bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of communication network topology in controlling microbial population in consortia
Authors: Ren Xinying , Murray Richard M. 
Published: March 2018

AbstractEngineering microbial consortia is an important new frontier for synthetic biology given its efficiency in performing complex tasks and endurance to environmental uncertainty. Most synthetic circuits regulate populational behaviors via cell-to-cell communications, which are affected by spatially heterogenous environments. Therefore, it is important to understand the limits on controlling system dynamics that are determined by interconnections among cell agents and provide a control strategy for engineering consortia. Here, we build a network model for a fractional population control circuit in two-strain consortia, and characterize the cell-to-cell communication network by topological properties, such as symmetry, locality and connectivity. Using linear network control theory, we relate the network topology to system output’s tracking performance. We analytically and numerically demonstrate that the minimum network control energy for accurate tracking depends on locality difference between two cell population’s spatial distributions and how strongly the controller node contributes to communication strength. To realize a robust consortia, we can manipulate the communication network topology and construct strongly connected consortia by altering chemicals in environments. Our results ground the expected cell population dynamics in its spatially organized communication network, and inspire directions in cooperative control in microbial consortia.
Can you make morphometrics work when you know the right answer? Pick and mix approaches for apple identification
Authors: Christodoulou Maria D. , Battey Nicholas H. , Culham Alastair 
Published: March 2018

AbstractMorphological classification of living things has challenged science for several centuries and has led to a wide range of objective morphometric approaches in data gathering and analysis. In this paper we explore those methods using apple cultivars, a model biological system in which discrete groups are pre-defined but in which there is a high level of overall morphological similarity. The effectiveness of morphometric techniques in discovering the groups is evaluated using statistical learning tools. No one technique proved optimal in classification on every occasion, linear morphometric techniques slightly out-performing geometric (72.6% accuracy on test set versus 66.7%). The combined use of these techniques with post-hoc knowledge of their individual successes with particular cultivars achieves a notably higher classification accuracy (77.8%). From this we conclude that even with pre-determined discrete categories, a range of approaches is needed where those categories are intrinsically similar to each other, and we raise the question of whether in studies where potentially continuous natural variation is being categorised the level of match between categories is routinely set too high.
Counteracting estimation bias and social influence to improve the wisdom of crowds
Authors: Kao Albert B. , Berdahl Andrew M. , Hartnett Andrew T. , Lutz Matthew J. , Bak-Coleman Joseph B. , Ioannou Christos C. , Giam Xingli , Couzin Iain D. 
Published: March 2018

AbstractAggregating multiple non-expert opinions into a collective estimate can improve accuracy across many contexts. However, two sources of error can diminish collective wisdom: individual estimation biases and information sharing between individuals. Here we measure individual biases and social influence rules in multiple experiments involving hundreds of individuals performing a classic numerosity estimation task. We first investigate how existing aggregation methods, such as calculating the arithmetic mean or the median, are influenced by these sources of error. We show that the mean tends to overestimate, and the median underestimate, the true value for a wide range of numerosities. Quantifying estimation bias, and mapping individual bias to collective bias, allows us to develop and validate three new aggregation measures that effectively counter sources of collective estimation error. In addition, we present results from a further experiment that quantifies the social influence rules that individuals employ when incorporating personal estimates with social information. We show that the corrected mean is remarkably robust to social influence, retaining high accuracy in the presence or absence of social influence, across numerosities, and across different methods for averaging social information. Utilizing knowledge of estimation biases and social influence rules may therefore be an inexpensive and general strategy to improve the wisdom of crowds.
csuWGCNA: a combination of signed and unsigned WGCNA to capture negative correlations
Authors: Dai Rujia , Xia Yan , Liu Chunyu , Chen Chao 
Published: March 2018

AbstractNetwork analysis helps us to understand how genes jointly affect biological functions. Weighted Gene Co-expression Network Analysis (WGCNA) is a frequently used method to build gene co-expression networks. WGCNA may be calculated with signed or unsigned correlations, with both methods having strengths and weaknesses, but both methods fail to capture weak and moderate negative correlations, which may be important in gene regulation. Combining the advantages and removing the disadvantages of both methods in one analysis would be desirable. In this study, we present a combination of signed and unsigned WGCNA (csuWGCNA), which combines the signed and unsigned methods and improves the detection of negative correlations. We applied csuWGCNA in 14 simulated datasets, six ground truth datasets and two large human brain datasets. Multiple metrics were used to evaluate csuWGCNA at gene pair and gene module levels. We found that csuWGCNA provides robust module detection and captures more negative correlations than the other methods, and is especially useful for non-coding RNA such as microRNA (miRNA) and long non-coding RNA (lncRNA). csuWGCNA enables detection of more informative modules with biological functions than signed or unsigned WGCNA, which enables discovery of novel gene regulation and helps interpretations in systems biology.
PP-2, a src-kinase inhibitor, is a potential corrector for F508del-CFTR in cystic fibrosis
Authors: Wang Yunguan , Arora Kavisha , Yang Fanmuyi , Shin Woong-Hee , Chen Jing , Kihara Daisuke , Naren Anjaparavanda P. , Jegga Anil G. 
Published: March 2018

AbstractCystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The most common mutation in CF, an in-frame deletion of phenylalanine 508, leads to a trafficking defect and endoplasmic reticulum retention of the protein where it becomes targeted for degradation. Successful clinical deployments of ivacaftor and ivacaftor/lumacaftor combination have been an exciting translational development in treating CF. However, their therapeutic effects are variable between subjects and remain insufficient. We used the Library of Integrated Network-based Cellular Signatures (LINCS) database as our chemical pool to screen for candidates. For in silico screening, we integrated connectivity mapping and CF systems biology to identify candidate therapeutic compounds for CF. Following in silico screening, we validated our candidate compounds with (i) an enteroid-based compound screening assay using CF (ΔF508/ΔF508-CFTR) patient-derived enteroids, (ii) short-circuit current analysis using polarized CF primary human airway epithelial cells and (iii) Western blots to measure F508-del-CFTR protein maturation. We identified 184 candidate compounds with in silico screening and tested 24 of them with enteroid-based forskolin-induced swelling (FIS) assay. The top hit compound was PP2, a known src-kinase inhibitor that induced swelling in enteroid comparable to known CF corrector (lumacaftor). Further validation with Western blot and short-circuit current analysis showed that PP-2 could correct mutant CFTR mis-folding and restore CFTR-mediated transmembrane current. We have identified PP2, a known src-kinase inhibitor, as a novel corrector of ΔF508-CFTR. Based on our studies and previous reports, src kinase inhibition may represent a novel paradigm of multi-action therapeutics – corrector, anti-inflammatory, and anti-infective – in CF.
Reducing effects of particle adsorption to the air-water interface in cryoEM
Authors: Noble Alex J. , Wei Hui , Dandey Venkata P. , Zhang Zhening , Potter Clinton S. , Carragher Bridget 
Published: March 2018

AbstractMost protein particles prepared in vitreous ice for single particle cryo-electron microscopy are adsorbed to air-water or substrate-water interfaces, potentially causing particles to adopt preferred orientations. Using the Spotiton robot and nanowire grids, we can significantly reduce air-water interface issues by decreasing the dwell time of particles in thin liquid films. We demonstrate this by using single particle cryoEM and cryoET on three biological samples.
The rhesus monkey hippocampus critically contributes to scene memory retrieval, but not new learning
Authors: Froudist-Walsh Sean , Browning Philip G. F. , Croxson Paula L. , Murphy Kathy L. , Shamy Jul Lea , Veuthey Tess L. , Wilson Charles R. E. , Baxter Mark G. 
Published: March 2018

AbstractHumans can recall a large number of memories years after the events that triggered them. Early studies of humans with amnesia led to the hippocampus being viewed as the critical structure for episodic memory, but human lesions are imprecise, making it difficult to identify the anatomical structures underlying memory impairments. Rodent studies enable great temporal and anatomical precision in hippocampal manipulations, but not investigation of the rich assortment of interleaved memories that occurs in humans. Thus it is not known how lesions restricted to the hippocampus affect the retrieval of multiple sequentially encoded memories. Furthermore, disagreement exists as to whether hippocampal inactivations lead to a temporally graded, or ungraded amnesia, which could be a consequence of different types hippocampal disruption observed in rodent and human studies. In the current study, four rhesus monkeys received bilateral neurotoxic lesions of the hippocampus, and were compared to thirteen unoperated controls on recognition and new learning of visual object-in-place scenes. Monkeys with hippocampal lesions were significantly impaired compared to controls at remembering scenes that were encoded before the lesion. We did not observe any temporal gradient effect of the lesion on memory recognition, with recent and remote memories being equally affected by the lesion. Monkeys with hippocampal lesions showed no deficits in learning and later recognising new scenes. Thus, the hippocampus, like other cortical regions, may be engaged in the acquisition and storage of new memories, but its role can be taken over by spared regions following a lesion. These findings illustrate the utility of experimental paradigms for studying retrograde and anterograde amnesia that make use of the capacity of nonhuman primates to rapidly acquire many distinct visual memories.
Rapid evolution of learning and reproduction in natural populations ofDrosophila melanogaster
Authors: Behrman Emily L. , Kawecki Tadeusz J. , Schmidt Paul 
Published: March 2018

AbstractLearning is a general mechanism of adaptive behavioural plasticity whose benefits and costs depend on the environment. Thus, seasonal oscillations in temperate environments between winter and summer might produce cyclical selection pressures that would drive rapid evolution of learning performance in multivoltine populations. To test this hypothesis, we investigated the evolutionary dynamics of learning ability over this rapid seasonal timescale in a natural population ofDrosophila melanogaster. Associative learning was tested in common garden-raised flies collected from nature in the spring and fall over three consecutive years. The spring flies consistently learned better than fall flies, revealing seasonal evolution of improved learning performance in nature. Fecundity showed the opposite seasonal pattern, suggesting a trade-off between learning and reproduction. This trade-off also held within population: more fecund individual females learned less well. This trade-off is mediated at least in part by natural polymorphism in the RNA binding proteincouch potato(cpo), with a genotype favoured during summer showing poorer learning performance and higher fecundity than a genotype favoured over winter. Thus, seasonal environments can drive rapid cyclical evolution of learning performance, but the evolutionary dynamics may be driven by trade-offs generated by pleiotropic effects of causative alleles selected for other reasons.
Interaction modulation through arrays of clustered methyl-arginine protein modifications
Authors: Woodsmith Jonathan , Casado-Medrano Victoria , Benlasfer Nouhad , Eccles Rebecca L. , Hutten Saskia , Heine Christian L. , Thormann Verena , Abou-Ajram Claudia , Rocks Oliver , Dormann Dorothee , Stelzl Ulrich 
Published: March 2018

AbstractSystematic analysis of human arginine methylation identifies two distinct signaling modes; either isolated modifications akin to canonical PTM regulation, or clustered arrays within disordered protein sequence. Hundreds of proteins contain these methyl-arginine arrays and are more prone to accumulate mutations and more tightly expression-regulated than dispersed methylation targets. Arginines within an array in the highly methylated RNA binding protein SYNCRIP were experimentally shown to function in concert providing a tunable protein interaction interface. Quantitative immuno-precipitation assays defined two distinct cumulative binding mechanisms operating across 18 proximal arginine-glycine (RG) motifs in SYNCRIP. Functional binding to the methyl-transferase PRMT1 was promoted by continual arginine stretches while interaction with the methyl-binding protein SMN1 was arginine content dependent irrespective of linear position within the unstructured region. This study highlights how highly-repetitive modifiable amino acid arrays in low structural complexity regions can provide regulatory platforms, with SYNCRIP as an extreme example how arginine methylation leverages these disordered sequences to mediate cellular interactions.
Monoclonal antibody 7D5 recognizes the R147 epitope on the gp91phox, phagocyte flavocytochrome b558 large subunit
Authors: Kawai Chikage , Yamauchi Akira , Kuribayashi Futoshi 
Published: March 2018

ABSTRACTHuman phagocyte flavocytochrome b558 (Cyt b), the catalytic center of nicotinamide adenine dinucleotide phosphate oxidase, consists of a heavily glycosylated large subunit (gp91phox; Nox2) and a small subunit (p22phox). Cyt b is a membrane‐spanning complex enzyme. Chronic granulomatous disease (CGD) is predominantly caused by a mutation in the CYBB gene encoding gp91phox on the X‐chromosome. Because the phagocytes of patients with CGD are not able to generate the superoxide anion, these patients are susceptible to severe infections that can be fatal. It has been suggested that the extracellular region of gp91phox is necessary for and critical to forming the epitope of mAb 7D5 and that 7D5 provides a useful tool for rapid screening of X‐linked CGD by FACS. To further elucidate the mAb 7D5 epitope on human gp91phox, chimeric DNA expressed human and mouse gp91phox recombinant protein were constructed. The fusion proteins were immunostained for mAb 7D5 and analyzed by FACS and western blot analysis. The 143ELGDRQNES151 region was found to reside at the extracellular surface on human gp91phox and to be an important epitope for the interaction with mAb 7D5, as analyzed by FACS analysis. In particular, amino acid R147 is a unique epitope on the membrane‐associated Cyt b for mAb 7D5. In conclusion, it is proposed that FACS analysis using mAb 7D5 is a valuable tool for early diagnosis of CGD.
The impact of development on patterns of nutrient limitation
Authors: Richard Romain , de Roos André M. 
Published: March 2018

Abstract

Development is often accompanied by major changes in an organism's functioning and in the way it interacts with its environment. We consider how developmental events such as allocation changes at maturity, ontogenetic diet shift or metamorphosis may affect the likelihood and nature of nutrient limitation and explore the consequences of these changes in nutrient limitation for individual life history and patterns of biomass production.

To this purpose, we develop a general model for individual growth and reproduction that is based on the assumption that biomass production and metabolism require several nutrients and that individuals may require them in different proportion at different stages of their lives.

We parameterize this model for Daphnia based on its physiological requirements for carbon (C) and phosphorus (P). Growth and reproduction have different nutrient requirements, and this affects the likelihood of C vs. P limitation of differently sized individuals. This translates into a size‐dependent threshold elemental ratio (TER), with a difference of up to twofold between juveniles and adults, a difference comparable to measured interspecific differences.

The main implications of these findings are that, at the population level, co‐limitation of biomass production by several nutrients is likely to occur under a wide range of food qualities. In addition, different regimes of nutrient limitation strongly influence the relative difference in biomass production of differently sized individuals, which has been shown to be a major driver of population and community dynamics. Our results point to development as a key determinant of a population's response to food quality.

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Male stress response is related to ornamentation but not resistance to oxidative stress in a warbler
Authors: Henschen Amberleigh E. , Whittingham Linda A. , Dunn Peter O. 
Published: March 2018

Abstract

Ornaments are thought to honestly signal individual quality to potential mates. Individual quality may include the ability to cope with stress through the production of glucocorticoids (GCs), such as corticosterone (CORT), which help to redirect resources from growth or reproduction to survival during an acute stress response. However, elevated levels of CORT may also increase oxidative stress and reduce immune function. Thus, an important question is whether high‐quality individuals, with more elaborate ornaments, signal their ability to produce a strong stress response and mitigate some of the negative effects of doing so through higher resistance to oxidative stress.

We tested whether ornamentation and resistance to oxidative stress were related to the increase in CORT during an acute stress response in a warbler, the common yellowthroat (Geothlypis trichas). Males in this species have two plumage ornaments, a black (eumelanin‐based) facial mask and a yellow (carotenoid‐based) bib. We measured the increase in CORT in response to the stress of capture and handling.

Males with more elaborate ornaments (larger masks and more colourful bibs) had a greater increase in CORT during an acute stress response. However, the increase in CORT was not related to resistance to oxidative stress.

These results suggest that both melanin‐ and carotenoid‐based plumage ornaments can signal the ability of a male to cope with stressors through a greater increase in CORT. Thus, the association between ornamentation and stress‐induced CORT is not likely due to a mechanism specific to a particular colour (melanin or carotenoid), but instead may result from more general interactions between CORT and health or condition.

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Transgenerational effects and acclimation affect dispersal in guppies
Authors: Le Roy Amélie , Seebacher Frank 
Published: March 2018

Abstract

Evolutionary theory predicts that intergenerational environmental fluctuations lead to transgenerational effects where offspring phenotypes are matched to conditions experienced by previous generations. However, in fluctuating environments, transgenerational effects can be detrimental by causing mismatches between ancestral and offspring environments. Acclimation in offspring could alleviate these negative effects.

We determined whether the interaction between transgenerational effects and acclimation affects locomotor performance and dispersal in guppies (Poecilia reticulata). In a fully factorial experiment, we tested the interaction between ancestral (22 or 30°C for six to eight generations), acclimation (22 or 30°C for 4 weeks) and acute test temperatures (two to five temperatures across 18–34°C). We predicted that matching ancestral and acclimation temperatures to acute environmental temperature maximises physiological capacities (swimming performance [Ucrit] and metabolic enzyme activities), and dispersal in an artificial stream. Alternatively, when ancestral and acute temperatures were mismatched, we predicted that thermal acclimation compensates for this mismatch by shifting performance curves. Finally, we hypothesised that physiological capacities are positively related to dispersal. We measured dispersal as a combination of traits characterising the departure and transient phases of dispersal (time taken to leave the introductory pool, voluntary speed against the current, number of dispersal decisions taken) in an 8‐m artificial stream.

As hypothesised, Ucrit was greatest when ancestral, acclimation and acute temperatures matched. Cold acclimation reduced the decrement in Ucrit resulting from a mismatch between ancestral and acute test temperatures. In both sexes, the interaction between ancestral and acclimation temperatures determined Ucrit, but not metabolic enzyme activities, and it affected the number of dispersal decisions in males only. Contrary to our hypothesis, physiological capacities did not constrain dispersal. Males were more likely to initiate dispersal when the acute temperatures mismatched their ancestral temperature. After initiating dispersal, males moved at a greater voluntary speed and made more dispersal decisions in environments matching their ancestral environment.

Our findings imply that although the interaction between transgenerational effects and acclimation modulates locomotor capacities, these relationships do not necessarily translate to all ecologically relevant locomotor tasks. Instead, sex‐specific life‐history traits such as life span are more likely to influence dispersal, and males in particular may initiate dispersal to escape suboptimal conditions.

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