bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological network assembly: how the regional metaweb influences local food webs
Authors: Saravia Leonardo A. , Marina Tomás I. , Kristensen Nadiah P. , De Troch Marleen , Momo Fernando R. 
Published: June 2018

AbstractLocal food webs result from a sequence of colonisations and extinctions by species from the regional pool or metaweb, i.e., the assembly process. Assembly is theorised to be a selective process: whether or not certain species or network structures can persist is partly determined by local processes including habitat filtering and dynamical constraints. Consequently, local food web structure should reflect these processes.The goal of this study was to test evidence for these selective processes by comparing the structural properties of real food webs to the expected distribution given the metaweb. We were particularly interested in ecological dynamics; if the network properties commonly associated with dynamical stability are indeed the result of stability constraints, then they should deviate from expectation in the direction predicted by theory.To create a null expectation, we used the novel approach of randomly assembling model webs by drawing species and interactions from the empirical metaweb. The assembly model permitted colonisation and extinction, and required a consumer species to have at least one prey, but had no habitat type nor population dynamical constraints. Three data sets were used: (1) the marine Antarctic metaweb, with 2 local food-webs; (2) the 50 lakes of the Adirondacks; and (3) the arthropod community from Florida Keys’ classic defaunation experiment.Contrary to our expectations, we found that there were almost no differences between empirical webs and those resulting from the null assembly model. Few empirical food webs showed significant differences with network properties, motif representations and topological roles. Network properties associated with stability did not deviate from expectation in the direction predicted by theory.Our results suggest that — for the commonly used metrics we considered — local food web structure is not strongly influenced by dynamical nor habitat restrictions. Instead, the structure is inherited from the metaweb. This suggests that the network properties typically attributed as causes or consequences of ecological stability are instead a by-product of the assembly process (i.e., spandrels), and may potentially be too coarse to detect the true signal of dynamical constraint.
Revisiting the phylogeny of Ficus (Moraceae): When Next Generation Sequencing corroborates Past Generation Botanists
Authors: Rasplus Jean-Yves , Rodriguez Lillian Jennifer , Tollon-Cordet Christine , Cruaud Astrid 
Published: June 2018

ABSTRACTDespite their ecological and evolutionary importance, fig trees still lack a resolved phylogeny. We used multiple analytical approaches and 600 conserved RAD-seq loci collected across 40 representative species to infer phylogenetic relationships among the major clades of Ficus. Our results converged on a fully resolved phylogeny that contradicts previous hypotheses by not placing section Pharmacosycea sister to all other fig trees. Instead, we find that subgenus Sycomorus is sister to two clades, one comprising all other gynodioecious sections, and the other containing all monoecious sections. Our results corroborate earlier botanists’ hypotheses and provide a baseline for future classification. We infer the evolution of key traits (growth form, breeding system and pollination mode) and find that, contrary to previous hypotheses, the ancestor of extant fig trees was likely a gynodioecious and actively pollinated tree. Our results open new opportunities to explore diversification patterns in fig trees and better understand their mutualistic interaction with wasps.
Brain regions modulated during covert visual attention in the macaque
Authors: Bogadhi Amarender R. , Bollimunta Anil , Leopold David A. , Krauzlis Richard J. 
Published: June 2018

AbstractNeurophysiology studies of covert visual attention in monkeys have emphasized the modulation of sensory neural responses in the visual cortex. At the same time, electrophysiological correlates of attention have been reported in other cortical and subcortical structures, and recent fMRI studies have identified regions across the brain modulated by attention. Here we used fMRI in two monkeys performing covert attention tasks to reproduce and extend these findings in order to help establish a more complete list of brain structures involved in the control of attention. As expected from previous studies, we found attention-related modulation in frontal, parietal and visual cortical areas as well as the superior colliculus and pulvinar. We also found significant attention-related modulation in cortical regions not traditionally linked to attention – mid-STS areas (anterior FST and parts of IPa, PGa, TPO), as well as the caudate nucleus. A control experiment using a second-order orientation stimulus showed that the observed modulation in a subset of these mid-STS areas did not depend on visual motion. These results identify the mid-STS areas (anterior FST and parts of IPa, PGa, TPO) and caudate nucleus as potentially important brain regions in the control of covert visual attention in monkeys.
Multiple myeloma immunoglobulin λ translocations portend poor prognosis
Authors: Barwick Benjamin G. , Neri Paola , Bahlis Nizar J. , Nooka Ajay K. , Kaufman Jonathan L. , Gupta Vikas A. , Auclair Daniel , Keats Jonathan J. , Lonial Sagar , Vertino Paula M. , Boise Lawrence H. 
Published: June 2018

AbstractMultiple myeloma is a malignancy of antibody-secreting plasma cells. Most patients benefit from current therapies, however, 20% of patients relapse or die within two years and are deemed ‘high-risk’. To better understand and identify high-risk myeloma, we analyzed the translocation landscape of 826 newly-diagnosed patients by whole genome sequencing as part of the CoMMpass study. Translocations at the IgL locus were present in 10% of myeloma patients, and corresponded with poor prognosis. Importantly, 70% of IgL translocations co-occurred with hyperdiploid disease, a marker of standard risk, which is routinely diagnosed clinically whereas IgL-translocations are not. Thus, it is likely that the majority of IgL-translocated myeloma is being misclassified. The IgL enhancer is among the strongest in myeloma cells, indicating it can robustly drive oncogene expression when translocated. Consistent with this, IgL-translocated patients failed to benefit from immunomodulatory imide drugs (IMiDs), which target the lymphocyte-specific transcription factor Ikaros. These data implicate the IgL enhancer as resistant to IMiD-inhibition, and when translocated, as a driver of poor prognosis.
Increased adaptability to rapid environmental change can more than make up for the two-fold cost of males
Authors: Holmes Caroline M. , Nemenman Ilya , Weissman Daniel B. 
Published: June 2018

AbstractThe famous “two-fold cost of sex” is really the cost of anisogamy – why should females mate with males who do not contribute resources to offspring, rather than isogamous partners who contribute equally? In typical anisogamous populations, a single very fit male can have an enormous number of offspring, far larger than is possible for any female or isogamous individual. If the sexual selection on males aligns with the natural selection on females, anisogamy thus allows much more rapid adaptation via super-successful males. We show via simulations that this effect can be sufficient to overcome the two-fold cost and maintain anisogamy against isogamy in populations adapting to environmental change. The key quantity is the variance in male fitness – if this exceeds what is possible in an isogamous population, anisogamous populations can win out in direct competition by adapting faster.
Multiple optic gland signaling pathways implicated in octopus maternal behaviors and death
Authors: Wang Z Yan , Ragsdale Clifton W 
Published: June 2018

0. Summary statementOctopus optic glands employ a multiplex progression of signaling molecules to regulate maternal behaviors.1. AbstractPost-reproductive life in the female octopus is characterized by an extreme pattern of maternal care: the mother cares for her clutch of eggs without feeding until her death. These maternal behaviors are completely eradicated if the optic glands, the octopus analog of the vertebrate pituitary gland, are removed from brooding females. Despite the optic gland’s importance in regulating maternal behavior, the molecular features underlying optic gland function are unknown. Here, we identify major signaling systems of theOctopus bimaculoidesoptic gland. Through behavioral analyses and transcriptome sequencing, we report that the optic gland undergoes remarkable molecular changes that coincide with transitions between behavioral stages. These include the dramatic up- and down-regulation of catecholamine, steroid, insulin, and feeding peptide pathways. Transcriptome analyses in other tissues demonstrate that these molecular changes are not generalized markers of aging and senescence, but instead, specific features of the optic glands. Our results provide strong evidence for the functional conservation of signaling molecules across evolutionarily distant species. For example, elevated levels of insulin growth factor binding proteins are associated with cachexia-like tissue wasting in flies, humans, and, reported here, octopuses. Our study expands the classic optic gland-pituitary gland analogy and indicates that, rather than a single “self-destruct” hormone, the maternal optic glands employ multiple pathways as systemic hormonal signals of behavioral control.
Ketamine disrupts neuromodulatory control of glutamatergic synaptic transmission
Authors: Lur Gyorgy , Higley Michael J. 
Published: June 2018

AbstractA growing body of literature has demonstrated the potential for ketamine in the treatment of major depression. Sub-anesthetic doses produce rapid and sustained changes in depressive behavior, both in patients and rodent models, associated with reorganization of glutamatergic synapses in the prefrontal cortex (PFC). While ketamine is known to regulate NMDA-type glutamate receptors (NMDARs), the full complement of downstream cellular consequences for ketamine administration are not well understood. Here, we combine electrophysiology with 2-photon imaging and glutamate uncaging in acute slices of mouse PFC to further examine how ketamine alters glutamatergic synaptic transmission. We find that four hours after ketamine treatment, glutamatergic synapses themselves are not significantly affected. However, expression levels of the neuromodulatory Regulator of G-protein Signaling (RGS4) are dramatically reduced. This loss of RGS4 activity disrupts the normal compartmentalization of synaptic neuromodulation. Thus, under control conditions, α2 adrenergic receptors and GABABreceptors selectively inhibit AMPA-type glutamate receptors (AMPARs) and NMDARs, respectively. After ketamine-induced loss of RGS4 activity, this selectivity is lost, with both modulatory systems broadly inhibiting glutamatergic transmission. These results demonstrate a novel mechanism by which ketamine can influence synaptic signaling and provide new avenues for the exploration of therapeutics directed at treating neuropsychiatric disorders, such as depression.
PI(4,5)P2 Binding Sites in the Ebola Virus Matrix Protein Modulate Assembly and Budding
Authors: Johnson Kristen A. , Budicini Melissa R. , Urata Sarah , Bhattarai Nisha , Gerstman Bernard S. , Chapagain Prem P. , Li Sheng , Stahelin Robert V. 
Published: June 2018

AbstractEbola virus (EBOV) causes sever hemorrhagic fever in humans, can cause death in a large percentage of those infected, and still lacks FDA approved treatment options. In this study, we investigated how the essential EBOV protein, VP40, forms stable oligomers to mediate budding and assembly from the host cell plasma membrane. An array of in vitro and cellular assays identified and characterized two lysine rich regions that bind to PI(4,5)P2 and serve distinct functions through the lipid binding and assembly of the viral matrix layer. We found that when VP40 binds PI(4,5)P2, VP40 oligomers become extremely stable and long lived. Together, this work characterizes the molecular basis of PI(4,5)P2 binding by VP40, which stabilizes formation of VP40 oligomers necessary for viral assembly and budding. Quercetin, a natural product that lowers PI(4,5)P2 in the plasma membrane, inhibited budding of VP40 VLPs and may inform future treatment strategies against EBOV.
Pan-cancer analysis of RNA binding proteins (RBPs) reveals the involvement of the core pre-mRNA splicing and translation machinery in tumorigenesis
Authors: Zhang Bin , Babu Kamesh R. , Lim Chun You , Kwok Zhi Hao , Li Jia , Zhou Siqin , Yang Henry , Tay Yvonne 
Published: June 2018

AbstractRNA binding proteins (RBPs) are key regulators of posttranscriptional processes such as RNA maturation, transport, localization, turnover and translation. Despite their dysregulation in various diseases including cancer, the landscape of RBP expression and regulatory mechanisms in human cancer has not been well characterized. Here, we analyzed mRNA expression of 1487 RBPs in ~6700 clinical samples across 16 human cancer types and found that there were significantly more upregulated RBPs than downregulated ones in tumors when compared to their adjacent normal tissues. Across almost all of the 16 cancer types, 109 RBPs were consistently upregulated (cuRBPs) while only 41 RBPs were consistently downregulated (cdRBPs). Integrating expression with the copy number and DNA methylation data, we found that the overexpression of cuRBPs is largely associated with the amplification of copy number, whereas the downregulation of cdRBPs may be a result of epigenetic silencing mediated by DNA methylation. Furthermore, our results indicated that cuRBPs could work together to promote cancer progression potentially through the involvement of splicing and translation machinery, while cdRBPs might function independently to suppress tumorigenesis. Additionally, we focused on colon cancer and identified several novel potential oncogenic RBPs, such as PABPC1L which might promote cancer development via regulating the core splicing machinery. In summary, we showed distinct expression landscapes, regulatory mechanisms and characteristics of cuRBPs and cdRBPs and implicated several novel RBPs in cancer pathogenesis. Moreover, our results suggest that the involvement of the core pre-mRNA splicing and translation machinery could be critical in tumorigenesis.
Mitochondrial citrate transporters CtpA and YhmA are involved in lysine biosynthesis in the white koji fungus,Aspergillus luchuensismut. kawachii
Authors: Kadooka Chihiro , Izumitsu Kosuke , Onoue Masahira , Okutsu Kayu , Yoshizaki Yumiko , Takamine Kazunori , Goto Masatoshi , Tamaki Hisanori , Futagami Taiki 
Published: June 2018

ABSTRACTAspergillus luchuensismut. kawachiiproduces a large amount of citric acid during the process of fermenting shochu, a traditional Japanese distilled spirit. In this study, we characterizedA. kawachiiCtpA and YhmA, which are homologous to the yeastSaccharomyces cerevisiaemitochondrial citrate transporters Ctp1 and Yhm2, respectively. CtpA and YhmA were purified fromA. kawachiiand reconstituted into liposomes. The proteoliposomes exhibited only counter-exchange transport activity; CtpA transported citrate using counter substrates especially forcis-aconitate and malate, whereas YhmA transported citrate using a wider variety of counter substrates, including citrate, 2-oxoglutarate, malate,cis-aconitate, and succinate. Disruption ofctpAandyhmAcaused deficient hyphal growth and conidia formation with reduced mycelial weight–normalized citrate production. Because we could not obtain a ΔctpAΔyhmAstrain, we constructed actpA-Sconditional expression strain in the ΔyhmAbackground using the Tet-On promoter system. Knockdown ofctpA-Sin ΔyhmAresulted in a severe growth defect on minimal medium, indicating that double disruption ofctpAandyhmAleads to synthetic lethality; however, we subsequently found that the severe growth defect was relieved by addition of lysine. Our results indicate that CtpA and YhmA are mitochondrial citrate transporters involved in citric acid production and that transport of citrate from mitochondria to the cytosol plays an important role in lysine biogenesis inA. kawachii.IMPORTANCECitrate transport is believed to play a significant role in citrate production by filamentous fungi; however, details of the process remain unclear. This study characterized two citrate transporters fromAspergillus luchuensismut. kawachii. Biochemical and gene disruption analyses showed that CtpA and YhmA are mitochondrial citrate transporters required for normal hyphal growth, conidia formation, and citric acid production. In addition, this study provided insights into the links between citrate transport and lysine biosynthesis. The characteristics of fungal citrate transporters elucidated in this study will help expand our understanding of the citrate production mechanism and facilitate the development and optimization of industrial organic acid fermentation processes.
Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments
Authors: Antti Karkman , Katariina Pärnänen , Joakim Larsson D.G. 
Published: June 2018

AbstractDischarge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. Such pollution can directly contribute to increased morbidity caused by the transmission of resistant fecal pathogens. Residual antibiotics in wastewaters have been speculated to select for resistant bacteria and thereby promote the evolution and emergence of new resistance factors. Increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments may, however, simply be a result of fecal contamination with resistant bacteria rather than caused by an on-site selection pressure. In this study we have disentangled these two alternative scenarios by relating the relative resistance gene abundance to the accompanying extent of fecal pollution in publicly available metagenomic data. This was possible by analyzing the abundance of a newly discovered phage which is exceptionally abundant in, and specific to, human feces. The presence of resistance genes could largely be explained by fecal pollution, with no clear signs of selection in the environment, the only exception being environments polluted by very high levels of antibiotics from manufacturing where selection is evident. Our results demonstrate the necessity to take in to account the fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance. The presence or absence of selection pressure has major implications for what the risk scenarios are (transmission versus evolution) and for what mitigations (reducing pathogenic bacteria or selective agents) should be prioritized to reduce health risks related to antibiotic resistance in the environment.
Influence of miR-520e-mediated MAPK signaling pathway on HBV replication and regulation of hepatocellular carcinoma cells via targeting EphA2
Authors: Tian Jing-hui , Liu Wen-dong , Zhang Zhi-yong , Tang Li-hua , Li Dong , Tian Zhao-ju , Lin Shao-wei , Li Ying-jie 
Published: June 2018

AbstractThis paper aims to determine the role of miR-520e in the replication of hepatitis B virus (HBV) and the growth of hepatocellular carcinoma (HCC) cells. MiR-520e and EphA2 in HBV-positive HCC tissues and cells were detected. HepG2.2.15 and Huh7 cells transfected with pHBV1.2 were divided into Mock, NC, miR-520e mimic, miR-520e inhibitor, si-EphA2, and miR-520e inhibitor + si-EphA2 groups. MiR-520e, HBV DNA content, HBsAg and HBeAg levels, cell proliferation, apoptosis and protein expression of EphA2 and MAPK pathways were evaluated. Furthermore, rAAV81.3HBV infected-mouse model was established to detect HBV-DNA levels. MiR-520e was up-regulated and EphA2 was down-regulated in HBV-positive HCC tissues and cells (HepG2.2.15 and HepAD38). MiR-520e was decreased in Huh7-X and HepG2-X cells in which HBx was stably expressed, but miR-520e was dose-dependently elevated in Huh7-X, HepG2-X, and HepG2.2.15 cells after interfering HBx. Additionally, miR-520e mimic and si-EphA2 groups were apparently reduced in HBV DNA content, HBsAg and HBeAg levels, cell proliferation, and were enhanced in the expressions of EphA2, MAPK pathways and cell apoptosis. Furthermore, si-EphA2 can reverse the promotion effect of miR-520e inhibitor on the HBV replication and tumor cell growth Up-regulating miR-520e in rAAV81.3HBV infected-mouse resulted in the reduced EphA2 in liver tissues and HBV DNA content in serum. MiR-520e was found to be decreased in HBV-positive HCC tissues and cells, while over-expression of miR-520e blocked MAPK pathways via inhibiting EphA2, ultimately reducing HBV replication and inhibiting tumor cell growth.
Spatiotemporally controlled genetic perturbation for efficient large-scale studies of cell non-autonomous effects
Authors: Chai Andrea , Mateus Ana M. , Oozeer Fazal , Sousa-Nunes Rita 
Published: June 2018

AbstractStudies in genetic model organisms have revealed much about the development and pathology of complex tissues. Most have focused on cell-intrinsic gene functions and mechanisms. Much less is known about how transformed, or otherwise functionally disrupted, cells interact with healthy ones towards a favorable or pathological outcome. This is largely due to technical limitations. We developed new genetic tools in Drosophila melanogaster that permit efficient multiplexed gain- and loss-of-function genetic perturbations with separable spatial and temporal control. Importantly, our novel tool-set is independent of the commonly used GAL4/UAS system, freeing the latter for additional, non-autonomous, genetic manipulations; and is built into a single strain, allowing one-generation interrogation of non-autonomous effects. Altogether, our design opens up efficient genome-wide screens on any deleterious phenotype. Specifically, we developed tools to study extrinsic effects on neural tumor growth but the strategy presented has endless applications within and beyond neurobiology, and in other model organisms.Impact statementA novel genetic strategy for induction of reproducible neural tumors (or any other deleterious phenotype) in a singleDrosophilastock (applicable to other organisms).