bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Kinetics of Xylem Ion Loading and Its Regulation in Halophytes and Glycophytes
Authors: Zarei Mahvash , Shabala Sergey , Zeng Fanrong , Chen Xiaohui , Zhang Shuo , Azizi Majid , Rahemi Majid , Davarpanah Sohrab , Yu Min , Shabala Lana 
Published: October 2019

Abstract
Although control of xylem ion loading is essential to confer salinity stress tolerance, specific details behind this process remain elusive. In this work, we compared the kinetics of xylem Na+ and K+ loading between two halophytes (Atriplex lentiformis and quinoa) and two glycophyte (pea and beans) species, to understand the mechanistic basis of the above process. Halophyte plants had high initial amounts of Na+ in the leaf, even when grown in the absence of the salt stress. This was matched by 7-fold higher xylem sap Na+ concentration compared with glycophyte plants. Upon salinity exposure, the xylem sap Na+ concentration increased rapidly but transiently in halophytes, while in glycophytes this increase was much delayed. Electrophysiological experiments using the microelectrode ion flux measuring technique showed that glycophyte plants tend to re-absorb Na+ back into the stele, thus reducing xylem Na+ load at the early stages of salinity exposure. The halophyte plants, however, were capable to release Na+ even in the presence of high Na+ concentrations in the xylem. The presence of hydrogen peroxide (H2O2) [mimicking NaCl stress-induced reactive oxygen species (ROS) accumulation in the root] caused a massive Na+ and Ca2+ uptake into the root stele, while triggering a substantial K+ efflux from the cytosol into apoplast in glycophyte but not halophytes species. The peak in H2O2 production was achieved faster in halophytes (30 min vs 4 h) and was attributed to the increased transcript levels of RbohE. Pharmacological data suggested that non-selective cation channels are unlikely to play a major role in ROS-mediated xylem Na+ loading.
Epigenetic Flexibility Underlies Somaclonal Sex Conversions in Hexaploid Persimmon
Authors: Masuda Kanae , Akagi Takashi , Esumi Tomoya , Tao Ryutaro 
Published: October 2019

AbstractEpigenetic regulation adds a flexible layer to genetic variations, potentially enabling long-term, but reversible, changes to a trait, while maintaining genetic information. In the hexaploid Oriental persimmon (Diospyros kaki), genetically monoecious cultivars bearing male flowers require the Y-encoded small RNA (smRNA) gene, OGI. This gene represses the expression of its autosomal counterpart gene, MeGI, as part of the canonical male production system. However, a D. kaki cultivar, Saijo, which lacks the OGI gene and originally bears only female flowers, occasionally produces somaclonal mutant male and revertant female (RF) branches. In this study, we investigated the mechanisms underlying these somaclonal sex conversions in persimmon. Specifically, we aimed to unravel how a genetically female tree without the OGI gene can produce male flowers and RF flowers. Applying multi-omics approaches, we revealed that this noncanonical male production system is basically consistent with the canonical system, in which the accumulation of smRNA targeting MeGI and the considerable DNA methylation of MeGI are involved. The epigenetic status of MeGI on CGN and CHG was synchronized to the genome-wide methylation patterns, both in transition to and from the male production system. These results suggest that the somaclonal sex conversions in persimmon are driven by the genome-wide epigenetic regulatory activities. Moreover, flexibility in the epigenetic layers of long-lived plant species (e.g. trees) is important for overcoming genetic robustness.
Striatal histamine mechanism in the pathogenesis of restless legs syndrome
Authors: Lai Yuan-Yang , Hsieh Kung-Chiao , Cheng Yu-Hsuan , Chew Keng-Tee , Nguyen Darian , Ramanathan Lalini , Siegel Jerome M 
Published: October 2019

AbstractStudy ObjectivesRestless legs syndrome (RLS) has been hypothesized to be generated by abnormal striatal dopamine transmission. Dopaminergic drugs are effective for the treatment of RLS. However, long-term use of dopaminergic drugs causes adverse effects. We used iron-deficient (ID) and iron-replacement (IR) rats to address the neuropathology of RLS and to determine if a histamine H3 receptor (H3R) antagonist might be a useful treatment. Histamine H3R antagonists have been shown to decrease motor activity.MethodsControl and ID rats were surgically implanted with electrodes for polysomnographic recording. After 3 days of baseline polysomnographic recordings, rats were systemically injected with the H3R agonist, α-methylhistamine, and antagonist, thioperamide. Recordings were continued after drug injection. Striatal H3R levels from control, ID, and IR rats were determined by western blots. Blood from control, ID, and IR rats was collected for the measurement of hematocrit levels.Resultsα-Methylhistamine and thioperamide increased and decreased motor activity, respectively, in control rats. In ID rats, α-methylhistamine had no effect on motor activity, whereas thioperamide decreased periodic leg movement (PLM) in sleep. Sleep–wake states were not significantly altered under any conditions. Striatal H3R levels were highest in ID rats, moderate to low in IR rats, and lowest in control rats. Striatal H3R levels were also found to positively and negatively correlate with PLM in sleep and hematocrit levels, respectively.ConclusionsA striatal histamine mechanism may be involved in ID anemia-induced RLS. Histamine H3R antagonists may be useful for the treatment of RLS.
Origin and adaptive radiation of the exceptional and threatened bembidiine beetle fauna of St Helena (Coleoptera: Carabidae)
Authors: Maddison David R , Sproul John S , Mendel Howard 
Published: October 2019

AbstractThe central peaks of the isolated island of St Helena (south Atlantic Ocean) are home to an extraordinary set of ground beetles of the tribe Bembidiini, which belong to three endemic genus-group taxa. These beetles are strikingly different in overall body form from the many bembidiines found elsewhere in the world. At least some of the St Helena species are likely to be extinct, and all are threatened by habitat destruction and invasive species. Through next-generation sequencing of historical museum specimens, we examine the phylogenetic relationships of the St Helena fauna. We find that, in spite of their morphological disparities, the endemic bembidiines of St Helena form a clade of genetically similar species, with their sister group being Bembidion alsium from the Indian Ocean island of La Réunion, and the sister group of this pair being the African subgenus Omotaphus. We propose that the St Helena Peaks Bembidion are an adaptive radiation that arose from a single dispersal event to St Helena from a now-extinct African lineage (sister to Omotaphus) and that this extinct lineage also served as the ancestral source of B. alsium. Given that the St Helena Peaks Bembidion are deeply nested in the genus Bembidion, we move the three taxa back in that genus as subgenera and provide a new name (Bembidion shepherdae) for the now-homonymous Bembidion wollastoni.
Revision of the Ropalopus ungaricus/insubricus group (Coleoptera: Cerambycidae: Callidiini) from the western Palaearctic region
Authors: Karpiński Lech , Szczepański Wojciech T , Kruszelnicki Lech 
Published: October 2019

Abstract
This paper revises the taxonomy and phylogeny of Ropalopus (Coleoptera: Cerambycidae: Callidiini) species belonging to the taxonomically intricate Ropalopus ungaricus/insubricus group from the western Palaearctic. Specimens from all taxa were studied and compared. The key characters, including the male terminalia, were examined by means of scanning electron microscopy. High-quality stacked photographs of the habitus of the specimens (dorsal, ventral) are presented. The phylogenetic analyses were based on 34 adult morphological characters. Both the strict and majority consensus trees revealed the monophyly of the revised group. Identification keys are provided for every taxon from this group, and their geographical distributions are also mapped. All European populations are reduced to subspecies of Ropalopus ungaricus. Additionally, a new subspecies from Greece, Ropalopus ungaricus ossae subsp. nov., is described and illustrated. A new synonymy for Ropalopus insubricus fischeri is proposed: Callidium insubricum = Callidium fischeri. Ropalopus nataliyae, which was described based on only a single female, is herein redescribed owing to the collection of abundant new material. Apart from geographical barriers, the main differentiating factor in this group is proved to be the elevation above sea level. Taxa of the R. ungaricus/insubricus group are therefore allopatric or, when parapatric, are isolated by elevation.
Primary visual cortex excitability is not atypical in acquired synaesthesia
Authors: Lungu Laura , Stewart Ryan , Luke David P. , Terhune Devin B. 
Published: October 2019

AbstractA wealth of data suggests that psychedelic drugs elicit spontaneous perceptual states that resemble synaesthesia although it is unclear whether these different forms of synaesthesia share overlapping neural mechanisms. Multiple studies have shown that developmental and trained synaesthesia is characterized by selective hyperexcitability in primary visual cortex and it has been proposed that cortical hyperexcitability may contribute to induced and acquired synaesthesia. This study tested the prediction that a case of acquired synaesthesia (LW) would display selectively elevated primary visual cortex excitability, as reflected in lower transcranial magnetic stimulation (TMS) phosphene thresholds, but no difference in motor thresholds, relative to controls. In contrast to this prediction, LW’s phosphene threshold was well within the threshold range of controls. These results suggest that acquired synaesthesia is not characterized by atypical visual cortex excitability.
Biophysical mechanisms governing large-scale brain network dynamics underlying individual-specific variability of perception
Authors: Vinodh Kumar G. , Dutta Shrey , Talwar Siddharth , Roy Dipanjan , Banerjee Arpan 
Published: October 2019

AbstractPerception necessitates interaction amongst neuronal ensembles, the dynamics of which can be conceptualized as the emergent behavior of coupled dynamical systems. Here, we propose a detailed neurobiologically realistic model that captures the neural mechanisms of inter-individual variability observed in cross-modal speech perception. From raw EEG signals recorded from human participants when they were presented with speech vocalizations of McGurk-incongruent and congruent audio-visual (AV) stimuli, we computed the global coherence metric to capture the neural variability of large-scale networks. We identified that participants’ McGurk susceptibility was negatively correlated to their alpha-band global coherence. The proposed biophysical model conceptualized the global coherence dynamics emerge from coupling between the interacting neural masses - representing the sensory specific auditory/visual areas and modality non-specific associative/integrative regions. Subsequently, we could predict that an extremely weak direct AV coupling result in a decrease in alpha band global coherence - mimicking the cortical dynamics of participants with higher McGurk susceptibility. Source connectivity analysis also showed decreased connectivity between sensory specific regions in participants more susceptible to McGurk effect, thus establishing an empirical validation to the prediction. Overall, our study provides an outline to link variability in structural and functional connectivity metrics to variability of performance that can be useful for several perception & action task paradigms.
On islands, evolutionary but not functional originality is rare
Authors: Veron S. , Pellens R. , Kondratyeva A. , Grandcolas P. , Govaerts Rafaël , Robuchon M. , Haevermans T. , Mouchet M. 
Published: October 2019

AbstractFunctionally and evolutionary original species are those whose traits or evolutionary history are shared by few others in a given set. These original species promote ecosystem multifunctionality, the ability to cope with an uncertain future, future benefits to society and therefore have a high conservation value. A potential signal of their extinction risks is their rarity (stating for geographic range-restriction in this study). On islands, life in isolation conducted to the rise of a multitude of original forms and functions as well as to high rates of endemism. Not only patterns and processes of insular originality are unexplained but the relationship between originality and rarity is still unknown. The aim of this study is to assess how original insular species are, to explore whether original species are rare or not and to investigate the factors that may explain the rarity of original species. We first compared the functional and evolutionary originality of monocotyledon species and whether continental or insular species were more original. We found that species restricted to islands were more original than continental species and, although functionally and evolutionary original species were dissimilar, many occurred on similar territories so that regional conservation strategies may allow to conserve these distinct forms. Yet, evolutionary original species were significantly more range-restricted than those which were distinct in their traits. Reflecting their rarity, evolutionary original species had low dispersal abilities and were found on islands where settlement may have been facilitated. On the opposite, functionally original species could reach a wider set of islands by being transported on long-distances. While some mechanisms may both explain rarity and originality such as extinctions, others may be specific to each of these biodiversity facets, in particular diversification, niche shift and expansion, and dispersal power. Implications for conservation are huge: original species are range-restricted and mostly found in the most threatened systems of the world, i.e. islands, endangering the reservoir of features against an uncertain future.
In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions
Authors: Nobori Tatsuya , Wang Yiming , Wu Jingni , Stolze Sara Christina , Tsuda Yayoi , Finkemeier Iris , Nakagami Hirofumi , Tsuda Kenichi 
Published: October 2019

AbstractUnderstanding how gene expression is regulated in plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found instances of both concordant and discordant regulation of bacterial mRNAs and proteins. Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.
Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease
Authors: Zhang Tian-hao , Dai Lei , Barton John P. , Du Yushen , Tan Yuxiang , Pang Wenwen , Chakraborty Arup K. , Lloyd-Smith James O. , Sun Ren 
Published: October 2019

AbstractDrug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies orin vitroselection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance.
Mathematical modeling of the protective coloration of animals with usage of parameters of diversity and evenness
Authors: Bespalov Yu. , Nosov K. , Levchenko O. , Grigoriev O. , Hnoievyi I. , Kabalyants P. 
Published: October 2019

AbstractAdaptive mechanisms performing at different levels of organization of living matter play an important role in theoretical biology. One of the important cases of such mechanisms is the protective coloration of animals, that masks them on the ground.The article aims at building mathematical models of the performance of the protective coloration of animals, depending on the specific situations of their adaptation to a particular area. The results of the study can be used to create remote technologies for detecting animals of certain species at a considerable distance.
Structural basis of UCUU RNA motif recognition by splicing factor RBM20
Authors: Upadhyay Santosh Kumar , Mackereth Cameron D. 
Published: October 2019

ABSTRACTThe vertebrate splicing factor RBM20 (RNA Binding Motif protein 20) regulates protein isoforms important for heart development and function, with mutations in the gene linked to cardiomyopathy. Previous studies have identified the four base RNA motif UCUU as a common element in pre-mRNA targeted by RBM20. Here, we have determined the structure of the RNA Recognition Motif (RRM) domain from mouse RBM20 bound to RNA containing a UCUU sequence. The atomic details show that the RRM domain spans a larger region than initially proposed in order to interact with the complete UCUU motif, with a well-folded C-terminal helix encoded by exon 8 critical for high affinity binding. This helix only forms upon binding RNA with the final uracil, and removing the helix reduces affinity as well as specificity. We therefore find that RBM20 uses a coupled folding-binding mechanism by the C-terminal helix to specifically recognize the UCUU RNA motif.
RNA polymerase I passage through nucleosomes depends on its lobe binding subunits
Authors: Merkl Philipp E. , Pilsl Michael , Fremter Tobias , Schwank Katrin , Engel Christoph , Längst Gernot , Milkereit Philipp , Griesenbeck Joachim , Tschochner Herbert 
Published: October 2019

AbstractRNA polymerase I (Pol I) is a highly efficient enzyme specialized to synthesize most of the ribosomal RNA. After nucleosome deposition at each round of replication the Pol I transcription machinery has to deal with nucleosomal barriers. It was suggested that Pol I-associated factors facilitate chromatin transcription, but it is not known whether Pol I has an intrinsic capacity to transcribe through nucleosomes. Here we used in vitro transcription assays to study purified Pol I of the yeast S. cerevisiae and Pol I mutants in comparison to Pol II and Pol III to pass a nucleosome. Under identical conditions, purified Pol I and Pol III, but not Pol II, were able to transcribe nucleosomal templates. Pol I mutants lacking either the heterodimeric subunit Rpa34.5/Rpa49 or the C-terminal part of the specific subunit Rpa12.2 showed a lower processivity on naked DNA templates, which was even more reduced in the presence of a nucleosome. The contribution of Pol I specific subunit domains to efficient passage through nucleosomes in context with transcription rate and processivity is discussed.
Extensive functional repertoire underpins complex behaviours: insights from Parkinson’s disease
Authors: Sorrentino Pierpaolo , Rucco Rosaria , Baselice Fabio , De Micco Rosa , Tessitore Alessandro , Hillebrand Arjan , Mandolesi Laura , Breakspear Michael , Gollo Leonardo L. , Sorrentino Giuseppe 
Published: October 2019

AbstractRapid reconfigurations of brain activity support efficient neuronal communication and flexible behaviour. Suboptimal brain dynamics impair this adaptability, possibly leading to functional deficiencies. We hypothesize that impaired flexibility in brain activity can lead to motor and cognitive symptoms of Parkinson’s disease (PD). To test this hypothesis, we studied the ‘functional repertoire’ – the number of distinct configurations of neural activity – using source-reconstructed magnetoencephalography in PD patients and controls. We found stereotyped brain dynamics and reduced flexibility in PD. The intensity of this reduction was proportional to symptoms severity, which can be explained by beta-band hyper-synchronization. Moreover, the basal ganglia were prominently involved in the abnormal patterns of brain activity. Our findings support the hypotheses that: symptoms in PD reflect impaired brain flexibility, this impairment preferentially involves the basal ganglia, and beta-band hypersynchronization is associated with reduced brain flexibility. These findings highlight the importance of extensive functional repertoires for behaviour and motor.