence files, or which annotations share a compatible coordinate system? Here, we describe a novel approach to establish identity and compatibility of reference genome resources. We approach this with three advances: First, we derive unique identifiers for each resource; second, we record parent-child relationships among resources; and third, we describe recursive identifiers that determine identity as well as compatibility of coordinate systems and sequence names. These advances facilitate portability, reproducibility, and re-use of genome reference data.

Availability

https://refgenie.databio.org
Reconstruction of Contemporary Human Stem Cell Dynamics with Oscillatory Molecular Clocks
Authors: Gabbutt Calum , Schenck Ryan O , Weisenberger Dan , Kimberley Christopher , Berner Alison , Househam Jacob , Lakatos Eszter , Robertson-Tessi Mark , Martin Isabel , Patel Roshani , Clark Sue , Latchford Andrew , Barnes Christopher , Leedham Simon J , Anderson Alexander RA , Graham Trevor A , Shibata Darryl
Published: March 2021

Molecular clocks record cellular ancestry. However, currently used clocks ‘tick too slowly’ to measure the short-timescale dynamics of cellular renewal in adult tissues. Here we develop ‘rapidly oscillating DNA methylation clocks’ where ongoing (de)methylation causes the clock to ‘tick-tock’ back-and-forth between methylated and unmethylated states like a pendulum. We identify oscillators using standard methylation arrays and develop a mathematical modelling framework to quantitatively measure human adult stem cell dynamics from these data. Small intestinal crypts were inferred to contain slightly more stem cells than colon (6.5 ± 1.0 vs 5.8 ± 1.7 stem cells/crypt) with slower stem cell replacement in small intestine (0.79 ± 0.5 vs 1.1 ± 0.8 replacements/stem cell/year). GermlineAPCmutation increased the number of replacements per crypt (13.0 ± 2.4 replacements/crypt/year vs 6.9 ± 4.6 for healthy colon). In blood, we measure rapid expansion of acute leukaemia and slower growth of chronic disease. Rapidly oscillating molecular clocks are a new methodology to quantitatively measure human somatic cell dynamics.
Time series analysis of trial-to-trial variability of MEG power spectrum during rest state, unattented listening and frequency-modulated tones classification
Authors: Kipiński Lech , Kordecki Wojciech
Published: March 2021

The nonstationarity of EEG/MEG signals is important for understanding the functioning of human brain. From the previous research we know that even very short, i.e. 250—500ms MEG signals are variance-nonstationary. The covariance of stochastic process is mathematically associated with its spectral density, therefore we investigate how the spectrum of such nonstationary signals varies in time.

We analyze the data from 148-channel MEG, that represent rest state, unattented listening and frequency-modulated tones classification. We transform short-time MEG signals to the frequency domain using the FFT algorithm and for the dominant frequencies 8—12 Hz we prepare the time series representing their trial-to-trial variability. Then, we test them for level- and trend-stationarity, unit root, heteroscedasticity and gaussianity and based on their properties we propose the ARMA-modelling for their description.

The analyzed time series have the weakly stationary properties independently of the functional state of brain and localization. Only their small percentage, mostly related to the cognitive task, still presents nonstationarity. The obtained mathematical models show that the spectral density of analyzed signals depends on only 2—3 previous trials.

The presented method has limitations related to FFT resolution and univariate models, but it is not computationally complicated and allows to obtain a low-complex stochastic models of the EEG/MEG spectrum variability.

Although the physiological short-time MEG signals are in principle nonstationary in time domain, its power spectrum at the dominant frequencies varies as weakly stationary stochastic process. Described technique has the possible applications in prediction of the EEG/MEG spectral properties in theoretical and clinical neuroscience.
Spontaneous Eye Blink Rate during the Working Memory Delay Period Predicts Task Accuracy
Authors: Ortega Jefferson , Plaska Chelsea Reichert , Gomes Bernard A. , Ellmore Timothy M.
Published: March 2021

Spontaneous eye blink rate (sEBR) has been linked to attention and memory, specifically working memory (WM). sEBR is also related to striatal dopamine (DA) activity with schizophrenia and Parkinson’s disease showing increases and decreases respectively in sEBR. A weakness of past studies of sEBR and WM is that correlations have been reported using blink rates taken at baseline either before or after performance of the tasks used to assess WM. The goal of the present study was to understand how fluctuations in sEBR during different phases of a visual WM task predict task accuracy. In two experiments, with recordings of sEBR collected inside and outside of a magnetic resonance imaging bore, we observed sEBR to be positively correlated with WM task accuracy during the WM delay period. We also found task-related modulation of sEBR, including higher sEBR during the delay period compared to rest, and lower sEBR during task phases (e.g., stimulus encoding) that place demands on visual attention. These results provide further evidence that sEBR could be an important predictor of WM task performance with the changes during the delay period suggesting a role in WM maintenance. The relationship of sEBR to DA activity and WM maintenance is discussed.
An integrative transcriptional logic model of hepatic insulin resistance
Authors: Kitamoto Takumi , Kuo Taiyi , Okabe Atsushi , Kaneda Atsushi , Accili Domenico
Published: March 2021

Abnormalities of lipid/lipoprotein and glucose metabolism are hallmarks of hepatic insulin resistance in type 2 diabetes. The former antedate the latter, but the latter become progressively refractory to treatment and contribute to therapeutic failures. It’s unclear whether the two processes share a common pathogenesis and what underlies their progressive nature. In this study, we investigated the hypothesis that genes in the lipid/lipoprotein pathway and those in the glucose metabolic pathway are governed by different transcriptional logics that affect their response to physiologic (fasting/refeeding) as well as pathophysiologic cues (insulin resistance and hyperglycemia). To this end, we obtained genomic and transcriptomic maps of the key insulin-regulated transcription factor, FoxO1, and integrated them with those of CREB, PPARα, and glucocorticoid receptor. We found an enrichment of glucose metabolic genes among those regulated by intergenic and promoter enhancers in a fasting-dependent manner, while lipid genes were enriched among fasting-dependent intron enhancers and fasting-independent enhancer-less introns. Glucose genes also showed a remarkable transcriptional resiliency, i.e., an enrichment of active marks at shared PPARα/FoxO1 regulatory elements when FoxO1 was inactivated. Surprisingly, the main features associated with insulin resistance and hyperglycemia were a “spreading” of FoxO1 binding to enhancers, and the emergence of target sites unique to this condition. We surmise that this unusual pattern correlates with the progressively intractable nature of hepatic insulin resistance. This transcriptional logic provides an integrated model to interpret the combined lipid and glucose abnormalities of type 2 diabetes.

Significance Statement

The liver is a source of excess lipid, atherogenic lipoproteins, and glucose in patients with type 2 diabetes. These factors predispose to micro- and macrovascular complications. The underlying pathophysiology is not well understood, and mechanistic insight into it may provide better tools to prevent, treat, and reverse the disease. Here we propose an alternative explanation for this pathophysiologic conundrum by illustrating a transcriptional “logic” underlying the regulation of different classes of genes. These findings can be interpreted to provide an integrated stepwise model for the coexistence of lipid and glucose abnormalities in hepatic insulin resistance.

Highlights

Foxo1 regulates liver metabolism through active enhancers, and hepatocyte maintenance through core promoters

Foxo1 regulates glucose genes through fasting-dependent intergenic enhancers

Bipartite intron regulation of lipid genes is partly fasting-independent

Pparαcontributes to the transcriptional resiliency of Foxo1 metabolic targets

Insulin resistance causes de novo recruitment of Foxo1 to active enhancers

A stepwise model of insulin resistance
Rationally designed immunogens enable immune focusing to the SARS-CoV-2 receptor binding motif
Authors: Hauser Blake M. , Sangesland Maya , Denis Kerri J. St. , Windsor Ian W. , Feldman Jared , Lam Evan C. , Kannegieter Ty , Balazs Alejandro B. , Lingwood Daniel , Schmidt Aaron G.
Published: March 2021

Eliciting antibodies to surface-exposed viral glycoproteins can lead to protective responses that ultimately control and prevent future infections. Targeting functionally conserved epitopes may help reduce the likelihood of viral escape and aid in preventing the spread of related viruses with pandemic potential. One such functionally conserved viral epitope is the site to which a receptor must bind to facilitate viral entry. Here, we leveraged rational immunogen design strategies to focus humoral responses to the receptor binding motif (RBM) on the SARS-CoV-2 spike. Using glycan engineering and epitope scaffolding, we find an improved targeting of the serum response to the RBM in context of SARS-CoV-2 spike imprinting. Furthermore, we observed a robust SARS-CoV-2-neutralizing serum response with increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses and represents an adaptable design approach for targeting conserved epitopes on other viral glycoproteins.

One Sentence Summary

SARS-CoV-2 immune focusing with engineered immunogens
Insights into the genetic architecture of complex traits in Napier grass (Cenchrus purpureus) and QTL regions governing forage biomass yield, water use efficiency and feed quality traits
Authors: Muktar Meki S. , Habte Ermias , Teshome Abel , Assefa Yilikal , Negawo Alemayehu T. , Lee Ki-Won , Zhang Jiyu , Jones Chris S.
Published: March 2021

Napier grass is the most important perennial tropical grass native to Sub-Saharan Africa and widely grown in tropical and subtropical regions around the world, primarily as a forage crop for animal feed, but with potential as an energy crop and in a wide range of other areas. Genomic resources have recently been developed for Napier grass that need to be deployed for genetic improvement and molecular dissection of important agro-morphological and feed quality traits. From a diverse set of Napier grass genotypes assembled from two independent collections, a subset of 84 genotypes that best represents the genetic diversity of the collections were selected and evaluated for two years in dry (DS) and wet (WS) seasons under three soil moisture conditions: moderate water stress in DS (DS-MWS); severe water stress in DS (DS-SWS) and, under rainfed (RF) conditions in WS (WS-RF). Data for agro-morphological and feed quality traits, adjusted for the spatial heterogeneity in the experimental blocks, were collected over a two-year period from 2018 to 2020. A total of 135,706 molecular markers were filtered, after removing markers with missing values > 10% and a minor allele frequency (MAF) < 5 %, from the high-density genome-wide markers generated previously using the genotyping by sequencing (GBS) method of the DArTseq platform. A genome-wide association study (GWAS), using two different mixed linear model algorithms, identified more than 58 QTL regions and markers associated with agronomic, morphological and water-use efficiency traits. QTL regions governing purple pigmentation and feed quality traits were also identified. The identified markers will be useful in the genetic improvement of Napier grass through the application of marker-assisted selection and for further characterization and map-based cloning of the QTLs.
MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging
Authors: Schapiro Denis , Sokolov Artem , Yapp Clarence , Muhlich Jeremy L. , Hess Joshua , Lin Jia-Ren , Chen Yu-An , Nariya Maulik K. , Baker Gregory J. , Ruokonen Juha , Maliga Zoltan , Jacobson Connor A. , Farhi Samouil L. , Abbondanza Domenic , McKinley Eliot T. , Betts Courtney , Regev Aviv , Coffey Robert J. , Coussens Lisa M. , Santagata Sandro , Sorger Peter K.
Published: March 2021

Highly multiplexed tissue imaging makes molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of the underlying data poses a substantial computational challenge. Here we describe a modular and open-source computational pipeline (MCMICRO) for performing the sequential steps needed to transform large, multi-channel whole slide images into single-cell data. We demonstrate use of MCMICRO on images of different tissues and tumors acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.
Killed whole genome-reduced bacteria surface-expressed coronavirus fusion peptide vaccines protect against disease in a porcine model
Authors: Maeda Denicar Lina Nascimento Fabris , Tian Debin , Yu Hanna , Dar Nakul , Rajasekaran Vignesh , Meng Sarah , Mahsoub Hassan , Sooryanarain Harini , Wang Bo , Heffron C. Lynn , Hassebroek Anna , LeRoith Tanya , Meng Xiang-Jin , Zeichner Steven L.
Published: March 2021

As the coronavirus disease 2019 (COVID-19) pandemic rages on, it is important to explore new evolution-resistant vaccine antigens and new vaccine platforms that can produce readily scalable, inexpensive vaccines with easier storage and transport. We report here a synthetic biology-based vaccine platform that employs an expression vector with an inducible Gram-negative autotransporter to express vaccine antigens on surface of genome-reduced bacteria to enhance interaction of vaccine antigen with immune system. As a proof of principle, we utilized genome-reducedE. colito express SARS-CoV-2 and porcine epidemic diarrhea virus (PEDV) fusion peptide (FP) on the cell surface, and evaluated their use as a killed whole cell vaccine. The FP sequence is highly conserved across coronaviruses; the 6 FP core amino acid residues along with the 4 adjacent residues upstream and the 3 residues downstream the core are identical between SARS-CoV-2 and PEDV. We tested the efficacy of PEDV FP and SARS-CoV-2 FP vaccines in a PEDV challenge pig model. We demonstrated that both vaccines induced potent anamnestic responses upon virus challenge, potentiated IFN-γ responses, reduced viral RNA loads in jejunum tissue, and provided significant protection against clinical disease. However, neither vaccines elicited sterilizing immunity. Since SARS-CoV-2 FP and PEDV FP vaccines provided similar clinical protection, the coronavirus FP could be a target for a broadly-protective vaccine using any platform. Importantly, the genome-reduced bacterial surface-expressed vaccine platform, when using a vaccine appropriate bacterial vector, has potential utility as an inexpensive, readily manufactured, and rapid vaccine platform for other pathogens.

Significance Statement

We report a new vaccine platform to express vaccine antigens on surface of genome-reduced bacteria to enhance vaccine immunogenicity. We demonstrated the utility of this vaccine platform by expressing the highly conserved fusion peptide (FP) of SARS-CoV-2 and porcine epidemic diarrhea virus on the surface ofE.colito produce killed whole cell bacterial vaccines. The vaccine primes a potent anamnestic response, potentiates IFN-γ responses, and provides significant protection in pigs against disease following virus challenge. The FP could be a target for a broadly-protective coronavirus vaccine since a Betacoronavirus SARS-CoV-2 FP vaccine provided cross-protection against Alphacoronavirus PEDV. When using a vaccine appropriate bacteria vector, this inexpensive new vaccine platform offers the potential for use in developing countries.
BREAKTHROUGH REPORT - Large scale measurement of protein synthesis rates over the diurnal cycle reveal pathway specific regulation of translation
Authors: Duncan Owen , Millar A. Harvey
Published: March 2021

Plants have a diurnal separation of metabolic fluxes and a need for differential maintenance of protein machinery in the day and night. To directly assess aggregate protein translation and degradation for specific proteins and to estimate the ATP investment involved, the individual rates of synthesis and degradation of hundreds of different proteins were measured inArabidopsis thalianarosettes. This quantification of translation control through incorporation of heavy hydrogen into newly synthesised protein confirmed that most protein synthesis occurs during the day hours (~3:1 day:night), but revealed it was highly divergent across functional categories. Proteins involved in photosynthesis, especially components of the light harvesting complexes, were synthesized much faster in the day (~10:1), while the protein components of carbon metabolism and vesicle trafficking were translated at similar rates day or night. Comparison of aggregate translation with a range of comparable studies using polysomal loading of transcripts or transcript abundance suggests that translational control is a major contributor to effective gene expression over the diurnal cycle. Diurnal protein degradation rate was observed to be tightly coordinated with protein synthesis rate as few leaf proteins changed in abundance despite reduced translation rates during the night. The direct, quantitative and aggregate analysis of protein synthesis provides an integration of transcriptional, post-transcriptional and translational control of leaf proteome homeostasis and an opportunity to assess the ATP investments involved. The data reveals how the pausing of photosystem synthesis and degradation at night allows the redirection of a decreased energy budget to a selective night-time maintenance schedule.

One sentence summary

Advances in collection and processing of stable isotope incorporation data has allowed characterisation of differential protein synthesis rates over the diurnal cycle which reveal both global and specific translational regulation programs of core biochemical pathways.
Dynamic accumulation of a helper NLR at the plant-pathogen interface underpins pathogen recognition
Authors: Duggan Cian , Moratto Eleonora , Savage Zachary , Hamilton Eranthika , Adachi Hiroaki , Wu Chih-Hang , Leary Alexandre Y , Tumtas Yasin , Rothery Stephen M , Maqbool Abbas , Nohut Seda , Kamoun Sophien , Bozkurt Tolga Osman
Published: March 2021

Plants employ sensor-helper pairs of NLR immune receptors to recognize pathogen effectors and activate immune responses. Yet the subcellular localization of NLRs pre- and post-activation during pathogen infection remains poorly known. Here we show that NRC4, from the ‘NRC’ solanaceous helper NLR family, undergoes dynamic changes in subcellular localization by shuttling to and from the plant-pathogen haustorium interface established during infection by the Irish potato famine pathogenPhytophthora infestans.Specifically, prior to activation, NRC4 accumulates at the extra-haustorial membrane (EHM), presumably to mediate response to perihaustorial effectors, that are recognized by NRC4-dependent sensor NLRs. However not all NLRs accumulate at the EHM, as the closely related helper NRC2, and the distantly related ZAR1, did not accumulate at the EHM. NRC4 required an intact N-terminal coiled coil domain to accumulate at the EHM, whereas the functionally conserved MADA motif implicated in cell death activation and membrane insertion was dispensable for this process. Strikingly, a constitutively autoactive NRC4 mutant did not accumulate at the EHM and showed punctate distribution that mainly associated with the plasma membrane, suggesting that post-activation, NRC4 probably undergoes a conformation switch to form clusters that do not preferentially associate with the EHM. When NRC4 is activated by a sensor NLR during infection however, NRC4 formed puncta mainly at the EHM and to a lesser extent at the plasma membrane. We conclude that following activation at the EHM, NRC4 may spread to other cellular membranes from its primary site of activation to trigger immune responses.

Significance statement

Plant NLR immune receptors function as intracellular sensors of pathogen virulence factors known as effectors. In resting state, NLRs localize to subcellular sites where the effectors they sense operate. However, the extent to which NLRs alter their subcellular distribution during infection remains elusive. We describe dynamic changes in spatiotemporal localization of an NLR protein in infected plant cells. Specifically, the NLR protein accumulates at the newly synthesized plant-pathogen interface membrane, where the corresponding effectors are deployed. Following immune recognition, the activated receptor re-organizes to form punctate structures that target the cell periphery. We propose that NLRs are not necessarily stationary immune receptors, but instead may spread to other cellular membranes from the primary site of activation to boost immune responses.
Plasma proteome analyses in individuals of European and African ancestry identifycis-pQTLs and models for proteome-wide association studies
Authors: Zhang Jingning , Dutta Diptavo , Köttgen Anna , Tin Adrienne , Schlosser Pascal , Grams Morgan E. , Harvey Benjamin ,   CKDGen Consortium, Yu Bing , Boerwinkle Eric , Coresh Josef , Chatterjee Nilanjan
Published: March 2021

Improved understanding of genetic regulation of proteome can facilitate the identification of causal mechanisms for complex traits. We analyzed data on 4,657 plasma proteins from 7,213 European American (EA) and 1,871 African American (AA) individuals from the ARIC study, and further replicated findings on 467 AA individuals from the AASK study. Here we identified 2,004 proteins in EA and 1,618 in AA, with majority overlapping, which showed associations with common variants incis-regions. Availability of AA samples led to smaller credible sets and significant number of population-specificcis-pQTLs. Elastic-net produced powerful models for protein prediction in both populations. An application of proteome-wide association studies (PWAS) to serum urate and gout, implicated several proteins, includingIL1RN,revealing the promise of the drug anakinra to treat acute gout flares. Our study demonstrates the value of large and diverse ancestry study for genetic mechanisms of molecular phenotypes and their relationship with complex traits.
Discovery of SARS-CoV-2 papain-like protease inhibitors through a combination of high-throughput screening and FlipGFP-based reporter assay
Authors: Xia Zilei , Sacco Michael Dominic , Ma Chunlong , Townsend Julia Alma , Kitamura Naoya , Hu Yanmei , Ba Mandy , Szeto Tommy , Zhang Xiujun , Meng Xiangzhi , Zhang Fushun , Xiang Yan , Marty Michael Thomas , Chen Yu , Wang Jun
Published: March 2021

The papain-like protease (PLpro) of SARS-CoV-2 is a validated antiviral drug target. PLprois involved in the cleavage of viral polyproteins and antagonizing host innate immune response through its deubiquitinating and deISG15ylating activities, rendering it a high profile antiviral drug target. Through a FRET-based high-throughput screening, several hits were identified as PLproinhibitors with IC50values at the single-digit micromolar range. Subsequent lead optimization led to potent inhibitors with IC50values ranging from 0.56 to 0.90 µM. To help prioritize lead compounds for the cellular antiviral assay against SARS-CoV-2, we developed the cell-based FlipGFP assay that is suitable for quantifying the intracellular enzymatic inhibition potency of PLproinhibitors in the BSL-2 setting. Two compounds selected from the FlipGFP-PLproassay, Jun9-53-2 and Jun9-72-2, inhibited SARS-CoV-2 replication in Caco-2 hACE2 cells with EC50values of 8.89 and 8.32 µM, respectively, which were 3-fold more potent than GRL0617 (EC50= 25.1 µM). The X-ray crystal structures of PLproin complex with GRL0617 showed that binding of GRL0617 to SARS-CoV-2 induced a conformational change in the BL2 loop to the more closed conformation. Overall, the PLproinhibitors identified in this study represent promising starting points for further development as SARS-CoV-2 antivirals, and FlipGFP-PLproassay might be a suitable surrogate for screening PLproinhibitors in the BSL-2 setting.
Antibiotic Resistance inBacillus-based Biopesticide Products
Authors: Kaze Mo , Brooks Lauren , Sistrom Mark
Published: March 2021

The crisis of antibiotic resistant bacterial infections is one of the most pressing public health issues. Common agricultural practices have been implicated in the generation of antibiotic resistant bacteria. Biopesticides, live bacteria used for pest control, are non-pathogenic and considered safe for consumption. Application of bacteria-based pesticides to crops in high concentrations raises the possibility of unintentional contributions to the movement and generation of antibiotic resistance genes in the environment. However, the presence of clinically relevant antibiotic resistance genes and their resistance phenotypes are currently unknown. Here we use a combination of multiple bioinformatic and microbiological techniques to define resistomes of widely used biopesticides and determine how the presence of suspected antibiotic resistance genes translates to observable resistance phenotypes in several biopesticide products. Our results demonstrate that biopesticide products are reservoirs of clinically relevant antibiotic resistance genes and bear resistance to multiple drug classes.

Importance

This is the first study to specifically address antibiotic resistance in widely distributed bacterial strains used as commercial biopesticides. Safety assessments of commercial live bacterial biopesticide products do not include antibiotic resistance phenotype identification. We identify antibiotic resistance genes in all live bacterial strains examined, and resistant phenotypes in all strains tested for antibiotic susceptibility. This work demonstrates that biopesticides potentially play a critical role as reservoirs and vectors of antibiotic resistance in the broader environmental resistome that is to date, unstudied.
The course of the UK COVID 19 pandemic; no measurable impact of new variants
Authors: Ellis D , Papadopoulos D , Mukherjee S , Ukwu U , Chari N , Charitopoulos K , Donkov I , Bishara S
Published: March 2021

Introduction

In November 2020, a new SARS-COV-2 variant or the ‘Kent variant’ emerged in the UK, and became the dominant UK SARS-COV-2 variant, demonstrating faster transmission than the original variant, which rapidly died out. However, it is unknown if this altered the overall course of the pandemic as genomic analysis was not common place at the outset and other factors such as the climate could alter the viral transmission rate over time. We aimed to test the hypothesis that the overall observed viral transmission was not altered by the emergence of the new variant, by testing a model generated earlier in the pandemic based on lockdown stringency, temperature and humidity.

Methods

From 1/1/20 to 4/2/21, the daily incidence of SARS-COV-2 deaths and the overall stringency of National Lockdown policy on each day was extracted from the Oxford University Government response tracker. The daily average temperature and humidity for London was extracted from Wunderground.com.

The viral reproductive rate was calculated on a daily basis from the daily mortality data for each day. The correlation between log10 of viral reproductive rate and lockdown stringency and weather parameters were compared by Pearson correlation to determine the time lag associated with the greatest correlation.

A multivariate model for the log10 of viral reproductive rate was constructed using lockdown stringency, temperature and humidity for the period 1/1/20 to 30/9/20. This model was extrapolated forward from 1/10/20 to 4/2/21 and the predicted viral reproductive rate, daily mortality and cumulative mortality were compared with official data.

Results

On multivariate linear regression, the optimal model had and R2 0f 0.833 for prediction of log10 viral reproductive rate 13 days later in the model construction period, with (coefficient, probability) lockdown stringency (−0.0109, p=0.0000), humidity (0.0038, p=0.0041) and temperature (−0.0035, p=0.0008). When extrapolated to the validation period (1/10/20 to 4/2/21), the model was highly correlated with daily (Pearson coefficient 0.88, p=0.0000) and cumulated SARS-COV-2 mortality (Pearson coefficient 0.99, p=0.0000).

Conclusion

The course of the SARS-COV-2 pandemic in the UK seems highly predicted by an earlier model based on the lockdown stringency, humidity and temperature and unaltered by the emergence of a newer viral genotype.
Associations of the BNT162b2 COVID-19 vaccine effectiveness with patient age and comorbidities
Authors: Yelin Idan , Katz Rachel , Herzel Esma , Berman-Zilberstein Tamar , Ben-Tov Amir , Kuint Jacob , Gazit Sivan , Patalon Tal , Chodick Gabriel , Kishony Roy
Published: March 2021

Vaccinations are considered the major tool to curb the current SARS-CoV-2 pandemic. A randomized placebo-controlled trial of the Pfizer BNT162b2 vaccine has demonstrated a 95% efficacy in preventing COVID-19 disease. These results are now corroborated with statistical analyses of real-world vaccination rollouts, but resolving vaccine effectiveness across demographic groups and its interaction with comorbidities is challenging. Here, applying a multivariable logistic regression analysis approach to a large patient-level dataset, including SARS-CoV-2 tests, vaccine inoculations and personalized demographics, we model vaccine effectiveness at daily resolution and its interaction with sex, age and comorbidities. Vaccine effectiveness gradually increased post day 12 of inoculation, then plateaued, around 35 days, reaching 95.0% [CI 93.4%-96.3%] for all infections and 99.5% [CI 97.0%-99.9%] for symptomatic infections. While effectiveness was on average uniform for men and women, it declined mildly but significantly with age especially for males. Effectiveness further declined for people with type 2 diabetes, COPD, and immunosuppression, as well as cardiac disease in females. Quantifying real-world vaccine effectiveness, including both biological and behavioral effects, our analysis provides initial measurement of vaccine effectiveness across demographic groups.
Patterns of compliance with COVID-19 preventive behaviours: a latent class analysis of 20,000 UK adults
Authors: Wright Liam , Steptoe Andrew , Fancourt Daisy
Published: March 2021

Background

Governments have implemented a range of measure to tackle COVID-19, primarily focusing on changing citizens’ behaviours in order to lower transmission of the virus. Few studies have looked at the patterns of compliance with different measures within individuals: whether people comply with all measures or selectively choose some but not others. Such research is important for designing interventions to increase compliance.

Methods

We used cross-sectional data from 20,947 UK adults in the COVID-19 Social Study collected 17 November – 23 December 2020. Self-report compliance was assessed with six behaviours: mask wearing, hand washing, indoor household mixing, outdoor household mixing, social distancing, and compliance with other guidelines. Patterns of compliance behaviour were identified using latent class analysis, and multinomial logistic regression was used to assess demographic, socioeconomic and personality predictors of behaviour patterns.

Results

We selected a four latent class solution. Most individuals reported similar levels of compliance across the six behaviour measures. High levels of compliance was the modal response. Lower self-reported compliance was related to young age, high risk-taking behaviour, low confidence in government, and low empathy, among other factors. Looking at individual behaviours, mask wearing had the highest level of compliance whilst compliance with social distancing was relatively low.

Conclusion

Results suggest that individuals choose to comply with all guidelines, rather than some but not others. Strategies to increase compliance should focus on increasing general motivations to comply alongside specifically encouraging social distancing.
RCytoGPS: An R Package for Reading and Visualizing Cytogenetics Data
Authors: Abrams Zachary B. , Tally Dwayne G. , Abruzzo Lynne V. , Coombes Kevin R.
Published: March 2021

Cytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology.

Availability and Implementation

Freely available athttps://CRAN.R-project.org/package=RCytoGPS

Supplementary information

Supplementary data are available atBioinformaticsonline.
BugSeq 16S: NanoCLUST with Improved Consensus Sequence Classification
Authors: Jung Ana , Chorlton Samuel D
Published: March 2021

NanoCLUST has enabled species-level taxonomic classification from noisy nanopore 16S sequencing data for BugSeq’s users and the broader nanopore sequencing community. We noticed a high misclassification rate of NanoCLUST-derived consensus 16S sequences due to its use of BLAST top hit taxonomy assignment. We replaced the consensus sequence classifier of NanoCLUST with QIIME2’s VSEARCH-based classifier to enable greater accuracy. We use mock microbial community and clinical 16S sequencing data to show that this replacement results in significantly improved nanopore 16S accuracy (over 5% recall and 19% precision), and make this new tool (BugSeq 16S) freely available for academic use atBugSeq.com/free.
Response of soil and vegetation in a warm-temperate Pine forest to intensive biomass harvests, phosphorus fertilisation, and wood ash application
Authors: Augusto Laurent , Beaumont Florent , Nguyen Christophe , Fraysse Jean-Yves , Trichet Pierre , Meredieu Céline , Vidal David , Sappin-Didier Valérie
Published: March 2021

Background and Aims

Concerns about climate change and carbon economy have prompted the promotion of alternative energy sources, including forest-based bioenergy. An evaluation of the environmental consequences of intensive harvests (stumps and roots, and also branches and foliage) for energy wood supply, and use of wood-ash recycling as a compensatory practice, helps in the evaluation of the use of forest biomass for energy production.

Methods

We made use of records from a split-plot experimental site crossing four different intensities of biomass harvesting (Stem-Only Harvest [SOH], Aboveground Additional Harvest [AAH], Belowground Additional Harvest [BAH], and Whole-Tree Harvest [WTH]) and three compensation methods (control [C], wood ash application [A] and phosphorus fertilisation [P]) to evaluate, in the 11-years-old stand (maritime pine:Pinus pinaster) that followed the biomass exports of the former stand, their effects on nutrient budgets, tree growth, soil fertility, chemical properties and soil carbon. This site is located in a forest on a poor soil, under a warm temperate climate (SW France).

Key results

Despite their low additional biomass exports (+10% for AAH to +34% for WTH), the non-conventional harvest practices exported much higher quantities of nutrients than the conventional SOH technique (for example +145% for N and K in WTH). Consequently, these treatments had negative effects on the soil nutritive status. Additional biomass harvests impacted the soil organic matter content, with negative effects on P-organic, soil cation exchange capacity, exchangeable Ca, and most extractible nutrients. However, data suggested that tree growth and foliage nutrient content had not yet been significantly impacted by harvest treatments, whereas tree nutritional status was improved by P-fertiliser or wood ash. As expected, we observed a positive effect of wood ash application on soil pH and nutrient content but, like additional harvests, wood ash application decreased the pool of soil organic carbon (~10% of the initial stock with ~7% of N-totallosses).

Conclusions

Overall, this factorial experiment showed that exporting more forest biomass due to the additional harvesting of tree canopies, stumps and roots had negative consequences on the ecosystem biogeochemistry. Additional harvests have aggravated the poverty of the already oligotrophic soil, and decreased the soil organic carbon content. Importantly, applying nutrients as fertiliser or wood ash did not compensate for all the negative impacts of biomass exports and the method of wood ash recycling in forests could even decrease the soil organic carbon.
Response ofrhizobialstrains on biochemical traits and nutrient uptake in Mungbean Vigna radiata L. Wilczek under moisture stress
Authors: Sapna  , Sharma K. D
Published: March 2021

The present study was conducted to assess the biochemical responses and nutrient uptake in response torhizobialinoculations in mungbean, and to screen therhizobialisolates for drought tolerance. A field experiment was designed in randomized block design and replicated thrice duringkharif2016 at Crop Physiology Field Area, CCS, Hisar. The experiment consisted of two levels of treatments (1) without inoculation (only RDF) and (2) with inoculation (RDF with combination of fiverhizobialstrains viz.Vigna703 + PSB strain P-36, MR 63, MR 54, MB 17a and MH 8b2) and two environments i.e. rainfed (no post sowing irrigation) and irrigated. Membrane stability index, leghaemoglobin content, chlorophyll content reduced by 17.7 %, 24.5% and 2.9% resp. under rainfed conditions while the plants inoculated withrhizobialisolate MR63 and MB 17a showed greater chlorophyll content (20.2% and 16.2%), LHb (29.1% and 22.9%) and MSI (19.4% and 17.9%) and enhanced nutrient uptake over RDF.
Thermal biology of two sympatric Lacertids lizards (Lacerta diplochondrodesandParvilacerta parva) from Western Anatolia
Authors: Şahin Mehmet Kürşat , Kuyucu Arda Cem
Published: March 2021

Sympatric lizard species differing in morphology present convenient models for studying the differentiation in thermal behavior and the role of morphological differences in thermal biology. Here we studied the thermal biology of two sympatric lizard species which occur together sympatrically in western Anatolia, Frig Valley. These two species differ in body size, with the largerLacerta diplochondrodesand smallerParvilacerta parva. Field body temperatures of the individuals belonging to both species were recorded in the activity period. Additionally, several environmental parameters including solar radiation, substrate temperature, air temperature and wind speed were also monitored to investigate the relative effect of these abiotic parameters on thermal biology of the two species. The field body temperature and temperature excess (difference between body and substrate temperature) of two species while being relatively close to each other, showed seasonal differences. Solar radiation, substrate temperature and air temperature were the main effective factors on thermal biology in the field. Additionally, although body size did not have a direct significant effect on body temperature or temperature excess, the interaction between body size and wind were effective on temperature excess. In conclusion, our study partially supports the conservation of thermal biology of related lizard species.
Proteome remodeling in theMycobacterium tuberculosisPknG knockout: molecular evidence for the role of this kinase in cell envelope biogenesis and hypoxia response
Authors: Lima Analía , Leyva Alejandro , Rivera Bernardina , Portela María Magdalena , Gil Magdalena , Cascioferro Alessandro , Lisa María-Natalia , Wehenkel Annemarie , Bellinzoni Marco , Carvalho Paulo C. , Batthyány Carlos , Alvarez María N. , Brosch Roland , Alzari Pedro M. , Durán Rosario
Published: March 2021

Mycobacterium tuberculosis, the etiological agent of tuberculosis, is among the deadliest human pathogens. One ofM. tuberculosis’s pathogenic hallmarks is its ability to persist in a dormant state in the host for long periods, reinitiating the infectious cycle when favorable environmental conditions are found. Thus, it is not surprising that this pathogen has developed different mechanisms to withstand the stressful conditions found in the host. In particular, the Ser/Thr protein kinase PknG has gained special relevance since it regulates nitrogen metabolism and facilitates bacterial survival inside macrophages. Nevertheless, the molecular mechanisms underlying these effects are far from being elucidated. To further investigate these issues, we performed quantitative proteomics analyses of protein extracts fromM. tuberculosisH37Rv and a mutant derivative lackingpknG. Our results showed that in the absence of PknG the mycobacterial proteome was remodeled since 5.7% of the proteins encoded byM. tuberculosispresented significant changes in its relative abundance when compared to the wild-type strain. The main biological processes affected bypknGdeletion were the biosynthesis of cell envelope components and the response to hypoxic conditions. As many as 13 DosR-regulated proteins were underrepresented in thepknGdeletion mutant, including the distinctive Hrp-1, which was found to be 12-fold decreased according to Parallel Reaction Monitoring experiments. Altogether, the results presented here allow us to postulate that PknG regulation of bacterial adaptation to stress conditions might be an important mechanism underlying its reported effect on intracellular bacterial survival.