bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using genomic data to revisit an early example of reproductive character displacement inHaitianAnolislizards
Authors: Lambert Shea M. , Geneva Anthony J. , Luke Mahler D. , Glor Richard E. 
Published: March 2013

AbstractThe pattern of reproductive character displacement (RCD)—in which traits associated with reproductive isolation are more different where two species occur together than where they occur in isolation—is frequently attributed to reinforcement, a process during which natural selection acting against maladaptive mating events leads to enhanced prezygotic isolation between species or incipient species. One of the first studies ofRCDto include molecular genetic data was described 40 years ago in a complex of Haitian trunk anole lizards using a small number of allozyme loci. In this example,Anolis caudalisappears to experience divergence in the color and pattern of an extensible throat fan, or dewlap, in areas of contact with closely related species at the northern and southern limits of its range. However, this case study has been largely overlooked for decades; meanwhile, explanations for geographic variation in dewlap color and pattern have focused primarily on adaptation to local signalling environments. We reinvestigate this example using amplified fragment length polymorphism (AFLP) genome scans, mtDNAsequence data, information on dewlap phenotypes andGISdata on environmental variation to test the hypothesis ofRCDgenerated by reinforcement in Haitian trunk anoles. Together, our phenotypic and genetic results are consistent withRCDat the southern and northern limits of the range ofA. caudalis. We evaluate the evidence for reinforcement as the explanation forRCDin Haitian trunk anoles, consider alternative explanations and provide suggestions for future work on the relationship between dewlap variation and speciation inHaitian trunk anoles.
Mucormycosis after scorpion sting: case report
Authors: Pourahmad Morteza , Sepidkar Abdolali , Farokhnia Mohmmad H. , Tadayon Seyed M. K. , Salehi Hassan , Zabetian Hassan 
Published: March 2013

SummaryMucor is a fungus, which give rise to opportunistic infection in immunocompromised patients. We described a 55‐year‐old immunocompetent woman with cutaneous mucormycosis after scorpion sting. Mucormycosis may happen in patients with intact immunity and is not allocated only to patients with immune deficiency.
Impaired heme oxygenase‐1 induction in the gastric antrum induces disruption of the interstitial cells of Cajal network in a rat model of streptozotocin‐induced diabetes
Authors: Mogami S. , Suzuki H. , Tsugawa H. , Fukuhara S. , Hibi T. 
Published: March 2013

AbstractBackgroundStreptozotocin (STZ) is known to induce type I diabetes and the loss of the interstitial cells of Cajal (ICC). However, the regulation of heme oxygenase‐1 (HO‐1) expression, which is reported to protect ICC, has not yet been elucidated in this model. The aim of this study was to investigate the alterations of HO‐1 expression and clarify the mechanism of ICC loss in the stomach using the rat model of STZ‐induced diabetes.MethodsStreptozotocin (65 mg kg−1) was intraperitoneally administered to 8‐week‐old female Wistar rats. Cobalt protoporphyrin (CoPP), an HO‐1 inducer, was administered subcutaneously once a week after the STZ injection. The expressions of HO‐1 and the receptor tyrosine kinase c‐Kit (a marker for ICC) proteins were investigated by western blot analysis and immunofluorescence staining.Key ResultsExpression of c‐Kit, particularly in the gastric antrum, was significantly decreased at 8 weeks, not at 1 week, compared to those of the control group. Significantly increased induction of HO‐1 expression, especially in the gastric corpus but not in the antrum, was observed in the STZ group at 8 weeks after the STZ injection relative to control. CoPP administration significantly up‐regulated HO‐1 expression in the STZ diabetic group and significantly restored the previously reduced ICC in the gastric antrum.Conclusions & InferencesUp‐regulation of HO‐1 expression in the STZ diabetic model was limited to the gastric corpus and impaired up‐regulation of HO‐1 expression in the gastric antrum likely induced the disruption of the ICC network.
First ReliableRe–OsAges of Pyrite and Stable Isotope Compositions ofFe(‐Cu) Deposits in theHami Region,EasternTianshanOrogenicBelt,NW China
Authors: Huang Xiao‐Wen , Qi Liang , Gao Jian‐Feng , Zhou Mei‐Fu 
Published: March 2013

AbstractTheEasternTianshanOrogenicBelt (ETOB) inNW China is composed of theDananhu–Tousuquanarc belt, theKanggurtag belt, theAqishan–Yamansubelt and theCentralTianshan belt from north to south. These tectonic belts have formed through arc–continent or arc–arc collisions during thePaleozoic. A number ofFe(‐Cu) deposits in theAqishan–Yamansubelt, including theHeifengshan,Shuangfengshan andShaquanziFe(‐Cu) deposits, are associated withCarboniferous–EarlyPermian volcanic rocks and are composed of vein‐type magnetite ores. Metallic minerals are dominated by magnetite and pyrite, with minor chalcopyrite. Calcite, chlorite, and epidote are the dominant gangue minerals. Pyrite separates of ores from those three deposits have relatively high and variableRe contents ranging from 3.7 to 184 ppb. All pyrite separates have very low commonOs, allowing us calculation of single mineral model ages for each sample. Pyrite separates from theHeifengshanFe deposit have an187Re–187Os isochron age of 310 ± 23 Ma (MSWD= 0.04) and a weighted mean model age of 302 ± 5 Ma (MSWD= 0.17). Those from the ShuangfengshanFe deposit have an isochron age of 295 ± 7 Ma (MSWD= 0.28) and a weighted mean model age of 292 ± 5 Ma (MSWD= 0.33). TheShaquanziFe‐Cu deposit has pyrite with an isochron age of 295 ± 7 Ma (MSWD= 0.26) and a weighted mean model age of 295 ± 6 Ma (MSWD= 0.23). Pyrite separates from theseFe(‐Cu) deposits have δ34SCDTranging from −0.41‰ to 4.7‰ except for two outliers. Calcite from theHeifengshanFe deposit andShaquanziFe‐Cu deposit have similarCandOisotope compositions with δ13CPDBand δ18OSMOWranging from −5.5‰ to −1.0‰ and from 10‰ to 12.7‰, respectively. These stable isotopic data suggest thatS,C,andOare magmatic‐hydrothermal in origin. The association of low‐Ti magnetite andFe/Cu‐sulfides resembles those ofIron–Oxide–Copper–Gold (IOCG) deposits elsewhere. Our reliableRe–Os ages of pyrite suggest that theFe(‐Cu) deposits in theAqishan–Yamansubelt formed at ∼296Ma, probably in a back‐arc extensional environment.
Urban Structure Generalization in Multi‐Agent Process by Use of Reactional Agents
Authors: Renard Jérémy , Duchêne Cécile 
Published: March 2013

AbstractThis article proposes an improvement of automated cartographic generalization using multi‐agent sytems in urban areas. Indeed the AGENT model, whose robustness has been tested and approved through the European project AGENT, gives very good results in generalizing dense urban areas by means of enlargement, removal and displacement of buildings. But this model does not tackle the question of including particular structures like building alignments in the process, which is a crucial issue. The problem is that integrating such structures does not fit into the accurate top‐down hierarchy of urban agents. In order to face this problem, we propose to partly re‐engineer the model by introducing the concept of reactional agents whose behavior is very different from hierarchical agents of the original model as they use bottom‐up activation. In this view, urban alignment is considered to be a reactional agent activated only by its inner buildings, which generalizes the aligned buildings together into one entire structure. Associating reactional alignment behavior with new generalization actions on alignments significantly improves the model and gives better results in dense urban areas. Moreover, the idea could probably be used for other applications.
Analyzing Relatedness by Toponym Co‐Occurrences on Web Pages
Authors: Liu Yu , Wang Fahui , Kang Chaogui , Gao Yong , Lu Yongmei 
Published: March 2013

AbstractThis research proposes a method for capturing “relatedness between geographical entities” based on the co‐occurrences of their names on web pages. The basic assumption is that a higher count of co‐occurrences of two geographical places implies a stronger relatedness between them. The spatial structure of China at the provincial level is explored from the co‐occurrences of two provincial units in one document, extracted by a web information retrieval engine. Analysis on the co‐occurrences and topological distances between all pairs of provinces indicates that: (1) spatially close provinces generally have similar co‐occurrence patterns; (2) the frequency of co‐occurrences exhibits a power law distance decay effect with the exponent of 0.2; and (3) the co‐occurrence matrix can be used to capture the similarity/linkage between neighboring provinces and fed into a regionalization method to examine the spatial organization of China. The proposed method provides a promising approach to extracting valuable geographical information from massive web pages.
Lymphoid-Tissue Stromal Cells Coordinate Innate Defense to Cytomegalovirus
Authors: Verma Shilpi , Wang Qiao , Chodaczek Grzegorz , Benedict Chris A. 
Published: March 2013

ABSTRACTDuring mouse cytomegalovirus (MCMV) infection, the first wave of type I interferon (IFN-I) production peaks at ∼8 h. This IFN-I emanates from splenic stromal cells located in the marginal zone (MZ) and requires B cells that express lymphotoxin. The amount of IFN-I produced at these initial times is at least equivalent in magnitude to that produced later by dendritic cells (∼36 to 48 h), but the relative roles of these two IFN-I sources in regulating MCMV defense remain unclear. Here we show that IFN-I produced by MZ stromal cells dramatically restricts the first measurable burst of viral production, which occurs at ∼32 h. This primary innate control by IFN-I is partially mediated through the activation of natural killer (NK) cells, which produce gamma interferon in an IFN-I-dependent fashion, and is independent of Ly49H. Strikingly, MCMV production in the spleens of immunocompetent mice never increases at times after 32 h. These results highlight the critical importance of lymphoid-tissue stromal cells in orchestrating the earliest phase of innate defense to MCMV infection, capping replication levels, and blocking spread until infection is ultimately controlled.
Identification and Characterization of Genetically Divergent Members of the Newly Established Family Mesoniviridae
Authors: Zirkel Florian , Roth Hanna , Kurth Andreas , Drosten Christian , Ziebuhr John , Junglen Sandra 
Published: March 2013

ABSTRACT

The recently established family
Mesoniviridae
(order
Nidovirales
) contains a single species represented by two closely related viruses, Cavally virus (CavV) and Nam Dinh virus (NDiV), which were isolated from mosquitoes collected in Côte d'Ivoire and Vietnam, respectively. They represent the first nidoviruses to be discovered in insects. Here, we report the molecular characterization of four novel mesoniviruses, Hana virus, Méno virus, Nsé virus, and Moumo virus, all of which were identified in a geographical region in Côte d'Ivoire with high CavV prevalence. The viruses were found with prevalences between 0.5 and 2.8%, and genome sequence analyses and phylogenetic studies suggest that they represent at least three novel species. Electron microscopy revealed prominent club-shaped surface projections protruding from spherical, enveloped virions of about 120 nm. Northern blot data show that the four mesoniviruses analyzed in this study produce two major 3′-coterminal subgenomic mRNAs containing two types of 5′ leader sequences resulting from the use of different pairs of leader and body transcription-regulating sequences that are conserved among mesoniviruses. Protein sequencing, mass spectroscopy, and Western blot data show that mesonivirus particles contain eight major structural protein species, including the putative nucleocapsid protein (25 kDa), differentially glycosylated forms of the putative membrane protein (20, 19, 18, and 17 kDa), and the putative spike (S) protein (77 kDa), which is proteolytically cleaved at a conserved site to produce S protein subunits of 23 and 57 kDa. The data provide fundamental new insight into common and distinguishing biological properties of members of this newly identified virus family.
Integration of the Second Messenger c-di-GMP into the Chemotactic Signaling Pathway
Authors: Russell Matthew H. , Bible Amber N. , Fang Xin , Gooding Jessica R. , Campagna Shawn R. , Gomelsky Mark , Alexandre Gladys 
Published: March 2013

ABSTRACT

Elevated intracellular levels of the bacterial second messenger c-di-GMP are known to suppress motility and promote sessility. Bacterial chemotaxis guides motile cells in gradients of attractants and repellents over broad concentration ranges, thus allowing bacteria to quickly adapt to changes in their surroundings. Here, we describe a chemotaxis receptor that enhances, as opposed to suppresses, motility in response to temporary increases in intracellular c-di-GMP.
Azospirillum brasilense
’s preferred metabolism is adapted to microaerophily, and these motile cells quickly navigate to zones of low oxygen concentration by aerotaxis. We observed that changes in oxygen concentration result in rapid changes in intracellular c-di-GMP levels. The aerotaxis and chemotaxis receptor, Tlp1, binds c-di-GMP via its C-terminal PilZ domain and promotes persistent motility by increasing swimming velocity and decreasing swimming reversal frequency, which helps
A. brasilense
reach low-oxygen zones. If c-di-GMP levels remain high for extended periods,
A. brasilense
forms nonmotile clumps or biofilms on abiotic surfaces. These results suggest that association of increased c-di-GMP levels with sessility is correct on a long-term scale, while in the short-term c-di-GMP may actually promote, as opposed to suppress, motility. Our data suggest that sensing c-di-GMP by Tlp1 functions similar to methylation-based adaptation. Numerous chemotaxis receptors contain C-terminal PilZ domains or other sensory domains, suggesting that intracellular c-di-GMP as well as additional stimuli can be used to modulate adaptation of bacterial chemotaxis receptors.

IMPORTANCE
To adapt and compete under changing conditions, bacteria must not only detect and respond to various environmental cues but also be able to remain sensitive to further changes in the environmental conditions. In bacterial chemotaxis, chemosensory sensitivity is typically brought about by changes in the methylation status of chemotaxis receptors capable of modulating the ability of motile cells to navigate in gradients of various physicochemical cues. Here, we show that the ubiquitous second messenger c-di-GMP functions to modulate chemosensory sensitivity of a bacterial chemotaxis receptor in the alphaproteobacterium
Azospirillum brasilense
. Binding of c-di-GMP to the chemotaxis receptor promotes motility under conditions of elevated intracellular c-di-GMP levels. Our results revealed that the role of c-di-GMP as a sessile signal is overly simplistic. We also show that adaptation by sensing an intracellular metabolic cue, via PilZ or other domains, is likely widespread among bacterial chemotaxis receptors.
A Multifaceted Study of Pseudomonas aeruginosa Shutdown by Virulent Podovirus LUZ19
Authors: Lavigne Rob , Lecoutere Elke , Wagemans Jeroen , Cenens William , Aertsen Abram , Schoofs Liliane , Landuyt Bart , Paeshuyse Jan , Scheer Maurice , Schobert Max , Ceyssens Pieter-Jan 
Published: March 2013

ABSTRACT

In contrast to the rapidly increasing knowledge on genome content and diversity of bacterial viruses, insights in intracellular phage development and its impact on bacterial physiology are very limited. We present a multifaceted study combining quantitative PCR (qPCR), microarray, RNA-seq, and two-dimensional gel electrophoresis (2D-GE), to obtain a global overview of alterations in DNA, RNA, and protein content in
Pseudomonas aeruginosa
PAO1 cells upon infection with the strictly lytic phage LUZ19. Viral genome replication occurs in the second half of the phage infection cycle and coincides with degradation of the bacterial genome. At the RNA level, there is a sharp increase in viral mRNAs from 23 to 60% of all transcripts after 5 and 15 min of infection, respectively. Although microarray analysis revealed a complex pattern of bacterial up- and downregulated genes, the accumulation of viral mRNA clearly coincides with a general breakdown of abundant bacterial transcripts. Two-dimensional gel electrophoretic analyses shows no bacterial protein degradation during phage infection, and seven stress-related bacterial proteins appear. Moreover, the two most abundantly expressed early and late-early phage proteins, LUZ19 gene product 13 (Gp13) and Gp21, completely inhibit
P. aeruginosa
growth when expressed from a single-copy plasmid. Since Gp13 encodes a predicted GNAT acetyltransferase, this observation points at a crucial but yet unexplored level of posttranslational viral control during infection.

IMPORTANCE
Massive genome sequencing has led to important insights into the enormous genetic diversity of bacterial viruses (bacteriophages). However, for nearly all known phages, information on the impact of the phage infection on host physiology and intracellular phage development is scarce. This aspect of phage research should be revitalized, as phages evolved genes which can shut down or redirect bacterial processes in a very efficient way, which can be exploited towards antibacterial design. In this context, we initiated a study of the human opportunistic pathogen
Pseudomonas aeruginosa
under attack by one its most common predators, the
Phikmvlikevirus
. By analyzing various stages of infection at different levels, this study uncovers new features of phage infection, representing a cornerstone for future studies on members of this phage genus.
Microanatomy at Cellular Resolution and Spatial Order of Physiological Differentiation in a Bacterial Biofilm
Authors: Serra Diego O. , Richter Anja M. , Klauck Gisela , Mika Franziska , Hengge Regine 
Published: March 2013

ABSTRACT

Bacterial biofilms are highly structured multicellular communities whose formation involves flagella and an extracellular matrix of adhesins, amyloid fibers, and exopolysaccharides. Flagella are produced by still-dividing rod-shaped
Escherichia coli
cells during postexponential growth when nutrients become suboptimal. Upon entry into stationary phase, however, cells stop producing flagella, become ovoid, and generate amyloid curli fibers. These morphological changes, as well as accompanying global changes in gene expression and cellular physiology, depend on the induction of the stationary-phase sigma subunit of RNA polymerase, σ
S
(RpoS), the nucleotide second messengers cyclic AMP (cAMP), ppGpp, and cyclic-di-GMP, and a biofilm-controlling transcription factor, CsgD. Using flagella, curli fibers, a CsgD::GFP reporter, and cell morphology as “anatomical” hallmarks in fluorescence and scanning electron microscopy, different physiological zones in macrocolony biofilms of
E. coli
K-12 can be distinguished at cellular resolution. Small ovoid cells encased in a network of curli fibers form the outer biofilm layer. Inner regions are characterized by heterogeneous CsgD::GFP and curli expression. The bottom zone of the macrocolonies features elongated dividing cells and a tight mesh of entangled flagella, the formation of which requires flagellar motor function. Also, the cells in the outer-rim growth zone produce flagella, which wrap around and tether cells together. Adjacent to this growth zone, small chains and patches of shorter curli-surrounded cells appear side by side with flagellated curli-free cells before curli coverage finally becomes confluent, with essentially all cells in the surface layer being encased in “curli baskets.”

IMPORTANCE
Heterogeneity or cellular differentiation in biofilms is a commonly accepted concept, but direct evidence at the microscale has been difficult to obtain. Our study reveals the microanatomy and microphysiology of an
Escherichia coli
macrocolony biofilm at an unprecedented cellular resolution, with physiologically different zones and strata forming as a function of known global regulatory networks that respond to biofilm-intrinsic gradients of nutrient supply. In addition, this study identifies zones of heterogeneous and potentially bistable CsgD and curli expression, shows bacterial curli networks to strikingly resemble Alzheimer plaques, and suggests a new role of flagella as an architectural element in biofilms.
Living and Thriving on the Skin:
Malassezia
Genomes Tell the Story
Authors: Coelho Marco A. , Sampaio José Paulo , Gonçalves Paula 
Published: March 2013

ABSTRACT

Our understanding of the interactions between normal skin microbiota and the human host has been greatly extended by recent investigations. In their recent study in
mBio
, A. Gioti et al. (mBio 4[1]:e00572-12, 2013) sequenced the genome of the atopic eczema-associated yeast,
Malassezia sympodialis
, and compared its gene content and organization with that of
Malassezia globosa
, a species implicated in dandruff. Their findings were also contrasted with those previously obtained for
Ustilago maydis
, which is a close relative but ecologically distinct plant parasite. Besides gaining additional insight into key host-specific adaptations and the particular function and molecular evolution of allergens related to atopic eczema, Gioti et al. also uncovered several lines of evidence that elegantly suggest the presence of an extant sexual cycle, with important implications in disease.