bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep conservation ofHid-like RHG gene family homologs in winged insects
Authors: Friedrich Markus
Published: April 2021

Together withsickle(skl), theDrosophilaparalogsreaper(rpr),head involution defective(hid), andgrim(RHG) control a critical switch in the induction of programmed cell death. RHG homologs have been identified in other dipteran and lepidopteran species but not beyond. Revisiting this issue with a “taxon hopping” BLAST search strategy in current genome and transcriptome resources, I detected high confidence RHG homologs in Coleoptera (beetles), Hymenoptera (bees+wasps), Hemiptera (true bugs), termites, and cockroaches. Analyses of gene structure and protein sequence conservation revealed a shared ancestral splicing pattern and highly conserved amino acid residues at both the N- and C-terminal ends that identifyhidas the most ancestrally organized RHG gene family member inDrosophila. hid-like RHG homologs were also detected in mosquitoes, redefining theirmichelob_x(mx) genes as an expansion of derived RHG homologs. Only singleton homologs were detected in the large majority of other insect clades. Lepidopteran RHG homologs, however, stand out by producing an evolutionarily derived splice isoform, identified in previous work, in addition to the newly detectedhid-like isoform. Exceptional sequence diversification of select RHG homologs at the family- and genus-level explain their elusiveness in important insect genome model species like the red flour beetleTribolium castaneumand the pea aphidAcyrthosiphon pisum. Combined, these findings expand the minimal age of the RHG gene family by about 100 million years and open new avenues for molecular cell death studies in insects.
A Hierarchical Process Model Links Behavioral Aging and Lifespan inC. elegans
Authors: Oswal Natasha , Martin Olivier M.F. , Stroustrup Sofia , Matusiak Bruckner Monika Anna , Stroustrup Nicholas
Published: April 2021

Individuals who remain vigorous longer tend to live longer, supporting the design of predictive behavioral biomarkers of aging. InC. elegans, the timing of age-associated vigorous movement cessation (VMC) and lifespan correlate strongly between individuals. However, many genetic and pharmaceutical interventions that alter aging produce disproportional effects on VMC and lifespan, appearing to “uncouple” the rate of behavioral aging and lifespan. To study the causal structure underlying such uncoupling, we developed a high-throughput, automated imaging platform to quantify behavioral aging and lifespan at an unprecedented scale. Our method reveals an inverse correlation between each individuals’ vigorous movement span and their remaining lifespan. Robust across many lifespan-altering interventions including a new RNA-polymerase II auxin-inducible degron system, our data shows that individualC. elegansexperience at least two distinct but coupled physical declines—one governing VMC and the other governing lifespan. Through simulations and modeling, we clarify the causal relationship between these two “biological ages” and highlight a crucial but often untested assumption in conventional aging biomarker research: predictive biomarkers may not always report on the same biological age as that which determines long-term health outcomes.
Racial differences in androgen metabolism and receptor signaling in prostate cancer
Authors: Ramakrishnan Swathi , Cortes-Gomez Eduardo , Attwood Kristopher , Kittles Rick A , Wang Jianmin , Rosario Spencer R , Smiraglia Dominic J , Azabdaftari Gissou , Mohler James L , Huss Wendy J , Woloszynska Anna
Published: April 2021

Dihydrotestosterone (DHT) and testosterone (T) mediated androgen receptor (AR) nuclear translocation initiates transcription of AR target genes that are pivotal for prostate cancer (PrCa) development and progression. Here we provide data indicating that in contrast to European American (EA) men, African American (AA) men with localized PrCa can exploit an alternative progesterone-androsterone-5α-androstanedione pathway for DHT biosynthesis. Enzymes that are involved in alternate pathways of DHT biosynthesis are elevated in PrCa tissues from AA men, compared to EA men, and also correlated with increased serum DHT levels. In addition, higher serum DHT levels reflect increased RNA expression of AR target genes in PrCa tissues from AA men. Interestingly, serum T but not DHT levels are significantly lower in AA men compared to EA men with PrCa. Furthermore, serum progesterone and related intermediate metabolites levels that are produced during alternate pathways of DHT biosynthesis are significantly lower in AA men with PrCa and associated with a shorter time to disease progression. These data highlight that androgen biosynthesis is altered in therapy naïve localized PrCa in AA men, and can potentially serve as prognostic indicators of disease progression.

Significance

Our work provides a rationale to examine potential pharmacological interventions that target androgen biosynthesis and AR signaling earlier in the disease continuum in AA men with PrCa. Additionally, our study lays the groundwork for developing serum measurements of intermediate androgen metabolites as PrCa prognostic biomarkers.
Precise and pervasive phasic bursting in locus coeruleus during maternal behavior
Authors: Dvorkin Roman , Shea Stephen D.
Published: April 2021

The noradrenergic locus coeruleus (LC) mediates key aspects of arousal, memory, and cognition in structured tasks, but its contribution to natural behavior remains unclear. Neuronal activity in LC is organized into sustained (‘tonic’) firing patterns reflecting global brain states and rapidly fluctuating (‘phasic’) bursts signaling discrete behaviorally significant events. LC’s broad participation in social behavior including maternal behavior is well-established, yet the temporal relationship of its activity to sensory events and behavioral decisions in this context is unknown. Here, we made electrical and optical recordings from LC in female mice during maternal interaction with pups. We find that pup retrieval stably elicits precisely timed and pervasive phasic activation of LC that can’t be attributed to sensory stimuli, motor activity, or reward. Correlation of LC activity with retrieval events shows that phasic events are most closely related to subsequent behavior. We conclude that LC likely drives goal-directed action selection during social behavior with globally-broadcast noradrenaline release.
Rapid mosaic brain evolution under artificial selection for relative telencephalon size in the guppy (Poecilia reticulata)
Authors: Fong Stephanie , Rogell Björn , Amcoff Mirjam , Kotrschal Alexander , van der Bijl Wouter , Buechel Séverine D. , Kolm Niclas
Published: April 2021

The vertebrate brain displays enormous morphological variation and the quest to understand the evolutionary causes and consequences of this variation has spurred much research. The mosaic brain evolution hypothesis, stating that brain regions can evolve relatively independently, is an important idea in this research field. Here we provide experimental support for this hypothesis through an artificial selection experiment in the guppy (Poecilia reticulata). After four generations of selection on relative telencephalon volume (relative to brain size) in replicated up-selected, down-selected and control-lines, we found substantial changes in telencephalon size, but no changes in other regions. Comparisons revealed that up-selected lines had larger telencephalon while down-selected lines had smaller telencephalon than wild Trinidadian populations. No cost of increasing telencephalon size was detected in offspring production. Our results support that independent evolutionary changes in specific brain regions through mosaic brain evolution can be important facilitators of cognitive evolution.
A new method for obtaining bankable and expandable adult-like microglial cells
Authors: You Min-Jung , Rim Chan , Kang Youn-Jung , Kwon Min-Soo
Published: April 2021

The emerging role of microglia in neurological disorders requires a novel method for obtaining massive amounts of adult microglia because currentin vitromethods for microglial study have many limitations, including a limited proliferative capacity, low cell yield, immature form, and too many experimental animals use. Here, we developed a new method for obtaining bankable and expandable adult-like microglial cells using the head neuroepithelial layer (NEL) of mouse E13.5. The NEL includes microglia progenitors that proliferate and ramify over time. Functional validation with a magnetic-activated cell sorting system using the NEL showed that the isolated CD11b-positive cells (NEL-MG) exhibited microglial functions, such as phagocytosis (microbeads, amyloid β, synaptosome), migration, and inflammatory changes following lipopolysaccharide (LPS) stimulation. NEL was subcultured and the NEL-MG exhibited a higher expression of microglia signature genes than the neonatal microglia, a widely usedin vitrosurrogate. Banking or long-term subculture of NEL did not affect NEL-MG characteristics. Transcriptome analysis revealed that NEL-MG exhibited better conservation of microglia signature genes with a closer fidelity to freshly isolated adult microglia than neonatal microglia. This new method effectively contributes to obtaining adult-like microglial cells, even when only a small number of experimental animals are available, leading to a broad application in neuroscience-associated fields.
Simultaneous suppression of ribosome biogenesis and Tor activation by TRIM-NHL proteins promotes terminal differentiation
Authors: Gui Jinghua , Samuels Tamsin J , Grobicki Katarina ZA , Teixeira Felipe Karam
Published: April 2021

Proper tissue development and homeostasis depends on the balance between growth and terminal differentiation, but the mechanisms coordinating these processes remain elusive. Accumulating evidence indicates that ribosome biogenesis (RiBi) and protein synthesis, two of the most energy-consuming cellular processes sustaining growth, are tightly regulated and yet can be uncoupled during stem cell fate transitions. Here, using theDrosophilaadult female germline stem cell (GSC) and larval neuroblast (NB) systems, we show that Mei-P26 and Brat, twoDrosophilaTRIM-NHL paralogs of the mammalian TRIM32 protein family, are responsible for uncoupling RiBi and protein synthesis during GSC and NB differentiation, respectively. Mei-P26 and Brat modify the metabolism of differentiating cells by activating the Target of rapamycin (Tor) kinase to promote translation, while concomitantly repressing RiBi. Depletion of Mei-P26 or Brat results in excessive cellular growth and defective terminal differentiation, which can be rescued by ectopic activation of Tor together with suppression of RiBi. Our results indicate that the anabolic reprogramming established by TRIM-NHL activity by uncoupling RiBi and translation activities creates the conditions required for terminal differentiation.
Effects of adhesive drying methods to reduce aerosol generation during resin bonding on enamel bond strength
Authors: Ayar Muhammet Kerim , Yesil Onder
Published: April 2021

Objective

In order to reduce the amount of aerosol during the use of dental adhesives, which are widely used in minimally invasive procedures, the effects of air stream-free adhesive drying methods on the enamel bond strength of resin adhesive systems were evaluated.

Materials and Methods

The four adhesive drying techniques used were an air-stream, a micro-applicator, a cotton pellet and an absorbent paper. Adhesive systems were Single Bond Universal and Optibond All-in-one. The group in which the adhesive was not dried served as the negative control group. Enamel shear bond strength was performed with a universal tester with a crosshead speed of 1 mm/min (n=12). A two-way analysis of variance and the Tukey post-hoc test were used for analysis of the SBS data.

Results

For both adhesives, drying the adhesive with cotton pellet or micro-applicator provided a SBS mean values similar to air-stream drying, while statistically significantly lower SBS mean values were observed in the negative control group and in the absorbent paper-dry group compared to the air-drying group.

Conclusions

Drying the adhesive with micro-applicator and cotton pellets creates less aerosol and thus can be used in the COVID-19 pandemic as it provides enamel bonding strength similar to air drying.

CLINICAL SIGNIFICANCE

To provide safer dental care during COVID-19 pandemic, it is highly recommended to use non-aerosol-generating alternatives, instead of aerosolgenerating dental procedures. In this study, we found that the aerosol generation-free methods for adhesive-drying such as cotton pellet and micro applicator drying methods provide similar enamel bonding with conventional drying method. We think that our findings will contribute to the realization of safer adhesive dentistry practice, especially during the COVID-19 pandemic.
Methane, a gut bacteria-produced gas, does not affect arterial blood pressure in normotensive anaesthetized rats
Authors: Zaorska Ewelina , Gawryś-Kopczyńska Marta , Ostaszewski Ryszard , Koszelewski Dominik , Ufnal Marcin
Published: April 2021

Methane is produced by carbohydrate fermentation in the gastrointestinal tract through the metabolism of methanogenic microbiota. Several lines of evidence suggest that methane exerts anti-inflammatory, anti-apoptotic and anti-oxidative effects. The effect of methane on cardiovascular system is obscure. The objective of the present study was to evaluate the hemodynamic response to methane. A vehicle or methane-rich saline were administered intravenously or intraperitoneally in normotensive anaesthetized rats. We have found no significant effect of the acute administration of methane-rich saline on arterial blood pressure and heart rate in anaesthetized rats. Our study suggests that methane does not influence the control of arterial blood pressure. However, further chronic studies may be needed to fully understand hemodynamic effects of the gas.
TheXanthomonastype-III effector protein XopS stabilizesCaWRKY40a to regulate defense hormone responses and preinvasion immunity in pepper (Capsicum annuum)
Authors: Raffeiner Margot , Üstün Suayib , Guerra Tiziana , Spinti Daniela , Fitzner Maria , Sonnewald Sophia , Baldermann Susanne , Börnke Frederik
Published: April 2021

A critical component of plant immunity against invading pathogens is the rapid transcriptional reprogramming of the attacked cell to minimize virulence. Many adapted plant bacterial pathogens use type III effector (T3E) proteins to interfere with plant defense responses, including the induction of immunity genes. The elucidation of effector function is essential to understanding bacterial pathogenesis. Here, we show that XopS, a T3E ofXanthomonas campestrispv.vesicatoria(Xcv), interacts with and inhibits the proteasomal degradation of the transcriptional regulator of defense gene expression WRKY40. Virus-induced gene silencing ofWRKY40in pepper enhanced plant tolerance towardsXcvinfection, indicating it represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets including salicylic acid (SA)-responsive genes and the jasmonic acid (JA) signaling repressorJAZ8.Xcvbacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery byXcv, as well as ectopic expression of XopS in Arabidopsis orNicotiana benthamianaprevented stomatal closure in response to bacteria and biotic elicitors in a WRKY40 dependent manner. This suggests that XopS interferes with preinvasion as well as with apoplastic defense by manipulating WRKY40 stability and gene expression eventually altering phytohormone crosstalk to promote pathogen proliferation.
Towards deciphering the structure of long homozygous stretches in cattle genome
Authors: Smaragdov Michael Grigorievich
Published: April 2021

Up-to-day there is no as universally accepted software tool and threshold parameters to identify runs of homozygosity (ROH). The relative position of POH segments in the cattle genome has not been studied extensively. Specific objective of this study was to evaluate the effect of allowed missing and heterozygous SNPs in ROH on their number, on the estimate of inbreeding level, and on structure of ROH segments in the cattle genome. In this study 371 Holsteinized cows from six herds were genotyped with BovineSNP50 array. To identify ROH, the consecutive and sliding runs were carried out with detectRUNS and Plink tools. Neither effect was shown for missing SNPs genotype calls. Allowing even one heterozygous SNP resulted in significant bias of ROH data. Furthermore, the sliding runs identified less ROH than consecutive runs. The mean coefficient of inbreeding across herds was 0.111 ± 0.003 and 0.104 ± 0.003 based on consecutive and sliding runs respectively. It was shown how, using the heterozygous SNPs in ROH, may be possible to derive a distribution of ROH segments in the cow genome. We suggested it was similar to normal distribution. Furthermore, frequency of ROH in the chromosomes did not depend on their length. Of 29 chromosomes, the most abundant with ROH were BTA 14, BTA 7, and BTA 18. The result of this study confirmed more accurately identification of ROH with consecutive runs, uneven their distribution in the cattle genome, significant bias of the data due to allowing heterozygous SNPs in ROH.
Isolation and characterization of a novelWolbachiabacteriophage fromAllonemobius sociuscrickets in Missouri
Authors: Kupritz Jonah , Martin John , Fischer Kerstin , Curtis Kurt C , Fauver Joseph R , Huang Yuefang , Choi Young-Jun , Beatty Wandy L , Mitreva Makedonka , Fischer Peter U
Published: April 2021

Wolbachiaare endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected inWolbachia, but particles ofWolbachiabacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket,Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screenedA. sociusabdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR forWolbachiasurface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies againstWolbachiasurface protein showed manyWolbachiaclusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOKue of the Mediterranean flour mothEphestia kuehniella(94.18% identity) and WOLig of the coronet moth,Craniophora ligustri(96.86% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles withinWolbachiacells. Isolation of phage WO revealed particles characterized by 40-62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.
Molecular characterization of a complex of Apoptosis Inducing Factor 1 (AIFM1) with cytochrome c oxidase of the mitochondrial respiratory chain
Authors: Hevler Johannes F. , Chiozzi Riccardo Zenezeni , Cabrera-Orefice Alfredo , Brandt Ulrich , Arnold Susanne , Heck Albert J.R.
Published: April 2021

Combining mass spectrometry based chemical cross-linking and complexome profiling, we analyzed the interactome of heart mitochondria. We focused on complexes of oxidative phosphorylation and found that dimeric apoptosis inducing factor 1 (AIFM1) forms a defined complex with ~10% of monomeric cytochromecoxidase (COX), but hardly interacts with respiratory chain supercomplexes. Multiple AIFM1 inter-crosslinks engaging six different COX subunits provided structural restraints to build a detailed atomic model of the COX-AIFM12complex. Application of two complementary proteomic approaches thus provided unexpected insight into the macromolecular organization of the mitochondrial complexome. Our structural model excludes direct electron transfer between AIFM1 and COX. Notably however, the binding site of cytochromecremains accessible allowing formation of a ternary complex. The discovery of the previously overlooked COX-AIFM12complex and clues provided by the structural model hint at a role of AIFM1 in OXPHOS biogenesis and in programmed cell death.
The genetic basis ofDrosophila melanogasterdefense againstBeauveria bassianaexplored through evolve and resequence and quantitative trait locus mapping
Authors: Shahrestani Parvin , King Elizabeth , Ramezan Reza , Phillips Mark , Riddle Melissa , Thornburg Marisa , Greenspan Zachary , Estrella Yonathan , Garcia Kelly , Chowdhury Pratik , Malarat Glen , Zhu Ming , Rottshaefer Susan M. , Wraight Stephen , Griggs Michael , Vandenberg John , Long Anthony D. , Clark Andrew G. , Lazzaro Brian P.
Published: April 2021

Many of the molecular mechanisms for antifungal immunity inDrosophila melanogasterhave been defined, but relatively little is known about the genetic basis for variation in antifungal immunity in natural populations. Using two population genetic approaches, Quantitative Trait Locus (QTL) Mapping and Evolve and Resequence (E&R), we explored the genetics underlyingD. melanogasterimmune defense against infection with the fungusBeauveria bassiana. Immune defense was highly variable both in the recombinant inbred lines from the Drosophila Synthetic Population Resource used for our QTL Mapping and in the synthetic outbred populations used in our E&R study. Survivorship of infection improved dramatically over just 10 generations in the E&R study, and continued to increase for an additional 9 generations, revealing a trade-off with uninfected longevity. Populations selected for increased defense againstB. bassianaevolved cross resistance to a second, distinctB. bassianastrain but not to bacterial pathogens. The QTL mapping study revealed that sexual dimorphism in defense depends on host genotype, and the E&R study indicated that dimorphism also depends on the specific pathogen to which the host is exposed. Both the QTL Mapping and E&R experiments generated lists of potentially causal candidate genes, although these lists were non-overlapping.
Ankle muscles drive mediolateral center of pressure control to ensure stable steady state gait
Authors: van Leeuwen A.M. , van Dieën J.H. , Daffertshofer A. , Bruijn S.M.
Published: April 2021

During steady-state walking, mediolateral gait stability can be maintained by controlling the center of pressure (CoP). The CoP modulates the moment of the ground reaction force, which brakes and reverses movement of the center of mass (CoM) towards the lateral border of the base of support. In addition to foot placement, ankle moments serve to control the CoP. We hypothesized that, during steady-state walking, single stance ankle moments establish a CoP shift to correct for errors in foot placement. We expected ankle muscle activity to be associated with this complementary CoP shift. During treadmill walking, full-body kinematics, ground reaction forces and electromyography were recorded in thirty healthy participants. We found a negative relationship between preceding foot placement error and CoP displacement during single stance; steps that were too medial were compensated for by a lateral CoP shift and vice versa, steps that were too lateral were compensated for by a medial CoP shift. Peroneus longus, soleus and tibialis anterior activity correlated with these CoP shifts. As such, we identified an (active) ankle strategy during steady-state walking. As expected, absolute explained CoP variance by foot placement error decreased when walking with shoes constraining ankle moments. Yet, contrary to our expectations that ankle moment control would compensate for constrained foot placement, the absolute explained CoP variance by foot placement error did not increase when foot placement was constrained. We argue that this lack of compensation reflects the interdependent nature of ankle moment and foot placement control. We suggest that single stance ankle moments do not only compensate for preceding foot placement errors, but also assist control of the subsequent foot placement. Foot placement and ankle moment control are ‘caught’ in a circular relationship, in which constraints imposed on one will also influence the other.
Glycosylated Antibiotics: New Promising Bacterial Efflux Pumps Inhibitors
Authors: Kamaz Zahraa Ali , Umar Haruna Isiyaku , Doshi Parth , Suri Praveenya
Published: April 2021

Background

Antimicrobial resistance is considered a major concern problem; bacteria have evolved mechanisms to overcome antibiotics’ action through evolutionary process. One main resistance mechanism that bacteria developed is the pumping of the antibiotics out of bacterial cells by transmembrane transporter proteins known as efflux pumps.

Materials and methods

To overcome bacterial resistance guided by efflux pumps, efflux pumps inhibitors (EPIs) are small molecules that obstruct efflux pumps binding sites and its structural assembly leading to disability in the efflux pumps normal function, new EPIs which under the current study are created by modifying the chemical structure of most common antibiotics including Ampicillin, Penicillin, Chloramphenicol, Ciprofloxacin and Tetracycline, such antibiotics are modified by adding N-acetyl glucose amine moiety to acceptor OH group of the respective antibiotic, the newly modified antibiotics are glycosylated EPIs. To test the effectiveness of the new EPIs in inhibiting AcrB-TolC and MexA-OprM efflux pumps functions, ADME properties for all of glycosylated antibiotics have been measured through applying Lipinski’s role of 5, docking and simulation studies have been included as well.

Results

Docked glycosylated tetracycline has given the highest binding energy in the active sites of both pumps, with −9.4 against AcrB and −8.8 against MexA. The simulation study has confirmed the binding of the glycosylated tetracycline in the active sites of both pumps, as well as its stability during the biological dynamicity of both pumps (opening and closing channels).

Conclusion

The results validation requires a long simulation time about 50 ns or more which was un applicable due to cost limitation, however, the newly glycosylated antibiotics have promising results that might make it eligible as drug candidates to overcome bacterial resistance.
Unipolar peptidoglycan synthesis in the Rhizobiales requires an essential class A penicillin-binding protein
Authors: Williams Michelle A. , Aliashkevich Alena , Krol Elizaveta , Kuru Erkin , Bouchier Jacob M. , Rittichier Jonathan , Brun Yves V. , VanNieuwenhze Michael S. , Becker Anke , Cava Felipe , Brown Pamela J. B.
Published: April 2021

Members of the Rhizobiales are polarly-growing bacteria that lack homologs of the canonical rod complex. To investigate the mechanisms underlying polar cell wall synthesis, we systematically probed the function of cell wall synthesis enzymes in the plant-pathogenAgrobacterium tumefaciens. The development of fluorescentd-amino acid dipeptide (FDAAD) probes, which are incorporated into peptidoglycan by penicillin-binding proteins inA. tumefaciens, enabled us to monitor changes in growth patterns in the mutants. Use of these fluorescent cell wall probes and peptidoglycan compositional analysis convincingly demonstrate that a single class A penicillin-binding protein is essential for polar peptidoglycan synthesis. Furthermore, we find evidence of an alternative mode of cell wall synthesis that likely requiresld-transpeptidase activity. Genetic analysis and cell wall targeting antibiotics reveal that the mechanism of unipolar growth is conserved inSinorhizobiumandBrucella. This work provides insights into unipolar peptidoglycan biosynthesis employed by the Rhizobiales during cell elongation.
Competitive dynamics underlie cognitive improvements during sleep
Authors: Chen Pin-Chun , Niknazar Hamid , Alaynick William A. , Whitehurst Lauren N. , Mednick Sara C.
Published: April 2021

We provide evidence that human sleep is a competitive arena where cognitive domains vie for limited resources. Using pharmacology and effective connectivity analysis, we demonstrate that long-term memory and working memory are served by distinct offline neural mechanisms that are mutually antagonistic. Specifically, we administered zolpidem to increase central sigma activity and demonstrated targeted suppression of autonomic vagal activity. With effective connectivity, we determined the central activity has greater causal influence over autonomic activity, and the magnitude of this influence during sleep produced a behavioral trade-off between offline long-term and working memory processing. These findings show the first evidence of a sleep switch mechanism that toggles between central sigma-dependent long-term memory and autonomic vagal-dependent working memory processing.

Significant Statement

Sleep facilitates both long-term episodic memory consolidation and short-term working memory functioning. However, the mechanism by which the sleeping brain performs both complex feats, and which sleep features are associated with these processes remain unclear. Using a pharmacological approach, we demonstrate that long-term and working memory are served by distinct offline neural mechanisms, and that these mechanisms are mutually antagonistic. We propose a Sleep Switch model in which the brain toggles between the two memory processes via a complex interaction at the synaptic, systems, and mechanistic level, with implications for research on cognitive disturbances observed in neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease, both of which involve the decline of sleep.
Antagonistic inhibitory subnetworks control cooperation and competition across cortical space
Authors: Mossing Daniel P. , Veit Julia , Palmigiano Agostina , Miller Kenneth D. , Adesnik Hillel
Published: April 2021

The cortical microcircuit can dynamically adjust to dramatic changes in the strength, scale, and complexity of its input. In the primary visual cortex (V1), pyramidal cells (PCs) integrate widely across space when signals are weak, but narrowly when signals are strong, a phenomenon known as contrast-dependent surround suppression. Theoretical work has proposed that local interneurons could mediate a shift from cooperation to competition of PCs across cortical space, underlying this computation. We combined calcium imaging and electrophysiology to constrain a stabilized supralinear network model that explains how the four principal cell types in layer 2/3 (L2/3) of mouse V1– somatostatin (SST), parvalbumin (PV), and vasoactive intestinal peptide (VIP) interneurons, and PCs– transform inputs from layer 4 (L4) PCs to encode drifting gratings of varying size and contrast. Using bidirectional optogenetic perturbations, we confirmed key predictions of the model. Our data and modeling showed that recurrent amplification drives a transition from a positive PC→VIP⊣SST⊣PC feedback loop at small size and low contrast to a negative PC→SST⊣PC feedback loop at large size and high contrast to contribute to this flexible computation. This may represent a widespread mechanism for gating competition across cortical space to optimally meet task demands.
An alphavirus replicon-based vaccine expressing a stabilized Spike antigen induces sterile immunity and prevents transmission of SARS-CoV-2 between cats
Authors: Langereis Martijn A. , Stachura Ken , Miller Suzan , Bosco-Lauth Angela M. , Albulescu Irina C. , Hartwig Airn E. , Porter Stephanie M. , Stammen-Vogelzangs Judith , Mogler Mark , van Kuppeveld Frank J.M. , Bosch Berend-Jan , Vermeij Paul , de Groof Ad , Bowen Richard A. , Davis Randy , Xu Zach , Tarpey Ian
Published: April 2021

Early in the global SARS-CoV-2 pandemic concerns were raised regarding infection of other animal hosts and whether these could play a significant role in the viral epidemiology. Infection of animals could be detrimental by causing clinical disease but also of concern if they become a viral reservoir allowing further mutations, plus having the potential to infect other animals or humans. The first reported animals to be infected both under experimental conditions and from anecdotal field evidence were cats described in China early in 2020. Given the concerns this finding raised and the close contacts between humans and cats, we aimed to determine whether a vaccine candidate could be developed that was suitable for use in multiple susceptible animal species and whether this vaccine could reduce infection of cats in addition to preventing spread to other cats.

Here we report that a Replicon Particle (RP) vaccine based on Venezuelan equine encephalitis virus (VEEV), known to be safe and efficacious for use in a variety of animals, expressing a stabilised Spike antigen, could induce neutralising antibody titers in guinea pigs and cats. After two intramuscular vaccinations, virus neutralising antibodies were detected in the respiratory tract of the guinea pigs and a cell mediated immune response was induced. The design of the SARS-CoV-2 antigen was shown to be critical in developing a strong neutralising antibody response. Vaccination of cats was able to induce a serum neutralising antibody response which lasted for the course of the experiment. Interestingly, in contrast to control animals, infectious virus could not be detected in oropharyngeal or nasal swabs of vaccinated cats after challenge. Moreover, the challenged control cats spread the virus to in-contact cats whereas the vaccinated cats did not transmit virus. The results show that the RP vaccine induces sterile immunity preventing SARS-CoV-2 infection and transmission. This data suggests that this RP vaccine could be a multi-species vaccine useful for preventing spread to and between other animals should that approach be required.
The neutralization potency of anti-SARS-CoV-2 therapeutic human monoclonal antibodies is retained against novel viral variants
Authors: Makdasi Efi , Zvi Anat , Alcalay Ron , Noy-Porat Tal , Peretz Eldar , Mechaly Adva , Levy Yinon , Epstein Eyal , Chitlaru Theodor , Tennenhouse Ariel , Aftalion Moshe , Gur David , Paran Nir , Tamir Hadas , Zimhony Oren , Weiss Shay , Mandelboim Michal , Mendelson Ella , Zuckerman Neta , Nemet Ital , Kliker Limor , Yitzhaki Shmuel , Shapira Shmuel C. , Israely Tomer , Fleishman Sarel J. , Mazor Ohad , Rosenfeld Ronit
Published: April 2021

A wide range of SARS-CoV-2 neutralizing monoclonal antibodies (mAbs) were reported to date, most of which target the spike glycoprotein and in particular its receptor binding domain (RBD) and N-terminal domain (NTD) of the S1 subunit. The therapeutic implementation of these antibodies has been recently challenged by emerging SARS-CoV-2 variants that harbor extensively mutated spike versions. Consequently, the re-assessment of mAbs, previously reported to neutralize the original early-version of the virus, is of high priority.

Four previously selected mAbs targeting non-overlapping epitopes, were evaluated for their binding potency to RBD versions harboring individual mutations at spike positions 417, 439, 453, 477, 484 and 501. Mutations at these positions represent the prevailing worldwide distributed modifications of the RBD, previously reported to mediate escape from antibody neutralization. Additionally, thein vitroneutralization potencies of the four RBD-specific mAbs, as well as two NTD-specific mAbs, were evaluated against two frequent SARS-CoV-2 variants of concern (VOCs): (i) the B.1.1.7 variant, emerged in the UK and (ii) the B.1.351 variant, emerged in South Africa. Variant B.1.351 was previously suggested to escape many therapeutic mAbs, including those authorized for clinical use. The possible impact of RBD mutations on recognition by mAbs is addressed by comparative structural modelling. Finally, we demonstrate the therapeutic potential of three selected mAbs by treatment of K18-hACE2 transgenic mice two days post infection with each of the virus strains.

Our results clearly indicate that despite the accumulation of spike mutations, some neutralizing mAbs preserve their potency against SARS-CoV-2. In particular, the highly potent MD65 and BL6 mAbs are shown to retain their ability to bind the prevalent novel viral mutations and to effectively protect against B.1.1.7 and B.1.351 variants of high clinical concern.
Tension mediated mechanical activation and pocket delipidation lead to an analogous MscL state
Authors: Wang Bolin , Lane Benjamin J. , Kapsalis Charalampos , Ault James R. , Sobott Frank , El Mkami Hassane , Calabrese Antonio N. , Kalli Antreas C. , Pliotas Christos
Published: April 2021

The MscL channel gates in response to membrane tension changes to allow the exchange of molecules through its pore. Lipid removal from transmembrane pockets leads to a MscL response. However, it is unknown whether there is correlation between the tension mediated state and the state derived by pocket delipidation in the absence of tension. Transitions between MscL states may follow a similar pathway to cover the available conformational space but may not necessarily sample the same discrete intermediates. Here, we combined pulsed-EPR and HDX-MS measurements on MscL, coupled with molecular dynamics under membrane tension, to investigate the changes associated with the distinctively derived states. Whether it is tension or pocket delipidation, we find that MscL samples a similar expanded state, which is the final step of the delipidation pathway but only an intermediate stop of the tension mediated path. Our findings hint at synergistic modes of regulation in mechanosensitive channels.
Cloning Polymerase Chain Reaction (PCR) Products: Blunt-End Cloning
Authors: Green Michael R. , Sambrook Joseph
Published: April 2021

The following is an elegant and simple protocol for generating and cloning blunt-ended DNA. Incubation of a ligation reaction in the presence of an excess amount of restriction enzyme can dramatically increase the yield of recombinant plasmids. The role of the restriction enzyme is to cleave circular and linear concatemers at restriction sites that are regenerated when plasmid molecules ligate to themselves. The method requires that ligation of the plasmid to a target DNA molecule destroys the restriction site, so preventing the restriction enzyme from digesting recombinants generated during the ligation reaction. The net effect of constant reclamation of unit-length linear vector molecules is to drive the equilibrium of the ligation reaction strongly in favor of recombinants between vector and insert. The method is efficient because regeneration of vector DNA, ligation, and polishing the termini of PCR-generated fragments of DNA all occur simultaneously in the same reaction mixture.
Heritage assets in financial reporting: a critical analysis of the IPSASB's consultation paper
Authors: Biondi Lucia , Grandis Fabio Giulio , Mattei Giorgia
Published: April 2021

Purpose

Within the stream of research on public sector accounting standards, heritage asset accounting represents a difficult and challenging issue. This paper intends to join the debate on heritage reporting by carrying out a critical review of the Consultation Paper (CP) “Financial Reporting for Heritage in the Public Sector” issued by the International Public Sector Accounting Standards Board (IPSASB) in order to highlight its strengths and weaknesses and to make recommendations.

Design/methodology/approach

To this end, the current study adopts document analysis as a qualitative research method by referring to Italy as a typical and critical case study. Moreover, the authors actively took part in the Italian working group on heritage assets reporting, so they are well-informed people about the Italian point of view as well as the broad discussion underpinning the Italian response.

Findings

Evidence demonstrates that, although the proposals included in the CP represent a new step towards an organic regulation of heritage asset reporting, if these preliminary views are confronted with the reality of an emblematic context, as in the Italian case, much room for improvement remains regarding the definition, recognition, measurement and disclosure of such assets.

Originality/value

The originality of the paper lies in its contribution to overcoming the current controversial aspects of heritage assets reporting and the issuing of an accounting standard. In doing so, the authors also attempt to answer the call made by Anessi-Pessina et al. (2019) to investigate in detail an individual country experience to better understand the state of the art in national and international accounting standards on heritage assets.
Cable reverberations during wireline distributed acoustic sensing measurements: their nature and methods for elimination
Authors: Martuganova Evgeniia , Stiller Manfred , Bauer Klaus , Henninges Jan , Krawczyk Charlotte M.
Published: April 2021

The application of distributed acoustic sensing in borehole measurements allows for the use of fibre optic cables to measure strain. This is more efficient in terms of time and costs compared with the deploying of conventional borehole seismometers. Nevertheless, one known drawback for temporary deployment is represented by the freely hanging wireline cable slapping and ringing inside the casing, which introduces additional coherent coupling noise to the data. The present study proposes an explanation for the mechanism of noise generation and draws an analogy with similar wave propagation processes and phenomena, such as ghost waves in marine seismics. This observation allows to derive a ringing noise filter function, to study its behaviour and to consider known effects of the gauge length filter. After examining existing methods aimed at eliminating ringing noise and results of their application, we propose a two‐step approach: (1) developing a denoising method based on a matching pursuit decomposition with Gabor atoms and (2) subtracting the noise model for imaging improvement. The matching pursuit method focuses on decomposing the original input signal into a weighted sum of Gabor functions. Analysing Gabor atoms properties for frequency, amplitude and position in time provides the opportunity to distinguish parts of the original signal denoting noise caused by the vibrating cable. The matching pursuit decomposition applied to the distributed acoustic sensing‐vertical seismic profiling data at the geothermal test site Groß Schönebeck provides a versatile processing instrument for noise suppression.
Temperature, emergence phenology and consumption drive seasonal shifts in fish growth and production across riverscapes
Authors: Kaylor Matthew J. , Justice Casey , Armstrong Jonathan B. , Staton Benjamin A. , Burns Lauren A. , Sedell Edwin , White Seth M.
Published: April 2021

Changes in biophysical conditions through time generate spatial and temporal variability in habitat quality across landscapes. For river ecosystems, researchers are increasingly able to characterize spatial and temporal patterns in habitat conditions, referred to as shifting habitat mosaics, yet rarely demonstrate how this translates into corresponding biological processes such as organism growth and production.

We assessed spatial patterns and processes determining seasonal changes in juvenile Chinook Salmon Oncorhynchus tshawytscha size, growth and production over 30–40 km in two NE Oregon subbasins.

We quantified seasonal patterns of growth by combining estimated emergence dates and body size distributions in July and September. We then used analysis of bioenergetics, empirical fish diets and spatial models incorporating temperature, habitat and population density to evaluate mechanisms driving spatiotemporal patterns of growth. Lastly, we quantified seasonal contributions to individual fish growth and to total production as a function of position within the stream network.

Spatial heterogeneity in incubation temperatures corresponded to later estimated emergence timing with distance upstream in both subbasins. During spring, estimated growth rates decreased with distance upstream, and coupled with emergence patterns, resulted in pronounced longitudinal gradients in body size by July. During summer, spatial patterns of growth reversed, with greater diet ration sizes and growth efficiencies upstream than downstream. These opposing spatiotemporal patterns of emergence timing and seasonal growth rates produced longitudinal gradients in the proportion of fish growth achieved in spring versus summer, with up to 80% of an individual's growth occurring in spring at downstream sites but as low as 10% at upstream sites. Coupling longitudinal patterns of fish density and growth revealed that in one subbasin the majority (65%) of total production occurred in spring, while in the other, in which fish were concentrated in headwaters, the majority (60%) of production occurred in summer.

While recent work has emphasized inter‐annual shifts in fish production across large spatial scales, this study demonstrates that longitudinal gradients of fish growth and production can reverse across seasons, and reveals important contributions of warmer, downstream habitats to overall production that occurred during cooler times of the year.
Chile, October and November 2019: ‘Feel’ and field‐work in times of crisis
Authors: SEPULVEDA SANCHEZ DENISSE , LAVANCHY ANNE , HEINI CÉLINE , ACEVEDO ALINE
Published: April 2021

One of the most important social upheavals in Chile since the end of the dictatorship started in October 2019, and continued until the coronavirus outbreak in March 2020. The event affected the ethnographic fieldwork that we, four anthropologists, were conducting at that time. This article draws on the recognition that, while being in different geographical locations, our respective experiences involve similar affects. Drawing on feminist epistemology, we have utilized these emotional experiences as a methodological tool to spark curiosity and open up a space for reconsidering fieldwork as ‘feel‐work’. Our respective positioning, in terms of national and emotional feelings of belonging as well as physical location, created affective dissonances that raised uneasiness while at the same time opening up a productive space to think about fieldwork as an experience of ‘out‐of‐place’ bodies and ‘out‐of‐place’ feelings.