bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity and composition of methanotroph communities in caves
Authors: Webster Kevin D. , Schimmelmann Arndt , Drobniak Agnieszka , Mastalerz Maria , Lagarde Laura Rosales , Boston Penelope J. , Lennon Jay T. 
Published: September 2018

ABSTRACTMethane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated that methanotrophs are abundant and contribute to CH4dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98 %) of the samples, including cave sites where CH4concentrations were at or below detection limits (≤ 0.3 ppmv). We identified a core methanotroph community among caves that was comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4concentrations varied. We also observed that methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Last, the relative abundance of methanotrophs was positively correlated with cave-air CH4concentrations suggesting that these microorganisms contribute to CH4flux in subterranean ecosystems.IMPORTANCERecent observations have shown that the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14 % of Earth’s land surface area, and therefore may represent a potentially important, but overlooked CH4sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show that the members of the USC-γclade are dominant in cave communities and can easily disperse through the environment, that methanotroph relative abundance was correlated with local scale mineralogy of soils, and that the relative abundance of methanotrophs was positively correlated with CH4concentrations in cave air.
A tale of two species: human and peafowl interactions in human dominated landscape influence each other’s behaviour
Authors: Paranjpe Dhanashree , Dange Priyanka 
Published: September 2018

AbstractWild life is increasingly coming in contact with humans in many parts of the world. Human perception of wild life may be an important factor in population management and conservation practices in urban and semi-urban areas. Human attitude towards bird species may vary from non-violent coexistence to a perception of birds as pests. Based on the data collected from survey interviews, we studied the perceptions of local communities in Rajasthan, India towards Indian Peafowl. Local communities in Rajasthan reported Indian Peafowl as crop pest and this perception varied across seasons. The crop loss incurred due to Indian Peafowl also varied across seasons according to the respondents. Despite reporting peafowls as a crop pest, locals regularly offered grains for them as a traditional practice. Thus, at our study sites locals have mostly positive perception about Indian peafowl around them.Food provisioning by local human population influenced diet composition and time-budget of Indian Peafowls at food provision and non-provision sites. Sites at which food provisioning was less or absent, peafowl spent more time in walking in search of food and more than half of their diet consisted of natural food. In contrast, the sites at which plenty of grains were available, time spent in walking was significantly less, while time spent in feeding was significantly more; and over 70% of their diet consisted of carbohydrate and protein-rich provisioned grains. Food provisioning changed the benefit: cost ratio (measured as time spent in feeding to time spent in all other behaviours) between provision and non-provision sites. Thus, food provisioning by humans can change feeding ecology of native Indian peafowl populations, while the presence of peafowl in human dominated landscape changes how humans interact with wild life around them.
Genetic correlation between sea age at maturity and iteroparity in Atlantic salmon
Authors: Aykanat Tutku , Ozerov Mikhail , Vähä Juha-Pekka , Orell Panu , Niemelä Eero , Erkinaro Jaakko , Primmer Craig R. 
Published: September 2018

AbstractGenetic correlations in life history traits may result in unpredictable evolutionary trajectories if not accounted for in life-history models. Iteroparity (the reproductive strategy of reproducing more than once) in Atlantic salmon (Salmo salar) is a fitness trait with substantial variation within and among populations. In the Teno River in northern Europe, iteroparous individuals constitute an important component of many populations and have experienced a sharp increase in abundance in the last 20 years, partly overlapping with a general decrease in age structure. The physiological basis of iteroparity bears similarities to that of age at first maturity, another life history trait with substantial fitness effects in salmon. Sea age at maturity in Atlantic salmon is controlled by a major locus around thevgll3gene, and we used this opportunity demonstrate that the two traits are genetically correlated around this genome region. The odds ratio of survival until second reproduction was up to 2.4 (1.8-3.5 90% CI) times higher for fish with the early-maturingvgll3genotype (EE) compared to fish with the late-maturing genotype(LL). The association had a dominance architecture, although the dominant allele was reversed in the late-maturing group compared to younger groups that stayed only one year at sea before maturation.Post hocanalysis indicated that iteroparous fish with theEEgenotype had accelerated growth prior to first reproduction compared to first-time spawners, across all age groups, while this effect was not detected in fish with theLLgenotype. These results broaden the functional link around thevgll3genome region and help us understand constraints in the evolution of life history variation in salmon. Our results further highlight the need to account for genetic correlations between fitness traits when predicting demographic changes in changing environments.
The true size of placebo analgesia: Concordant neural and behavioural measures of placebo analgesia during experimental acute pain
Authors: Valentini E , Aglioti SM , Chakrabarti B 
Published: September 2018

Abstract‘Placebo analgesia’ refers to the reduction of pain following the administration of an inactive treatment. While most clinical trials compare a drug treatment against a placebo to determine the efficacy of the analgesic, most experimental studies of placebo analgesia do not include a real analgesic condition. A direct comparison of placebo against a real analgesic can inform us about the true size of the placebo effect. To this end, we aimed to provide a robust estimate of placebo analgesia by contrasting the effect of pain relief expectation from an inert cream (vaseline) against a real topical analgesic agent (lidocaine) applied on two different limbs and their respective control conditions. Pain reports and electroencephalography (EEG) responses triggered by laser nociceptive stimulation were collected. Forty typical healthy adults were enrolled in a double-blind randomized within-subject study where a standard placebo induction script of verbal suggestions in a sham medical setting was used to enhance the expectation on treatment outcome. In line with the earliest studies of placebo analgesia, majority (30 of 40) of participants was placebo responders, i.e. they reported lower pain to the placebo treatment. Placebo responders reported low pain and displayed low laser evoked potentials (LEPs) amplitude for both the analgesic and placebo treatment limbs compared to the respective control limbs. Placebo analgesia correlated positively with the amplitude of the LEPs, thus establishing convergent validity of the findings. This study provides a robust estimate of the neural and behavioural measures of placebo analgesia, in comparison to a real analgesic. These estimates can help inform the quantitative criteria for similar neural and behavioural measures in assessing the effectiveness of a real drug in placebo controlled trials.
Chemical signatures of honey bee group membership develop via a socially-modulated innate process
Authors: Vernier Cassondra L. , Krupp Joshua J. , Marcus Katelyn , Hefetz Abraham , Levine Joel D. , Ben-Shahar Yehuda 
Published: September 2018

AbstractLarge social insect colonies exhibit a remarkable ability for recognizing group members via colony-specific cuticular hydrocarbon (CHC) pheromonal signatures. Previous work suggested that in some ant species colony-specific signatures are generated through a “gestalt” mechanism via the passive transfer and homogenization of CHCs across all individual members of the colony. In contrast, we demonstrate that nestmate recognition cues of worker honey bees (Apis mellifera) mature in foragers via a sequence of stereotypic age-dependent quantitative and qualitative chemical transitions, which are driven by intrinsic biosynthetic pathways. Therefore, in contrast to predictions of the “Gestalt” model, nestmate recognition cues in honey bee colonies do not represent a passive “average” signature that is carried and recognized by all colony members. Instead, specific colony members develop the relevant cues via an innately-determined developmental program that can be modulated by colony-specific social environmental factors.
Reduced Medial Frontal Positivity During the Stimulus-Response Interval Precedes Action Errors and Explains Task Deficits in Attention-Deficit Hyperactivity Disorder
Authors: Burwell Scott J. , Makeig Scott , Iacono William G. , Malone Stephen M. 
Published: September 2018

AbstractBrain mechanisms responsible for errors during cognitive tasks are poorly understood, particularly in adolescents with attention-deficit hyperactivity disorder (ADHD). Using subject-specific multimodal imaging (EEG, MRI, behavior) during flanker task performance by a sample of 94 human adolescents (mean age = 15.5 years, 50% female) with varying degrees of ADHD symptomatology, we examined the degree to which amplitudes of source-resolved event-related potentials (ERPs) from brain independent components within a critical (but often ignored) period in the action selection process, the stimulus-response interval, predicted motor response errors (across trials) and error rates (across individuals). Reduced amplitudes of Frontocentral P3 (peaking at approximately 390 milliseconds in stimulus-locked ERPs) and Pre-Movement Positivity (PMP, peaking at approximately 110 milliseconds pre-response in response-locked ERPs) in projections from posterior medial frontal cortex (pMFC) predicted erroneous responses, and reduced amplitude of PMP predicted a larger participant error rate. After regressing stimulus-from response-locked ERPs, we concluded that errors primarily depended upon response selection processes reflected in PMP amplitude. Finally, mediation analyses showed that smaller PMPs on correct response trials was associated with the higher frequency of errors committed by adolescents with more ADHD symptoms. These results bolster the importance of pMFC in action selection and support the possible value of using PMP as an intervention target to remediate performance deficits in ADHD.
Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity
Authors: Li Pan , Wei Yifan , Mei Miao , Tang Lei , Sun Lei , Huang Wenze , Zhou Jianyu , Zou Chunlin , Zhang Shaojun , Qin Cheng-feng , Jiang Tao , Dai Jianfeng , Tan Xu , Zhang Qiangfeng Cliff 
Published: September 2018

SUMMARYSince its outbreak in 2007, Zika virus (ZIKV) has become a global health threat that causes severe neurological conditions. Here we perform a comparativein vivostructural analysis of the RNA genomes of two ZIKV strains to decipher the regulation of their infection at the RNA level. Our analysis identified both known and novel functional RNA structural elements. We discovered a functional long-range intramolecular interaction specific for the Asian epidemic strains, which contributes to their infectivity. Our findings illuminate the structural basis of ZIKV regulation and provide a rich resource for the discovery of RNA structural elements that are important for ZIKV infection.
Embryonic Exposure to Valproic Acid impairs Social Predispositions for Dynamic Cues of Animate Motion in Newly-Hatched Chicks
Authors: Lorenzi Elena , Pross Alessandra , Rosa-Salva Orsola , Versace Elisabetta , Sgadò Paola , Vallortigara Giorgio 
Published: September 2018

AbstractPredispositions to preferentially orient towards cues associated with social partners, such as face-like stimuli or biological and animate motion, appear to guide social behavior from the onset of life. These predispositions have been documented in several vertebrate species including human neonates, young monkeys and newly-hatched domestic chicks. Human newborns at high familiar risk of Autism Spectrum Disorder (ASD) show a remarkable deficit in their attention toward these predisposed stimuli, either static and dynamic, compared to newborns at low risk. A previous study showed that prenatal exposure to valproic acid (VPA) (that in humans increases the risk of developing ASD) impairs the chicks’ predisposition to approach naturalistic social stimuli that convey static configurations of features (a stuffed hen), without impairing general cognitive and learning abilities. Here we investigated the effect of VPA exposure on another class of social predispositions, i.e. the spontaneous preference to approach self-propelled objects, namely objects that display autonomous changes in speed. We observed that the preference for stimuli displaying autonomous changes in speed was impaired in VPA-compared to vehicle-injected chicks. Our results indicate an effect of VPA on the development of predisposed orienting mechanisms towards dynamic stimuli, that could be used to investigate the molecular and neurobiological mechanisms underlying ASD early symptoms.
Network analysis of canine brain morphometry links tumour risk to oestrogen deficiency and accelerated brain ageing
Authors: Rzechorzek Nina M. , Saunders Olivia M. , Hisco Lucy , Schwarz Tobias , Marioni-Henry Katia , Argyle David J. , Schoenebeck Jeffery J. , Freeman Tom C. 
Published: September 2018

AbstractBackgroundStructural ‘brain age’ is a valuable but complex biomarker for several brain disorders. The dog is an unrivalled comparator for neurological disease modeling, however brain phenotypic diversity among pedigrees creates computational and statistical challenges.MethodsWe applied unbiased network correlation analysis in dogs to explore complex interactions between brain morphometrics, patient metadata, and neurological disease. Twenty-four parameters measured from each of 286 brain magnetic resonance imaging scans generated 9,438 data points that were used to cluster canine patients according to their brain morphometry profiles. The network was then explored for statistically significant enrichments within breed, sex, age, and diagnostic categories.FindingsMorphometric comparisons revealed an advanced ‘aged-brain’ profile in the Boxer breed, consisting of a small brain length, width, and volume, combined with ventriculomegaly. Key features of this profile were paralleled in neutered female dogs which, relative to un-neutered females, had an 11-fold greater risk of developing primary brain tumours. Enrichment analysis confirmed that Boxers and geriatric individuals were enriched for brain tumour diagnoses, despite a lack of geriatric Boxers within the cohort.InterpretationThese findings suggest that accelerated brain ageing might contribute to tumour risk in Boxers and may be influenced by oestrogen deficiency — a risk factor for dementia and brain tumours in humans. We propose that morphometric features of brain ageing in dogs, like humans, might better predict neurological disease risk than a patient’s chronological age.FundingWellcome Trust Integrated Training Fellowship for Veterinarians (096409/Z/11/Z to N.M.R) and an MSD Animal Health Connect Bursary (to O.M.S.).
Revealing the critical regulators of cell identity in the mouse cell atlas
Authors: Suo Shengbao , Zhu Qian , Saadatpour Assieh , Fei Lijiang , Guo Guoji , Yuan Guo-Cheng 
Published: September 2018

AbstractRecent progress in single-cell technologies has enabled the identification of all major cell types in mouse. However, for most cell types, the regulatory mechanism underlying their identity remains poorly understood. By computational analysis of the recently published mouse cell atlas data, we have identified 202 gene regulatory networks whose activities are highly variable across different cell types, and more importantly, predicted a small set of essential regulators for each of over 800 cell types in mouse for the first time. Systematic validation by automated literature- and data-mining provides strong additional support for our predictions. Thus, these predictions serve as a valuable resource that would be useful for the broad biological community. Finally, we have built a user-friendly, interactive, web-portal to enable users to navigate this mouse cell network atlas.
Heterogeneity of Sonic Hedgehog response dynamics and fate specification in single neural progenitors
Authors: Xiong Fengzhu , Tentner Andrea R. , Nandagopal Sandy , Hiscock Tom W. , Huang Peng , Megason Sean G. 
Published: September 2018

SUMMARYDuring neural tube patterning, a gradient of Sonic hedgehog (Shh) signaling specifies ventral progenitor fates. The cellular response to Shh is processed through a genetic regulatory network (GRN) to specify distinct fate decisions. This process integrates Shh response level, duration and other inputs and is affected by noise in signaling and cell position. How reliably Shh response profile predicts the fate choice of a single cell is unclear. Here we use live imaging to track neural progenitors in developing zebrafish and quantify both Shh and fate reporters in single cells over time. We found that there is significant heterogeneity between Shh response and fate choice in single cells. We quantitatively modeled reporter intensities to obtain single cell response levels over time and systematically evaluated their correlation with cell fate specification. Motor neuron progenitors (pMN) exhibit a high degree of variability in their Shh responses, which is particularly prominent in the posterior neural tube where the Shh response dynamics are similar to those of the more ventrally fated lateral floor plate cells (LFPs). Our results highlight the precision limit of morphogen-interpretation GRNs in small and dynamic target cell fields.
Cell type-specific complement expression from healthy and diseased retinae
Authors: Pauly Diana , Schäfer Nicole , Grassmann Felix , Pfaller Anna M. , Straub Tobias , Weber Bernhard H. F. , Hauck Stefanie M. , Grosche Antje 
Published: September 2018

AbstractRetinal degeneration is associated with complement system activation, but retinal sources of complement are unknown. Here, we describe the human and murine complement transcriptomes of Müller cells, microglia/macrophages, vascular cells, neurons and retinal pigment epithelium (RPE) in health and disease. All cell populations expressedc1s, c3, cfb, cfp, cfhandcfi. Murine Müller cells contributed the highest amount of complement activators (c1s, c3, cfb). RPE mainly expressedcfh,whilecfiandcfptranscripts were most abundant in neurons. The main complement negative regulator in the human retina wascfi, whilecfhdominated in the murine retina. Importantly, the expression ofc1s, cfb, cfp, cfiincreased and that ofcfhdecreased with aging. Impaired photoreceptor recycling led to an enhancedc3expression in RPE and to a reducedcfiexpression in microglia/macrophages. Expression of complement components was massively upregulated after transient retinal ischemia in murine microglia, Müller cells and RPE. The individual signature of complement expression in distinct murine and human retinal cell types indicates a local, well-orchestrated regulation of the complement system in both species.
Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in non-model species
Authors: Plese Bruna , Rossi Maria Eleonora , Kenny Nathan James , Taboada Sergi , Koutsouveli Vasiliki , Riesgo Ana 
Published: September 2018

AbstractMitochondrial resources are of known utility to many fields of phylogenetic, population and molecular biology. Their combination of faster and slower-evolving regions and high copy number enables them to be used in many situations where other loci are unsuitable, with degraded samples and after recent speciation events.The advent of next-generation sequencing technologies (and notably the Illumina platform) has led to an explosion in the number of samples that can be studied at transcriptomic level, at relatively low cost. Here we describe a robust pipeline for the recovery of mitochondrial genomes from these RNA-seq resources. This pipeline can be used on sequencing of a variety of depths, and reliably recovers the protein coding and ribosomal gene complements of mitochondria from almost any transcriptomic sequencing experiment. The complete sequence of the mitochondrial genome can also be recovered when sequencing is performed in sufficient depth. We evidence the efficacy of our pipeline using data from a number of non-model invertebrates of four disparate phyla, namely Porifera, Nemertea, Mollusca and Annelida. Interestingly, among our poriferan data, where microbiological symbionts are known empirically to make mitochondrial assembly difficult, this pipeline proved especially useful.Our pipeline will allow the recovery of mitochondrial data from a variety of previously-sequenced samples, and add an additional angle of enquiry to future RNA-seq efforts, simplifying the process of mitochondrial genome assembly for even the most recalcitrant clades and adding this data to the scientific record for a range of future uses.
Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type-2 diabetes
Authors: Diamanti Klev , Cavalli Marco , Pan Gang , Pereira Maria J , Kumar Chanchal , Skrtic Stanko , Grabherr Manfred , Risérus Ulf , Eriksson Jan W , Komorowski Jan , Wadelius Claes 
Published: September 2018

ABSTRACTType-2 diabetes (T2D) mellitus is a complex metabolic disease commonly caused by insulin resistance in several tissues. We performed a matched two-dimensional metabolic screening in tissue samples from a cohort of 43 multi-organ donors. The intra-individual analysis was assessed across five key-metabolic tissues (serum, adipose tissue, liver, pancreatic islets and muscle), and the inter-individual across three different groups reflecting T2D progression. We identified 92 metabolites differing significantly between non-diabetes and T2D subjects. Carnitines were significantly higher in liver, while lysophosphatidylcholines significantly lower in muscle and serum. An investigation of the progression to overt T2D showed that deoxycholic acid glycine conjugate was significantly higher in liver of pre-diabetes samples while additional increase in T2D was insignificant. A subset of lysophosphatidylcholines were significantly lower in the muscle of pre-diabetes subjects. Overall, the analysis of this unique dataset can increase the understanding of the metabolic interplay between organs in the development of T2D.