bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic architecture of habitat‐related divergence and signature of directional selection in the body shapes ofGnathopogonfishes
Authors: Kakioka Ryo , Kokita Tomoyuki , Kumada Hiroki , Watanabe Katsutoshi , Okuda Noboru 
Published: July 2015

AbstractEvolution of ecomorphologically relevant traits such as body shapes is important to colonize and persist in a novel environment. Habitat‐related adaptive divergence of these traits is therefore common among animals. We studied the genomic architecture of habitat‐related divergence in the body shape ofGnathopogonfishes, a novel example of lake–stream ecomorphological divergence, and tested for the action of directional selection on body shape differentiation. Compared to stream‐dwellingGnathopogon elongatus,the sister speciesGnathopogon caerulescens,exclusively inhabiting a large ancient lake, had an elongated body, increased proportion of the caudal region and small head, which would be advantageous in the limnetic environment. Using an F2interspecific cross between the twoGnathopogonspecies (195 individuals), quantitative trait locus (QTL) analysis with geometric morphometric quantification of body shape and restriction‐site associatedDNAsequencing‐derived markers (1622 loci) identified 26 significantQTLs associated with the interspecific differences of body shape‐related traits. TheseQTLs had small to moderate effects, supporting polygenic inheritance of the body shape‐related traits. EachQTLwas mostly located on different genomic regions, while colocalizedQTLs were detected for some ecomorphologically relevant traits that are proxy of body and caudal peduncle depths, suggesting different degree of modularity among traits. The directions of the body shapeQTLs were mostly consistent with the interspecific difference, andQTLsign test suggested a genetic signature of directional selection in the body shape divergence. Thus, we successfully elucidated the genomic architecture underlying the adaptive changes of the quantitative and complex morphological trait in a novel system.
A population study of killer viruses reveals different evolutionary histories of two closely related Saccharomyces sensu stricto yeasts
Authors: Chang Shang‐Lin , Leu Jun‐Yi , Chang Tien‐Hsien 
Published: July 2015

AbstractMicrobes have evolved ways of interference competition to gain advantage over their ecological competitors. The use of secreted killer toxins by yeast cells through acquiring double‐stranded RNA viruses is one such prominent example. Although the killer behaviour has been well studied in laboratory yeast strains, our knowledge regarding how killer viruses are spread and maintained in nature and how yeast cells co‐evolve with viruses remains limited. We investigated these issues using a panel of 81 yeast populations belonging to three Saccharomyces sensu stricto species isolated from diverse ecological niches and geographic locations. We found that killer strains are rare among all three species. In contrast, killer toxin resistance is widespread in Saccharomyces paradoxus populations, but not in Saccharomyces cerevisiae or Saccharomyces eubayanus populations. Genetic analyses revealed that toxin resistance in S. paradoxus is often caused by dominant alleles that have independently evolved in different populations. Molecular typing identified one M28 and two types of M1 killer viruses in those killer strains. We further showed that killer viruses of the same type could lead to distinct killer phenotypes under different host backgrounds, suggesting co‐evolution between the viruses and hosts in different populations. Taken together, our data suggest that killer viruses vary in their evolutionary histories even within closely related yeast species.
History matters more when explaining genetic diversity within the context of the core–periphery hypothesis
Authors: Duncan Sarah I. , Crespi Erica J. , Mattheus Nichole M. , Rissler Leslie J. 
Published: July 2015

AbstractThe core–periphery hypothesis (CPH) predicts that populations located at the periphery of a species' range should have lower levels of genetic variation than those at the centre of the range. However, most of the research on the CPH focuses on geographic distance and not on ecological distance, or uses categorical definitions of core and periphery to explain the distribution of genetic diversity. We use current climate data and historical climate data from the last glacial maxima to develop quantitative estimates of contemporary and historical ecological suitability using ecological niche models. We analysed genetic diversity using 12 polymorphic microsatellites to estimate changes in heterozygosity, allelic richness and population differentiation in 31 populations of the wood frog (Lithobates sylvaticus) spanning the species’ entire eastern clade (33o to 45o latitude) from Alabama, USA, to Nova Scotia, Canada. Our data support predictions based on the CPH. Populations showed significant differences in genetic diversity across the range, with lower levels of genetic variation at the geographic range edge and in areas with lower levels of historical and contemporary ecological suitability. However, history and geography (not current ecological suitability) best explain the patterns. This study highlights the importance of examining more than just geography when assessing the CPH, and the importance of historical ecological suitability in the maintenance of genetic diversity and population differentiation.
SuhB is a novel ribosome associated protein that regulates expression of MexXY by modulating ribosome stalling in Pseudomonas aeruginosa
Authors: Shi Jing , Jin Yongxin , Bian Ting , Li Kewei , Sun Ziyu , Cheng Zhihui , Jin Shouguang , Wu Weihui 
Published: July 2015

SummaryTranslation elongation is modulated by various ribosome‐binding proteins. Environmental stresses, such as starvation and antibiotics, can cause stalling of bacterial ribosomes, which may alter gene expression through a transcription or translation attenuation mechanism. In Pseudomonas aeruginosa, the expression of MexXY multidrug efflux system, which plays a significant role in resistance against aminoglycoside antibiotics, is controlled by a translation surveillance mechanism. Stalling of ribosome at the PA5471 leader peptide (PA5471.1) mRNA leads to transcription of PA5471, which subsequently up‐regulates the expression of MexXY. In this study, we found that mutation in a suhB gene leads to decreased susceptibility to aminoglycosides. Transcriptomic analysis revealed an up‐regulation of MexXY and PA5471, which were demonstrated to be responsible for the decreased susceptibility of the suhB mutant. We further demonstrated that PA5471.1 is essential for the up‐regulation of PA5471 in the suhB mutant. Co‐immunoprecipitation assay revealed an interaction between SuhB and ribosome, suggesting a role of SuhB in translation. Indeed, higher amount of PA5471.1 mRNA was found to associate with ribosome isolated from the suhB mutant, indicating increased ribosome stalling. Therefore, this study identified SuhB as a novel ribosome associated protein that is involved in modulating ribosome activity.
Ribosomal protein S6 phosphorylation is controlled by TOR and modulated by PKA in Candida albicans
Authors: Chowdhury Tahmeena , Köhler Julia R. 
Published: July 2015

SummaryTOR and PKA signaling pathways control eukaryotic cell growth and proliferation. TOR activity in model fungi, such as Saccharomyces cerevisiae, responds principally to nutrients, e.g., nitrogen and phosphate sources, which are incorporated into the growing cell mass; PKA signaling responds to the availability of the cells' major energy source, glucose. In the fungal commensal and pathogen, Candida albicans, little is known of how these pathways interact. Here, the signal from phosphorylated ribosomal protein S6 (P‐S6) was defined as a surrogate marker for TOR‐dependent anabolic activity in C. albicans. Nutritional, pharmacologic and genetic modulation of TOR activity elicited corresponding changes in P‐S6 levels. The P‐S6 signal corresponded to translational activity of a GFP reporter protein. Contributions of four PKA pathway components to anabolic activation were then examined. In high glucose concentrations, only Tpk2 was required to upregulate P‐S6 to physiologic levels, whereas all four tested components were required to downregulate P‐S6 in low glucose. TOR was epistatic to PKA components with respect to P‐S6. In many host niches inhabited by C. albicans, glucose is scarce, with protein being available as a nitrogen source. We speculate that PKA may modulate TOR‐dependent cell growth to a rate sustainable by available energy sources, when monomers of anabolic processes, such as amino acids, are abundant.
Dorsal root enhancement in paraneoplastic sensory ataxic neuropathy with anti‐Hu antibody
Authors: Shibui Aya , Kobayashi Junpei , Kuroda Hiroshi , Aoki Masashi 
Published: July 2015

AbstractMagnetic resonance imaging findings of paraneoplastic sensory ataxic neuropathy have previously shown that spinal cord lesions are located in the dorsal column. We report a 65‐year‐old man with paraneoplastic sensory ataxic neuropathy of subacute onset presenting dorsal root enhancement on magnetic resonance imaging. Pathological studies found that, in patients with sensory ataxic neuropathy associated with lung cancer, the dorsal roots and ganglia were severely degenerated with inflammatory cell infiltration, whereas the dorsal columns of the spinal cord were simply degenerated without inflammatory reaction, indicating centripetal Wallerian degeneration. There have been no radiological reports describing the preceding steps of Wallerian degeneration in the dorsal column, indicating the disruption of dorsal root ganglia. In the present case, we showed direct evidence of root inflammation detected as dorsal root enhancement in a patient with paraneoplastic sensory ataxic neuropathy of subacute onset.
Case of hereditary neuropathy with liability to pressure palsies presenting progressive muscular atrophy with lower motor neuron degeneration in the spinal cord and the brainstem
Authors: Tohge Rie , Shinoto Yuya , Takahashi Makio 
Published: July 2015

AbstractWe present a case of hereditary neuropathy with liability to pressure palsies developing progressive muscular atrophy, caused by the deletion of peripheral myelin protein‐22. The patient had a history of episodic peripheral nerve palsies during adolescence, and later manifested progressive bulbar palsy and muscular atrophy in all extremities in his 70s. Peripheral myelin protein‐22 is known to be expressed in Schwann cells, and its messenger ribonucleic acid is also expressed in lower motor neurons in the spinal cord and the brainstem. Therefore, the presented case suggests that the deletion of peripheral myelin protein‐22 facilitated impairment of peripheral nerves and lower motor neurons with aging and/or genetic stress, which could contribute to the pathogenesis of progressive muscular atrophy.
Resting anal pressure, not outlet obstruction or transit, predicts healthcare utilization in chronic constipation: a retrospective cohort analysis
Authors: Staller K. , Barshop K. , Kuo B. , Ananthakrishnan A. N. 
Published: July 2015

AbstractBackgroundChronic constipation is common and exerts a considerable burden on health‐related quality of life and healthcare resource utilization. Anorectal manometry (ARM) and colonic transit testing have allowed classification of subtypes of constipation, raising promise of targeted treatments. There has been limited study of the correlation between physiological parameters and healthcare utilization.MethodsAll patients undergoing ARM and colonic transit testing for chronic constipation at two tertiary care centers from 2000 to 2014 were included in this retrospective study. Our primary outcomes included number of constipation‐related and gastroenterology visits per year. Multivariate linear regression adjusting for confounders defined independent effect of measures of colonic and anorectal function on healthcare utilization.Key ResultsOur study included 612 patients with chronic constipation. More than 50% (n = 333) of patients had outlet obstruction by means of balloon expulsion testing and 43.5% (n = 266) had slow colonic transit. On unadjusted analysis, outlet obstruction (1.98 vs 1.68), slow transit (2.40 vs 2.07) and high resting anal pressure (2.16 vs 1.76) were all associated with greater constipation‐related visits/year compared to patients without each of those parameters (p < 0.05 for all). Outlet obstruction and high resting anal pressure were also associated with greater number of gastroenterology visits/year. After multivariate adjustment, high resting anal pressure was the only independent predictor of increased constipation‐related visits/year (p = 0.02) and gastroenterology visits/year (p = 0.04).Conclusions & InferencesAmong patients with chronic constipation, high resting anal pressure, rather than outlet obstruction or slow transit, predicts healthcare resource utilization.
Integration of photosynthesis, development and stress as an opportunity for plant biology
Authors: Allahverdiyeva Yagut , Battchikova Natalia , Brosché Mikael , Fujii Hiroaki , Kangasjärvi Saijaliisa , Mulo Paula , Mähönen Ari Pekka , Nieminen Kaisa , Overmyer Kirk , Salojärvi Jarkko , Wrzaczek Michael 
Published: July 2015

SummaryWith the tremendous progress of the past decades, molecular plant science is becoming more unified than ever. We now have the exciting opportunity to further connect subdisciplines and understand plants as whole organisms, as will be required to efficiently utilize them in natural and agricultural systems to meet human needs. The subfields of photosynthesis, plant developmental biology and plant stress are used as examples to discuss how plant science can become better integrated. The challenges, strategies and rich opportunities for the integration of the plant sciences are discussed. In recent years, more and more overlap between various subdisciplines has been inadvertently discovered including tradeoffs that may occur in plants engineered for biotechnological applications. Already important, bioinformatics and computational modelling will become even more central to structuring and understanding the ever growing amounts of data. The process of integrating and overlapping fields in plant biology research is advancing, but plant science will benefit from dedicating more effort and urgency to reach across its boundaries.
Betylmania? – Small Standing Stones and the Megaliths ofSouth‐WestBritain
Authors: Gillings Mark 
Published: July 2015

SummaryThis paper calls attention to a previously neglected element of the broad repertoire of monumental megalithic structures that characterize the later third and second millenniaBCacross theBritishIsles – extremely small standing stones. Despite their frequency and the complex arrangements and associations they embody, these miniliths are rarely recorded in detail and frequently marginalized to a generic background. As a result, they are largely absent from interpretative accounts. Drawing upon recent debates regarding materiality and monument form, alongside the results of excavations explicitly targeting tiny stone settings, the discussion argues that the phenomenon of raising and fixing small uprights was not only widespread and persistent, but sheds important light upon the beliefs and ideas driving monument construction during the laterNeolithic andBronzeAges.
Early Specialized Production? A Chalcolithic Stone Bracelet Workshop at Kanlitaş, Turkey
Authors: Baysal Emma , Baysal Adnan , Türkcan Ali Umut , Nazaroff Adam 
Published: July 2015

SummaryAn assemblage of marble bracelets, at various stages of manufacture, recovered during surface survey of the site of Kanlıtaş in Turkey, indicates that there was specialized production activity at the site during the Chalcolithic period. In this article we present the assemblage, evidence about material procurement, technology and manufacturing processes. We discuss the significance of the assemblage in relation to other sites in the area and as an example of production intended for inter‐site trade or exchange. We also address the wider issues of both the production of stone bracelets as a widespread practice in Anatolia from the Neolithic onwards, and the phenomenon of early specialized production.
Absence of capsule reveals glycan‐mediated binding and recognition of salivary mucin MUC7 by Streptococcus pneumoniae
Authors: Thamadilok S. , Roche‐Håkansson H. , Håkansson A.P. , Ruhl S. 
Published: July 2015

SummarySalivary proteins modulate bacterial colonization in the oral cavity and interact with systemic pathogens that pass through the oropharynx. An interesting example is the opportunistic respiratory pathogen Streptococcus pneumoniae that normally resides in the nasopharynx, but belongs to the greater Mitis group of streptococci, most of which colonize the oral cavity. Streptococcus pneumoniae also expresses a serine‐rich repeat (SRR) adhesin, PsrP, which is a homologue to oral Mitis group SRR adhesins, such as Hsa of Streptococcus gordonii and SrpA of Streptococcus sanguinis. As the latter bind to salivary glycoproteins through recognition of terminal sialic acids, we wanted to determine whether S. pneumoniae also binds to salivary proteins through possibly the same mechanism. We found that only a capsule‐free mutant of S. pneumoniae TIGR4 binds to salivary proteins, most prominently to mucin MUC7, but that this binding was not mediated through PsrP or recognition of sialic acid. We also found, however, that PsrP is involved in agglutination of human red blood cells (RBCs). After removal of PsrP, an additional previously masked lectin‐like adhesin activity mediating agglutination of sialidase‐treated RBCs becomes revealed. Using a custom‐spotted glycoprotein and neoglycoprotein dot blot array, we identify candidate glycan motifs recognized by PsrP and by the putative S. pneumoniae adhesin that could perhaps be responsible for pneumococcal binding to salivary MUC7 and glycoproteins on RBCs.
TLR4, NOD1 and NOD2 mediate immune recognition of putative newly identified periodontal pathogens
Authors: Marchesan J. , Jiao Y.Z. , Schaff R.A. , Hao J. , Morelli T. , Kinney J.S. , Gerow E. , Sheridan R. , Rodrigues V. , Paster B.J. , Inohara N. , Giannobile W.V. 
Published: July 2015

SummaryPeriodontitis is a polymicrobial inflammatory disease that results from the interaction between the oral microbiota and the host immunity. Although the innate immune response is important for disease initiation and progression, the innate immune receptors that recognize both classical and putative periodontal pathogens that elicit an immune response have not been elucidated. By using the Human Oral Microbe Identification Microarray (HOMIM), we identified multiple predominant oral bacterial species in human plaque biofilm that strongly associate with severe periodontitis. Ten of the identified species were evaluated in greater depth, six being classical pathogens and four putative novel pathogens. Using human peripheral blood monocytes (HPBM) and murine bone‐marrow‐derived macrophages (BMDM) from wild‐type (WT) and Toll‐like receptor (TLR)‐specific and MyD88 knockouts (KOs), we demonstrated that heat‐killed Campylobacter concisus, Campylobacter rectus, Selenomonas infelix, Porphyromonas endodontalis, Porphyromonas gingivalis, and Tannerella forsythia mediate high immunostimulatory activity. Campylobacter concisus, C. rectus, and S. infelix exhibited robust TLR4 stimulatory activity. Studies using mesothelial cells from WT and NOD1‐specific KOs and NOD2‐expressing human embryonic kidney cells demonstrated that Eubacterium saphenum, Eubacterium nodatum and Filifactor alocis exhibit robust NOD1 stimulatory activity, and that Porphyromonas endodontalis and Parvimonas micra have the highest NOD2 stimulatory activity. These studies allowed us to provide important evidence on newly identified putative pathogens in periodontal disease pathogenesis showing that these bacteria exhibit different immunostimulatory activity via TLR4, NOD1, and NOD2 (Clinicaltrials.gov NCT01154855).
Caregivers of children with no food allergy—their experiences and perception of food allergy
Authors: Yamamoto‐Hanada Kiwako , Futamura Masaki , Takahashi Osamu , Narita Masami , Kobayashi Fumio , Ohya Yukihiro 
Published: July 2015

AbstractBackgroundFood allergy (FA) is one of the most important health issues in schoolchildren. Although one of the most common places where pediatric anaphylaxis occurs is the home of a peer, the perception and experiences of caregivers who do not have a child with FA are unclear.MethodsAn anonymous paper‐based questionnaire was distributed to caregivers of FA children (FA caregivers) in the National Center for Child Health and Development and caregivers of non‐FA children (non‐FA caregivers) in public school in Tokyo. We examined the perception and experiences of FA among three groups: Group 1, non‐FA caregiver who had not witnessed adverse reactions and near‐miss events related to FA; Group 2, non‐FA caregivers who had witnessed adverse reactions and near‐miss events related to FA; and Group 3, caregivers who had a child with FA.ResultsEpinephrine auto‐injector was recognized by 43.6% non‐FA caregivers. Only 2.8% of non‐FA caregivers had experienced a child being bullied, harassed, or refused by a school because of FA. There were more caregivers in Group 2 who thought they could take the appropriate action if they witnessed a child with adverse response to causal food than in Group 1 (p < 0.05). All groups felt anxious over adverse events related to FA.ConclusionThe experiences and perception of FA were lacking among non‐FA caregivers. Therefore, it is also important to provide FA education for non‐FA caregivers to improve the quality of life of FA children.
Two Kinds of Stakes
Authors: Worsnip Alex 
Published: July 2015

AbstractI distinguish two different kinds of practical stakes associated with propositions. The W‐stakes (world) track what is at stake with respect to whether the proposition is true or false. The A‐stakes (attitude) track what is at stake with respect to whether an agent believes (or relies on) the proposition. This poses a dilemma for those who claim that whether a proposition is known can depend on the stakes associated with it. Only the W‐stakes reading of this view preserves intuitions about knowledge‐attributions, but only the A‐stakes reading preserves the putative link between knowledge and practical reasoning that has motivated it.