bluuebunny/crossref_metadata_2025 huggingface dataset:
Prefrontal cortical activity predicts the extra-place field spiking of hippocampal place cells
Authors: Yu Jai Y. , Frank Loren M.
Published: November 2020

The receptive field of a neuron describes the regions of a stimulus space where the neuron is consistently active. Sparse spiking outside of the receptive field is often considered to be noise, rather than a reflection of information processing. Whether this characterization is accurate remains unclear. We therefore contrasted the sparse, temporally isolated spiking of hippocampal CA1 place cells to the consistent, temporally adjacent spiking seen within their spatial receptive fields (“place fields”). We found that isolated spikes, which occur during locomotion, are more strongly phase coupled to hippocampal theta oscillations than adjacent spikes and, surprisingly, transiently express coherent representations of non-local spatial representations. Further, prefrontal cortical activity is coordinated with, and can predict the occurrence of future isolated spiking events. Rather than local noise within the hippocampus, sparse, isolated place cell spiking reflects a coordinated cortical-hippocampal process consistent with the generation of non-local scenario representations during active navigation.
Taxonomy of the apicomplexan symbionts of coral, including Corallicolida ord. nov., reassignment of the genus Gemmocystis, and description of new species Corallicola aquarius gen. nov. sp. nov. and Anthozoaphila gnarlus gen. nov. sp. nov
Authors: Kwong Waldan K. , Irwin Nicholas A.T. , Mathur Varsha , Na Ina , Okomoto Noriko , Vermeij Mark J.A. , Keeling Patrick J.
Published: November 2020

Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called ‘corallicolids’, are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, Gemmocystis cylindrus (described from the coral Dendrogyra cylindrus), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, Corallicola aquarius gen. nov. sp. nov. from its Rhodactis sp. host, and also describe a second species, Anthozoaphila gnarlus gen. nov. sp. nov., from the coral host Madracis mirabilis. Finally, we propose reassigning the incertae sedis taxon G. cylindrus from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.
Excess mortality across regions of Europe during the first wave of the COVID-19 pandemic – impact of the winter holiday travelling and government responses
Authors: Björk Jonas , Mattisson Kristoffer , Ahlbom Anders
Published: November 2020

Background

This aggregated population study of 219 regions in 11 European countries investigated the effect of the seemingly quasi-randomly assigned school winter holiday week on excess mortality associated with the COVID-19 pandemic during spring 2020. A secondary aim was to evaluate the impact of stringency and timing of the government responses to the early inflow of infected cases.

Methods

Regional data on mortality week 14-23 in 2020 compared with the same period 2015-2019 were retrieved from Eurostat and national statistical agencies. Data on initial government responses were obtained from the Oxford COVID-19 Government Response Tracker. Variance-weighted least square regression was used with further adjustment for population density and age distribution.

Results

Being a region with winter holiday exclusively in week 9 was in the adjusted analysis associated with 16 weekly excess deaths (95% confidence interval 13 to 20) per million inhabitants, which corresponds to 38% of the excess mortality during the study period in these regions. A more stringent response implemented in week 11, corresponding to 10 additional units on the 0-100 ordinal scale, was associated with 20 fewer weekly deaths (95% confidence interval 18 to 22) per million inhabitants.

Conclusions

Travelling during winter holiday in week 9 was an amplifying event that contributed importantly to the excess mortality observed in the study area during the spring 2020. Timely government responses to the resulting early inflow of cases was associated with lower excess mortality.
First results on diversity patterns and selective sweeps in a Southeast European panel of maize inbred lines as combined with two West European panels
Authors: Galić Vlatko , Anđelković Violeta , Kravić Natalija , Grčić Nikola , Ledenčan Tatjana , Jambrović Antun , Zdunić Zvonimir , Nicolas Stéphane D , Charcosset Alain , Šatović Zlatko , Šimić Domagoj
Published: November 2020

Abstract: More than one third of European grain maize is produced in South Eastearn Europe (SEE) and utilization of historical maize material developed in SEE for its favorable alleles and diversity has long been speculated. However, molecular information on diversity of the SEE maize genetic material is scarce. The objectives of this study were i) to analyze diversity patterns in a large panel of densely genotyped historical accessions from SEE, ii) to compare the data with those obtained from other two European panels, and iii) to identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to SEE conditions. 572 accessions of the historical inbred lines from Maize Research Institute Zemun Polje gene bank representing the SEE material were genotyped using the 600k maize genotyping Axiom array. The genotyping results were merged with two European panels DROPS and TUM. Genetic structure and diversity were analyzed using neighbor-joining cladogram, PcoA, Admixture, Structure and sNMF. To detect the selective sweep signals, Tajima's D statistic and RAiSD were employed. The best number of ancestral populations was K=7, whereby one of them is a subpopulation containing inbreds belong exclusively to the SEE panel. The prevalence of inbreds linked to historical US inbred lines Wf9, Oh43, Pa91 and A374 was detected in SEE. Possible soft selective sweep was detected in chromosome 2 in region harboring a gene linked to promotion of flowering FPF1. Additional scan for selective sweeps using the RAiSD methodology yielded four signals in chromosomes 5 and 6, all in gene-rich regions. Several candidates of selection were identified, influencing the plant morphology and adaptation. Our study provides the first step towards the re-utilization of the SEE genetic materials for use in modern maize breeding. Phenotypic analysis is needed for assessment of SEE accessions for favorable alleles, and identification of breeding targets.
Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics
Authors: Markin C.J. , Mokhtari D.A. , Sunden F. , Appel M.J. , Akiva E. , Longwell S.A. , Sabatti C. , Herschlag D. , Fordyce P.M.
Published: November 2020

Systematic and extensive investigation of enzymes is needed to understand their extraordinary efficiency and meet current challenges in medicine and engineering. We present HT-MEK, a microfluidic platform for high-throughput expression, purification, and characterization of >1500 enzyme variants per experiment. For 1036 mutants of the alkaline phosphatase PafA, we performed >670,000 reactions to determine >5000 kinetic and physical constants for multiple substrates and inhibitors. These constants allowed us to uncover extensive kinetic partitioning to a misfolded state and isolate catalytic effects, revealing spatially contiguous “regions” of residues linked to particular aspects of function. These regions included active-site proximal residues but also extended to the enzyme surface, providing a map of underlying architecture that could not be derived from existing approaches. HT-MEK, using direct and coupled fluorescent assays, has future applications to a wide variety of problems ranging from understanding molecular mechanisms to medicine to engineering and design.

One Sentence Summary

HT-MEK, a microfluidic platform for high-throughput, quantitative biochemistry, reveals enzyme architectures shaping function.
The rocaglate CR-31-B (-) inhibits SARS-CoV-2 replication at non-cytotoxic, low nanomolar concentrationsin vitroandex vivo
Authors: Müller Christin , Obermann Wiebke , Karl Nadja , Wendel Hans-Guido , Taroncher-Oldenburg Gaspar , Pleschka Stephan , Hartmann Roland K. , Grünweller Arnold , Ziebuhr John
Published: November 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus in the subgenusSarbecoviruscauses a respiratory disease with varying symptoms referred to as coronavirus disease 2019 (COVID-19) and is responsible for a pandemic that started in early 2020. With no vaccines or effective antiviral treatments available, and infection and fatality numbers continuing to increase globally, the quest for novel therapeutic solutions remains an urgent priority. Rocaglates, a class of plant-derived cyclopenta[b]benzofurans, exhibit broad-spectrum antiviral activity against positive- and negative-sense RNA viruses. This compound class inhibits eukaryotic initiation factor 4A (eIF4A)-dependent mRNA translation initiation, resulting in strongly reduced viral RNA translation. The synthetic rocaglate CR-31-B (-) has previously been shown to inhibit the replication of human coronaviruses, such as HCoV-229E and MERS-CoV, as well as Zika-, Lassa-, Crimean Congo hemorrhagic fever virus in primary cells. Here, we assessed the antiviral activity of CR-31-B (-) against SARS-CoV-2 using bothin vitroandex vivocell culture models. In African green monkey Vero E6 cells, CR-31-B (-) inhibited SARS-CoV-2 replication with an EC50of ~1.8 nM. In line with this, viral protein accumulation and replication/transcription complex formation were found to be strongly reduced by this compound. In anex vivoinfection system using human airway epithelial cells, CR-31-B (-) was found to cause a massive reduction of SARS-CoV-2 titers by about 4 logs to nearly non-detectable levels. The data reveal a potent anti-SARS-CoV-2 activity by CR-31-B (-), corroborating previous results obtained for other coronaviruses and supporting the idea that rocaglates may be used in first-line antiviral intervention strategies against novel and emerging RNA virus outbreaks.
Ipomoeassin-F inhibits thein vitrobiogenesis of the SARS-CoV-2 spike protein and its host cell membrane receptor
Authors: O’Keefe Sarah , Roboti Peristera , Duah Kwabena B. , Zong Guanghui , Schneider Hayden , Shi Wei Q. , High Stephen
Published: November 2020

In order to produce proteins essential for their propagation, many pathogenic human viruses, including SARS-CoV-2 the causative agent of COVID-19 respiratory disease, commandeer host biosynthetic machineries and mechanisms. Three major structural proteins, the spike, envelope and membrane proteins, are amongst several SARS-CoV-2 components synthesised at the endoplasmic reticulum (ER) of infected human cells prior to the assembly of new viral particles. Hence, the inhibition of membrane protein synthesis at the ER is an attractive strategy for reducing the pathogenicity of SARS-CoV-2 and other obligate viral pathogens. Using anin vitrosystem, we demonstrate that the small molecule inhibitor ipomoeassin F (Ipom-F) potently blocks the Sec61-mediated ER membrane translocation/insertion of three therapeutic protein targets for SARS-CoV-2 infection; the viral spike and ORF8 proteins together with angiotensin-converting enzyme 2, the host cell plasma membrane receptor. Our findings highlight the potential for using ER protein translocation inhibitors such as Ipom-F as host-targeting, broad-spectrum, antiviral agents.
High-throughput phenotyping methods for quantifying hair fiber morphology
Authors: Lasisi Tina , Zaidi Arslan A. , Webster Timothy Harding , Stephens Nicholas Bradley , Routch Kendall , Jablonski Nina Grace , Shriver Mark David
Published: November 2020

Quantifying the continuous variation in human scalp hair morphology is of interest to anthropologists, geneticists, dermatologists and forensic scientists, but existing methods for studying hair form are time-consuming and not widely used. Here, we present a high-throughput sample preparation protocol for the imaging of both longitudinal (curvature) and cross-sectional scalp hair morphology. Additionally, we describe and validate a new Python package designed to process longitudinal and cross-sectional hair images, segment them, and provide measurements of interest. Lastly, we apply our methods to an admixed African-European sample (n=140), demonstrating the benefit of quantifying hair morphology over qualitative classification or racial categories, and providing evidence against the long-held belief that cross-sectional morphology predicts curvature.
High-throughput characterization of photocrosslinker-bearing ion channel variants to map residues critical for function and pharmacology
Authors: Braun Nina , Friis Søren , Ihling Christian , Sinz Andrea , Andersen Jacob , Pless Stephan A.
Published: November 2020

Incorporation of non-canonical amino acids (ncAAs) can endow proteins with novel functionalities, such as crosslinking or fluorescence. In ion channels, the function of these variants can be studied with great precision using standard electrophysiology, but this approach is typically labor intensive and low throughput. Here, we establish a high-throughput protocol to conduct functional and pharmacological investigations of ncAA-containing hASIC1a (human acid-sensing ion channel 1a) variants in transiently transfected mammalian cells. We introduce three different photocrosslinking ncAAs into 103 positions and assess the function of the resulting 309 variants with automated patch-clamp (APC). We demonstrate that the approach is efficient and versatile, as it is amenable to assessing even complex pharmacological modulation by peptides. The data show that the acidic pocket is a major determinant for current decay and live-cell crosslinking provides insight into the hASIC1a-psalmotoxin-1 interaction. Further, we provide evidence that the protocol can be applied to other ion channels, such as P2X2 and GluA2 receptors. We therefore anticipate the approach to enable future APC-based studies of ncAA-containing ion channels in mammalian cells.
Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking
Authors: Schuller Marion , Correy Galen J. , Gahbauer Stefan , Fearon Daren , Wu Taiasean , Díaz Roberto Efraín , Young Iris D. , Martins Luan Carvalho , Smith Dominique H. , Schulze-Gahmen Ursula , Owens Tristan W. , Deshpande Ishan , Merz Gregory E. , Thwin Aye C. , Biel Justin T. , Peters Jessica K. , Moritz Michelle , Herrera Nadia , Kratochvil Huong T. ,   QCRG Structural Biology Consortium, Aimon Anthony , Bennett James M. , Neto Jose Brandao , Cohen Aina E. , Dias Alexandre , Douangamath Alice , Dunnett Louise , Fedorov Oleg , Ferla Matteo P. , Fuchs Martin , Gorrie-Stone Tyler J. , Holton James M. , Johnson Michael G. , Krojer Tobias , Meigs George , Powell Ailsa J. , Rack Johannes Gregor Matthias , Rangel Victor L , Russi Silvia , Skyner Rachael E. , Smith Clyde A. , Soares Alexei S. , Wierman Jennifer L. , Zhu Kang , Jura Natalia , Ashworth Alan , Irwin John , Thompson Michael C. , Gestwicki Jason E. , von Delft Frank , Shoichet Brian K. , Fraser James S. , Ahel Ivan
Published: November 2020

The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
Adsorption of Azo Dyes by a Novel Bio-Nanocomposite Based on Whey Protein Nanofibrils and Nano-clay: Equilibrium Isotherm and Kinetic Modeling
Authors: Aqdam ShabBoo Rahimi , Otzen Daniel E. , Mahmoodi Niyaz Mohammad , Morshedi Dina
Published: November 2020

Excessive discharge of hazardous azo dyes into the aquatic ecosystem is a global environmental concern. Here, we develop a green approach to remediate dye pollutions in water by fabricating an easy-separable bio-nanocomposite, based on whey protein concentrate, its nanofibrils, and montmorillonite nano-clay. To characterize the nanocomposite, we used SEM, FT-IR, XRD, and BET techniques. Nanofibrils lead to a uniform dispersion of montmorillonite in the whey protein matrix and also reinforce the nanocomposite. The adsorption efficacy was monitored in a batch system, using cationic dyes (Chrysoidine-G, Bismarck brown-R), reactive dyes (reactive black-5, reactive orange-16), acid dyes (acid red-88, acid red-114), and direct dyes (direct violet-51, Congo red). This nanocomposite adsorbed different dye classes, cationic dyes quicker (> 82%, after 4 h), and reactive dyes slower. Then, the effect of initial dye concentration, pH, contact time, adsorbent dose, and temperature on Chrysoidine-G adsorption was explored. The adsorbent showed a high removal (>93%) for a wide concentration range of Chrysoidine-G, also acidic pH and higher temperature are more favorable for the process. Equilibrium adsorption parameters were reasonably fitted with a linear (Nernst) isotherm model. The results indicated the existence of an unlimited number of absorption sites,i.e.no saturation was achieved under our experimental conditions (qmax(Exp)= 731 mg/g). Kinetic data were fitted with pseudo-second-order and intra-particle diffusion models. We conclude that this nanocomposite is a green adsorbent with potential use for wastewater treatment and related purposes.

Highlights

We produced an easy-separable bio-nanocomposite using whey nanofibrils and MMT, with high adsorption capacity

Nanofibrils help disperse MMT particles uniformly in the WP matrix

The adsorbent’s performance was compared to the adsorbents in absence of MMT and nanofibrils

This composite adsorbs cationic, anionic, direct and reactive azo dyes with different kinetics

Adsorption isotherms and kinetics are studied in detail
A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro
Authors: Cheng Mary Hongying , Porritt Rebecca A. , Rivas Magali Noval , Krieger James M , Ozdemir Asli Beyza , Garcia Gustavo , Arumugaswami Vaithilingaraja , Fries Bettina C. , Arditi Moshe , Bahar Ivet
Published: November 2020

We recently discovered a superantigen-like motif, similar to Staphylococcal enterotoxin B (SEB), near the S1/S2 cleavage site of SARS-CoV-2 Spike protein, which might explain the multisystem-inflammatory syndrome (MIS-C) observed in children and cytokine storm in severe COVID-19 patients. We show here that an anti-SEB monoclonal antibody (mAb), 6D3, can bind this viral motif, and in particular its PRRA insert, to inhibit infection by blocking the access of host cell proteases, TMPRSS2 or furin, to the cleavage site. The high affinity of 6D3 for the furin-cleavage site originates from a poly-acidic segment at its heavy chain CDR2, a feature shared with SARS-CoV-2-neutralizing mAb 4A8. The affinity of 6D3 and 4A8 for this site points to their potential utility as therapeutics for treating COVID-19, MIS-C, or common cold caused by human coronaviruses (HCoVs) that possess a furin-like cleavage site.
Protease OMA1 Modulates Mitochondrial Bioenergetics and Ultrastructure through Dynamic Association with MICOS Complex
Authors: Viana Martonio Ponte , Levytskyy Roman M. , Anand Ruchika , Reichert Andreas S. , Khalimonchuk Oleh
Published: November 2020

Remodeling of mitochondrial ultrastructure is a complex dynamic process that is critical for a variety of mitochondrial functions and apoptosis. Although the key regulators of this process - mitochondrial contact site and cristae junction organizing system (MICOS) and GTPase Optic Atrophy 1 (OPA1) have been characterized, the mechanisms behind this regulation remain incompletely defined. Here, we found that in addition to its role in mitochondrial division, metallopeptidase OMA1 is required for maintenance of contacts between the inner and outer membranes through a dynamic association with MICOS. This association is independent of OPA1, appears to be mediated via the MICOS subunit MIC60, and is important for stability of MICOS machinery and the inner-outer mitochondrial membrane contacts. We find that OMA1-MICOS relay is required for stability of respiratory supercomplexes, optimal bioenergetic output in response to cellular insults, and apoptosis. Loss of OMA1 affects these activities; remarkably it can be partially compensated for by an artificial MICOS-emulating tether protein that bridges the inner and outer mitochondrial membranes. Our data show that OMA1-mediated support of mitochondrial ultrastructure is required for maintenance of mitochondrial architecture and bioenergetics under both basal and homeostasis-challenging conditions, and suggest a previously unrecognized role for this protease in mitochondrial physiology.
Snowball Earths, population bottlenecks, andProchlorococcusevolution
Authors: Zhang Hao , Sun Ying , Zeng Qinglu , Crowe Sean A. , Luo Haiwei
Published: November 2020

Prochlorococcusare the most abundant photosynthetic organisms in the modern ocean. A massive DNA loss event occurred in their early evolutionary history, leading to highly reduced genomes in nearly all lineages, as well as enhanced efficiency in both nutrient uptake and light absorption. The environmental landscape that shaped this ancient genome reduction, however, remained unknown. Through careful molecular clock analyses, we established that thisProchlorococcusgenome reduction occurred during the Neoproterozoic Snowball Earth climate catastrophe. The lethally low temperature and exceedingly dim light during the Snowball Earth event would have inhibitedProchlorococcusgrowth and proliferation and caused severe population bottlenecks. These bottlenecks are recorded as an excess of deleterious mutations that accumulated across genomic regions in the descendant lineages.Prochlorococcusadaptation to extreme environmental conditions during Snowball Earth intervals can be inferred by tracing the evolutionary paths of genes that encode key metabolic potential. This metabolic potential includes modified lipopolysaccharide structure, strengthened peptidoglycan biosynthesis, the replacement of a sophisticated circadian clock with an hourglass-like mechanism that resets daily for dim light adaption, and the adoption of ammonia diffusion as an efficient membrane transporter-independent mode of nitrogen acquisition. In this way, the Neoproterozoic Snowball Earth event altered the physiological characters ofProchlorococcus, shaping their ecologically vital role as the most abundant primary producers in the modern oceans.
Activation of ARTD2/PARP2 by DNA damage induces conformational changes relieving enzyme autoinhibition
Authors: Obaji Ezeogo , Maksimainen Mirko M. , Galera-Prat Albert , Lehtiö Lari
Published: November 2020

Human ARTD2/PARP2 is an ADP-ribosyltransferase which, when activated by 5’- phosphorylated DNA ends, catalyzes poly-ADP-ribosylation of itself, other proteins and DNA. A crystal structure of ARTD2 in complex with an activating 5’-phosphorylated DNA shows that the WGR domain bridges the dsDNA gap and joins the DNA ends. This DNA binding results in major conformational changes, reorganization of helical fragments, in the ARTD2 regulatory domain. Comparison of ARTD1-3 crystal structures reveal how binding to a DNA damage site leads to formation of a catalytically competent conformation capable of binding substrate NAD+and histone PARylation factor 1 changing the ARTD2 residue specificity from glutamate to serine when initiating DNA repair processes. The structure also reveals how the conformational changes in the autoinhibitory regulatory domain would promote the flexibility needed by the enzyme to reach the target macromolecule for ADP-ribosylation.
A comprehensive analysis of vomeronasal organ transcriptome reveals variable gene expression depending on age and function in rabbits
Authors: Villamayor PR , Robledo D , Fernández C , Gullón J , Quintela L , Sánchez-Quinteiro P , Martínez P
Published: November 2020

The vomeronasal organ (VNO) is a chemosensory organ specialized in the detection of pheromones and consequently the regulation of behavioural responses mostly related to reproduction. VNO shows a broad variation on its organization, functionality and gene expression in vertebrates, and although the species analyzed to date have shown very specific features, its expression patterns have only been well-characterized in mice. Despite rabbits represent a model of chemocommunication, unfortunately no genomic studies have been performed on VNO of this species to date. The capacity of VNO to detect a great variety of different stimuli suggests a large number of genes with complex organization to support this function. Here we provide the first comprehensive gene expression analysis of the rabbit VNO through RNA-seq across different sexual maturation stages. We characterized the VNO transcriptome, updating the number of the two main vomeronasal receptor (VR) families, 129 V1R and 70 V2R. Among others, the expression of transient receptor potential channel 2 (TRPC2), a crucial cation channel generating electrical responses to sensory stimulation in vomeronasal neurons, along with the specific expression of some fomyl-peptide receptors and H2-Mv genes, both known to have specific roles in the VNO, revealed a the particular gene expression repertoire of this organ, but also its singularity in rabbits. Moreover, juvenile and adult VNO transcriptome showed consistent differences, which may indicate that these receptors are tuned to fulfill specific functions depending on maturation age. We also identified VNO-specific genes, including most VR and TRPC2, thus confirming their functional association with the VNO. Overall, these results represent the genomic baseline for future investigations which seek to understand the genetic basis of behavioural responses canalized through the VNO.

HIGHLIGHTS

First description of the rabbit vomeronasal organ (VNO) transcriptome

VNO contains a unique gene repertoire depending on the species

High fluctuation of the VNO gene expression reveals changes dependent on age and specific functions

Most vomeronasal-receptors (VR) and transient receptor potential channel 2 (TRPC2) genes are VNO-specific

Reproduction-related genes shows a wide expression pattern
Evidence for co-evolution of masking and circadian phase inDrosophila melanogaster
Authors: Ghosh Arijit , Sharma Pragya , Dansana Shephali , Sheeba Vasu
Published: November 2020

Heritable variation in the timing or circadian phases of rhythmic events with respect to daily time cues gives rise to chronotypes. Despite its importance, the mechanisms (clock or non-clock) regulating chronotypes remain elusive. Using artificial laboratory selection for divergent phasing of emergence of adults from pupae, our group has derived populations ofDrosophila melanogasterwhich areearlyandlatechronotypes for eclosion rhythm. Several circadian rhythm characteristics of these populations have since been described. We hypothesized that our selection protocol has inadvertently resulted in selection for masking, a non-clock phenomenon, in theearlychronotype due to the placement of our selection window (which includes the lights-ON transition). Based on theoretical predictions and previous studies on our populations, we designed experiments to discriminate between enhanced masking to light versus circadian clock mediated changes in determining enhanced emergence in the morning window in ourearlychronotypes. Using a series of phase-shift protocols, LD-DD transition, andT-cycle experiments, we find that ourearlychronotypes have evolved positive masking, and their apparent entrained phases are largely contributed by masking. Through skeletonT-cycle experiments, we find that in addition to the evolution of greater masking, ourearlychronotypes have also evolved advanced phase of entrainment. Furthermore, our study systematically outlines experimental approaches to examine relative contributions of clock versus non-clock control of an entrained behavior. Although it has previously been suggested that masking may confer an adaptive advantage to organisms, here we provide experimental evidence for the evolution of masking as a mean of phasing of an entrained rhythm that can complement clock control of an entrained behavior.
Expression of type I interferon-associated genes at point of antiretroviral therapy interruption predicts time to HIV virological rebound
Authors: Zacharapoulou Panagiota , Marchi Emanuele , Ogbe Ane , Robinson Nicola , Brown Helen , Jones Mathew , Parolini Lucia , Pace Matthew , Grayson Nicholas , Kaleebu Pontiano , Rees Helen , Fidler Sarah , Goulder Philip , Klenerman Paul , Frater John
Published: November 2020

Although certain individuals with HIV infection can stop antiretroviral therapy (ART) without evidence of viral load rebound, the mechanisms under-pinning ‘post-treatment control’ remain unclear. Twelve individuals who had received 12 months of ART from primary HIV infection and then undertook a TI were sampled at the time of stopping therapy. Using RNA-Seq we explored gene expression in CD4 T cells to look for evidence of a mechanism that might underpin virological rebound and lead to discovery of an associated biomarker. Using independent analysis tools, genes associated with the type I interferon response were strongly associated with a delayed time to viral rebound following TI. These are the first data we are aware of that link transcriptomic signatures associated with innate immunity with control following TI. While these results need to be confirmed in larger trials, they could help define a strategy for new therapies and identify new biomarkers for remission.
Comparing short and long batteries to assess deficits and their neural bases in stroke aphasia
Authors: Halai Ajay D. , De Dios Perez Blanca , Stefaniak James D. , Lambon Ralph Matthew A.
Published: November 2020

Multiple language assessments are necessary for diagnosing, characterising and quantifying the multifaceted deficits observed in many patients’ post-stroke. Current language batteries, however, tend to be an imperfect trade-off between time and sensitivity of assessment. There have hitherto been two main types of battery. Extensive batteries provide thorough information but are impractically long for application in clinical settings or large-scale research studies. Clinically-targeted batteries tend to provide superficial information about a large number of language skills in a relatively short period of time by reducing the depth of each test but, consequently, can struggle to identify mild deficits, qualify the level of each impairment or reveal the underlying component structure. In the current study, we compared these batteries across a large group of individuals with chronic stroke aphasia to determine their utility. In addition, we developed a data-driven reduced version of an extensive battery that maintained sensitivity to mild impairment, ability to grade deficits and the component structure. The underlying structure of these three language batteries (extensive, shallow and data-reduced) was analysed using cross-validation analysis and principal component analysis. This revealed a four-factor solution for the extensive and data-reduced batteries, identifying phonology, semantic skills, fluency and executive function in contrast to a two-factor solution using the shallow battery (phonological/language severity and cognitive severity). Lesion symptom mapping using participants’ factor scores identified convergent neural structures based on existing language models for phonology (superior temporal gyrus), semantics (inferior temporal gyrus), speech fluency (precentral gyrus) and executive function (lateral occipitotemporal cortex) based on the extensive and data-reduced batteries. The two components in the shallow battery converged with the phonology and executive function clusters. In addition, we show that multivariate prediction models could be utilised to predict the component scores using neural data, however not for every component score within every test battery. Overall, the data-reduced battery appears to be an effective way to save assessment time yet retain the underlying structure of language and cognitive deficits observed in post stroke aphasia.
A highly efficient gene disruption strategy reveals lipid co-regulatory networks
Authors: Harayama Takeshi , Hashidate-Yoshida Tomomi , Fleuriot Lucile , Aguilera-Romero Auxiliadora , Hamano Fumie , Ri Keiken , Morimoto Ryo , Debayle Delphine , Shimizu Takao , Riezman Howard
Published: November 2020

Gene disruption has been dramatically facilitated by genome editing tools. Despite improvements in gene disruption rates in cultured cells, clone isolation remains routinely performed to obtain mutants, potentially leading to artifacts due to clonal variation in cellular phenotypes. Here we report GENF, a highly efficient strategy to disrupt genes without isolating clones, which can be multiplexed. Using it, we obtained reliable lipidomics datasets from mutant cells without being affected by variances related to clone isolation. Through this, we found that an enzyme involved in congenital generalized lipodystrophy regulates glycerophospholipids with specific acyl-chains. We also demonstrate the possibility to dissect complex lipid co-regulatory mechanisms, explaining cell adaptations to altered lipid metabolism. With its simplicity and the avoidance of cloning-related artifacts, GENF is likely to contribute to many cell biology studies, especially those involving -omics approaches.
Missing pieces in the full annual cycle of fish ecology: a systematic review of the phenology of freshwater fish research
Authors: Brady Megan E. , Chione Andrew M. , Armstrong Jonathan B.
Published: November 2020

In recent decades, fish ecologists have become increasingly aware of the need for spatially comprehensive sampling. However, a corresponding reflection on the temporal aspects of research has been lacking. We quantified the seasonal timing and extent of freshwater fish research. Since reviewing all prior work was not feasible, we considered two different subsets. First, we compiled the last 30 years of ecological research on juvenile Pacific salmon and trout (Oncorhynchusspp.) (n = 371 studies). In addition to the aggregate, we compared groups classified by subject matter. Next, to evaluate whether riverscape ecology has embraced space at the expense of time, we compiled research across taxa in which fish were enumerated in a spatially continuous fashion (n = 46). We found that ecologicalOncorhynchusspp. research was biased towards summer (40% occurred during June-August) and the month of June in particular, at the expense of winter work (only 13% occurred during December-February). Riverscape studies were also biased toward summer (47% of studies) and against winter (11%). It was less common for studies to encompass multiple seasons (43% of ecologicalOncorhynchusspp. studies and 54% of riverscape studies) and most were shorter than 4 months (73% of ecologicalOncorhynchusspp. studies and 81% of riverscape studies). These temporal biases may cause researchers to overemphasize ecological phenomena observed during summer and limit our ability to recognize seasonal interactions such as carry-over effects or compensatory responses. Full year and winter studies likely hold valuable insights for conservation and management.
Application of Microencapsulation Technology in Mushroom Powder Cake Processing
Authors: Zifei Liu , Hongyan Ye , Wei Yue , Li Ning
Published: November 2020

In this study,Lentinus edodes(or mushroom) powder and carrot juice were used as raw materials to prepare a new type of nutritious cakes. Microencapsulation was applied in embedding vitamin C to prevent the loss of this vitamin during baking at high temperatures. The most suitable addition amount of each materials was optimized via single-factor test and response surface analysis. The optimal microencapsulation of shiitake mushroom powder with carrot juice required 10 g of mushroom powder, 35 g of soft sugar, 50 mL of carrot juice and 160 g of egg white. The cake prepared herein was rich in nutrient and exuded a unique flavor. This cake was prepared via modern processing technologies and efficient detection techniques. Microencapsulation not only improves the nutritional value of traditional flour products but also expands the scope of research on food processing technologies.

Practical applications

Lentinus edodesis a nutritious food with low fat content and rich in polysaccharides and vitamins. Consumption of this mushroom improves immunity, lowers blood pressure, and prevents the development of various types of cancer. GroundL. edodespowder is also called mushroom powder, which has the same nutrient composition and efficacy asL.entinus edodes. Carrots produce a fresh aroma, and the large amounts of β -carotene in carrots improve the nutritional value of carrot-based food and also exert beneficial effects, such as preventing xerophthalmia, night blindness, and oral ulcer. A new cake made of carrot juice and mushroom powder can effectively improve the nutritional and economic values of carrot and mushroom powder. However, vitamin C easily loses its function at high temperatures. In this study, vitamin C was microencapsulated to reduce its outflow. The purpose of this study was to expand the applications of microencapsulation technology, provide a scientific basis for the production of nutritious functional foods, and offer new research ideas for the development of new cakes.
Temporal Requirements of SKN-1/NRF as a Regulator of Lifespan and Proteostasis inCaenorhabditis elegans
Authors: Grushko Danielle , Levine Amir , Boocholez Hana , Cohen Ehud
Published: November 2020

Lowering the activity of the Insulin/IGF-1 Signaling (IIS) cascade results in elevated stress resistance, enhanced protein homeostasis (proteostasis) and extended lifespan of worms, flies and mice. In the nematodeCaenorhabditis elegans(C. elegans), the longevity phenotype that stems from IIS reduction is entirely dependent upon the activities of a subset of transcription factors including the Forkhead factor DAF-16/FOXO (DAF-16), Heat Shock Factor-1 (HSF-1), SKiNhead/Nrf (SKN-1) and ParaQuat Methylviologen responsive (PQM-1). While DAF-16 determines lifespan exclusively during early adulthood and governs proteostasis in early adulthood and midlife, HSF-1 executes these functions foremost during development. Despite the central roles of SKN-1 as a regulator of lifespan and proteostasis, the temporal requirements of this transcription factor were unknown. Here we employed conditional knockdown techniques and discovered that inC. elegans, SKN-1 is primarily important for longevity and proteostasis during late larval development through early adulthood. Our findings indicate that events that occur during late larval developmental through early adulthood affect lifespan and proteostasis and suggest that subsequent to HSF-1, SKN-1 sets the conditions, partially overlapping temporally with DAF-16, that enable IIS reduction to promote longevity and proteostasis. Our findings raise the intriguing possibility that HSF-1, SKN-1 and DAF-16 function in a coordinated and sequential manner to promote healthy aging.
EoRNA, a barley gene and transcript abundance database
Authors: Milne Linda , Bayer Micha , Rapazote-Flores Paulo , Mayer Claus-Dieter , Waugh Robbie , Simpson Craig G
Published: November 2020

A high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EoRNA* – Expression of RNA) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EoRNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eòrna is the Scottish Gaelic word for Barley
The ESCRT-III machinery participates in the production of extracellular vesicles and protein export duringPlasmodium falciparuminfection
Authors: Avalos-Padilla Yunuen , Georgiev Vasil N. , Lantero Elena , Pujals Silvia , Verhoef René , Borgheti-Cardoso Livia N. , Albertazzi Lorenzo , Dimova Rumiana , Fernàndez-Busquets Xavier
Published: November 2020

Infection withPlasmodium falciparumenhances extracellular vesicles (EVs) production in parasitized red blood cells (pRBC), an important mechanism for parasite-to-parasite communication during the asexual intraerythrocytic life cycle. Theendosomalsortingcomplexrequired fortransport (ESCRT), and in particular the ESCRT-III sub-complex, participates in the formation of EVs in higher eukaryotes. However, RBCs have lost the majority of their organelles through the maturation process, including an important reduction in their vesicular network. Therefore, the mechanism of EV production inP. falciparum-infected RBCs remains to be elucidated. Here we demonstrate thatP. falciparumpossesses a functional ESCRT-III machinery that is activated by an alternative recruitment pathway involving the action of PfBro1 and PfVps32/PfVps60 proteins. Additionally, multivesicular bodies formation and membrane shedding, both reported mechanisms of EVs production, were reconstituted in the membrane model of giant unilamellar vesicles using the purified recombinant proteins. Moreover, the presence of PfVps32, PfVps60 and PfBro1 in EVs purified from a pRBC culture was confirmed by super-resolution microscopy. In accordance, disruption of thePfvps60gene led to a reduction in the number of the produced EVs in the KO strain when compared with the parental 3D7 strain. Overall, our results increase the knowledge on the underlying molecular mechanisms during malaria pathogenesis and demonstrate that ESCRT-IIIP. falciparumproteins participate in EVs production.
Separation and enrichment of sodium-motile bacteria using cost-effective microfluidics
Authors: Gurung Jyoti P , Kashani Moein Navvab , Agarwal Sanaz , Peralta Gonzalo , Gel Murat , Baker Matthew AB
Published: November 2020

Many motile bacteria are propelled by the rotation of flagellar filaments. This rotation is driven by a membrane protein known as the stator-complex, which drives the rotor of the bacterial flagellar motor. Torque generation is powered in most cases by proton transit through membrane protein complexes known as stators, with the next most common ionic power source being sodium. Sodium-powered stators can be studied through the use synthetic chimeric stators that combine parts of sodium- and proton-powered stator proteins. The most well studied example is the use of the sodium powered PomA-PotB chimeric stator unit in the naturally proton-poweredE. coli. Here we designed a fluidics system at low cost for rapid prototyping to separate motile and non-motile populations of bacteria while varying the ionic composition of the media and thus the sodium-motive-force available to drive this chimeric flagellar motor. We measured separation efficiencies at varying ionic concentrations and confirmed using fluorescence that our device delivered eight-fold enrichment of the motile proportion of a mixed population. Furthermore, our results showed that we could select bacteria from reservoirs where sodium was not initially present. Overall, this technique can be used to implement selection of highly-motile fractions from mixed liquid cultures, with applications in directed evolution to investigate the adaptation of motility in bacterial ecosystems.
Diverse natural variants suppress mutations in hundreds of essential genes
Authors: Parts Leopold , Batté Amandine , Lopes Maykel , Yuen Michael W. , Laver Meredith , San Luis Bryan-Joseph , Yue Jia-Xing , Pons Carles , Eray Elise , Aloy Patrick , Liti Gianni , van Leeuwen Jolanda
Published: November 2020

The consequence of a mutation can be influenced by the context in which it operates. For example, loss of gene function may be tolerated in one genetic background, but lead to lethality in another. The extent to which mutant phenotypes are malleable, the complexity of the architecture of modifiers, and the identities of causal genes and pathways remain largely unknown. Here, we measure the fitness effects of ~1,500 temperature sensitive alleles of yeast essential genes in the context of variation from ten different natural genetic backgrounds, and map the modifiers for 19 combinations. Altogether, fitness defects for 183 of the 530 tested genes (35%) could be suppressed by standing genetic variation in at least one wild strain. Suppression was generally driven by gain-of-function of a single, strong modifier gene. The validated causes included both variants in protein interaction partners or pathway members suppressing specific genes, as well as general modifiers altering the effect of many temperature sensitive alleles. The emerging frequency of suppression and range of possible suppression mechanisms suggest that a substantial fraction of monogenic diseases could be repressed by modulating other gene products.