bluuebunny/crossref_metadata_2025 huggingface dataset:
Tissue-Engineered Bone Tumor as a Reproducible Human in Vitro Model for Studies of Anticancer Drugs
Authors: Sakolish Courtney , House John S , Chramiec Alan , Liu Yizhong , Chen Zunwei , Halligan Susan P , Vunjak-Novakovic Gordana , Rusyn Ivan
Published: October 2019

Studies of anticancer therapies in traditional cell culture models can demonstrate efficacy of direct-acting compounds but lack the 3-dimensional arrangement of the tumor cells and their tissue-specific microenvironments, both of which are important modulators of treatment effects in vivo. Bone cells reside in complex environments that regulate their fate and function. A bioengineered human bone-tumor model has been shown to provide a microphysiological niche for studies of cancer cell behavior. Here, we demonstrate successful transfer between 2 laboratories and utility of this model in efficacy studies using well-established chemotherapeutic agents. The bioengineered human bone-tumor model consisted of Ewing sarcoma (RD-ES) cancer cell aggregates infused into tissue-engineered bone that was grown from human mesenchymal stem cell-derived differentiated into osteoblasts within mineralized bone scaffolds. The tumor model was maintained in culture for over 5 weeks and subjected to clinically relevant doses of linsitinib, doxorubicin, cisplatin, methotrexate, vincristine, dexamethasone, or MAP (methotrexate, doxorubicin, and cisplatin combination). Drug administration cycles were designed to mimic clinical treatment regimens. The bioengineered tumors were evaluated days to weeks after the cessation of treatment to monitor the potential for relapse, using bioengineered bone and ES cell monolayers as controls. Drug binding to the scaffolds and media proteins and gene expression were also evaluated. We show that a bioengineered human bone tumor can be used as a microphysiological model for preclinical studies of anticancer drugs. We found that anticancer efficacy was achieved at concentrations approximating the human Cmax, in contrast to traditional ES cell monolayers. These studies show that the bone-tumor model can be successfully transferred between laboratories and has predictive power in preclinical studies. The effects of drugs on the bone tumors and healthy bone were studied in parallel, in support of the utility of this model for identification of new therapeutic targets.
Raw meat-based diets for companion animals: a potential source of transmission of pathogenic and antimicrobial-resistant Enterobacteriaceae
Authors: Nüesch-Inderbinen Magdalena , Treier Andrea , Zurfluh Katrin , Stephan Roger
Published: October 2019

Feeding pets raw meat-based diets (RMBDs) has become increasingly popular but may constitute a risk due to the contamination with pathogenic and antimicrobial-resistant (AMR) bacteria. The aim of this study was to evaluate commercially available RMBDs with regard to microbiological quality and occurrence of AMR Enterobacteriaceae. Of 51 RMBD samples, 72.5% did not meet the microbiological standards for Enterobacteriaceae set out by EU regulations for animal by-products intended for pet food. Furthermore,
Salmonella
was detected in 3.9% of the samples. AMR bacteria were found in 62.7% of the samples, the majority thereof were resistant to third-generation cephalosporins due to the production of extended-spectrum β-lactamases (ESBLs) including CTX-M-1, which is widespread in livestock, and CTX-M-15, which is the most common ESBL variant worldwide. Colistin- and aminoglycoside-resistant isolates, producing MCR-1 and RMTB, were identified in 3.9 and 2% of the samples, respectively. The majority of the AMR
Escherichia coli
belonged to commensal groups A or B1 and were associated with clonal complexes CC155 and CC10. Two belonged to the emerging extraintestinal pathogenic CC648, and one to the globally disseminated uropathogenic
E. coli
sequence type ST69, suggesting zoonotic potential. The microbiological quality and the high prevalence of AMR producing Enterobacteriaceae in RMBDs raise concerns for animal and public health.
Facile synthesis of 2-arylimidazo[1,2-a]pyridines catalysed by DBU in aqueous ethanol
Authors: Veer Babita , Singh Ram
Published: October 2019

A facile protocol for the synthesis of 2-arylimidazo[1,2-a]pyridines was developed using two-component cyclization of substituted 2-aminopyridines and substituted phenacyl bromides in 65–94% yield. The reaction was DBU catalysed using green solvent, aqueous ethanol (1 : 1 v/v) at room temperature. The atom economy of the products was calculated to be 66.25–73.41%. The developed protocol successfully exhibits a broad substrate scope, less reaction time, high to moderate yield and multigram scale synthesis.
Mechanics of bed particle saltation in turbulent wall-shear flow
Authors: Padhi Ellora , Ali Sk Zeeshan , Dey Subhasish
Published: October 2019

In this paper, we explore the mechanics of bed particle saltation in turbulent wall-shear flow, analysing the forces on a particle to perform saltation. The hydrodynamic drag encompasses the form drag and turbulent drag. The hydrodynamic lift comprises the Saffman lift, Magnus lift and turbulent lift. The subtle role of the Basset force in governing the particle trajectory is accounted for in the analysis. The bedload flux, emanating from the mathematical analysis of bed particle saltation, is determined. The results reveal that for the particle parameter range 20–100, the transport stage function equalling unity corroborates the threshold of bed particle saltation, where the saltation height and length are 1.3 and 9 times the particle size. For a given transport stage function, the relative saltation height and length decrease with an increase in particle parameter. For the particle parameter range 20–100, the relative saltation height and length increase with an increase in transport stage function, reaching their peaks, and then, they decrease. For a given particle parameter, the peak and mean particle densimetric Froude numbers increase as the transport stage function increases. The bedload flux curves for particle parameters 26 and 63 produce the upper and lower bound curves, respectively.
Spiral wave unpinning facilitated by wave emitting sites in cardiac monolayers
Authors: Punacha Shreyas , Berg Sebastian , Sebastian Anupama , Krinski Valentin I. , Luther Stefan , Shajahan T. K.
Published: October 2019

Rotating spiral waves of electrical activity in the heart can anchor to unexcitable tissue (an obstacle) and become stable pinned waves. A pinned rotating wave can be unpinned either by a local electrical stimulus applied close to the spiral core, or by an electric field pulse that excites the core of a pinned wave independently of its localization. The wave will be unpinned only when the pulse is delivered inside a narrow time interval called the unpinning window (UW) of the spiral. In experiments with cardiac monolayers, we found that other obstacles situated near the pinning centre of the spiral can facilitate unpinning. In numerical simulations, we found increasing or decreasing of the UW depending on the location, orientation and distance between the pinning centre and an obstacle. Our study indicates that multiple obstacles could contribute to unpinning in experiments with intact hearts.
Assessing the multi-pathway threat from an invasive agricultural pest:
Tuta absoluta
in Asia
Authors: McNitt Joseph , Chungbaek Young Yun , Mortveit Henning , Marathe Madhav , Campos Mateus R. , Desneux Nicolas , Brévault Thierry , Muniappan Rangaswamy , Adiga Abhijin
Published: October 2019

Modern food systems facilitate rapid dispersal of pests and pathogens through multiple pathways. The complexity of spread dynamics and data inadequacy make it challenging to model the phenomenon and also to prepare for emerging invasions. We present a generic framework to study the spatio-temporal spread of invasive species as a multi-scale propagation process over a time-varying network accounting for climate, biology, seasonal production, trade and demographic information. Machine learning techniques are used in a novel manner to capture model variability and analyse parameter sensitivity. We applied the framework to understand the spread of a devastating pest of tomato,
Tuta absoluta
, in South and Southeast Asia, a region at the frontier of its current range. Analysis with respect to historical invasion records suggests that even with modest self-mediated spread capabilities, the pest can quickly expand its range through domestic city-to-city vegetable trade. Our models forecast that within 5–7 years,
Tuta absoluta
will invade all major vegetable growing areas of mainland Southeast Asia assuming unmitigated spread. Monitoring high-consumption areas can help in early detection, and targeted interventions at major production areas can effectively reduce the rate of spread.
Carotenoid pigmentation in salmon: variation in expression at
BCO2-l
locus controls a key fitness trait affecting red coloration
Authors: Lehnert S. J. , Christensen K. A. , Vandersteen W. E. , Sakhrani D. , Pitcher T. E. , Heath J. W. , Koop B. F. , Heath D. D. , Devlin R. H.
Published: October 2019

Carotenoids are primarily responsible for the characteristic red flesh coloration of salmon. Flesh coloration is an economically and evolutionarily significant trait that varies inter- and intra-specifically, yet the underlying genetic mechanism is unknown. Chinook salmon (
Oncorhynchus tshawytscha
) represents an ideal system to study carotenoid variation as, unlike other salmonids, they exhibit extreme differences in carotenoid utilization due to genetic polymorphisms. Here, we crossed populations of Chinook salmon with fixed differences in flesh coloration (red versus white) for a genome-wide association study to identify loci associated with pigmentation. Here, the
beta-carotene oxygenase 2-like
(
BCO2-l
) gene was significantly associated with flesh colour, with the most significant single nucleotide polymorphism explaining 66% of the variation in colour.
BCO2
gene disruption is linked to carotenoid accumulation in other taxa, therefore we hypothesize that an ancestral mutation partially disrupting
BCO2-l
activity (i.e. hypomorphic mutation) allowed the deposition and accumulation of carotenoids within Salmonidae. Indeed, we found elevated transcript levels of
BCO2-l
in white Chinook salmon relative to red. The long-standing mystery of why salmon are red, while no other fishes are, is thus probably explained by a hypomorphic mutation in the proto-salmonid at the time of divergence of red-fleshed salmonid genera (approx. 30 Ma).
Pleiotropic effects of sex-determining genes in the evolution of dioecy in two plant species
Authors: Akagi Takashi , Charlesworth Deborah
Published: October 2019

One reason for studying sex chromosomes of flowering plants is that they have often evolved separate sexes recently, and the genomes of dioecious species may not yet have evolved adaptations to their changes from the ancestral state. An unstudied question concerns the relative importance of such adaptation, versus the effects of the mutations that led to separate sexes in the first place. Theoretical models for such an evolutionary change make the prediction that the mutations that created males must have sexually antagonistic effects, not only abolishing female functions, but also increasing male functions relative to the ancestral functional hermaphrodites. It is important to test this critical assumption. Moreover, the involvement of sexual antagonism also implies that plant sex-determining genes may directly cause some of the sexual dimorphisms observed in dioecious plants. Sex-determining genes are starting to be uncovered in plants, including species in the generaDiospyrosandActinidia(families Ebenaceae and Actinidiaceae, respectively). Here, we describe transgenic experiments in which the effects of the very different male-determining genes of these two dioecious species were studied in a non-dioecious plant,Nicotiana tabacum. The results indeed support the critical assumption outlined above.
Predicting population responses to environmental change from individual-level mechanisms: towards a standardized mechanistic approach
Authors: Johnston A. S. A. , Boyd R. J. , Watson J. W. , Paul A. , Evans L. C. , Gardner E. L. , Boult V. L.
Published: October 2019

Animal populations will mediate the response of global biodiversity to environmental changes. Population models are thus important tools for both understanding and predicting animal responses to uncertain future conditions. Most approaches, however, are correlative and ignore the individual-level mechanisms that give rise to population dynamics. Here, we assess several existing population modelling approaches and find limitations to both ‘correlative’ and ‘mechanistic’ models. We advocate the need for a standardized mechanistic approach for linking individual mechanisms (physiology, behaviour, and evolution) to population dynamics in spatially explicit landscapes. Such an approach is potentially more flexible and informative than current population models. Key to realizing this goal, however, is overcoming current data limitations, the development and testing of eco-evolutionary theory to represent interactions between individual mechanisms, and standardized multi-dimensional environmental change scenarios which incorporate multiple stressors. Such progress is essential in supporting environmental decisions in uncertain future conditions.
Variation at an adhesin locus suggests sociality in natural populations of the yeast
Saccharomyces cerevisiae
Authors: Oppler Zachary J. , Parrish Meadow E. , Murphy Helen A.
Published: October 2019

Microbes engage in numerous social behaviours that are critical for survival and reproduction, and that require individuals to act as a collective. Various mechanisms ensure that collectives are composed of related, cooperating cells, thus allowing for the evolution and stability of these traits, and for selection to favour traits beneficial to the collective. Since microbes are difficult to observe directly, sociality in natural populations can instead be investigated using evolutionary genetic signatures, as social loci can be evolutionary hotspots. The budding yeast has been studied for over a century, yet little is known about its social behaviour in nature. Flo11 is a highly regulated cell adhesin required for most laboratory social phenotypes; studies suggest it may function in cell recognition and its heterogeneous expression may be adaptive for collectives such as biofilms. We investigated this locus and found positive selection in the areas implicated in cell–cell interaction, suggesting selection for kin discrimination. We also found balancing selection at an upstream activation site, suggesting selection on the level of variegated gene expression. Our results suggest this model yeast is surprisingly social in natural environments and is probably engaging in various forms of sociality. By using genomic data, this research provides a glimpse of otherwise unobservable interactions.
How do World and European Standard Populations impact Burden of Disease studies? A case study of Disability-Adjusted Life Years in Scotland
Authors: Wyper Grant MA , Grant Ian , Fletcher Eilidh , McCartney Gerry , Fischbacher Colin , Stockton Diane L
Published: October 2019

Background

Disability-Adjusted Life Years (DALYs) are an established method for quantifying population health needs and guiding prioritisation decisions. Global Burden of Disease (GBD) estimates aim to ensure comparability between countries and over time by using age-standardised rates (ASR) to account for differences in the age structure of different populations. Different standard populations are used for this purpose but it is not widely appreciated that the choice of standard may affect not only the resulting rates but also the rankings of causes of DALYs. We aimed to evaluate the impact of the choice of standard, using the example of Scotland.

Methods

DALY estimates were derived from the 2016 Scottish Burden of Disease (SBOD) study for an abridged list of 68 causes of disease/injury, representing a three-year annual average across 2014-16. Crude DALY rates were calculated using Scottish national population estimates. DALY ASRs standardised using the GBD World Standard Population (GBD WSP) were compared to those using the 2013 European Standard Population (ESP2013). Differences in ASR and in rank order within the cause list were summarised across all-causes and for each individual cause.

Results

The ranking of causes by DALYs were similar using crude rates or ASR (ESP2013). As expected, all-cause DALY rates using ASR (GBD WSP) were around 26% lower. Overall 58 out of 68 causes had a lower ASR using GBD WSP compared with ESP2013, with the largest falls occurring for leading causes of mortality observed in older ages. Gains in ASR were much smaller in scale and largely affected causes that operated early in life. These differences were associated with a substantial change to the ranking of causes when GBD WSP was used compared with ESP2013.

Conclusion

Disease rankings based on DALY ASRs are strongly influenced by the choice of standard population. While GBD WSP offers international comparability, within-country analyses based on DALY ASRs should reflect local age structures. For European countries including Scotland, ESP2013 may better guide local priority setting.
Idea Paper: Predicting culturability of microbes from population dynamics under field conditions
Authors: Ushio Masayuki
Published: October 2019

Isolation and cultivation of microbes from environmental samples have been fundamental and important for species identification and investigating functions and ecology of target microbes. While cultivation and isolation of microbes are not easy, the natural environment can “culture” any endemic microbes, and thus key information for culturing and isolating microbes may be encoded in the natural population dynamics of microbes. In this paper, I present the idea that culturability of microbes may be inferred by quantifying dynamics properties of microbes using nonlinear time series analytical tools. To briefly demonstrate the idea, I analyzed high-frequency, quantitative microbial time series obtained for artificial rice plots established at Kyoto University, Japan. I selected bacterial phyla that included sufficient numbers of microbial taxa, and analyzed 398 microbial taxa using empirical dynamic modeling. The nine phyla analyzed generally followed a similar pattern: many microbial taxa fell into the “Simple” dynamics category, and a small proportion of taxa were categorized in “Simple but nonlinear” or “Nearly random” dynamics categories. The present analysis suggested that many microbes in the study system might be cultivated by modifying a relatively small number of conditions. However, the present idea as well as the result is preliminary and premature, and more precise taxonomic information (i.e., species-level identification) and a culturability dataset will help to validate the idea. If the present idea was found to be valid, a priori evaluation of the culturability of microbes would become possible, which would avoid unnecessary costs (labor, time and money) of attempts to cultivate microbes.
While shoot herbivory mitigates, root herbivory exacerbates eutrophication’s impact on diversity in a grassland model
Authors: Crawford Michael , Schlägel Ulrike E. , May Felix , Wurst Susanne , Grimm Volker , Jeltsch Florian
Published: October 2019

1

Eutrophication is widespread throughout grassland systems and expected to increase during the Anthropocene. Trophic interactions, like aboveground herbivory, have been shown to mitigate its effect on plant diversity. Belowground herbivory may also impact these habitats’ response to eutrophication, but the direction of its influence is much less understood, and likely to depend on factors such as the herbivores’ preference for dominant species and the symmetry of belowground competition. If preferential towards the dominant, fastest growing species, root herbivores may reduce these species’ relative fitness and support diversity during eutrophication. However, as plant competition belowground is commonly considered to be symmetric, root herbivores may be less impactful than shoot herbivores because they do not reduce any competitive asymmetry between the dominant and subordinate plants.

To better understand this system, we used an established, two-layer, grassland community model to run a full-factorially designed simulation experiment, crossing the complete removal of aboveground herbivores and belowground herbivores with eutrophication. After 100 years of simulation, we analyzed communities’ diversity, competition on the individual-level, as well as their resistance and recovery. The model reproduced both observed general effects of eutrophication in grasslands and the short-term trends of specific experiments. We found that belowground herbivores exacerbate the negative influence of eutrophication on Shannon diversity within our model grasslands, while aboveground herbivores mitigate its effect. Indeed, data on individuals’ above- and belowground resource uptake reveals that root herbivory reduces resource limitation belowground. As with eutrophication, this shifts competition aboveground. Since shoot competition is asymmetric—with larger, taller individuals gathering disproportionate resources compared to their smaller, shorter counterparts—this shift promotes the exclusion of the smallest species. While increasing the root herbivores’ preferences towards dominant species lessens their negative impact, at best they are only mildly advantageous, and they do very little reduce the negative consequences of eutrophication. Because our model’s belowground competition is symmetric, we hypothesize that root herbivores may be beneficial when root competition is asymmetric. Future research into belowground herbivory should account for the nature of competition belowground to better understand the herbivores’ true influence.
Hippocampal spike-time correlations and place-field overlaps during open field foraging
Authors: Monsalve-Mercado Mauro M. , Roudi Yasser
Published: October 2019

Phase precessing place cells encode spatial information on fine timescales via the timing of their spikes. This phase code has been extensively studied on linear tracks and for short runs in the open field. However, less is known about the phase code on unconstrained trajectories lasting tens of minutes, typical of open field foraging. In previous work (Monsalve-Mercado and Leibold, 2017), an analytic expression was derived for the spike-time cross-correlation between phase precessing place cells during natural foraging in the open field. This expression makes two predictions on how this phase code differs from the linear track case: cross-correlations are symmetric with respect to time, and they represent the distance between pairs of place fields in that the theta-filtered cross-correlations around zero time-lag are positive for cells with nearby fields while they are negative for those with fields further apart. Here we analyze several available open field recordings and show that these predictions hold for pairs of CA1 place cells. We also show that the relationship remains during remapping in CA1, and it is also present in place cells in area CA3. For CA1 place cells of Fmr1-null mice, which exhibit normal place fields but somewhat weaker temporal coordination with respect to theta compared to wild type, the cross-correlations still remain symmetric but the relationship to place field overlap is largely lost. The relationship discussed here describes how spatial information is communicated by place cells to downstream areas in a finer theta-timescale, relevant for learning and memory formation in behavioural tasks lasting tens of minutes in the open field.
Switchgrass Rhizosphere Metabolite Chemistry Driven by Nitrogen Availability
Authors: Smercina Darian N. , Bowsher Alan W. , Evans Sarah E. , Friesen Maren L. , Eder Elizabeth K. , Hoyt David W. , Tiemann Lisa K.
Published: October 2019

Plants and soil microorganisms interact closely in the rhizosphere where plants may exchange carbon (C) for functional benefits from the microbial community. For example, the bioenergy crop, switchgrass (Panicum virgatum) is thought to exchange root-exuded C for nitrogen (N) fixed by diazotrophs (free-living N-fixers). However, this interaction is not well characterized and it is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions. We found switchgrass root exudate chemistry to be more responsive to N availability than to diazotroph presence. Total metabolite concentrations were generally greater under high N versus low N and unaffected by inoculation. Examination of rhizosphere chemical fingerprints indicates metabolite chemistry was also driven strongly by N availability with a greater relative abundance of carbohydrates under high N and greater relative abundance of organic acids under low N. We also found evidence of changes in rhizosphere chemical fingerprints by inoculation treatment suggesting a potential for switchgrass to respond or even recruit diazotrophs. However, we found little evidence of N treatment and inoculation interaction effects which suggests switchgrass response to diazotroph presence is not mediated by N availability.
In situ protein identification and mapping using secondary ion mass spectrometry
Authors: Kotowska Anna M. , Williams Philip M. , Aylott Jonathan W. , Shard Alexander G. , Alexander Morgan R. , Scurr David J.
Published: October 2019

Protein characterisation at surfaces currently requires digestion prior to either liquid extraction of the protein for mass spectrometry analysis or in situ matrix-assisted desorption/ionisation. Here, we show that direct assignment of individual proteins and mixtures at surfaces can be achieved by employing secondary ion mass spectrometry (SIMS) with gas cluster ion beam (GCIB) bombardment and an Orbitrap™ analyser. Potential applications of the method are illustrated by demonstrating imaging of a protein film masked by a gold grid and the analysis of a protein monolayer biochip.
An Enzymatic Active Site Embedded in a DNA Nanostructure
Authors: Kekic Tadija , Ahmadi Yasaman , Barisic Ivan
Published: October 2019

Artificial enzymes hold a great potential in the field of biotechnology. The currently available design strategies are limited to recruit and organise secondary and tertiary structural elements, and functional motifs of native enzymes. Here, we demonstrate an approach towards the bottom-up development of an artificial enzyme based on DNA nanotechnology. Structural analyses of the FlaI ATPase were used to identify a set of amino acids essential for the catalytic reaction. The selected amino acids were used to design four peptide-oligonucleotide conjugates (POCs). The POCs were integrated into a DNA nanostructure and reconstituted the catalytic site of FlaI. DNA origami technology was employed to maintain the relative orientations of the amino acids and their positions analogous to those in the protein catalytic site. The substrate turnover rates were found to be comparable in our artificial nanozyme (kcat = 0.3622 s-1) and the native enzyme (kcat ≈ 0.016 s-1). The nanozymes could be recycled using an ultrafiltration protocol and reused in multiple experiments allowing a reliable reproduction of the measurements. The emulation of enzymatic activity, by this novel and computable technological framework, can be of high relevance in many different areas.
The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network
Authors: Codato Roberta , Perichon Martine , Divol Arnaud , Fung Ella , Sotiropoulos Athanassia , Bigot Anne , Weitzman Jonathan B. , Medjkane Souhila
Published: October 2019

The coordinated expression of myogenic regulatory factors, including MyoD and myogenin, orchestrates the steps of skeletal muscle development, from myoblast proliferation and cell-cycle exit, to myoblast fusion and myotubes maturation. Yet, it remains unclear how key transcription factors and epigenetic enzymes cooperate to guide myogenic differentiation. Proteins of the SMYD (SET and MYND domain-containing) methyltransferase family participate in cardiac and skeletal myogenesis during development in zebrafish, Drosophila and mice. Here, we show that the mammalian SMYD3 methyltransferase coordinates skeletal muscle differentiation in vitro. Overexpression of SMYD3 in myoblasts promoted muscle differentiation and myoblasts fusion. Conversely, silencing of endogenous SMYD3 or its pharmacological inhibition impaired muscle differentiation. Genome-wide transcriptomic analysis of murine myoblasts, with silenced or overexpressed SMYD3, revealed that SMYD3 impacts skeletal muscle differentiation by targeting the key muscle regulatory factor myogenin. The role of SMYD3 in the regulation of skeletal muscle differentiation and myotube formation, partially via the myogenin transcriptional network, highlights the importance of methyltransferases in mammalian myogenesis.
Prophage induction mediated by quorum sensing signals alters soil bacterial community structure
Authors: Liang Xiaolong , Wagner Regan E. , Li Bingxue , Zhang Ning , Radosevich Mark
Published: October 2019

Recent findings have revealed a role for bacterial quorum sensing communication in bacteriophage (phage) reproduction decisions. However quorum sensing based phage-host interactions remain largely unknown, with the mechanistic details revealed for only a few phage-host pairs and a dearth of information available at the microbial community level. Here we report on the specific action of individual quorum-sensing signals (acyl-homoserine lactones; AHLs varying in acyl-chain length from four to 14 carbon atoms) on prophage induction in soil microbial communities. AHL treatment significantly decreased the bacterial diversity (Shannon Index) but did not significantly impact species richness. Exposure to short chain-length AHLs resulted in a decrease in the abundance of different taxa than exposure to higher molecular weight AHLs. Each AHL targeted a different subset of bacterial taxa. Our observations demonstrate that individual AHLs trigger prophage induction in different bacterial taxa leading to changes in microbial community structure.
Microtubule polymerization state and clathrin-dependent internalization regulate dynamics of cardiac potassium channel
Authors: Melgari Dario , Barbier Camille , Dilanian Gilles , Rücker-Martin Catherine , Doisne Nicolas , Coulombe Alain , Hatem Stéphane N. , Balse Elise
Published: October 2019

Ion channel trafficking powerfully influences cardiac electrical activity as it regulates the number of available channels at the plasma membrane. Studies have largely focused on identifying the molecular determinants of the trafficking of the atria-specific KV1.5 channel, the molecular basis of the ultra-rapid delayed rectifier current IKur. Besides, regulated KV1.5 channel recycling upon changes in homeostatic state and mechanical constraints in native cardiomyocytes has been well documented. Here, using cutting-edge imaging in live myocytes, we investigated the dynamics of this channel in the plasma membrane. We demonstrate that the clathrin pathway is a major regulator of the functional expression of KV1.5 channels in atrial myocytes, with the microtubule network as the prominent organizer of KV1.5 transport within the membrane. Both clathrin blockade and microtubule disruption result in channel clusturization with reduced membrane mobility and internalization, whereas disassembly of the actin cytoskeleton does not. Mobile KV1.5 channels are associated with the microtubule plus-end tracking protein EB1 whereas static KV1.5 clusters are associated with stable acetylated microtubules. In human biopsies from patients in atrial fibrillation associated with atrial remodeling, drastic modifications in the trafficking balance occurs together with alteration in microtubule polymerization state resulting in modest reduced endocytosis and increased recycling. Consequently, hallmark of atrial KV1.5 dynamics within the membrane is clathrin- and microtubule-dependent. During atrial remodeling, predominance of anterograde trafficking activity over retrograde trafficking could result in accumulation ok KV1.5 channels in the plasma membrane.
Modulated efficacy CRISPRi reveals evolutionary conservation of essential gene expression-fitness relationships in bacteria
Authors: Hawkins John S. , Silvis Melanie R. , Koo Byoung-Mo , Peters Jason M. , Jost Marco , Hearne Cameron C. , Weissman Jonathan S. , Todor Horia , Gross Carol A.
Published: October 2019

Essential genes are the central hubs of cellular networks. Despite their importance, the lack of high-throughput methods for titrating their expression has limited our understanding of the fitness landscapes against which essential gene expression levels are optimized. We developed a modified CRISPRi system leveraging the predictable reduction in efficacy of imperfectly matched sgRNAs to generate specific levels of CRISPRi activity and demonstrate its broad applicability in bacteria. Using libraries of mismatched sgRNAs, we characterized the expression-fitness relationships of essential genes inEscherichia coliandBacillus subtilis. Remarkably, these relationships co-vary by pathway and are predominantly conserved betweenE. coliandB. subtilisdespite ~ 2 billion years of evolutionary separation, suggesting that deeply conserved tradeoffs underlie bacterial homeostasis.

One Sentence Summary

Bacterial essential genes have varying responses to CRISPRi knockdown that are largely conserved across ~2 billion years of evolution.
A weak link with actin organizes tight junctions to control epithelial permeability
Authors: Belardi Brian , Hamkins-Indik Tiama , Harris Andrew R. , Fletcher Daniel A.
Published: October 2019

In vertebrates, epithelial permeability is regulated by the tight junction (TJ) formed by specialized adhesive membrane proteins, adaptor proteins, and the actin cytoskeleton. Despite the TJ’s critical physiological role, a molecular-level understanding of how TJ assembly sets the permeability of epithelial tissue is lacking. Here, we identify a 28-amino acid sequence in the TJ adaptor protein ZO-1 that is responsible for actin binding and show that this interaction is essential for TJ permeability. In contrast to the strong interactions at the adherens junction, we find that the affinity between ZO-1 and actin is surprisingly weak, and we propose a model based on kinetic trapping to explain how affinity could affect TJ assembly. Finally, by tuning the affinity of ZO-1 to actin, we demonstrate that epithelial monolayers can be engineered with a spectrum of permeabilities, which points to a new target for treating transport disorders and improving drug delivery.
AKT2 deficiency causes sarcopenia and metabolic disorder of skeletal muscle
Authors: Chen Miao , Ji Caoyu , Xiao Fei , Chen Dandan , Gao Shuya , Yang Qingchen , Peng Yue , Sanchis Daniel , Yan Fangrong , Ye Junmei
Published: October 2019

Skeletal muscle is responsible for the majority of glucose disposal in the body. Insulin resistance in the skeletal muscle accounts for 85-90% of the impairment of total body glucose disposal in patients with tye 2 diabetes (T2D). However, the mechanism remains controversial. AKT2 is a protein kinase performing important functions in the regulation of glucose metabolism. We observed that mice deficient for AKT2 (AKT2 KO) exhibited decreased body weight and lean mass and showed impaired glucose tolerance, compared to their age- and gender-matched wild type mice (WT). Therefore, to test whether AKT2 deficiency causes deficits in skeletal muscle development and metabolism, we analyzed the expression of molecules related to skeletal muscle development, glucose uptake and metabolism in young (3 months) and old (8 months) mice. We found that AMPK phosphorylation and MEF2A expression were downregulated in young AKT2 KO mice, and this downregulation was inverted by AMPK activation. We also observed reduced mtDNA abundance and reduced expression of genes involved in mitochondrial biogenesis in the skeletal muscle of adult AKT2 KO mice, which was prevented by AMPK activation. However, GLUT4 expression was regulated by AKT2 in an AMPK-independent manner in skeletal muscle. During high-fat-diet (HFD)-induced obesity, AKT2 KO mice exhibited increased insulin resistance compared to WT mice. Our study establishes a new and important function of AKT2 in regulating glucose uptake and AMPK-dependent development and mitochondrial biogenesis in skeletal muscle.
Dis3L2 regulates cellular proliferation through a PI3-Kinase dependent signalling pathway
Authors: Towler Benjamin P. , Pashler Amy L. , Haime Hope J. , Przybyl Katarzyna M. , Viegas Sandra C. , Matos Rute G. , Morley Simon J. , Arraiano Cecilia M. , Newbury Sarah F.
Published: October 2019

Dis3L2 is a highly conserved 3’-5’ exoribonuclease which is mutated in the human overgrowth disorders Perlman syndrome and Wilms’ tumour. Here, we have generated a newdis3L2 null mutant and a UAS-nuclease-dead line inDrosophilato demonstrate that the catalytic activity of Dis3L2 is required to control proliferation in imaginal discs. Using RNA-seq ondis3L2mutant wing discs, we show that the imaginal disc growth factor Idgf2 is responsible for driving the wing overgrowth observed indis3L2null mutants. IDGFs are conserved proteins homologous to human chitinase-like proteins such as CHI3L1/YKL-40 which are implicated in tissue regeneration as well as cancers including colon cancer and non-small cell lung cancer. We also show that loss of DIS3L2 in human HEK-293T cells results in cell proliferation, illustrating the conservation of this important cell proliferation pathway. Using these human cells we show that loss of DIS3L2 results in an increase in the activity of the PI3-Kinase/AKT signalling pathway, which we subsequently show to also have a role in driving the proliferation phenotype inDrosophila. Our work therefore provides the first mechanistic explanation for DIS3L2-induced overgrowth in humans and flies and identifies an ancient proliferation pathway controlled by Dis3L2 to regulate cell proliferation and tissue growth.
Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals
Authors: Vaga Stefania , Lee Sunjae , Ji Boyang , Andreasson Anna , Talley Nicholas J , Agréus Lars , Bidkhori Gholamreza , Kovatcheva-Datchary Petia , Park Junseok , Lee Doheon , Proctor Gordon , Ehrlich Dusko , Nielsen Jens , Engstrand Lars , Shoaie Saeed
Published: October 2019

Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.
Curling of epithelial monolayers reveals coupling between active bending and tissue tension
Authors: Fouchard Jonathan , Wyatt Tom , Proag Amsha , Lisica Ana , Khalilgharibi Nargess , Recho Pierre , Suzanne Magali , Kabla Alexandre , Charras Guillaume
Published: October 2019

Epithelial monolayers are two-dimensional cell sheets which compartmentalise the body and organs of multi-cellular organisms. Their morphogenesis during development or pathology results from patterned endogenous and exogenous forces and their interplay with tissue mechanical properties. In particular, bending of epithelia is thought to results from active torques generated by the polarization of myosin motors along their apico-basal axis. However, the contribution of these out-of-plane forces to morphogenesis remains challenging to evaluate because of the lack of direct mechanical measurement. Here, we use epithelial curling to characterize the out-of-plane mechan ics of epithelial monolayers. We find that curls of high curvature form spontaneously at the free edge of epithelial monolayers devoid of substrate in vivo and in vitro. Curling originates from an enrichment of myosin in the basal domain that generates an active spontaneous curvature. By measuring the force necessary to flatten curls, we can then estimate the active torques and the bending modulus of the tissue. Finally, we show that the extent of curling is controlled by the interplay between in-plane and out-of-plane stresses in the monolayer. Such mechanical coupling implies an unexpected role for in-plane stresses in shaping epithelia during morphogenesis.
Neev, a novel long non-coding RNA, is expressed in chaetoblasts during regeneration of Eisenia fetida
Authors: Patel Surendra Singh , Zunjarrao Sanyami , Pillai Beena
Published: October 2019

Eisenia fetida, the common vermicomposting earthworm, shows robust regeneration of posterior segments removed by amputation. During the period of regeneration, the newly formed tissue initially contains only undifferentiated cells but subsequently differentiates into a variety of cell types including muscle, nerve and vasculature. Transcriptomics analysis, reported previously, provided a number of candidate non-coding RNAs that were induced during regeneration. We found that one such long non-coding RNA (lncRNA) is expressed in the skin, only at the base of newly formed chaetae. The spatial organization and precise arrangement of the regenerating chaetae and the cells expressing the lncRNA on the ventral side clearly support a model wherein the regenerating tissue contains a zone of growth and cell division at the tip and a zone of differentiation at the site of amputation. The temporal expression pattern of the lncRNA, christened Neev, closely resembled the pattern of chitin synthase genes, implicated in chaetae formation. We found that the lncRNA harbours 49 sites for binding a set of four miRNAs while the Chitin Synthase 8 mRNA comprises 478 sites. The over-representation of shared miRNA sites suggests that lncRNA Neev may act as a miRNA sponge to transiently de-repress chitin synthase 8 during formation of new chaetae in the regenerating segments of Eisenia fetida.

Summary statement

The earthworm, Eisenia fetida, regenerates posterior segments following amputation. The transcriptome of the regenerating worm revealed a novel lncRNA, expressed only at the base of regenerating chaetae. We propose that this lncRNA is a miRNA sponge that modulates chitin synthesis.
Essentiality of local topology and regulation in kinetic metabolic modeling
Authors: Li Gaoyang , Du Wei , Cao Huansheng
Published: October 2019

Genome-scale metabolic networks (GSMs) are mathematic representation of a set of stoichiometrically balanced reactions. However, such static GSMs do not reflect or incorporate functional organization of genes and their dynamic regulation (e.g., operons and regulons). Specifically, there are numerous topologically coupled local reactions through which fluxes are coordinated; and downstream metabolites often dynamically regulate the gene expression of their reactions via feedback. Here, we present a method which reconstructs GSMs with locally coupled reactions and transcriptional regulation of metabolism by key metabolites. The proposed method has outstanding performance in phenotype prediction of wild-type and mutants inEscherichia coli(E. coli),Saccharomyces cerevisiae(S. cerevisiae) andBacillus subtilis(B. subtilis) growing in various conditions, outperforming existing methods. The predicted growth rate and metabolic fluxes are highly correlated with those experimentally measured. More importantly, our method can also explain the observed growth rates by capturing the ‘real’ (experimentally measured) changes in flux between the wild-types and mutants. Overall, by identifying and incorporating locally organized and regulated functional modules into GSMs, Decrem achieves accurate predictions of phenotypes and has broad applications in bioengineering, synthetic biology and microbial pathology.
Differential contribution of p300 and CBP to regulatory elements in mESCs
Authors: Martire Sara , Sundaresan Aishwarya , Banaszynski Laura A.
Published: October 2019

The transcription coactivators CREB binding protein (CBP) and p300 are highly homologous acetyltransferases that mediate histone 3 lysine 27 acetylation (H3K27ac) at regulatory elements such as enhancers and promoters. Although in most cases, CBP and p300 are considered to be functionally identical, both proteins are indispensable for development and there is evidence of tissue-specific nonredundancy. However, characterization of chromatin and transcription states regulated by each protein is lacking. In this study we analyze the individual contribution of p300 and CBP to the H3K27ac landscape, chromatin accessibility, and transcription in mouse embryonic stem cells (mESC). We demonstrate that p300 is responsible for the majority of H3K27ac in mESCs and that loss of acetylation in p300-depleted mESCs is more pronounced at enhancers compared to promoters. While loss of either CBP or p300 has little effect on the open state of chromatin, we observe that distinct gene sets are transcriptionally dysregulated upon depletion of p300 or CBP. Transcriptional dysregulation is generally correlated with dysregulation of promoter acetylation upon depletion of p300 (but not CBP) and appears to be relatively independent of dysregulated enhancer acetylation. Interestingly, both our transcriptional and genomic analyses demonstrate that targets of the p53 pathway are stabilized upon deletion of p300, suggesting that this pathway is highly prioritized when p300 levels are limited.
Analysis of multi-tissue transcriptomes reveals candidate genes and pathways influenced by cerebrovascular diseases
Authors: Pan Zhi-Lin , Chen Cho-Yi
Published: October 2019

Cerebrovascular diseases (CVD) are a group of medical conditions that impair circulation of blood to the brain, including stroke, transient ischemic attack (TIA), embolism, aneurysm, and other circulatory disorders affecting the brain. Here, we investigated the effects of having CVD history on the molecular signature of brain regions by comparing gene expression profiles from several brain tissues between cohorts with and without CVD history. We first merged tissue samples from GTEx RNA-Seq dataset into clusters based on the overall gene expression similarity. Then we performed differential expression (DE) analyses for each cluster using a linear mixed model that controls covariates and the individual random effect. Cross-region DE genes were ranked by the combined q-values derived from the mixed model using Fisher’s method. Functional enrichment analyses were performed using Gene Set Enrichment Analysis (GSEA) program. We identified hundreds of DE genes, and many of them are related to endothelial or brain functions and associated diseases. We found that STAB1 was highly overexpressed across brain regions in the CVD cohort, and the upregulation of STAB1 in brain tissues may contribute to weaker self-defense mechanisms against lesions in the brain. Our results suggest a list of candidate genes and pathways that may be dysregulated in the brains of people with CVD history, implying that suffering from CVD could pose potential hazard to the brain.