bluuebunny/crossref_metadata_2025 huggingface dataset:
Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate
Authors: Seim Ian , Posey Ammon E. , Snead Wilton T. , Stormo Benjamin M. , Klotsa Daphne , Pappu Rohit V. , Gladfelter Amy S.
Published: April 2021

Ribonucleoprotein bodies are exemplars of membraneless biomolecular condensates that can form via spontaneous or driven phase transitions. The fungal protein Whi3 forms ribonucleoprotein condensates with different RNA molecules, and these condensates are implicated in key processes such as cell-cycle control and generating cell polarity. Whi3 has a modular architecture that includes a Q-rich intrinsically disordered region (IDR) and a tandem RNA recognition module. Here, we demonstrate that a 21-residue stretch within the Q-rich IDR has a weak intrinsic preference for forming alpha-helical conformations. Through mutagenesis, we find that increased alpha helicity enhances oligomerization in the dilute phase. One consequence of enhanced oligomerization is a dilution of Whi3 in the dense phase. The opposite behavior is observed when helicity within the 21-residue stretch of the Q-rich region is abrogated. Thus, the formation of dilute phase oligomers, driven by a specific sequence motif and potential synergies with the rest of the IDR, opposes incorporation of the Whi3 protein into the dense phase, thereby altering the dense phase stoichiometry of protein to RNA. Our findings, which stand in contrast to other systems where oligomerization has been shown to enhance the drive for phase separation, point to a novel mechanism that might be operative for influencing compositions of condensates. Our work also points to routes for designing synthetic ribonucleoprotein condensates whereby modulation of protein oligomerization via homotypic interactions can impact dense phase concentrations, stoichiometries, and material properties.

Significance

A large sub-class of biomolecular condensates are linked to RNA regulation and are known as ribonucleoprotein (RNP) bodies. While extensive work has identified driving forces for biomolecular condensate formation, relatively little is known about forces that oppose assembly. Here, using a fungal RNP protein, Whi3, we show that a portion of its intrinsically disordered, glutamine-rich region modulates phase separation by forming transient alpha helical structures that promote the assembly of dilute phase oligomers. These oligomers detour Whi3 proteins from condensates, thereby impacting the driving forces for phase separation, the protein-to-RNA ratio in condensates, and the material properties of condensates. Our findings show how nanoscale conformational and oligomerization equilibria can influence mesoscale phase equilibria.
Working Memory Performance after Daily Caffeine Intake: Compromised Performance and Reduced Hippocampal Activity
Authors: Lin Yu-Shiuan , Weibel Janine , Landolt Hans-Peter , Santini Francesco , Slawik Helen , Borgwardt Stefan , Cajochen Christian , Reichert Carolin
Published: April 2021

Neuroprotective effects of caffeine have been frequently reported in the context of disease and cognitive dysfunction as well as in epidemiological studies in humans. However, evidence on caffeine effects on neural and memory functions during daily intake in a healthy cognitive state remains scarce. This randomized double-blind placebo-controlled crossover study investigated working memory functions by N-back tasks and functional magnetic resonance imaging (fMRI) after daily caffeine intake compared to a placebo baseline and to acute caffeine withdrawal in 20 young healthy volunteers. Each volunteer was given 3 times 150 mg caffeine for 10 days in the daily caffeine condition, 3 times 150 mg mannitol for 10 days in the placebo condition, and 9-day caffeine plus 1-day mannitol in the acute withdrawal condition. During the 10thday, participants performed 4 N-back sessions (two loads each: 0- and 3-back) under controlled laboratory conditions. During the 4thsession of N-Back (i.e. at 5.5 h, 36.5 h and > 10 days after the last caffeine intake in the caffeine, withdrawal, and placebo condition, respectively) we assessed blood-oxygen-level-dependent (BOLD) activity. During the entire 10thday, in 0-back tasks, we observed longer reaction times (RTs) in the withdrawal compared to the placebo (Cohen’s d = 0.7) and caffeine condition (Cohen’s d = 0.6), but no significant effects of conditions on error rates. In contrast, in 3-back tasks (controlled for 0-back), the RTs in the caffeine condition were longer compared to placebo (Cohen’s d = 0.6) and withdrawal (Cohen’s d = 0.5). Error rates were higher during both caffeine and withdrawal conditions compared to placebo (Cohen’s d of both contrasts = 0.4). Whole-brain analyses on fMRI data did not reveal significant condition-dependent differences in activities between task loads. Across task loads, however, we observed a reduced hippocampal activation (Cohen’s d = −1.3) during the caffeine condition compared to placebo, while no significant difference in brain activities between withdrawal and placebo conditions. Taken together, the worse working memory function and the hippocampal hypoactivation implicate a potential detrimental effect of daily caffeine intake on neurocognitive functions of healthy adults. Moreover, they echo the hippocampal volumetric reduction reported previously in the same volunteers. Lastly, acute withdrawal from daily caffeine intake impairs both low-order cognitive processes and working memory performance. Taking earlier studies on acute caffeine effects into account, our findings indicate that daily caffeine intake elicits a dynamic change in cerebral activities during the course of repeated consumption, with unknown consequences in the long run.
Neuromodulation-induced burst firing in parvalbumin interneurons of the basolateral amygdala mediates transition between fear-associated network and behavioral states
Authors: Fu Xin , Teboul Eric , Maguire Jamie , Tasker Jeffrey G.
Published: April 2021

Patterned coordination of network activity in the basolateral amygdala (BLA) is important for fear expression. Neuromodulatory systems play an essential role in regulating changes between behavioral states, however the mechanisms underlying the neuromodulatory control of BLA circuits that mediates transitions between brain and behavioral states remain largely unknown. We examined the role of neuromodulation of parvalbumin (PV)-expressing interneurons in the BLA in coordinating network and behavioral states using combined chemogenetics,ex vivopatch clamp recordings, andin vivoandex vivolocal field potential recordings. We show that Gq signaling, whether by the designer receptor, hM3D, α1A adrenoreceptors, or 5-HT2a serotonergic receptors, induces a previously undescribed, highly stereotyped bursting pattern of activity in BLA PV interneurons that generates synchronous bursts of inhibitory postsynaptic currents and phasic firing in the BLA principal neurons. The Gq activation in PV interneurons induced a transition from tonic to phasic firing in the BLA PV neurons and principal neurons and suppressed BLA gamma oscillations in slices and suppressed BLA gamma and potentiated theta powerin vivo. Gq activation in BLA PV interneurons also facilitated fear memory recall, consistent with previous reports of BLA gamma suppression and theta potentiation during conditioned fear expression. Thus, our data reveal a BLA parvalbumin neuron-specific Gq neuromodulatory mechanism that mediates the transition to a fear-associated network and behavioral state.
Gene editing in Farm Animals: A Step Change for Eliminating Epidemics on our Doorstep?
Authors: Leony Petersen Gertje Eta , Buntjer Jaap , Hely Fiona S. , Byrne Timothy John , Whitelaw Bruce , Doeschl-Wilson Andrea
Published: April 2021

Recent breakthroughs in gene-editing technologies that can render individuals fully resistant to infections may offer unprecedented opportunities for controlling future epidemics. Yet, their potential for reducing disease spread are poorly understood as the necessary theoretical framework for estimating epidemiological effects arising from gene editing applications is currently lacking. Here, we develop semi-stochastic modelling approaches to investigate how the adoption of gene editing may affect infectious disease prevalence in farmed animal populations and the prospects and time-scale for disease elimination. We apply our models to the Porcine Reproductive and Respiratory Syndrome PRRS, one of the most persistent global livestock diseases to date. Whereas extensive control efforts have shown limited success, recent production of gene-edited pigs that are fully resistant to the PRRS virus have raised expectations for eliminating this deadly disease.

Our models predict that disease elimination on a national scale would be difficult to achieve if gene editing was used as the only disease control. However, when complemented with vaccination, the introduction of 10% of genetically resistant animals in a fraction of herds could be sufficient for eliminating the disease within 3-6 years. Besides strategic distribution of genetically resistant animals, several other key determinants underpinning the epidemiological impact of gene-editing were identified.
Programmable Microbial Ink for 3D Printing of Living Materials Produced from Genetically Engineered Protein Nanofibers
Authors: Duraj-Thatte Anna M. , Manjula-Basavanna Avinash , Rutledge Jarod , Xia Jing , Hassan Shabir , Sourlis Arjirios , Rubio Andrés G. , Lesha Ami , Zenkl Michael , Kan Anton , Weitz David A. , Zhang Yu Shrike , Joshi Neel S.
Published: April 2021

Living cells have the capability to synthesize molecular components and precisely assemble them from the nanoscale to build macroscopic living functional architectures under ambient conditions.1–3The emerging field of living materials has leveraged microbial engineering to produce materials for various applications, but building 3D structures in arbitrary patterns and shapes has been a major challenge.1–14We set out to develop a new bioink, termed as “microbial ink” that is produced entirely from genetically engineered microbial cells, programmed to perform a bottom-up, hierarchical self-assembly of protein monomers into nanofibers, and further into nanofiber networks that comprise extrudable hydrogels. We further demonstrate the 3D printing of functional living materials by embedding programmedEscherichia coli(E. coli) cells and nanofibers into microbial ink, which can sequester toxic moieties, release biologics and regulate its own cell growth through the chemical induction of rationally designed genetic circuits. This report showcases the advanced capabilities of nanobiotechnology and living materials technology to 3D-print functional living architectures.
When good mutations go bad: how population size can change the direction of natural selection
Authors: Raynes Yevgeniy , Burch Christina L. , Weinreich Daniel M.
Published: April 2021

Classical evolutionary theory holds that the efficiency, but not the direction, of natural selection depends on population size. In small populations, drift overwhelms selection, rendering all fitness-affecting mutations selectively neutral. Yet, beneficial mutations never become deleterious and deleterious mutations never become beneficial. Remarkably, several mutations, including in modifiers of recombination and mutation rate, have now been shown to be favored at some population sizes but disfavored at others, challenging established theory. Previously, we have designated this phenomenon sign inversion. Here we show that, unlike selected mutations in the classical framework, mutations susceptible to sign inversion confer both fitness costs and fitness benefits, that vary among their carriers. Furthermore, all such mutations can be classified based on whether their effects differ between or within mutant lineages. Using computer simulations, we demonstrate that both between-lineage and within-lineage variability can cause sign inversion and elucidate the common underlying mechanism. Our results confirm that variability in the sign of selective effects is necessary for sign inversion, which occurs because drift overwhelms selection on carriers bearing the cost and carriers enjoying the benefit at different population sizes.
Ruxolitinib versus Dexamethasone in Hospitalized Adults with Covid-19: multicenter matched-controlled study
Authors: Stanevich O.V. , Fomina D.S. , Bakulin I.G. , Galeev Sh. I. , Bakin E.A. , Belash V.A. , Kulikov A.N. , Lebedeva A.A. , Lioznov D.A. , Polushin Yu S. , Shlyk I.V. , Vorobyev E.A. , Vorobyeva S.V. , Surovceva T.V. , Bakulina N.V. , Lysenko M.A. , Moiseev I.S.
Published: April 2021

Background

Several anti-cytokine therapies were tested in the randomized trials in hospitalized patients with severe acute respiratory syndrome coronavirus 2 infection (COVID-19). Both janus kinase (JAK) inhibitor, baricitinib, and dexamethasone demonstrated the reduction of mortality. In this matched control study we compared dexamethasone to another JAK inhibitor, ruxolitinib.

Methods

The study included 146 hospitalized patients with COVID-19 and oxygen support requirement. The control group was selected 1:1 from 1355 dexamethasone-treated patients and was matched by 29 clinical and laboratory parameters predicting survival.

Results

Ruxolitinib treatment in the general cohort of patients was associated with equivalent to dexamethasone mortality rate: 9,6% (95% CI 4,6-14,6%) vs 13,0% (95% CI 7,5-18,5%, superiority p=0.35, non-inferiority p=0.0137), respectively. Time to discharge without oxygen support requirement was also not different between these groups: 13 vs 11 days (p=0.13). Subgroup analysis without adjustment for multiple comparisons demonstrated reduced mortality in ruxolitnib-treated patients with febrile fever (OR 0.33, 95%CI 0.11-1.00). Except higher incidence of grade 1 thrombocytopenia (37% vs 23%, p=0.042), ruxolitinib therapy was associated with better safety profile due to reduced rate of severe cardiovascular adverse events (6.8% vs 15%, p=0.025).

Conclusions

Ruxolitinib may be an alternative anti-cytokine therapy with comparable efficacy in patients with potential risks of steroid administration. Patients with febrile fever at admission may benefit from ruxolitinib administration.

Funding

Ruxolitinib was obtained from Novartis through Managed Access Program (MAP).
Simulation of aerosol and droplet spread during upper airway and gastrointestinal endoscopy
Authors: Heymer Johannes , Dengler Florian , Krohn Alexander , Jaki Christina , Schilling Tobias , Müller-Schilling Martina , Kandulski Arne , Ott Matthias
Published: April 2021

Objective

Aerosols and droplets are the main vectors in transmission of highly contagious SARS-Cov-2. Invasive diagnostic procedures like upper airway and gastrointestinal endoscopy have been declared as aerosol generating procedures. Protection of health care workers is crucial in times of COVID-19 pandemic.

Methods

We simulated aerosol and droplet spread during upper airway and gastrointestinal endoscopy with and without physico-mechanical barriers using a simulation model.

Results

A clear plastic drape as used for central venous access markedly reduced visualized aerosol and droplet spread during endoscopy.

Conclusion

A simple and cheap drape has the potential to reduce aerosol and droplet spread during endoscopy. In terms of health care worker protection, this may be important particularly in low- or moderate-income countries.
Transient dopamine neuron activity precedes and encodes the vigor of contralateral movements
Authors: Mendonça Marcelo D , da Silva Joaquim Alves , Hernandez Ledia F. , Castela Ivan , Obeso José , Costa Rui M
Published: April 2021

Dopamine neurons (DANs) in the substantia nigra pars compacta (SNc) have been related to movement vigor, and loss of these neurons leads to bradykinesia in Parkinson’s disease. However, it remains unclear whether DANs encode a general motivation signal or modulate movement kinematics. We imaged activity of SNc DANs in mice trained in a novel operant task which relies on individual forelimb sequences. We uncovered that a similar proportion of SNc DANs increased their activity before ipsi-vs. contralateral sequences. However, the magnitude of this activity was higher for contralateral actions, and was related to contralateral but not ipsilateral sequence length. In contrast, the activity of reward-related DANs, largely distinct from those modulated by movement, was not lateralized. Finally, unilateral dopamine depletion impaired contralateral, but not ipsilateral, sequence length. These results indicate that movement-initiation DANs encode more than a general motivation signal, and invigorate kinematic aspects of contralateral movements.

Teaser

Transient activity in substantia nigra compacta dopamine neurons encodes contralateral, but not ipsilateral action vigor.
Untargeted1H NMR Metabolomics and Pathway Analysis Reveals Dysregulated Proteostasis in Cyclophilin D (CypD)-deficient Mice Tissues
Authors: Adegbite YI , Adegbite OS , Ouyang Y , Sutton R , Criddle DN , Lian LY
Published: April 2021

Cyclophilin D (CypD) is a nuclear-encoded mitochondrial protein. Although best known as a regulator of the mitochondrial permeability transition pore (MPTP), it is also implicated in the regulation of cellular bioenergetics and extramitochondrial activities. In addition, being a peptidyl prolylcis-transisomerase (PPIase), deletion of CypD is likely to affect protein stability in the mitochondria; however, there is little direct evidence of this. In this study, untargeted1H NMR metabolomics, coupled with multivariate analysis, was used to describe simultaneous changes in the metabolic system of CypD-deficient mice liver, heart, and pancreas, with data from the serum to identify systematic changes. Metabolomics Pathway Analyses (MetPA) revealed commonly perturbed metabolites in the different mouse tissues lacking CypD, with significantly enriched pathways that are related to amino acid, glucose and purine metabolisms, and bioenergetics. Serum from CypD-deficient mice confirmed changes in tissue urea cycle, lipid metabolism and ketogenesis. Overall this study reveals the role of CypD in maintaining protein homeostasis, concurring with its biochemical property as a peptidyl-prolyl isomerase and also demonstrates the wider metabolic adaptations induced by the deletion of theppifgene, resulting in a CypD-deficient mice metabolome that is different from the wild-type system.
Burkholderia PglL enzymes are serine preferring oligosaccharidetransferases which target conserved proteins across the Burkholderia genus
Authors: Hayes Andrew J. , Lewis Jessica M. , Davies Mark R. , Scott Nichollas E.
Published: April 2021

Glycosylation is increasingly recognised as a common protein modification within bacterial proteomes. While great strides have been made in identifying species that contain glycosylation systems, our understanding of the proteins and sites targeted by these enzymes is far more limited. Within this work we explore the conservation of glycoproteins andO-linked glycosylation sites across the pan-Burkholderiaglycoproteome. Using a multi-protease glycoproteomic approach we generate high-confidence glycoproteomes and associated glycosylation sites in two widely utilizedB. cenocepaciastrains, K56-2 and H111. This resource reveals glycosylation occurs exclusively at serine residues and that glycoproteins/glycosylation sites are highly conserved across 294 publicly availableB. cenocepaciagenomes. Consistent with this we demonstrate that the substitution of Serine for Threonine residues in a model protein results in a dramatic decrease in glycosylation efficiency by the oligosaccharidetransferase pglLBCeven when pglLBCis overexpressed. This preference for glycosylation at Serine residues is observed across at least 9Burkholderiaglycoproteomes supporting that Serine is the dominant residue targeted by pglL-mediated glycosylation across theBurkholderiagenus. Using population genomics we observe that pglL targeted glycosylated proteins are common acrossBurkholderiaspecies. Combined, this work demonstrates that PglL enzymes of the Burkholderia genus are Serine-preferring oligosaccharidetransferases that target conserved and shared protein substrates across theBurkholderiagenus.
Modular biosynthesis of plant hemicellulose and its impact on yeast cells
Authors: Robert Madalen , Waldhauer Julian , Stritt Fabian , Yang Bo , Pauly Markus , Voiniciuc Cătălin
Published: April 2021

Background

The carbohydrate polymers that encapsulate plants cells have benefited humans for centuries and have valuable biotechnological uses. In the past five years, exciting possibilities have emerged in the engineering of polysaccharide-based biomaterials. Despite impressive advances on bacterial cellulose-based hydrogels, comparatively little is known about how plant hemicelluloses can be reconstituted and modulated in cells suitable for biotechnological purposes.

Results

Here, we assembled cellulose synthase-like A (CSLA) enzymes using an optimizedPichia pastorisplatform to produce tunable heteromannan (HM) polysaccharides in yeast. By swapping the domains of plant mannan and glucomannan synthases, we engineered chimeric CSLA proteins that made β-1,4-linked mannan in quantities surpassing those of the native enzymes while minimizing the burden on yeast growth. Prolonged expression of a glucomannan synthase fromAmorphophallus konjacwas toxic to yeast cells: reducing biomass accumulation and ultimately leading to compromised cell viability. However, an engineered glucomannan synthase as well as CSLA pure mannan synthases and a CSLC glucan synthase did not inhibit growth. Interestingly,Pichiacell size could be increased or decreased depending on the composition of the CSLA protein sequence. HM yield and glucose incorporation could be further increased by co-expressing chimeric CSLA proteins with a MANNAN-SYNTHESIS-RELATED (MSR) co-factor fromArabidopsis thaliana.

Conclusion

The results provide novel routes for the engineering of polysaccharide-based biomaterials that are needed for a sustainable bioeconomy. The characterization of chimeric cellulose synthase-like enzymes in yeast offers an exciting avenue to produce plant polysaccharides in a tunable manner. Furthermore, cells modified with non-toxic plant polysaccharides such as β-mannan offer a modular chassis to produce and encapsulate sensitive cargo such as therapeutic proteins.
Sox8 remodels the cranial ectoderm to generate the ear
Authors: Buzzi Ailin Leticia , Chen Jingchen , Thiery Alexandre , Delile Julien , Streit Andrea
Published: April 2021

The vertebrate inner ear arises from a pool of progenitors with the potential to contribute to all the sense organs and cranial ganglia in the head. Here we explore the molecular mechanisms that control ear specification from these precursors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with the first genome-wide characterization of non-coding elements that integrate this information. This analysis places the transcription factor Sox8 at the top of the ear determination network. Introducing Sox8 into cranial ectoderm not only converts non-ear cells into ear progenitors, but also activates the cellular programs for ear morphogenesis and neurogenesis. Thus, Sox8 has the unique ability to remodel transcriptional networks in the cranial ectoderm towards ear identity.
Identification of druggable host targets needed for SARS-CoV-2 infection by combined pharmacological evaluation and cellular network directed prioritization both in vitro and in vivo
Authors: Patten J.J. , Keiser Patrick T. , Gysi Deisy , Menichetti Giulia , Mori Hiroyuki , Donahue Callie J. , Gan Xiao , Valle Italo do , Geoghegan-Barek Kathleen , Anantpadma Manu , Boytz RuthMabel , Berrigan Jacob L. , Hulsey-Stubbs Sarah , Ayazika Tess , O’Leary Colin , Jalloh Sallieu , Wagner Florence , Ayehunie Seyoum , Elledge Stephen J. , Anderson Deborah , Loscalzo Joseph , Zitnik Marinka , Gummuluru Suryaram , Namchuk Mark N. , Barabási Albert-László , Davey Robert A.
Published: April 2021

Identification of host factors contributing to replication of viruses and resulting disease progression remains a promising approach for development of new therapeutics. Here, we evaluated 6710 clinical and preclinical compounds targeting 2183 host proteins by immunocytofluorescence-based screening to identify SARS-CoV-2 infection inhibitors. Computationally integrating relationships between small molecule structure, dose-response antiviral activity, host target and cell interactome networking produced cellular networks important for infection. This analysis revealed 389 small molecules, >12 scaffold classes and 813 host targets with micromolar to low nanomolar activities. From these classes, representatives were extensively evaluated for mechanism of action in stable and primary human cell models, and additionally against Beta and Delta SARS-CoV-2 variants and MERS-CoV. One promising candidate, obatoclax, significantly reduced SARS-CoV-2 viral lung load in mice. Ultimately, this work establishes a rigorous approach for future pharmacological and computational identification of novel host factor dependencies and treatments for viral diseases.
Energy Penalties Enhance Flexible Receptor Docking in a Model Cavity
Authors: Kamenik Anna S. , Singh Isha , Lak Parnian , Balius Trent E. , Liedl Klaus R. , Shoichet Brian K.
Published: April 2021

Protein flexibility remains a major challenge in library docking due to difficulties in sampling conformational ensembles with accurate probabilities. Here we use the model cavity site of T4 Lysozyme L99A to test flexible receptor docking with energy penalties from molecular dynamics (MD) simulations. Crystallography with larger and smaller ligands indicates that this cavity can adopt three major conformations, open, intermediate, and closed. Since smaller ligands typically bind better to the cavity site, we anticipate an energy penalty for cavity opening. To estimate its magnitude, we calculate conformational preferences from MD simulations. We find that including a penalty term is essential for retrospective ligand enrichment, otherwise high-energy states dominate the docking. We then prospectively docked a library of over 900,000 compounds for new molecules binding to each conformational state. Absent a penalty term, the open conformation dominated the docking results; inclusion of this term led to a balanced sampling of ligands against each state. High ranked molecules were experimentally tested by Tm-upshift and X-ray crystallography. From 33 selected molecules, we identified 18 new ligands and determined 13 crystal structures. Most interesting were those bound to the open cavity, where the buried site opens to bulk solvent. Here, highly unusual ligands for this cavity had been predicted, including large ligands with polar tails; these were confirmed both by binding and by crystallography. In docking, incorporating protein flexibility with thermodynamic weightings may thus access new ligand chemotypes. The MD approach to accessing and, crucially, weighting such alternative states may find general applicability.

Significance Statement

The dynamic nature of biomolecules is typically neglected in docking screens for ligand discovery. Key to benefitting from various receptor conformations is not only structural but also thermodynamic information. Here we test a general approach that uses conformational preferences from enhanced and conventional MD simulations to account for the cost of transitions to high energy states. Including this information as a conformational penalty term in a docking scoring function, we perform retrospective and prospective screens and experimentally confirm novel ligands with Tm-upshift and X-ray crystallography.
Structure and dynamics of FCHo2 docking on membranes
Authors: Alaoui F. El , Casuso I. , Sanchez-Fuentes D. , André-Arpin C. , Rathar R. , Baecker V. , Castro A. , Lorca T. , Viaud J. , Vassilopoulos S. , Carretero-Genevrier A. , Picas. L.
Published: April 2021

Clathrin-mediated endocytosis (CME) is a central trafficking pathway in eukaryotic cells regulated by phosphoinositides. The plasma membrane phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an instrumental role in driving CME initiation. The F-BAR domain only protein 1 and 2 complex (FCHo1/2) is among the early proteins that reach the plasma membrane, but the exact mechanisms triggering its recruitment remains elusive. Here, we show the molecular dynamics of FCHo2 self-assembly on membranes by combining bottom-up synthetic approaches on in vitro and cellular membranes. Our results indicate that PI(4,5)P2 domains assist FCHo2 docking at specific membrane regions, where it self-assembles into ring-like shape protein patches. We show that binding of FCHo2 on cellular membranes promotes PI(4,5)P2 clustering at the boundary of cargo receptors and that this accumulation enhances clathrin assembly. Thus, our results provide a mechanistic framework that could explain the recruitment of early PI(4,5)P2-interacting proteins at endocytic sites.
Pseudogene-mediated gene conversion after CRISPR-Cas9 editing demonstrated by partialCD33conversion withSIGLEC22P
Authors: Shaw Benjamin C. , Estus Steven
Published: April 2021

Although gene editing workflows typically consider the possibility of off-target editing, pseudogene-directed homology repair has not, to our knowledge, been reported previously. Here, we employed a CRISPR-Cas9 strategy for targeted excision of exon 2 inCD33in U937 human monocyte cell line. Candidate clonal cell lines were screened by using a clinically relevant antibody known to label the IgV domain encoded by exon 2 (P67.6, gemtuzumab). In addition to the anticipated deletion of exon 2, we also found unexpected P67.6-negative cell lines which had apparently retained CD33 exon 2. Sequencing revealed that these lines underwent gene conversion from the nearby SIGLEC22P pseudogene during homology repair that resulted in three missense mutations relative to CD33. Ectopic expression studies confirmed that the P67.6 epitope is dependent upon these amino acids. In summation, we report that pseudogene-directed homology repair can lead to aberrant CRISPR gene editing.
Group size influences individual metabolic traits in a social fish
Authors: Chrétien Emmanuelle , Boisclair Daniel , Cooke Steven J. , Killen Shaun S.
Published: April 2021

Group living is widespread among animal species and yields both costs and benefits. Presence of conspecifics can restrict or enhance the expression of individual behaviour, and the recent social environment is thought to affect behavioural responses in later contexts, even when individuals are alone. However, little is known about how social dynamics influence the expression of individual physiological traits, including metabolic rates.

There is some evidence that shoaling can reduce fish metabolic rates, but habitat conditions such as shelter availability may generate density-dependent influences on individual metabolic rates.

We investigated how social group size and availability of shelter influence Eurasian minnowPhoxinus phoxinusmetabolic rates estimated by respirometry in the presence or absence of plant shelter. Respirometry trials were conducted before and after we housed fish for three weeks in a social treatment consisting in a specific group size (n= 4 or 8) and shelter availability (presence or absence of plant shelter in the holding tank).

Minimum day-time and night-time metabolic rates estimated while in presence of plant shelter were lower than when estimated in absence of plant shelter, both before and after individuals were housed in their social group size and shelter availability treatment. Standard metabolic rate was higher for fish held in groups of four as compared to fish held in groups of eight while maximum metabolic rate showed no difference. Shelter availability during the social treatments did not influence standard or maximum metabolic rates.

Our results suggest that group size may directly influence energy demands of individuals, highlighting the importance of understanding the role of social dynamics on variations in physiological traits associated with energy expenditure.
Compartmentalized control of Cdk1 drives mitotic spindle assembly
Authors: Serpico Angela Flavia , Febbraro Francesco , Pisauro Caterina , Grieco Domenico
Published: April 2021

During cell division, dramatic microtubular rearrangements driven by cyclin B-cdk1 (Cdk1) kinase activity mark mitosis onset leading to interphase cytoskeleton dissolution and mitotic spindle assembly. Once activated by Cdc25, that reverses inhibitory phosphorylation operated by Wee1/Myt1, Cdk1 clears the cytoplasm from microtubules by inhibiting microtubule associated proteins (MAPs) with microtubule growth-promoting properties. Nevertheless, some of these MAPs are required for spindle assembly, creating quite a conundrum. We show here that a Cdk1 fraction bound to spindle structures escaped Cdc25 action and remained inhibited by phosphorylation (i-Cdk1) in mitotic human cells. Loss or restoration of i-Cdk1 inhibited or promoted spindle assembly, respectively. Furthermore, polymerizing spindle microtubules fostered i-Cdk1 by aggregating with Wee1 and excluding Cdc25. Our data reveal that spindle assembly relies on compartmentalized control of Cdk1 activity.
MBNL1 and RBFOX1 co-regulate alternative splicing events transcriptome-wide through a conserved buffering mechanism
Authors: Hale Melissa , Ellis Joseph , Meng Ryan , McDaniel Sunny , Mahady Amy , Wagner Stacey , Richardson Jared , McConnell Ona , Wang Eric , Berglund J. Andrew
Published: April 2021

Alternative splicing (AS) is controlled bycis-regulatory elements recognized by networks oftrans-acting factors. Here we investigate modes and mechanisms of AS co-regulation by MBNL1 and RBFOX1, two RNA binding proteins (RBPs) critical for developmental AS transitions. We generated two cell models that express each RBP under separate inducible promoters. Transcriptome-wide categorization of the impacts of RBFOX1 expression on MBNL1 splicing revealed a common co-regulatory mode through which RBFOX1buffersMBNL1 dose-dependent splicing regulation by reducing the total range of exon inclusion or exclusion. Minigene mutational analysis andin vitrobinding experiments suggest that thisbufferingmechanism occurs through a sharedcis-regulatory element previously unidentified as critical for MBNL1-dependent activity. Overall, our studies define a conserved co-regulatory mechanism through which RBFOX1 and MBNL1 can fine-tune and provide redundancy for AS outcomes. These studies indicate overlapping use of RNA motifs with potential implications for when activity of RBPs is disrupted.
TheDrosophilaanterior-posterior axis is polarized by asymmetric myosin activation
Authors: Doerflinger Hélène , Zimyanin Vitaly , Johnston Daniel St
Published: April 2021

TheDrosophilaanterior-posterior (AP) axis is specified at mid-oogenesis when Par-1 kinase is recruited to the posterior cortex of the oocyte, where it polarises the microtubule cytoskeleton to define where the axis determinants,bicoidandoskarmRNAs localise. This polarity is established in response to an unknown signal from the follicle cells, but how this occurs is unclear. Here we show that the myosin chaperone, Unc-45 and Non-Muscle Myosin II (MyoII) are required in the germ line upstream of Par-1 in polarity establishment. Furthermore, the Myosin regulatory Light Chain (MRLC) is di-phosphorylated at the oocyte posterior in response to the follicle cell signal, inducing longer pulses of myosin contractility at the posterior and increased cortical tension. Over-expression of MRLC-T21A that cannot be di-phosphorylated or acute treatment with the Myosin light chain kinase inhibitor ML-7 abolish Par-1 localisation, indicating that posterior of MRLC di-phosphorylation is essential for polarity. Thus, asymmetric myosin activation polarizes the anterior-posterior axis by recruiting and maintaining Par-1 at the posterior cortex. This raises an intriguing parallel with AP axis formation inC. eleganswhere MyoII is also required to establish polarity, but functions to localize the anterior PAR proteins rather than PAR-1.
Dielectric barrier discharge cold atmospheric plasma: Influence of processing parameters on microbial inactivation in meat and meat products
Authors: Nasiru Mustapha Muhammad , Frimpong Evans Boateng , Muhammad Umair , Qian Jing , Mustapha Abdullateef Taiye , Yan Wenjing , Zhuang Hong , Zhang Jianhao
Published: April 2021

Decontamination of meat is commonly practiced to get rid of or decrease the microbial presence on the meat surface. Dielectric barrier discharge cold atmospheric plasma (DBD‐CAP) as innovative technology is a food microbial inactivation technique considered in high regard by food scientists and engineers in present times. However, cold atmospheric plasma application is at the experimental stage, due to lack of sufficient information on its mode of action in inactivating microbes, food shelf‐life extensibility, whereas, the nutritional value of food is preserved. In this review, we have appraised recent work on DBD‐CAP concerning the decontamination treatment of meat products, highlighting the processing value results on the efficacy of the DBD‐CAP microbial inactivation technique. Also, the paper will review the configurations, proposed mechanisms, and chemistry of DBD‐CAP. Satisfactory microbial inactivation was observed. In terms of DBD‐CAP application on sensory evaluation, inferences from reviewed literature showed that DBD has no significant effect on meat color and tenderness, whereas in contrast, TBARS values of fresh and processed meat are affected. DBD seems economically efficient and environmentally sustainable.
Prey decline leads to diet shift in the largest population of Indo‐Pacific humpback dolphins?
Authors: LIN Wenzhi , KARCZMARSKI Leszek , ZHOU Ruilian , MO Yaqian , GUO Lang , YIU Sam King Fung , NING Xi , WAI Tak‐Cheung , WU Yuping
Published: April 2021

The Pearl River Delta (PRD) region on the southeast coast of China has long been known as a highly productive fishing ground. Since the late 1980s, fishing pressure in the PRD has been intense, which warrants concerns of potential fishery‐related impacts on the food resources and foraging ecology of apex marine predators in this region, such as the Indo‐Pacific humpback dolphin (Sousa chinensis). In this study, we examined 54 stomachs with food remains, collected from beached carcasses of humpback dolphins recovered during fifteen years between 2003 and 2017. The 6043 identified prey items represent 62 teleost taxa, primarily small estuarine fish, but also larger reef fish. The dolphins appear to be opportunistic foragers, hunting across the water‐column, with preference for shoaling and meaty fishes (e.g.Collichthys lucidusIRI% = 38.6%,Johnius belangeriiIRI% = 23.1%,Mugil cephalusIRI% = 14.0%). Our findings suggest a dietary shift in recent years, from primarily demersal (as previously reported) to greater intake of neritic and pelagic fish. Dolphin foraging group size has decreased in recent years, which corresponds with declining size and numbers of prey items retrieved from dolphin stomachs. We suggest that these are indicators of declining food resources. Faced with a shortage of preferred prey, humpback dolphins may have broadened their dietary spectrum to maintain their daily energy intake, while their foraging group size decreased in response to the altered tradeoff between the costs and benefits of group foraging.
The clinical relevance of IgM and IgA anti-pneumococcal polysaccharide ELISA assays in patients with suspected antibody deficiency
Authors: Janssen Lisanne M A , Heron Michiel , Murk Jean-Luc , Leenders Alexander C A P , Rijkers Ger T , de Vries Esther
Published: April 2021

Unlike immunoglobulin (Ig)G pneumococcal polysaccharide (PnPS)-antibodies, PnPS IgA and IgM-antibodies are not routinely determined for the assessment of immunocompetence. It is not yet known whether an isolated inability to mount a normal IgM or IgA-PnPS response should be considered a relevant primary antibody deficiency (PAD). We studied the clinical relevance of anti-PnPS IgM and IgA-assays in patients with suspected primary immunodeficiency in a large teaching hospital in ’s-Hertogenbosch, the Netherlands. Serotype-specific-PnPS IgG assays were performed; subsequently, 23-valent-PnPS IgG assays (anti-PnPS IgG assays), and later anti-PnPS IgA and IgM assays, were performed in archived material (240 patients; 304 samples). Eleven of 65 pre- and six of 10 post-immunization samples from good responders to PnPS serotype-specific IgG testing had decreased anti-PnPS IgA and/or IgM titres. Of these, three pre- and no post-immunization samples were from patients previously classified as ‘no PAD’. Determination of anti-PnPS IgA and IgM in addition to anti-PnPS IgG did not reduce the need for serotype-specific PnPS IgG testing to assess immunocompetence [receiver operating characteristic (ROC) analysis of post-immunization samples: anti-PnPS IgA + IgG area under the curve (AUC) = 0.80, 95% confidence interval (CI) = 0.63–0.97; anti-PnPS IgM + IgG AUC 0.80, 95% CI = 0.62–0.98; anti-PnPS IgA + IgG + IgM AUC = 0.71, 95% CI = 0.51–0.91; anti-PnPS IgG AUC = 0.93, 95% CI = 0.85–1.00]. Our data show that patients classified as having an intact antibody response based on measurement of serotype-specific PnPS IgG can still display impaired anti-PnPS IgM and IgA responses, and that the additional measurement of anti-PnPS IgA and IgM could not reduce the need for serotype-specific IgG testing. Future studies are needed to investigate the clinical relevance of potential ‘specific IgA or IgM antibody deficiency’ in patients with recurrent airway infections in whom no PAD could be diagnosed according to the current definitions.
Common and distinct neural trends of allocentric and egocentric spatial coding: An ALE meta‐analysis
Authors: Derbie Abiot Y. , Chau Bolton K .H. , Wong Clive H. Y. , Chen Li‐Dian , Ting Kin‐hung , Lam Bess Y. H. , Lee Tatia M. C. , Chan Chetwyn C. H. , Smith Yoland
Published: April 2021

The uniqueness of neural processes between allocentric and egocentric spatial coding has been controversial. The distinctive paradigms used in previous studies for manipulating spatial coding could have attributed for the inconsistent results. This study was aimed to generate converging evidence from previous functional brain imaging experiments for collating neural substrates associated with these two types of spatial coding. An additional aim was to test whether test‐taking processes would have influenced the results. We obtained coordinate‐based functional neuroimaging data for 447 subjects and performed activation likelihood estimation (ALE) meta‐analysis. Among the 28 experiments, the results indicate two common clusters of convergence. They were the right precuneus and the right superior frontal gyrus as parts of the parieto‐frontal circuit. Between‐type differences were in the parieto‐occipital circuit, with allocentric showing convergence in the superior occipital gyrus (SOG) cluster compared with egocentric showing convergence in the middle occipital gyrus (MOG) cluster. Task‐specific influences were only found in allocentric spatial coding. Spatial judgment‐oriented tasks seem to increase the demands on manipulating spatial relationships among the visual objects, while spatial navigation tasks seem to increase the demands on maintaining object representations. Our findings address the theoretical controversies on spatial coding that both the allocentric and egocentric types are common in their processes mediated by the parieto‐frontal network, while unique and additional processes in the allocentric type are mediated by the parieto‐occipital network. The positive results on possible task‐specific confound offer insights into the future design of spatial tasks for eliciting spatial coding processes.
A thermal trade‐off between viral production and degradation drives virus‐phytoplankton population dynamics
Authors: Demory David , Weitz Joshua S. , Baudoux Anne‐Claire , Touzeau Suzanne , Simon Natalie , Rabouille Sophie , Sciandra Antoine , Bernard Olivier
Published: April 2021

Marine viruses interact with microbial hosts in dynamic environments shaped by variation in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modelling with experiments to explore the effect of temperature on virus‐phytoplankton interactions. Our model shows the negative consequences of high temperatures on infection and suggests a temperature‐dependent threshold between viral production and degradation. Modelling long‐term dynamics in environments with different average temperatures revealed the potential for long‐term host‐virus coexistence, epidemic free or habitat loss states. We generalised our model to variation in global sea surface temperatures corresponding to present and future seas and show that climate change may differentially influence virus‐host dynamics depending on the virus‐host pair. Temperature‐dependent changes in the infectivity of virus particles may lead to shifts in virus‐host habitats in warmer oceans, analogous to projected changes in the habitats of macro‐, microorganisms and pathogens.
The American robin (Turdus migratorius): A focal species for anti‐parasitic egg rejection studies among hosts of the brown‐headed cowbird (Molothrus ater)
Authors: Turner Abbigail M. , Hauber Mark E.
Published: April 2021

Obligate avian brood parasites lay their eggs in the nest of other species and impose reproductive costs upon their hosts. In response, many hosts have evolved a variety of defenses to avoid or reduce the costs associated with parasitism, including the rejection of parasitic eggs. Here, we review the different sensory and contextual cues involved in egg rejection by the American robin (Turdus migratorius), one of the handful of rejecter host species of the brood parasitic brown‐headed cowbird (Molothrus ater) in North America. Robins are an open‐cup nesting species whose eggs dramatically differ in appearance from the cowbirds' eggs; therefore, we expect that visual cues would be the primary sensory modality used when rejecting foreign eggs. The results of our comprehensive review confirm that visual cues, including eggshell color and maculation, are strong predictors of robins' egg rejection responses. Egg size, egg shape, and other contextual traits (including clutch composition, maternal status, and sympatry with the parasite) also affect egg rejection in this host species. Future research into this species' egg rejection mechanisms would benefit from comparisons to other strongly and moderately egg rejecter host species of brown‐headed cowbirds, as well as from seeking to understand further why so many hosts of this particular parasitic lineage accept foreign eggs. We also discuss the implications of this review for other egg rejecter and non‐rejecter hosts of diverse avian brood parasites.