bluuebunny/crossref_metadata_2025 huggingface dataset:
Influenza-associated mortality for circulatory and respiratory causes during the 2013-2014 through the 2018-2019 influenza seasons in Russia
Authors: Goldstein Edward
Published: November 2019

Background

Information on influenza-associated mortality in Russia is limited and largely related to deaths with influenza in the diagnosis that represent a small fraction of all influenza-associated deaths.

Methods

Using previously developed methodology (Goldstein et al., Epidemiology 2012), we regressed the monthly rates of mortality for respiratory causes, as well as circulatory causes (available from the Russian Federal State Statistics Service (Rosstat)) during the 2013/14 through the 2018/19 influenza seasons linearly against the monthly proxies for the incidence of influenza A/H3N2, A/H1N1 and B (obtained using data from the Smorodintsev Research Institute of Influenza (RII) on influenza/ARI consultations, testing of respiratory specimens and genetic/antigenic characterization of influenza viruses), adjusting for the baseline rates of mortality not associated with influenza circulation and temporal trends.

Results

For the 2013/14 through the 2018/19 seasons, influenza circulation was associated with an average annual 17636 (95% CI (9482,25790)) deaths for circulatory causes and 4179 (3250,5109) deaths for respiratory causes, with the largest number of deaths (32298 (18071,46525) for circulatory causes and 6689 (5019,8359) for respiratory causes) estimated during the 2014/15 influenza season. Influenza A/H3N2 was responsible for 51.8% of all circulatory influenza-associated deaths and 37.2% of all respiratory influenza-associated deaths. Influenza A/H1N1 was responsible for 23.4% of all circulatory influenza-associated deaths and 29.5% of all respiratory influenza-associated deaths. Influenza B was responsible for 24.9% of all circulatory influenza-associated deaths and 33.3% of all respiratory influenza-associated deaths, with the overwhelming majority of those deaths being caused by the B/Yamagata viruses. Compared to the 2013/14 through the 2015/16 seasons, during the 2016/17 through the 2018/19 seasons (when levels of influenza vaccination were significantly higher), the volume of influenza-associated mortality declined by about 16.1%, or 3809 annual respiratory and circulatory deaths.

Conclusions

Influenza circulation is associated with a substantial mortality burden in Russia, particularly for circulatory deaths, with some reduction in mortality rates observed following the major increase in influenza vaccination coverage. Those results support the potential utility of further extending the levels of influenza vaccination, the use of quadrivalent influenza vaccines, and extra efforts for protecting individuals with circulatory disease in Russia, including vaccination and the use of antiviral medications.
Attention-related modulation of caudate neurons depends on superior colliculus activity
Authors: Herman James P. , Arcizet Fabrice , Krauzlis Richard J.
Published: November 2019

Recent work has implicated the basal ganglia in visual perception and attention, in addition to their traditional role in motor control. The basal ganglia, especially the caudate nucleus “head” (CDh) of the striatum, receive indirect anatomical connections from the superior colliculus, a midbrain structure that is known to play a crucial role in the control of visual attention. To test the possible functional relationship between these subcortical structures, we recorded CDh neuronal activity before and during unilateral SC inactivation in a spatial attention task. SC inactivation significantly altered the attention-related modulation of CDh neurons and strongly impaired the classification of task epochs based on CDh activity. Only inactivation of the same-side of SC as recorded CDh neurons, not the opposite-side, had these effects. These results demonstrate a novel interaction between SC activity and attention-related visual processing in the basal ganglia.
Histone deacetylase 9 promoter hypomethylation associated with adipocyte dysfunction is a statin-related metabolic effect
Authors: Khamis Amna , Boutry Raphael , Canouil Mickaël , Mathew Sumi , Lobbens Stephane , Crouch Hutokshi , Andrew Toby , Abderrahmani Amar , Tamanini Filippo , Froguel Philippe
Published: November 2019

Background

Adipogenesis, the process whereby preadipocytes differentiate into mature adipocytes, is crucial for maintaining metabolic homeostasis. Cholesterol lowering statins increase type 2 diabetes (T2D) risk possibly by affecting adipogenesis and insulin resistance but the (epi)genetic mechanisms involved are unknown. Here, we characterised the effects of statin treatment on adipocyte differentiation using in vitro human preadipocytes cell model to identify putative effective genes.

Results

Statin treatment during adipocyte differentiation caused a reduction in key genes involved in adipogenesis, such as ADIPOQ, GLUT4 and ABCG1. Using Illumina’s Infinium ‘850K’ Methylation EPIC array, we found a significant hypomethylation of cg14566882, located in the promoter of the histone deacetylase 9 (HDAC9) gene, in response to two types of statins (atorvastatin and mevastatin), which correlates with an increased HDAC9 mRNA expression. HDAC9 is a transcriptional repressor of the cholesterol efflux ABCG1 gene expression, which is epigenetically modified in obesity and prediabetic states. Thus, we assessed the putative impact of ABCG1 knockdown in mimicking the effect of statin in adipogenesis. ABCG1 KD reduced the expression of key genes involved in adipocyte differentiation and decreased insulin signalling and glucose uptake. In human blood cells from two cohorts, ABCG1 expression was impaired in response to statins, confirming that ABCG1 is in vivo targeted by these drugs.

Conclusions

We identified an epigenetic link between adipogenesis and adipose tissue insulin resistance in the context of T2D risk associated with statin use, which has important implications as HDAC9 and ABCG1 are considered potential therapeutic targets for obesity and metabolic diseases.
NLRP7 Plays A Functional Role in Regulating BMP4 Signaling During Differentiation of Patient-Derived Trophoblasts
Authors: Alici-Garipcan Aybuke , Özçimen Burcu , Suder Ilke , Ülker Volkan , Önder Tamer T. , Özören Nesrin
Published: November 2019

Complete Hydatidiform Mole (HM) is a gestational trophoblastic disease resulting in hyper proliferation of trophoblast cells and absence of embryo development. Mutations in the primate specific-maternal effect gene NLRP7 are the major cause of familial recurrent complete HM. Here, we established an in vitro model of HM using NLRP7 deficient patient-specific induced pluripotent stem cells (iPSCs) derived trophoblasts. Using whole transcriptome profiling during trophoblast differentiation, we showed that NLRP7 deficiency results in precocious downregulation of pluripotency factors, activation of trophoblast lineage markers and promotes maturation of differentiated extraembryonic cell types such as syncytiotrophoblasts. Interestingly, we found that these phenotypes are dependent on BMP4 signaling and BMP pathway inhibition corrected the excessive trophoblast differentiation of patient derived iPSCs. Our human iPSC model of a genetic placental disease recapitulates aspects of trophoblast biology, highlights the broad utility of iPSC-derived trophoblasts for modeling human placental diseases and identifies NLRP7 as an essential modulator of key developmental cell fate regulators.
NorK, a novel norfloxacin efflux pump in Staphylococcus aureus
Authors: Briaud Paul , Baude Jessica , Bastien Sylvère , Camus Laura , Vandenesch François , Moreau Karen
Published: November 2019

A novel efflux pump similar to Nor efflux pumps and designated as NorK was identified in Staphylococcus aureus. It contributes to norfloxacin resistance and presents a high level of expression in different strains. Its expression is not regulated by MgrA, unlike other genes of the nor gene family, suggesting that NorK could be important in the absence of expression of other nor genes.
Phase variation-based biosensors for bacteriophage detection and phage receptor discrimination
Authors: Olivenza David R. , Casadesús Josep , Ansaldi Mireille
Published: November 2019

Environmental monitoring of bacteria using phage-based biosensors has been widely developed for many different species. However, there are only a few available methods to detect specific bacteriophages in raw environmental samples. In this work, we developed a simple and efficient assay to rapidly monitor the phage content of a given sample. The assay is based on the bistable expression of theSalmonella enterica opvABoperon. Under regular growth conditions,opvABis only expressed by a small fraction of the bacterial subpopulation. In the OpvABONsubpopulation, synthesis of the OpvA and OpvB products shortens the O-antigen in the lipopolysaccharide and confers resistance to phages that use LPS as a receptor. As a consequence, the OpvABONsubpopulation is selected in the presence of such phages. Using anopvAB::gfpfusion, we could monitor LPS-binding phages in various media, including raw water samples. To enlarge our phage-biosensor panoply, we also developed several coliphage biosensors that proved efficient to detect LPS- as well as protein-binding coliphages. Moreover, the combination of these tools allows to identify what is the bacterial receptor triggering phage infection. TheopvAB::gfpbiosensor thus comes in different flavours to efficiently detect a wide range of bacteriophages and identify the type of receptor they recognize.

Importance

Detection and accurate counting of bacteriophages, the viruses that specifically infect bacteria, from environmental samples still constitutes a challenge for those interested in isolating and characterizing bacteriophages for ecological or biotechnological purposes. This work provides a simple and accurate method based on the bi-stable expression of genes that confer resistance to certain classes of bacteriophages in different bacterial models. It paves the way for future development of highly efficient phage biosensors that can discriminate among several receptor-binding phages and that could be declined in many more versions. In a context where phage ecology, research, and therapy are flourishing again, it becomes essential to possess simple and efficient tools for phage detection.
Mildew Locus O facilitates colonization by arbuscular mycorrhiza in angiosperms
Authors: Jacott Catherine N. , Charpentier Myriam , Murray Jeremy D. , Ridout Christopher J.
Published: November 2019

Loss of barley Mildew Resistance Locus O (MLO) is known to confer durable and robust resistance to powdery mildew (Blumeria graminis), a biotrophic fungal leaf pathogen. Based on the increased expression of MLO in mycorrhizal roots and its presence in a clade of the MLO family that is specific to mycorrhizal-host species, we investigated the potential role of MLO in arbuscular mycorrhizal interactions.

Using mutants from barley, wheat, and Medicago truncatula, we demonstrate a role for MLO in colonization by the arbuscular mycorrhizal fungi Rhizophagus irregularis.

Early mycorrhizal colonization was reduced in mlo mutants of barley, wheat and Medicago truncatula, and this was accompanied by a pronounced decrease in the expression of many of the key genes required for intracellular accommodation of arbuscular mycorrhizal fungi.

These findings suggest that the primary role of MLO in angiosperms is in the establishment of symbiotic associations with beneficial fungi, which has been appropriated by powdery mildew.
The neural computation of human prosocial choices in complex motivational states
Authors: Saulin Anne , Horn Ulrike , Lotze Martin , Kaiser Jochen , Hein Grit
Published: November 2019

Motives motivate human behavior. Most behaviors are driven by more than one motive, yet it is unclear how different motives interact and how such motive combinations affect the neural computation of the behaviors they drive. To answer this question, we induced two prosocial motives simultaneously (multi-motive condition) and separately (single motive conditions). After the different motive inductions, participants performed the same choice task in which they allocated points in favor of the other person (prosocial choice) or in favor of themselves (egoistic choice). We used fMRI to assess prosocial choice-related brain responses and drift diffusion modelling to specify how motive combinations affect individual components of the choice process. Our results showed that the combination of the two motives in the multi-motive condition increased participants’ choice biases prior to the behavior itself. On the neural level, these changes in initial prosocial bias were associated with neural responses in the bilateral dorsal striatum. In contrast, the efficiency of the prosocial decision process was comparable between the multi-motive and the single-motive conditions. These findings provide insights into the computation of prosocial choices in complex motivational states, the motivational setting that drives most human behaviors.

Highlights

Activating different social motives simultaneously can enhance prosocial choices

Multi-motive combinations change initial prosocial biases

Dorso-striatal activation increases with larger increase of prosocial bias

Multi-motive combinations modulate relative response caution
The effect of experimental lead pollution on DNA methylation in a wild bird population
Authors: Mäkinen Hannu , van Oers Kees , Eeva Tapio , Laine Veronika N. , Ruuskanen Suvi
Published: November 2019

Anthropogenic pollution is known to negatively influence an organism’s physiology, behavior and fitness. Epigenetic regulation, such as DNA methylation, has been hypothesized as one mechanism to mediate such effects, yet studies in wild species are lacking. We first investigated the effects of early-life exposure to the heavy metal lead (Pb) on DNA methylation levels in a wild population of great tits (Parus major), by experimentally exposing nestlings to lead at environmentally relevant levels. Secondly, we studied the effects of heavy metal exposure in a population close to a copper smelter, where birds suffer from pollution-related decrease in food quality. For both comparisons, the analysis of about million CpGs covering most of the annotated genes, revealed that regions enriched for developmental processes showed pollution-related changes in DNA methylation, but the results were not consistent with binomial and beta binomial regression. Our study indicates that post-natal anthropogenic heavy metal exposure can affect methylation levels of development related genes in a wild bird population.
Antimicrobial solid media for screening non-sterile Arabidopsis thaliana seeds
Authors: Behrendorff James B. Y. H. , Borràs-Gas Guillem , Pribil Mathias
Published: November 2019

Background

Stable genetic transformation of plants is a low-efficiency process, and identification of positive transformants usually relies on screening for expression of a co-transformed marker gene. Often this involves germinating seeds on solid media containing a selection reagent. Germination on solid media requires surface sterilization of seeds and careful aseptic technique to prevent microbial contamination, but surface sterilization techniques are time consuming and can cause seed mortality if not performed carefully. We developed an antimicrobial cocktail that can be added to solid media to inhibit bacterial and fungal growth without impairing germination, allowing us to bypass the surface sterilization step.

Results

Adding a combination of terbinafine (1 µM) and timentin (200 mg/L) to solid media delayed the onset of observable microbial growth and did not affect germination of non-sterile seeds from ten different wild-type and mutant Arabidopsis thaliana accessions. The method was also compatible with Nicotiana tabacum germination. Seedlings sown in non-sterile conditions could be maintained on antimicrobial media for up to a week without observable contamination. The antimicrobial cocktail was compatible with rapid screening methods for hygromycin B, phosphinothricin (BASTA) and nourseothricin resistance genes, meaning that positive transformants can be identified from non-sterile seeds in as little as four days after stratification and transferred to soil before the onset of visible microbial contamination.

Conclusion

The antimicrobial cocktail presented here delays microbial growth for long enough to permit germination of non-sterile Arabidopsis thaliana seedlings on solid media and it is compatible with rapid screening methods. We were able to select genetic transformants on solid media without seed surface sterilization, eliminating a tedious and time-consuming step.
A novel pH-regulated, unusual 603 bp overlapping protein coding gene pop is encoded antisense to ompA in Escherichia coli O157:H7 (EHEC)
Authors: Zehentner Barbara , Ardern Zachary , Kreitmeier Michaela , Scherer Siegfried , Neuhaus Klaus
Published: November 2019

Antisense transcription is well known in bacteria. However, translation of antisense RNAs is typically not considered, as the implied overlapping coding at a DNA locus is assumed to be highly improbable. Therefore, such overlapping genes are systematically excluded in prokaryotic genome annotation. Here we report an exceptional 603 bp long open reading frame completely embedded in antisense to the gene of the outer membrane protein ompA. Ribosomal profiling revealed translation of the mRNA and the protein was detected in Western blots. A σ70 promoter, transcription start site, Shine-Dalgarno motif and rho-independent terminator were experimentally validated. A pH-dependent phenotype conferred by the protein was shown in competitive overexpression growth experiments of a translationally arrested mutant versus wild type. We designate this novel gene pop (pH-regulated overlapping protein-coding gene). Increasing evidence based on ribosome-profiling indicates translation of antisense RNA, suggesting that more overlapping genes of unknown function may exist in bacteria.
Hormonal control of motivational circuitry orchestrates the transition to sexuality in Drosophila
Authors: Zhang Stephen X. , Glantz Ethan H. , Rogulja Dragana , Crickmore Michael A.
Published: November 2019

Newborns and hatchlings of many species perform incredibly sophisticated behaviors, but all vertebrates and many invertebrates selectively abstain from sexual activity at the beginning of life. Hormonal changes have long been associated with adolescence, but it is not clear how these circulating factors create a new motivation and drive its associated behaviors. We show that the transition to sexuality in maleDrosophilais controlled by juvenile hormone, which spikes at eclosion and declines over days as the propensity for courtship gradually increases. Juvenile hormone directly inhibits the activity of at least three courtship-motivating circuit elements, ensuring the complete suppression of sexual motivation and behavior. Blocking or overriding these inhibitory mechanisms evokes immediate and robust sexual behavior from very young and otherwise asexual males. These results provide a first example of hormonal changes gating the transition to sexuality by activating latent, but largely developed and functional, motivational circuitry.
Model-based inference of punctuated molecular evolution
Authors: Manceau Marc , Marin Julie , Morlon Hélène , Lambert Amaury
Published: November 2019

In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a time-varying rate (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary time scale. Here, we develop a model combining basal, clock-like molecular evolution with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) co-occurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular evolution and from temporal variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.
Intra-Species Differences in Population Size shape Life History and Genome Evolution
Authors: Willemsen David , Cui Rongfeng , Reichard Martin , Valenzano Dario Riccardo
Published: November 2019

The evolutionary forces shaping life history trait divergence within species are largely unknown. Killifish (oviparous Cyprinodontiformes) evolved an annual life cycle as an exceptional adaptation to life in arid savannah environments characterized by seasonal water availability. The turquoise killifish (Nothobranchius furzeri) is the shortest-lived vertebrate known to science and displays differences in lifespan among wild populations, representing an ideal natural experiment in the evolution and diversification of life history. Here, by combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among turquoise killifish populations. We generate an improved reference assembly for the turquoise killifish genome, trace the evolutionary origin of the sex chromosome, and identify genes under strong positive and purifying selection, as well as those evolving neutrally. We find that the shortest-lived turquoise killifish populations, which dwell in fragmented and isolated habitats at the outer margin of the geographical range of the species, are characterized by small effective population size and accumulate throughout the genome several small to large-effect deleterious mutations due to genetic drift. The genes most affected by drift in the shortest-lived turquoise killifish populations are involved in the WNT signalling pathway, neurodegenerative disorders, cancer and the mTOR pathway. As the populations under stronger genetic drift are the shortest-lived ones, we propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by causing the genome-wide accumulation of deleterious mutations, cumulatively contribute to the short adult lifespan in turquoise killifish populations.
Energy Expenditure during Cell Spreading Regulates the Stem Cells Responses to Matrix Stiffness
Authors: Xie Jing , Bao Min , Hu Xinyu , Koopman Werner J. H. , Huck Wilhelm T. S.
Published: November 2019

Cells respond to the mechanical properties of the extracellular matrix (ECM) through formation of focal adhesions (FAs), re-organization of the actin cytoskeleton and adjustment of cell contractility. These are energy-demanding processes, but a potential causality between mechanical cues (matrix stiffness) and cellular (energy) metabolism remains largely unexplored. Here, we culture human mesenchymal stem cells (hMSCs) on stiff (20 kPa) or soft (1 kPa) substrate and demonstrate that cytoskeletal reorganization and FA formation spreading on stiff substrates lead to a drop in intracellular ATP levels, correlates with the activation of AMP-activated protein kinase (AMPK). The resulting increase in ATP levels further facilitates cell spreading and reinforces cell tension of the steady state, and coincides with nuclear localization of YAP/TAZ and Runx2. While on soft substrates (1 kPa), lowered ATP levels limit these cellular mechanoresponses. Furthermore, genetic ablation of AMPK lowered cellular ATP levels on stiff substrate and strongly reduced responses to substrate stiffness. Together, these findings reveal a hitherto unidentified relationship between energy expenditure and the cellular mechanoresponse, and point to AMPK as a key mediator of stem cell fate in response to ECM mechanics.
A novel transplantable model of lung cancer associated tissue loss and disrupted muscle regeneration
Authors: Arneson Paige C , Ducharme Alexandra M , Doles Jason D
Published: November 2019

Background

Cancer-associated muscle wasting (CAW), a symptom of cancer cachexia, is associated with approximately 20% of lung cancer deaths, and remains poorly characterized on a mechanistic level. Current animal models for lung cancer-associated cachexia are limited in that they: 1) primarily employ flank transplantation methods, 2) have short survival times not reflective of the patient condition, and 3) are typically performed in young mice not representative of mean patient age. This study investigates a new model for lung cancer-associated cachexia that can address these issues and also implicates muscle regeneration as a contributor to CAW.

Methods

We used tail vein injection as a method to introduce tumor cells that seed primarily in the lungs of mice. Body composition of tumor bearing mice was longitudinally tracked using NMR-based, echo magnetic resonance imaging (echoMRI). These data were combined with histological and molecular assessments of skeletal muscle to provide a complete analysis of muscle wasting.

Results

In this new lung CAW model we observed 1) progressive loss in whole body weight, 2) progressive loss of lean and fat mass, 3) a circulating cytokine/inflammatory profile similar to that seen in other models of CAW, 4) histological changes associated with muscle wasting, and 5) molecular changes in muscle that implicate suppression of muscle repair/regeneration. Finally, we show that survival can be extended without lessening CAW by titrating injected cell number.

Conclusions

Overall, this study describes a new model of CAW that could be useful for further studies of lung cancer-associated wasting and accompanying changes in the regenerative capacity of muscle. Additionally, this model addresses many recent concerns with existing models such as immunocompetence, tumor location, and survival time.
Transcranial Direct current stimulation does not modulate performance on a tongue twister task
Authors: Wiltshire Charlotte E. E. , Watkins Kate E.
Published: November 2019

Background

TDCS modulates cortical excitability in a polarity-specific way. When used in combination with a behavioural task, it can also alter performance. Previously, tDCS modulated the performance of older adults on a complex speech motor learning task, which involved repetition of tongue twisters [1].

Objective

We aimed to replicate this finding in healthy young participants and to extend it by measuring tDCS-induced changes in motor excitability using transcranial magnetic stimulation and motor-evoked potentials elicited in the lips.

Method

In a double-blind randomized sham-controlled study, three groups of 20 participants received: 1) anodal tDCS to the left IFG/LipM1 and cathodal tDCS to the right hemisphere homologue; or 2) cathodal tDCS over the left and anodal over the right; or 3) sham stimulation. Participants heard and repeated tongue twisters and matched simple sentences before, during and 10 minutes after the stimulation. Motor excitability was measured before and immediately after the tDCS.

Results

The improvement in performance of tongue twister repetition from baseline to after stimulation was significantly greater than for the simple sentences but did not differ among the three groups. Motor excitability significantly decreased to a small but similar extent across the three groups.

Conclusions

TDCS did not modulate performance on a complex articulation task in healthy young adults. TDCS applied concurrently with task learning also failed to modulate motor excitability in expected ways. TDCS may be most effective in brains where brain function is sub-optimal due to age-related declines or pathology.
Visualizing a protonated RNA state that modulates microRNA-21 maturation
Authors: Baisden Jared T. , Boyer Joshua A. , Zhao Bo , Zhang Qi
Published: November 2019

MicroRNAs are evolutionarily conserved small, non-coding RNAs that regulate diverse biological processes. Due to their essential regulatory roles, microRNA biogenesis is tightly regulated, where protein factors are often found to interact with specific primary and precursor microRNAs for regulation. Here, using NMR relaxation dispersion spectroscopy and mutagenesis, we reveal that the precursor of oncogenic microRNA-21 exists as a pH-dependent ensemble that spontaneously reshuffles the secondary structure of the entire apical stem-loop region, including the Dicer cleavage site. We show that the alternative excited conformation transiently sequesters the bulged adenine into a non-canonical protonated A+–G mismatch, conferring a two-fold enhancement in Dicer processing over its ground conformational state. These results indicate that microRNA maturation efficiency may be encoded in the intrinsic dynamic ensemble of primary and precursor microRNAs, providing potential means of regulating microRNA biogenesis in response to environmental and cellular stimuli.
A novel, ultrasensitive approach for quantitative carbohydrate composition and linkage analysis using LC-ESI ion trap tandem mass spectrometry
Authors: Alagesan Kathirvel , Silva Daniel Varon , Seeberger Peter H , Kolarich Daniel
Published: November 2019

Glycan identification and characterisation is essential to correlate glycoconjugate structure to biological function. The structural assignment of carbohydrates is often based on MS composition analyses and knowledge on well-studied glycosylation pathways. Nevertheless, many monosaccharide building blocks are indistinguishable by mass alone and detailed linkage information is also not easily obtained by MS/MS analyses, in particular when organisms are studied where the glycosylation pathways are less well defined. Here, we present a novel, simple and sensitive method using Reversed Phase (RP) – Liquid Chromatography Electrospray ionisation tandem mass spectrometry (LC–ESI-MS/MS) for unambiguous identification and linkage determination of monosaccharides including N-acetylneuraminic acids. Sequential permethylation and reductive amination steps are employed prior and after acid hydrolysis to enable separation and differentiation of the various monosaccharides and their respective linkage positions. The well-established, monosaccharide specific methylation patterns allowed for the identification of the various derivatised monosaccharide alditols based on their retention time and tandem mass spectrometry fingerprint. Absolute quantitation can also be accomplished by including a set of internal standards, thus simultaneously providing qualitative and quantitative information on the monosaccharide residues present.
Viscoelastic properties of ECM-rich embryonic microenvironments
Authors: Akos Zsuzsa , Isai Dona G. , Rajasingh Sheeja , Kosa Edina , Ghazvini Saba , Dhar Prajna , Czirok Andras
Published: November 2019

The material properties of tissues and their mechanical state is an important factor during development, disease, regenerative medicine and tissue engineering. Here we describe a microrheological measurement technique utilizing aggregates of microinjected ferromagnetic nickel particles to probe the viscoelastic properties of embryonic tissues. Quail embryos were cultured in a plastic incubator chamber located at the center of two pairs of crossed electromagnets. We estimate the Young’s modulus of the ECM-rich region separating the mesoderm and endoderm in Hamburger Hamilton stage 6-10 quail embryos as 300±100 Pa. We found a pronounced viscoelastic behavior consistent with a Zener (standard generalized solid) model. The viscoelastic response is about 45% of the total response, with a characteristic relaxation time of 1.3 sec.
Microtubule Nucleation by Single Human γTuRC in a Partly Open Asymmetric Conformation
Authors: Consolati Tanja , Locke Julia , Roostalu Johanna , Asthana Jayant , Lim Wei Ming , Gannon Julian , Martino Fabrizio , Costa Alessandro , Surrey Thomas
Published: November 2019

The γ-tubulin ring complex (γTuRC) is the major microtubule nucleator in cells. However, the mechanism of its regulation is not understood. Here, we purified human γTuRC and quantitatively characterized its nucleation properties in a TIRF microscopy-based real-time nucleation assay. We find that microtubule nucleation by γTuRC is kinetically inhibited compared to microtubule elongation. Determining the cryo-EM structure of γTuRC at 4 Å resolution reveals an asymmetric conformation with only part of the complex in a ‘closed’ conformation matching the microtubule geometry. Several factors stabilise the closed conformation. One is actin in the core of the complex and others, likely MZT1 or MZT2, line the outer perimeter of the closed part of γTuRC. The opposed side of γTuRC is in an ‘open’, nucleation-incompetent conformation, leading to a structural asymmetry, explaining the kinetic inhibition of nucleation by human γTuRC. Our data suggest possible regulatory mechanisms for microtubule nucleation by γTuRC closure.
Calcium-induced calcium release in noradrenergic neurons of the locus coeruleus
Authors: Kawano Hiroyuki , Mitchell Sara B. , Koh Jin-Young , Goodman Kirsty M. , Harata N. Charles
Published: November 2019

The locus coeruleus (LC) is a nucleus within the brainstem that consists of norepinephrine-releasing neurons. It is involved in broad processes including autonomic regulation, and cognitive and emotional functions such as arousal, attention and anxiety. Understanding the mechanisms that control the excitability of LC neurons is important because they innervate widespread regions of the central nervous system. One of the key regulators is the cytosolic calcium concentration ([Ca2+]c), the increases in which can be amplified by calcium-induced calcium release (CICR) from the intracellular calcium stores. Although the electrical activities of LC neurons are regulated by changes in [Ca2+]c, the extent of CICR involvement in this regulation has remained unclear. Here we show that CICR hyperpolarizes acutely dissociated LC neurons of the rat brain and demonstrate the pathway whereby it does this. When CICR was activated by extracellular application of 10 mM caffeine, LC neurons were hyperpolarized in the current-clamp mode of the patch-clamp recording, and the majority of neurons showed an outward current in the voltage-clamp mode. This outward current was accompanied by an increase in membrane conductance, and its reversal potential was close to the K+ equilibrium potential, indicating that it is mediated by the opening of K+ channels. The outward current was generated in the absence of extracellular calcium and was blocked when the calcium stores were inhibited by applying ryanodine. Pharmacological experiments indicated that the outward current was mediated by Ca2+-activated K+ channels of the non-small conductance type. Finally, the application of caffeine led to an increase in the [Ca2+]c in these neurons, as visualized by fluorescence microscopy. These findings delineate a mechanism whereby CICR suppresses the electrical activity of LC neurons, and indicate that it could play a dynamic role in modulating the LC-mediated noradrenergic tone in the brain.
NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale
Authors: Varga Matthew J. , Loggia Spencer , Fu Yiben , Yogurtcu Osman N , Johnson Margaret E.
Published: November 2019

Currently, a significant barrier to building predictive models of cell-based self-assembly processes is that molecular models cannot capture minutes-long cellular dynamics that couple distinct components with active processes, while reaction-diffusion models lack sufficient detail for capturing assembly structures. Here we introduce the Non-Equilibrium Reaction-Diffusion Self-assembly Simulator (NERDSS), which addresses this gap by integrating a structure-resolved reaction-diffusion algorithm with rule-based model construction. By representing proteins as rigid, multi-site molecules that adopt well-defined orientations upon binding, NERDSS simulates formation of large reversible structures with sites that can be acted on by reaction rules. We show how NERDSS allows for directly comparing and optimizing models of multi-component assembly against time-dependent experimental data. Applying NERDSS to assembly steps in clathrin-mediated endocytosis, we capture how the formation of clathrin caged structures can be driven by modulating the strength of clathrin-clathrin interactions, by adding cooperativity, or by localizing clathrin to the membrane. NERDSS further predicts how clathrin lattice disassembly can be driven by enzymes that irreversibly change lipid populations on the membrane. By modeling viral lattice assembly and recapitulating oscillations in protein expression levels for a circadian clock model, we illustrate the wide usability and adaptability of NERDSS. NERDSS simulates user-defined assembly models that were previously inaccessible to existing software tools, with broad applications to predicting self-assembly in vivo and designing high-yield assemblies in vitro.
Melanoma-secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis
Authors: Kleffman Kevin , Levinson Grace , Wong Eitan , Galán-Echevarría Francisco , Von-Itter Richard , Rose Indigo , Blumenberg Lili , Floristán Alfredo , Tranos James , Argibay Diana , Chen Jenny , Dhabaria Avantika , de Miera Sainz de Vega Eleazar , Rogers Robert , Zaim-Wadghiri Youssef , Mathews Paul , Osman Iman , Ruggles Kelly , Ueberheide Beatrix , Liddelow Shane A. , DeMattos Ronald , Li Yue Ming , Schneider Robert J. , Hernando Eva
Published: November 2019

Brain metastasis is a significant cause of morbidity and mortality in multiple cancer types and represents an unmet clinical need. The mechanisms that mediate metastatic cancer growth in the brain parenchyma are largely unknown. Melanoma, which has the highest rate of brain metastasis among common cancer types, is an ideal model to study how cancer cells adapt to the brain parenchyma. We performed unbiased proteomics analysis of melanoma short-term cultures, a novel model for the study of brain metastasis. Intriguingly, we found that proteins implicated in neurodegenerative pathologies are differentially expressed in melanoma cells explanted from brain metastases compared to those derived from extracranial metastases. This raised the exciting hypothesis that molecular pathways implicated in neurodegenerative disorders are critical for metastatic adaptation to the brain.

Here, we show that melanoma cells require amyloid beta (Aβ), a polypeptide heavily implicated in Alzheimer’s disease, for growth and survival in the brain parenchyma. Melanoma cells produce and secrete Aβ, which activates surrounding astrocytes to a pro-metastatic, anti-inflammatory phenotype. Furthermore, we show that pharmacological inhibition of Aβ decreases brain metastatic burden.

Our results reveal a mechanistic connection between brain metastasis and Alzheimer’s disease – two previously unrelated pathologies, establish Aβ as a promising therapeutic target for brain metastasis, and demonstrate suppression of neuroinflammation as a critical feature of metastatic adaptation to the brain parenchyma.
3DGV: Immersive Exploration of 3D Genome Structures using Virtual Reality
Authors: Zhang Éric , Drogaris Chrisostomos , Gédon Antoine , Sossin Aaron , Faraj Rajae , Chen Haifen , Cyr Yan , Majewski Jacek , Blanchette Mathieu , Waldispühl Jérôme
Published: November 2019

The analysis of 3D genomic data is expected to revolutionize our understanding of genome organization and regulatory mechanisms. Yet, the complex spatial organization of this information can be difficult to interpret with 2D viewers. Virtual Reality (VR) technologies offer an opportunity to rethink our methods to visualize and navigate 3D objects. In this paper, we introduce the Virtual Reality 3D Genome Viewer (3DGV), an open platform to experiment and develop VR solutions to explore 3D genome structures.

Availability

http://3dgv.cs.mcgill.ca/
Lysates ofMethylococcus capsulatusBath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+Tregs and improve metabolism
Authors: Jensen Benjamin. A. H. , Holm Jacob B. , Larsen Ida S. , von Burg Nicole , Derer Stefanie , Rivollier Aymeric , Agrinier Anne Laure , Sulek Karolina , Indrelid Stine A. , Arnoldussen Yke J. , Sonne Si B. , Fjære Even , Damgaard Mads T. F. , Pærregaard Simone I. , Angell Inga L. , Rudi Knut , Marette André , Treebak Jonas T. , Madsen Lise , Åkesson Caroline Piercey , Agace William , Sina Christian , Kleiveland Charlotte R. , Kristiansen Karsten , Lea Tor E.
Published: November 2019

Interactions between host and gut microbial communities may be modulated by diets and play pivotal roles in securing immunological homeostasis and health. Here we show that intake of feed based on whole-cell lysates of the non-commensal bacteriumMethylococcus capsulatusBath (McB) as protein source reversed high fat high sucrose-induced changes in the gut microbiota to a state resembling that of lean, low fat diet-fed mice, both under mild thermal stress (T22°C) and at thermoneutrality (T30°C). McB feeding selectively upregulated triple positive (Foxp3+RORγt+IL-17+) regulatory T cells in the small intestine and colon, and enhanced mucus production and glycosylation status suggesting improved gut health. Mice receiving McB lysates further exhibited improved glucose regulation, reduced body and liver fat along with diminished hepatic immune infiltration. Collectively, these data points towards profound whole-body effects elicited by the McB lysate suggesting that it may serve as a potent modulator of immunometabolic homeostasis.
Inoculation with a microbe isolated from the Negev Desert enhances corn growth
Authors: Khan Noor , Martínez-Hidalgo Pilar , Humm Ethan A. , Maymon Maskit , Kaplan Drora , Hirsch Ann M.
Published: November 2019

Corn (Zea mays L.) is not only an important food source, but also has numerous uses, including for biofuels, fillers for cosmetics, glues, and so on. The amount of corn grown in the U.S. has significantly increased since the 1960s and with it, the demand for synthetic fertilizers and pesticides/fungicides to enhance its production. However, the downside of the continuous use of these products, especially N and P fertilizers, has been an increase in N2O emissions and other greenhouse gases into the atmosphere as well as run-off into waterways that fuel pollution and algal blooms. These approaches to agriculture, especially if exacerbated by climate change, will result in decreased soil health as well as human health. We searched for microbes from arid, native environments that are not being used for agriculture because we reasoned that indigenous microbes from such soils could promote plant growth and help restore degraded soils. Employing cultivation-dependent methods to isolate bacteria from the Negev Desert in Israel, we tested the effects of several microbial isolates on corn in both greenhouse and small field studies. One strain, Dietzia cinnamea 55, originally identified as Planomicrobium chinensis, significantly enhanced corn growth over the uninoculated control in both greenhouse and outside garden experiments. We sequenced and analyzed the genome of this bacterial species to elucidate some of the mechanisms whereby D. cinnamea 55 promoted plant growth. In addition, to ensure the biosafety of this previously unknown plant growth promoting bacterial (PGPB) strain as a potential bioinoculant, we tested the survival and growth of Caenorhabditis elegans (a test for virulence) in response to D. cinnamea 55. We also looked for genes for potential virulence determinants as well as for growth promotion.
Expansion of a subset within C2 clade of Escherichia coli sequence type 131 (ST131) is driving the increasing rates of Aminoglycoside resistance: a molecular epidemiology report from Iran
Authors: Hojabri Zoya , Darabi Narges , Mirmohammadkhani Majid , Hemmati Romina , saeedi Zahra , Roustaee Kiarash , Pajand Omid
Published: November 2019

The most important lineage of Escherichia coli, named sequence type 131 (ST131) is a pandemic clone which drives the increasing rates of antibiotic resistance. While the pervasiveness of ST131 clade C, especially subclades C2 and C1-M27 has been demonstrated in numerous global surveys, no report about the ST131 clades and its virotypes has been published from Iran, so far. So, in this study we investigated and compared the virotypes, antibiotic susceptibility patterns, resistance/virulence determinants and clonality of ST131 clades collected during one-year surveillance study.

Most of isolates belonged to clade C2 (34/76 [44.7%]), with the highest virulence factor (VF) scores and resistance rates. The distinctive profiles of clade C2 virulence genes were revealed by “principle coordinates analysis” (PcoA) test. The distribution of hlyA/cnf1virulence genes among clade C2 was not uniform, so that positive strains showed significantly higher rates of resistance markers (blaCTX-M-15, blaOXA-1, aac6Ib/Ib-cr and aac3IIa) and ampicillin- sulbactam/gentamicin/tobramycin resistance. Virotype C as the most common virotype (48.7%) was predominant among clade C1 population, while almost all of virotypes E and F [(22/23), 95.6%] strains belonged to clade C2, with the highest VF scores and aminoglycoside resistance rates. “Multi locus variable Number tandem repeats analysis” (MLVA) clustered clades C1 and C2 together, while clades A and B strains were mostly identified as singletons.

Appearance of virotypes E and F among clade C2 strains with higher rates of aminoglycoside resistance/virulence genes content demonstrate the shifting dynamics of this pandemic clone in response to antibiotic selection pressure by establishing the newly-emerged subsets.
Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons
Authors: Turelli Priscilla , Playfoot Christopher , Grun Dephine , Raclot Charlène , Pontis Julien , Coudray Alexandre , Thorball Christian , Duc Julien , Pankevich Eugenia , Deplancke Bart , Busskamp Volker , Trono Didier
Published: November 2019

In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB)-zinc finger proteins (KZFPs). Many TEeRS are subsequently coopted in transcription networks, but how KZFPs influence this process is largely unknown. We identify ZNF417 and ZNF587 as primate-specific KZFPs repressing HERVK (human endogenous retrovirus K) and SVA (SINE-VNTR-Alu) integrants in human embryonic stem cells (ESC). Expressed in specific regions of the human developing and adult brain, ZNF417/587 keep controlling TEeRS in ESC-derived neurons and brain organoids, secondarily influencing the differentiation and neurotransmission profile of neurons and preventing the induction of neurotoxic retroviral proteins and an interferon-like response. Thus, evolutionarily recent KZFPs and their TE targets partner up to influence human neuronal differentiation and physiology.

One Sentence Summary

Young transposable elements and their protein controllers team up to regulate the differentiation and function of human neurons.