bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel features of pressure relaxation in nonequilibrium helium crystals
Authors: Bisrchenko A. P. , Mikhin N. P. , Rudavskii E. Ya. , Smirnov S. N. , Fysun Ya. Yu.
Published: September 2018

The method of precision barometry has been used to study the structural relaxation processes in nonequilibrium helium crystals obtained by liquid crystallization during rapid cooling in the temperature range of 1.3–1.7 K. The pressure at the ends of a cylindrical measuring cell with solid helium and their variation with time during stepwise heating of the sample were measured. The experimental results for the relaxation kinetics, when the pressure values recorded by both sensors increased with time, were analyzed. Analysis of the experimental results provides estimates of the average atomic concentration of vacancies in the crystal, the vacancy diffusion coefficient values, and the activation energy of vacancy motion. The present work continues the study of structural pressure relaxation initiated in a previous work (LTP 44, 402 (2018)), where a model describing the relaxation of internal stresses in nonequilibrium helium crystals associated with the diffusion of vacancies was proposed for interpretation of the experimental data.
Thermally activated deformation of nanocrystalline and coarse grained CoCrFeNiMn high entropy alloy in the temperature range 4.2–350 K
Authors: Podolskiy A. V. , Schafler E. , Tabachnikova E. D. , Tikhonovsky M. A. , Zehetbauer M. J.
Published: September 2018

Mechanical properties of a nanocrystalline (∼ 60 nm) and a coarse grained (grain sizes ∼ 4 µm) CoCrFeNiMn high entropy alloys were studied in uniaxial compression in the temperature range 4.2–350 K. Temperature dependences of yield strength, flow stress and strain rate sensitivity have been registered and analyzed in the framework of two thermal activation deformation models, that of thermal activation of local barrier overcoming, and that of Peierls valley double kink formation. Microscopic parameters of dislocation interaction with the barriers for thermally activated motion are estimated and low temperature deformation mechanisms are discussed.
Estimation of desired feed intake for growth and reproductive organ development in pre-laying hens
Authors: Palma Bendezu Hilda , Sakomura Nilva Kazue , Malheiros Euclides Braga , Dorigam Juliano Cesar De Paula , Da Silva Edney Pereira , Reis Matheus De Paula
Published: September 2018

The objective of the present study was to describe the growth of reproductive organs and, on the basis of this information, predict feed intake during the pre-laying phase of laying-type pullets and to evaluate the results of the models. Ninety-six ISA-Brown pullets from 15 to 28 weeks of age were used in the first experiment. The weights of the birds with and without feathers, ovaries and oviducts were measured, and samples were taken to analyse dry matter, gross energy and crude protein. Seventy-six ISA-Brown and 76 Hy-Line pullets from 15 to 24 weeks of age were used in the second experiment. Feed intake was measured daily for each hen until the first egg was laid. The energy for maintenance (EEM) was calculated on the basis of the actual protein content and protein weight at maturity. The effective energy (EE) requirement was calculated as EER = EEM + 50 deposition of protein (DP) + 56 deposition of lipids (DL). Feed intake was calculated by dividing the EE requirement by the EE content in the feed. The simulation of feed intake overestimated values of 0.41 g/day (P > 0.05) and 2.65 g/day (P < 0.001) for Hy-Line and ISA-Brown respectively. A significant linear bias was observed for Hy-Line (P < 0.001) but not for ISA-Brown (P > 0.05). The assessment of the results indicated that the models for predicting feed intake were more accurate and less precise for Hy-Line than for ISA-Brown. Thus, there was an agreement between the calculated and measured values for feed intake, which shows that the models provide a true estimation of feed intake during the pre-laying phase.
End-Blocked Silanization of Side-Chain Fluoroalkyl Oligoether and its Surface Properties
Authors: Wang Lei , Chen Lei , Li Zhanxiong
Published: September 2018

In this study, three novel side-chain fluoroalkyl oligoethers with different molecular weights were synthesised via a ring-opening reaction of 2,2,3,3,4,4,5,5,5-nonafluoropentyloxirane. The fluorooligoethers were then silanized and characterised by FT-IR,1H, and 19F NMR spectroscopies. These silanlized fluorooligoethers were used to fabricate hydrophobic coatings on silicon substrates, which were pre-treated with O2 plasma, by the method of liquid phase deposition. The chemical compositions and structures of the film surfaces were analysed by X-ray photoelectron spectroscopy and the results showed that silanized fluorooligoethers formed self-assembled films on the silicon wafer. The surface wettability of the coatings was measured by water contact angles. It is noted that the annealing process can improve the hydrophobicity with the highest water contact angle being 115.2 ± 1° and hexadecane contact angle being 67.2 ± 1°. The surface morphologies and roughness of the self-assembled films were measured by atomic force microscopy (AFM), as a result, the surface was found to be rougher with the increment of the molecular weight of the fluorooligoethers.
Thioamide Derivative of the Potent Antitubercular 2-(Decylsulfonyl)acetamide is Less Active Against Mycobacterium tuberculosis, but a More Potent Antistaphylococcal Agent
Authors: Sun Hsien-Kuo , Pang Angel , Farr Dylan C. , Mosaiab Tamim , Britton Warwick J. , Anoopkumar-Dukie Shailendra , Grice I. Darren , Kiefel Milton J. , West Nick P. , Grant Gary D. , Houston Todd A.
Published: September 2018

Due to the prevalence of thioamides in antibacterial compounds, we chose to convert the amide in the antitubercular compound 2-(decylsulfonyl)acetamide to a thioamide using Lawesson’s reagent to study its activity against a range of microorganisms. This derivative (8) had significantly diminished activity against tuberculosis but slightly better activity than the parent compound against the Gram positive species Staphylococcus aureus. This activity against a second major pathogen is remarkable considering the structural simplicity of these compounds.
Exploring agricultural development and climate adaptation in northern Australia under climatic risks
Authors: Mathew Supriya , Zeng Benxiang , Zander Kerstin K. , Singh Ranjay K.
Published: September 2018

The agriculture sector in northern Australia is vulnerable to the impacts of climate change and climate variability. Climate change risks for future agricultural development include higher atmospheric temperature, increased rainfall variability and an increase in the frequency and severity of extreme weather events such as floods, droughts, heatwaves and fires. An uncertain future climate can affect agricultural production, efficient resource use and sustainable livelihoods. A balance needs to be achieved between resource use and livelihood security for sustainable agricultural development amid stressors such as climate change. This paper examines sustainable agricultural development in northern Australia using the environmental livelihood framework, a new approach that explores the relationships between water, energy and food resources and the livelihoods they sustain. The study shows that developments in the renewable energy sector, water infrastructure sector and advances in research and development for climate resilient infrastructure and climate resilient species are likely to improve agricultural production in northern Australia. Measures to attract and retain agricultural workforce is also key to maintaining a sustainable agricultural workforce in northern Australia. Adequate monitoring and evaluation of agricultural investments is important as future climatic impacts remain uncertain.
Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen
Authors: Pishchany Gleb , Mevers Emily , Ndousse-Fetter Sula , Horvath Dennis J. , Paludo Camila R. , Silva-Junior Eduardo A. , Koren Sergey , Skaar Eric P. , Clardy Jon , Kolter Roberto
Published: September 2018

The rapid emergence of antibiotic-resistant pathogenic bacteria has accelerated the search for new antibiotics. Many clinically used antibacterials were discovered through culturing a single microbial species under nutrient-rich conditions, but in the environment, bacteria constantly encounter poor nutrient conditions and interact with neighboring microbial species. In an effort to recapitulate this environment, we generated a nine-strain actinomycete community and used 16S rDNA sequencing to deconvolute the stochastic production of antimicrobial activity that was not observed from any of the axenic cultures. We subsequently simplified the community to just two strains and identifiedAmycolatopsissp. AA4 as the producing strain andStreptomyces coelicolorM145 as an inducing strain. Bioassay-guided isolation identified amycomicin (AMY), a highly modified fatty acid containing an epoxide isonitrile warhead as a potent and specific inhibitor ofStaphylococcus aureus. Amycomicin targets an essential enzyme (FabH) in fatty acid biosynthesis and reducesS. aureusinfection in a mouse skin-infection model. The discovery of AMY demonstrates the utility of screening complex communities against specific targets to discover small-molecule antibiotics.
Conductively coupled flexible silicon electronic systems for chronic neural electrophysiology
Authors: Li Jinghua , Song Enming , Chiang Chia-Han , Yu Ki Jun , Koo Jahyun , Du Haina , Zhong Yishan , Hill Mackenna , Wang Charles , Zhang Jize , Chen Yisong , Tian Limei , Zhong Yiding , Fang Guanhua , Viventi Jonathan , Rogers John A.
Published: September 2018

Significance

A critical challenge for flexible biomedical implants is in the development of materials and structures that enable intimate coupling to biotissues with long-term stability. The results presented here address this problem through a materials and integration strategy that combines highly doped silicon nanomembranes chemically bonded to thin films of thermal silicon dioxide in a construct that simultaneously serves as a biofluid barrier and a conductively coupled biointerface. Use of this approach with various flexible electronic systems, including passive and active electrodes for electrophysiological sensing and electrical stimulation, illustrate capabilities in high-fidelity operation. Systematic accelerated lifetime studies in artificial biofluids highlight the stability of these systems for chronic operation, without electrical leakage or other forms of degradation.
High Sensitivity Mapping of Cortical Dopamine D2 Receptor Expressing Neurons
Authors: Khlghatyan Jivan , Quintana Clémentine , Parent Martin , Beaulieu Jean-Martin
Published: September 2018

Cortical D2 dopamine receptor (Drd2) have mostly been examined in the context of cognitive function regulation and neurotransmission modulation of medial prefrontal cortex by principal neurons and parvalbumin positive, fast-spiking, interneurons in schizophrenia. Early studies suggested the presence of D2 receptors in several cortical areas, albeit with major technical limitations. We used combinations of transgenic reporter systems, recombinase activated viral vectors, quantitative translatome analysis, and high sensitivity in situ hybridization to identify D2 receptor expressing cells and establish a map of their respective projections. Our results identified previously uncharacterized clusters of D2 expressing neurons in limbic and sensory regions of the adult mouse brain cortex. Characterization of these clusters by translatome analysis and cell type specific labeling revealed highly heterogeneous expression of D2 receptors in principal neurons and various populations of interneurons across cortical areas. Transcript enrichment analysis also demonstrated variable levels of D2 receptor expression and several orphan G-protein-coupled receptors coexpression in different neuronal clusters, thus suggesting strategies for genetic and therapeutic targeting of D2 expressing neurons in specific cortical areas. These results pave the way for a thorough re-examination of cortical D2 receptor functions, which could provide information about neuronal circuits involved in psychotic and mood disorders.
Incidence of infective endocarditis in patients considered at moderate risk
Authors: Østergaard Lauge , Valeur Nana , Wang Andrew , Bundgaard Henning , Aslam Mohsin , Gislason Gunnar , Torp-Pedersen Christian , Bruun Niels Eske , Søndergaard Lars , Køber Lars , Fosbøl Emil Loldrup
Published: September 2018

Aims

Stratification of patients at risk of infective endocarditis (IE) remains a cornerstone in guidance of prophylactic strategies of IE. However, little attention has been given to patients considered at moderate risk.

Methods and results

Using Danish nationwide registries, we assessed the risk of IE in patients with aortic and mitral valve disorders, a cardiac implantable electronic device (CIED), or hypertrophic cardiomyopathy (HCM) and compared these patient groups with (i) controls from the background population using risk-set matching and (ii) a high-risk population (prosthetic heart valve). Cumulative incidence plots and multivariable adjusted Cox proportional hazard analysis were used to compare risk of IE between risk groups. We identified 83 453 patients with aortic or mitral valve disorder, 50 828 with a CIED, and 3620 with HCM. The cumulative risk of IE after 10 years was 0.9% in valve disorder, 1.3% in CIED, and 0.5% in HCM patients. Compared with the background population, valve disorder, CIED, and HCM carried a higher associated risk of IE, hazard ratio (HR) = 8.75 [95% confidence interval (CI) 6.36–12.02], HR = 6.63 (95% CI 4.41–9.96), and HR = 6.57 (95% CI 2.33–18.56), respectively. All three study groups were associated with a lower risk of IE compared with high-risk patients, HR = 0.27 (95% CI 0.23–0.32) for valve disorder, HR = 0.28 (95% CI 0.23–0.33) for CIED, and HR = 0.13 (95% CI 0.06–0.29) for HCM.

Conclusions

Heart valve disorder, CIED, and patients with HCM were associated with a higher risk of IE compared with the background population but have a lower associated risk of IE compared with high-risk patients.
The Cycle Structure of Unicritical Polynomials
Authors: Bridy Andrew , Garton Derek
Published: September 2018

A polynomial with integer coefficients yields a family of dynamical systems indexed by primes as follows: for any prime $p$, reduce its coefficients mod $p$ and consider its action on the field $ {{\mathbb{F}}}_p$. The questions of whether and in what sense these families are random have been studied extensively, spurred in part by Pollard’s famous “rho” algorithm for integer factorization (the heuristic justification of which is the conjectural randomness of one such family). However, the cycle structure of these families cannot be random, since in any such family, the number of cycles of a fixed length in any dynamical system in that family is bounded. In this paper, we show that the cycle statistics of many of these families are as random as possible. As a corollary, we show that most members of these families have many cycles, addressing a conjecture of Mans et al.
The SLC transporter in nutrient and metabolic sensing, regulation, and drug development
Authors: Zhang Yong , Zhang Yuping , Sun Kun , Meng Ziyi , Chen Ligong
Published: September 2018

The prevalence of metabolic diseases is growing worldwide. Accumulating evidence suggests that solute carrier (SLC) transporters contribute to the etiology of various metabolic diseases. Consistent with metabolic characteristics, the top five organs in which SLC transporters are highly expressed are the kidney, brain, liver, gut, and heart. We aim to understand the molecular mechanisms of important SLC transporter-mediated physiological processes and their potentials as drug targets. SLC transporters serve as ‘metabolic gate’ of cells and mediate the transport of a wide range of essential nutrients and metabolites such as glucose, amino acids, vitamins, neurotransmitters, and inorganic/metal ions. Gene-modified animal models have demonstrated that SLC transporters participate in many important physiological functions including nutrient supply, metabolic transformation, energy homeostasis, tissue development, oxidative stress, host defense, and neurological regulation. Furthermore, the human genomic studies have identified that SLC transporters are susceptible or causative genes in various diseases like cancer, metabolic disease, cardiovascular disease, immunological disorders, and neurological dysfunction. Importantly, a number of SLC transporters have been successfully targeted for drug developments. This review will focus on the current understanding of SLCs in regulating physiology, nutrient sensing and uptake, and risk of diseases.
Jian-Wei Pan: building the quantum internet
Authors: Ball Philip
Published: September 2018

For many decades since its inception in the early twentieth century, quantum mechanics seemed to be an exotic and peculiarly non-intuitive kind of physics that applied to matter at the smallest scales: the laws that govern atoms, photons and subatomic particles. All our engineering, meanwhile, was dominated by the familiar rules of classical physics, in which objects have definite positions, trajectories and properties.

 But, in the past several decades, scientists have started to harness quantum rules in practical technologies. In 1985, the physicist Richard Feynman suggested that computers governed by quantum rules might be capable of computations beyond the means of classical ones like those in use today. At much the same time, other researchers showed that information encoded in quantum states could be transmitted between a sender and receiver using a kind of encryption that could not be intercepted and read without that being detected. Quantum computers and quantum cryptography have now become central components of a real-world quantum-information technology that may soon find scientific, industrial and social uses.

 These applications could be increasingly enabled by a global information network with quantum capability: a quantum internet. China is at the forefront of that enterprise, and one of the scientific leaders in this effort is Jian-Wei Pan of the University of Science and Technology of China in Hefei. Pan studied for his PhD with quantum-information pioneer Anton Zeilinger in Vienna before returning to China to implement these nascent technologies. In 2012, he won the International Quantum Communication Award and, in 2017, he was included in Nature’s annual list of the ‘ten people who mattered in science’ over the past year. That July, he and his colleagues reported ‘quantum teleportation’ of photons from a ground-based station to a satellite 1400 km away.

 NSR recently interviewed Professor Pan about the current achievements and future prospects for quantum-information technologies.
Probability
Authors: Eagle Antony
Published: September 2018

Rather than entailing that a particular outcome will occur, many scientific theories only entail that an outcome will occur with a certain probability. Because scientific evidence inevitably falls short of conclusive proof, when choosing between different theories it is standard to make reference to how probable the various options are in light of the evidence. A full understanding of probability in science needs to address both the role of probabilities in theories, or chances, as well as the role of probabilistic judgment in theory choice. In this chapter, the author introduces and distinguishes the two sorts of probability from one another and attempt to offer a satisfactory characterization of how the different uses for probability in science are to be understood. A closing section turns to the question of how views about the chance of some outcome should guide our confidence in that outcome.
The changing face of risk factors for non-communicable disease in Myanmar: findings from the 2009 and 2014 WHO STEP Surveys
Authors: Grover Shekhar , Sinha Dhirendra N , Gupta Sanjay , Gupta Prakash C , Mehrotra Ravi
Published: September 2018

Background

Myanmar is burdened with the dual problem of communicable and non-communicable diseases (NCD), and is constantly endeavoring to attain its health objectives with limited resources. This study compares the results for the 2009 and 2014 WHO STEPs surveys (the ‘stepwise’ approach to adult risk factor surveillance) in Myanmar to determine the change in NCD risk factors over time.

Methodology

The proportion of individuals with major NCD risk factors such as current tobacco and alcohol consumption, <5 fruit/vegetable servings, physical activity, raised blood pressure (BP) and overweight and obesity from the year 2009 (n = 6414) and year 2014 (n = 8757) WHO STEP surveys were compared for the age group 25–64 and relative changes (RC) calculated.

Results

Tobacco and alcohol consumption has increased significantly (25 and 49% RC, respectively) over the years. Individuals with low fruit/vegetable consumption (<5 servings) have declined (4.3% RC) and physical activity has increased significantly (46.5% RC). The prevalence of overweight, obese and hypertensive individuals has reduced significantly during this period with a RC reduction of 18, 28 and 20%, respectively.

Conclusion

Reductions in some NCD risk factors are encouraging but control of tobacco use and alcohol consumption requires more stringent policies in order to prevent NCDs in the future.
Integration Host Factor Is Essential for Biofilm Formation, Extracellular Enzyme, Zeamine Production, and Virulence in Dickeya zeae
Authors: Chen Xuefeng , Yu Chengpeng , Li Shuangchun , Li Xinwei , Liu Qiongguang
Published: September 2018

Dickeya zeae is a globally important pathogenic bacterium that infects many crops, including rice, maize, potato, and banana. Bacterial foot rot of rice caused by D. zeae is one of the most important bacterial diseases of rice in China and some Southeast Asian countries. To investigate the functions of integration host factor (IHF) in D. zeae, we generated knockout mutants of ihfA and ihfB. Phenotypic assays showed that both the ΔihfA and ΔihfB strains had greatly reduced mobility, biofilm formation, extracellular protease, and pectinase activities, and toxin production compared with the wild-type strain. In addition, the mutants did not inhibit the germination of rice seeds, failed to cause soft rot in potatoes and a hypersensitive response in tobacco, and were avirulent in rice. Quantitative reverse-transcription polymerase chain reaction analysis demonstrated that IHF positively regulates the expression of zmsA, hrpN/Y, pelA/B/C, pehX, celZ, prtG, fliC, and DGC (diguanylate cyclase). Electrophoretic mobility shift assays further confirmed that IhfA binds to the promoter region of the DGC gene and may alter the levels of a second bacterial messenger, c-di-GMP, to regulate the pathogenicity or other physiological functions of D. zeae. In summary, IHF is an important integrated regulator of pathogenicity in D. zeae.
MLST Reveals a Separate and Novel Clonal Group forAcidovorax avenaeStrains Causing Red Stripe in Sugarcane from Argentina
Authors: Fontana Paola D. , Tomasini Nicolás , Fontana Cecilia A. , Di Pauli Valentina , Cocconcelli Pier S. , Vignolo Graciela M. , Salazar Sergio M.
Published: September 2018

Acidovorax spp. cause a wide range of economically important diseases in monocotyledonous and dicotyledonous plants, including sugarcane, corn, rice, oat, millet, foxtail watermelon, and orchid. In Argentina, the red stripe disease of sugarcane caused by Acidovorax avenae affects 30% of the milling stems with important economic losses. To explore the genetic diversity of this bacterium associated with red stripe in Argentina, multilocus sequence typing (MLST) was applied. This study included 15 local strains isolated from four different sugarcane planting regions and selected after random amplified polymorphic DNA analysis and reference strains of A. citrulli, A. avenae, and A. oryzae to investigate their phylogenetic relationships. MLST analysis resulted in five sequence types among the sugarcane A. avenae strains which constitute a clonal complex, meaning a common and close origin. Sugarcane strains were related to A. avenae from other hosts and distant to A. citrulli. Signals of frequent recombination in several lineages of A. avenae was detected and we observed that A. oryzae is closely related to A. avenae strains. This study provides valuable data in the field of epidemiological and evolutionary investigations of novel clone of A. avenae strains causing sugarcane red stripe. The knowledge of the genetic diversity and strain-host specificity are important to select the genotypes with the best response to the red stripe disease.
Quantifying the Influence of Mutation Detection on Tumour Subclonal Reconstruction
Authors: Liu Lydia Y. , Bhandari Vinayak , Salcedo Adriana , Espiritu Shadrielle M. G. , Morris Quaid D. , Kislinger Thomas , Boutros Paul C.
Published: September 2018

Whole-genome sequencing can be used to estimate subclonal populations in tumours and this intra-tumoural heterogeneity is linked to clinical outcomes. Many algorithms have been developed for subclonal reconstruction, but their variabilities and consistencies are largely unknown. We evaluated sixteen pipelines for reconstructing the evolutionary histories of 293 localized prostate cancers from single samples, and eighteen pipelines for the reconstruction of 10 tumours with multi-region sampling. We show that predictions of subclonal architecture and timing of somatic mutations vary extensively across pipelines. Pipelines show consistent types of biases, with those incorporating SomaticSniper and Battenberg preferentially predicting homogenous cancer cell populations and those using MuTect tending to predict multiple populations of cancer cells. Subclonal reconstructions using multi-region sampling confirm that single-sample reconstructions systematically underestimate intra-tumoural heterogeneity, predicting on average fewer than half of the cancer cell populations identified by multi-region sequencing. Overall, these biases suggest caution in interpreting specific architectures and subclonal variants.
An ABC method for whole-genome sequence data: inferring paleolithic and neolithic human expansions
Authors: Jay Flora , Boitard Simon , Austerlitz Frédéric
Published: September 2018

Species generally undergo a complex demographic history, consisting, in particular, of multiple changes in population size. Genome-wide sequencing data are potentially highly informative for reconstructing this demographic history. A crucial point is to extract the relevant information from these very large datasets. Here we designed an approach for inferring past demographic events from a moderate number of fully sequenced genomes. Our new approach uses Approximate Bayesian Computation (ABC), a simulation-based statistical framework that allows (i) identifying the best demographic scenario among several competing scenarios, and (ii) estimating the best-fitting parameters under the chosen scenario. ABC relies on the computation of summary statistics. Using a cross-validation approach, we showed that statistics such as the lengths of haplotypes shared between individuals, or the decay of linkage disequilibrium with distance, can be combined with classical statistics (eg heterozygosity, Tajima’s D) to accurately infer complex demographic scenarios including bottlenecks and expansion periods. We also demonstrated the importance of simultaneously estimating the genotyping error rate. Applying our method on genome-wide human-sequence databases, we finally showed that a model consisting in a bottleneck followed by a Paleolithic and a Neolithic expansion was the most relevant for Eurasian populations.
Dominance in dogs as rated by owners corresponds to ethologically valid markers of dominance
Authors: Kubinyi Enikő , Wallis Lisa J
Published: September 2018

Dominance is well defined in ethology, debated in psychology, and is often unclear among the dog owning public and in the press. However, to date, no study has examined how owners perceive dominance in dogs, and what different behaviours and personality types are used to describe dominant and subordinate individuals. A questionnaire study was launched to investigate the external validity of owner-derived estimates of dominance in dog dyads sharing the same household (N = 1151). According to the owners, dogs rated as dominant (87%) have priority access to resources (resting place, food, and rewards), undertake certain tasks (defend and lead the group, bark more), display dominance (win fights, lick the other’s mouth less, and mark over the other’s urine), share certain personality traits (smarter, more aggressive and impulsive), and are older than their partner dog (all p < 0.0001). An age-related hypothesis has been suggested to explain dominance in dogs, but we found that dog age did not explain the occurrence of dominance-related behaviours over the owners’ estimate of dominance status. Results suggest that owner-derived reports of dominance ranks of dogs living in multi-dog households correspond to ethologically valid behavioural markers of dominance. Size and physical condition were unrelated to the perceived dominance. Surprisingly, in mixed-sex dyads, females were more frequently rated as dominant than males, which might correspond to a higher proportion of neutered females in this subgroup. For future studies that wish to allocate dominance status using owner report, we offer a novel survey.
Insulin Producing Cells Monitor the Cold and Compensate the Cold-Induced Sleep in Drosophila
Authors: Zhang Xu O. , Cui Xinyue , Zhu Dikai
Published: September 2018

Sleep is regulated by environmental factors including temperature, but the neural circuits that receive the sensory signal and mediate the regulation remain unclear. We examined how cold could influence Drosophila sleep patterns and its neural mechanism. The results showed that Drosophila has more sleep duration, less sleep latency and deeper sleep depth under cold condition. We identified the Insulin-producing Cells (IPCs) can be activated by cold, and receive the cold signal from the 11216 cold-sensing neuron without a direct synaptic connection. Elevation of IPCs’ sensitivity to cold impairs the sleep-promoting effect of cold while blocking of IPCs enhance the effect mostly on sleep circadian, suggesting that the cold activated IPCs have a compensative role in sleep regulation. Our finding revealed a potential neural circuit that help maintain sleep circadian in detrimental environment and may give new insight to the complicated sleep regulation mechanism.
The NSL complex mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise
Authors: Lam Kin Chung , Chung Ho-Ryun , Semplicio Giuseppe , Bhardwaj Vivek , Iyer Shantanu S. , Holz Herbert , Georgiev Plamen , Akhtar Asifa
Published: September 2018

Nucleosomal organization at gene promoters is critical for transcription, with a nucleosome-depleted region (NDR) at transcription start sites (TSSs) being required for transcription initiation. How NDR and the precise positioning of the +1 nucleosome is maintained on active genes remains unclear. Here, we report that the Drosophila Non-Specific Lethal (NSL) complex is necessary to maintain this stereotypical nucleosomal organization at promoters. Upon NSL1 depletion, nucleosomes invade the NDRs at TSSs of NSL-bound genes. NSL complex member NSL3 binds to TATA-less promoters in a sequence-dependent manner. The NSL complex interacts with the NURF chromatin remodeling complex and is necessary and sufficient to recruit NURF to target promoters. The NSL complex is not only essential for transcription but is required for accurate TSS selection for genes with multiple TSSs. Further, loss of NSL complex leads to an increase in transcriptional noise. Thus, the NSL complex establishes a canonical nucleosomal organization that enables transcription and determines TSS fidelity.
Efficient transposon mutagenesis mediated by an IPTG-controlled conditional suicide plasmid
Authors: Naorem Santa S. , Han Jin , Zhang Stephanie Y. , Zhang Junyi , Graham Lindsey B. , Song Angelou , Smith Cameron V. , Rashid Fariha , Guo Huatao
Published: September 2018

Background

Transposon mutagenesis is highly valuable for bacterial genetic and genomic studies. The transposons are usually delivered into host cells through conjugation or electroporation of a suicide plasmid. However, many bacterial species cannot be efficiently conjugated or transformed for transposon saturation mutagenesis. For this reason, temperature-sensitive (ts) plasmids have also been developed for transposon mutagenesis, but prolonged incubation at high temperatures to induce ts plasmid loss can be harmful to the hosts and lead to enrichment of mutants with adaptive genetic changes. In addition, the ts phenotype of a plasmid is often strain- or species-specific, as it may become non-ts or suicidal in different bacterial species.

Results

We have engineered several conditional suicide plasmids that have a broad host range and whose loss is IPTG-controlled. One construct, which has the highest stability in the absence of IPTG induction, was then used as a curable vector to deliver hyperactive miniTn5 transposons for insertional mutagenesis. Our analyses show that these new tools can be used for efficient and regulatable transposon mutagenesis in Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. In P. aeruginosa PAO1, we have used this method to generate a Tn5 insertion library with an estimated diversity of ~108, which is ~2 logs larger than the best transposon insertional library of PAO1 and related Pseudomonas strains previously reported.

Conclusion

We have developed a number of IPTG-controlled conditional suicide plasmids. By exploiting one of them for transposon delivery, a highly efficient and broadly useful mutagenesis system has been developed. As the assay condition is mild, we believe that our methodology will have broad applications in microbiology research.
Cell-Type Switches Induced by Stochastic Histone Modification Inheritance
Authors: Huang Rongsheng , Lei Jinzhi , Pei-Yuan Zhou
Published: September 2018

ABSTRACT

Cell plasticity is important for tissue developments during which somatic cells may switch between distinct states. Genetic networks to yield multistable states are usually required to yield multiple states, and either external stimuli or noise in gene expressions are trigger signals to induce cell-type switches between the states. In many biological systems, cells show highly plasticity and can switch between different state spontaneously, but maintaining the dynamic equilibrium of the cell population. Here, we considered a mechanism of spontaneous cell-type switches through the combination between gene regulation network and stochastic epigenetic state transitions. We presented a mathematical model that consists of a standard positive feedback loop with changes of histone modifications during with cell cycling. Based on the model, nucleosome state of an associated gene is a random process during cell cycling, and hence introduces an inherent noise to gene expression, which can automatically induce cell-type switches in cell cycling. Our model reveals a simple mechanism of spontaneous cell-type switches through a stochastic histone modification inheritance during cell cycle. This mechanism is inherent to the normal cell cycle process, and is independent to the external signals.
Bayesian Inference of Other Minds Explains Human Choices in Group Decision Making
Authors: Khalvati Koosha , Park Seongmin A. , Mirbagheri Saghar , Philippe Remi , Sestito Mariateresa , Dreher Jean-Claude , Rao Rajesh P. N.
Published: September 2018

To make decisions in a social context, humans have to predict the behavior of others, an ability that is thought to rely on having a model of other minds known as theory of mind. Such a model becomes especially complex when the number of people one simultaneously interacts is large and the actions are anonymous. Here, we show that in order to make decisions within a large group, humans employ Bayesian inference to model the “mind of the group,” making predictions of others’ decisions while also considering the effects of their own actions on the group as a whole. We present results from a group decision making task known as the Volunteers Dilemma and demonstrate that a Bayesian model based on partially observable Markov decision processes outperforms existing models in quantitatively explaining human behavior. Our results suggest that in group decision making, rather than acting based solely on the rewards received thus far, humans maintain a model of the group and simulate the group’s dynamics into the future in order to choose an action as a member of the group.
PERK Signaling Regulates Extracellular Proteostasis of an Amyloidogenic Protein During Endoplasmic Reticulum Stress
Authors: Romine Isabelle C. , Wiseman R. Luke
Published: September 2018

The PERK arm of the unfolded protein response (UPR) regulates cellular proteostasis and survival in response to endoplasmic reticulum (ER) stress. However, the impact of PERK signaling on extracellular proteostasis is poorly understood. We define how PERK signaling influences extracellular proteostasis during ER stress using a conformational reporter of the secreted amyloidogenic protein transthyretin (TTR). We show that inhibiting PERK signaling impairs ER stress-dependent secretion of destabilized TTR by increasing its ER retention in chaperone-bound complexes. Interestingly, PERK inhibition promotes the ER stress-dependent secretion of TTR in non-native conformations that accumulate extracellularly as soluble oligomers. Pharmacologic or genetic TTR stabilization partially restores secretion of native TTR tetramers. However, PERK inhibition still increases the ER stress-dependent secretion of TTR in non-native conformations under these conditions, indicating that the conformation of stable secreted proteins can also be affected by inhibiting PERK. Our results define a role for PERK in regulating extracellular proteostasis during ER stress and indicate that genetic or aging-related alterations in PERK signaling can exacerbate ER stress-related imbalances in extracellular proteostasis implicated in diverse diseases.
Quantitative study of the somitogenetic wavefront in zebrafish
Authors: Zhang Weiting , Ducos Bertrand , Delagrange Marine , Vriz Sophie , Bensimon David
Published: September 2018

A quantitative description of the molecular networks that sustain morphogenesis is one of the challenges of developmental biology. Specifically, a molecular understanding of the segmentation of the antero-posterior axis in vertebrates has yet to be achieved. This process known as somitogenesis is believed to result from the interactions between a genetic oscillator and a posterior-moving determination wavefront. Here we quantitatively study and perturb the network in zebrafish that sustains this wavefront and compare our observations to a model whereby the wavefront is due to a switch between stable states resulting from reciprocal negative feedbacks of Retinoic Acid (RA) on the activation of ERK and of ERK on RA synthesis. This model quantitatively accounts for the near linear shortening of the post-somitic mesoderm (PSM) in response to the observed exponential decrease during somitogenesis of the mRNA concentration of a morphogen (Fgf8). It also accounts for the observed dynamics of the PSM when the molecular components of the network are perturbed. The generality of our model and its robustness allows for its test in other model organisms.
Co-translation drives the assembly of mammalian nuclear multisubunit complexes
Authors: Kamenova Ivanka , Mukherjee Pooja , Conic Sascha , Mueller Florian , El-Saafin Farrah , Bardot Paul , Garnier Jean-Marie , Dembele Doulaye , Capponi Simona , Timmers H.T. Marc , Vincent Stéphane D. , Tora László
Published: September 2018

Abstract

Cells dedicate significant energy to build proteins often organized in multiprotein assemblies with tightly regulated stoichiometries. As genes encoding proteins assembling in the same multisubunit complexes are dispersed in the genome of eukaryotes, it is unclear how multisubunit complexes assemble. We show that mammalian nuclear transcription complexes (TFIID, TREX-2 and SAGA) composed of a large number of subunits but lacking precise architectural details are built co-translationally. We demonstrate that the dimerization domains and their positions in the interacting subunits determine the co-translational assembly pathway (simultaneous or sequential). Our results indicate that protein translation and complex assembly are linked in building mammalian multisubunit complexes and suggest that co-translational assembly is a general principle in mammalian cells to avoid non-specific interactions and protein aggregation. These findings will significantly advance structural biology by defining endogenous co-translational building blocks in the architecture of multisubunit complexes.
Arabidopsis Class I Formin FH1 Relocates Between Membrane Compartments During Root Cell Ontogeny And Associates With Plasmodesmata
Authors: Oulehlová Denisa , Kollárová Eva , Cifrová Petra , Pejchar Přemysl , Žárský Viktor , Cvrčková Fatima
Published: September 2018

Formins are evolutionarily conserved eukaryotic proteins engaged in actin nucleation and other aspects of cytoskeletal organization. Angiosperms have two formin clades with multiple paralogs; typical plant Class I formins are integral membrane proteins that can anchor cytoskeletal structures to membranes. For the main Arabidopsis housekeeping Class I formin, FH1 (At3g25500), plasmalemma localization was documented in heterologous expression and overexpression studies. We previously showed that loss of FH1 function increases cotyledon epidermal pavement cell shape complexity via modification of actin and microtubule organization and dynamics. Here we employ transgenic Arabidopsis expressing green fluorescent protein-tagged FH1 (FH1-GFP) from its native promoter to investigatein vivobehaviour of this formin using advanced microscopy techniques. The fusion protein is functional, since its expression complements thefh1loss-of-function mutant phenotype. Accidental overexpression of FH1-GFP results in a decrease in trichome branch number, whilefh1mutation has the opposite effect, indicating a general role of this formin in controlling cell shape complexity. Consistent with previous reports, FH1-GFP associates with membranes. However, the protein exhibits surprising actin- and secretory pathway-dependent dynamic localization and relocates between cellular endomembranes and the plasmalemma during cell division and differentiation in root tissues, with transient tonoplast localization at the transition/elongation zones border. FH1-GFP also accumulates in actin-rich regions of cortical cytoplasm and associates with plasmodesmata in both the cotyledon epidermis and root tissues. Together with previous reports from metazoan systems, this suggests that formins might have an ancestral role at cell-cell junctions.
The Dlg-module and clathrin-mediated endocytosis regulate EGFR signaling and cyst cell-germline coordination in theDrosophilatestis
Authors: Papagiannouli Fani , Berry Cameron Wynn , Fuller Margaret T.
Published: September 2018

Tissue homeostasis and repair relies on proper communication of stem cells and their differentiating daughters with the local tissue microenvironment. In theDrosophilamale germline adult stem cell lineage, germ cells proliferate and progressively differentiate enclosed in supportive somatic cyst cells, forming a small organoid, the functional unit of differentiation. Here we show that cell polarity and vesicle trafficking influence signal transduction in cyst cells, with profound effects on the germ cells they enclose. Our data suggest that both the cortical components Dlg, Scrib, Lgl and the clathrin-mediated endocytic (CME) machinery downregulate EGFR signaling. Knockdown ofdlg, scrib, lglor CME components in cyst cells resulted in germ cell death, similar to increased signal transduction via the EGFR, while lowering EGFR or downstream signaling components rescued the defects. This work provides new insights on how cell polarity and endocytosis cooperate to regulate signal transduction and sculpt developing tissues.
Deacetylation of catalytic lysine in CDK1 is essential for Cyclin-B binding and cell cycle
Authors: Deota Shaunak , Rathnachalam Sivasudhan , Namrata Kanojia , Boob Mayank , Fulzele Amit , Radhika S , Ganguli Shubhra , Balaji Chinthapalli , Kaypee Stephanie , Vishwakarma Krishna Kant , Kundu Tapas Kumar , Bhandari Rashna , de Peredo Anne Gonzalez , Mishra Mithilesh , Venkatramani Ravindra , Kolthur-Seetharam Ullas
Published: September 2018

Cyclin-dependent-kinases (CDKs) are essential for cell cycle progression. While dependence of CDK activity on Cyclin levels is established, molecular mechanisms that regulate their binding are less studied. Here, we show that CDKl:Cyclin-B interactions are regulated by acetylation, which was hitherto unknown. We demonstrate that cell cycle dependent acetylation of the evolutionarily conserved catalytic lysine in CDK1 or eliminating its charge state abrogates Cyclin-B binding. Opposing activities of SIRT1 and P300 regulate acetylation, which marks a reserved pool of CDK1. Our high resolution structural analyses into the formation of kinase competent CDK1: Cyclin-B complex have unveiled long-range effects of catalytic lysine in configuring the CDK1 interface for Cyclin-B binding. Cells expressing acetylation mimic mutant of Cdc2 in yeast are arrested in G2 and fail to divide. Thus, by illustrating cell cycle dependent deacetylation as a determinant of CDK1:Cyclin-B interaction, our results redefine the current model of CDK1 activation and cell cycle progression.