bluuebunny/crossref_metadata_2025_split huggingface dataset:
Different pioneer plant species select specific rhizosphere bacterial communities in a high mountain environment
Authors: Ciccazzo Sonia , Esposito Alfonso , Rolli Eleonora , Zerbe Stefan , Daffonchio Daniele , Brusetti Lorenzo 
Published: July 2014

Abstract
The rhizobacterial communities of 29 pioneer plants belonging to 12 species were investigated in an alpine ecosystem to assess if plants from different species could select for specific rhizobacterial communities. Rhizospheres and unvegetated soils were collected from a floristic pioneer stage plot at 2,400 m a.s.l. in the forefield of Weisskugel Glacier (Matsch Valley, South Tyrol, Italy), after 160 years of glacier retreat. To allow for a culture-independent perspective, total environmental DNA was extracted from both rhizosphere and bare soil samples and analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and Denaturing Gradient Gel Electrophoresis (DGGE). ARISA fingerprinting showed that rhizobacterial genetic structure was extremely different from bare soil bacterial communities while rhizobacterial communities clustered strictly together according to the plant species. Sequencing of DGGE bands showed that rhizobacterial communities were mainly composed of Acidobacteria and Proteobacteria whereas bare soil was colonized by Acidobacteria and Clostridia. UniFrac significance calculated on DGGE results confirmed the rhizosphere effect exerted by the 12 species and showed different bacterial communities (P < 0.05) associated with all the plant species. These results pointed out that specific rhizobacterial communities were selected by pioneer plants of different species in a high mountain ecosystem characterized by oligotrophic and harsh environmental conditions, during an early primary succession.
The Kardashian index: a measure of discrepant social media profile for scientists
Authors: Hall Neil 
Published: July 2014

AbstractIn the era of social media there are now many different ways that a scientist can build their public profile; the publication of high-quality scientific papers being just one. While social media is a valuable tool for outreach and the sharing of ideas, there is a danger that this form of communication is gaining too high a value and that we are losing sight of key metrics of scientific value, such as citation indices. To help quantify this, I propose the ‘Kardashian Index’, a measure of discrepancy between a scientist’s social media profile and publication record based on the direct comparison of numbers of citations and Twitter followers.
A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening
Authors: Jeon Jouhyun , Nim Satra , Teyra Joan , Datti Alessandro , Wrana Jeffrey L , Sidhu Sachdev S , Moffat Jason , Kim Philip M 
Published: July 2014

AbstractWe present an integrated approach that predicts and validates novel anti-cancer drug targets. We first built a classifier that integrates a variety of genomic and systematic datasets to prioritize drug targets specific for breast, pancreatic and ovarian cancer. We then devised strategies to inhibit these anti-cancer drug targets and selected a set of targets that are amenable to inhibition by small molecules, antibodies and synthetic peptides. We validated the predicted drug targets by showing strong anti-proliferative effects of both synthetic peptide and small molecule inhibitors against our predicted targets.
Tumor Stage After Neoadjuvant Chemotherapy Determines Survival After Surgery for Adenocarcinoma of the Esophagus and Esophagogastric Junction
Authors: Davies Andrew R. , Gossage James A. , Zylstra Janine , Mattsson Fredrik , Lagergren Jesper , Maisey Nick , Smyth Elizabeth C. , Cunningham David , Allum William H. , Mason Robert C. 
Published: July 2014

Purpose Neoadjuvant chemotherapy is established in the management of most resectable esophageal and esophagogastric junction adenocarcinomas. However, assessing the downstaging effects of chemotherapy and predicting response to treatment remain challenging, and the relative importance of tumor stage before and after chemotherapy is debatable. Methods We analyzed consecutive resections for esophageal or esophagogastric junction adenocarcinomas performed at two high-volume cancer centers in London between 2000 and 2010. After standard investigations and multidisciplinary team consensus, all patients were allocated a clinical tumor stage before treatment, which was compared with pathologic stage after surgical resection. Survival analysis was conducted using Kaplan-Meier analysis and Cox regression analysis. Results Among 584 included patients, 400 patients (68%) received neoadjuvant chemotherapy. Patients with downstaged tumors after neoadjuvant chemotherapy experienced improved survival compared with patients without response (P < .001), and such downstaging (hazard ratio, 0.43; 95% CI, 0.31 to 0.59) was the strongest independent predictor of survival after adjusting for patient age, tumor grade, clinical tumor stage, lymphovascular invasion, resection margin status, and surgical resection type. Patients downstaged by chemotherapy, compared with patients with no response, experienced lower rates of local recurrence (6% v 13%, respectively; P = .030) and systemic recurrence (19% v 29%, respectively; P = .027) and improved Mandard tumor regression scores (P < .001). Survival was strongly dictated by stage after neoadjuvant chemotherapy, rather than clinical stage at presentation. Conclusion The stage of esophageal or esophagogastric junction adenocarcinoma after neoadjuvant chemotherapy determines prognosis rather than the clinical stage before neoadjuvant chemotherapy, indicating the importance of focusing on postchemotherapy staging to more accurately predict outcome and eligibility for surgery. Patients who are downstaged by neoadjuvant chemotherapy benefit from reduced rates of local and systemic recurrence.
MiR-153 targets the nuclear factor-1 family and protects against teratogenic effects of ethanol exposure in fetal neural stem cells
Authors: Tsai Pai-Chi , Bake Shameena , Balaraman Sridevi , Rawlings Jeremy , Holgate Rhonda R. , Dubois Dustin , Miranda Rajesh C. 
Published: July 2014

ABSTRACT
Ethanol exposure during pregnancy is an established cause of birth defects, including neurodevelopmental defects. Most adult neurons are produced during the second trimester-equivalent period. The fetal neural stem cells (NSCs) that generate these neurons are an important but poorly understood target for teratogenesis. A cohort of miRNAs, including miR-153, may serve as mediators of teratogenesis. We previously showed that ethanol decreased, while nicotine increased miR-153 expression in NSCs. To understand the role of miR-153 in the etiology of teratology, we first screened fetal cortical NSCs cultured ex vivo, by microarray and quantitative RT-PCR analyses, to identify cell-signaling mRNAs and gene networks as important miR-153 targets. Moreover, miR-153 over-expression prevented neuronal differentiation without altering neuroepithelial cell survival or proliferation. Analysis of 3′UTRs and in utero over-expression of pre-miR-153 in fetal mouse brain identified Nfia (nuclear factor-1A) and its paralog, Nfib, as direct targets of miR-153. In utero ethanol exposure resulted in a predicted expansion of Nfia and Nfib expression in the fetal telencephalon. In turn, miR-153 over-expression prevented, and partly reversed, the effects of ethanol exposure on miR-153 target transcripts. Varenicline, a partial nicotinic acetylcholine receptor agonist that, like nicotine, induces miR-153 expression, also prevented and reversed the effects of ethanol exposure. These data collectively provide evidence for a role for miR-153 in preventing premature NSC differentiation. Moreover, they provide the first evidence in a preclinical model that direct or pharmacological manipulation of miRNAs have the potential to prevent or even reverse effects of a teratogen like ethanol on fetal development.
Deafness in occludin-deficient mice with dislocation of tricellulin and progressive apoptosis of the hair cells
Authors: Kitajiri Shin-ichiro , Katsuno Tatsuya , Sasaki Hiroyuki , Ito Juichi , Furuse Mikio , Tsukita Shoichiro 
Published: July 2014

ABSTRACT
Occludin is the first identified protein in the tight junction (TJ), but its function has remained for the most part obscure. TJs have been demonstrated to play important roles in the inner ear function, and occludin is expressed in all the epithelial TJs in the inner ear. Thus, we examined the inner ears of occludin-deficient (Occ−/−) mice. Although inner ears initially developed normally in Occ−/− mice, apoptosis occurs in hair cells in the organ of Corti around day 12 after birth, and deafness develops. Since hair cell degeneration was not observed in cochlear explant cultures of Occ−/− mice, environmental changes were considered to be the trigger of cell death. As for the vestibular system, both the morphologies and functions are normal in Occ−/− mice. These phenotypes of Occ−/− mice are very similar with those of claudin-14 or claudin-9 deficient mice, leading us to speculate on the existence of imbalance induced by TJ abnormalities, such as localized ionic components. Moreover, the occludin deficiency led to dislocalization of tricellulin, a gene responsible for human deafness DFNB49. The deafness in Occ−/− mice may be due to this dislocalization of tricellulin.
Potentiated Hsp104 variants suppress toxicity of diverse neurodegenerative disease-linked proteins
Authors: Jackrel Meredith E. , Shorter James 
Published: July 2014

Abstract
Protein misfolding is implicated in numerous lethal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and Parkinson disease (PD). There are no therapies that reverse these protein-misfolding events. We aim to apply Hsp104, a hexameric AAA+ protein from yeast, to target misfolded conformers for reactivation. Hsp104 solubilizes disordered aggregates and amyloid, but has limited activity against human neurodegenerative disease proteins. Thus, we have previously engineered potentiated Hsp104 variants that suppress aggregation, proteotoxicity and restore proper protein localization of ALS and PD proteins in Saccharomyces cerevisiae, and mitigate neurodegeneration in an animal PD model. Here, we establish that potentiated Hsp104 variants possess broad substrate specificity and, in yeast, suppress toxicity and aggregation induced by wild-type TDP-43, FUS and α-synuclein, as well as missense mutant versions of these proteins that cause neurodegenerative disease. Potentiated Hsp104 variants also rescue toxicity and aggregation of TAF15 but not EWSR1, two RNA-binding proteins with a prion-like domain that are connected with development of ALS and frontotemporal dementia. Thus, potentiated Hsp104 variants are not entirely non-specific. Indeed, they do not unfold just any natively folded protein. Rather, potentiated Hsp104 variants are finely tuned to unfold proteins bearing short unstructured tracts that are not recognized by wild-type Hsp104. Our studies establish the broad utility of potentiated Hsp104 variants.
Body size effects on the oxygen-sensitivity of dragonfly flight
Authors: Henry Joanna Randyl , Harrison Jon F. 
Published: July 2014

AbstractOne hypothesis for the small size of insects relative to vertebrates, and the existence of giant fossil insects, is that atmospheric oxygen levels constrain insect body sizes because oxygen delivery is more challenging in larger insects. This study tested this hypothesis in dragonflies by measuring the oxygen-sensitivity of flight metabolic rates and behavior during hovering for 11 species of dragonflies that ranged in mass by an order of magnitude. We measured flight times and flight metabolic rates in 7 oxygen concentrations ranging from 30% to 2.5% to assess the sensitivity of their flight to atmospheric oxygen. We also assessed the oxygen-sensitivity of flight in low-density air (nitrogen replaced with helium) in order to increase the metabolic demands of hovering flight. Lowered atmospheric densities did induce higher flight metabolic rates. Flight behavior was more sensitive to decreasing oxygen levels than flight metabolic rate. The oxygen-sensitivity of flight metabolic rates and behaviors were not correlated with body size, indicating that larger insects are able to maintain oxygen supply-to-demand even during flight.
Mitochondrial uncoupling as a regulator of life history trajectories in birds: An experimental study in the zebra finch
Authors: Stier Antoine , Bize Pierre , Roussel Damien , Schull Quentin , Massemin Sylvie , Criscuolo Francois 
Published: July 2014

Abstract
Mitochondria have a fundamental role in the transduction of energy from food into ATP. The coupling between food oxidation and ATP production is however never perfect but may nevertheless be of evolutionary significance. The 'uncoupling to survive' hypothesis suggests that 'mild' mitochondrial uncoupling evolved as a protective mechanism against the excessive production of damaging reactive oxygen species (ROS). Because resource allocation and ROS production are thought to shape animal life histories, alternative life history trajectories might be driven by individual variation in the degree of mitochondrial uncoupling. We tested this hypothesis in a small bird species, the zebra finch (Taeniopygia guttata), by treating adults with the artificial mitochondrial uncoupler 2,4-dinitrophenol (DNP) over a 32-months period. In agreement with our expectations, the uncoupling treatment increased metabolic rate. However, we found no evidence that treated birds enjoyed lower oxidative stress levels or greater survival rates, in contrast to previous results in other taxa. In vitro experiments revealed lower sensitivity of ROS production to DNP in mitochondria isolated from skeletal muscles of zebra finch than mouse. In addition, we found significant reductions in the number of eggs laid and in the inflammatory immune response in treated birds. Altogether, our data suggest that the 'uncoupling to survive' hypothesis may not be applicable for zebra finches, presumably due to lower effects of mitochondrial uncoupling on mitochondrial ROS production in birds than mammals. Mitochondrial uncoupling appeared nevertheless as a potential life-history regulator of traits such as fecundity and immunity at adulthood, even with food supplied ad-libitum.
Host orientation using volatiles in the phoretic nematode Caenorhabditis japonica
Authors: Okumura Etsuko , Yoshiga Toyoshi 
Published: July 2014

Abstract
Host orientation is the most important step in host-searching nematodes; however, information on direct cues from hosts to evoke this behavior is limited. Caenorhabditis japonica establishes a species-specific phoresy with Parastrachia japonensis. Dauer larvae (DL), the non-feeding and phoretic stage of C. japonica, are predominantly found on female phoretic hosts, but the mechanisms underlying the establishment of this phoresy remain unknown. To determine if C. japonica DL are able to recognize and orient themselves to a host using a volatile cue from the host, we developed a Y-tube olfactory assay system in which C. japonica DL were significantly attracted to the air from P. japonensis but not to the air from three other insects or to CO2. These results demonstrated that C. japonica DL utilize volatiles for host recognition and orientation and that the presence of a specific volatile kairomone released by the host attracts C. japonica DL.
A superfast muscle in the complex sonic apparatus of Ophidion rochei (Ophidiiformes): histological and physiological approaches
Authors: Kéver Loïc , Boyle Kelly S. , Dragičević Branko , Dulčić Jakov , Parmentier Eric 
Published: July 2014

Abstract
In teleosts, superfast muscles are generally associated with the swimbladder wall whose vibrations result in sound production. In Ophidion rochei, three pairs of muscles were named 'sonic' because their contractions affect swimbladder position: the dorsal sonic muscle (DSM), the intermediate sonic muscle (ISM), and the ventral sonic muscle (VSM). These muscles were investigated thanks to electron microscopy and electromyography in order to determine their function in sound production. Fibers of the VSM and DSM were much thinner than the fibers of the ISM and epaxial musculature. However, only VSM fibers had the typical ultrastructure of superfast muscles: low proportion of myofibrils, and high proportions of sarcoplasmic reticulum and mitochondria. In females, each sound onset was preceded by the onset of electrical activity in the VSM and the DSM (ISM was not tested). The electromyograms of the VSM were very similar to the waveforms of the sounds: means for the pulse period were 3.6±0.5 ms and 3.6±0.7 ms, respectively. This shows that the fast VSM (ca. 280 Hz) is responsible for the pulse period and fundamental frequency of female sounds. DSM electromyograms were generally characterized by one or two main peaks followed by periods of lower electrical activity which suggests a sustained contraction over the course of the sound. The fiber morphology of the ISM and its antagonistic position relative to the DSM are not indicative of a muscle capable of superfast contractions. Overall, this study experimentally shows the complexity of the sound production mechanism in the nocturnal fish O. rochei.
Parasitic and immune-modulation of flight activity in honey bees tracked with optical counters
Authors: Alaux Cédric , Crauser Didier , Pioz Maryline , Saulnier Cyril , Le Conte Yves 
Published: July 2014

AbstractHost-parasite interactions are often characterized by changes in the host behaviour, which are either beneficial to the parasite or the host, or a non-adaptive byproduct of parasitism. Those interactions are further complicated in animal society since the individual fitness is associated with the group performance. However, a better understanding of host-parasite interaction in animal society first requires to identify individual host behavioural modification. Therefore, we challenged honey bee (Apis mellifera) workers with the parasite Nosema ceranae or an immune stimulation and tracked their flight activity over their lifetime with an optic counter. We found that bees responded differently to each stress: both Nosema-infected and immune-challenged bees performed a lower number of daily flights compared to control bees, but the duration of their flights increased and decreased over time, respectively. Overall, parasitized bees spent more time in the field each day than control bees and inversely for immune-challenged bees. Despite the stress due to immune challenge, bees had a survival similar to control bees likely due to their restricted activity. We discuss how those different behavioural modifications could be adaptive phenotypes. This study provides new insights into how biological stress can affect the behaviour of individuals living in society and how host responses evolved.
Scavenging ROS dramatically increases NMDA receptor whole cell currents in painted turtle cortical neurons
Authors: Dukoff David J. , Hogg David W. , Hawrsyh Peter J. , Buck Leslie T. 
Published: July 2014

AbstractOxygen deprivation triggers excitotoxic cell death in mammal neurons through excessive calcium loading via over-activation of N-methyl-D-aspartate (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. This does not occur in the western painted turtle which overwinters for months without oxygen. Neurological damage is avoided through anoxia-mediated decreases in NMDA and AMPA receptor currents that are dependent upon a modest rise in intracellular Ca2+ concentrations ([Ca2+]i) originating from mitochondria. Anoxia also blocks mitochondrial reactive oxygen species (ROS) generation which is another potential signaling mechanism to regulate glutamate receptors. To assess the effects of decreased intracellular [ROS] on NMDA and AMPA receptor currents we scavenged ROS with N-2-mercaptopropionylglycine (MPG) or N-acetylcysteine (NAC). Unlike anoxia, ROS scavengers increased NMDA receptor whole-cell currents by 100% while hydrogen peroxide decreased currents. AMPA receptor currents and [Ca2+]i concentrations were unaffected by ROS manipulation. Since decreases in [ROS] increased NMDA receptor currents we next asked if mitochondrial Ca2+ release prevents receptor potentiation during anoxia. Normoxic activation of mitochondrial ATP-sensitive potassium (mKATP) channels with diazoxide decreased NMDA receptor currents and was unaffected by subsequent ROS scavenging. Diazoxide application following ROS scavenging did not rescue scavenger-mediated increases in NMDA receptor currents. Fluorescent measurement of [Ca2+]i and ROS levels demonstrated that [Ca2+]i increases before ROS decreases. We conclude that decreases in ROS concentration are not linked to anoxia-mediated decreases in NMDA / AMPA receptor currents but are rather associated with an increase in NMDA receptor currents that is prevented during anoxia by mitochondrial Ca2+ release.
Cardiac responses to hypercapnia in larval zebrafish (Danio rerio): The links between CO2 chemoreception, catecholamines and carbonic anhydrase
Authors: Miller Scott , Pollack Jacob , Bradshaw Julia , Kumai Yusuke , Perry Steve F. 
Published: July 2014

AbstractThe ontogeny of carbon dioxide (CO2) sensing in zebrafish (Danio rerio) has not been examined. In this study, CO2-mediated increases in heart rate were used to gauge the capacity of zebrafish larvae to sense CO2. CO2 is thought to be detected via neuroepithelial cells (NECs), which are homologous to mammalian carotid body glomus cells. Larvae at 5 days post-fertilization (dpf) exhibited tachycardia when exposed for 30 min to 0.75% CO2 (~ 5.63 mm Hg); at 7 dpf, tachycardia was elicited by 0.5% CO2 (~ 3.75 mm Hg). Based on pharmacological evidence using β-adrenergic receptor (β1-AR) antagonists, and confirmed by β1-AR translational gene knockdown using morpholinos, the reflex tachycardia accompanying hypercapnia was likely mediated by the interaction of catecholamines with cardiac β1 receptors. Because the cardiac response to hypercapnia was abolished by the ganglionic blocker, hexamethonium, it is probable that the reflex cardio-acceleration was mediated by catecholamines derived from sympathetic adrenergic neurons. Owing to its likely role in facilitating intracellular acidification during exposure to hypercapnia, it was hypothesized that carbonic anhydrase (CA) is involved in CO2 sensing, and that inhibition of CA activity would blunt the downstream responses. Indeed, the cardiac response to hypercapnia (0.75% CO2) was reduced in fish at 5 dpf exposed to acetazolamide, a CA inhibitor, and in fish experiencing zCAc (CA2-like a) knockdown. Successful knockdown of zCAc was confirmed by CA activity measurements, western blotting and immunocytochemistry. Co-injection of embryos with zCAc morpholino and mRNA modified at the morpholino binding site, restored normal levels of CA activity and protein levels, and restored (rescued) the usual cardiac responses to hypercapnia. These data, combined with the finding that zCAc is expressed in NEC's located on the skin, suggest that the afferent limb of the CO2-induced cardiac reflex in zebrafish larvae is initiated by coetaneous CO2-sensing neuroepithelial cells.