bluuebunny/crossref_metadata_2025 huggingface dataset:
First Report of a 16Sr I-B Phytoplasma Associated with Phyllody and Stem Fasciation of Flax (Linum usitatissimum) in India
Authors: Biswas C. , Dey P. , Mandal K. , Mitra J. , Satpathy S. , Karmakar P. G.
Published: July 2014

Flax or linseed is grown as a fiber or oilseed crop in tropical and temperate regions. It is commercially cultivated in many countries of the world including Canada, China, India, the United States, Ethiopia, Pakistan, Russia, Poland, and Argentina (1). In December 2013, symptoms suggestive of phytoplasma infection were noticed on flax in different experimental fields of Central Research Institute for Jute and Allied Fibres (CRIJAF) research farm, Barrackpore, India, and the incidence was less than 2%. Because incidence of phytoplasma diseases are increasing worldwide, occurrence of a phytoplasma in a new geographical area poses an imminent threat. The infected plants showed floral virescence, phyllody, and stem fasciation (flattened stem). Floral malformation was very conspicuous with abnormal structures replacing normal flowers. All the floral parts, including petals, turned into green leaves. Total DNA was extracted from leaf mid veins of three symptomatic and three asymptomatic plants using a DNeasy Plant Mini Kit (Qiagen). PCR was carried out with the phytoplasma-specific universal P1/P7 primer set followed by nested primer pair R16F2n/R16R2 (2), resulting in DNA amplicons that were 1.8 kb and 1.2 kb, respectively, in all symptomatic samples tested. No amplification was observed with DNA from symptomless samples. This suggested association of a phytoplasma with the disease. The five purified nested PCR products were cloned in a pGEM-T Easy vector (Promega) and sequenced. One of the sequences that proved to be identical to the others was deposited in GenBank (Accession No. KJ417660). The consensus sequence was analyzed by NCBI BLAST and found to share 99% similarity with the 16Sr DNA sequence of the ‘Candidatus Phytoplasma asteris' reference strain (GenBank HQ828108), which belongs to 16SrI group. The phylogenetic tree based on 16SrDNA sequence of phytoplasmas belonging to group 16SrI and other distinct phytoplasma groups also showed that the phytoplasma clustered with members of group 16SrI (3). The nested PCR product of R16F2n/R16R2 was digested using restriction enzymes AluI, BfaI, BstU, HhaI, HpaI, KpnI, MseI, and RsaI. The RFLP patterns were compared with those of known phytoplasma strains (2) and they matched the patterns for aster yellows subgroup B (16Sr I-B). Subsequently, the iPhyClassifier 16Sr group/subgroup classification based on similarity (4) analyses showed that the studied strain had 16SrDNA sequences in the 16SrI-B group with a similarity coefficient of 1.00. To the best of our knowledge, this is the first report of 16SrI-B phytoplasma associated with flax in India.

References: (1) K. P. Akhtar et al. Phytoparasitica 41:383, 2013. (2) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (3) N. Saitou and M. Nei. Mol. Biol. Evol. 4:406, 1987. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
Evaluation of a Diverse, Worldwide Collection of Wild, Cultivated, and Landrace Pepper (Capsicum annuum) for Resistance to Phytophthora Fruit Rot, Genetic Diversity, and Population Structure
Authors: Naegele R. P. , Tomlinson A. J. , Hausbeck M. K.
Published: July 2014

Pepper is the third most important solanaceous crop in the United States and fourth most important worldwide. To identify sources of resistance for commercial breeding, 170 pepper genotypes from five continents and 45 countries were evaluated for Phytophthora fruit rot resistance using two isolates of Phytophthora capsici. Genetic diversity and population structure were assessed on a subset of 157 genotypes using 23 polymorphic simple sequence repeats. Partial resistance and isolate-specific interactions were identified in the population at both 3 and 5 days postinoculation (dpi). Plant introductions (PIs) 640833 and 566811 were the most resistant lines evaluated at 5 dpi to isolates 12889 and OP97, with mean lesion areas less than Criollo de Morelos. Genetic diversity was moderate (0.44) in the population. The program STRUCTURE inferred four genetic clusters with moderate to very great differentiation among clusters. Most lines evaluated were susceptible or moderately susceptible at 5 dpi, and no lines evaluated were completely resistant to Phytophthora fruit rot. Significant population structure was detected when pepper varieties were grouped by predefined categories of disease resistance, continent, and country of origin. Moderately resistant or resistant PIs to both isolates of P. capsici at 5 dpi were in genetic clusters one and two.
Ungulate saliva inhibits a grass–endophyte mutualism
Authors: Tanentzap Andrew J. , Vicari Mark , Bazely Dawn R.
Published: July 2014

Fungal endophytes modify plant–herbivore interactions by producing toxic alkaloids that deter herbivory. However, studies have neglected the direct effects herbivores may have on endophytes. Antifungal properties and signalling effectors in herbivore saliva suggest that evolutionary pressures may select for animals that mitigate the effects of endophyte-produced alkaloids. Here, we tested whether saliva of moose (
Alces alces
) and European reindeer (
Rangifer tarandus
) reduced hyphal elongation and production of ergot alkaloids by the foliar endophyte
Epichloë festucae
associated with the globally distributed red fescue
Festuca rubra
. Both moose and reindeer saliva reduced the growth of isolated endophyte hyphae when compared with a treatment of distilled water. Induction of the highly toxic alkaloid ergovaline was also inhibited in plants from the core of
F. rubra
's distribution when treated with moose saliva following simulated grazing. In genotypes from the southern limit of the species' distribution, ergovaline was constitutively expressed, as predicted where growth is environmentally limited. Our results now present the first evidence, to our knowledge, that ungulate saliva can combat plant defences produced by a grass–endophyte mutualism.
Sir Kenneth Murray. 30 December 1930 — 7 April 2013
Authors: Brammar W. J. , Gratzer W. B.
Published: July 2014

Sir Kenneth Murray—Ken to his friends—was held in high esteem and affection by all who knew him. In a remarkable career, which began after he left school at the age of 16 years, he played a prominent part, through his elegant and meticulous research, in the evolution of biotechnology; he trained and inspired generations of students entering this bright new discipline; he developed the means of diagnosing, preventing and treating a feared disease, thereby saving many thousands of lives; he was one of a small coterie that founded the first Europe-based biotechnology company; and he used the profits that this yielded to enrich his university and promote, through the charity that he founded, the careers of promising young scientists. He remained, throughout, modest, unassuming and ever willing to give of his time and knowledge to all who asked.
Malcolm Roy Clarke. 24 October 1930 — 10 May 2013
Authors: Herring Peter J.
Published: July 2014

Malcolm Clarke was a leading authority on cephalopods and their significance in the world oceans. Much of his knowledge of their abundance was gained through a study of their beaks from the stomachs of predators, particularly sperm whales. He had a lifelong enthusiasm for sperm whales (and for other cetaceans), leading him to reappraise their buoyancy control. Postgraduate experience as a whaling inspector in the Antarctic led to his joining the National Institute of oceanography in 1958 to work on oceanic squids. In 1972 he moved to the Marine Biological association’s Plymouth laboratory, where he was elected FRS in 1981 and was awarded a Special Merit promotion. He remained there until retirement in 1987, during which time he set up the Cephalopod International Advisory Council (CIAC). After retirement he travelled widely and continued his research on whales and squids, based first at home in Plymouth and later at his house in Pico, in the Azores.
Geomagnetic imprinting predicts spatio-temporal variation in homing migration of pink and sockeye salmon
Authors: Putman Nathan F. , Jenkins Erica S. , Michielsens Catherine G. J. , Noakes David L. G.
Published: July 2014

Animals navigate using a variety of sensory cues, but how each is weighted during different phases of movement (e.g. dispersal, foraging, homing) is controversial. Here, we examine the geomagnetic and olfactory imprinting hypotheses of natal homing with datasets that recorded variation in the migratory routes of sockeye (Oncorhynchus nerka) and pink (Oncorhynchus gorbuscha) salmon returning from the Pacific Ocean to the Fraser River, British Columbia. Drift of the magnetic field (i.e. geomagnetic imprinting) uniquely accounted for 23.2% and 44.0% of the variation in migration routes for sockeye and pink salmon, respectively. Ocean circulation (i.e. olfactory imprinting) predicted 6.1% and 0.1% of the variation in sockeye and pink migration routes, respectively. Sea surface temperature (a variable influencing salmon distribution but not navigation, directly) accounted for 13.0% of the variation in sockeye migration but was unrelated to pink migration. These findings suggest that geomagnetic navigation plays an important role in long-distance homing in salmon and that consideration of navigation mechanisms can aid in the management of migratory fishes by better predicting movement patterns. Finally, given the diversity of animals that use the Earth's magnetic field for navigation, geomagnetic drift may provide a unifying explanation for spatio-temporal variation in the movement patterns of many species.
Walking in circles: a modelling approach
Authors: Maus Horst-Moritz , Seyfarth Andre
Published: July 2014

Blindfolded or disoriented people have the tendency to walk in circles rather than on a straight line even if they wanted to. Here, we use a minimalistic walking model to examine this phenomenon. The bipedal spring-loaded inverted pendulum exhibits asymptotically stable gaits with centre of mass (CoM) dynamics and ground reaction forces similar to human walking in the sagittal plane. We extend this model into three dimensions, and show that stable walking patterns persist if the leg is aligned with respect to the body (here: CoM velocity) instead of a world reference frame. Further, we demonstrate that asymmetric leg configurations, which are common in humans, will typically lead to walking in circles. The diameter of these circles depends strongly on parameter configuration, but is in line with empirical data from human walkers. Simulation results suggest that walking radius and especially direction of rotation are highly dependent on leg configuration and walking velocity, which explains inconsistent veering behaviour in repeated trials in human data. Finally, we discuss the relation between findings in the model and implications for human walking.
Geckoprinting: assembly of microelectronic devices on unconventional surfaces by transfer printing with isolated gecko setal arrays
Authors: Jeong Jaeyoung , Kim Juho , Song Kwangsun , Autumn Kellar , Lee Jongho
Published: July 2014

Developing electronics in unconventional forms provides opportunities to expand the use of electronics in diverse applications including bio-integrated or implanted electronics. One of the key challenges lies in integrating semiconductor microdevices onto unconventional substrates without glue, high pressure or temperature that may cause damage to microdevices, substrates or interfaces. This paper describes a solution based on natural gecko setal arrays that switch adhesion mechanically on and off, enabling pick and place manipulation of thin microscale semiconductor materials onto diverse surfaces including plants and insects whose surfaces are usually rough and irregular. A demonstration of functional ‘geckoprinted’ microelectronic devices provides a proof of concept of our results in practical applications.
Relaxation of the single-slip condition in strain-gradient plasticity
Authors: Anguige Keith , Dondl Patrick W.
Published: July 2014

We consider the variational formulation of both geometrically linear and geometrically nonlinear elasto-plasticity subject to a class of hard single-slip conditions. Such side conditions typically render the associated boundary-value problems non-convex. We show that, for a large class of non-smooth plastic distortions, a given single-slip condition (specification of Burgers vectors) can be relaxed by introducing a microstructure through a two-stage process of mollification and lamination. The relaxed model can be thought of as an aid to simulating macroscopic plastic behaviour without the need to resolve arbitrarily fine spatial scales.
Amygdaloid and non-amygdaloid fear both influence avoidance of risky foraging in hungry rats
Authors: Kim Earnest , Kim Eun Joo , Yeh Regina , Shin Minkyung , Bobman Jake , Krasne Franklin B. , Kim Jeansok J.
Published: July 2014

Considerable evidence seems to show that emotional and reflex reactions to feared situations are mediated by the amygdala. It might therefore seem plausible to expect that amygdala-coded fear should also influence decisions when animals make choices about instrumental actions. However, there is not good evidence of this. In particular, it appears, though the literature is conflicted, that once learning is complete, the amygdala may often not be involved in instrumental avoidance behaviours. It is therefore of interest that we have found in rats living for extended periods in a semi-naturalistic ‘closed economy’, where they were given random shocks in regions that had to be entered to obtain food, choices about feeding behaviour were in fact influenced by amygdala-coded fear, in spite of the null effect of amygdalar lesions on fear of dangerous location
per se
. We suggest that avoidance of highly motivated voluntary behaviour does depend in part on fear signals originating in the amygdala. Such signalling may be one role of well-known projections from amygdala to cortico-striate circuitry.
The dynamics of sperm cooperation in a competitive environment
Authors: Fisher Heidi S. , Giomi Luca , Hoekstra Hopi E. , Mahadevan L.
Published: July 2014

Sperm cooperation has evolved in a variety of taxa and is often considered a response to sperm competition, yet the benefit of this form of collective movement remains unclear. Here, we use fine-scale imaging and a minimal mathematical model to study sperm aggregation in the rodent genusPeromyscus. We demonstrate that as the number of sperm cells in an aggregate increase, the group moves with more persistent linearity but without increasing speed. This benefit, however, is offset in larger aggregates as the geometry of the group forces sperm to swim against one another. The result is a non-monotonic relationship between aggregate size and average velocity with both a theoretically predicted and empirically observed optimum of six to seven sperm per aggregate. To understand the role of sexual selection in driving these sperm group dynamics, we compared two sister-species with divergent mating systems. We find that sperm ofPeromyscus maniculatus(highly promiscuous), which have evolved under intense competition, form optimal-sized aggregates more often than sperm ofPeromyscus polionotus(strictly monogamous), which lack competition. Our combined mathematical and experimental study of coordinated sperm movement reveals the importance of geometry, motion and group size on sperm velocity and suggests how these physical variables interact with evolutionary selective pressures to regulate cooperation in competitive environments.
Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish
Authors: Fraser Dylan J. , Debes Paul V. , Bernatchez Louis , Hutchings Jeffrey A.
Published: July 2014

Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, single-nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest.
Mortality trajectory analysis reveals the drivers of sex-specific epidemiology in natural wildlife–disease interactions
Authors: McDonald Jennifer L. , Smith Graham C. , McDonald Robbie A. , Delahay Richard J. , Hodgson Dave
Published: July 2014

In animal populations, males are commonly more susceptible to disease-induced mortality than females. However, three competing mechanisms can cause this sex bias: weak males may simultaneously be more prone to exposure to infection and mortality; being ‘male’ may be an imperfect proxy for the underlying driver of disease-induced mortality; or males may experience increased severity of disease-induced effects compared with females. Here, we infer the drivers of sex-specific epidemiology by decomposing fixed mortality rates into mortality trajectories and comparing their parameters. We applied Bayesian survival trajectory analysis to a 22-year longitudinal study of a population of badgers (
Meles meles
) naturally infected with bovine tuberculosis (bTB). At the point of infection, infected male and female badgers had equal mortality risk, refuting the hypothesis that acquisition of infection occurs in males with coincidentally high mortality. Males and females exhibited similar levels of heterogeneity in mortality risk, refuting the hypothesis that maleness is only a proxy for disease susceptibility. Instead, sex differences were caused by a more rapid increase in male mortality rates following infection. Males are indeed more susceptible to bTB, probably due to immunological differences between the sexes. We recommend this mortality trajectory approach for the study of infection in animal populations.
Molecular analysis of ancient caries
Authors: Simón Marc , Montiel Rafael , Smerling Andrea , Solórzano Eduvigis , Díaz Nancy , Álvarez-Sandoval Brenda A. , Jiménez-Marín Andrea R. , Malgosa Assumpció
Published: July 2014

An 84 base pair sequence of theStreptococcus mutansvirulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains.
Male receiver bias for red agonistic signalling in a yellow-signalling widowbird: a field experiment
Authors: Ninnes C. E. , Andersson S.
Published: July 2014

Receiver bias models of signal evolution are typically regarded as alternatives or complements to ornament evolution due to coevolving mate choice, whereas sexually or socially selected agonistic signals are rarely studied with respect to receiver psychology. Against the background of convergent evolution of red agonistic signals from yellow ancestors in the genus
Euplectes
(widowbirds and bishops), we experimentally test the function of a yellow signal in the montane marsh widowbird (
E. psammocromius
), as well as a hypothesized receiver bias for redder (longer wavelength) hues. In a field experiment in southern Tanzania, males that had their yellow wing patches blackened lost their territories or lost territorial contests more often than controls or reddened males, which together with a longer wavelength hue in territory holders, indicates an agonistic signal function. Males painted a novel red hue, matching that of red-signalling congeners, retained their territories and won contests more often than controls. To our knowledge, this is the first demonstration of a receiver bias driving agonistic signal evolution. Although the sensory or cognitive origin of this bias is yet unknown, it strengthens our view that genetically constrained signal production (i.e. carotenoid metabolism), rather than differential selection, explains the carotenoid colour diversification in
Euplectes
.
Pacific-wide contrast highlights resistance of reef calcifiers to ocean acidification
Authors: Comeau S. , Carpenter R. C. , Nojiri Y , Putnam H. M. , Sakai K. , Edmunds P. J.
Published: July 2014

Ocean acidification (OA) and its associated decline in calcium carbonate saturation states is one of the major threats that tropical coral reefs face this century. Previous studies of the effect of OA on coral reef calcifiers have described a wide variety of outcomes for studies using comparable partial pressure of CO
2
(
p
CO
2
) ranges, suggesting that key questions remain unresolved. One unresolved hypothesis posits that heterogeneity in the response of reef calcifiers to high
p
CO
2
is a result of regional-scale variation in the responses to OA. To test this hypothesis, we incubated two coral taxa (
Pocillopora damicornis
and massive
Porites
) and two calcified algae (
Porolithon onkodes
and
Halimeda macroloba
) under 400, 700 and 1000 μatm
p
CO
2
levels in experiments in Moorea (French Polynesia), Hawaii (USA) and Okinawa (Japan), where environmental conditions differ. Both corals and
H. macroloba
were insensitive to OA at all three locations, while the effects of OA on
P. onkodes
were location-specific. In Moorea and Hawaii, calcification of
P. onkodes
was depressed by high
p
CO
2
, but for specimens in Okinawa, there was no effect of OA. Using a study of large geographical scale, we show that resistance to OA of some reef species is a constitutive character expressed across the Pacific.
Tessaracoccus lapidicaptus sp. nov., an actinobacterium isolated from the deep subsurface of the Iberian pyrite belt
Authors: Puente-Sánchez Fernando , Sánchez-Román Mónica , Amils Ricardo , Parro Víctor
Published: July 2014

A novel actinobacterium, designated IPBSL-7T, was isolated from a drilling core 297 m deep obtained from the Iberian Pyrite Belt. The strain was isolated anaerobically using nitrate as the electron acceptor. 16S rRNA gene sequence analysis revealed that it was related to

Tessaracoccus flavescens

SST-39T (95.7 % similarity),

Tessaracoccus bendigoensis

Ben 106T (95.7 %),

Tessaracoccus lubricantis

KSS-17SeT (95.6 %) and

Tessaracoccus oleiagri

SL014B-20A1T (95.0 %), while its similarity to any other member of the family

Propionibacteriaceae

was less than 94 %. Cells were non-motile, non-spore-forming, Gram-positive, oval to rod-shaped, and often appeared in pairs or small groups. The strain was facultatively anaerobic, oxidase-negative, catalase-positive and capable of reducing nitrate. Colonies were circular, convex, smooth and colourless. The organism could grow at between 15 and 40 °C, with an optimal growth at 37 °C. The pH range for growth was from pH 6 to 9, with pH 8 being the optimal value. Strain IPBSL-7T had peptidoglycan type A3-γ′, with ll-diaminopimelic acid as the diagnostic diamino-acid and glycine at position 1 of the peptide subunit. The dominant menaquinone was MK-9(H4) (93.8 %). The major cellular fatty acid was anteiso-C15 : 0 (55.0 %). The DNA G+C content was 70.3 mol%. On the basis of phenotypic and phylogenetic results, strain IPBSL-7T can be differentiated from previously described species of the genus

Tessaracoccus

and, therefore, represents a novel species, for which the name Tessaracoccus
lapidicaptus sp. nov. is proposed. The type strain is IPBSL-7T ( = CECT 8385T = DSM 27266T).
Gordonia iterans sp. nov., isolated from a patient with pneumonia
Authors: Kang Ying-Qian , Ming Hong , Gonoi Tohru , Chen Yuru , Cao Yu , Wang Yan-Yan , Cheng Juan , Koga Takeharu , Mikami Yuzuru , Li Wen-Jun
Published: July 2014

A second novel clinical actinobacterial strain, designated IFM 10348T, was isolated from the sputum of the same Japanese patient with bacterial pneumonia from whom the type strain of

Gordonia araii

had been isolated. The strains differed in phylogenetic position and drug-resistance profiles. The taxonomic position of strain IFM 10348T was clarified by phenotypic, chemotaxonomic and phylogenetic studies. Phylogenetic analyses based on 16S rRNA gene sequences clearly demonstrated that strain IFM 10348T occupied a distinct clade within the genus

Gordonia

and was related closely to

Gordonia malaquae

DSM 45064T and

Gordonia hirsuta

DSM 44140T (97.3 and 97.1 % similarities, respectively). Strain IFM 10348T was also clearly differentiated from

G. malaquae

DSM 45064T and

G. hirsuta

DSM 44140T based on gyrB and secA1 gene sequence similarity values. Strain IFM 10348T had MK-9(H2) as the predominant menaquonine, contained meso-diaminopimelic acid, arabinose, galactose and glucosamine as cell-wall components, and contained C18 : 1ω9c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major cellular fatty acids. Mycolic acids were present. The DNA G+C content of strain IFM 10348T was 68.0 mol%. DNA–DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that strain IFM 10348T represents a novel species of the genus

Gordonia

, for which the name Gordonia iterans sp. nov. is proposed. The type strain is IFM 10348T ( = CCTCC M2011245T = NCCB 100436T).
Veillonella seminalis sp. nov., a novel anaerobic Gram-stain-negative coccus from human clinical samples, and emended description of the genus Veillonella
Authors: Aujoulat Fabien , Bouvet Philippe , Jumas-Bilak Estelle , Jean-Pierre Hélène , Marchandin Hélène
Published: July 2014

Ten isolates of unknown, Gram-stain-negative, anaerobic cocci were recovered from human clinical samples, mainly from semen. On the basis of their phenotypic features, including morphology, main metabolic end products, gas production, nitrate reduction and decarboxylation of succinate, the strains were identified as members of the genusVeillonella.Multi-locus sequence analysis and corresponding phylogenies were based on 16S rRNA,dnaKandrpoBgenes, and on the newly proposedgltAgene. The strains shared high levels of genetic sequence similarity and were related most closely toVeillonella ratti. The strains could not be differentiated fromV. rattion the basis of 16S rRNA gene sequence analysis whilegltA,rpoBanddnaKgene sequences showed 85.1, 93.5 and 90.2 % similarity with those of the type strain ofV. ratti, respectively. Phylogenetic analyses revealed that the isolates formed a robust clade in theV. ratti–Veillonella criceti–Veillonella magnasubgroup of the genusVeillonella. As observed forV. criceti, the isolates were able to ferment fructose. In contrast to other members of the genusVeillonella, the 10 strains were not able to metabolize lactate. Cellular fatty acid composition was consistent with that of other species of the genusVeillonella. From these data, the 10 isolates are considered to belong to a novel species in the genusVeillonella, for which the nameVeillonella seminalissp. nov. is proposed. The type strain is ADV 4313.2T( = CIP 107810T = LMG 28162T).Veillonellastrain ACS-216-V-Col6b subjected to whole genome sequencing as part as the Human Microbiome Project is another representative ofV. seminalissp. nov. An emended description of the genusVeillonellais also proposed.
Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake
Authors: Ganzert Lars , Schirmack Janosch , Alawi Mashal , Mangelsdorf Kai , Sand Wolfgang , Hillebrand-Voiculescu Alexandra , Wagner Dirk
Published: July 2014

A novel methanogenic archaeon, strain MC-15T, was isolated from a floating biofilm on a sulphurous subsurface lake in Movile Cave (Mangalia, Romania). Cells were non-motile sarcina-like cocci with a diameter of 2–4 µm, occurring in aggregates. The strain was able to grow autotrophically on H2/CO2. Additionally, acetate, methanol, monomethylamine, dimethylamine and trimethylamine were utilized, but not formate or dimethyl sulfide. Trypticase peptone and yeast extract were not required for growth. Optimal growth was observed at 33 °C, pH 6.5 and a salt concentration of 0.05 M NaCl. The predominant membrane lipids of MC-15Twere archaeol and hydroxyarchaeol phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol as well as hydroxyarchaeol phosphatidylserine and archaeol glycosaminyl phosphatidylinositol. The closely related species,Methanosarcina vacuolataandMethanosarcina horonobensis,had a similar composition of major membrane lipids to strain MC-15T. The 16S rRNA gene sequence of strain MC-15Twas similar to those ofMethanosarcina vacuolataDSM 1232T(sequence similarity 99.3 %),Methanosarcina horonobensisHB-1T(98.8 %),Methanosarcina barkeriDSM 800T(98.7 %) andMethanosarcina siciliaeT4/MT(98.4 %). DNA–DNA hybridization revealed 43.3 % relatedness between strain MC-15TandMethanosarcina vacuolataDSM 1232T. The G+C content of the genomic DNA was 39.0 mol%. Based on physiological, phenotypic and genotypic differences, strain MC-15Trepresents a novel species of the genusMethanosarcina, for which the nameMethanosarcinaspelaeisp. nov. is proposed. The type strain is MC-15T( = DSM 26047T = JCM 18469T).
Allokutzneria oryzae sp. nov., isolated from rhizospheric soil of Oryza sativa L.
Authors: Duangmal Kannika , Poomthongdee Nalin , Pathom-aree Wasu , Takè Akira , Thamchaipenet Arinthip , Matsumoto Atsuko , Takahashi Yoko
Published: July 2014

The taxonomic status of a rhizospheric soil actinomycete, designated R8-39T, was established using a polyphasic approach. The organism had phenotypic and morphological characteristics consistent with its classification in the genus

Allokutzneria

. Phylogenetic analysis based on an almost complete 16S rRNA gene sequence showed that the strain formed a monophyletic clade with the type strains of members of the genus

Allokutzneria

. Strain R8-39T displayed the highest levels of 16S rRNA gene sequence similarity to

Allokutzneria albata

DSM 44149T (98.8 %) and

Allokutzneria multivorans

YIM 120521T (98.3 %). However, the DNA–DNA hybridization values between strain R8-39T and

A. albata

and

A. multivorans

were clearly below the 70 % threshold. The organism was found to have chemical characteristics consistent with its classification in the genus

Allokutzneria

. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose, galactose, glucose, mannose, rhamnose and ribose. The main menaquinone was MK-9(H4). No mycolic acid was detected. The G+C content of the genomic DNA was 71.8 mol%. In addition, strain R8-39T had a phenotypic profile that readily distinguished it from recognized representatives of the genus

Allokutzneria

. It is evident from the combined genotypic and phenotypic properties that strain R8-39T represents a novel species of the genus

Allokutzneria

. The proposed name for this species is Allokutzneria oryzae sp. nov.; the type strain is R8-39T ( = BCC 60399T = NBRC 109649T).
Genotypically defined β-lactamase-negative ampicillin-resistant isolates of non-typable Haemophilus influenzae are associated with increased invasion of bronchial epithelial cells in vitro
Authors: Atkins Nicola A. , Kunde Dale A. , Zosky Graeme , Tristram Stephen G.
Published: July 2014

The aim of the study was to investigate the association between the presence of altered penicillin-binding protein 3 (PBP3) in non-typable Haemophilus influenzae (NTHi) and an increased capacity to invade bronchial epithelial cells in vitro. A collection of 40 clinical isolates of NTHi comprised of 20 with normal PBP3 and 20 with altered PBP3 (defined by an N526K substitution) was established. The isolates were tested for the ability to invade bronchial epithelial cells in vitro using a 4 h gentamicin survival assay. Invasion was measured as the percentage of intracellular organisms relative to the initial inoculum. The mean invasion rate was 0.00–14.79 % in the normal PBP3 isolates and 0.02–36.69 % in the altered PBP3 isolates. The altered PBP3 isolates had a higher (P = 0.003) mean invasion rate (6.86 %, n = 20) than the normal PBP3 isolates (1.31 %, n = 20). Subsequently, two variants of altered PBP3 (transformant 1, N526K; transformant 2, M377I, S385T, L389F and N526K) were cloned into three of the initial isolates (parents) with normal PBP3 and relatively low invasive ability, and the parents and transformants tested for invasion as above. There was no difference (P = 0.89) in the mean invasion rates for the parents (0.81 %, n = 3), transformants 1 (0.90 %, n = 3) and transformants 2 (1.38 %, n = 3). There was an association between the presence of altered PBP3 in NTHi and an increased capacity to invade BEAS-2B cells in vitro, but cloning experiments suggested that the altered PBP3 was not involved directly in enhanced invasion.
Mutant USA strain of porcine circovirus type 2 (mPCV2) exhibits similar virulence to the classical PCV2a and PCV2b strains in caesarean-derived, colostrum-deprived pigs
Authors: Opriessnig Tanja , Xiao Chao-Ting , Gerber Priscilla F. , Halbur Patrick G. , Matzinger Shannon R. , Meng Xiang-Jin
Published: July 2014

In 2012, a mutant porcine circovirus type 2 (mPCV2) strain was identified in cases of PCV-associated disease (PCVAD) in the USA. The mPCV2 had an additional amino acid, lysine (K), in the capsid at position 234. The objectives of this study were to compare the pathogenicity of mPCV2, PCV2a and PCV2b in pigs using biologically pure infectious virus stocks derived from respective infectious DNA clones, and to investigate the importance of genotype-specific ORF2 and the presence of lysine at position 234 of the capsid. A total of 47, 2-week-old, caesarean-derived, colostrum-deprived (CDCD) pigs were assigned to one of seven groups. At 3 weeks of age, the pigs were experimentally inoculated with saline, PCV2a, PCV2b, mPCV2, PCV2b-234-K (lysine addition in ORF2), chimeric PCV2b-ORF1/mPCV2-ORF2 or reciprocal chimeric mPCV2-ORF1/PCV2b-ORF2. All pigs were necropsied 21 days post-infection (p.i.). Gross lesions were limited to visible icterus and loss of body condition in a portion of the mPCV2 pigs. The amount of PCV2 DNA was significantly higher in pigs inoculated with mPCV2 compared with PCV2b in sera at 7 days p.i. and faecal swabs at 14 days p.i. Based on lymphoid lesions, a higher prevalence of PCVAD was seen in pigs infected with PCV2s containing the additional 234-K (64.3 %) compared with those infected with a PCV2 with the regular 233 bp ORF2 (40 %). Results indicated that all PCV2 isolates were capable of inducing severe lesions and disease in the CDCD pig model, and there was no significant difference in virulence.
Neuraminidase gene homology contributes to the protective activity of influenza vaccines prepared from the influenza virus library
Authors: Haredy Ahmad M. , Yamada Hiroshi , Sakoda Yoshihiro , Okamatsu Masatoshi , Yamamoto Naoki , Omasa Takeshi , Mori Yasuko , Kida Hiroshi , Okamoto Shigefumi , Okuno Yoshinobu , Yamanishi Koichi
Published: July 2014

Whole-virus (WV) vaccines from influenza A/duck/Hokkaido/77 (H3N2), and its reassortant strains H3N4, H3N5 and H3N7, which have the same haemagglutinin (HA) gene but different neuraminidase (NA) genes, were prepared from our influenza virus library. Mice were intranasally immunized with equivalent doses of each vaccine (1–0.01 µg per mouse). All of the mice that received the highest dose of each vaccine (1 µg per mouse) showed equivalent high HA-inhibiting (HI) antibody titres and survived the H3N2 challenge viruses. However, mice that received lower doses of vaccine (0.1 or 0.01 µg per mouse) containing a heterologous NA had lower survival rates than those given the H3N2-based vaccine. The lungs of mice challenged with H3N2 virus showed a significantly higher virus clearance rate when the vaccine contained the homologous NA (N2) versus a heterologous NA, suggesting that NA contributed to the protection, especially when the HI antibody level was low. These results suggested that, even if vaccines prepared for a possible upcoming pandemic do not induce sufficient HI antibodies, WV vaccines can still be effective through other matched proteins such as NA.
Single-stranded positive-sense RNA viruses generated in days using infectious subgenomic amplicons
Authors: Aubry Fabien , Nougairède Antoine , de Fabritus Lauriane , Querat Gilles , Gould Ernest A. , de Lamballerie Xavier
Published: July 2014

Reverse genetics is a key methodology for producing genetically modified RNA viruses and deciphering cellular and viral biological properties, but methods based on the preparation of plasmid-based complete viral genomes are laborious and unpredictable. Here, both wild-type and genetically modified infectious RNA viruses were generated in days using the newly described ISA (infectious-subgenomic-amplicons) method. This new versatile and simple procedure may enhance our capacity to obtain infectious RNA viruses from PCR-amplified genetic material.
Critical role for bone marrow stromal antigen 2 in acute Chikungunya virus infection
Authors: Mahauad-Fernandez Wadie D. , Jones Philip H. , Okeoma Chioma M.
Published: July 2014

Bone marrow stromal antigen 2 (BST-2; also known as tetherin or CD317) is an IFN-inducible gene that functions to block the release of a range of nascent enveloped virions from infected host cells. However, the role of BST-2 in viral pathogenesis remains poorly understood. BST-2 plays a multifaceted role in innate immunity, as it hinders retroviral infection and possibly promotes infection with some rhabdo- and orthomyxoviruses. This paradoxical role has probably hindered exploration of BST-2 antiviral functionin vivo. We reported previously that BST-2 tethers Chikungunya virus (CHIKV)-like particles on the cell plasma membrane. To explore the role of BST-2 in CHIKV replication and host protection, we utilized CHIKV strain 181/25 to examine early events during CHIKV infection in a BST-2−/−mouse model. We observed an interesting dichotomy between WT and BST-2−/−mice. BST-2 deficiency increased inoculation site viral load, culminating in higher systemic viraemia and increased lymphoid tissues tropism. A suppressed inflammatory innate response demonstrated by impaired expression of IFN-α, IFN-γ and CD40 ligand was observed in BST-2−/−mice compared with the WT controls. These findings suggested that, in part, BST-2 protects lymphoid tissues from CHIKV infection and regulates CHIKV-induced inflammatory response by the host.
Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes
Authors: Treangen Todd J. , Ondov Brian D. , Koren Sergey , Phillippy Adam M.
Published: July 2014

Though many microbial species or clades now have hundreds of sequenced genomes, existing whole-genome alignment methods do not efficiently handle comparisons on this scale. Here we present the Harvest suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Combined they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.
Comparative analysis of principal components can be misleading
Authors: Uyeda Josef C. , Caetano Daniel S. , Pennell Matthew W.
Published: July 2014

Quantitative geneticists long ago recognized the value of studying evolution in a multivariate framework (Pearson, 1903). Due tolinkage, pleiotropy, coordinated selection and mutational covariance, the evolutionary response in any phenotypic trait can only be properly understood in the context ofother traits (Lande, 1979; Lynch and Walsh, 1998). This is of course also well-appreciated bycomparative biologists. However, unlike in quantitative genetics, most of the statistical and conceptual tools for analyzing phylogenetic comparative data (recently reviewed in Pennell and Harmon, 2013) are designed for analyzing a single trait (but see, for example Revell and Harmon, 2008; Revell and Harrison, 2008; Hohenlohe and Arnold, 2008; Revell and Collar, 2009; Schmitz and Motani, 2011; Adams, 2014b). Indeed, even classical approaches for testing for correlated evolution between two traits (e.g., Felsenstein, 1985; Grafen, 1989; Harvey and Pagel, 1991) are not actually multivariate as each trait is assumed to have evolved under a process that is independent of the state of the other (Hansen and Orzack, 2005; Hansen and Bartoszek, 2012). As a result of these limitations, researchers with multivariate datasets are often faced with a choice: analyze each trait as if they were independent or else decompose the dataset into statistically independent set of traits, such that each set can be analyzed with the univariate methods.
Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics
Authors: Sen Shaunak , Murray Richard M.
Published: July 2014

Temporal dynamics in many biomolecular circuits can change with temperature because of the temperature dependence of underlying reaction rate parameters. It is generally unclear what circuit mechanisms can inherently facilitate robustness in the dynamics to variations in temperature. Here, we address this issue using a combination of mathematical models and experimental measurements in a cell-free transcription-translation system. We find that negative transcriptional feedback can reduce the effect of temperature variation on circuit dynamics. Further, we find that effective negative feedback due to first-order degradation mechanisms can also enable such a temperature robustness effect. Finally, we estimate temperature dependence of key parameters mediating such negative feedback mechanisms. These results should be useful in the design of temperature robust circuit dynamics.
Geranyllinalool Synthases in Solanaceae and Other Angiosperms Constitute an Ancient Branch of Diterpene Synthases Involved in the Synthesis of Defensive Compounds
Authors: Falara Vasiliki , Alba Juan M. , Kant Merijn R. , Schuurink Robert C. , Pichersky Eran
Published: July 2014

Many angiosperm plants, including basal dicots, eudicots, and monocots, emit (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene, which is derived from geranyllinalool, in response to biotic challenge. An Arabidopsis (Arabidopsis thaliana) geranyllinalool synthase (GLS) belonging to the e/f clade of the terpene synthase (TPS) family and two Fabaceae GLSs that belong to the TPS-g clade have been reported, making it unclear which is the main route to geranyllinalool in plants. We characterized a tomato (Solanum lycopersicum) TPS-e/f gene, TPS46, encoding GLS (SlGLS) and its homolog (NaGLS) from Nicotiana attenuata. The K  m value of SlGLS for geranylgeranyl diphosphate was 18.7 µm, with a turnover rate value of 6.85 s–1. In leaves and flowers of N. attenuata, which constitutively synthesize 17-hydroxygeranyllinalool glycosides, NaGLS is expressed constitutively, but the gene can be induced in leaves with methyl jasmonate. In tomato, SlGLS is not expressed in any tissue under normal growth but is induced in leaves by alamethicin and methyl jasmonate treatments. SlGLS, NaGLS, AtGLSs, and several other GLSs characterized only in vitro come from four different eudicot families and constitute a separate branch of the TPS-e/f clade that diverged from kaurene synthases, also in the TPS-e/f clade, before the gymnosperm-angiosperm split. The early divergence of this branch and the GLS activity of genes in this branch in diverse eudicot families suggest that GLS activity encoded by these genes predates the angiosperm-gymnosperm split. However, although a TPS sequence belonging to this GLS lineage was recently reported from a basal dicot, no representative sequences have yet been found in monocot or nonangiospermous plants.
Long-Term Evolution of Nucleotide-Binding Site-Leucine-Rich Repeat Genes: Understanding Gained from and beyond the Legume Family
Authors: Shao Zhu-Qing , Zhang Yan-Mei , Hang Yue-Yu , Xue Jia-Yu , Zhou Guang-Can , Wu Ping , Wu Xiao-Yi , Wu Xun-Zong , Wang Qiang , Wang Bin , Chen Jian-Qun
Published: July 2014

Proper utilization of plant disease resistance genes requires a good understanding of their short- and long-term evolution. Here we present a comprehensive study of the long-term evolutionary history of nucleotide-binding site (NBS)-leucine-rich repeat (LRR) genes within and beyond the legume family. The small group of NBS-LRR genes with an amino-terminal RESISTANCE TO POWDERY MILDEW8 (RPW8)-like domain (referred to as RNL) was first revealed as a basal clade sister to both coiled-coil-NBS-LRR (CNL) and Toll/Interleukin1 receptor-NBS-LRR (TNL) clades. Using Arabidopsis (Arabidopsis thaliana) as an outgroup, this study explicitly recovered 31 ancestral NBS lineages (two RNL, 21 CNL, and eight TNL) that had existed in the rosid common ancestor and 119 ancestral lineages (nine RNL, 55 CNL, and 55 TNL) that had diverged in the legume common ancestor. It was shown that, during their evolution in the past 54 million years, approximately 94% (112 of 119) of the ancestral legume NBS lineages experienced deletions or significant expansions, while seven original lineages were maintained in a conservative manner. The NBS gene duplication pattern was further examined. The local tandem duplications dominated NBS gene gains in the total number of genes (more than 75%), which was not surprising. However, it was interesting from our study that ectopic duplications had created many novel NBS gene loci in individual legume genomes, which occurred at a significant frequency of 8% to 20% in different legume lineages. Finally, by surveying the legume microRNAs that can potentially regulate NBS genes, we found that the microRNA-NBS gene interaction also exhibited a gain-and-loss pattern during the legume evolution.