bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host nutrition mediates interactions between plant viruses, altering transmission and predicted disease spread
Authors: Kendig Amy E. , Borer Elizabeth T. , Boak Emily N. , Picard Tashina C. , Seabloom Eric W. 
Published: September 2019

AbstractInteractions among co-infecting pathogens are common across host taxa and can affect infectious disease dynamics. Host nutrition can mediate these among-pathogen interactions, altering the establishment and growth of pathogens within hosts. It is unclear, however, how nutrition-mediated among-pathogen interactions affect transmission and the spread of disease through populations. We manipulated the nitrogen (N) and phosphorus (P) supplies to oat plants in growth chambers and evaluated interactions between two aphid-vectored Barley and Cereal Yellow Dwarf Viruses: PAV and RPV. We quantified the effect of each virus on the other’s establishment, within-plant density, and transmission. Co-inoculation significantly increased PAV density when N and P supplies were low and tended to increase RPV density when N supply was high. Co-infection increased PAV transmission when N and P supplies were low and tended to increase RPV transmission when N supply was high. Despite the parallels between the effects of among-pathogen interactions on density and transmission, changes in virus density only partially explained changes in transmission, suggesting that virus density–independent processes contribute to transmission. A mathematical model describing the spread of two viruses through a plant population, parameterized with empirically derived transmission values, demonstrated that nutrition-mediated among-pathogen interactions could affect disease spread. Interactions that altered transmission through virus density–independent processes determined overall disease dynamics. Our work suggests that host nutrition alters disease spread through among-pathogen interactions that modify transmission.
ECM-body: A cell-free 3D biomimetic scaffold derived from intact planarian body
Authors: Sonpho Ekasit , Wootthichairangsan Chanida , Ishida Miyuki , Inoue Takeshi , Agata Kiyokazu , Maleehuan Anchuleerat , Charngkaew Komgrid , Chomanee Nusara , Moonsom Saengduen , Wongtrakoongate Patompon , Chairoungdua Arthit , Ounjai Puey 
Published: September 2019

AbstractExtracellular matrix (ECM) plays key roles in shaping fates of stem cells, not only by providing suitable niche but also by mediating physical and biochemical cues. Despite intensive investigations on regeneration, the roles of ECM on fate determination of stem cells in animal with great regenerative potency, such as planarian, remained unclear. Here, we developed a method to decellularizing and isolating extracellular matrix from planarians. Although the isolated scaffold appears translucent, it contains all the internal features, resembling the structure of intact planarian, and which we thus called “ECM-body”. Nuclear staining demonstrated that ECM-body contains very little or no cell remained. Histological sections displayed a well-preserved morphological integrity of the specimen. Scanning electron microscope showed porous surface on ECM-body, potentially suitable for housing cells. Furthermore, our preliminary experiment suggested that ECM-body can be utilized as biomimetic scaffold for cell culture as it may support survival of injected neoblasts.
Exploiting a Mechanical Perturbation of Titin Domain to Identify How Force Field Parameterization Affects Protein Refolding Pathways
Authors: Wang David , Marszalek Piotr E. 
Published: September 2019

AbstractMolecular mechanics force fields have been shown to differ in their predictions of processes such as protein folding. To test how force field differences affect predicted protein behavior, we created a mechanically perturbed model of the beta-stranded I91 titin domain based on atomic force spectroscopy data and examined its refolding behavior using six different force fields. To examine the transferability of the force field discrepancies identified by this model, we compared the results to equilibrium simulations of the weakly helical peptide Ac-(AAQAA)3-NH2. The total simulation time was 80 µs. From these simulations we found significant differences in I91 perturbation refolding ability between force fields. Concurrently, Ac-(AAQAA)3-NH2 equilibration experiments indicated that although force fields have similar overall helical frequencies, they can differ in helical lifetimes. The combination of these results suggests that differences in force field parameterization may allow a more direct transition between the beta and alpha regions of the Ramachandran plot thereby affecting both beta-strand refolding ability and helical lifetimes. Furthermore, the combination of results suggests that using mechanically perturbed models can provide a controlled method to gain more insight into how force fields affect protein behavior.
Mapping the Global Network of Extracellular Protease Regulation inStaphylococcus aureus
Authors: Gimza Brittney D. , Larias Maria I. , Budny Bridget G. , Shaw Lindsey N. 
Published: September 2019

AbstractA primary function of the extracellular proteases ofStaphylococcus aureusis to control the progression of infection by selectively modulating the stability of virulence factors. Consequently, a regulatory network exists to titrate protease abundance/activity, to influence accumulation, or lack thereof, of individual virulence factors. Herein, we comprehensively map this system, exploring regulation of the four protease loci by known and novel factors. In so doing, we determine that seven major elements (SarS, SarR, Rot, MgrA, CodY, SaeR, and SarA) form the primary network of control, with the latter three being the most powerful. We note that expression of aureolysin is largely repressed by these factors, whilst thesploperon is subject to the strongest upregulation of any protease loci, particularly by SarR and SaeR. Furthermore, when exploringscpAexpression, we find it to be profoundly influenced in opposing fashions by SarA (repressor) and SarR (activator). We also present the screening of >100 regulator mutants ofS. aureus, identifying 7 additional factors (ArgR2, AtlR, MntR, Rex, XdrA, Rbf, and SarU) that form a secondary circuit of protease control. Primarily these elements serve as activators, although we reveal XdrA as a new repressor of protease expression. With the exception or ArgR2, each of the new effectors appear to work through the primary network of regulation to influence protease production. Collectively, we present a comprehensive regulatory circuit that emphasizes the complexity of protease regulation and suggest that its existence speaks to the importance of these enzymes toS. aureusphysiology and pathogenic potential.ImportanceThe complex regulatory role of the proteases necessitates very tight coordination and control of their expression. Whilst this process has been well studied, a major oversight has been the consideration of proteases as a single entity, rather than 10 enzymes produced from four different promoters. As such, in this study we comprehensively characterized the regulation of each protease promoter, discovering vast differences in the way each protease operon is controlled. Additionally, we broaden the picture of protease regulation using a global screen to identify novel loci controlling protease activity, uncovering a cadre of new effectors of protease expression. The impact of these elements on the activity of proteases and known regulators was characterized producing a comprehensive regulatory circuit that emphasizes the complexity of protease regulation inStaphylococcus aureus.
Attention to rhythms: sensory-specific constrained sampling of temporal regularities
Authors: Zalta Arnaud , Petkoski Spase , Morillon Benjamin 
Published: September 2019

AbstractThat attention is a fundamentally rhythmic process has recently received abundant empirical evidence. The essence of temporal attention, however, is to flexibly focus in time. Whether this function is hampered by an underlying rhythmic mechanism is unknown. In six interrelated experiments, we behaviourally quantify the sampling capacities of periodic temporal attention during auditory or visual perception. We reveal the presence of limited attentional capacities, with an optimal sampling rate of ~1.4 Hz in audition and ~0.7 Hz in vision. Investigating the motor contribution to temporal attention, we show that it scales with motor rhythmic precision, maximal at ~1.7 Hz. Critically, the motor modulation is beneficial to auditory but detrimental to visual temporal attention. These results are captured by a computational model of coupled oscillators, that reveals the underlying structural constraints governing the temporal alignment between motor and attention fluctuations.
A Ponceau Staining based Dot-Blot Assay for reliable and cost-effective Protein Quantification
Authors: Helbing Dario-Lucas , Böhm Leopold , Cui Yan , Stabenow Leonie Karoline , Morrison Helen 
Published: September 2019

AbstractReliable quantification of protein extracts from tissues can be a challenge e.g. due to interference of the high fat content in tissues of the nervous system. Further problems like under- or overerstimation of protein concentrations in protein quantification kits like the bicinchoninic acid (BCA) assay can occur. In addition, common lysis buffers such as RIPA buffer are known to be unable to solubilize a large amount of proteins (~10-30%) leading to unsatisfactory and unreliable experimental results with techniques such as immunoblotting. In this work, we have developed a Ponceau S staining based protein quantification assay. This assay is compatible with tissues or cells directly lysed in 2x SDS gel loading buffer, containing bromophenolblue, leading to more complete protein extraction. Protein concentrations of several samples can be determined in a fast and cost-effective manner and subsequent experiments (e.g. Western blot) can be performed without loss of proteins. The presented protein quantification method is highly reliable, fast and economical. Using this method, it is possible to save between 2300 to 3200€ per 1000 lysates as compared to the costs of a commercial BCA kit.
Dynactin p150 promotes processive motility of DDB complexes by minimizing diffusional behavior of dynein
Authors: Feng Qingzhou , Gicking Allison M. , Hancock William O. 
Published: September 2019

AbstractCytoplasmic dynein is activated by forming a complex with dynactin and the adaptor protein BicD2. We used Interferometric Scattering (iSCAT) microscopy to track dynein-dynactin-BicD2 (DDB) complexes in vitro and developed a regression-based algorithm to classify switching between processive, diffusive and stuck motility states. We find that DDB spends 65% of its time undergoing processive stepping, 4% undergoing 1D diffusion, and the remaining time transiently stuck to the microtubule. Although the p150 subunit was previously shown to enable dynactin diffusion along microtubules, blocking p150 enhanced the proportion of time DDB diffused and reduced the time DDB processively walked. Thus, DDB diffusive behavior most likely results from dynein switching into an inactive (diffusive) state, rather than p150 tethering the complex to the microtubule. DDB - kinesin-1 complexes, formed using a DNA adapter, moved slowly and persistently, and blocking p150 led to a 70 nm/s plus-end shift in the average velocity, in quantitative agreement with the increase in diffusivity seen in isolated DDB. The data suggest a DDB activation model in which engagement of dynactin p150 with the microtubule promotes dynein processivity, serves as an allosteric activator of dynein, and enhances processive minus-end motility during intracellular bidirectional transport.TOC HighlightDynein-dynactin-BicD2 (DDB) is highly processive, but also shows transient pausing and diffusion, which we analyzed using iSCAT microscopy. Blocking dynactin p150 results in more diffusion of isolated DDB and a plus-end shift of kinesin-1 – DDB complexes. Thus, we conclude that p150 is an allosteric activator of dynein in the DDB complex.
MADloy: Robust detection of mosaic loss of chromosome Y from genotype-array-intensity data
Authors: González Juan R , López-Sánchez Marcos , Cáceres Alejandro , Puig Pere , Esko Tonu , Pérez-Jurado Luis A 
Published: September 2019

AbstractAccurate protocols and methods to robustly detect the mosaic loss of chromosome Y (mLOY) are needed given its reported role in cancer, several age-related disorders and overall male mortality. Intensity SNP-array data have been used to infer mLOY status and to determine its prominent role in male disease. However, discrepancies of reported findings can be due to the uncertainty and variability of the methods used for mLOY detection and to the differences in the tissue-matrix used. We proposed MADloy, the first publicly available software tool that incorporates previous methods and includes a new robust approach, allowing efficient calling in large studies and comparisons between methods. The new method implemented in MADloy optimizes mLOY calling by correctly modeling the underlying reference population with no-mLOY status and incorporating B-deviation information. We observed improvements in the calling accuracy with respect to previous methods, using experimentally validated samples, and an increment in the statistical power to detect associations with disease and mortality, using simulation studies and real dataset analyses. We applied MADloy to detect the increment of mLOY cellularity in blood on 18 individuals after 3 years, and to confirm that its detection in saliva was sub-optimal (41%). We illustrate the use of MADloy to detect the down-regulation genes in the chromosome Y in kidney and bladder tumors with mLOY, and to perform pathway analyses for the detection of mLOY in blood. MADloy is a new software tool implemented in R for easy and robust calling of mLOY status in men aimed to facilitate its study in large epidemiological studies.
Integrated transcriptomic correlation network analysis identifies COPD molecular determinants
Authors: Paci Paola , Fiscon Giulia , Conte Federica , Licursi Valerio , Morrow Jarrett , Hersh Craig , Cho Michael , Castaldi Peter , Glass Kimberly , Silverman Edwin K. , Farina Lorenzo 
Published: September 2019

AbstractChronic obstructive pulmonary disease (COPD) is a heterogeneous and complex syndrome. Network-based analysis implemented by SWIM software can be exploited to identify key molecular switches - called “switch genes” - for disease. Genes contributing to common biological processes or define given cell types are frequently co-regulated and co-expressed, giving rise to expression network modules. Consistently, we found that the COPD correlation network built by SWIM consists of three well-characterized modules: one populated by switch genes, all up-regulated in COPD cases and related to the regulation of immune response, inflammatory response, and hypoxia (like TIMP1, HIF1A, SYK, LY96, BLNK and PRDX4); one populated by well-recognized immune signature genes, all up-regulated in COPD cases; one where the GWAS genes AGER and CAVIN1 are the most representative module genes, both down-regulated in COPD cases. Interestingly, 70% of AGER negative interactors are switch genes including PRDX4, whose activation strongly correlates with the activation of known COPD GWAS interactors SERPINE2, CD79A, and POUF2AF1. These results suggest that SWIM analysis can identify key network modules related to complex diseases like COPD.
Neurocognitive patterns dissociating semantic processing from executive control are linked to more detailed off-task mental time travel
Authors: Wang Hao-Ting , Ping Ho Nerissa Siu , Bzdok Danilo , Bernhardt Boris C. , Margulies Daniel S. , Jefferies Elizabeth , Smallwood Jonathan 
Published: September 2019

1ABSTRACTFeatures of ongoing experience are common across individuals and cultures. However, certain people express specific patterns to a greater extent than others. The current psychological theory assumes that individual differences in thought patterns occur because different types of experience depend on differences in associated neurocognitive mechanisms. Consequently, individual variation in the underlying neurocognitive architecture is hypothesised to determine the ease with which certain thought patterns are generated or maintained. Our study (N=178) tested this hypothesis using multivariate pattern analysis to infer shared variance among measures of cognitive function and neural organisation and examined whether these hidden structures explain reports of the patterns of on-going thoughts people experienced in the lab. We found that relatively better performance on tasks requiring primarily semantic knowledge, rather than executive control, was linked to a neural functional organisation that was associated, via meta-analysis, with task labels related to semantic associations (sentence processing, reading and verbal semantics). Variability of this functional mode predicted significant individual variation in the types of thoughts that individuals experienced in the laboratory: Neurocognitive patterns linked to better performance at tasks that required guidance from semantic representation, rather than those dependent on executive control, were associated with patterns of thought characterised by greater subjective detail and a focus on time periods other than the here and now. These relationships were consistent across different days and did not vary with task condition, indicating they are relatively stable features of an individual’s cognitive profile. Together these data confirm that individual variation in aspects of ongoing experience can be inferred from hidden neurocognitive architecture and demonstrate that performance trade-offs between executive control and long term semantic knowledge are linked to a person’s tendency to imagine situations that transcend the here and now.
Static growth alters PrrF- and 2-alkyl-4(1H)-quinolone regulation of virulence trait expression in Pseudomonas aeruginosa
Authors: Brewer Luke K. , Huang Weiliang , Hackert Brandy , Kane Maureen A. , Oglesby Amanda G. 
Published: September 2019

ABSTRACTPseudomonas aeruginosa is an opportunistic pathogen that is frequently associated with both acute and chronic infections, the latter of which are often polymicrobial. P. aeruginosa possesses a complex regulatory network that modulates nutrient acquisition and virulence, but our knowledge of these networks is largely based on studies with shaking cultures, which are not likely representative of conditions during infection. Here, we provide proteomic, metabolic, and genetic evidence that regulation by iron, a critical metallo-nutrient, is altered in static P. aeruginosa cultures. We identified type VI secretion as a target of iron regulation in P. aeruginosa in static but not shaking conditions, and we present evidence that this regulation occurs via PrrF sRNA-dependent production of 2-alkyl-4(1H)-quinolone metabolites. We further discovered that iron-regulated interactions between P. aeruginosa and a Gram-positive opportunistic pathogen, Staphylococcus aureus, are mediated by distinct factors in shaking versus static bacterial cultures. These results yield new bacterial iron regulation paradigms and highlight the need to re-define iron homeostasis in static microbial communities.
Testosterone and cortisol are negatively associated with ritualized bonding behavior in male macaques
Authors: Rincon Alan V. , Heistermann Michael , Schülke Oliver , Ostner Julia 
Published: September 2019

AbstractNeuroendocrine research on the formation of social bonds has primarily focused on the role of nonapeptides. However, steroid hormones often act simultaneously to either inhibit or facilitate bonding. Testosterone is proposed to mediate a trade-off between male mating effort and nurturing behavior; therefore, low levels are predicted during periods of nurturing infant care and social bonding. In species where social bonding and support regulates hypothalamic-pituitary-adrenal axis activity, we also expect glucocorticoid levels to be low during bonding periods. We investigated how immunoreactive urinary testosterone (iuT) and cortisol (iuC) were related to triadic male-infant-male interactions – a ritualized male bonding behavior – as well as infant care in male Barbary macaques (Macaca sylvanus). We collected >3000 hours of behavioral observation data during full-day focal animal follows from 14 adult males and quantified iuT and iuC from 650 urine samples. As predicted, both iuT and iuC were negatively correlated with rates of triadic interactions within-subjects in the hours preceding urination. We found no relationship between iuT and iuC with triadic interactions between-subjects. Infant care was weakly positively correlated to iuT and iuC within-subjects, but not between-subjects. The observed negative relationship between iuT and triadic interactions may be beneficial to lower competitive tendencies between adult males and to not inhibit bond formation. Lowered iuC could reflect increased bonding and perceived social support as triadic interactions predict future coalition formation in this species. Additionally, lowered iuC may be reflective of buffered tensions between males. The positive relationship of iuT and iuC with infant care suggests that the handling of infants in may be less nurturing but rather protective or competitive in this species. Measuring steroid hormones in relation to bonding and nurturing can help us interpret behaviors within the ecological contexts that they occur.
Acid-Sensing Ion Channels Mediate Type III Adenylyl Cyclase-Independent Acid-Sensing of Mouse Olfactory Sensory Neurons
Authors: Yang Juan , Qiu Liyan , Strobel Matthew , Kabel Amanda , Zha Xiangming , Chen Xuanmao 
Published: September 2019

AbstractAcids can disturb the ecosystem of wild animals through altering their olfaction and olfaction-related survival behaviors. It is known that the main olfactory epithelia (MOE) of mammals rely on odorant receptors and type III adenylyl cyclase (AC3) to detect general odorants. However, it is unknown how the olfactory system sense protons or acidic odorants. Here we show that the mouse MOE responded to acidic volatile stimuli in the presence and the absence of AC3. Acetic acid-induced electro-olfactogram (EOG) responses in wild type (WT) MOE can be dissected into two components: one dependent on the AC3-mediated cAMP pathway and the other not. MOE of AC3 knockout (KO) mice retained an acid-evoked EOG response but failed to respond to an odor mix. The acid-evoked responses of the AC3 KO could be blocked by diminazene, an inhibitor of acid-sensing ion channels (ASICs), but not by forskolin/IBMX, which desensitize the cAMP pathway. AC3 KO mice lost their sensitivity to detect pungent odorants but maintained sniffing behavior to acetic acid. Immunofluorescence staining demonstrated that ASIC1 proteins were highly expressed in olfactory sensory neurons (OSNs), mostly enriched in the knobs, dendrites, and somata, but not in olfactory cilia. Moreover, mice exhibited reduced preference to attractive objects when placed in an environment with acidic volatiles. Together, we conclude that the mouse olfactory system has a non-conventional, ASICs-mediated mechanism for acid-sensing. Acid stimulation of ASICs may unselectively depolarize different OSNs and interfere with the anatomical logic for odor perception.