bluuebunny/crossref_metadata_2025 huggingface dataset:
The novel PII-interacting protein PirA regulates flux into the cyanobacterial ornithine-ammonia cycle
Authors: Bolay Paul , Muro-Pastor M. Isabel , Rozbeh Rokhsareh , Timm Stefan , Hagemann Martin , Florencio Francisco J. , Forchhammer Karl , Klähn Stephan
Published: November 2020

Among prokaryotes, cyanobacteria have an exclusive position due to the fact that they perform oxygenic photosynthesis. Cyanobacteria substantially differ from other bacteria in further aspects, e.g. they evolved a plethora of unique regulatory mechanisms to control primary metabolism. This is exemplified by the regulation of glutamine synthetase (GS) via small proteins termed inactivating factors (IFs). Here we reveal another small, 51 amino acid protein, which is encoded by thessr0692gene, to regulate flux into the ornithine-ammonia cycle (OAC), the key hub of cyanobacterial nitrogen stockpiling and remobilization. This regulation is achieved by the interaction with the central carbon/nitrogen control protein PII, which commonly controls the entry into the OAC by activating the key enzyme of arginine synthesis, N-acetyl-L-glutamate kinase (NAGK). We suggest that Ssr0692 competes with NAGK for PIIbinding and thereby prevents NAGK activation, which in turn lowers arginine synthesis. Accordingly, we termed itPII-interacting regulator ofarginine synthesis (PirA). Similar to the GS IFs, PirA accumulates in response to ammonium upshift due to relief from repression by the global nitrogen-control transcription factor NtcA. Consistently, deletion of PirA affects the cell to balance metabolite pools of the OAC in response to ammonium shocks. Moreover, its interaction with PIIrequires ADP and is prevented by PIImutations affecting the T-loop conformation, the major protein-interaction surface of this signal processing protein. Thus, we propose that PirA is an integrator determining flux into N storage compounds not only depending on the N availability but also the energy state of the cell.

Importance

Cyanobacteria contribute a significant portion to the annual oxygen yield and play important roles in biogeochemical cycles, e.g. as major primary producers. Due to their photosynthetic lifestyle cyanobacteria also arouse interest as hosts for the sustainable production of fuel components and high-value chemicals. However, their broad application as microbial cell factories is hampered by limited knowledge about the regulation of metabolic fluxes in these organisms. Our research identified a novel regulatory protein that controls nitrogen flux, in particular arginine synthesis in the cyanobacterial model strainSynechocystissp. PCC 6803. Beside its role as proteinogenic amino acid, arginine is a precursor for the cyanobacterial storage compound cyanophycin, which is of potential interest to biotechnology. The obtained results will therefore not only enhance our understanding of flux control in these organisms, it will also help to provide a scientific fundament for targeted metabolic engineering and hence the design of photosynthesis-driven biotechnological applications.
Bidirectional redox cycling of phenazine-1-carboxylic acid byCitrobacter portucalensisMBL drives increased nitrate reduction
Authors: Tsypin Lev M. , Newman Dianne K.
Published: November 2020

Phenazines are secreted metabolites that microbes use in diverse ways, from quorum sensing to antimicrobial warfare to energy conservation. Phenazines are able to contribute to these activities due to their redox activity. The physiological consequences of cellular phenazine reduction have been extensively studied, but the counterpart phenazine oxidation has been largely overlooked. Phenazine-1-carboxylic acid (PCA) is common in the environment and readily reduced by its producers. Here, we describe its anaerobic oxidation byCitrobacter portucalensisstrain MBL, which was isolated from topsoil in Falmouth, MA, and which does not produce phenazines itself. This activity depends on the availability of a suitable terminal electron acceptor, specifically nitrate or fumarate. WhenC. portucalensisMBL is provided reduced PCA and either nitrate or fumarate, it continuously oxidizes the PCA. We compared this terminal electron acceptor-dependent PCA-oxidizing activity ofC. portucalensisMBL to that of several other γ-proteobacteria with varying capacities to respire nitrate and/or fumarate. We found that PCA oxidation by these strains in a fumarate-or nitrate-dependent manner is decoupled from growth and correlated with their possession of the fumarate or periplasmic nitrate reductases, respectively. We infer that bacterial PCA oxidation is widespread and genetically determined. Notably, reduced PCA enhances the rate of nitrate reduction to nitrite byC. portucalensisMBL beyond the stoichiometric prediction, which we attribute toC. portucalensisMBL’s ability to also reduce oxidized PCA, thereby catalyzing a complete PCA redox cycle. This bidirectionality highlights the versatility of PCA as a biological redox agent.

IMPORTANCE

Phenazines are increasingly appreciated for their roles in structuring microbial communities. These tricyclic aromatic molecules have been found to regulate gene expression, be toxic, promote antibiotic tolerance, and promote survival under oxygen starvation. In all of these contexts, however, phenazines are studied as electron acceptors. Even if their utility arises primarily from being readily reduced, they would need to be oxidized in order to be recycled. While oxygen and ferric iron can oxidize phenazines abiotically, biotic oxidation of phenazines has not been studied previously. We observed bacteria that readily oxidize phenazine-1-carboxylic acid (PCA) in a nitrate-dependent fashion, concomitantly increasing the rate of nitrate reduction to nitrite. Because nitrate is a prevalent terminal electron acceptor in diverse anoxic environments, including soils, and phenazine-producers are widespread, this observation of linked phenazine and nitrogen redox cycling suggests an underappreciated role for redox-active secreted metabolites in the environment.
The experience of distress during the COVID-19 outbreak: a cross-country examination on the fear of COVID-19 and the sense of loneliness
Authors: Coco Gianluca Lo , Gentile Ambra , Bosnar Ksenija , Milovanovic Ivana , Bianco Antonino , Drid Patrik , Pišot Saša
Published: November 2020

Objectives

To examine gender, age and cross-country differences in fear of COVID-19 and sense of loneliness during the lockdown, by comparing people from countries with a high rate of infections and deaths (i.e. Spain and Italy) and from countries with a mild spread of infection (i.e. Croatia, Serbia, Slovakia, Slovenia, Bosnia and Herzegovina).

Methods

A total of 3876 participants (63% female) completed an online survey on “Everyday life practices in COVID-19 time” in April 2020, including measures of fear of COVID-19 and loneliness.

Results

Males and females of all age groups in countries suffering from a strong impact of the COVID-19 pandemic reported higher fear of COVID-19 and sense of loneliness. In less endangered countries females and elder stated more symptoms than males and younger; in Spanish and Italian sample the pattern of differences is considerably more complex.

Conclusion

Future research should thoroughly examine different age and gender groups. The analysis of emotional well-being in groups at risk of mental health issues can help to lessen the long term social and economic costs due to the COVID-19 outbreak.
Embryo classification beyond pregnancy: Early prediction of first trimester miscarriage using machine learning
Authors: Amitai Tamar , Kan-Tor Yoav , Srebnik Naama , Buxboim Amnon
Published: November 2020

Objective

Develop a machine learning classifier for predicting the risk of cleavage-stage embryos to undergo first trimester miscarriage based on time-lapse images of preimplantation development.

Design

Retrospective study of a 4-year multi-center cohort of women undergoing intra-cytoplasmatic sperm injection (ICSI). The study included embryos with positive indication of clinical implantation based on gestational sac visualization either with first trimester miscarriage or live birth outcome. Miscarriage was determined based on negative fetal heartbeat indication during the first trimester.

Setting

Data were recorded and obtained in hospital setting and research was performed in university setting.

Patient(s)

Data from 391 women who underwent fresh single or double embryo transfers were included.

Intervention(s)

None.

Main Outcome Measure(s)

A minimal subset of six non-redundant morphodynamic features were screened that maintain high prediction capacity. Using this feature subset, XGBoost and Random Forest models were trained following a 100-fold Monte-Carlo cross validation scheme. Feature importance was scored using the SHapley Additive exPlanations (SHAP) methodology. Miscarriage versus live-birth outcome prediction was evaluated using a non-contaminated balanced test set and quantified in terms of the area under the receiver operating characteristic (ROC) curve (AUC), precision-recall curve, positive predictive value (PPV), and confusion matrices.

Result(s)

Features that account for the distribution of the nucleolus precursor bodies within the small pronucleus and pronuclei dynamics were highly predictive of miscarriage outcome. AUC for miscarriage prediction of validation and test set embryos using both models was 0.68-to-0.69. Clinical utility was tested by setting two classification thresholds accounting for high sensitivity 0.73 with 0.6 specificity and high specificity 0.93 with 0.33 sensitivity.

Conclusion(s)

We report the development of a decision-support tool for identifying the embryos with high risk of miscarriage. Prioritizing embryos for transfer based on their predicted risk of miscarriage in combination with their predicted implantation potential will improve live-birth rates and shorten time-to-pregnancy.

Capsule

The risk of first trimester miscarriage of cleavage stage embryos is predicted with AUC 68% by screening a minimal subset of six non-redundant morpho-dynamic features and training a machine-learning classifier.
Glucolipotoxicity-induced Mig6 desensitizes EGFR signaling and promotes pancreatic beta cell death
Authors: Chen Yi-Chun , Lutkewitte Andrew J. , Basavarajappa Halesha D. , Fueger Patrick T.
Published: November 2020

A loss of functional beta cell mass is a final etiological event in the development of frank type 2 diabetes (T2D). To preserve or expand beta cells and therefore treat/prevent T2D, growth factors have been considered therapeutically but have largely failed to achieve robust clinical success. The molecular mechanisms preventing the activation of mitogenic signaling pathways from maintaining functional beta cell mass during the development of T2D remain unknown. We speculated that endogenous negative effectors of mitogenic signaling cascades impede beta cell survival/expansion. Thus, we tested the hypothesis that a stress-inducible epidermal growth factor receptor (EGFR) inhibitor, Mitogen-inducible gene 6 (Mig6), regulates beta cell fate in a T2D milieu. To this end, we determined that: 1) glucolipotoxicity (GLT) induces Mig6, thereby blunting EGFR signaling cascades, and 2) Mig6 mediates molecular events regulating beta cell survival/death. We discovered that GLT impairs EGFR activation, and Mig6 is elevated in human islets from T2D donors as well as GLT-treated rodent islets and 832/13 INS-1 beta cells. Mig6 is essential for GLT-induced EGFR desensitization, as Mig6 suppression rescued the GLT-impaired EGFR and ERK1/2 activation. Further, Mig6 mediated EGFR but not insulin-like growth factor-1 receptor nor hepatocyte growth factor receptor activity in beta cells. Finally, we identified that elevated Mig6 augmented beta cell apoptosis, as Mig6 suppression reduced apoptosis during GLT. In conclusion, we established that T2D and GLT induce Mig6 in pancreatic beta cells. The elevated Mig6 desensitizes EGFR signaling and induces beta cell death. Our findings suggest that Mig6 could be a novel therapeutic target for T2D, as blocking Mig6 could possibly enhance mitogenic signaling cascades in a diabetic milieu to promote beta cell survival and prevent beta cell death.
Hacking The Diversity Of SARS-CoV-2 And SARS-Like Coronaviruses In Human, Bat And Pangolin Populations
Authors: Dimonaco Nicholas J. , Salavati Mazdak , Shih Barbara
Published: November 2020

In 2019, a novel coronavirus, SARS-CoV-2/nCoV-19, emerged in Wuhan, China, and has been responsible for the current COVID-19 pandemic. The evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development. As part of the international “CoronaHack” in April 2020 (https://www.coronahack.co.uk/), we employed a collection of contemporary methodologies to compare the genomic sequences of coronaviruses isolated from human (SARS-CoV-2;n=163), bat (bat-CoV;n=215) and pangolin (pangolin-CoV;n=7) available in public repositories. Followingde novogene annotation prediction, analyses of gene-gene similarity network, codon usage bias and variant discovery were undertaken. Strong host-associated divergences were noted in ORF3a, ORF6, ORF7a, ORF8 and S, and in codon usage bias profiles. Lastly, we have characterised several high impact variants (inframe insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and may be highlighting loci of potential functional relevance.
Identifying genetic variants associated with cerebellar volume in 33,265 individuals from the UK-Biobank
Authors: Chambers Tom , Escott-Price Valentina , Legge Sophie , Baker Emily , Singh Krish D. , Walters James TR , Caseras Xavier , Anney Richard JL
Published: November 2020

There is expanding interest in researching the cerebellum given accumulating evidence of its important contributions to cognitive and emotional functions, in addition to more established sensorimotor roles. While large genome-wide association studies (GWAS) have shed light on the common allele architecture of cortical and subcortical brain structures, the cerebellum remains under investigated. We conducted a meta-GWAS of cerebellar volume in 33,265 UK-Biobank European participants. Results show cerebellar volume to be moderately heritable (h2SNP=50.6%). We identified 33 independent genome-wide associated SNPs with total cerebellar volume, with 6 of these SNPs mapped to protein-coding genes and 5 more shown to alter cerebellar gene expression. We highlight 21 unique candidate genes for follow-up analysis. Cerebellar volume showed significant genetic correlation with brainstem, pallidum and thalamus volumes, but no significant correlations with neuropsychiatric phenotypes. Our results provide important new knowledge of the genetic architecture of cerebellar volume and its relationship with other brain phenotypes.
In vitro immunization approach to generate specific murine monoclonal IgG antibodies
Authors: Michelchen Sophia , Micheel Burkhard , Hanack Katja
Published: November 2020

Generating monoclonal antibodies to date is a time intense process requiring immunization of laboratory animals. The transfer of the humoral immune response intoin vitrosettings shortens this process and circumvents the necessity of animal immunization. However, orchestrating the complex interplay of immune cellsin vitrois very challenging. We aimed for a simplified approach focusing on the protagonist of antibody production: the B lymphocyte. We activated purified murine B lymphocytesin vitrowith combinations of antigen and stimuli. Within ten days of culture we induced specific IgM and IgG antibody responses against a viral coat protein. Permanently antibody-producing hybridomas were generated. Furthermore we used this method to induce a specific antibody response againstLegionella pneumophila. We thus established an effective protocol to generate monoclonal antibodiesin vitro. By overcoming the necessity ofin vivoimmunization it may be the first step towards a universal strategy to generate antibodies from various species.
PARKIN REGULATES DRUG TAKING-BEHAVIOR IN RAT MODEL OF METHAMPHETAMINE USE DISORDER
Authors: Sharma Akhil , Harutyunyan Arman , Schneider Bernard L. , Moszczynska Anna
Published: November 2020

There is no FDA-approved medication for Methamphetamine (METH) Use Disorder. New therapeutic approaches are needed, especially for people who use METH heavily and are at high risk for overdose. This study used genetically engineered rats to evaluate PARKIN as a potential target for METH Use Disorder. PARKIN knockout, PARKIN-overexpressing and wild-type young adult male Long Evans rats were trained to self-administer high doses of METH using an extended-access METH self-administration paradigm. Reinforcing/rewarding properties of METH were assessed by quantifying drug-taking behavior and time spent in a METH-paired environment. PARKIN knockout rats self-administered more METH and spent more time in the METH-paired environment than wild-type rats. Wild-type rats overexpressing PARKIN self-administered less METH and spent less time in the METH-paired environment. PARKIN knockout rats overexpressing PARKIN self-administered less METH during the first half of drug self-administration days than PARKIN-deficient rats. The results indicate that rats with PARKIN excess or PARKIN deficit are useful models for studying neural substrates underlying “resilience” or vulnerability to METH Use Disorder, and identify PARKIN as a novel potential drug target to treat heavy use of METH.
Chromatin Accessibility Maps Provide Evidence of Multilineage Gene Priming in Hematopoietic Stem Cells
Authors: Martin Eric W. , Krietsch Jana , Reggiardo Roman E. , Sousae Rebekah , Kim Daniel H. , Forsberg E. Camilla
Published: November 2020

Hematopoietic stem cells (HSCs) have the capacity to differentiate into vastly different types of mature blood cells. The epigenetic mechanisms regulating the multilineage ability, or multipotency of HSCs are not well understood. To test the hypothesis thatcisregulatory elements that control fate decisions for all lineages are primed in HSCs, we used ATAC-seq to compare chromatin accessibility of HSCs with five unipotent cell types. We observed the highest similarity in accessibility profiles between Megakaryocyte Progenitors and HSCs, whereas B cells had the greatest number of regions withde novogain in accessibility during differentiation. Despite these differences, we identifiedcisregulatory elements from all lineages that displayed epigenetic priming in HSCs. These findings provide new insights into the regulation of stem cell multipotency, as well as a resource to identify functional drivers of lineage fate.

HIGHLIGHTS

HSCs have higher global chromatin accessibility than any unilineage progeny

Megakaryocyte Progenitors are the most closely related unipotent cell type to HSCs

B cell commitment involvesde novochromatin accessibility

Evidence ofciselement priming of lineage-specific genes in HSCs
Reproducible abnormalities of functional gradient reliably predict clinical and cognitive symptoms in schizophrenia
Authors: Wang Meng , Li Ang , Liu Yong , Yan Hao , Sun Yuqing , Song Ming , Chen Jun , Chen Yunchun , Wang Huaning , Guo Hua , Wan Ping , Lv Luxian , Yang Yongfeng , Li Peng , Lu Lin , Yan Jun , Wang Huiling , Zhang Hongxing , Zhang Dai , Jiang Tianzi , Liu Bing
Published: November 2020

Background

Schizophrenia (SZ) typically manifests heterogeneous phenotypes involving positive, negative and cognitive symptoms. However, the underlying neural mechanisms of these symptoms keep unclear. Functional gradient is a fascinating measure to characterize continuous, hierarchical organization of brain.

Methods

We aimed to investigate whether reproducible disruptions of functional gradient existed in SZ compared to normal controls (NC), and these abnormalities were associated with severity of clinical and cognitive symptoms in SZ. All analyses were implemented in two independent large-sample multi-site datasets (discovery dataset, 400 SZ and 336 NC; replication dataset, 279 SZ and 262 NC). First, functional gradient across cerebral cortex was calculated in each subject. Second, vertex-wise comparisons of cortical gradient between SZ and NC groups were performed to identify abnormalities in SZ. Meanwhile, reproducible and robustness analyses were implemented to validate these abnormalities. Finally, regression analyses were performed using generalized additive models to link these abnormalities to severity of clinical and cognitive symptoms in SZ.

Results

We found an abnormal gradient map in SZ in the discovery dataset, which was reproducible in the replication dataset. The abnormal gradient pattern was also robust when performing methodological alternatives and control analyses. Further, these reproducible abnormalities can reliably predict symptoms of clinical and cognitive domains across the two independent datasets.

Conclusion

These findings demonstrated that alterations in functional gradient can provide a reliable signature of SZ, characterizing the heterogenous symptoms of clinical or cognitive domains, and may be further investigated to understand the neurobiological mechanisms of these symptoms.

Impact Statement

In our study, using functional gradient measure and statistical learning technology and two independent multi-site case-control resting-state fMRI datasets (discovery dataset: 736 subjects; replication dataset: 541 subjects), we comprehensively investigated functional hierarchical organization in the cerebral cortex of SZ and its association with interindividual severity of symptoms. We found reproducible and robust abnormalities of functional gradient existed in SZ, which provided a reliable signature to characterize negative and general psychopathology symptoms, as well as cognitive deficits. Our findings can provide new insights to understand the neurobiological mechanisms of clinical and cognitive symptoms in SZ.
Memory Transfer of Random Time Patterns Across Modalities
Authors: HiJee Kang , Ryszard Auksztulewicz , Chi Hong Chan , Drew Cappotto , Vani Gurusamy Rajendran , Jan Wilbert Hendrik Schnupp
Published: November 2020

Perception is sensitive to statistical regularities in the environment, including temporal characteristics of sensory inputs. Interestingly, temporal patterns implicitly learned within one modality can also be recognised in another modality. However, it is unclear how cross-modal learning transfer affects neural responses to sensory stimuli. Here, we recorded neural activity of human volunteers (N=24, 12 females, 12 males) using electroencephalography (EEG), while participants were exposed to brief sequences of randomly-timed auditory or visual pulses. Some trials consisted of a repetition of the temporal pattern within the sequence, and subjects were tasked with detecting these trials. Unknown to the participants, some trials reappeared throughout the experiment, enabling implicit learning. Replicating previous behavioural findings, we showed that participants benefit from temporal information learned in audition, and that they can apply this information to stimuli presented in vision. Such memory transfer was not observed from vision to audition. However, using an analysis of EEG response learning curves, we showed that learning temporal structures both within and across modalities modulates single-trial EEG response amplitudes in both conditions (audition to vision and vision to audition). Interestingly, the neural correlates of temporal learning within modalities relied on modality-specific brain regions, while learning transfer affected activity in frontal regions, suggesting distinct mechanisms. The cross-modal effect could be linked to frontal beta-band activity. The neural effects of learning transfer were similar both when temporal information learned in audition was transferred to visual stimuli and vice versa. Thus, both modality-specific mechanisms for learning of temporal information, and general mechanisms which mediate learning transfer across modalities, have distinct physiological signatures that are observable in the EEG.
Competition-based screening secures the evolutionary stability of a defensive microbiome
Authors: Worsley Sarah F. , Innocent Tabitha M. , Holmes Neil A. , Al-Bassam Mahmoud M. , Wilkinson Barrie , Murrell J. Colin , Boomsma Jacobus J. , Yu Douglas W. , Hutchings Matthew I.
Published: November 2020

Cuticular microbiomes ofAcromyrmexleaf-cutting ants are exceptional because they are freely colonizable, and yet the prevalence ofPseudonocardia, a native vertically transmitted symbiont that controlsEscovopsisfungus-garden disease, is never compromised. Game theory suggests thatcompetition-based screeningcan allow the selective recruitment of antibiotic-producing bacteria from the environment, by fomenting and biasing competition for abundant host resources. Mutual symbiont aggression benefits the host and also maintains native symbiont viability. Here we use RNA-stable isotope probing (RNA-SIP) to confirm predictions thatAcromyrmexcuticles can maintain a range of microbial symbionts. We then used dual-RNA-sequencing and bioassays to show that vertically transmittedPseudonocardiastrains produce antibacterials that differentially reduce the growth rates of other microbes, ultimately eliminating non-antibiotic-producing strains that might parasitize the symbiosis while still allowing antibiotic-producingStreptomycesstrains to survive. Open cuticular microbiomes can thus maintain a specific co-evolved mutualism by restricting access for other bacterial strains.
Insights into kinetics, release, and behavioral effects of brain-targeted hybrid nanoparticles for cholesterol delivery in Huntington’s disease
Authors: Birolini Giulia , Valenza Marta , Ottonelli Ilaria , Passoni Alice , Favagrossa Monica , Duskey Jason T. , Bombaci Mauro , Vandelli Maria Angela , Colombo Laura , Bagnati Renzo , Caccia Claudio , Leoni Valerio , Taroni Franco , Forni Flavio , Ruozi Barbara , Salmona Mario , Tosi Giovanni , Cattaneo Elena
Published: November 2020

Supplementing brain cholesterol is emerging as a potential treatment for Huntington’s disease (HD), a genetic neurodegenerative disorder characterized, among other abnormalities, by inefficient brain cholesterol biosynthesis. However, delivering cholesterol to the brain is challenging due to the bloodbrain barrier (BBB), which prevents it from reaching the striatum, especially, with therapeutically relevant doses.

Here we describe the distribution, kinetics, release, and safety of novel hybrid polymeric nanoparticles made of PLGA and cholesterol which were modified with an heptapeptide (g7) for BBB transit (hybrid-g7-NPs-chol). We show that these NPs rapidly reach the brain and target neural cells. Moreover, deuterium-labeled cholesterol from hybrid-g7-NPs-chol is released in a controlled manner within the brain and accumulates over time, while being rapidly removed from peripheral tissues and plasma. We confirm that systemic and repeated injections of the new hybrid-g7-NPs-chol enhanced endogenous cholesterol biosynthesis, prevented cognitive decline, and ameliorated motor defects in HD animals, without any inflammatory reaction.

In summary, this study provides insights about the benefits and safety of cholesterol delivery through advanced brain-permeable nanoparticles for HD treatment.
Polymerization of misfolded protein lowers CX3CR1 expression in human PBMCs
Authors: Tumpara Srinu , Ballmaier Matthias , Wrenger Sabine , König Mandy , Lehmann Matthias , Lichtinghagen Ralf , Martinez-Delgado Beatriz , DeLuca David , Jedicke Nils , Welte Tobias , Fromme Malin , Strnad Pavel , Stolk Jan , Janciauskiene Sabina
Published: November 2020

The CX3CR1 (chemokine (C-X3-C motif) receptor 1) expression levels on immune cells have significant importance in maintaining tissue homeostasis under physiological and pathological conditions. The factors implicated in the regulation of CX3CR1 and its specific ligand CX3CL1 (fractalkine) expression remain largely unknown. Recent studies provide evidence that host‘s misfolded proteins occurring in the forms of polymers or amyloid fibrils can regulate CX3CR1 expression. Herein, we present a novel example that polymers of human ZZ alpha1-antitrypsin (Z-AAT) protein, resulting from its conformational misfolding due to the Z (Glu342Lys) mutation inSERPINA1gene, strongly lower CX3CR1 expression in human PBMCs. We also show that extracellular polymers of Z-AAT are internalized by PBMCs, which parallels with increased intracellular levels of CX3CR1 protein. Our findings support the role of extracellular misfolded proteins in CX3CR1 regulation and encourage conducting further studies on this issue.
Deuterium-depletion has no significant impact on the mutation rate ofEscherichia coli, invalidating the Double D-Bridge Hypothesis
Authors: Ajibola Walliyulahi , Karcagi Ildikó , Somlyai Gábor , Somlyai Ildikó , Fehér Tamás
Published: November 2020

Deuterium (D), the second most abundant isotope of hydrogen is present in natural waters at an approximate concentration of 145-155 ppm (cca. 1.5E-4 atom/atom). D is known to influence various biological processes due to its physical and chemical properties, which significantly differ from those of hydrogen. For example, increasing D-concentration to >1000-fold above its natural abundance has been shown to increase the frequency of genetic mutations in several species. The Double D-Bridge Hypothesis, formulated with the intent of explaining the mechanism of D-mutagenicity is based on the calculation that the theoretical frequency of A:T base pairs that comprise two D-bridges instead of H-bridges is 2E-8, which is equal to the mutation rate of certain species. To experimentally challenge this hypothesis, and to infer the mutagenicity of D present at natural concentrations, we investigated the effect of a nearly 100-fold reduction of D concentration on the bacterial mutation rate. Using fluctuation tests, we measured the mutation rate of threeEscherichia coligenes (cycA, ackAandgalK) in media containing D at either <2 ppm or 150 ppm concentrations. Out of 15 pair-wise fluctuation analyses, nine indicated a significant decrease, while three marked the significant increase of the mutation/culture value upon D-depletion. Overall, growth in D-depleted minimal medium led to a geometric mean of 0.663-fold (95% confidence interval: 0.483-0.911) change in the mutation rate. This falls nowhere near the expected 10,000-fold reduction, indicating that the Double D-Bridge Hypothesis does not hold. In addition, the combined results did not display a statistically significant change in the mutation/culture value, the mutation rate or the mutant frequency upon D-depletion. The potential mutagenic effect of D present at natural concentrations onE. coliis therefore below the limit of detection using the indicated methods.
Genetic dissection of the mitochondrial lipoylation pathway in yeast
Authors: Pietikäinen Laura P. , Rahman M. Tanvir , Hiltunen J. Kalervo , Dieckmann Carol L. , Kastaniotis Alexander J.
Published: November 2020

Background

Lipoylation of 2-ketoacid dehydrogenases is essential for mitochondrial function in eukaryotes. While the basic principles of the lipoylation processes have been worked out, we still lack a thorough understanding of the details of this important post-translational modification pathway. Here we used yeast as a model organism to characterize substrate usage by the highly conserved eukaryotic octanoyl/lipoyl transferasesin vivoand queried how amenable the lipoylation system is to supplementation with exogenous substrate.

Results

We show that the requirement for mitochondrial fatty acid synthesis to provide substrates for lipoylation of the 2-ketoacid dehydrogenases can be bypassed by supplying the cells with free lipoic acid (LA) or octanoic acid (C8) and a mitochondrially targeted fatty acyl/lipoyl activating enzyme. We also provide evidence that theS. cerevisiaelipoyl transferase Lip3, in addition to transferring LA from the glycine cleavage system H protein to the pyruvate dehydrogenase (PDH) and α-ketoglutarate dehydrogenase (KGD) E2 subunits, can transfer this cofactor from the PDH complex to the KGD complex. In support of yeast as a model system for human metabolism, we demonstrate that the human octanoyl/lipoyl transferases can substitute for their counterparts in yeast to support respiratory growth and protein lipoylation. Like the wild-type yeast enzyme, the human lipoyl transferase LIPT1 responds to LA supplementation in the presence of the activating enzyme LplA.

Conclusions

In the yeast model system, the eukaryotic lipoylation pathway can use free LA and C8 as substrates when fatty/lipoic acid activating enzymes are targeted to mitochondria. Lip3 LA transferase has a wider substrate specificity than previously recognized. We show that these features of the lipoylation mechanism in yeast are conserved in mammalian mitochondria. Our findings have important implications for the development of effective therapies for the treatment of LA or mtFAS deficiency-related disorders.
ThePhyscomitrium (Physcomitrella) patensPpKAI2L receptors for strigolactones and related compounds highlight MAX2 dependent and independent pathways
Authors: Lopez-Obando Mauricio , Guillory Ambre , Boyer François-Didier , Cornu David , Hoffmann Beate , Le Bris Philippe , Pouvreau Jean-Bernard , Delavault Philippe , Rameau Catherine , de Saint Germain Alexandre , Bonhomme Sandrine
Published: November 2020

In flowering plants, the α/β hydrolase DWARF14 (D14) perceives strigolactone (SL) hormones and interacts with the F-box protein MORE AXILLARY GROWTH2 (MAX2) to regulate developmental processes. The key SL biosynthetic enzyme, CAROTENOID CLEAVAGE DEOXYGENASE8 (CCD8), is present in the mossPhyscomitrium (Physcomitrella) patens,and PpCCD8-derived compounds regulate plant extension. Based on germination assays using seeds of the parasitic plantPhelipanche ramosa,we propose that these compounds are non-canonical SLs. Perception of PpCCD8-derived compounds does not require the PpMAX2 homolog. Candidate receptors are among the 13PpKAI2LIKE-A to -Lgenes, homologous to the ancestralD14paralogKARRIKIN INSENSITIVE2 (KAI2).In Arabidopsis, AtKAI2 is the receptor for a still elusive endogenous KAI2-Ligand (KL). We show that inP. patens,among SL analogs, the (+)-GR24 enantiomer is a good mimic for PpCCD8-derived compounds, while the effects of the (-)-GR24 enantiomer, a KL mimic in flowering plants, are opposite. Interaction and binding assays of seven PpKAI2L proteins using pure enantiomers pinpoint at stereoselectivity towards (-)-GR24 for the (A-E) clade. Enzyme assays highlight strong hydrolytic activity of the PpKAI2L-H protein. Moss mutants for allPpKAI2Lgene subclades were obtained and tested for their response to both enantiomers. We show thatPpKAI2L-Ato-Egenes are not involved in PpCCD8-derived compound perception, but act in a PpMAX2-dependant pathway. In contrast, mutations inPpKAI2L-G, and-Jgenes abolish the response to (+)-GR24, suggesting that encoded proteins are receptors for PpCCD8-derived SLs.
Protective face mask filter capable of inactivating SARS-CoV-2, and methicillin-resistantStaphylococcus aureusandStaphylococcus epidermidis
Authors: Martí Miguel , Tuñón-Molina Alberto , Aachmann Finn Lillelund , Muramoto Yukiko , Noda Takeshi , Takayama Kazuo , Serrano-Aroca Ángel
Published: November 2020

Face masks have globally been accepted to be an effective protective tool to prevent bacterial and viral transmission, especially against indoor aerosol transmission. However, commercial face masks contain filters that are made of materials that are not capable of inactivating neither SARS-CoV-2 nor multidrug-resistant bacteria. Therefore, symptomatic and asymptomatic individuals can infect other people even if they wear them because some viable viral or bacterial loads can escape from the masks. Furthermore, viral or bacterial contact transmission can occur after touching the mask, which constitutes an increasing source of contaminated biological waste. Additionally, bacterial pathogens contribute to the SARS-CoV-2 mediated pneumonia disease complex and their resistance to antibiotics in pneumonia treatment is increasing at an alarming rate. In this regard, herein, we report the development of a novel protective non-woven face mask filter fabricated with a biofunctional coating of benzalkonium chloride that is capable of inactivating SARS-CoV-2 in one minute of contact, and the life-threatening methicillin-resistantStaphylococcus aureusandStaphylococcus epidermidis.Nonetheless, despite the results obtained, further studies are needed to ensure the safety and correct use of this technology for the mass production and commercialization of this broad-spectrum antimicrobial face mask filter. Our novel protective non-woven face mask filter would be useful for many health care workers and researchers working in this urgent and challenging field.
Loss of cortical control over the descending pain modulatory system determines the development of the neuropathic pain state in rats
Authors: Drake RAR , Steel KAJ , Apps R , Lumb BM , Pickering AE
Published: November 2020

The loss of descending inhibitory control is thought critical to the development of chronic pain but what causes this loss in function is not well understood. We have investigated the dynamic contribution of prelimbic cortical neuronal projections to the periaqueductal grey (PrL-P) to the development of neuropathic pain in rats using combined opto- and chemo-genetic approaches. We found PrL-P neurons to exert a tonic inhibitory control on thermal withdrawal thresholds in uninjured animals. Following nerve injury, ongoing activity in PrL-P neurons masked latent hypersensitivity and improved affective state. However, this function is lost as the development of sensory hypersensitivity emerges. Despite this loss of tonic control, opto-activation of PrL-P neurons at late post-injury timepoints could restore the anti-allodynic effects by inhibition of spinal nociceptive processing. We suggest that the loss of cortical drive to the descending pain modulatory system underpins the expression of neuropathic sensitisation after nerve injury.
Acetylcholine Signaling Genes are Required for Cocaine-Stimulated Egg Laying inCaenorhabditis elegans
Authors: Emerson Soren , Hay Megan , Smith Mark , Granger Ricky , Blauch David , Snyder Nicole , El Bejjani Rachid
Published: November 2020

The toxicity and addictive liability associated with cocaine abuse are well known. However, its mode of action is not completely understood, and effective pharmacotherapeutic interventions remain elusive. The cholinergic effects of cocaine on acetylcholine receptors, synthetic enzymes, and degradative enzymes have been the focus of relatively little empirical investigation. Due to its genetic tractability and anatomical simplicity, the egg laying circuit of the hermaphroditic nematode,Caenorhabditis elegans, is a powerful model system to precisely examine the genetic and molecular targets of cocainein vivo. Here, we report a novel cocaine-induced behavioral phenotype inCaenorhabditis elegans, cocaine-stimulated egg laying. In addition, we present the results of anin vivocandidate suppression screen of synthetic enzymes, receptors, degradative enzymes, and downstream components of the intracellular signaling cascades of the main neurotransmitter systems that controlCaenorhabditis elegansegg laying. Our results show that cocaine-stimulated egg laying is dependent on acetylcholine synthesis and synaptic release, functional nicotinic acetylcholine receptors, and theCaenorhabditis elegansacetylcholinesterases.
Protein Detection and Localization in Plant Cells Using Spot-Tagging
Authors: Mentzelopoulou Andriani , Liu Chen , Moschou Panagiotis Nikolaou
Published: November 2020

Fluorescent labelling of proteins without compromising their activity is crucial for determining their spatiotemporal localization while retaining their functionality. Spot-tag is a 12-amino acid peptide recognized by a single-domain nanobody. Here we introduce the spot-tag as a labelling strategy for proteins in fixed and living plant cells, using as an example the microtubule motor centromeric protein E-related Kinesin 7.3. Spot-tagging of ectopically introduced Kinesin 7.3 does not interfere with microtubules and spot staining results in a close-grained fluorophore labelling revealing a localization pattern that resembles “beads-on-a-string”. We anticipate that our protocol will apply to many more demanding protein cellular targets, offsetting activity perturbations and low photon quantum yields imposed by other protein-tagging approaches.
Cortical processing of reference in language revealed by computational models
Authors: Li Jixing , Wang Shaonan , Luh Wen-Ming , Pylkkänen Liina , Yang Yiming , Hale John
Published: November 2020

Human language processing involves not only combining word meanings in accordance with semantic and syntactic constraints, but also figuring out who and what is being referred to. Here we present a first study towards a mechanistic understanding of the neural basis for referential processing. Using both functional MRI and magnetoencephalography (MEG), we identified a consistent increase of activity in a network spanning the anterior and posterior left middle temporal gyrus and the angular gyrus for pronoun processing during naturalistic listening for both English and Chinese speakers. We then adopted a “reverse-engineering” approach to examine the cognitive processes underlying pronoun resolution. We evaluated the neural fit of three symbolic models that each formalizes a different strand of explanation for pronoun resolution in the cognitive and linguistic literature, as well as two deep neural network models with an LSTM or a Transformer architecture. Our results favor the memory-based symbolic model, suggesting a domain-general mechanism of pronoun resolution that resembles memory retrieval.
Structural basis of resistance to lincosamide, streptogramin A, and pleuromutilin antibiotics by ABCF ATPases in Gram-positive pathogens
Authors: Crowe-McAuliffe Caillan , Murina Victoriia , Turnbull Kathryn Jane , Kasari Marje , Mohamad Merianne , Polte Christine , Takada Hiraku , Vaitkevicius Karolis , Johansson Jörgen , Ignatova Zoya , Atkinson Gemma C. , O’Neill Alex J. , Hauryliuk Vasili , Wilson Daniel N.
Published: November 2020

Target protection proteins bind to antibiotic targets and confer resistance to the host organism. One class of such proteins, termedantibioticresistance (ARE) ATP binding cassette (ABC) proteins of the F-subtype (ARE ABCFs), are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition by antibiotics that target the large ribosomal subunit. Using single-particle cryo-EM, we have solved the structure of ARE ABCF–ribosome complexes from three Gram-positive pathogens:Enterococcus faecalisLsaA,Staphylococcus haemolyticusVgaALCandListeria monocytogenesVgaL. Supported by extensive mutagenesis analysis, these structures enable a comparative approach to understanding how these proteins mediate antibiotic resistance on the ribosome. We present evidence of mechanistically diverse allosteric relays converging on a few peptidyltransferase center (PTC) nucleotides, and propose a general model of antibiotic resistance mediated by these ARE ABCFs.
ssc-micorRNA-132 suppresses theClostridium perfringensbeta2 toxin induced inflammation and apoptosis of IPEC-J2 cells via targetingDACH1
Authors: Xie Kaihui , Yan Zunqiang , wang Wei , Luo Ruirui , Gao Xiaoli , Wang Pengfei , Yang Qiaoli , Huang Xiaoyu , Zhang Juanli , Yang Jiaojiao , Gun Shuangbao
Published: November 2020

Clostridium perfringens(C. perfringens) beta2 (CPB2) is the main virulence factor secreted fromC. perfringenstype C, which caused diarrhea characterized by high mortality in pig, especially newborn piglets. Our previous research found that ssc-miR-132 displayed decreased expression in piglets diarrhea after infected withC. perfringenstype C compared with normal piglets. We speculated that ssc-miR-132 may play an important role in the diarrhea. However, the function of ssc-miR-132 in the diarrhea is limited. Thus, we overexpressed and knocked down ssc-miR-132 in intestinal porcine epithelial (IPEC-J2) cells, and then treated the cells with recombinant CPB2 (rCPB2) toxin (20 μg/mL). Our results showed that ssc-miR-132 was significantly decreased after treated with rCPB2 toxin. In addition, overexpression of ssc-miR-132 reduced the expression of lactate dehydrogenase (LDH) and tumor necrosis factor (TNF-α), interleukin-6 (IL-6) and interleukin-8 (IL-8) caused by rCPB2 toxin. The CCK8, Edu and TUNEL staining showed that overexpression of ssc-miR-132 weakened the inhibition of rCPB2 toxin on cell proliferation and reduced the promotion of cell apoptosis; while inhibition of ssc-miR-132 had opposite results. The dual luciferase experiment showed that dachshund family transcription factor 1 (DACH1) was the target gene of ssc-miR-132. SilencingDACH1was consistent with the results of overexpression of ssc-miR-132, and reversed the apoptosis and inflammation caused by rCPB2 toxin. Overexpression ofDACH1weakened the role of ssc-miR-132 in rCPB2 toxin -induced inflammation and apoptosis. In summary, ssc-miR-132 inhibited rCPB2 toxin-induced apoptosis and inflammation in IPEC-J2 cells by targetingDACH1.
Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells
Authors: Swygert Sarah G. , Lin Dejun , Portillo-Ledesma Stephanie , Lin Po-Yen , Hunt Dakota R. , Kao Cheng-Fu , Schlick Tamar , Noble William S. , Tsukiyama Toshio
Published: November 2020

Determining the conformation of chromatin in cells at the nucleosome level and its relationship to cellular processes has been a central challenge in biology. We show that in quiescent yeast, widespread transcriptional repression coincides with the local compaction of chromatin fibers into structures that are less condensed and more heteromorphic than canonical 30-nanometer forms. Acetylation or substitution of H4 tail residues decompacts fibers and leads to global transcriptional de-repression. Fiber decompaction also increases the rate of loop extrusion by condensin. These findings establish a role for H4 tail-dependent local chromatin fiber folding in regulating transcription and loop extrusion in cells. They also demonstrate the physiological relevance of canonical chromatin fiber folding mechanisms even in the absence of regular 30-nanometer structures.
Dissecting genomic determinants of positive selection with an evolution-guided regression model
Authors: Huang Yi-Fei
Published: November 2020

In evolutionary genomics, it is fundamentally important to understand how characteristics of genomic sequences, such as gene expression level, determine the rate of adaptive evolution. While numerous statistical methods, such as the McDonald-Kreitman test, are available to examine the association between genomic features and the rate of adaptation, we currently lack a statistical approach to disentangle the independent effect of a genomic feature from the effects of other correlated genomic features. To address this problem, I present a novel statistical model, the MK regression, which augments the McDonald-Kreitman test with a generalized linear model. Analogous to the classical multiple regression model, the MK regression can analyze multiple genomic features simultaneously to infer the independent effect of a genomic feature, holding constant all other genomic features. Using the MK regression, I identify numerous genomic features driving positive selection in chimpanzees. These features include well-known ones, such as local mutation rate, residue exposure level, tissue specificity, and immune genes, as well as new features not previously reported, such as gene expression level and metabolic genes. In particular, I show that highly expressed genes may have a higher adaptation rate than their weakly expressed counterparts, even though a higher expression level may impose stronger negative selection. Also, I show that metabolic genes may have a higher adaptation rate than their non-metabolic counterparts, possibly due to recent changes in diet in primate evolution. Overall, the MK regression is a powerful approach to elucidate the genomic basis of adaptation.