bluuebunny/crossref_metadata_2025 huggingface dataset:
Dipeptides promote folding and peptide binding of MHC class I molecules
Authors: Saini Sunil Kumar , Ostermeir Katja , Ramnarayan Venkat Raman , Schuster Heiko , Zacharias Martin , Springer Sebastian
Published: September 2013

MHC class I molecules bind only those peptides with high affinity that conform to stringent length and sequence requirements. We have now investigated which peptides can aid the in vitro folding of class I molecules, and we find that the dipeptide glycyl-leucine efficiently supports the folding of HLA-A*02:01 and H-2Kbinto a peptide-receptive conformation that rapidly binds high-affinity peptides. Treatment of cells with glycyl-leucine induces accumulation of peptide-receptive H-2Kband HLA-A*02:01 at the surface of cells. Other dipeptides with a hydrophobic second amino acid show similar enhancement effects. Our data suggest that the dipeptides bind into the F pocket like the C-terminal amino acids of a high-affinity peptide.
Model projections of atmospheric steering of Sandy-like superstorms
Authors: Barnes Elizabeth A. , Polvani Lorenzo M. , Sobel Adam H.
Published: September 2013

Superstorm Sandy ravaged the eastern seaboard of the United States, costing a great number of lives and billions of dollars in damage. Whether events like Sandy will become more frequent as anthropogenic greenhouse gases continue to increase remains an open and complex question. Here we consider whether the persistent large-scale atmospheric patterns that steered Sandy onto the coast will become more frequent in the coming decades. Using the Coupled Model Intercomparison Project, phase 5 multimodel ensemble, we demonstrate that climate models consistently project a decrease in the frequency and persistence of the westward flow that led to Sandy’s unprecedented track, implying that future atmospheric conditions are less likely than at present to propel storms westward into the coast.
Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P
Authors: Peil Lauri , Starosta Agata L. , Lassak Jürgen , Atkinson Gemma C. , Virumäe Kai , Spitzer Michaela , Tenson Tanel , Jung Kirsten , Remme Jaanus , Wilson Daniel N.
Published: September 2013

Significance

During protein synthesis, ribosomes catalyze peptide-bond formation between amino acids with differing efficiency. We show that two or more consecutive prolines induce ribosome stalling, and that stalling strength is influenced by the amino acid preceding and following the prolines. In bacteria, the elongation factor EF-P efficiently rescues the ribosome stalling irrespective of the XPP or PPX motif.
Genome-wide fitness profiling reveals adaptations required by
Haemophilus
in coinfection with influenza A virus in the murine lung
Authors: Wong Sandy M. , Bernui Mariana , Shen Hao , Akerley Brian J.
Published: September 2013

Significance

The upper respiratory tract is colonized by numerous bacteria that are usually confined to this site in healthy individuals. However, in coinfection with a preceding viral infection, these bacteria can colonize the lung, leading to lethal secondary bacterial pneumonia. In this report, a frequent pathogen in coinfections with influenza virus,
Haemophilus influenzae
, was examined at the whole-genome level to comparatively analyze genes conferring bacterial fitness in mice previously infected with influenza A virus vs. in non-virally infected mice. We identified altered requirements for many bacterial virulence factors and physiological adaptations, providing insight into conditions in the lung that exert selection on coinfecting pathogens. Bacterial factors required for colonization during coinfection represent potential targets for antimicrobials to combat secondary bacterial pneumonia.
Diagnosis of tumors during tissue-conserving surgery with integrated autofluorescence and Raman scattering microscopy
Authors: Kong Kenny , Rowlands Christopher J. , Varma Sandeep , Perkins William , Leach Iain H. , Koloydenko Alexey A. , Williams Hywel C. , Notingher Ioan
Published: September 2013

Significance

Histopathology is the standard method for diagnosis of cancer. However, this method requires time-consuming procedures for sectioning and staining of tissues, making histopathology impractical for use during surgery for most cancer types. We report a unique method based on two optical spectroscopy techniques—autofluorescence imaging and Raman scattering—that can accurately measure molecular differences between tumor cells and healthy tissue and allows diagnosis of tumors faster than histopathology, without requiring tissue sectioning or staining. Our study demonstrates the potential of this technique for diagnosis of tissues during cancer surgery, providing a quick and objective way to determine whether the tissue layers removed by the surgeon are clear of tumor.
Tissue- and cell-type–specific manifestations of heteroplasmic mtDNA 3243A>G mutation in human induced pluripotent stem cell-derived disease model
Authors: Hämäläinen Riikka H. , Manninen Tuula , Koivumäki Hanna , Kislin Mikhail , Otonkoski Timo , Suomalainen Anu
Published: September 2013

Significance

Mitochondrial DNA (mtDNA) mutations are a common cause of human inherited diseases and manifest with exceptional clinical heterogeneity and tissue specificity, the molecular basis of which are largely unknown. We produced induced pluripotent stem cells (iPSCs) from patients carrying the most common mtDNA mutation, m.3243A>G. During reprogramming, the cells underwent an mtDNA bottleneck, mimicking that in epiblast specification. We differentiated iPSCs to heteroplasmic human cells and tissues with isogenic nuclear background and show that the disease manifestation depends on cellular context. We show that upon neuronal differentiation, complex I is actively degraded by an autophagy-mediated mechanism. Our data indicate that cellular context actively modifies mtDNA segregation and manifestations, and that complex I is actively down-regulated in neurons with m.3243A>G mutation.
Protease homolog BepA (YfgC) promotes assembly and degradation of β-barrel membrane proteins in
Escherichia coli
Authors: Narita Shin-ichiro , Masui Chigusa , Suzuki Takehiro , Dohmae Naoshi , Akiyama Yoshinori
Published: September 2013

Significance

Outer membrane proteins (OMPs) are involved in important cellular activities in Gram-negative bacteria. Although the
bepA
(formerly
yfgC
) gene encoding a putative metalloprotease has been implicated in quality control of OMPs, its specific function remains unclear. This study reveals that BepA promotes assembly of LptD, an OMP involved in the transport of lipopolysaccharides, which undergoes intramolecular disulfide rearrangement during its biogenesis. BepA also promotes degradation of incorrectly folded LptD. BamA, another OMP involved in OMP assembly, is also degraded in a BepA-dependent manner in the absence of periplasmic chaperone SurA. BepA thus controls the quality of OMPs by promoting either the biogenesis or elimination of OMPs, depending on their folding state.
Benefits, costs, and livelihood implications of a regional payment for ecosystem service program
Authors: Zheng Hua , Robinson Brian E. , Liang Yi-Cheng , Polasky Stephen , Ma Dong-Chun , Wang Feng-Chun , Ruckelshaus Mary , Ouyang Zhi-Yun , Daily Gretchen C.
Published: September 2013

Despite broad interest in using payment for ecosystem services to promote changes in the use of natural capital, there are few expost assessments of impacts of payment for ecosystem services programs on ecosystem service provision, program cost, and changes in livelihoods resulting from program participation. In this paper, we evaluate the Paddy Land-to-Dry Land (PLDL) program in Beijing, China, and associated changes in service providers’ livelihood activities. The PLDL is a land use conversion program that aims to protect water quality and quantity for the only surface water reservoir that serves Beijing, China’s capital city with nearly 20 million residents. Our analysis integrates hydrologic data with household survey data and shows that the PLDL generates benefits of improved water quantity and quality that exceed the costs of reduced agricultural output. The PLDL has an overall benefit–cost ratio of 1.5, and both downstream beneficiaries and upstream providers gain from the program. Household data show that changes in livelihood activities may offset some of the desired effects of the program through increased expenditures on agricultural fertilizers. Overall, however, reductions in fertilizer leaching from land use change dominate so that the program still has a positive net impact on water quality. This program is a successful example of water users paying upstream landholders to improve water quantity and quality through land use change. Program evaluation also highlights the importance of considering behavioral changes by program participants.
Young infants have biological expectations about animals
Authors: Setoh Peipei , Wu Di , Baillargeon Renée , Gelman Rochel
Published: September 2013

Significance

We provide an experimental demonstration that young infants possess abstract biological expectations about animals. Our findings represent a major breakthrough in the study of the foundations of human knowledge. In four experiments, 8-mo-old infants expected novel objects they categorized as animals to have filled insides. Thus, infants detected a violation when objects that were self-propelled and agentive were revealed to be hollow, or when an object that was self-propelled and furry rattled when shaken, as though mostly hollow. We describe possible characterizations of infants’ expectations about animals’ insides, including a characterization that emphasizes human predator–prey adaptations. We also discuss how infants’ expectation that animals have insides lays a foundation for the development of more advanced biological knowledge.
Low-copy
piggyBac
transposon mutagenesis in mice identifies genes driving melanoma
Authors: Ni Thomas K. , Landrette Sean F. , Bjornson Robert D. , Bosenberg Marcus W. , Xu Tian
Published: September 2013

Significance

Passenger mutation rates are highly elevated in many human cancers, posing a significant hurdle for the identification of cancer-driving genes. In this study, we screened for melanomas in mice using a unique, low-copy transposon mutagenesis system that can induce tumors with few somatic mutations. We show that our experimental system accurately recapitulated the genetic basis of human melanomas with only five somatic mutations, thus circumventing hundreds of unrelated passengers. Using cross-species comparative analyses and functional studies in human cells, we identified three previously undescribed genes involved in melanoma and several dozen candidate genes. Our study demonstrates that the low-copy transposon mutagenesis approach can facilitate the identification of cancer-driving genes that are masked by high passenger mutation rates.
Effect of relationship experience on trust recovery following a breach
Authors: Schilke Oliver , Reimann Martin , Cook Karen S.
Published: September 2013

Significance

Will people be more likely to forgive a breach of trust in an earlier or later stage of an interpersonal relationship? The present article reports behavioral and neurophysiological experiments that speak to this important question. Results show that trust recovery is facilitated with increasing relationship experience. Differential activation in the controlled social cognition system (C-system) and the automatic social cognition system (X-system) indicate that decision making is less controlled and more automatic following a later as opposed to an earlier trust breach. These findings have important implications for the study of trust recovery after a breach, as well as the neuroscience of trust.
Positively selected FimH residues enhance virulence during urinary tract infection by altering FimH conformation
Authors: Schwartz Drew J. , Kalas Vasilios , Pinkner Jerome S. , Chen Swaine L. , Spaulding Caitlin N. , Dodson Karen W. , Hultgren Scott J.
Published: September 2013

Significance

The evolution of multidrug resistance in pathogenic bacteria, including uropathogenic
Escherichia coli
(UPEC), that cause most urinary tract infections is becoming a worldwide crisis. UPEC use a variety of virulence factors and adhesins, including the mannose-binding FimH adhesin, to colonize and invade bladder tissue, often forming intracellular biofilms and quiescent reservoirs that can contribute to recurrent infections recalcitrant to treatment. Using two prototypical UPEC strains, we discovered that positively selected residues outside of the FimH mannose-binding pocket affect transitions between low- and high-affinity FimH conformations, which extraordinarily impacts FimH function during pathogenesis. Thus, this work elucidates mechanistic and functional insights into pathoadaptation and evolutionary fine-tuning of critical virulence interactions.
Disputing while covering a dispute on television news
Authors: Shukrun-Nagar Pnina
Published: September 2013

This paper discusses the potential of semantic, pragmatic and grammatical devices used in the Israeli television news coverage of a dispute to promote one agenda, negate a contradictory one and position the correspondent as a participant in the dispute. Moreover, I argue that viewers of news identify at least some of these devices and attribute an argumentative role to them. To support this, I analyze questionnaires in which native speakers relate to a specific news item, focusing on the three most common devices interpreted: implicatures, emotionality and textual planning. The discussion sheds light on dialogical interactions between, first, correspondents and their addressees; second, between the correspondents’ words and their co-texts, contexts and other occurrences of these words or their synonyms in public discourse. The corpus includes 19 items on a struggle between ultra-Orthodox and secular Jews in Israel broadcast in 2009 on Israel’s Channel 2 television news.
Brand names and unconventional spelling
Authors: Wong Andrew D.
Published: September 2013

This article explores the creative use of unconventional spelling in brand names. Using insights from the indexical approach to the linguistic construction of identity, it demonstrates how unconventional spelling produces a myriad of effects and meanings, which in turn help construct brand identities. First, it identifies the various strategies of unconventional spelling, investigates their potential to convey distinctiveness, and examines other effects and meanings that they produce. It then presents a case study to further illustrate how unconventional spelling works with other marketing materials to create a unique brand identity. Unconventional spelling, because of its polarizing nature, can be a risky resource for constructing brand identities. Not only does this study contribute to an under-researched area in the sociolinguistics of orthography, but it also broadens the range of identities and linguistic resources examined in the sociolinguistic investigation of identity construction.
Infection Prevention and Control in Residential Facilities for Pediatric Patients and Their Families
Authors: Guzman-Cottrill Judith A. , Ravin Karen A. , Bryant Kristina A. , Zerr Danielle M. , Kociolek Larry , Siegel Jane D.
Published: September 2013

The Society for Healthcare Epidemiology of America (SHEA) guideline “Infection Prevention and Control in Residential Facilities for Pediatric Patients and Their Families” is the first infection prevention and control (IPC) guideline to address preventing transmission of infectious agents in “home away from home” residential settings, of which the Ronald McDonald Houses (RMHs) serve as a prototype. These types of facilities provide support services, including overnight lodging, for ill and injured children and their families. Food preparation occurs in common areas, and cleaning of rooms or apartments is performed by the occupants during their stay and before departure. Pediatricpatientsare frequent guests of the family-centered facilities while receiving or recovering from specialized medical therapy. Examples of high-risk populations served in these facilities include families of patients with cancer, recipients of stem cell or solid organ transplants, surgical and/or very-low-birthweight infants who receive care in neonatal intensive care units (NICUs), those with cystic fibrosis, and women with high-risk pregnancies awaiting delivery in a nearby medical center. Such facilities are located worldwide and vary in their physical structure and the predominant population served.
Metrics of positive scalar curvature and generalised Morse functions, Part II
Authors: Walsh Mark
Published: September 2013

The surgery technique of Gromov and Lawson may be used to construct families of positive scalar curvature metrics which are parameterised by Morse functions. This has played an important role in the study of the space of metrics of positive scalar curvature on a smooth manifold and its corresponding moduli spaces. In this paper, we extend this technique to work for families of generalised Morse functions, i.e. smooth functions with both Morse and birth-death singularities.
On 𝑞-normal operators and the quantum complex plane
Authors: Cimprič Jaka , Savchuk Yurii , Schmüdgen Konrad
Published: September 2013

For

q
>
0

q>0

let

A

\mathcal {A}

denote the unital

∗
*

-algebra with generator

x
x

and defining relation

x

x
∗

=
q

x
∗

x

xx^*=qx^*x

. Based on this algebra we study

q
q

-normal operators and the complex

q
q

-moment problem. Among other things, we prove a spectral theorem for

q
q

-normal operators, a variant of Haviland’s theorem and a strict Positivstellensatz for

A

.

\mathcal {A}.

We also construct an example of a positive element of

A

\mathcal {A}

which is not a sum of squares. It is used to prove the existence of a formally

q
q

-normal operator which is not extendable to a

q
q

-normal one in a larger Hilbert space and of a positive functional on

A

\mathcal {A}

which is not strongly positive.
Novel human lncRNA–disease association inference based on lncRNA expression profiles
Authors: Chen Xing , Yan Gui-Ying
Published: September 2013

Motivation: More and more evidences have indicated that long–non-coding RNAs (lncRNAs) play critical roles in many important biological processes. Therefore, mutations and dysregulations of these lncRNAs would contribute to the development of various complex diseases. Developing powerful computational models for potential disease-related lncRNAs identification would benefit biomarker identification and drug discovery for human disease diagnosis, treatment, prognosis and prevention.

Results: In this article, we proposed the assumption that similar diseases tend to be associated with functionally similar lncRNAs. Then, we further developed the method of Laplacian Regularized Least Squares for LncRNA–Disease Association (LRLSLDA) in the semisupervised learning framework. Although known disease–lncRNA associations in the database are rare, LRLSLDA still obtained an AUC of 0.7760 in the leave-one-out cross validation, significantly improving the performance of previous methods. We also illustrated the performance of LRLSLDA is not sensitive (even robust) to the parameters selection and it can obtain a reliable performance in all the test classes. Plenty of potential disease–lncRNA associations were publicly released and some of them have been confirmed by recent results in biological experiments. It is anticipated that LRLSLDA could be an effective and important biological tool for biomedical research.

Availability: The code of LRLSLDA is freely available at http://asdcd.amss.ac.cn/Software/Details/2.

Contact:  xingchen@amss.ac.cn or yangy@amt.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exploiting disjointness axioms to improve semantic similarity measures
Authors: Ferreira João D. , Hastings Janna , Couto Francisco M.
Published: September 2013

Motivation: Representing domain knowledge in biology has traditionally been accomplished by creating simple hierarchies of classes with textual annotations. Recently, expressive ontology languages, such as Web Ontology Language, have become more widely adopted, supporting axioms that express logical relationships other than class–subclass, e.g. disjointness. This is improving the coverage and validity of the knowledge contained in biological ontologies. However, current semantic tools still need to adapt to this more expressive information. In this article, we propose a method to integrate disjointness axioms, which are being incorporated in real-world ontologies, such as the Gene Ontology and the chemical entities of biological interest ontology, into semantic similarity, the measure that estimates the closeness in meaning between classes.

Results: We present a modification of the measure of shared information content, which extends the base measure to allow the incorporation of disjointness information. To evaluate our approach, we applied it to several randomly selected datasets extracted from the chemical entities of biological interest ontology. In 93.8% of these datasets, our measure performed better than the base measure of shared information content. This supports the idea that semantic similarity is more accurate if it extends beyond the hierarchy of classes of the ontology.

Contact: joao.ferreira@lasige.di.fc.ul.pt

Supplementary information:  Supplementary data are available at Bioinformatics online.
Metriculator: quality assessment for mass spectrometry-based proteomics
Authors: Taylor Ryan M. , Dance Jamison , Taylor Russ J. , Prince John T.
Published: September 2013

Summary: Quality control in mass spectrometry-based proteomics remains subjective, labor-intensive and inconsistent between laboratories. We introduce Metriculator, a software designed to facilitate long-term storage of extensive performance metrics as introduced by NIST in 2010. Metriculator features a web interface that generates interactive comparison plots for contextual understanding of metric values and an automated metric generation toolkit. The comparison plots are designed for at-a-glance determination of outliers and trends in the datasets, together with relevant statistical comparisons. Easy-to-use quantitative comparisons and a framework for integration plugins will encourage a culture of quality assurance within the proteomics community.

Availability and Implementation: Available under the MIT license at http://github.com/princelab/metriculator.

Contact:  jtprince@chem.byu.edu
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure
Authors: Suddala Krishna C. , Rinaldi Arlie J. , Feng Jun , Mustoe Anthony M. , Eichhorn Catherine D. , Liberman Joseph A. , Wedekind Joseph E. , Al-Hashimi Hashim M. , Brooks Charles L. , Walter Nils G.
Published: September 2013

Riboswitches are structural elements in the 5′ untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ1 riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at near-physiological Mg2+ concentration and pH, both ligand-free aptamers adopt similar pre-folded state ensembles that differ in their ligand-mediated folding. Structure-based Gō-model simulations of the two aptamers suggest that the ligand binds late (Bacillus subtilis) and early (Thermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the principal distinction between the two riboswitches lies in their relative tendencies to fold via mechanisms of conformational selection and induced fit, respectively. These mechanistic insights are put to the test by rationally designing a single nucleotide swap distal from the ligand binding pocket that we find to predictably control the aptamers′ pre-folded states and their ligand binding affinities.
The Role of Oxytocin in Psychiatric Disorders
Authors: Cochran David M. , Fallon Daniel , Hill Michael , Frazier Jean A.
Published: September 2013

Learning Objectives

After participating in this educational activity, the physician should be better able to

Oxytocin is a peptide hormone integral in parturition, milk letdown, and maternal behaviors that has been demonstrated in animal studies to be important in the formation of pair bonds and in social behaviors. This hormone is increasingly recognized as an important regulator of human social behaviors, including social decision making, evaluating and responding to social stimuli, mediating social interactions, and forming social memories. In addition, oxytocin is intricately involved in a broad array of neuropsychiatric functions and may be a common factor important in multiple psychiatric disorders such as autism, schizophrenia, and mood and anxiety disorders. This review article examines the extant literature on the evidence for oxytocin dysfunction in a variety of psychiatric disorders and highlights the need for further research to understand the complex role of the oxytocin system in psychiatric disease and thus pave the way for developing new therapeutic modalities. Articles were selected that involved human participants with various psychiatric disorders and that either compared oxytocin biology to healthy controls or examined the effects of exogenous oxytocin administration.
Curriculum Development and Implementation of a National Interprofessional Fellowship in Patient Safety
Authors: Watts Bradley V. , Williams Linda , Mills Peter D. , Paull Douglas E. , Cully Jeffrey A. , Gilman Stuart C. , Hemphill Robin R.
Published: September 2013

Objectives

Developing a workforce skilled in improving the safety of medical care has often been cited as an important means to achieve safer care. Although some educational programs geared toward patient safety have been developed, few advanced training programs have been described in the literature. We describe the development of a patient safety fellowship program.

Methods

We describe the development and curriculum of an Interprofessional Fellowship in Patient Safety. The 1-year in residence fellowship focuses on domains such as leadership, spreading innovations, medical improvement, patient safety culture, reliability science, and understanding errors.

Results

Specific training in patient safety is available and has been delivered to 48 fellows from a wide range of backgrounds. Fellows have accomplished much in terms of improvement projects, educational innovations, and publications. After completing the fellowship program, fellows are obtaining positions within health-care quality and safety and are likely to make long-term contributions.

Conclusions

We offer a curriculum and fellowship design for the topic of patient safety. Available evidence suggests that the fellowship results in the development of patient safety professionals.
The diminishing role of hubs in dynamical processes on complex networks
Authors: Quax Rick , Apolloni Andrea , Sloot Peter M. A.
Published: September 2013

It is notoriously difficult to predict the behaviour of a complex self-organizing system, where the interactions among dynamical units form a heterogeneous topology. Even if the dynamics of each microscopic unit is known, a real understanding of their contributions to the macroscopic system behaviour is still lacking. Here, we develop information-theoretical methods to distinguish the contribution of each individual unit to the collective out-of-equilibrium dynamics. We show that for a system of units connected by a network of interaction potentials with an arbitrary degree distribution, highly connected units have less impact on the system dynamics when compared with intermediately connected units. In an equilibrium setting, the hubs are often found to dictate the long-term behaviour. However, we find both analytically and experimentally that the instantaneous states of these units have a short-lasting effect on the state trajectory of the entire system. We present qualitative evidence of this phenomenon from empirical findings about a social network of product recommendations, a protein–protein interaction network and a neural network, suggesting that it might indeed be a widespread property in nature.
Lipid tubule growth by osmotic pressure
Authors: Rangamani Padmini , Zhang Di , Oster George , Shen Amy Q.
Published: September 2013

We present here a procedure for growing lipid tubules
in vitro
. This method allows us to grow tubules of consistent shape and structure, and thus can be a useful tool for nano-engineering applications. There are three stages during the tubule growth process: initiation, elongation and termination. Balancing the forces that act on the tubule head shows that the growth of tubules during the elongation phase depends on the balance between osmotic pressure and the viscous drag exerted on the membrane from the substrate and the external fluid. Using a combination of mathematical modelling and experiment, we identify the key forces that control tubule growth during the elongation phase.
Association of polyandry andsex-ratiodrive prevalence in natural populations ofDrosophila neotestacea
Authors: Pinzone Cheryl A. , Dyer Kelly A.
Published: September 2013

Selfish genetic elements bias their own transmission to the next generation, even at the expense of the fitness of their carrier.Sex-ratio(SR) meiotic drive occurs when an X-chromosome causes Y-bearing sperm to die during male spermatogenesis, so that it is passed on to all of the male's offspring, which are all daughters. How SR is maintained as a stable polymorphism in the absence of genetic suppressors of drive is unknown. Here, we investigate the potential for the female remating rate to affect SR dynamics in natural populations, using the flyDrosophila neotestacea. In controlled laboratory conditions, females from populations where SR is rare mate more often than females from populations where SR is common. Furthermore, only when males mate multiply does the average fertility of SR males relative to wild-type males decrease to a level that can prevent SR from spreading. Our results suggest that differences in the female mating rate among populations may contribute to SR dynamics in the wild, and thus also affect the outcome of this intragenomic conflict. In line with this, we also present evidence of a localized population crash due to SR that may have resulted from habitat fragmentation along with a reduced mating rate.
The impact of strain diversity and mixed infections on the evolution of resistance to
Bacillus thuringiensis
Authors: Raymond Ben , Wright Denis J. , Crickmore Neil , Bonsall Michael B.
Published: September 2013

Pesticide mixtures can reduce the rate at which insects evolve pesticide resistance. However, with live biopesticides such as the naturally abundant pathogen
Bacillus thuringiensis
(
Bt
), a range of additional biological considerations might affect the evolution of resistance. These can include ecological interactions in mixed infections, the different rates of transmission post-application and the impact of the native biodiversity on the frequency of mixed infections. Using multi-generation selection experiments, we tested how applications of single and mixed strains of
Bt
from diverse sources (natural isolates and biopesticides) affected the evolution of resistance in the diamondback moth,
Plutella xylostella,
to a focal strain. There was no significant difference in the rate of evolution of resistance between single and mixed-strain applications although the latter did result in lower insect populations. The relative survivorship of
Bt-
resistant genotypes was higher in the mixed-strain treatment, in part owing to elevated mortality of susceptible larvae in mixtures. Resistance evolved more quickly with treatments that contained natural isolates, and biological differences in transmission rate may have contributed to this. Our data indicate that the use of mixtures can have unexpected consequences on the fitness of resistant and susceptible insects.
When does fishing lead to more fish? Community consequences of bottom trawl fisheries in demersal food webs
Authors: van Denderen P. Daniel , van Kooten Tobias , Rijnsdorp Adriaan D.
Published: September 2013

Bottom trawls are a globally used fishing gear that physically disturb the seabed and kill non-target organisms, including those that are food for the targeted fish species. There are indications that ensuing changes to the benthic invertebrate community may increase the availability of food and promote growth and even fisheries yield of target fish species. If and how this occurs is the subject of ongoing debate, with evidence both in favour and against. We model the effects of trawling on a simple ecosystem of benthivorous fish and two food populations (benthos), susceptible and resistant to trawling. We show that the ecosystem response to trawling depends on whether the abundance of benthos is top-down or bottom-up controlled. Fishing may result in higher fish abundance, higher (maximum sustainable) yield and increased persistence of fish when the benthos which is the best-quality fish food is also more resistant to trawling. These positive effects occur in bottom-up controlled systems and systems with limited impact of fish feeding on benthos, resembling bottom-up control. Fishing leads to lower yields and fish persistence in all configurations where susceptible benthos are more profitable prey. Our results highlight the importance of mechanistic ecosystem knowledge as a requirement for successful management.
Salinibacillus xinjiangensis sp. nov., a halophilic bacterium from a hypersaline lake
Authors: Yang Na , Ren Biao , Liu Zhi-Heng , Dai Huan-Qin , Wang Jian , Zhou Yu-Guang , Song Fu-Hang , Zhang Li-Xin
Published: September 2013

A Gram-positive, endospore-forming, rod-shaped bacterium, designated isolate J4T, was isolated from a neutral saline lake sample from Xinjiang Uyghur Autonomous Region, China, and subjected to a polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain J4T is most closely related to

Salinibacillus aidingensis

25-7T (with 96.7 % similarity),

Salinibacillus kushneri

8-2T (96.5 %),

Ornithinibacillus scapharcae

TW25T (96.4 %),

Salirhabdus euzebyi

CVS-14T (96.4 %) and

Ornithinibacillus californiensis

MB-9T (96.2 %). Chemotaxonomic analysis showed menaquinone-7 (MK-7) to be the major isoprenoid quinone of strain J4T; diphosphatidylglycerol and phosphatidylglycerol were the major cellular polar lipids and the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of strain J4T was determined to be 36.2 mol%. Strain J4T was positive for catalase activity and negative for oxidase activity. Strain J4T was observed to grow at 25–50 °C (optimal 35–42 °C), pH 6.5–8.0 (optimal 7.0–7.5) and in media containing 1–21 % (w/v) NaCl (optimal 9–12 %). Based on these data, strain J4T represents a novel species of the genus

Salinibacillus

and the name Salinibacillus xinjiangensis sp. nov. is proposed. The type strain is J4T ( = CGMCC 1.12331T = JCM 18732T).
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
Authors: Nepal Chirag , Hadzhiev Yavor , Previti Christopher , Haberle Vanja , Li Nan , Takahashi Hazuki , Suzuki Ana Maria M. , Sheng Ying , Abdelhamid Rehab F. , Anand Santosh , Gehrig Jochen , Akalin Altuna , Kockx Christel E.M. , van der Sloot Antoine A.J. , van IJcken Wilfred F.J. , Armant Olivier , Rastegar Sepand , Watson Craig , Strähle Uwe , Stupka Elia , Carninci Piero , Lenhard Boris , Müller Ferenc
Published: September 2013

Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates.
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
Authors: Seitan Vlad C. , Faure Andre J. , Zhan Ye , McCord Rachel Patton , Lajoie Bryan R. , Ing-Simmons Elizabeth , Lenhard Boris , Giorgetti Luca , Heard Edith , Fisher Amanda G. , Flicek Paul , Dekker Job , Merkenschlager Matthias
Published: September 2013

Chromosome conformation capture approaches have shown that interphase chromatin is partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized topological domains. This compartmentalization is thought to facilitate the matching of genes and regulatory elements, but its precise function and mechanistic basis remain unknown. Cohesin controls chromosome topology to enable DNA repair and chromosome segregation in cycling cells. In addition, cohesin associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. Although these findings suggest an important role for cohesin in genome organization, this role has not been assessed on a global scale. Unexpectedly, we find that architectural compartments are maintained in noncycling mouse thymocytes after genetic depletion of cohesin in vivo. Cohesin was, however, required for specific long-range interactions within compartments where cohesin-regulated genes reside. Cohesin depletion diminished interactions between cohesin-bound sites, whereas alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete gene expression states within preexisting chromosomal compartments.
Biofilm formation and antibiotic production in Ruegeria mobilis are influenced by intracellular concentrations of cyclic dimeric guanosinmonophosphate
Authors: D'Alvise Paul W. , Magdenoska Olivera , Melchiorsen Jette , Nielsen Kristian F. , Gram Lone
Published: September 2013

In many species of the marine Roseobacter clade, periods of attached life, in association with phytoplankton or particles, are interspersed with planktonic phases. The purpose of this study was to determine whether shifts between motile and sessile life in the globally abundant Roseobacter clade species Ruegeria mobilis are associated with intracellular concentrations of the signal compound cyclic dimeric guanosinmonophosphate (c‐di‐GMP), which in bacteria regulates transitions between motile and sessile life stages. Genes for diguanylate cyclases and phosphodiesterases, which are involved in c‐di‐GMP signalling, were found in the genome of R. mobilis strain F1926. Ion pair chromatography‐tandem mass spectrometry revealed 20‐fold higher c‐di‐GMP concentrations per cell in biofilm‐containing cultures than in planktonic cells. An introduced diguanylate cyclase gene increased c‐di‐GMP and enhanced biofilm formation and production of the potent antibiotic tropodithietic acid (TDA). An introduced phosphodiesterase gene decreased c‐di‐GMP and reduced biofilm formation and TDA production. tdaC, a key gene for TDA biosynthesis, was expressed only in attached or biofilm‐forming cells, and expression was induced immediately after initial attachment. In conclusion, c‐di‐GMP signalling controls biofilm formation and biofilm‐associated traits in R. mobilis and, as suggested by presence of GGDEF and EAL domain protein genes, also in other Roseobacter clade species.
Exogenous 5,6‐dimethylbenzimidazole caused production of a non‐functional tetrachloroethene reductive dehalogenase in Sulfurospirillum multivorans
Authors: Keller Sebastian , Ruetz Markus , Kunze Cindy , Kräutler Bernhard , Diekert Gabriele , Schubert Torsten
Published: September 2013

Corrinoid‐dependent reductive dehalogenation is mediated by phylogenetically diverse anaerobic bacteria that either synthesize corrinoids de novo or are dependent on corrinoid salvaging from the environment. The tetrachloroethene (PCE) reductive dehalogenase (PceA) of the Gram‐negative Epsilonproteobacterium Sulfurospirillum multivorans harbours a norpseudo‐B12 as corrinoid cofactor. Norpseudo‐B12 differs from coenzyme B12 in the nucleotide loop structure. Adenine instead of 5,6‐dimethylbenzimidazole (DMB) serves as lower ligand base of the central cobalt ion, and the nucleotide loop of norpseudo‐B12 lacks a methyl group at position 176. In this study, S. multivorans was grown anaerobically with PCE in the presence of DMB. At a DMB concentration of 25 μM, the adenine moiety in the nucleotide loop of norpseudo‐B12 was quantitatively replaced by DMB. The formation of the DMB‐containing nor‐B12 severely affected PCE‐dependent growth and the PceA activity. In DMB‐treated cells processing of the cytoplasmic PceA precursor was impeded, a result pointing to retarded cofactor incorporation. PceA enriched from cells cultivated with DMB contained nor‐B12. Nor‐B12 purified from cells grown in the presence of DMB mediated the abiotic reductive dehalogenation of trichloroacetate to dichloroacetate at a 25‐fold lower rate in comparison with norpseudo‐B12, a fact underpinning the relevance of norpseudo‐B12 as efficient catalyst for reductive dehalogenation in general.
The logic of metabolism and its fuzzy consequences
Authors: Danchin Antoine , Sekowska Agnieszka
Published: September 2013

Intermediary metabolism molecules are orchestrated into logical pathways stemming from history (L‐amino acids, d‐sugars) and dynamic constraints (hydrolysis of pyrophosphate or amide groups is the driving force of anabolism). Beside essential metabolites, numerous variants derive from programmed or accidental changes. Broken down, variants enter standard pathways, producing further variants. Macromolecule modification alters enzyme reactions specificity. Metabolism conform thermodynamic laws, precluding strict accuracy. Hence, for each regular pathway, a wealth of variants inputs and produces metabolites that are similar to but not the exact replicas of core metabolites. As corollary, a shadow, paralogous metabolism, is associated to standard metabolism. We focus on a logic of paralogous metabolism based on diversion of the core metabolic mimics into pathways where they are modified to minimize their input in the core pathways where they create havoc. We propose that a significant proportion of paralogues of well‐characterized enzymes have evolved as the natural way to cope with paralogous metabolites. A second type of denouement uses a process where protecting/deprotecting unwanted metabolites – conceptually similar to the procedure used in the laboratory of an organic chemist – is used to enter a completely new catabolic pathway.
Surfactin triggers biofilm formation of Bacillus subtilis in melon phylloplane and contributes to the biocontrol activity
Authors: Zeriouh Houda , de Vicente Antonio , Pérez‐García Alejandro , Romero Diego
Published: September 2013

The biocontrol activity of many Bacillus species has been traditionally related to the direct antagonism of pathogens. In previous works, we reported that B. subtilis strain UMAF6614 was an efficient biocontrol agent that produced bacillomycin, fengycin and surfactin lipopeptides. Bacillomycins and fengycins were shown to have antagonistic activity towards fungal and bacterial pathogens of cucurbits; however, the functionality of surfactin remained unclear. In this study, the role of surfactin in the biocontrol activity of this strain was investigated. We observed that a deficiency in surfactin production led to a partial reduction of disease suppression by this biocontrol agent, which coincided with a defect in biofilm formation and the colonization of the melon phylloplane. These effects were due to a dramatic reduction in the production of exopolysaccharide and the TasA protein, which are the two major components of the extracellular matrix. We propose that the biocontrol activity of this strain is the result of the coordinated action of the three families of lipopeptides. B. subtilis UMAF6614 produces surfactin to trigger biofilm formation on melon phylloplane, which ensures the long‐term persistence and the adequate secretion of suppressive lipopeptides, bacillomycins and fengycins, which efficiently target pathogens.
NrsZ: a novel, processed, nitrogen‐dependent, small non‐coding RNA that regulates Pseudomonas aeruginosa PAO1 virulence
Authors: Wenner Nicolas , Maes Alexandre , Cotado‐Sampayo Marta , Lapouge Karine
Published: September 2013

The opportunistic pathogen Pseudomonas aeruginosa PAO1 has a remarkable capacity to adapt to various environments and to survive with limited nutrients. Here, we report the discovery and characterization of a novel small non‐coding RNA: NrsZ (nitrogen‐regulated sRNA). We show that under nitrogen limitation, NrsZ is induced by the NtrB/C two‐component system, an important regulator of nitrogen assimilation and P. aeruginosa's swarming motility, in concert with the alternative sigma factor RpoN. Furthermore, we demonstrate that NrsZ modulates P. aeruginosa motility by controlling the production of rhamnolipid surfactants, virulence factors notably needed for swarming motility. This regulation takes place through the post‐transcriptional control of rhlA, a gene essential for rhamnolipids synthesis. Interestingly, we also observed that NrsZ is processed in three similar short modules, and that the first short module encompassing the first 60 nucleotides is sufficient for NrsZ regulatory functions.