bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in MYB expression and gene abnormalities further confirm that salivary cribriform basal cell tumors and adenoid cystic carcinoma are two distinct tumor entities
Authors: Tian Zhen , Li Lei , Zhang Chun‐ye , Gu Ting , Li Jiang 
Published: December 2015

BackgroundIn practices, some cases of salivary basal cell tumors that consist mainly of cribriform growth pattern are difficult to differentiate from adenoid cystic carcinoma (AdCC). Identification of reliable molecular biomarkers for the differential diagnosis between them is required.MethodsTwenty‐two cases of cribriform salivary basal cell tumors (at least 10% cribriform pattern present in each tumor) comprising 18 cases of basal cell adenoma (BCA) and four cases of basal cell adenocarcinoma (BcAC) were collected between 1985 and 2008. Twenty cases of cribriform AdCC were retrieved from our archives. MYB protein expression and gene abnormalities were detected in all cases by immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) analyses, respectively.ResultsNeither MYB protein nor split genes were detected in any of the cases of cribriform basal cell tumors, while 55% (11/20) of cases of cribriform AdCC had MYB protein expression. High MYB expression was detected in 81.8% (9/11) cases, while low expression was found in the remaining cases. FISH analysis indicated that nine AdCC tumors with high MYB protein expression were split gene‐positive, while MYB gene splitting was not detected in the 11 cases with low or absent MYB protein expression.ConclusionThe molecular changes in AdCC differ from those associated with cribriform basal cell tumors, which further confirms that cribriform basal cell tumors and AdCC are two distinct tumor entities. Simultaneous detection of MYB protein expression and the associated molecular changes could be beneficial in differentiating salivary cribriform basal cell tumors from AdCC.
Refined assessment of the geographic distribution of Geoffroy's cat (Leopardus geoffroyi) (Mammalia: Felidae) in the Neotropics
Authors: Cuyckens G. A. E. , Pereira J. A. , Trigo T. C. , Da Silva M. , Gonçalves L. , Huaranca J. C. , Bou Pérez N. , Cartes J. L. , Eizirik E. 
Published: December 2015

AbstractUnderstanding the fine‐scale geographic distribution of a species has applications in biogeography, ecology, evolution and conservation. Species distribution models (SDM) have been widely used to predict geographic and climatic ranges of species. Geoffroy's cat Leopardus geoffroyi is a small felid of least concern that occupies a wide variety of habitat types in Argentina, Bolivia, Brazil, Chile, Paraguay and Uruguay. We evaluated the fine‐scale distribution of Geoffroy's cat at the sub‐continental level, estimated its current extent and area of occurrence and discussed the current and potential ranges developed with SDM. On the basis of species occurrences (n = 1502) and large‐scale environmental data, two model types (‘environmental’ and ‘land cover’) were developed using MaxEnt. The estimated extent of occurrence of Geoffroy's cat was 3 180 664 km2, but the potential area of occurrence predicted by our environmental model was 70% larger due to areas with high suitability (i.e. >0.5) compared to the species’ current range. The most important bioclimatic factors affecting Geoffroy's cat presence were temperature seasonality, mean temperature of the coldest quarter and annual precipitation. Two recent records obtained outside the known distribution of the species fell within the high‐suitability area (i.e. >0.5) predicted by our model. Our SDM suggest that this habitat‐generalist felid is probably expanding its distribution range by taking advantage of changes in human land use.
Performance of non‐invasive models of fibrosis in predicting mild to moderate fibrosis in patients with non‐alcoholic fatty liver disease
Authors: Siddiqui Mohammad S. , Patidar Kavish R. , Boyett Sherry , Luketic Velimir A. , Puri Puneet , Sanyal Arun J. 
Published: December 2015

AbstractBackground & AimsIn non‐alcoholic fatty liver disease, presence of fibrosis is predictive of long‐term liver–related complications. Currently, there are no reliable and non‐invasive means of quantifying fibrosis in those with non‐alcoholic fatty liver disease. Therefore, we aimed to evaluate the performance of a panel of non‐invasive models in predicting fibrosis in non‐alcoholic fatty liver disease.MethodsThe accuracy of FibroMeter non‐alcoholic fatty liver disease, fibrosis 4 and four other non‐invasive models in predicting fibrosis in those with biopsy proven non‐alcoholic fatty liver disease was compared. These models were constructed post hoc in patients who had necessary clinical information collected within 2 months of a liver biopsy. The areas under receiver operating characteristics curves were compared for each model using Delong analysis. Optimum cut‐off for each model and fibrosis stage were calculated using the Youden index.ResultsThe area under receiver operating characteristics curves for F ≥ 1 fibrosis for fibrosis 4 and FibroMeter non‐alcoholic fatty liver disease was 0.821 and 0.801 respectively. For F ≥ 3, the area under receiver operating characteristics curves was 0.866 for fibrosis 4 and 0.862 for FibroMeter non‐alcoholic fatty liver disease. Delong analysis showed the area under receiver operating characteristics curves was statistically different for fibrosis 4 and FibroMeter non‐alcoholic fatty liver disease compared with BARD, BAAT and aspartate aminotransferase:alanine aminotransferase ratio for F ≥ 1 and F ≥ 3. Area under receiver operating characteristics curves were significantly different for fibrosis 4 and FibroMeter non‐alcoholic fatty liver disease for F ≥ 3 compared with non‐alcoholic fatty liver disease fibrosis score. At a fixed sensitivity of 90%, FibroMeter non‐alcoholic fatty liver disease had the highest specificity for F ≥ 1 (52.4%) and F ≥ 3 (63.8%). In contrast, at a fixed specificity of 90%, fibrosis 4 outperformed other models with a sensitivity of 60.2% for F ≥ 1 and 70.6% for F ≥ 3 fibrosis.ConclusionThese non‐invasive models of fibrosis can predict varying degrees of fibrosis from routinely collected clinical information in non‐alcoholic fatty liver disease.
Ribosome‐associated pentatricopeptide repeat proteins function as translational activators in mitochondria of trypanosomes
Authors: Aphasizheva Inna , Maslov Dmitri A. , Qian Yu , Huang Lan , Wang Qi , Costello Catherine E. , Aphasizhev Ruslan 
Published: December 2015

SummaryMitochondrial ribosomes of Trypanosoma brucei are composed of 9S and 12S rRNAs, eubacterial‐type ribosomal proteins, polypeptides lacking discernible motifs and approximately 20 pentatricopeptide repeat (PPR) RNA binding proteins. Several PPRs also populate the polyadenylation complex; among these, KPAF1 and KPAF2 function as general mRNA 3′ adenylation/uridylation factors. The A/U‐tail enables mRNA binding to the small ribosomal subunit and is essential for translation. The presence of A/U‐tail also correlates with requirement for translation of certain mRNAs in mammalian and insect parasite stages. Here, we inquired whether additional PPRs activate translation of individual mRNAs. Proteomic analysis identified KRIPP1 and KRIPP8 as components of the small ribosomal subunit in mammalian and insect forms, but also revealed their association with the polyadenylation complex in the latter. RNAi knockdowns demonstrated essential functions of KRIPP1 and KRIPP8 in the actively respiring insect stage, but not in the mammalian stage. In the KRIPP1 knockdown, A/U‐tailed mRNA encoding cytochrome c oxidase subunit 1 declined concomitantly with the de novo synthesis of this subunit whereas polyadenylation and translation of cyb mRNA were unaffected. In contrast, the KRIPP8 knockdown inhibited A/U‐tailing and translation of both CO1 and cyb mRNAs. Our findings indicate that ribosome‐associated PPRs may selectively activate mRNAs for translation.
Transcriptional control of quorum sensing and associated metabolic interactions in Pseudomonas syringae strain B728a
Authors: Scott Russell A. , Lindow Steven E. 
Published: December 2015

SummaryPseudomonas syringae pv. syringae cell densities fluctuate regularly during host plant colonization. Previously we identified nine genes dependent on the quorum‐sensing‐associated luxR homolog ahlR during epiphytic and apoplastic stages of host colonization. Yet their contributions to host colonization remain obscure, despite ahlR regulon presence within and beyond the P. syringae pan‐genome. To elucidate AhIR regulon member functions, we characterized their regulation, interactions with each other, and contributions to the metabolome. We report Psyr_1625, encoding a functional pyruvate deydrogenase‐E1 subunit PdhQ, is required to prevent the accumulation of pyruvate in rich media. Furthermore it is exquisitely regulated by both repression of its own promoter by QrpR within a novel clade of the MarR regulator family, and co‐transcription on a 5kb transcript originating from the AhlR‐driven ahlI promoter, that reads over ahlR and qrpR. Metabolites accumulated during expression of the second AhlR‐driven operon (Psyr_1620‐1616, paoABCDE), only in a pdhQ mutant background, in addition to pyruvate, are herein associated with derepression of QrpR‐repressed pdhQ. AHL signaling, QrpR, and transcriptional read‐through events integrate to ensure AHL‐dependent expression of a novel metabolism in anticipation of environmental stress, while minimizing endogenously generated cytotoxicity.
The Legionella pneumophila CpxRA two‐component regulatory system: new insights into CpxR's function as a dual regulator and its connection to the effectors regulatory network
Authors: Feldheim Yaron S. , Zusman Tal , Speiser Yariv , Segal Gil 
Published: December 2015

SummaryLegionella pneumophila utilizes the Icm/Dot type‐IV secretion system to translocate approximately 300 effector proteins into host cells, and the CpxRA two‐component system (TCS) was previously shown to regulate the expression of several of these effectors. In this study, we expanded the pool of L. pneumophila CpxR‐regulated genes to 38, including 27 effector‐encoding genes. Our study demonstrates for the first time that the CpxR dual regulator has different requirements for activation and repression of target genes. These differences include the positioning of the CpxR regulatory element relative to the promoter element, and the effect of CpxR phosphate donors on the expression of CpxR target genes. In addition, unlike most response regulators, a mutant form of the L. pneumophila CpxR which cannot be phosphorylated was found to self‐interact, and to repress gene expression similarly to wild‐type CpxR, even though its ability to activate gene expression was reduced. Moreover, the CpxRA TCS was found to activate the expression of LetE which was found to function as a connector protein between the CpxRA TCS and the LetAS‐RsmYZ‐CsrA regulatory cascade. Our results show that CpxR plays a major role in L. pneumophila pathogenesis gene expression and functions as part of a regulatory network.
RNase III mediated cleavage of the coding region of mraZ mRNA is required for efficient cell division in Corynebacterium glutamicum
Authors: Maeda Tomoya , Tanaka Yuya , Takemoto Norihiko , Hamamoto Nagisa , Inui Masayuki 
Published: December 2015

SummaryThe Corynebacterium glutamicum R cgR_1959 gene encodes an endoribonuclease of the RNase III family. Deletion mutant of cgR_1959 (Δrnc mutant) showed an elongated cell shape, and presence of several lines on the cell surface, indicating a required of RNase III for maintaining normal cell morphology in C. glutamicum. The level of mraZ mRNA was increased, whereas cgR_1596 mRNA encoding a putative cell wall hydrolase and ftsEX mRNA were decreased in the Δrnc mutant. The half‐life of mraZ mRNA was significantly prolonged in the Δrnc and the Δpnp mutant strains. This indicated that the degradation of mraZ mRNA was performed by RNase III and the 3′‐to‐5′ exoribonuclease, PNPase. Northern hybridization and primer extension analysis revealed that the cleavage site for mraZ mRNA by RNase III is in the coding region. Overproduction of MraZ resulted in an elongated cell shape. The expression of ftsEX decreased while that of cgR_1596 unchanged in an MraZ‐overexpressing strain. An electrophoretic mobility shift assay and a transcriptional reporter assay indicate that MraZ is a transcriptional repressor of ftsEX in C. glutamicum. These results indicate that RNase III is required for efficient expression of MraZ‐dependent ftsEX and MraZ‐independent cgR_1596.
ZAP1‐mediated modulation of triacylglycerol levels in yeast by transcriptional control of mitochondrial fatty acid biosynthesis
Authors: Singh Neelima , Yadav Kamlesh Kumar , Rajasekharan Ram 
Published: December 2015

SummaryThe transcriptional activator Zap1p maintains zinc homeostasis in Saccharomyces cerevisiae. In this study, we examined the role of Zap1p in triacylglycerol (TAG) metabolism. The expression of ETR1 is reduced in zap1Δ. The altered expression of ETR1 results in reduced mitochondrial fatty acid biosynthesis and reduction in lipoic acid content in zap1Δ. The transcription factor Zap1 positively regulates ETR1 expression. Deletion of ETR1 also causes the accumulation of TAG, and the introduction of ETR1 in zap1Δ strain rescues the TAG level. These results demonstrated that the compromised mitochondrial fatty acid biosynthesis causes a reduction in lipoic acid and loss of mitochondrial function in zap1Δ. Functional mitochondria are required for the ATP production and defect in mitochondria slow down the process which may channeled carbon towards lipid biosynthesis and stored in the form of TAG.
Hydrogen sulfide is a novel potential virulence factor of Mycoplasma pneumoniae: characterization of the unusual cysteine desulfurase/desulfhydrase HapE
Authors: Großhennig Stephanie , Ischebeck Till , Gibhardt Johannes , Busse Julia , Feussner Ivo , Stülke Jörg 
Published: December 2015

SummaryMycoplasma pneumoniae is a human pathogen causing atypical pneumonia with a minimalized and highly streamlined genome. So far, hydrogen peroxide production, cytadherence, and the ADP‐ribosylating CARDS toxin have been identified as pathogenicity determinants. We have studied haemolysis caused by M. pneumoniae, and discovered that hydrogen peroxide is responsible for the oxidation of heme, but not for lysis of erythrocytes. This feature could be attributed to hydrogen sulfide, a compound that has previously not been identified as virulence factor in lung pathogens. Indeed, we observed hydrogen sulfide production by M. pneumoniae. The search for a hydrogen sulfide‐producing enzyme identified HapE, a protein with similarity to cysteine desulfurases. In contrast to typical cysteine desulfurases, HapE is a bifunctional enzyme: it has both the cysteine desulfurase activity to produce alanine and the cysteine desulfhydrase activity to produce pyruvate and hydrogen sulfide. Experiments with purified HapE showed that the enzymatic activity of the protein is responsible for haemolysis, demonstrating that HapE is a novel potential virulence factor of M. pneumoniae.
Salt‐sensitivity of σH and Spo0A prevents sporulation of Bacillus subtilis at high osmolarity avoiding death during cellular differentiation
Authors: Widderich Nils , Rodrigues Christopher D. A. , Commichau Fabian M. , Fischer Kathleen E. , Ramirez‐Guadiana Fernando H. , Rudner David Z. , Bremer Erhard 
Published: December 2015

SummaryThe spore‐forming bacterium Bacillus subtilis frequently experiences high osmolarity as a result of desiccation in the soil. The formation of a highly desiccation‐resistant endospore might serve as a logical osmostress escape route when vegetative growth is no longer possible. However, sporulation efficiency drastically decreases concomitant with an increase in the external salinity. Fluorescence microscopy of sporulation‐specific promoter fusions to gfp revealed that high salinity blocks entry into the sporulation pathway at a very early stage. Specifically, we show that both Spo0A‐ and SigH‐dependent transcription are impaired. Furthermore, we demonstrate that the association of SigH with core RNA polymerase is reduced under these conditions. Suppressors that modestly increase sporulation efficiency at high salinity map to the coding region of sigH and in the regulatory region of kinA, encoding one the sensor kinases that activates Spo0A. These findings led us to discover that B. subtilis cells that overproduce KinA can bypass the salt‐imposed block in sporulation. Importantly, these cells are impaired in the morphological process of engulfment and late forespore gene expression and frequently undergo lysis. Altogether our data indicate that B. subtilis blocks entry into sporulation in high‐salinity environments preventing commitment to a developmental program that it cannot complete.
A minimized motile machinery for Mycoplasma genitalium
Authors: García‐Morales Luis , González‐González Luis , Querol Enrique , Piñol Jaume 
Published: December 2015

SummaryThe cell wall‐less bacterium Mycoplasma genitalium uses specialized adhesins located at the terminal organelle to adhere to host cells and surfaces. The terminal organelle is a polar structure protruding from the cell body that is internally supported by a cytoskeleton and also has an important role in cell motility. We have engineered a M. genitalium null mutant for MG491 protein showing a massive downstream destabilization of proteins involved in the terminal organelle organization. This mutant strain exhibited striking similarities with the previously isolated MG_218 null mutant strain. Upon introduction of an extra copy of MG_318 gene in both strains, the amount of main adhesins P140 and P110 dramatically increased. These strains were characterized by microcinematography, epifluorescence microscopy and cryo‐electron microcopy, revealing the presence of motile cells and filaments in the absence of many proteins considered essential for cell adhesion and motility. These results indicate that adhesin complexes play a major role in the motile machinery of M. genitalium and demonstrate that the rod element of the cytoskeleton core is not the molecular motor propelling mycoplasma cells. These strains containing a minimized motile machinery also provide a valuable cell model to investigate the adhesion and gliding properties of this human pathogen.
Expression of IroN, the salmochelin siderophore receptor, requires mRNA activation by RyhB small RNA homologues
Authors: Balbontín Roberto , Villagra Nicolás , Pardos de la Gándara Maria , Mora Guido , Figueroa‐Bossi Nara , Bossi Lionello 
Published: December 2015

SummaryThe iroN gene of Salmonella enterica and uropathogenic Escherichia coli encodes the outer membrane receptor of Fe3+‐bound salmochelin, a siderophore tailored to evade capture by the host's immune system. The iroN gene is under negative control of the Fur repressor and transcribed under iron limiting conditions. We show here that transcriptional de‐repression is not sufficient to allow iroN expression, as this also requires activation by either of two partially homologous small RNAs (sRNAs), RyhB1 and RyhB2. The two sRNAs target the same sequence segment approximately in the middle of the 94‐nucleotide 5′ untranslated region (UTR) of iroN mRNA. Several lines of evidence suggest that base pair interaction stimulates iroN mRNA translation. Activation does not result from the disruption of a secondary structure masking the ribosome binding site; rather it involves sequences at the 5′ end of iroN 5′ UTR. In vitro ‘toeprint’ assays revealed that this upstream site binds the 30S ribosomal subunit provided that RyhB1 is paired with the mRNA. Altogether, our data suggest that RyhB1, and to lesser extent RyhB2, activate iroN mRNA translation by promoting entry of the ribosome at an upstream ‘standby’ site. These findings add yet an additional nuance to the polychromatic landscape of sRNA‐mediated regulation.
Clinically silent seizures in a neonate with tuberous sclerosis
Authors: Ikeno Mitsuru , Okumura Akihisa , Abe Shinpei , Igarashi Ayuko , Hisata Ken , Shoji Hiromichi , Shimizu Toshiaki 
Published: December 2015

AbstractAlthough seizures during infancy in patients with tuberous sclerosis complex are common, seizures in neonates are infrequent. Here, we report the clinical course and electroencephalography (EEG) findings of a neonate with tuberous sclerosis complex associated with clinically silent seizures. The patient was a girl in whom cardiac tumors were detected on fetal ultrasonography. Brain magnetic resonance imaging during the neonatal period showed subependymal and cortical tubers. Routine EEG indicated unexpected ictal changes with no noticeable clinical symptoms. Ictal EEG was associated with a subtle increase in heart rate and a brief increase in chin electromyogram. These changes were difficult to identify clinically. The patient later developed focal seizures and epileptic spasms and had severe psychomotor delay. The present case suggests the occurrence of clinically silent seizures before the appearance of epileptic spasms in infants with tuberous sclerosis, and that EEG is an option for neonates with a prenatal diagnosis.
Acute oral complications in a pediatric patient with acute lymphoid leukemia
Authors: Kamasaki Yoko , Satoh Kyoko , Nishiguchi Miyuki , Hoshino Tomonori , Fujiwara Taku 
Published: December 2015

AbstractPseudomonas aeruginosa is a low‐virulence pathogen that can cause infection in immunocompromised patients. Among pediatric hematologists, it is known that careful attention should be paid to P. aeruginosa as the bacteria responsible for intraoral inflammation, and antibiotic therapy targeting P. aeruginosa is the first‐line treatment during neutropenia in patients with hematological malignancy. Immunosuppressed patients, however, are at high risk of developing inflammation. Here, we report a case involving a 10‐year‐old patient with acute lymphoid leukemia (ALL), in which P. aeruginosa synergistically acted with pre‐existing gingivitis to induce unusual oral necrotic lesions, leading to acute buccal cellulitis and pus discharge from external sinus tracts.
Conceptualizing Social Attention in Developmental Research
Authors: Salley Brenda , Colombo John 
Published: December 2015

AbstractThe term social attention has become widely used during the last decade, appearing within behavioral neuroscience and developmental neurocognitive literatures to characterize a variety of activities and cognitive processes that emerge in the presence of conspecifics. We provide here an overview of the current status of social attention as a construct, as reflected in its appearance in research studies, and we offer a framework for characterizing the extant literature based on the functions of social attention processes: as behavior for social communication, as motivation to engage in social communication, and as a form of basic visual attention in the context of other social agents. We then provide two overarching questions to guide future research efforts directed toward establishing the utility of social attention as an independent and/or unified construct. We then consider implications and recommendations for future research efforts.