Association of Bartonella Species with Wild and Synanthropic Rodents in Different Brazilian Biomes

ABSTRACTBartonellaspp. comprise an ecologically successful group of microorganisms that infect erythrocytes and have adapted to different hosts, which include a wide range of mammals, besides humans. Rodents are reservoirs of about two-thirds ofBartonellaspp. described to date; and some of them have been implicated as causative agents of human diseases. In our study, we performed molecular and phylogenetic analyses ofBartonellaspp. infecting wild rodents from five different Brazilian biomes. In order to characterize the genetic diversity ofBartonellaspp., we performed a robust analysis based on three target genes, followed by sequencing, Bayesian inference, and maximum likelihood analysis.Bartonellaspp. were detected in 25.6% (117/457) of rodent spleen samples analyzed, and this occurrence varied among different biomes. The diversity analysis ofgltAsequences showed the presence of 15 different haplotypes. Analysis of the phylogenetic relationship ofgltAsequences performed by Bayesian inference and maximum likelihood showed that theBartonellaspecies detected in rodents from Brazil was closely related to the phylogenetic group A detected in other cricetid rodents from North America, probably constituting only one species. Last, theBartonellaspecies genogroup identified in the present study formed a monophyletic group that includedBartonellasamples from seven different rodent species distributed in three distinct biomes. In conclusion, our study showed that the occurrence ofBartonellabacteria in rodents is much more frequent and widespread than previously recognized.IMPORTANCEIn the present study, we reported the occurrence ofBartonellaspp. in some sites in Brazil. The identification and understanding of the distribution of this important group of bacteria may allow the Brazilian authorities to recognize potential regions with the risk of transmission of these pathogens among wild and domestic animals and humans. In addition, our study accessed important gaps in the biology of this group of bacteria in Brazil, such as its low host specificity, high genetic diversity, and relationship with otherBartonellaspp. detected in rodents trapped in America. Considering the diversity of newly discoveredBartonellaspecies and the great ecological plasticity of these bacteria, new studies with the aim of revealing the biological aspects unknown until now are needed and must be performed around the world. In this context, the impact ofBartonellaspp. associated with rodents in human health should be assessed in future studies.

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Evaluating undergraduate research conferences as vehicles for novice researcher development

International Journal for Researcher Development ◽

10.1108/ijrd-10-2015-0026 ◽

2016 ◽

Vol 7 (2) ◽

pp. 159-177 ◽

Cited By ~ 9

Author(s):

Pauline Kneale ◽

Andrew Edwards-Jones ◽

Helen Walkington ◽

Jennifer Hill

Keyword(s):

Undergraduate Students ◽

Undergraduate Research ◽

Skills Development ◽

Learning Context ◽

Content Type ◽

Research Conference ◽

Researcher Development ◽

Development Framework ◽

Wide Range ◽

The Impact

Purpose This paper aims to focus on the undergraduate research conference as its sphere of study and investigate the impact of significance of participation and socialisation in such activities on student attitudes and professional development. Using situated learning to theoretically position the undergraduate research conference as an authentic learning context, connection is also made with the concept of graduate attributes. Design/methodology/approach The Vitae (2014) Researcher Development Framework (RDF) is used to provide a template for charting the experiences and development of undergraduate students as researchers. This can be applied to short-term activities and programmes and to long-term career plans. The insights from 90 undergraduate students participating in three national undergraduate research conferences were obtained through interviews, and thematically analysed to map the students’ skills development against the RDF criteria. Findings Three main aspects of undergraduate research conference participation were considered particularly important by the students: the value of paper presentations, the value of poster presentations and the value of the overall conference experience. Within these themes, participants identified a wide range of skills and attributes they felt they had developed as a result of either preparing for or participating in the conferences. The majority of these skills and attributes could be mapped against the different domains of the RDF, using a public engagement lens for comparing actual with expected developmental areas. Research limitations/implications This research helps undergraduate research conference organisers construct programme content and form it in such a way that students’ skill development can be maximised prior to, and during, the course of an event. Learning developers can also use these findings to help understand the support needs of students preparing to deliver papers at such conferences. So far, little empirical research has examined students’ skills development within the undergraduate research conference arena. Originality/value The outcomes of this study show the diversity of the skills that students developed and the value of the conference format for offering networking practice and enhancing the communication skills which employers value.

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In VivoEfficacy of Anuran Trypsin Inhibitory Peptides against Staphylococcal Skin Infection and the Impact of Peptide Cyclization

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04324-14 ◽

2015 ◽

Vol 59 (4) ◽

pp. 2113-2121 ◽

Cited By ~ 9

Author(s):

U. Malik ◽

O. N. Silva ◽

I. C. M. Fensterseifer ◽

L. Y. Chan ◽

R. J. Clark ◽

...

Keyword(s):

Antimicrobial Agents ◽

Cyclic Peptide ◽

Sequence Similarity ◽

Infection Model ◽

Content Type ◽

Wide Range ◽

Inhibitory Activities ◽

The Impact

ABSTRACTStaphylococcus aureusis a virulent pathogen that is responsible for a wide range of superficial and invasive infections. Its resistance to existing antimicrobial drugs is a global problem, and the development of novel antimicrobial agents is crucial. Antimicrobial peptides from natural resources offer potential as new treatments against staphylococcal infections. In the current study, we have examined the antimicrobial properties of peptides isolated from anuran skin secretions and cyclized synthetic analogues of these peptides. The structures of the peptides were elucidated by nuclear magnetic resonance (NMR) spectroscopy, revealing high structural and sequence similarity with each other and with sunflower trypsin inhibitor 1 (SFTI-1). SFTI-1 is an ultrastable cyclic peptide isolated from sunflower seeds that has subnanomolar trypsin inhibitory activity, and this scaffold offers pharmaceutically relevant characteristics. The five anuran peptides were nonhemolytic and noncytotoxic and had trypsin inhibitory activities similar to that of SFTI-1. They demonstrated weakin vitroinhibitory activities againstS. aureus, but several had strong antibacterial activities againstS. aureusin anin vivomurine wound infection model. pYR, an immunomodulatory peptide fromRana sevosa, was the most potent, with complete bacterial clearance at 3 mg · kg−1. Cyclization of the peptides improved their stability but was associated with a concomitant decrease in antimicrobial activity. In summary, these anuran peptides are promising as novel therapeutic agents for treating infections from a clinically resistant pathogen.

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Xylodon bambusinus and X. xinpingensis spp. nov. (Hymenochaetales) from southern China

Phytotaxa ◽

10.11646/phytotaxa.511.3.3 ◽

2021 ◽

Vol 511 (3) ◽

Author(s):

XIANG MA ◽

CHANG-LIN ZHAO

Keyword(s):

New Species ◽

Bayesian Inference ◽

Maximum Likelihood ◽

Growth Habit ◽

Southern China ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Two New Species ◽

Thin Walled ◽

Inference Methods

Two new species, Xylodon bambusinus and X. xinpingensis, are proposed based on morphological and molecular evidences. Both species share the annual growth habit, resupinate basidiomata and monomitic hyphal system with clamped, colorless generative hyphae, smooth, thin-walled basidiospores, but X. bambusinus is characterized by the smooth to tuberculate hymenial surface, presence of capitate and fusiform cystidia, broad ellipsoid basidiospores, while X. xinpingensis by the reticulate hymenophore with cream hymenial surface, and subglobose basidiospores (4.5–6 × 3.5–5 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on molecular data of ITS and ITS+nLSU sequences showed that X. bambusinus was sister to X. subclavatus, while X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus. The nLSU dataset revealed that X. bambusinus grouped with X. asperus and X. brevisetus with lower supports, and that X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus and then with X. rimosissimus without supports. Both morphological and molecular evidences confirmed the placement of two new species in Xylodon. Description and figures from the new species and a key to the known species of Xylodon from China are presented.

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An Adaptive Bitrate Switching Algorithm for Speech Applications in Context of WebRTC

ACM Transactions on Multimedia Computing Communications and Applications ◽

10.1145/3458751 ◽

2021 ◽

Vol 17 (4) ◽

pp. 1-21

Author(s):

Mohannad Alahmadi ◽

Peter Pocta ◽

Hugh Melvin

Keyword(s):

Real Time ◽

Data Exchange ◽

Quality Of Experience ◽

End User ◽

High Quality ◽

Content Type ◽

Switching Algorithm ◽

Wide Range ◽

The Impact

Web Real-Time Communication (WebRTC) combines a set of standards and technologies to enable high-quality audio, video, and auxiliary data exchange in web browsers and mobile applications. It enables peer-to-peer multimedia sessions over IP networks without the need for additional plugins. The Opus codec, which is deployed as the default audio codec for speech and music streaming in WebRTC, supports a wide range of bitrates. This range of bitrates covers narrowband, wideband, and super-wideband up to fullband bandwidths. Users of IP-based telephony always demand high-quality audio. In addition to users’ expectation, their emotional state, content type, and many other psychological factors; network quality of service; and distortions introduced at the end terminals could determine their quality of experience. To measure the quality experienced by the end user for voice transmission service, the E-model standardized in the ITU-T Rec. G.107 (a narrowband version), ITU-T Rec. G.107.1 (a wideband version), and the most recent ITU-T Rec. G.107.2 extension for the super-wideband E-model can be used. In this work, we present a quality of experience model built on the E-model to measure the impact of coding and packet loss to assess the quality perceived by the end user in WebRTC speech applications. Based on the computed Mean Opinion Score, a real-time adaptive codec parameter switching mechanism is used to switch to the most optimum codec bitrate under the present network conditions. We present the evaluation results to show the effectiveness of the proposed approach when compared with the default codec configuration in WebRTC.

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Dynamics in Copy Numbers of Five Plasmids of a DairyLactococcus lactisStrain under Dairy-Related Conditions Including Near-Zero Growth Rates

Applied and Environmental Microbiology ◽

10.1128/aem.00314-18 ◽

2018 ◽

Vol 84 (11) ◽

Cited By ~ 1

Author(s):

Oscar van Mastrigt ◽

Marcel M. A. N. Lommers ◽

Yorick C. de Vries ◽

Tjakko Abee ◽

Eddy J. Smid

Keyword(s):

Nutrient Limitation ◽

Lactococcus Lactis ◽

Growth Rates ◽

Copy Number ◽

Plasmid Copy ◽

Content Type ◽

Copy Numbers ◽

Wide Range ◽

Zero Growth ◽

The Impact

ABSTRACTLactic acid bacteria can carry multiple plasmids affecting their performance in dairy fermentations. The expression of plasmid-borne genes and the activity of the corresponding proteins are severely affected by changes in the numbers of plasmid copies. We studied the impact of growth rate on the dynamics of plasmid copy numbers at high growth rates in chemostat cultures and down to near-zero growth rates in retentostat cultures. Five plasmids of the dairy strainLactococcus lactisFM03-V1 were selected, and these varied in size (3 to 39 kb), in replication mechanism (theta or rolling circle), and in putative (dairy-associated) functions. The copy numbers ranged from 1.5 to 40.5, and the copy number of theta-type replicating plasmids was negatively correlated to the plasmid size. Despite the extremely wide range of growth rates (0.0003 h−1to 0.6 h−1), the copy numbers of the five plasmids were stable and only slightly increased at near-zero growth rates, showing that the plasmid replication rate was strictly controlled. One low-copy-number plasmid, carrying a large exopolysaccharide gene cluster, was segregationally unstable during retentostat cultivations, reflected in a complete loss of the plasmid in one of the retentostat cultures. The copy number of the five plasmids was also hardly affected by varying the pH value, nutrient limitation, or the presence of citrate (maximum 2.2-fold), signifying the stability in copy number of the plasmids.IMPORTANCELactococcus lactisis extensively used in starter cultures for dairy fermentations. Important traits for the growth and survival ofL. lactisin dairy fermentations are encoded by genes located on plasmids, such as genes involved in lactose and citrate metabolism, protein degradation, oligopeptide uptake, and bacteriophage resistance. Because the number of plasmid copies could affect the expression of plasmid-borne genes, it is important to know the factors that influence the plasmid copy numbers. We monitored the plasmid copy numbers ofL. lactisat near-zero growth rates, characteristic for cheese ripening. Moreover, we analyzed the effects of pH, nutrient limitation, and the presence of citrate. This showed that the plasmid copy numbers were stable, giving insight into plasmid copy number dynamics in dairy fermentations.

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Natural resource governance, accountability and legitimising propensity: insights from Ghana's oil and gas sector

Journal of Accounting in Emerging Economies ◽

10.1108/jaee-08-2019-0153 ◽

2021 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Emmanuel Asare ◽

Bruce Burton ◽

Theresa Dunne

Keyword(s):

Natural Resource ◽

Oil And Gas ◽

Oil And Gas Industry ◽

Resource Discovery ◽

Legitimacy Theory ◽

Structured Interviews ◽

Content Type ◽

Resource Governance ◽

Wide Range ◽

The Impact

PurposeThis study explores Ghanaian views about accountability discharge by firms and government in the context of the nation's newly discovered oil and gas resources. The research focusses on a range of issues relating to stakeholder interaction, communication flows and the impact of decision-making on Ghanaian lives, as perceived by individuals on the ground.Design/methodology/approachThe paper adapts elements of legitimacy theory to interpret the outcome of a series of semi-structured interviews with members of key accountee and accountor groups including citizens and representatives of the state and private firms in the oil and gas industry in Ghana.FindingsThe results indicate that rather than attempting to effect substantive accountability discharge, Ghana's government and oil and gas firms employ a wide range of legitimation strategies despite the apparently complete absence of the accountee power normally seen as driving the need for social contract repair.Research limitations/implicationsThe findings suggest that accountability discharge in Ghana is cursory at best, with several legitimising strategies in evidence. The representatives from state institutions appear to share some of the concerns, suggesting that the problems are entrenched and will require robust enforcement of a strengthened regulatory approach to effect meaningful change.Originality/valueThis paper contributes to the literature on the discharge of institutional accountability by building on earlier conceptualisations of legitimacy theory to explore perceptions around a recent natural resource discovery. The analysis highlights grave concerns regarding the behaviour of state and corporate actors, one that runs counter to sub-Saharan African tradition.

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Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran

Applied and Environmental Microbiology ◽

10.1128/aem.01518-19 ◽

2019 ◽

Vol 85 (20) ◽

Cited By ~ 2

Author(s):

Moein Khojasteh ◽

S. Mohsen Taghavi ◽

Pejman Khodaygan ◽

Habiballah Hamzehzarghani ◽

Gongyou Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Global Scale ◽

Population Diversity ◽

Bacterial Leaf Streak ◽

High Genetic Diversity ◽

Center Of Origin ◽

Content Type ◽

Xanthomonas Translucens ◽

Insight Into

ABSTRACT This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding’s grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding’s grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen. IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads—namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens—have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.

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Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains

Applied and Environmental Microbiology ◽

10.1128/aem.02873-19 ◽

2020 ◽

Vol 86 (6) ◽

Cited By ~ 3

Author(s):

Ebrahim Osdaghi ◽

Touraj Rahimi ◽

S. Mohsen Taghavi ◽

Maryam Ansari ◽

Sadegh Zarei ◽

...

Keyword(s):

Genetic Diversity ◽

Comparative Genomics ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Sensu Stricto ◽

Bacterial Canker ◽

Agricultural Crops ◽

Content Type ◽

Canker Disease

ABSTRACT Members of the genus Clavibacter are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g., alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter sp. strains account for a great portion of the genetic diversity of the genus, and C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis), causing bacterial canker disease, is considered one of the most destructive seed-borne agents for the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory results in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter sp. strains, including the type strains of newly described subspecies, to provide precise insight into the diversity of tomato-associated members of the genus and further clarify the taxonomic status of the strains using genotypic and phenotypic features. The results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensis sensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the nonpathogenic strains, a number of pathogenicity-related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results indicate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter sp. strains to facilitate differentiation of the lineages in quarantine inspections. IMPORTANCE Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops, such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant-pathogenic members of the genus (e.g., C. michiganensis sensu stricto and C. sepedonicus, infecting tomato and potato plants, respectively) are included in the A2 (high-risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. account for a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and are subjected to the quarantine inspections. Hence, discrimination between the pathogenic and nonpathogenic Clavibacter sp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost-efficient management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview of the phylogenetic and genomic differences between the pathogenic and nonpathogenic tomato-associated Clavibacter sp. strains. We also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) should be reconsidered.

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Sensitivity of automatic control of emergency manoeuvre to parametric uncertainty of the airplane model

Aircraft Engineering and Aerospace Technology ◽

10.1108/aeat-01-2018-0017 ◽

2019 ◽

Vol 91 (3) ◽

pp. 407-419

Author(s):

Jerzy Graffstein ◽

Piotr Maslowski

Keyword(s):

Control System ◽

Automatic Control ◽

Flight Control ◽

Parametric Uncertainty ◽

Second Phase ◽

Flight Control System ◽

Content Type ◽

Control Quality ◽

Wide Range ◽

The Impact

Purpose The main purpose of this work was elaboration and verification of a method of assessing the sensitivity of automatic control laws to parametric uncertainty of an airplane’s mathematical model. The linear quadratic regulator (LQR) methodology was used as an example design procedure for the automatic control of an emergency manoeuvre. Such a manoeuvre is assumed to be pre-designed for the selected airplane. Design/methodology/approach The presented method of investigating the control systems’ sensitivity comprises two main phases. The first one consists in computation of the largest variations of gain factors, defined as differences between their nominal values (defined for the assumed model) and the values obtained for the assumed range of parametric uncertainty. The second phase focuses on investigating the impact of the variations of these factors on the behaviour of automatic control in the manoeuvre considered. Findings The results obtained allow for a robustness assessment of automatic control based on an LQR design. Similar procedures can be used to assess in automatic control arrived at through varying design methods (including methods other than LQR) used to control various manoeuvres in a wide range of flight conditions. Practical implications It is expected that the presented methodology will contribute to improvement of automatic flight control quality. Moreover, such methods should reduce the costs of the mathematical nonlinear model of an airplane through determining the necessary accuracy of the model identification process, needed for assuring the assumed control quality. Originality/value The presented method allows for the investigation of the impact of the parametric uncertainty of the airplane’s model on the variations of the gain-factors of an automatic flight control system. This also allows for the observation of the effects of such variations on the course of the selected manoeuvre or phase of flight. This might be a useful tool for the design of crucial elements of an automatic flight control system.

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Complete Genome Sequence of Psittacine Adenovirus 1, Identified from Poicephalus senegalus in Italy

Microbiology Resource Announcements ◽

10.1128/mra.01037-18 ◽

2018 ◽

Vol 7 (11) ◽

Cited By ~ 5

Author(s):

Adelaide Milani ◽

Gianpiero Zamperin ◽

Alice Fusaro ◽

Annalisa Salviato ◽

Luca Bano ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Full Genome Sequence ◽

Full Genome ◽

High Genetic Diversity ◽

Content Type ◽

First Time

Using a metagenomics approach, we were able to determine for the first time the full-genome sequence of a psittacine adenovirus 1 isolate that was recovered from the liver of a dead Senegal parrot (Poicephalus senegalus) in Italy. The results of the phylogenetic investigations revealed the existence of high genetic diversity among adenoviruses circulating in psittacine birds.

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