bluuebunny/crossref_metadata_2025 huggingface dataset:
Enriching and aggregating purple non-sulfur bacteria in an anaerobic sequencing-batch photobioreactor for nutrient capture from wastewater
Authors: Cerruti Marta , Stevens Berber , Ebrahimi Sirous , Alloul Abbas , Vlaeminck Siegfried E. , Weissbrodt David G.
Published: January 2020

Purple non-sulfur bacteria (PNSB), a guild of anoxygenic photomixotrophic organisms, rise interest to capture nutrients from wastewater in mixed-culture bioprocesses. One challenge targets the aggregation of PNSB biomass through gravitational separation from the treated water to facilitate its retention and accumulation, while avoiding the need for membranes. We aimed to produce an enriched, concentrated, well-settling, nutrient-removing PNSB biomass using sequencing batch regimes (SBR) in an anaerobic photobioreactor. The stirred tank was fed with a synthetic influent mimicking loaded municipal wastewater (430-860 mg CODAcLInf-1, COD:N:P ratio of 100:36:4-100:11:2 m/m/m), operated at 30°C and pH 7, and continuously irradiated with infrared (IR) light (>700 nm) at 375 W m-2. After inoculation with activated sludge at 0.1 g VSS L-1, PNSB were rapidly enriched in a first batch of 24 h: the genusRhodobacterreached 54% of amplicon sequencing read counts. SBR operations at volume exchange ratio of 50% with decreasing hydraulic retention times (48 to 16 h; 1 to 3 cycles d-1) and increasing volumetric organic loading rates (0.2 to 1.3 kg COD m-3d-1) stimulated the aggregation (compact granules of 50-150 μm), settling (sedimentation G-flux of 4.7 kg h-1m-2), and accumulation (as high as 3.8 g VSS L-1) of biomass. The sludge retention time (SRT) increased freely from 2.5 to 11 d without controlled sludge wasting. Acetate, ammonium, and orthophosphate were removed simultaneously (up to 96% at a rate of 1.1 kg COD m-3d-1, 77% at 113 g N m-3d-1, and 73% at 15 g P m-3d-1) with a COD:N:P assimilation ratio of 100:6.7:0.9 (m/m/m). Competition for substrate and photons occurred in the PNSB guild. SBR regime shifts sequentially selected forRhodobacter(90%) under shorter SRT and non-limiting acetate concentrations during reaction phases,Rhodopseudomonas(70%) under longer SRT and acetate limitation, andBlastochloris(10%) under higher biomass concentrations. We highlighted the benefits of a PNSB-based SBR process for biomass accumulation and simultaneous nutrient capture at substantial rates, and its underlying microbial ecology.

Graphical abstract

Highlights

PNSB were highly enriched (90%) in an anaerobic stirred-tank photobioreactor.

The mixed-culture SBR process fostered PNSB biomass aggregation and accumulation.

PNSB sludge reached 3.8 g VSS L-1and a sedimentation G-flux of 4.7 kg h-1m-2.

PNSB enabled a high simultaneous removal of COD (96%), N (77%), and P (73%).

Rhodobacter,Rhodopseudomonas, andBlastochloriscompeted for acetate and photons.
Motile ghosts of the halophilic archaeon,Haloferax volcanii
Authors: Kinosita Yoshiaki , Mikami Nagisa , Li Zhengqun , Braun Frank , Quax Tessa EF. , van der Does Chris , Ishmukhametov Robert , Albers Sonja-Verena , Berry Richard M.
Published: January 2020

Motility is seen across all domains of life1. Prokaryotes exhibit various types of motilities, such as gliding, swimming, and twitching, driven by supramolecular motility machinery composed of multiple different proteins2. In archaea only swimming motility is reported, driven by the archaellum (archaeal flagellum), a reversible rotary motor consisting of a torque-generating motor and a helical filament which acts as a propeller3,4. Unlike the bacterial flagellar motor (BFM), adenosine triphosphate (ATP) hydrolysis probably drives both motor rotation and filamentous assembly in the archaellum5,6. However, direct evidence is still lacking due to the lack of a versatile model system. Here we present a membrane-permeabilized ghost system that enables the manipulation of intracellular contents, analogous to the triton model in eukaryotic flagella7and glidingMycoplasma8,9. We observed high nucleotide selectivity for ATP driving motor rotation, negative cooperativity in ATP hydrolysis and the energetic requirement for at least 12 ATP molecules to be hydrolyzed per revolution of the motor. The response regulator CheY increased motor switching from counterclockwise (CCW) to clockwise (CW) rotation, which is the opposite of a previous report10. Finally, we constructed the torque-speed curve at various [ATP]s and discuss rotary models in which the archaellum has characteristics of both the BFM and F1-ATPase. Because archaea share similar cell division and chemotaxis machinery with other domains of life11,12, our ghost model will be an important tool for the exploration of the universality, diversity, and evolution of biomolecular machinery.
Neuroretinal-derived caveolin-1 promotes endotoxin-induced inflammation in the murine retina
Authors: Gurley Jami M. , Gmyrek Grzegorz , McClellan Mark E. , Hauck Stefanie M. , Dozmorov Mikhail G. , Wren Jonathan D. , Carr Daniel J. J. , Elliott Michael H.
Published: January 2020

Chronic ocular inflammation is associated with many retinal degenerative diseases that result in vision loss. The immune-privileged environment and complex organization of retinal tissue allow for the retina’s essential role in visual function processes, yet confound inquiries into cell-specific inflammatory effects that lead to retinal dysfunction and degeneration. Caveolin-1 (Cav1) is an integral membrane protein expressed in many retinal cell populations and has been implicated in retinal immune regulation. However, the direction (i.e., promotion or inhibition) in which Cav1 regulates inflammatory processes in the retina (as well as in other tissues) remains unclear. Previously, we showed that global-Cav1 depletion in the retina paradoxically resulted in reduced retinal inflammatory cytokine production with concurrent elevated retinal immune cell infiltration. We hypothesized that our previous results could be explained by cell-specific Cav1 functions in the retina. Here, we utilized our Chx10 (visual system homeobox 2)-Cre knockout model to deplete Cav1 specifically in the neural retinal (NR) compartment in order to clarify the role of neural retinal-specific Cav1 (NR-Cav1) in the retinal immune response to intravitreal LPS (lipopolysaccharide) challenge. Our data support that neural retinal-derived Cav1promotesretinal tissue inflammation as Chx10-mediated Cav1 depletion was sufficient to suppressbothretinal cytokine production and immune cell infiltration following inflammatory stimulation. Additionally, we identify Traf3 (tumor necrosis factor (TNF) receptor-associated factor 3) as a highly expressed potential immune modulator in retinal tissue that is upregulated with NR-Cav1 depletion. Furthermore, this study highlights the importance for understanding the role of Cav1 (and other proteins) in cell-specific contexts.
Interruption of thymic activity in adults improves responses to tumor immunotherapy
Authors: Almeida-Santos José , Bergman Marie-Louise , Cabral Inês Amendoeira , Demengeot Jocelyne
Published: January 2020

The thymus produces precursors of both effectors and regulatory T cells (Tconv and Treg, respectively) whose interactions prevents autoimmunity while allowing efficient protective immune responses. Tumors express a composite of self- and tumor-specific antigens and engage both Tconv and Treg cells. Along the aging process, the thymus involutes, and tumor incidence increases, a correlation proposed previously to be causal and the result of effector cell decline. In this work, we directly tested whether interruption of thymic activity in adult mice affects Foxp3 expressing Treg composition and function, and alters tumor immune surveillance. Young adult mice, on two different genetic backgrounds, were surgically thymectomized (TxT) and analyzed or challenged 2 months later. Cellular analysis revealed a 10-fold decrease in both Tconv and Treg numbers and a bias for activated cells. The persisting Treg displayed reduced stability of Foxp3 expression and, as a population, showed compromised return to homeostasis upon induced perturbations. We next tested the growth of three tumor models from different origin and presenting distinct degrees of spontaneous immunogenicity. In none of these conditions adult TxT facilitated tumor growth. Rather TxT enhanced the efficacy of anti-tumor immunotherapies targeting Treg and/or the checkpoint CTLA4, as evidenced by increased frequency of responder mice and decreased intra-tumoral Treg to CD8+IFNγ+cell ratio. Together, our findings point to a scenario where abrogation of thymic activities affects preferentially the regulatory over the ridding arm of the immune activities elicited by tumors, and argues that higher incidence of tumors with age cannot be solely attributed to thymic output decline.
RAD sequencing data reveal a radiation of willow species (SalixL., Salicaceae) in the Hengduan Mountains and adjacent areas
Authors: He Li , Wagner Natascha Dorothea , Hörandl Elvira
Published: January 2020

The Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and endemism and considered to be a secondary diversification center for the woody plant genusSalix(Salicaceae). This study aimed to reconstruct the spatio-temporal evolution of theSalix Chamaetia-Vetrixclade in the HDM and to test for the occurrence of a radiation. We inferred phylogenetic relationships based on more than 34,000 RAD loci of 27 species. Phylogenetic analyses recovered a well-resolved tree topology with two major clades, the Eurasian and the HDM clade and a divergence time of c. 23.9 Ma. The HDM clade comprises two subclades. The species of the HDM clade originated in north HDM and adjacent areas and then dispersed into the south HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses revealed that during the last glacial maximum, range contractions were observed in the northern areas, while southward expansions resulted in range overlaps. The reconstruction of putative adaptive character evolution of plant height, inflorescence and flower morphology indicate that adaptations to altitudinal distribution contributed to the diversification of the HDM willows. Our data indicate that a radiation occurred in HDM within theSalix Chamaetia-Vetrixclade. Dispersal within the mountain system and to adjacent regions as well as survival in glacial refugia have shaped the biogeographical history of the clade. Differentiation along altitudinal zonation concomitant to morphological adaptations to colder climates may be important ecological factors for the high species diversity ofSalixin this area.
Drug repurposing for mitochondrial diseases using a pharmacological model of complex I deficiency in the yeastYarrowia lipolytica
Authors: Perlstein Ethan O.
Published: January 2020

Mitochondrial diseases affect 1 in 5,000 live births around the world. They are caused by inherited orde novomutations in over 350 nuclear-encoded and mtDNA-encoded genes. There is no approved treatment to stop the progression of any mitochondrial disease despite the enormous global unmet need. Affected families often self-compound cocktails of over-the-counter vitamins and generally recognized as safe nutritional supplements that have not received regulatory approval for efficacy. Finding a new use for an approved drug is called repurposing, an attractive path for mitochondrial diseases because of the reduced safety risks, low costs and fast timelines to a clinic-ready therapy or combination of therapies. Here I describe the first-ever drug repurposing screen for mitochondrial diseases involving complex I deficiency, e.g., Leigh syndrome, using the yeastYarrowia lipolyticaas a model system. Unlike the more commonly used yeastSaccharomyces cerevisiaebut like humans,Yarrowia lipolyticahas a functional and metabolically integrated respiratory complex I and is an obligate aerobe. In 384-well-plate liquid culture format without shaking,Yarrowia lipolyticacells grown in either glucose-containing media or acetate-containing media were treated with a half-maximal inhibitory concentration (3µM and 6μM, respectively) of the natural product and complex I inhibitor piericidin A. Out of 2,560 compounds in the Microsource Spectrum collection, 24 suppressors of piercidin A reached statistical significance in one or both media conditions. The suppressors include calcium channel blockers nisoldipine, amiodarone and tetrandrine as well as the farnesol-like sesquiterpenoids parthenolide, nerolidol and bisabolol, which may all be modulating mitochondrial calcium homeostasis. Estradiols and synthetic estrogen receptor agonists are the largest class of suppressors that rescue growth of piericidin-A-treatedYarrowia lipolyticacells in both glucose-containing and acetate-containing media. Analysis of structure-activity relationships suggests that estrogens may enhance bioenergetics by evolutionarily conserved interactions with mitochondrial membranes that promote mitochondrial filamentation and mitochondrial DNA replication.
Virtual screening of MAP-Tauprotein inhibitors fromSemecarpus anacardiumLinn. leaf extract for cancer prevention
Authors: Singh Rajesh Kumar , Singh Anil Kumar , Ranjan Amit , Srivastava Akhileshwar Kumar , Singh Monika , Kumar Abhishek , Dwivedi Kamal Nayan
Published: January 2020

Semecarpus anacardiumis a well known Indian medicinal plant with various medicinal properties like hypoglycemic, antioxidant, anticancer, anti-inflammatory, anti-geriatric, antimicrobial and hair growth promoter, etc. The molecular mechanism of metabolites from fruiting bodies ofS. anacardiumagainst cancer has been described but anticancerous properties in its leaves are still unknown. The leaves were extracted in petroleum ether, ethyl acetate and methanol and assayed for anticancer activity using MTT assay. The active extract was evaluated for mode of cell death induction using EtBr-AO double staining and analyzed for phytochemical constituents using GC-MS, followed by molecular docking studies for exploration of possibility for anticancer agents and Drugability. In this study, ethyl acetate extract of leaf was found potent cytotoxic in MCF-7 cells and also induced apoptosis. It has also found the SLE is safe for normal cells. The molecular docking studies were done to explore the probable mechanism of action of the extract which showed 9 compounds are targeting the microtubule-associated protein tau (MAPT). MAPT promotes assembling and prevents disassembling to arrest the cell cycle. The overexpression of MAPT induces chemoresistance to cancerous cells against conventional drugs like paclitaxel. We have identified 17 compounds from ethyl acetate extract ofS. anacardiumleaves and drawn its chemical structure by using chembiodraw software to transform into pdb format. Further, the compounds have been subjected for molecular docking study to investigate its interactive efficiency with MAPT protein. The compound 13 had higher interactive potential to MAPT with binding energy −31.75 kcal/mol and lowest binding energy (−15.44 kcal/mol) was observed in compound 6. The present study suggested that the compounds from leaves ofS. anacardiumcould be alternative approach of conventional drug for cancer treatment with cost effective and less side effect.
Protein S-nitrosylation of Human Cytomegalovirus pp71 inhibits its ability to limit STING antiviral responses
Authors: Nukui Masatoshi , Roche Kathryn L. , Jia Jie , Fox Paul L. , Murphy Eain A.
Published: January 2020

Human Cytomegalovirus (HCMV) is a ubiquitous pathogen that has co-evolved with its host and in doing so, is highly efficient in undermining antiviral responses that limit successful infections. As a result, HCMV infections are highly problematic in individuals with weakened or underdeveloped immune systems including transplant recipients and newborns. Understanding how HCMV controls the microenvironment of an infected cell so as to favor productive replication is of critical importance. To this end, we took an unbiased proteomics approach to identify the highly reversible, stress induced, post-translational modification (PTM), protein S-nitrosylation, on viral proteins to determine the biological impact on viral replication.

We identified protein S-nitrosylation of 13 viral proteins during infection of highly permissive fibroblasts. One of these proteins, pp71, is critical for efficient viral replication, as it undermines host antiviral responses, including STING activation. By exploiting site-directed mutagenesis of the specific amino acids we identified in pp71 as protein S-nitrosylated, we found this pp71 PTM diminishes its ability to undermine antiviral responses induced by the STING pathway. Our results suggest a model in which protein S-nitrosylation may function as a host response to viral infection that limits viral spread.

IMPORTANCE

In order for a pathogen to establish a successful infection, it must undermine the host cell responses inhibitory to the pathogen. As such, herpesviruses encode multiple viral proteins that antagonize each host antiviral response, thereby allowing for efficient viral replication. Human Cytomegalovirus encodes several factors that limit host countermeasures to infection, including pp71. We identified a previously unreported modification of pp71 residues within the protein are protein S-nitrosylated. Using site-directed mutagenesis, we mutated the specific sites of this modification thereby blocking this pp71 post-translational modification. In contexts where pp71 is not protein S-nitrosylated, host antiviral response was inhibited. The net result of this post-translational modification is to render a viral protein with diminished abilities to block host responses to infection. This novel work supports a model in which protein S-nitrosylation may be an additional mechanism in which a cell inhibits a pathogen during the course of infection.
Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPσ
Authors: Karki Sudeep , Shkumatov Alexander V. , Bae Sungwon , Ko Jaewon , Kajander Tommi
Published: January 2020

Synaptic adhesion molecules play an important role in the formation, maintenance and refinement of neuronal connectivity. Recently, several leucine rich repeat (LRR) domain containing neuronal adhesion molecules have been characterized including netrin G-ligands, SLITRKs and the synaptic adhesion-like molecules (SALMs). Dysregulation of these adhesion molecules have been genetically and functionally linked to various neurological disorders. Here we investigated the molecular structure and mechanism of ligand interactions for the postsynaptic SALM3 adhesion protein with its presynaptic ligand, receptor protein tyrosine phosphatase σ (PTPσ). We solved the crystal structure of the dimerized leucine rich repeat (LRR) domain of SALM3, revealing the conserved structural features and mechanism of dimerization. Furthermore, we determined the complex structure of SALM3 with PTPσ using small angle X-ray scattering, revealing a 2:2 complex similar to that observed for SALM5. Solution studies unraveled additional flexibility for the complex structure, but validated the uniform mode of action for SALM3 and SALM5 to promote synapse formation. The relevance of the key interface residues was further confirmed by mutational analysis with cellular binding assays and artificial synapse formation assays. Collectively, our results suggest that SALM3 dimerization is a pre-requisite for the SALM3-PTPσ complex to exert synaptogenic activity.
Centrosome impairment causes DNA replication stress through MLK3/MK2 signaling and R-loop formation
Authors: Tayeh Zainab , Stegmann Kim , Kleeberg Antonia , Friedrich Mascha , Choo Josephine Ann Mun Yee , Wollnik Bernd , Dobbelstein Matthias
Published: January 2020

Abstract

Centrosomes function as organizing centers of microtubules and support accurate mitosis in many animal cells. However, it remains to be explored whether and how centrosomes also facilitate the progression through different phases of the cell cycle. Here we show that impairing the composition of centrosomes, by depletion of centrosomal components or by inhibition of polo-like kinase 4 (PLK4), reduces the progression of DNA replication forks. This occurs even when the cell cycle is arrested before damaging the centrosomes, thus excluding mitotic failure as the source of replication stress. Mechanistically, the kinase MLK3 associates with centrosomes. When centrosomes are disintegrated, MLK3 activates the kinases p38 and MK2/MAPKAPK2. Transcription-dependent RNA:DNA hybrids (R-loops) are then causing DNA replication stress. Fibroblasts from patients with microcephalic primordial dwarfism (Seckel syndrome) harbouring defective centrosomes showed replication stress and diminished proliferation, which were each alleviated by inhibition of MK2. Thus, centrosomes not only facilitate mitosis, but their integrity is also supportive in DNA replication.

Highlights

Centrosome defects cause replication stress independent of mitosis.

MLK3, p38 and MK2 (alias MAPKAPK2) are signalling between centrosome defects and DNA replication stress through R-loop formation.

Patient-derived cells with defective centrosomes display replication stress, whereas inhibition of MK2 restores their DNA replication fork progression and proliferation.

Graphical abstract
Changes in partner traits drive variation in plant–nectar robber interactions across habitats
Authors: Fitch Gordon , Vandermeer John
Published: January 2020

The frequency and outcome of biotic interactions commonly vary with environmental conditions, even without changes to community composition. Yet the drivers of such environmentally-mediated change in biotic interactions are poorly understood, limiting our ability to predict how environmental change will impact communities. Studying nectar robbery by stingless bees ofOdontonema cuspidatum(Acanthaceae) in a coffee agroecosystem, we documented a temporally consistent difference in nectar robbing intensity between anthropogenic and seminatural habitats. Plants growing in coffee fields (anthropogenic habitat) experienced significantly more nectar robbery than plants growing in forest fragments (seminatural habitat). Using a combination of field surveys and manipulative experiments, we found that nectar robbery was higher in coffee fields primarily due to environmental effects on a) neighborhood floral context and b)O. cuspidatumfloral traits. This led to both preferential foraging by nectar robbers in coffee fields, and to changes in foraging behavior onO. cuspidatumthat increased robbery. Nectar robbery significantly reduced fruit set inO. cuspidatum. These results suggest that the effects of anthropogenic environmental change on species traits may be more important than its effect on species density in determining how interaction frequency and outcome are affected by such environmental change.
Photosynthetic protein classification using genome neighborhood-based machine learning feature
Authors: Sangphukieo Apiwat , Laomettachit Teeraphan , Ruengjitchatchawalya Marasri
Published: January 2020

Identification of novel photosynthetic proteins is important for understanding and improving photosynthetic efficiency. Synergistically, genomic context such as genome neighborhood can provide additional useful information to identify the photosynthetic proteins. We, therefore, expected that applying the computational approach, particularly machine learning (ML) with the genome neighborhood-based feature should facilitate the photosynthetic function assignment. Our results revealed a functional relationship between photosynthetic genes and their genomic neighbors, indicating the possibility to assign functions from their genome neighborhood profile. Therefore, we created a new method for extracting the patterns based on genome neighborhood network (GNN) and applied for the photosynthetic protein classification using ML algorithms. Random forest (RF) classifier using genome neighborhood-based features achieved the highest accuracy up to 94% in the classification of photosynthetic proteins and also showed better performance (Mathew’s correlation coefficient = 0.852) than other available tools including the sequence similarity search (0.497) and ML-based method (0.512). Furthermore, we demonstrated the ability of our model to identify novel photosynthetic proteins comparing to the other methods. Our classifier is available athttp://bicep.kmutt.ac.th/photomod_standalone,https://bit.ly/2S0I2Oxand DockerHub:https://hub.docker.com/r/asangphukieo/photomod
CRY1-CBS binding regulates circadian clock function and metabolism
Authors: Cal-Kayitmazbatir Sibel , Kulkoyluoglu-Cotul Eylem , Growe Jacqueline , Selby Christopher P. , Rhoades Seth D. , Malik Dania , Oner Hasimcan , Asimgil Hande , Francey Lauren J. , Sancar Aziz , Kruger Warren D. , Hogenesch John B. , Weljie Aalim , Anafi Ron C. , Kavakli Ibrahim Halil
Published: January 2020

Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here we report that Cystathionine β-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein Cryptochrome1 (CRY1). In cells, CBS augments CRY1 mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. TransgenicCbsZn/Znmice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts fromCry1−/−mice show reduced CBS activity that normalizes after the addition of exogenous wild type (WT) CRY1. Metabolomic analysis of WT,CbsZn/Zn,Cry1−/−, andCry2−/−samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1 induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control.
Disassembly and degradation of MinD oscillator complexes byEscherichia coliClpXP
Authors: LaBreck Christopher J. , Trebino Catherine E. , Ferreira Colby N. , Morrison Josiah J. , DiBiasio Eric C. , Conti Joseph , Camberg Jodi L.
Published: January 2020

MinD is a cell division ATPase inEscherichia colithat oscillates from pole to pole and regulates the spatial position of the cell division machinery. Together with MinC and MinE, the Min system restricts assembly of the FtsZ-ring to midcell, oscillating between the opposite ends of the cell and preventing FtsZ-ring misassembly at the poles. Here, we show that the ATP-dependent bacterial proteasome complex ClpXP degrades MinD in reconstituted degradation reactions in vitro, through direct recognition of the MinD N-terminal region, and in vivo. MinD degradation is enhanced during stationary phase, suggesting that ClpXP regulates levels of MinD in cells that are not actively dividing. MinC and MinD are known to co-assemble into linear polymers, therefore we monitored copolymers assembled in vitro after incubation with ClpXP and observed that ClpXP promotes rapid MinCD copolymer disassembly as a result of direct MinD degradation by ClpXP. The N-terminus of MinD, including residue Arg 3, which is near the ATP-binding site, is critical for degradation by ClpXP. Together, these results demonstrate that ClpXP degradation modifies conformational assemblies of MinD in vitro and depresses Min function in vivo during periods of reduced proliferation.
FTO-mediated cytoplasmic m6Amdemethylation adjusts stem-like properties in colorectal cancer cell
Authors: Relier Sébastien , Ripoll Julie , Guillorit Hélène , Amalric Amandine , Boissière Florence , Vialaret Jérôme , Attina Aurore , Debart Françoise , Choquet Armelle , Macari Françoise , Samalin Emmanuelle , Vasseur Jean-Jacques , Pannequin Julie , Crapez Evelyne , Hirtz Christophe , Rivals Eric , Bastide Amandine , David Alexandre
Published: January 2020

Cancer stem cells (CSCs) are a small but critical cell population for cancer biology since they display inherent resistance to standard therapies and give rise to metastases. Despite accruing evidence establishing a link between deregulation of epitranscriptome-related players and tumorigenic process, the role of messenger RNA (mRNA) modifications dynamic in the regulation of CSC properties remains poorly understood. Here, we show that the cytoplasmic pool of fat mass and obesity-associated protein (FTO) impedes CSC abilities in colorectal cancer through its m6Am(N6,2’-O-dimethyladenosine) demethylase activity. While m6Amis strategically located next to the m7G-mRNA cap, its biological function is not well understood and has not been addressed in cancer. Low FTO expression in patient-derived cell lines elevates m6Amlevel in mRNA which results in enhancedin vivotumorigenicity and chemoresistance. Inhibition of the nuclear m6Ammethyltransferase, PCIF1/CAPAM, partially reverses this phenotype. FTO-mediated regulation of m6Ammarking constitutes a novel, reversible pathway controlling CSC abilities that does not involve transcriptome remodeling, but could fine-tune translation efficiency of selected m6Ammarked transcripts. Altogether, our findings bring to light the first biological function of the m6Ammodification and its potential adverse consequences for colorectal cancer management.
Limb contraction drives fear perception
Authors: Solanas Marta Poyo , Vaessen Maarten , de Gelder Beatrice
Published: January 2020

Humans and other primate species are experts at recognizing affective information from body movements but the underlying brain mechanisms are still largely unknown. Previous research focusing on the brain representation of symbolic emotion categories has led to mixed results. This study used representational similarity and multi-voxel pattern analysis techniques to investigate how postural and kinematic features computed from affective whole-body movement videos are related to brain processes. We show that body posture and kinematics differentially activated brain regions indicating that this information might be selectively encoded in these regions. Most specifically, the feature limb contraction seemed to be particularly relevant for distinguishing fear and it was represented in several regions spanning affective, action observation and motor preparation networks. Our approach goes beyond traditional methods of mapping symbolic emotion categories to brain activation/deactivation by discovering which specific movement features are encoded in the brain, and possibly drive automatic emotion perception.
ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning
Authors: Abadi Shiran , Avram Oren , Rosset Saharon , Pupko Tal , Mayrose Itay
Published: January 2020

Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. While model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they are not always feasible, and sometimes depend on preliminary assumptions which do not hold for sequence data. Moreover, while these methods are dedicated to revealing the processes that underlie the sequence data, in most cases they do not produce the most accurate trees. Notably, phylogeny reconstruction consists of two related tasks, topology reconstruction and branch-length estimation. It was previously shown that in many cases the most complex model, GTR+I+G, leads to topologies that are as accurate as using existing model selection criteria, but overestimates branch lengths. Here, we present ModelTeller, a computational methodology for phylogenetic model selection, devised within the machine-learning framework, optimized to predict the most accurate model for branch-length estimation accuracy. ModelTeller relies on a readily implemented machine-learning model and thus the prediction according to features extracted from the sequence data results in a substantial decrease in running time compared to existing strategies. We show that on datasets simulated under simple homogenous substitution models ModelTeller leads to branch-length estimation that is as accurate as the statistical model selection criteria. We then demonstrate that ModelTeller outperforms these criteria when more intricate patterns – that aim at mimicking realistic processes – are considered.
Dual-light photodynamic therapy administered daily provides a sustained antibacterial effect on biofilm and preventsStreptococcus mutansadaptation
Authors: Nikinmaa S , Alapulli H , Auvinen P , Vaara M , Rantala J , Kankuri E , Sorsa T , Meurman J , Pätilä T
Published: January 2020

Introduction

Antibacterial photodynamic therapy (aPDT) and antibacterial blue light (aBL) are emerging treatment methods auxiliary to mechanical debridement for periodontitis. APDT provided with a near infrared (NIR) light in conjunction with an indocyanine green (ICG) photosensitizer has shown efficacy in several dental in-office-treatment protocols. In this study, we testedStreptococcus mutansbiofilm sensitivity to either single-light (aPDT or aBL) or dual-light aPDT (simultaneous aPDT and aBL) exposure.

Materials and Methods

Biofilm was cultured by pipeting dilutedStreptococcus mutanssuspension with growth medium on the bottom of well plates. Either a single-light aPDT (810-nm aPDT or 405-nm aBL) or a dual-light aPDT (simultaneous 810-nm aPDT and 405nm aBL) was applied, in both cases together with the ICG photosensitizer, while keeping the total light energy constant at 100J/cm2. Single-dose light exposures were given after one-day, four-day or fourteen-day biofilm incubations. Also, a repeated daily dose of the same light energy was applied during biofilm incubations on four-day and fourteen-day biofilms. Finally, antibacterial action of the dual-light aPDT with different relative ratios of 810 nm and 405 nm of light energy was examined on the single-day and four-day protocols. Biofilms were scraped, diluted into ratios between 1:1 to 1:100 000, and plated. After re-incubation, colony-forming units (CFUs) were counted, and confocal 3D biofilm imaging was performed.

Results

On a one-day biofilm, dual-light aPDT was significantly more efficient than single-light aBL or aPDT, although all modalities were bactericidal. On a four-day maturated biofilm, a single exposure of aPDT or dual-light aPDT was more efficient than aBL, resulting in a four logarithmic scale reduction in bacterial counts. Surprisingly, when the same amount of aPDT was repeated with a daily dosing on a four-day or a fourteen-day biofilm, bacterial viability improved significantly. A similar but milder response of improved bacterial viability was seen after repetitive aBL application. The viability improvement was eliminated when dual-light aPDT was applied. By changing the relative light energy ratios in dual-light aPDT, a relative increase in aBL improved the antibacterial action of dual-light aPDT when the biofilm was older.

Conclusion

When aPDT is administered repeatedly toS. mutansbiofilm, a single wavelength-based aBL or aPDT leads to a significant biofilm adaptation and increasedS. mutansviability. The combined use of aBL light in synchrony with aPDT arrests the adaptation and provides significantly improved and sustained antibacterial efficacy.
Limited dispersal and an unexpected aggression pattern in a native supercolonial ant
Authors: Hakala S. M. , Ittonen M. , Seppä P. , Helanterä H.
Published: January 2020

Understanding how social groups function requires studies on how individuals move across the landscape and interact with each other. Ant supercolonies are extreme cooperative units that may consist of thousands of interconnected nests, and their individuals cooperate over large spatial scales. However, the inner structure of suggested supercolonial (or unicolonial) societies has rarely been extensively studied using both genetic and behavioral analyses. We describe a dense supercolony-like aggregation of more than 1 300 nests of the antFormica(Coptoformica)pressilabris. We performed aggression bioassays and found that, while aggression levels were generally low, there was some aggression within the assumed supercolony. The occurrence of aggression increased with distance from the focal nest, in accordance with the genetically viscous population structure we observe by using 10 microsatellite markers. However, the aggressive interactions do not follow any clear pattern that would allow specifying colony borders within the area. The genetic data indicate limited gene flow within and away from the supercolony. Our results show that aFormicasupercolony is not necessarily a single unit but can be a more fluid mosaic of aggressive and amicable interactions instead, highlighting the need to study internest interactions in detail when describing supercolonies.
Physiotherapist and Podiatrist Independent Prescribing in the United Kingdom: A quasi experimental study
Authors: Carey Nicola , Edwards Judith , Otter Simon , Gage Heather , Williams Peter , Courtenay Molly , Moore Ann , Stenner Karen
Published: January 2020

Background

Increasing numbers of nurses, pharmacists and allied health professionals across the world have prescribing rights: over 90,000 of the eligible United Kingdom workforce are qualified as non-doctor prescribers. In order to inform future developments, it is important to understand the benefits and impact of prescribing by allied health professionals including physiotherapists and podiatrists.

Aim:to compare outcomes of Physiotherapist and Podiatrist Independent Prescriber (PP-IP) patients with those of Physiotherapist and Podiatrist non-prescribers (PP-NPs). Outcome measures included patient satisfaction, ease of access to services, quality of life and cost implications.

Design:a quasi-experimental, post-test control group design

Methods:Using mixed methods outcomes were compared between 7 sites where care was provided from a PP-IP (3 podiatrist and 4 physiotherapist IPs) and 7 sites from a PP-NP (3 podiatrist and 4 physiotherapist NPs). Patients were followed up for 2 months (2015-2016).

Results:489 patients were recruited: n=243 IP sites, and n=246 NP sites. Independent prescribing was found to be highly acceptable, and equivalent in terms of quality of life (p>0.05) and patient satisfaction (p≤0.05) compared to care provided by NPs. PP-IP care delivery was found to be more resource intensive than NP-PP, with longer consultation duration for IPs (around 6.5 mins), and a higher proportion of physiotherapy patients discussed with medical colleagues (around 9.5 minutes).

Conclusion

This study provides new knowledge that PP-IPs provide high levels of care. PP-IP care delivery was found to be more resource intensive. Further research is required to explore cost effectiveness. A more focussed exploration within each profession using targeted outcome measures would enable a more robust comparison, inform future developments around the world and help ensure non-doctor prescribing is recognised as an effective way to alleviate shortfalls in the global workforce.
G9a Promotes Breast Cancer Recurrence Through Repression of a Pro-inflammatory Program
Authors: Mabe Nathaniel W. , Wolery Shayna E. , Newcomb Rachel , Meingasner Ryan C. , Vilona Brittany A. , Lin Chao-Chieh , Lupo Ryan , Chi Jen-Tsan , Alvarez James V.
Published: January 2020

Epigenetic dysregulation is a common feature of cancer, and is thought to underlie many aspects of tumor progression. Using a genetically engineered mouse model of breast cancer recurrence, we show that recurrent mammary tumors undergo widespread epigenomic and transcriptional alterations, and acquire dependence on the G9a histone methyltransferase. Genetic ablation of G9a delays tumor recurrence, and pharmacologic inhibition of G9a slows the growth of recurrent tumors. Mechanistically, G9a activity is required to silence pro-inflammatory cytokines, including TNF, through H3K9 methylation at gene promoters. G9a inhibition induces re-expression of these cytokines, leading to p53 activation and necroptosis. Recurrent tumors upregulate receptor interacting protein kinase-3 (RIPK3) expression and are dependent upon RIPK3 activity. High RIPK3 expression renders recurrent tumors sensitive to necroptosis following G9a inhibition. These findings demonstrate that epigenetic rewiring – specifically G9a-mediated silencing of pro-necroptotic proteins – is a critical step in tumor recurrence and suggest that G9a is a targetable dependency in recurrent breast cancer.
A FOXO-dependent replication checkpoint restricts proliferation of damaged cells
Authors: Hornsveld Marten , Feringa Femke M , Krenning Lenno , van den Berg Jeroen , Smits Lydia MM , Nguyen Nguyen BT , Rodriguez-Colman Maria J , Dansen Tobias B , Medema Rene H , Burgering Boudewijn MT
Published: January 2020

DNA replication is challenged by numerous exogenous and endogenous factors that can interfere with the progression of replication forks. Stalling or slowing of the replication fork as a result of replication stress leads to formation of aberrant single-stranded DNA (ssDNA) stretches and potentially DNA double-stranded-breaks (DSBs). Accumulation of ssDNA activates the ATR-dependent DNA replication stress checkpoint response that slows progression from S/G2- to M-phase to protect genomic integrity (1). However, whether mild replication stress restricts proliferation remains controversial (2–6). Here we identify a novel cell cycle exit mechanism, that prevents S/G2 phase arrested cells from undergoing mitosis after exposure to mild replication stress through premature activation of the CDH1 bound Anaphase Promoting Complex / Cyclosome (APC/CCDH1). We find that replication stress causes a gradual decrease of the levels of the APC/CCDH1inhibitor EMI1/FBXO5 through Forkhead Box O (FOXOs) mediated repression of its transcriptional regulator E2F1. By doing so, FOXOs limit the time during which the replication stress checkpoint is reversible, and thereby play an important role in maintaining genomic stability.
PPM-Decay: A Computational Model of Auditory Prediction with Memory Decay
Authors: Harrison Peter M. C. , Bianco Roberta , Chait Maria , Pearce Marcus T.
Published: January 2020

Statistical learning and probabilistic prediction are fundamental processes in auditory cognition. A prominent computational model of these processes is Prediction by Partial Matching (PPM), a variable-order Markov model that learns by internalizingn-grams from training sequences. However, PPM has limitations as a cognitive model: in particular, it has a perfect memory that weights all historic observations equally, which is inconsistent with memory capacity constraints and recency effects observed in human cognition. We address these limitations with PPM-Decay, a new variant of PPM that introduces a customizable memory decay kernel. In three studies – one with artificially generated sequences, one with chord sequences from Western music, and one with new behavioral data from an auditory pattern detection experiment – we show how this decay kernel improves the model’s predictive performance for sequences whose underlying statistics change over time, and enables the model to capture effects of memory constraints on auditory pattern detection. The resulting model is available in our new open-source R package,ppm(https://github.com/pmcharrison/ppm).
Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes
Authors: Latorre Sergio M. , Reyes-Avila C. Sarai , Malmgren Angus , Win Joe , Kamoun Sophien , Burbano Hernán A.
Published: January 2020

Background

Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungusMagnaporthe(Syn.Pyricularia)oryzae—the causal agent of blast disease of cereals— is among the most destructive plant pathogens to world agriculture and a major threat to the production of rice, wheat and other cereals. AlthoughM. oryzaeis a multihost pathogen that infects more than 50 species of cereals and grasses, all rice-infecting isolates belong to a single genetically defined lineage. Here, we combined multiple genomics datasets to reconstruct the genetic history of the rice-infecting lineage ofM. oryzaebased on 131 isolates from 21 countries.

Results

The global population of the rice blast fungus consists of a diverse set of individuals and three well-defined genetic groups. Multiple population genetic tests revealed that the rice-infecting lineage of the blast fungus probably originated from a recombining diverse group in South East Asia followed by three independent clonal expansions that took place over the last ∼200 years. Patterns of allele sharing identified a subpopulation from the recombining diverse group that introgressed with one of the clonal lineages before its global expansion. Remarkably, the four genetic lineages of the rice blast fungus vary in the number and patterns of presence/absence of candidate effector genes. In particular, clonal lineages carry a reduced repertoire of effector genes compared with the diverse group, and specific combinations of effector presence/absence define each of the pandemic clonal lineages.

Conclusions

Our analyses reconstruct the genetic history of the rice-infecting lineage ofM. oryzaerevealing three clonal lineages associated with rice blast pandemics. Each of these lineages displays a specific pattern of presence/absence of effector genes that may have shaped their adaptation to the rice host and their evolutionary history.
A Simple and Robust Cell-Based Assay for the Discovery of Novel Cytokinesis Inhibitors
Authors: Radnai Laszlo , Stremel Rebecca F. , Vaissiere Thomas , Martin William H. , Rumbaugh Gavin , Kamenecka Theodore M. , Griffin Patrick R. , Miller Courtney A.
Published: January 2020

Cytokinesis is the last step of mitotic cell division that separates the cytoplasm of dividing cells. Small molecule inhibitors targeting either the elements of the regulatory pathways controlling cytokinesis, or the terminal effectors have been of interest as potential drug candidates for the treatment of various diseases. Here we have developed a cell-based assay for the discovery of novel cytokinesis inhibitors. The assay is performed in a 96-well plate format in 48 hours. Living cells, nuclei and nuclei of dead cells are revealed by a single staining step with three fluorescent dyes, followed by live cell imaging using an automated fluorescence microscope. The primary signal is the nuclei-to-cell ratio (NCR). In the presence of cytokinesis inhibitors, this ratio is expected to increase over time, as the ratio of multinucleated cells increases in the population. Cytotoxicity is quantified as the ratio of dead nuclei to total nuclei. A screening window coefficient (Z’) of 0.65 indicates that the assay is suitable for screening purposes, as the positive and negative controls are well-separated. EC50values for four compounds can be reliably determined in a single 96-well plate by using only six different compound concentrations. An excellent test-retest reliability (R2=0.998) was found for EC50values covering a ∼1500-fold range of potencies. The robustness, simplicity and flexibility of the assay is demonstrated here by using modulators of actin dynamics with different mechanisms of action (jasplakinolide, cytochalasin D and swinholide A) and derivatives of the nonmuscle myosin II inhibitor blebbistatin.