bluuebunny/crossref_metadata_2025_split huggingface dataset:
Invasion but not hybridisation is associated with ecological niche shift in monkeyflowers
Authors: Da Re Daniele , Olivares Angel P. , Smith William , Vallejo-Marín Mario 
Published: July 2019

AbstractBackgroundThe ecological niche occupied by novel hybrids can influence their establishment as well as the potential to coexist with their parents. Hybridisation generates new phenotypic combinations, which, in some cases, may allow them to occupy ecological niches outside the environmental envelope of parental taxa. In other cases, hybrids may retain similar ecological niches to their parents, resulting in competition and affecting their coexistence. To date, few studies have quantitatively assessed niche shifts associated with hybridisation in recently introduced populations while simultaneously characterising the niche of parental species in both native and introduced ranges.AimsIn this study, we compared the ecological niche of a novel hybrid plant with the niches of its two parental taxa in the non-native geographic range. We also characterised and compared the parental taxa’s ecological niche of native and introduced populations in order to assess potential niche changes during the invasion process independent of hybridisation.MethodsWe studied monkeyflowers (Mimulus spp., Phrymaceae) that were introduced from the Americas to Europe and New Zealand in the last 200 years. We focused on a novel hybrid, triploid, asexual taxon (M. × robertsii) that occurs only in the British Isles where its two parents (M. guttatusandM. luteus) come into secondary contact. We assembled more than 12,000 geo-referenced occurrence records and eight environmental variables of the three taxa across native and introduced ranges, and conducted ecological niche model analysis using maximum entropy, principal component and niche dynamics analysis.ResultsWe found no evidence of niche shift in the hybrid,M. × robertsiicompared to introduced populations of both of their parental taxa. The hybrid had a niche more similar toM. luteus, which is also the rarest of the parental taxa on the introduced range. Among parental monkeyflowers,M. guttatusshowed niche conservatism in introduced populations in Europe, but a niche shift in New Zealand, whileM. luteusshowed a niche shift in Europe. However, the evidence of niche shift should be treated with caution due to the occurence of non-analog climatic conditions, small population size and unfilling niche dynamics.ConclusionsOur results suggest that hybridisation in non-native monkyeflowers did not result in a shift in ecological niche. This niche conservation could create competition between parental and derived taxa, the outcome of which will depend on relative competitive abilities. Further work is needed to establish if the expansion of the hybrid in the introduced range is causally related to the apparent rarity of one of the parents (M.luteus). Finally, the comparison of native and non-native populations of parental taxa, suggest that whether invasions result in niche shifts or not depends on both taxon and geographic region, highlighting the idiosyncratic nature of biological invasions.
Time spent in distinct life-history stages has sex-specific effects on reproductive fitness in wild Atlantic salmon
Authors: Mobley Kenyon B. , Granroth-Wilding Hanna , Ellmen Mikko , Orell Panu , Erkinaro Jaakko , Primmer Craig R. 
Published: July 2019

AbstractIn species with complex life cycles, life history theory predicts that fitness is affected by conditions encountered in previous life history stages. Here, we use a four-year pedigree to investigate if time spent in two distinct life history stages has sex-specific reproductive fitness consequences in anadromous Atlantic salmon (Salmo salar). We determined the amount of years spent in fresh water as juveniles (freshwater age, FW), and years spent in the marine environment prior to sexual maturation (sea age, SW) on 264 spawning adults. We then estimated reproductive fitness as the number of offspring (reproductive success) and the number of mates (mating success) using genetic parentage analysis (>5000 offspring). Sea age is positively correlated with reproductive and mating success of both sexes whereby older and larger individuals gained the highest reproductive fitness benefits (females: increase of 16.5 offspring/SW and 0.86 mates/SW; males: increase of 12.4 offspring/SW and 0.43 mates/SW). Younger freshwater age was related to older sea age and thus increased reproductive fitness, but only among females (females: −9.0 offspring/FW and −0.80 mates/FW). This implies that females can obtain higher reproductive fitness by transitioning to the marine environment earlier. In contrast, male mating and reproductive success was unaffected by freshwater age and males returned to spawn earlier than females despite the fitness advantage of later sea age maturation. Our results show that the timing of transitions between juvenile and adult phases has a sex-specific consequence on female reproductive fitness, demonstrating a life-history trade-off between maturation and reproduction in wild Atlantic salmon.
Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and function of dairy calves
Authors: Foditsch Carla , Pereira Richard V.V. , Siler Julie D. , Altier Craig , Warnick Lorin D. 
Published: July 2019

AbstractThe increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), enrofloxacin, or tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sample preparation and sequencing was conducted. The effect of antibiotic treatment on each taxon and functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other treatment groups. The SEED database was used for functional analyses, which showed that calves in the enrofloxacin group started with a higher abundance of “Resistance to antibiotics and toxic compounds” function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. “Resistance to Fluoroquinolones” and “Erythromycin resistance”, of relevance given the study groups, were not statistically different in abundance between treatment groups. “Resistance to fluoroquinolones” increased during the study period regardless of treatment group. Despite small differences over the first weeks between treatment groups, at Day 112 the microbiota composition and functional profile was similar among all study groups. These findings show that metaphylaxis treatment of dairy calves with either enrofloxacin or tulathromycin have minimal impacts on the microbial composition and functional microbiota of dairy calves over time.
Lateral organ diversification in plants mediated by the ALOG protein family of transcription factors
Authors: Naramoto Satoshi , Jones Victor Arnold Shivas , Trozzi Nicola , Sato Mayuko , Toyooka Kiminori , Shimamura Masaki , Ishida Sakiko , Nishitani Kazuhiko , Ishizaki Kimitsune , Nishihama Ryuichi , Kohchi Takayuki , Dolan Liam , Kyozuka Junko 
Published: July 2019

AbstractLand plant shoot structures evolved a diversity of lateral organs as morphological adaptations to the terrestrial environment, in which lateral organs independently evolved in each lineage in the sporophyte or gametophyte generation. The gametophyte meristem of the basally-diverging plant Marchantia polymorpha produces axes with non-photosynthetic scale-like lateral organs instead of leaves. Here we report that an ALOG (Arabidopsis LSH1 and Oryza G1) family protein in Marchantia, MpTAWAWA1 (MpTAW1), regulates meristem maintenance and lateral organ development. A mutation in MpTAW1, preferentially expressed in lateral organs, induces lateral organs with mis-specified identity and increased cell number, and furthermore, causes defects in apical meristem maintenance. Remarkably, MpTAW1 expression rescued the elongated-spikelet phenotype of a rice mutant of MpTAW1 homologue. This suggests that ALOG genes are co-opted to specify lateral organ identities in both gametophyte and sporophyte shoots by repressing lateral organ growth. We propose that the recruitment of ALOG-mediated lateral organ modification was in part responsible for the convergent evolution of independently-evolved lateral organs among highly divergent plant lineages and contributed to the morphological diversification of land plants.
Structure-function analysis of the Escherichia coli β–barrel assembly enhancing protease BepA suggests a role for a self-inhibitory state
Authors: Bryant Jack A. , Cadby Ian T. , Chong Zhi-Soon , Sevastsyanovich Yana R. , Morris Faye C. , Cunningham Adam F. , Kritikos George , Meek Richard W. , Banzhaf Manuel , Chng Shu-Sin , Henderson Ian R. , Lovering Andrew L. 
Published: July 2019

AbstractThe asymmetric Gram-negative outer membrane (OM) is the first line of defence for the bacteria against environmental insults and attack by antimicrobials. The key component of the OM barrier is the surface exposed lipopolysaccharide, which is transported to the surface by the essential lipopolysaccharide transport (Lpt) system. Correct folding of the Lpt system OM component, LptD, is essential and is regulated by a periplasmic metalloprotease, BepA. Here we present the crystal structure of BepA, solved to a resolution of 1.9 Å. Our structure comprises the zinc-bound m48 protease domain and a tetratricopeptide repeat (TPR) domain, consisting of four 2-helix TPR motifs and four non-TPR helices, leading to a nautilus-like shape in which the TPR repeats cup the protease domain. Using targeted mutagenesis approaches, we demonstrate that the protein is auto-regulated by the active-site plug. Further to this we reveal that mutation of a negative pocket, formed at the interface between the m48 and TPR domains, impairs BepA activity suggesting the pocket as a possible substrate binding site. We also identify a potential protein interaction site within the TPR cavity as being important for BepA function. Lastly, we provide evidence to show that increased antibiotic susceptibility in the absence of correctly functioning BepA occurs through disruption of OM lipid asymmetry, leading to reduced barrier function and increased cell permeability.
Epstein Barr virus genomes reveal population structure and type 1 association with endemic Burkitt lymphoma
Authors: Kaymaz Yasin , Oduor Cliff I. , Aydemir Ozkan , Luftig Micah A. , Otieno Juliana A. , Ong’echa John Michael , Bailey Jeffrey A. , Moormann Ann M. 
Published: July 2019

AbstractEndemic Burkitt lymphoma (eBL), the most prevalent pediatric cancer in sub-Saharan Africa, is associated with malaria and Epstein Barr virus (EBV). In order to better understand the role of EBV in eBL, we improved viral DNA enrichment methods and generated a total of 98 new EBV genomes from both eBL cases (N=58) and healthy controls (N=40) residing in the same geographic region in Kenya. Comparing cases and controls, we found that EBV type 1 was significantly associated with eBL with 74.5% of patients (41/55) versus 47.5% of healthy children (19/40) carrying type 1 (OR=3.24, 95% CI=1.36 - 7.71,P=0.007). Controlling for EBV type, we also performed a genome-wide association study identifying 6 nonsynonymous variants in the genes EBNA1, EBNA2, BcLF1, and BARF1 that were enriched in eBL patients. Additionally, we observed that viruses isolated from plasma of eBL patients were identical to their tumor counterpart consistent with circulating viral DNA originating from the tumor. We also detected three intertypic recombinants carrying type 1 EBNA2 and type 2 EBNA3 regions as well as one novel genome with a 20 kb deletion resulting in the loss of multiple lytic and virion genes. Comparing EBV types, genes show differential variation rates as type 1 appears to be more divergent. Besides, type 2 demonstrates novel substructures. Overall, our findings address the complexities of EBV population structure and provide new insight into viral variation, which has the potential to influence eBL oncogenesis.Key PointsEBV type 1 is more prevalent in eBL patients compared to the geographically matched healthy control group.Genome-wide association analysis between cases and controls identifies 6 eBL-associated nonsynonymous variants in EBNA1, EBNA2, BcLF1, and BARF1 genes.Analysis of population structure reveals that EBV type 2 exists as two genomic sub groups.
Host-microbiome coevolution promotes cooperation in a rock-paper-scissor dynamic
Authors: Lewin-Epstein Ohad , Hadany Lilach 
Published: July 2019

AbstractCooperation is a fundamental behavior observed in all forms of life. The evolution of cooperation has been widely studied, but almost all theories focused on the cooperating individual and its genes. We suggest a different approach, taking into account the microbes carried by the interacting individuals. Accumulating evidence reveal that microbes can affect their host wellbeing and behavior, yet hosts can evolve mechanisms to resist the manipulations of their microbes. We thus propose that coevolution of microbes with their hosts may favor microbes that induce their host to cooperate. Using computational modeling, we show that microbe-induced cooperation can evolve and be maintained in a wide range of conditions, including when facing hosts’ resistance to the microbial effect. We find that host-microbe coevolution leads the population to a rock-paper-scissors dynamic, that enables maintenance of cooperation in a polymorphic state. This theory may help explain occurrences of cooperation in a wide variety of organisms, including in cases that are difficult to explain by current theories. In addition, this study provides a new perspective on the coevolution of hosts and their microbiome, emphasizing the potential role of microbes in shaping their host behavior.
DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines
Authors: Yukselen Onur , Turkyilmaz Osman , Ozturk Ahmet Rasit , Garber Manuel , Kucukural Alper 
Published: July 2019

ABSTRACTThe emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research. The dramatic increase in the volume of data makes analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for a highly-parallel, flexible, portable, and reproducible data processing frameworks. Flexibility ensures that pipelines can support a variety of applications without requiring one-off modifications. Portability ensures that users can leverage computationally available resources and work within economic constraints. Reproducibility warrants credibility to the results and is particularly challenging in the face of the sheer volume of data and the complexity of processing pipelines that vary widely between users.Several platforms currently exist for the design and execution of complex pipelines (e.g. Galaxy, GenePattern, GeneProf). Unfortunately, these platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, Nextflow was implemented to simplify portable, scalable, and reproducible scientific pipelines using containers. We have used Nextflow capabilities as leverage and developed a user interface, DolphinNext, for creating, deploying, and executing complex Nextflow pipelines for high throughput data processing. The guiding principle of DolphinNext is to facilitate the building and deployment of complex pipelines using a modular approach implemented in a graphical interface. DolphinNext provides: 1. A drag and drop user interface that abstracts pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. A user interface to monitor pipeline execution that allows the re-initiation of pipelines at intermediate steps 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Seamless portability to distributed computational environments such as high-performance clusters or cloud computing environments.
Mechanism of µ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation
Authors: Hu X. , Provasi D. , Filizola M. 
Published: July 2019

AbstractIn the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the µ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, are monovalent and divalent cations. Specifically, the monovalent sodium cation (Na+) has been known for decades to affect MOP receptor signaling by reducing agonist binding, whereas the divalent magnesium cation (Mg2+) has been shown to have the opposite effect, notwithstanding the presence of sodium chloride. While ultra-high resolution opioid receptor crystal structures have revealed a specific Na+ binding site and molecular dynamics (MD) simulation studies have supported the idea that this monovalent ion reduces agonist binding by stabilizing the receptor inactive state, the putative binding site of Mg2+ on the MOP receptor, as well as the molecular determinants responsible for its positive allosteric modulation of the receptor, are unknown. In this work, we carried out tens of microseconds of all-atom MD simulations to investigate the simultaneous binding of Mg2+ and Na+ cations to inactive and active crystal structures of the MOP receptor embedded in an explicit lipid/water environment. Analyses of these simulations shed light on (a) the preferred binding sites of Mg2+ on the MOP receptor, (b) details of the competition between Mg2+ and Na+ cations for specific sites, (c) estimates of binding affinities, and (d) testable hypotheses of the molecular mechanism underlying the positive allosteric modulation of the MOP receptor by the Mg2+ cation.Statement of SignificanceOverprescription of opioid drugs in the late 1990s, followed by abuse of both prescription and illicit opioid drugs, has led to what is nowadays called “opioid overdose crisis” or “opioid epidemic”, with more than 130 Americans dying daily from opioid overdose at the time of writing. To reduce opioid doses, and thereby prevent or treat overdose and opioid use disorders, attention has recently shifted to the use of co-analgesics. Understanding how opioid receptor targets can be allosterically modulated by these elements, including cations, is key to the development of improved therapeutics. Here, we provide an atomic-level understanding of the mechanism by which magnesium binds to the µ-opioid receptor and enhances opioid drug efficacy by stabilizing the receptor activated state.
Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping
Authors: Mollinari Marcelo , Olukolu Bode A. , da S. Pereira Guilherme , Khan Awais , Gemenet Dorcus , Yencho Craig , Zeng Zhao-Bang 
Published: July 2019

AbstractThe hexaploid sweetpotato (Ipomoea batatas(L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and has a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly implemented software, MAPpoly. The resulting genetic map revealed 96.5% collinearity betweenI. batatasand its diploid relativeI. trifida.We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%) were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.
Inhibition of adhesive nanofibrillar mediatedStreptococcus gordonii - Candida albicansmono- and dual-species biofilms
Authors: Veerapandian Raja , Vediyappan Govindsamy 
Published: July 2019

AbstractDental caries and periodontitis are the most common oral disease of all age groups, affecting billions of people worldwide. These oral diseases are mostly associated with the microbial biofilms in the oral cavity.Streptococcus gordonii, an early tooth colonizing bacterium andCandida albicans, an opportunistic pathogenic fungus, are the two abundant oral microbes form mixed biofilms and augment their virulence properties affecting oral health negatively. Understanding the molecular mechanisms of their interactions and blocking the growth of these biofilms by nontoxic compounds could help develop effective therapeutic approaches. We report in this study, inhibition of mono- or dual-species biofilms ofS. gordoniiandC. albicans, and biofilm eDNAin vitroby Gymnemic Acids (GAs), a nontoxic small molecule inhibitor of fungal hyphae. Scanning electron microscopic images of biofilms revealed attachment ofS. gordoniicells to the hyphal and on saliva-coated hydroxyapatite (sHA) surfaces via nanofibrils only in the untreated control but not in the GAs treated biofilms. Interestingly,C. albicansproduced fibrillar adhesive structures from hyphae when grown withS. gordoniias mixed biofilm and addition of GAs to this biofilm abrogates the nanofibrils, reduces the growth of hyphae, and biofilms. To our knowledge, this is a first report thatC. albicansproduces adhesive fibrils from hyphae in response toS. gordoniimixed biofilm growth. A semi-quantitative PCR data of selected genes related to biofilms of both microbes show their differential expression. Further evaluation of one of the gene products ofS. gordoniirevealed that GAs could inhibit its recombinant glyceraldehyde-3-phosphate dehydrogenase (GAPDH) enzyme activity. Taken together, our results suggest thatS. gordoniistimulates expression of adhesive materials inC. albicansby direct interaction and or by signaling mechanism(s), and these mechanisms can be inhibited by GAs. Further studies on global gene expression of these biofilms and their biochemical studies may reveal the molecular mechanism of their inhibition.