bluuebunny/crossref_metadata_2025_split huggingface dataset:
A newcis-acting regulatory element driving gene expression in the zebrafish pineal gland
Authors: Alon Shahar , Eisenberg Eli , Jacob-Hirsch Jasmine , Rechavi Gideon , Vatine Gad , Toyama Reiko , Coon Steven L. , Klein David C. , Gothilf Yoav 
Published: January 2009

AbstractMotivation: The identification of functional cis-acting DNA regulatory elements is a crucial step towards understanding gene regulation. Ab initio motif detection algorithms have been extensively used in search of regulatory elements. Yet, their success in providing experimentally validated regulatory elements in vertebrates has been limited.Results: Here we report in silico identification and in vivo validation of regulatory elements that determine enhanced gene expression in the pineal gland of zebrafish. Microarray data enabled detection of genes that exhibit high expression in the pineal gland. The promoter regions of these genes were computationally analyzed in order to identify overrepresented motifs. The highest ranking motif identified is a CRX/OTX binding site, known to govern expression in the pineal gland and retina. The second highest ranking motif was not reported before; we experimentally validated its function in vivo by mutational analysis. The methodology presented here may be applicable as a general scheme for finding regulatory elements that contribute to tissue-specific gene expression.Contacts: yoavg@tauex.tau.ac.il; elieis@post.tau.ac.ilSupplementary information: Supplementary data are available at Bioinformatics online.
DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins
Authors: Nishima Wataru , Qi Guoying , Hayward Steven , Kitao Akio 
Published: January 2009

Abstract
Motivation: The biological function of proteins is associated with a variety of motions, ranging from global domain motion to local motion of side chain. We propose a method, dihedral transition analysis (DTA), to identify significant dihedral angle changes between two distinct protein conformations and for characterization of the effect of these transitions on both local and global conformation.
Results: Applying DTA to a comprehensive and non-redundant dataset of 459 high-resolution pairs of protein structures, we found that a dihedral transition occurs in 82% of proteins. Multiple dihedral transitions are shown to occur cooperatively along the sequence, which allows us to separate a polypeptide chain into fragments with and without transitions, namely transition fragments (TFs) and stable fragments (SFs), respectively. By characterizing the magnitude of TF conformational change and the effect of the transition on the neighboring fragments, flap and hinge motions are identified as typical motions. DTA is also useful to detect protein motions, subtle in RMSD but significant in terms of dihedral angle changes, such as the peptide-plane flip, the side-chain flip and path-preserving motions. We conclude that DTA is a useful tool to extract potential functional motions, some of which might have been missed using conventional methods for protein motion analysis.
Availability: http://dynamics.iam.u-tokyo.ac.jp/DTA/
Contact: kitao@iam.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Morphological convergence and coexistence in three sympatric North American species of Microtus (Rodentia: Arvicolinae)
Authors: Spaeth Paula Ann 
Published: January 2009

AbstractAim  Niche theory predicts that ecologically identical species cannot stably coexist in local communities. My aim was to investigate morphological diversity as a possible factor enabling the coexistence of a species‐rich Microtus (Rodentia: Arvicolinae) fauna in a hotspot of North American mammalian diversity, the Greater Yellowstone Ecosystem (GYE).Location  The Greater Yellowstone Ecosystem, North America.Methods  Using in‐hand morphological measurements of size and shape, I compared the morphologies of three North American vole species (Microtus spp.), in sympatry in the GYE and in allopatry across their ranges, in order to examine: (1) whether morphologies are fixed or plastic and (2) the degree of morphological character displacement or convergence in sympatric species.Results  Support was found for plasticity of morphology for all three vole species: M. longicaudus, M. montanus and M. pennsylvanicus. However, Microtus individuals of all species from the GYE area of sympatry were more similar to each other than to allopatric individuals of the same species.Main conclusions  Competition among these congeners is not manifested in morphological overdispersion. The response of these congeneric species to the same local ecological conditions is convergent. The relative strength of environmental conditions appears to be stronger than the strength of competitive interactions among the study species.
Glycolipids are involved in biofilm accumulation and prolonged bacteraemia in Enterococcus faecalis
Authors: Theilacker Christian , Sanchez‐Carballo Patricia , Toma Ioana , Fabretti Francesca , Sava Irina , Kropec Andrea , Holst Otto , Huebner Johannes 
Published: January 2009

SummaryBiofilm production is thought to be an important step in many enterococcal infections. In several Gram‐positive bacteria, membrane glycolipids have been implicated in biofilm formation. We constructed a non‐polar deletion mutant of a putative glucosyltransferase designated biofilm‐associated glycolipid synthesis A (bgsA) in Enterococcus faecalis 12030. Analysis of major extracted glycolipids by nuclear magnetic resonance spectroscopy revealed that the cell membrane of 12030ΔbgsA was devoid of diglucosyl–diacylglycerol (DGlcDAG), while monoglucosyl–diacylglycerol was overrepresented. The cell walls of 12030ΔbgsA contained longer lipoteichoic acid molecules and were less hydrophobic than wild‐type bacteria. Inactivation of bgsA in E. faecalis 12030 and E. faecalis V583 led to an almost complete arrest of biofilm formation on plastic surfaces. Overexpression of bgsA, on the other hand, resulted in increased biofilm production. While initial adherence was not affected, bgsA‐deficient bacteria did not accumulate in the growing biofilm. Also, adherence of E. faecalisΔbgsA to Caco‐2 cells was impaired. In a mouse bacteraemia model, E. faecalis 12030ΔbgsA was cleared more rapidly from the bloodstream than the wild‐type strain. In summary, BgsA is a glycosyltransferase synthetizing DGlcDAG, a glycolipid and lipoteichoic acid precursor involved in biofilm accumulation, adherence to host cells, and virulence in vivo.
Cross‐immunity and immune mimicry as mechanisms of resistance to the lantibiotic lacticin 3147
Authors: Draper Lorraine A. , Grainger Karen , Deegan Lucy H. , Cotter Paul D. , Hill Colin , Ross R. Paul 
Published: January 2009

SummaryLantibiotics are antimicrobial peptides that possess great potential as clinical therapeutic agents. These peptides exhibit many beneficial traits and in many cases the emergence of resistance is extremely rare. In contrast, producers of lantibiotics synthesize dedicated immunity proteins to provide self‐protection. These proteins have very specific activities and cross‐immunity is rare. However, producers of two peptide lantibiotics, such as lacticin 3147, face the unusual challenge of exposure to two active peptides (α and β). Here, in addition to establishing the contribution of LtnI and LtnFE to lacticin 3147 immunity, investigations were carried out to determine if production of a closely related lantibiotic (i.e. staphylococcin C55) or possession of LtnI/LtnFE homologues could provide protection. Here we establish that not only are staphylococcin C55 producers cross‐immune to lacticin 3147, and therefore represent a natural repository of Staphylococcus aureus strains that are protected against lacticin 3147, but that functional immunity homologues are also produced by strains of Bacillus licheniformis and Enterococcus faecium. This result raises the spectre of resistance through immune mimicry, i.e. the emergence of lantibiotic‐resistant strains from the environment resulting from the possession/acquisition of immunity gene homologues. These phenomena will have to be considered carefully when developing lantibiotics for clinical application.
Microtubule‐severing proteins are involved in flagellar length control and mitosis in Trypanosomatids
Authors: Casanova Magali , Crobu Lucien , Blaineau Christine , Bourgeois Nathalie , Bastien Patrick , Pagès Michel 
Published: January 2009

SummaryMicrotubules are key players in the biology of Trypanosomatid parasites, not only as classical components of the mitotic spindle, microtubule‐organizing centres and flagellum but also as the essential constituent of the cytoskeleton. Their length dynamics are regulated by, among others, microtubule‐severing proteins. Four and six genes encoding microtubule‐severing proteins can be found bioinformatically in the Leishmania major and Trypanosoma brucei genome respectively. We investigated all these proteins in these organisms, which include the katanin, katanin‐like, spastin and fidgetin, and looked at their subcellular localization as well as their putative function by examining ‘loss‐of‐function’ phenotypes. The katanin‐like KAT60b was found implicated in flagellar length reduction, but not in its size increase, while the katanin p80 subunit appeared clearly involved in cytokinesis. Fidgetin and spastin homologues were both localized in the nucleus: the first as a discrete and variable number of dots during most of the cell cycle, redistributing to the spindle and midbody during mitosis; the second concentrated as ≤ 5 perinucleolar punctuations, similar to the electron‐dense plaques identified in T. brucei, which were assimilated to kinetochores. This first study of microtubule‐severing proteins in ‘divergent’ eukaryotes gives further insight into the multiple functions of these proteins identified in the hitherto studied models.
Single 23S rRNA mutations at the ribosomal peptidyl transferase centre confer resistance to valnemulin and other antibiotics in Mycobacterium smegmatis by perturbation of the drug binding pocket
Authors: Long Katherine S. , Poehlsgaard Jacob , Hansen Lykke H. , Hobbie Sven N. , Böttger Erik C. , Vester Birte 
Published: January 2009

SummaryTiamulin and valnemulin target the peptidyl transferase centre (PTC) on the bacterial ribosome. They are used in veterinary medicine to treat infections caused by a variety of bacterial pathogens, including the intestinal spirochetes Brachyspira spp. Mutations in ribosomal protein L3 and 23S rRNA have previously been associated with tiamulin resistance in Brachyspira spp. isolates, but as multiple mutations were isolated together, the roles of the individual mutations are unclear. In this work, individual 23S rRNA mutations associated with pleuromutilin resistance at positions 2055, 2447, 2504 and 2572 (Escherichia coli numbering) are introduced into a Mycobacterium smegmatis strain with a single rRNA operon. The single mutations each confer a significant and similar degree of valnemulin resistance and those at 2447 and 2504 also confer cross‐resistance to other antibiotics that bind to the PTC in M. smegmatis. Antibiotic footprinting experiments on mutant ribosomes show that the introduced mutations cause structural perturbations at the PTC and reduced binding of pleuromutilin antibiotics. This work underscores the fact that mutations at nucleotides distant from the pleuromutilin binding site can confer the same level of valnemulin resistance as those at nucleotides abutting the bound drug, and suggests that the former function indirectly by altering local structure and flexibility at the drug binding pocket.
Structural insights into the molecular organization of the S‐layer from Clostridium difficile
Authors: Fagan Robert P. , Albesa‐Jové David , Qazi Omar , Svergun Dmitri I. , Brown Katherine A. , Fairweather Neil F. 
Published: January 2009

Summary Clostridium difficile expresses a surface layer (S‐layer) which coats the surface of the bacterium and acts as an adhesin facilitating interaction of the bacterium with host enteric cells. The S‐layer contains a high‐molecular‐weight S‐layer protein (HMW SLP) and its low‐molecular‐weight partner protein (LMW SLP). We show that these proteins form a tightly associated non‐covalent complex, the H/L complex, and we identify the regions of both proteins responsible for complex formation. The 2.4 Å X‐ray crystal structure of a truncated derivative of the LMW SLP reveals two domains. Domain 1 has a two‐layer sandwich architecture while domain 2, predicted to orientate towards the external environment, contains a novel fold. Small‐angle X‐ray scattering analysis of the H/L complex shows an elongated molecule, with the two SLPs arranged ‘end‐to‐end’ interacting with each other through a small contact area. Alignment of LMW SLPs, which exhibit high sequence diversity, reveals a core of conserved residues that could reflect functional conservation, while allowing for immune evasion through sequence variation. These structures are the first described for the S‐layer of a bacterial pathogen, and provide insights into the assembly and biogenesis of the S‐layer.
Mycolic acid methyltransferase, MmaA4, is necessary for thiacetazone susceptibility in Mycobacterium tuberculosis
Authors: Alahari Anuradha , Alibaud Laeticia , Trivelli Xavier , Gupta Radhika , Lamichhane Gyanu , Reynolds Robert C. , Bishai William R. , Guerardel Yann , Kremer Laurent 
Published: January 2009

SummarySusceptibility of Mycobacterium tuberculosis to the second‐line antitubercular drug thiacetazone (TAC) requires activation by the monoxygenase, EthA. Here, we report isolation of spontaneous mutants in Mycobacterium bovis BCG that are highly resistant to TAC, but carry a functional EthA. Unexpectedly, a majority of the TAC‐resistant mutants lacked keto‐mycolic acids, which are long‐chain fatty acids associated with the cell wall and which contribute significantly to the physiopathology of tuberculosis. Predictably, causative mutations in the above mutants were in the gene encoding methyltransferase MmaA4, which is required for synthesis of keto‐ and methoxy‐mycolic acids. Drug‐resistant phenotype of the BCG mutants was reproduced in a mmaA4, but not in a mmaA3 null mutant of M. tuberculosis CDC1551. Susceptibility to TAC could be restored by complementation with a functional mmaA4 gene. Interestingly, overexpression of MmaA4 in M. bovis BCG made it more susceptible to TAC. We provide novel mechanistic insights into antitubercular drug activation by co‐ordinated actions of EthA and MmaA4. This study is the first demonstration of the participation of an enzyme linked to the synthesis of oxygenated mycolates in a drug activation process in M. tuberculosis, and highlights the interplay between mycolic acid synthesis, drug activation and mycobacterial virulence.
Functional characterization of cohesin SMC3 and separase and their roles in the segregation of large and minichromosomes in Trypanosoma brucei
Authors: Bessat Mohamed , Ersfeld Klaus 
Published: January 2009

SummaryMinichromosomes in the nuclear genome of Trypanosoma brucei exhibit unusual patterns of mitotic segregation. To address whether differences in their mode of segregation in relation to large chromosomes are reflected at a molecular level, we characterized two different proteins that have highly conserved functions in eukaryotic chromosomes segregation: the SMC3 protein, a component of the chromatid cohesion apparatus, and the protease separase that resolves the cohesin complex at the onset of anaphase and has, in other organisms, additional functions during mitosis. Using in situ hybridization we show that RNA interference‐mediated depletion of SMC3 has no visible effect on the segregation of the minichromosomal population but interferes with the faithful mitotic separation of large chromosomes. In contrast, separase depletion causes missegregation of both mini‐ and large chromosomes. We also show that SMC3 persists as a soluble protein throughout the cell cycle and only associates with chromatin between G1 and metaphase. Separase is present in the cell during the entire cell cycle, but is excluded from the nucleus until the metaphase–anaphase transition, thereby providing a potential control mechanism to prevent the untimely cleavage of the cohesin complex.
Rearing Environment Affects the Brain Size of Guppies: Lab‐Reared Guppies have Smaller Brains than Wild‐Caught Guppies
Authors: Burns James G. , Saravanan Arthy , Helen Rodd F. 
Published: January 2009

AbstractAnimals bred for captivity often have smaller brains and behave differently than their wild counterparts. These differences in brain size have been attributed to genetic changes resulting from, for example, inbreeding depression and pleiotropic effects of artificial selection for traits such as docility. A critical question, though, is whether these differences in brain size are due to plastic responses to the environment, not just genetic changes. We observed a large reduction in brain size in first generation, lab‐reared female guppies compared with wild‐caught ones (19% smaller telencephalon, 17% smaller optic tectum). We then reared first‐generation, lab‐born guppies in environments varying in spatial complexity and size in an attempt to isolate factors that might increase brain size and change temperament, but no significant differences in phenotype were observed. The results of these experiments show that, although the environmental factors responsible for the effect have not been found, even first generation lab‐reared individuals can have smaller brains than wild individuals.
Rut‐Induced Hypophagia in Male Bighorn Sheep and Mountain Goats: Foraging Under Time Budget Constraints
Authors: Pelletier Fanie , Mainguy Julien , Côté Steeve D. 
Published: January 2009

AbstractIn polygynous ungulates, the rut imposes constraints on male time budgets that generate a trade‐off between maintenance and reproduction, leading to a reduction in time spent foraging. As mating activities can incur substantial somatic costs, males are expected to spend their ‘non‐rutting’ time recovering during the breeding season. If the diminution in time allocated to foraging by males is only a consequence of time budget constraints, males should keep a similar ratio of time spent foraging to lying to that observed in the pre‐rut, leading to an overall reduction of these two activities (the ‘foraging constraint’ hypothesis). Alternatively, if males adopt an energy‐saving strategy, they should limit energy expenditures by reducing foraging but not lying time, as the energy gains of forage intake may not meet the basal energetic requirements, especially in northern and temperate regions (the ‘energy‐saving’ hypothesis). Here, we contrast these two hypotheses by comparing individual daily time budgets of marked adult bighorn sheep rams (Ovis canadensis) and male mountain goats (Oreamnos americanus) during the pre‐rut and the rut. Concordant results for both species support the ‘foraging constraint’ hypothesis, as sexually‐active males reduced time spent foraging and lying from the pre‐rut to the rut because of an increase in time spent in mating‐related activities. Bighorn sheep rams also increased time spent foraging when not engaged in mating tactics, providing further support for a ‘maximisation’ of energy intake in the absence of reproductive opportunities. Because there are also known physiological changes that occur during the rut which may cause appetite suppression, for example to produce metabolic compounds linked with olfactory communication (the ‘scent‐urination’ hypothesis) or to cope with increased burden of parasites (the ‘parasite‐induced anorexia’ hypothesis), further research should aim at simultaneously testing these current hypotheses to better understand rut‐induced hypophagia and its effects on the life histories of male ungulates.
Male Siamese Fighting Fish, Betta splendens, Increase Rather than Conceal Courtship Behavior when a Rival is Present
Authors: Dzieweczynski Teresa L. , Lyman Sarah , Poor Elysia A. 
Published: January 2009

AbstractThe impact of social environment on mating success is especially pronounced in species where both intraspecific and interspecific selection influence reproduction, such as the Siamese fighting fish. Males alter male–male interactions when either a male or female audience is present, but how males change their behavior toward a female when a rival male is present is unknown. This study addresses whether males alter their behavior toward a female in a way that would prevent a rival male from interrupting courtship. The behavior of male Siamese fighting fish toward a dummy female was examined under various degrees of visual cover, both in the presence and absence of a rival male, to investigate whether males use concealment provided by the structural environment to their advantage. While males did not use barriers to conceal courtship as hypothesized, males altered their behavior by increasing courtship and monitoring their nest when a rival was visible. This increase in courtship is in contrast to most studies on courtship in the presence of a rival that find a reduction in courtship behavior. Males spent more time opercular gill flaring when no barriers were present, suggesting that males may be trying to court the female and communicate to the rival simultaneously. There was also a trend for aggression toward the female and the rival to decrease as screen length increased. Thus, males compensate for the presence of a rival by adjusting their courtship and aggressive behaviors, which could have important implications for courtship success.
Evidence‐based medicine training in residency: a survey of urology programme directors
Authors: Dahm Philipp , Preminger Glenn M. , Scales Charles D. , Fesperman Susan F. , Yeung Lawrence L. , Cohen Marc S. 
Published: January 2009

OBJECTIVETo investigate whether and in what format urology residents receive formal training in evidence‐based clinical practice.METHODSIn 2007 we conducted a survey of the Accreditation Council for Graduate Medical Education (ACGME)‐accredited urology residency programmes in the USA. The survey instrument was sent to all programmes, using postal mailing, e‐mail and a web–based interface. Programme director and coordinator names and basic demographic information such as programme size and length were retrieved from the institutions’ websites and the ACGME database.RESULTSOf 117 ACGME‐accredited urology programmes, 108 responded (92.3%). Most respondents either agreed or strongly agreed with statements that formal evidence‐based medicine (EBM) training was valuable to urology residents (97, 89.8%) and should be part of all residency programme curricula (91, 84.3%). Eighty‐four programmes (77.8%) indicated that their curricula included formal educational activities related to EBM. These programmes provided a median (interquartile range) of 10 (4.8–25.0) h of EBM teaching per academic year. Most programmes (65.9%) provided fewer hours of EBM training than programme directors perceived as ideal. Asked what would make it easier to integrate EBM into the programme, respondents identified urology‐specific educational materials (33.3%), a formal curriculum (24.4%) and faculty development (16.3%) as central needs.CONCLUSIONIn this survey we found that most programme directors recognize formal EBM teaching as an important aspect of urology residency training. However, most programmes devote less time to EBM training than they would like, and urology‐specific resources have been lacking. These findings support increased efforts to provide urology residents with opportunities to learn EBM‐related knowledge and skills in a variety of educational formats.