bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of different exercise training modes on dentate gyrus neurodegeneration and synaptic plasticity in morphine-dependent rats
Authors: Ranjbar Kamal , Zarrinkalam Ebrahim , Asl Sara Soleimani , Salehi Iraj , Taheri Masoumeh , Komaki Alireza
Published: April 2021

Various impacts of exercise on brain performance have been documented following morphine dependence induction; however, the underlying neuronal mechanisms remain unclear. The present research was done to investigate the impact of different exercise training modes on neuronal maturation, and synaptic plasticity in the perforant pathway (PP)-dentate gyrus (DG) synapse in the morphine-dependent rats. Five groups, including a control group (Con, ten healthy rats) and forty morphine-dependent rats were considered as follows (n=10/group): 1) sedentary-dependent (Sed-D); 2) endurance exercise-dependent (En-D); 3) strength exercise-dependent (St-D); and 4) concurrent exercise-dependent (Co-D). The exercise training groups were subjected to endurance, strength, and concurrent training 5 days per week for 10 weeks. After training sessions, the field excitatory postsynaptic potential (fEPSP) slope and population spike (PS) amplitude in DG were determined in response to high-frequency stimulation (HFS) of the PP. For assessing neurogenesis NeuroD level was evaluated after performing all experiments. Concurrent training increased PS amplitude and EPSP than the control group. NeuroD in the morphine-dependent rats significantly decreased, but concurrent training returned the NeuroD to the healthy rat level. Concurrent training can ameliorate synaptic plasticity impairment in morphine-dependent rats through neurogenesis promotion. According to the results, concurrent training can be an appropriate novel candidate for treating opioid addiction.
Relationing of Labellum and Glossae Biomorphological characteristics of honeybee workers as breeding tool on honey collection potential ofApis melliferaL. honeybee colonies
Authors: Iqbal Aneela , Rafique Muhammad Khalid , Mahmood Rashid , Noreen Mamoona , Sarwar Ghulam , Ahmad Ishaq , Shahzad Anjum , Shah Muhammad Jahangir , Ahmed Agha Mushtaque , Lashari Muhammad Akbar
Published: April 2021

This study focused on the correlation of honey collection Potential and the length and width of labellum and glossae in worker honey bees (Apis melliferaLigustica). Sixty honeybeeA. melliferaL. colonies were selected, among these 60 colonies, 3 worker bees were sampled from each colony total numbers of samples collected were 180 adult worker foraging bees. Fifteen colonies for each group were used to check the correlation of honey production with length of labellum, width of labellum, length of glossae and the width of glossae respectively. These worker bees were bought to the laboratory frozen, boiled, dissected and mounted on the slides. Measurements of the labellum length, labellum width, glossae length and glossae width were taken by the stereomicroscope with ocular micrometer at 0.8X magnification. Correlation values for the honey collectionand length and width of labellum and glossae were high and positive. These Results support the perception that worker bees with larger labellum and glossae have more ability for honey collection Potential. It is concluded that Biomorphological characters of labellum and glossae are significantly correlated with the honeycollection Potential inA. melliferaL.
Clinical Efficacy of Prebiotics and Glycosaminoglycans versus Placebo In Dogs with Food Responsive Enteropathy Receiving a Hydrolyzed Diet: A Pilot Study
Authors: Glanemann Barbara , Seo Yeon-Jung , Priestnall Simon L. , Garden Oliver A. , Kilburn L. , Rossoni-Serao M. , Segarra Sergi , Mochel Jonathan P. , Allenspach Karin
Published: April 2021

Induction of remission is easily achieved with dietary treatment in dogs diagnosed with Food Responsive Chronic Enteropathy (FRD). Administration of prebiotics and glycosaminoglycans (GAGs) may improve epithelial cell integrity and therefore be useful as adjunct treatment. This study evaluated whether the relapse rate of FRD dogs that are switched back to a normal diet can be influenced using supplemental treatment with prebiotics and GAGs.

A randomized, controlled clinical trial (RCCT) was performed in dogs diagnosed with FRD. Dogs were diagnosed based on clinical exclusion diagnosis, endoscopic biopsies showing predominantly lymphoplasmacytic infiltration, and response to dietary treatment. Dogs were randomized to be fed a combination of prebiotics and GAGs (group 1) or placebo (group 2) in addition to a hydrolyzed diet. At week 10, a second endoscopy was performed and dogs were switched back to normal diet. Relapse rate was monitored every 2 weeks after that until week 18.

Statistical analysis was performed for each outcome (Canine Chronic Enteropathy Clinical Activity Index (CCECAI), clinicopathological data, endoscopic scoring, mWSAVA histological scoring index (mWSAVA), and number of relapses following switch to normal diet) using a linear mixed effects model for group comparison. Time, group, and their interactions were included as a fixed effect, whereas each dog was treated as a random effect.

Of the 35 dogs enrolled into the clinical trial, 10 in each group reached the point of second endoscopy. A total of 13 dogs (n=8 in group 1 and n=5 in group 2) reached the trial endpoint of 18 weeks. After switching back to normal diet, none of the dogs in either group relapsed. No significant differences were found over time or between groups for CCECAI, endoscopy scoring and histological scoring. Although there was a clinical worsening in the placebo group after switching back to the original diet, this was not statistically significant (CCECAI p=0.58). Post-hoc power calculation revealed that 63 dogs per group would have been needed to detect statistically significant differences in CIBDAI between treatment groups. Standard dietary treatment induced rapid clinical response in all cases, however, additional supplementation with prebiotics and GAGs did not significantly improve clinical outcome within 4 months after switching back to normal diet. Since there are very few RCCT published in CE in dogs, this pilot study provides important power analyses for planning of further studies.
Identification of the combining abilityof grain yield and its components in hybrid barley populations based on topcross analysis
Authors: Gulmira Akhmedova , Laura Tokhetova , Serikbai Umirzakov , Ainur Demesinova , Ibadulla Tautenov , Serik Bekzhanov , Omarov Kali , Bakhytzhan Shayanbekova
Published: April 2021

The topcross method for assessing combining abilityis more economical and less laborious compared to diallel analysis, and also allows the breeder to obtain quite valuable information about the inbred material. In this research, the determination of the general (GCA) and specific (SCA) combining ability of barley (Hordeum vulgare L.) hybridsin two regions of Kazakhstan contrasting in soil and climatic conditions,the role of additive and non-additive genes in the determination of thetraits understudyhas beenrevealed. It is concluded thatthe predominance of additive gene interactions in the control of the traits understudyin theconditions of the Aral Sea region indicates the possibility of effective selection already in the F2generation, and in the piedmontzone of the Almaty region, due to the high determination of these traits by dominant genes, it is necessary to differentiate the populations of hybrids, starting from the first generation and further selection shall be carried out in several cycles until the achievement of homozygosity of loci carrying dominant genes. Consequently, the genetic contribution of the additive and non-additive effects of genes to the determination and inheritance of the studied traits significantly depends on the conditions of growing the genotypes of spring barley. Of greatest practical interest are the varieties Rihane, WI2291/Roho/WI2269 from the International Center ICARDA and the variety-tester Odessa 100 (Odessa Selection and Genetic Institute, Ukraine) with high GCA and SCA effects, little dependent on growing conditions, which are recommended to be used as reliable donors in breeding programs.
Investigation of Different Free Image Analysis Software for High-Throughput Droplet Detection
Authors: Sanka Immanuel , Bartkova Simona , Pata Pille , Smolander Olli-Pekka , Scheler Ott
Published: April 2021

Droplet microfluidics has revealed innovative strategies in biology and chemistry. This advancement has delivered novel quantification methods, such as digital droplet polymerase chain reaction (ddPCR) and antibiotic heteroresistance analysis tool. For droplet analysis, researchers often use imaging techniques. Unfortunately, the analysis of images may require specific tools or programming skills to produce the expected results. In order to address the issue, we explore the potential use of standalone freely available software to detect droplets. We select four most popular software and classify them into instinctive and objective types based on their operation logic. We test and evaluate the software’s i) ability to detect droplets, ii) accuracy and precision, and iii) overall user-friendliness. In our experimental setting we find the objective type of software is better suited for droplet detection. The objective type of software also has simpler workflow or pipeline, especially aimed for non-experienced user. In our case, CellProfiler™(CP) offers the most user-friendly experience for both single image and batch processing analysis.
De novo genome assembly and functional annotation forFusarium langsethiae
Authors: Zuo Ya , Verheecke-Vaessen Carol , Molitor Corentin , Medina Angel , Magan Naresh , Mohareb Fady
Published: April 2021

Motivation

Fusarium langsethiaeis a T-2 and HT-2 mycotoxins producingFusariumspecies firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis inF. langsethiaeto help develop effective control strategies.

Results

TheF. langsethiaeassembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye; producing a genome assembly total length of 59Mb and N50 of 3.51Mb. A total of 19,336 coding genes were identified using RNA-Seq informedab-initiogene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene Ontology.

Contact

f.mohareb@cranfield.ac.uk

Data availability

Raw sequence reads and assembled genome can be downloaded from: GenBank under the accession JAFFKB000000000
Elasticity of dense actin networks produces nanonewton protrusive forces
Authors: Jasnin Marion , Hervy Jordan , Balor Stéphanie , Bouissou Anais , Proag Amsha , Voituriez Raphaël , Maridonneau-Parini Isabelle , Baumeister Wolfgang , Dmitrieff Serge , Poincloux Renaud
Published: April 2021

Actin filaments assemble into force-generating systems involved in diverse cellular functions, including cell motility, adhesion, contractility and division. It remains unclear how networks of actin filaments, which individually generate piconewton forces, can produce forces reaching tens of nanonewtons. Here we use in situ cryo-electron tomography to unveil how the nanoscale architecture of macrophage podosomes enables basal membrane protrusion. We show that the sum of the actin polymerization forces at the membrane is not sufficient to explain podosome protrusive forces. Quantitative analysis of podosome organization demonstrates that the core is composed of a dense network of bent actin filaments storing elastic energy. Theoretical modelling of the network as a spring-loaded elastic material reveals that it exerts forces of up to tens of nanonewtons, similar to those evaluated experimentally. Thus, taking into account not only the interface with the membrane but also the bulk of the network, is crucial to understand force generation by actin machineries. Our integrative approach sheds light on the elastic behavior of dense actin networks and opens new avenues to understand force production inside cells.
Effect of imputation on gene network reconstruction from single-cell RNA-seq data
Authors: Ly Lam-Ha , Vingron Martin
Published: April 2021

Despite the advances in single-cell transcriptomics the reconstruction of gene regulatory networks remains challenging. Both the large amount of zero counts in experimental data and the lack of a consensus preprocessing pipeline for single-cell RNA-seq data make it hard to infer networks from transcriptome data. Data imputation can be applied in order to enhance gene-gene correlations and facilitate downstream data analysis. However, it is unclear what consequences imputation methods have on the reconstruction of gene regulatory networks.

To study this question, we evaluate the effect of imputation methods on the performance and structure of the reconstructed networks in different experimental single-cell RNA-seq data sets. We use state-of-the-art algorithms for both imputation and network reconstruction and evaluate the difference in results before and after imputation. We observe an inflation of gene-gene correlations that affects the predicted network structures and may decrease the performance of network reconstruction in general. Yet, within the modest limits of achievable results, we also make a recommendation as to an advisable combination of algorithms, while warning against the indiscriminate use of imputation before network reconstruction in general.
A phased genome assembly for allele-specific analysis in Trypanosoma brucei
Authors: Cosentino RO , Brink BG , Siegel TN
Published: April 2021

Many eukaryotic organisms are diploid or even polyploid, i.e. they harbour two or more independent copies of each chromosome. Yet, to date most reference genome assemblies represent a mosaic consensus sequence in which the homologous chromosomes have been collapsed into one sequence. This procedure generates sequence artefacts and impedes analyses of allele-specific mechanisms. Here, we report the allele-specific genome assembly of the diploid unicellular protozoan parasite Trypanosoma brucei.

As a first step, we called variants on the allele-collapsed assembly of the T. brucei Lister 427 isolate using short-read error-corrected PacBio reads. We identified 96 thousand heterozygote variants across the genome (average of 4.2 variants / kb), and observed that the variant density along the chromosomes was highly uneven. Several long (>100 kb) regions of loss-of-heterozigosity (LOH) were identified, suggesting recent recombination events between the alleles. By analysing available genomic sequencing data of multiple Lister 427 derived clones, we found that most LOH regions were conserved, except for some that were specific to clones adapted to the insect lifecycle stage. Surprisingly, we also found that some Lister 427 clones were aneuploid. We found evidence of trisomy in chromosome five (chr 5), chr 2, chr 6 and chr 7. Moreover, by analysing RNA-seq data, we showed that the transcript level is proportional to the ploidy, evidencing the lack of a general expression control at the transcript level in T. brucei.

As a second step, to generate an allele-specific genome assembly, we used two powerful datatypes for haplotype reconstruction: raw long reads (PacBio) and chromosome conformation (Hi-C) data. With this approach, we were able to assign 99.5% of all heterozygote variants to a specific homologous chromosome, building a 66 Mb long T. brucei Lister 427 allele-specific genome assembly. Hereby, we identified genes with allele-specific premature termination codons and showed that differences in allele-specific expression at the level of transcription and translation can be accurately monitored with the fully phased genome assembly.

The obtained reference-grade allele-specific genome assembly of T. brucei will enable the analysis of allele-specific phenomena, as well as the better understanding of recombination and evolutionary processes. Furthermore, it will serve as a standard to ‘benchmark’ much needed automatic genome assembly pipelines for highly heterozygous wild species isolates.
Bistable host-pathogen interaction explains varied infection outcomes
Authors: Yu Guozhi , Hu Yingying , Wang Shizhong , Han Xingfa , Du Xiaogang , Xu Huailiang , Zeng Xianyin , Steiner Ulrich , Rolff Jens
Published: April 2021

Death or survival are the two outcomes of an infection. The development of an infection depends on multiple interplaying factors, including the temporal dynamic of host nutrition, immune response and pathogen proliferation, but how these factors collectively determine the outcome of an infection is less understood. To understand the underlying principle of infection, here, we took a systems approach by developing a simple mathematical model to understand multi-factored host-pathogen interaction. We find that nonlinear interactions feedback between host and pathogens resulting in two distinct trajectories of disease progression. We show that disease progression, measured by the pathogen load, responds in a bistable manner, by either proliferating or eventually being eliminated. We identified key processes accounting for bistability, including host’s resource assimilation, immune response and intrinsic noise. In addition, resource availability, immunity, and pathogen load at the onset of infection are also critical in determining the bistability. We then highlight, by discussing in the light of previous theoretical and experimental work, how our framework provides testable theories for host-pathogen interaction inside the host.
Structural basis for the ARF GAP activity and specificity of the C9orf72 complex
Authors: Su Ming-Yuan , Fromm Simon A. , Remis Jonathan , Toso Daniel B. , Hurley James H.
Published: April 2021

Mutation ofC9ORF72is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 forms a complex with SMCR8 and WDR41, which was reported to have GTPase activating protein activity toward ARF proteins, RAB8A, and RAB11A. We determined the cryo-EM structure of ARF1-GDP-BeF3-bound to C9orf72:SMCR8:WDR41. The SMCR8longinand C9orf72longindomains form the binding pocket for ARF1. One face of the C9orf72longindomain holds ARF1 in place, while the SMCR8longinpositions the catalytic finger Arg147 in the ARF1 active site. Mutations in interfacial residues of ARF1 and C9orf72 reduced or eliminated GAP activity. RAB8A GAP required ∼10-fold higher concentrations of the C9orf72 complex than for ARF1. These data support a specific function for the C9orf72 complex as an ARF GAP.
Changing microbial activities during low salinity acclimation in the brown algaEctocarpus subulatus
Authors: KleinJan Hetty , Caliafano Gianmaria , Aite Méziane , Fremy Enora , Frioux Clémence , Karimi Elham , Corre Erwan , Wichard Thomas , Siegel Anne , Boyen Catherine , Dittami Simon M.
Published: April 2021

Ectocarpus subulatusis one of the few brown algae found in river habitats. Its ability to tolerate freshwater is due, in part, to its uncultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grownE. subulatususing mild antibiotic treatments, which affected its ability to grow in low salinity. The acclimation to low salinity of fresh water-tolerant and intolerant holobionts was then compared. Salinity had a significant impact on bacterial gene expression as well as the expression of algae- and bacteria-associated viruses in all holobionts, albeit in different ways for each holobiont. On the other hand, gene expression of the algal host and metabolite profiles were affected almost exclusively in the fresh water intolerant holobiont. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, we identified vitamin K synthesis as one possible bacterial service missing specifically in the fresh water-intolerant holobiont in low salinity.

We also noticed an increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a compound that regulates quorum sensing. This could have caused a shift in bacterial behavior in the intolerant holobiont, resulting in virulence or dysbiosis.

Originality-Significance Statement

The importance of symbiotic microbes for the health and stress resistance of multicellular eukaryotes is widely acknowledged, but understanding the mechanisms underlying these interactions is challenging. They are especially difficult to separate in systems with one or more uncultivable components. We bridge the gap between fully controlled, cultivable model systems and purely environmental studies through the use of a multi-omics approach and metabolic models on experimentally modified “holobiont” systems. This allows us to generate two promising working hypotheses on the mechanisms by which uncultivated bacteria influence their brown algal host’s fresh water tolerance.
Retrotransposons as pathogenicity factors of the plant pathogenic fungusBotrytis cinerea
Authors: Porquier Antoine , Tisserant Constance , Salinas Francisco , Glassl Carla , Wange Lucas , Enard Wolfgang , Hauser Andreas , Hahn Matthias , Weiberg Arne
Published: April 2021

Background

Retrotransposons are genetic elements inducing mutations in all domains of life. Despite their detrimental effect, retrotransposons become temporarily active during epigenetic reprogramming and cellular stress response, which may accelerate host genome evolution. In fungal pathogens, a positive role has been attributed to retrotransposons when shaping genome architecture and expression of genes encoding pathogenicity factors; thus, retrotransposons are known to influence pathogenicity.

Results

We here uncovered a hitherto unknown role of fungal retrotransposons as being pathogenicity factors, themselves. Studying the aggressive fungal plant pathogenBotrytis cinerea, that is known to deliver some long-terminal repeat (LTR) deriving regulatory trans-species small RNAs (BcsRNAs) into plant cells to suppress host gene expression for infection we found that naturally occurring, less aggressiveB. cinereastrains possess considerably lower copy numbers of LTR retrotransposons and had lost retrotransposonBcsRNA production. By a transgenic proof-of-concept approach, we reconstituted retrotransposon expression in aBcsRNA-lackingB. cinereastrain, which resulted in enhanced aggressiveness in a retrotransposon andBcsRNA expression-dependent manner. Moreover, retrotransposon expression inB. cinerealed to suppression of plant defence-related genes during infection.

Conclusions

We propose that retrotransposons are pathogenicity factors that manipulate host plant gene expression by encoding trans-speciesBcsRNAs. Taken together, the novelty that retrotransposons are pathogenicity factors will have general impact on studies of host-microbe interactions and pathology.
Alpha oscillations reflect suppression of distractors with increased perceptual load
Authors: Gutteling Tjerk , Sillekens Lonieke , Lavie Nilli , Jensen Ole
Published: April 2021

Attention serves an essential role in cognition and behaviour allowing us to focus on behaviourally-relevant objects while ignoring distraction. Perceptual load theory states that attentional resources are allocated according to the requirements of the task, i.e. its ‘load’. The theory predicts that the resources left to process irrelevant, possibly distracting stimuli, are reduced when the perceptual load is high. However, it remains unclear how this allocation of attentional resources specifically relates to neural excitability and suppression mechanisms. In this magnetoencephalography (MEG) study, we show that brain oscillations in the alpha band (8-13Hz) implement the suppression of distracting objects when the perceptual load is high. In parallel, high load increased neuronal excitability for target objects, as reflected by rapid frequency tagging. We suggest that the allocation of resources in tasks with high perceptual load is implemented by a gain increase for targets, complemented by distractor suppression reflected by alpha band oscillations closing the ‘gate’ for interference.
Phosphoproteomics of ATR Signaling in Prophase I of Mouse Meiosis
Authors: Sims Jennie R. , Faça Vitor M. , Pereira Catalina , Arroyo-Martinez Gerardo A. , Freire Raimundo , Cohen Paula E. , Weiss Robert S. , Smolka Marcus B.
Published: April 2021

During mammalian meiosis, the ATR kinase plays crucial roles in the coordination of DNA repair, meiotic sex chromosome inactivation and checkpoint signaling. Despite the importance of ATR in meiosis, the meiotic ATR signaling network remains largely unknown. Here we defined ATR signaling during prophase I in mice. Quantitative analysis of phosphoproteomes obtained after genetic ablation of the ATR-activating 9-1-1 complex or chemical inhibition of ATR revealed over 12,000 phosphorylation sites, of which 863 phosphorylation sites were dependent on both 9-1-1 and ATR. ATR and 9-1-1-dependent signaling was enriched for S/T-Q and S/T-X-X-K motifs and included proteins involved in DNA damage signaling, DNA repair, and piRNA and mRNA metabolism. We find that ATR targets the RNA processing factors SETX and RANBP3 and regulate their localization to the sex body. Overall, our analysis establishes a comprehensive map of ATR signaling in spermatocytes and highlights potential meiotic-specific actions of ATR during prophase I.
MLL1 Methyltransferase Activity is Regulated by Distinct Nucleosome Binding Modes
Authors: Ayoub Alex , Park Sang Ho , Lee Young-Tae , Cho Uhn-Soo , Dou Yali
Published: April 2021

Here we solve the single particle cryoEM structure for the MLL1 complex with nucleosome core particle (NCP) carrying histone H3 lysine 4 to methionine mutation. The MLL1 complex displays significant rotational dynamics on the NCP, a feature distinct from the yeast SET1 complex. We identified two major binding modes of the MLL1 complex on the NCP. Both binding modes anchor on the NCP through ASH2L, but they differ drastically with regard to where the MLL1 SET domain and RbBP5 bind. We show that one of the binding modes is catalytically inactive since disrupting interactions unique to this binding mode does not affect overall MLL1 activity in an NCP-specific manner. Interestingly, the inactive binding mode is in a configuration similar to that of the ySET1- NCP complex, which is intrinsically inactive on an unmodified NCP. The high rotational dynamics of the MLL1 complex as well as distinction between MLL and yeast SET1 complexes may reflect the necessity for loci-specific regulation of H3K4 methylation states in higher eukaryotes.
Conformational landscape of full-length Smad proteins
Authors: Gomes Tiago , Martin-Malpartida Pau , Ruiz Lidia , Aragón Eric , Cordeiro Tiago N. , Macias Maria J.
Published: April 2021

Smad transcription factors, the main effectors of the TGFβ (transforming growth factor β) network, have been shaped along the evolution of multicellular animals to regulate essential processes. Smad proteins have a mixed architecture of globular domains and flexible linkers and adopt distinct quaternary structures depending on their activation state and cellular context. Here we studied the structures of full-length Smad4 and Smad2 proteins through an integrative approach combining small-angle X-ray scattering and detailed atomic information obtained from Nuclear Magnetic Resonance spectroscopy, X-ray and molecular dynamic simulations. Both Smad4 and Smad2 populate ensembles of expanded/compact conformations, with the MH1 and MH2 domains tethered by intrinsically disordered linkers that provide conformational freedom to the proteins. In solution, Smad4 is monomeric, whereas Smad2 coexists as monomer-dimer-trimer association states, even without activation. Smad2 dimers, which were previously overlooked, are proposed as key building blocks that define the functional quaternary structures of Smad proteins.

Highlights

Solution ensembles of full-length Smad2 and Smad4 proteins

Smad4 populates dynamic extended and compact monomeric conformations

Smad2 dimers may be the intermediate state to form heterotrimers with Smad4

New integrative methodological strategy for examining multi-domain and flexible proteins
Post-encoding reactivation promotes one-shot learning of episodes in humans
Authors: Wu Xiongbo , Viñals Xavier , Ben-Yakov Aya , Staresina Bernhard P. , Fuentemilla Lluís
Published: April 2021

Prior animal and human work have shown that post-encoding reinstatement plays an important role in organizing the temporal sequence of unfolding episodes in memory. Here, we investigated whether post-encoding reinstatement serves to promote the encoding of ‘one-shot’ episodic learning beyond the temporal structure in humans. In experiment 1, participants encoded sequences of pictures depicting unique and meaningful episodic-like events. We used representational similarity analysis on scalp electroencephalography recordings during encoding and found evidence of rapid picture elicited EEG patterns reinstatement at episodic offset (around 500ms post-episode). Memory reinstatement was not observed between successive elements within an episode and the degree of memory reinstatement at episodic offset predicted later recall for that episode. In experiment 2, participants encoded a shuffled version of the picture sequences from experiment 1, rendering each episode meaningless to the participant but temporally structured as in experiment 1, and we found no evidence of memory reinstatement at episodic offset. These results suggest that post-encoding memory reinstatement is akin to the rapid formation of unique and meaningful episodes that unfold over time.
Echoes of the late Pleistocene in a novel trophic cascade between cougars and feral donkeys
Authors: Lundgren Erick J. , Ramp Daniel , Middleton Owen M. , Balisi Mairin , Ripple William J. , Hasselerharm Chris D. , Sanchez Jessica N. , Wooster Eamonn I. F. , Mills Mystyn , Wallach Arian D.
Published: April 2021

Introduced large herbivores have partly filled ecological gaps formed in the late Pleistocene, when many of the Earth’s megafauna were driven extinct. However, surviving predators are widely considered unable to influence introduced megafauna, leading them to exert unusually strong herbivory and disturbance-related effects. We report on a behaviorally-mediated trophic cascade between cougars (Puma concolor) and feral donkeys (Equus africanus asinus) at desert wetlands in North America. In response to predation of juveniles, donkeys shifted from nocturnal to almost exclusively diurnal, thereby avoiding peaks in cougar activity. Furthermore, donkeys reduced the time they spent at desert wetlands by 87%: from 5.5 hours a day to 0.7 hours at sites with predation. These shifts in activity were associated with increased activity and richness of other mammal species and reduced disturbance and herbivory-related effects on these ecologically-distinct wetland ecosystems, including 49% fewer trails, 35% less trampled bare ground, and 227% more canopy cover. Cougar predation on introduced donkeys rewires an ancient food web, with diverse implications for modern ecosystems.
Chemoproteomic study uncovers HemK2/KMT9 as a new target for NTMT1 bisubstrate inhibitors
Authors: Chen Dongxing , Meng Ying , Yu Dan , Noinaj Nicholas , Cheng Xiaodong , Huang Rong
Published: April 2021

Understanding the selectivity of methyltransferase inhibitors is important to dissect the functions of each methyltransferase target. From this perspective, here we report a chemoproteomic study to profile the selectivity of a potent protein N-terminal methyltransferase 1 (NTMT1) bisubstrate inhibitor NAH-C3-GPKK (Ki, app= 7±1 nM) in endogenous proteomes. First, we describe the rational design, synthesis, and biochemical characterization of a new chemical probe6, a biotinylated analogue of NAH-C3-GPKK. Next, we systematically analyze protein networks that may selectively interact with the biotinylated probe6in concert with the competitor NAH-C3-GPKK. Besides NTMT1, the designated NTMT1 bisubstrate inhibitor NAH-C3-GPKK was found to also potently inhibit a methyltransferase complex HemK2-Trm112 (also known as KMT9-Trm112), highlighting the importance of systematic selectivity profiling. Furthermore, this is the first potent inhibitor for HemK2/KMT9 reported to date. Thus, our studies lay the foundation for future efforts towards the development of selective inhibitors for NTMT1 and HemK2/KMT9.

TOC
Correcting artifacts in ratiometric biosensor imaging; an improved approach for dividing noisy signals
Authors: Marston Daniel J. , Slattery Scott , Hahn Klaus M. , Tsygankov Denis
Published: April 2021

The accuracy of biosensor ratio imaging is limited by signal/noise. Signals can be weak when biosensor concentrations must be limited to avoid cell perturbation. This can be especially problematic in imaging of low volume regions, e.g., along the cell edge. The cell edge is an important imaging target in studies of cell motility. We show how the division of fluorescence intensities with low signal-to-noise at the cell edge creates specific artifacts due to background subtraction and division by small numbers, and that simply improving the accuracy of background subtraction cannot address these issues. We propose a new approach where, rather than simply subtracting background from the numerator and denominator, we subtract a noise correction factor (NCF) from the numerator only. This NCF can be derived from the analysis of noise distribution in the background near the cell edge or from ratio measurements in the cell regions where signal-to-noise is high. We test the performance of the method first by examining two noninteracting fluorophores distributed evenly in cells. This generated a uniform ratio that could provide a ground truth. We then analyzed actual protein activities reported by a single chain biosensor for the guanine exchange factor Asef, and a dual chain biosensor for the GTPase Cdc42. The reduction of edge artifacts revealed persistent Asef activity in a narrow band (∼640 nm wide) immediately adjacent to the cell edge. For Cdc42, the NCF method revealed an artefact that would have been obscured by traditional background subtraction approaches.
Inhibition of gibberellin accumulation by water deficiency promotes fast and long-term ‘drought avoidance’ responses in tomato
Authors: Shohat Hagai , Cheriker Hadar , Vasuki Himabindu , Illouz-Eliaz Natanella , Blum Shula , Amsellem Ziva , Tarkowská Danuše , Aharoni Asaph , Eshed Yuval , Weiss David
Published: April 2021

Plants reduce transpiration to avoid dehydration during drought episodes by stomatal closure and inhibition of canopy growth. While abscisic acid (ABA) has a primary role in ‘drought avoidance’, previous studies suggest that gibberellin (GA), might also be involved. Here we show in tomato (Solanum lycopersicum) that shortage of water inhibited the expression of the GA biosynthesis genesGA20 oxidase1(GA20ox1) andGA20ox2and induced the GA-deactivating geneGA2ox7in leaves and guard cells, resulting in reduced bioactive GA levels. Drought regulation of GA metabolism was mediated by ABA-dependent and independent pathways, and by the transcription factorDEHYDRATION RESPONSIVE ELEMENT BINDING (DREB), TINY1. Mutations inGA20ox1andGA20ox2reduced water loss due to the smaller canopy area. On the other hand, loss ofGA2ox7did not affect leaf size, but attenuated stomatal response to water deficiency; during soil dehydration,ga2ox7plants closed their stomata and reduced transpiration later than WT, suggesting thatga2ox7stomata are hyposensitive to soil dehydration. Together, the results suggest that drought-induced GA deactivation in guard cells contributes to stomatal closure at the early stages of soil dehydration, whereas inhibition of GA synthesis in leaves promotes mainly the long-term reduction in canopy growth to reduce transpiration area.
Accelerated electron transfer in nanostructured electrodes improves the sensitivity of electrochemical biosensors
Authors: Fu Kaiyu , Seo Ji-Won , Kesler Vladimir , Maganzini Nicolo , Wilson Brandon D. , Eisenstein Michael , Soh H. Tom
Published: April 2021

Electrochemical biosensors hold the exciting potential to integrate molecular detection with signal processing and wireless communication in a miniaturized, low-cost system. However, as electrochemical biosensors are miniaturized to the micron scale, their detection sensitivity degrades precipitously, thereby greatly reducing their utility in the context of molecular diagnostic applications. Studies have reported that nanostructured electrodes can greatly improve electrochemical biosensor sensitivity, but the underlying mechanism remains poorly understood, thus making it difficult to fully exploit this phenomenon to improve biosensor performance. In this work, we propose and experimentally validate a novel mechanism in which electron transfer is physically accelerated within nanostructured electrodes due to reduced charge screening, resulting in enhanced sensitivity. We show that this mechanism can be exploited to achieve up to 24-fold increase in signal and nearly four-fold lower limit-of-detection relative conventional planar electrodes. This accelerated electron transfer mechanism should prove broadly applicable for improving the performance of electrochemical biosensors.
Divergent Acyl Carrier Protein Decouples Mitochondrial Fe-S Cluster Biogenesis from Fatty Acid Synthesis in Malaria Parasites
Authors: Falekun Seyi , Sepulveda Jaime , Jami-Alahmadi Yasaman , Park Hahnbeom , Wohlschlegel James A. , Sigala Paul A.
Published: April 2021

Plasmodium falciparummalaria parasites are early-diverging eukaryotes with many unusual metabolic adaptations. Understanding these adaptations will give insight into parasite evolution and unveil new parasite-specific drug targets. Most eukaryotic cells retain a mitochondrial fatty acid synthesis (FASII) pathway whose acyl carrier protein (mACP) and 4-phosphopantetheine (Ppant) prosthetic group provide a soluble scaffold for acyl chain synthesis. In yeast and humans, mACP also functions to biochemically couple FASII activity to electron transport chain (ETC) assembly and Fe-S cluster biogenesis. In contrast to most eukaryotes, thePlasmodiummitochondrion lacks FASII enzymes yet curiously retains a divergent mACP lacking a Ppant group. We report that ligand-dependent knockdown of mACP is lethal to parasites, indicating an essential FASII-independent function. Decyl-ubiquinone rescues parasites temporarily from death, suggesting a dominant dysfunction of the mitochondrial ETC followed by broader cellular defects. Biochemical studies reveal thatPlasmodiummACP binds and stabilizes the Isd11-Nfs1 complex required for Fe-S cluster biosynthesis, despite lacking the Ppant group required for this association in other eukaryotes, and knockdown of parasite mACP causes loss of both Nfs1 and the Rieske Fe-S protein in ETC Complex III. This work reveals thatPlasmodiumparasites have evolved to decouple mitochondrial Fe-S cluster biogenesis from FASII activity, and this adaptation is a shared metabolic feature of otherApicomplexanpathogens, includingToxoplasmaandBabesia. This discovery also highlights the ancient, fundamental role of ACP in mitochondrial Fe-S cluster biogenesis and unveils an evolutionary driving force to retain this interaction with ACP independent of its eponymous function in FASII.

Significance Statement

Plasmodiummalaria parasites are single-celled eukaryotes that evolved unusual metabolic adaptations. Parasites require a mitochondrion for blood-stage viability, but essential functions beyond the electron transport chain are sparsely understood. Unlike yeast and human cells, thePlasmodiummitochondrion lacks fatty acid synthesis enzymes but retains a divergent acyl carrier protein (mACP) incapable of tethering acyl groups. Nevertheless, mACP is essential for parasite viability by binding and stabilizing the core mitochondrial Fe-S cluster biogenesis complex via a divergent molecular interface lacking an acyl-pantetheine group that contrasts with other eukaryotes. This discovery unveils an essential metabolic adaptation inPlasmodiumand other human parasites that decouples mitochondrial Fe-S cluster biogenesis from fatty acid synthesis and evolved at or near the emergence ofApicomplexanparasitism.
Limitations of the ABEGO representation: ambiguity between αα-corner and αα-hairpin
Authors: Sakuma Koya
Published: April 2021

ABEGO is a coarse-grained representation for polypeptide backbone dihedral angles. The Ramachandran map is divided into four segments denoted as A, B, E, and G to represent the local conformation of polypeptide chains in the character strings. Although the ABEGO representation is widely used in structural informatics and protein design, it cannot capture minor differences in backbone dihedral angles, which potentially leads to ambiguity between two structurally distinct fragments. Here, we show a nontrivial example of two local motifs that could not be distinguished by their ABEGO representations. We found that two well-known local motifs αα-hairpins and αα-corners are both represented as α-GBB-α and thus indistinguishable in the ABEGO representation, although they show distinct arrangements of the flanking α-helices. We also found that α-GBB-α motifs caused a loss of efficiency in the ABEGO-based fragment-assembly simulations for protein backbone design. Nevertheless, we designed amino-acid sequences that were predicted to fold into the target topologies that contained these α-GBB-α motifs. Our finding that certain local motifs bottleneck the ABEGO-based fragment-assembly simulations for construction of backbone structures suggests that finer representations of backbone torsion angles are required for efficiently generating diverse topologies containing such indistinguishable local motifs.
Changes in regional white matter volumetry and microstructure during the post-adolescence period: a cross-sectional study of a cohort of 1,713 university students
Authors: Tsuchida Ami , Laurent Alexandre , Crivello Fabrice , Petit Laurent , Pepe Antonietta , Beguedou Naka , Debette Stephanie , Tzourio Christophe , Mazoyer Bernard
Published: April 2021

Human brain white matter undergoes a protracted maturation that continues well into adulthood. Recent advances in diffusion-weighted imaging (DWI) methods allow detailed characterizations of the microstructural architecture of white matter, and they are increasingly utilised to study white matter changes during development and ageing. However, relatively little is known about the late maturational changes in the microstructural architecture of white matter during post-adolescence. Here we report on regional changes in white matter volume and microstructure in young adults undergoing university-level education. As part of the MRi-Share multi-modal brain MRI database, multi-shell, high angular resolution DWI data were acquired in a unique sample of 1,713 university students aged 18 to 26. We assessed the age and sex dependence, as well as hemispheric asymmetry of diffusion metrics derived from diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI), in the white matter regions as defined in the John Hopkins University (JHU) white matter labels atlas. We demonstrate that while regional white matter volume is relatively stable over the age range of our sample, the white matter microstructural properties show clear age-related variations. Globally, it is characterised by a robust increase in neurite density index (NDI), and to a lesser extent, orientation dispersion index (ODI). These changes are accompanied by a decrease in diffusivity. In contrast, there is minimal age-related variation in fractional anisotropy. There are regional variations in these microstructural changes: some tracts, most notably cingulum bundles, show a strong age-related increase in NDI coupled with decreases in radial and mean diffusivity, while others, mainly cortico-spinal projection tracts, primarily show an ODI increase and axial diffusivity decrease. These age-related variations are not different between males and females, but males show higher NDI and ODI and lower diffusivity than females across many tracts. We also report a robust hemispheric asymmetry in both the volume and microstructural properties in many regions. These findings emphasise the complexity of changes in white matter structure occurring in this critical period of late maturation in early adulthood.
Quantification and image-derived phenotyping of retinal ganglion cell nuclei in theneemouse model of congenital glaucoma
Authors: van der Heide Carly J. , Meyer Kacie J. , Hedberg-Buenz Adam , Pellack Danielle , Pomernackas Nicholas , Mercer Hannah E. , Anderson Michael G.
Published: April 2021

Theneemouse model exhibits characteristic features of congenital glaucoma, a common cause of childhood blindness. The current study ofneemice had two components. First, the time course of neurodegeneration inneeretinal flat-mounts was studied over time using a retinal ganglion cell (RGC)-marker, BRN3A; a pan-nuclear marker, TO-PRO-3; and H&E staining. Based on segmentation of nuclei using ImageJ and RetFM-J, this analysis identified a rapid loss of BRN3A+nuclei from 4–15 weeks of age, with the first statistically significant difference in average density compared to age-matched controls detected in 8-week-old cohorts (49% reduction innee). Consistent with a model of glaucoma, no reductions in BRN3A−nuclei were detected, but the combined analysis indicated that some RGCs lost BRN3A marker expression prior to actual cell loss. These results have a practical application in the design of experiments usingneemice to study mechanisms or potential therapies for congenital glaucoma. The second component of the study pertains to a discovery-based analysis of the large amount of image data with 748,782 segmented retinal nuclei. Using the automatedly collected region of interest feature data captured by ImageJ, we tested whether RGC density of glaucomatous mice was significantly correlated to average nuclear area, perimeter, Feret diameter, or MinFeret diameter. These results pointed to two events influencing nuclear size. For variations in RGC density above approximately 3,000 nuclei/mm2apparent spreading was observed, in which BRN3A−nuclei—regardless of genotype—became slightly larger as RGC density decreased. This same spreading occurred in BRN3A+nuclei of wild-type mice. For variation in RGC density below 3,000 nuclei/mm2, which only occurred in glaucomatousneemutants, BRN3A+nuclei became smaller as disease was progressively severe. These observations have relevance to defining RGCs of relatively higher sensitivity to glaucomatous cell death and the nuclear dynamics occurring during their demise.