Sequence and phylogenetic analysis of chicken anaemia virus obtained from backyard and commercial chickens in Nigeria.

PubMed

Oluwayelu, D O; Todd, D; Olaleye, O D

2008-12-01

This work reports the first molecular analysis study of chicken anaemia virus (CAV) in backyard chickens in Africa using molecular cloning and sequence analysis to characterize CAV strains obtained from commercial chickens and Nigerian backyard chickens. Partial VP1 gene sequences were determined for three CAVs from commercial chickens and for six CAV variants present in samples from a backyard chicken. Multiple alignment analysis revealed that the 6% and 4% nucleotide diversity obtained respectively for the commercial and backyard chicken strains translated to only 2% amino acid diversity for each breed. Overall, the amino acid composition of Nigerian CAVs was found to be highly conserved. Since the partial VP1 gene sequence of two backyard chicken cloned CAV strains (NGR/CI-8 and NGR/CI-9) were almost identical and evolutionarily closely related to the commercial chicken strains NGR-1, and NGR-4 and NGR-5, respectively, we concluded that CAV infections had crossed the farm boundary.

Earthquake potential in California-Nevada implied by correlation of strain rate and seismicity

USGS Publications Warehouse

Zeng, Yuehua; Petersen, Mark D.; Shen, Zheng-Kang

2018-01-01

Rock mechanics studies and dynamic earthquake simulations show that patterns of seismicity evolve with time through (1) accumulation phase, (2) localization phase, and (3) rupture phase. We observe a similar pattern of changes in seismicity during the past century across California and Nevada. To quantify these changes, we correlate GPS strain rates with seismicity. Earthquakes of M > 6.5 are collocated with regions of highest strain rates. By contrast, smaller magnitude earthquakes of M ≥ 4 show clear spatiotemporal changes. From 1933 to the late 1980s, earthquakes of M ≥ 4 were more diffused and broadly distributed in both high and low strain rate regions (accumulation phase). From the late 1980s to 2016, earthquakes were more concentrated within the high strain rate areas focused on the major fault strands (localization phase). In the same time period, the rate of M > 6.5 events also increased significantly in the high strain rate areas. The strong correlation between current strain rate and the later period of seismicity indicates that seismicity is closely related to the strain rate. The spatial patterns suggest that before the late 1980s, the strain rate field was also broadly distributed because of the stress shadows from previous large earthquakes. As the deformation field evolved out of the shadow in the late 1980s, strain has refocused on the major fault systems and we are entering a period of increased risk for large earthquakes in California.

Earthquake Potential in California-Nevada Implied by Correlation of Strain Rate and Seismicity

NASA Astrophysics Data System (ADS)

Zeng, Yuehua; Petersen, Mark D.; Shen, Zheng-Kang

2018-02-01

Rock mechanics studies and dynamic earthquake simulations show that patterns of seismicity evolve with time through (1) accumulation phase, (2) localization phase, and (3) rupture phase. We observe a similar pattern of changes in seismicity during the past century across California and Nevada. To quantify these changes, we correlate GPS strain rates with seismicity. Earthquakes of M > 6.5 are collocated with regions of highest strain rates. By contrast, smaller magnitude earthquakes of M ≥ 4 show clear spatiotemporal changes. From 1933 to the late 1980s, earthquakes of M ≥ 4 were more diffused and broadly distributed in both high and low strain rate regions (accumulation phase). From the late 1980s to 2016, earthquakes were more concentrated within the high strain rate areas focused on the major fault strands (localization phase). In the same time period, the rate of M > 6.5 events also increased significantly in the high strain rate areas. The strong correlation between current strain rate and the later period of seismicity indicates that seismicity is closely related to the strain rate. The spatial patterns suggest that before the late 1980s, the strain rate field was also broadly distributed because of the stress shadows from previous large earthquakes. As the deformation field evolved out of the shadow in the late 1980s, strain has refocused on the major fault systems and we are entering a period of increased risk for large earthquakes in California.

Mediational and Deviance Theories of Late High School Failure: Process Roles of Structural Strains, Academic Competence, and General versus Specific Problem Behavior

ERIC Educational Resources Information Center

Newcomb, Michael D.; Abbott, Robert D.; Catalano, Richard F.; Hawkins, J. David; Battin-Pearson, Sara; Hill, Karl

2002-01-01

Understanding and preventing high school failure is a national priority. Structural strain and general deviance theories attempt to explain late high school failure. The authors tested the hypotheses that general (vs. specific) deviance and academic competence mediate the relationships between structural strain factors (gender, ethnicity, and…

Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.

PubMed

Schaefke, Bernhard; Wang, Tzi-Yuan; Wang, Chuen-Yi; Li, Wen-Hsiung

2015-07-27

Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains). © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Autophagic degradation of dBruce controls DNA fragmentation in nurse cells during late Drosophila melanogaster oogenesis.

PubMed

Nezis, Ioannis P; Shravage, Bhupendra V; Sagona, Antonia P; Lamark, Trond; Bjørkøy, Geir; Johansen, Terje; Rusten, Tor Erik; Brech, Andreas; Baehrecke, Eric H; Stenmark, Harald

2010-08-23

Autophagy is an evolutionarily conserved pathway responsible for degradation of cytoplasmic material via the lysosome. Although autophagy has been reported to contribute to cell death, the underlying mechanisms remain largely unknown. In this study, we show that autophagy controls DNA fragmentation during late oogenesis in Drosophila melanogaster. Inhibition of autophagy by genetically removing the function of the autophagy genes atg1, atg13, and vps34 resulted in late stage egg chambers that contained persisting nurse cell nuclei without fragmented DNA and attenuation of caspase-3 cleavage. The Drosophila inhibitor of apoptosis (IAP) dBruce was found to colocalize with the autophagic marker GFP-Atg8a and accumulated in autophagy mutants. Nurse cells lacking Atg1 or Vps34 in addition to dBruce contained persisting nurse cell nuclei with fragmented DNA. This indicates that autophagic degradation of dBruce controls DNA fragmentation in nurse cells. Our results reveal autophagic degradation of an IAP as a novel mechanism of triggering cell death and thereby provide a mechanistic link between autophagy and cell death.

Conserved hypothetical protein Rv1977 in Mycobacterium tuberculosis strains contains sequence polymorphisms and might be involved in ongoing immune evasion.

PubMed

Jiang, Yi; Liu, Haican; Wang, Xuezhi; Li, Guilian; Qiu, Yan; Dou, Xiangfeng; Wan, Kanglin

2015-01-01

Host immune pressure and associated parasite immune evasion are key features of host-pathogen co-evolution. A previous study showed that human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved and thus it was deduced that M. tuberculosis lacks antigenic variation and immune evasion. Here, we selected 151 clinical Mycobacterium tuberculosis isolates from China, amplified gene encoding Rv1977 and compared the sequences. The results showed that Rv1977, a conserved hypothetical protein, is not conserved in M. tuberculosis strains and there are polymorphisms existed in the protein. Some mutations, especially one frameshift mutation, occurred in the antigen Rv1977, which is uncommon in M.tb strains and may lead to the protein function altering. Mutations and deletion in the gene all affect one of three T cell epitopes and the changed T cell epitope contained more than one variable position, which may suggest ongoing immune evasion.

Hatchery Contributions to Emerging Naturally Produced Lake Huron Lake Trout.

PubMed

Scribner, Kim; Tsehaye, Iyob; Brenden, Travis; Stott, Wendylee; Kanefsky, Jeannette; Bence, James

2018-06-19

Recent assessments indicate the emergence of naturally produced lake trout (Salvelinus namaycush) recruitment throughout Lake Huron in the North American Laurentian Great Lakes (>50% of fish <7 yrs). Because naturally produced fish derived from different stocked hatchery strains are unmarked, managers cannot distinguish strains contributing to natural recruitment. We used 15 microsatellite loci to identify strains of naturally produced lake trout (N=1567) collected in assessment fisheries during early (2002-2004) and late (2009-2012) sampling periods. Individuals from 13 American and Canadian hatchery strains (N=1143) were genotyped to develop standardized baseline information. Strain contributions were estimated using a Bayesian inferential approach. Deviance information criteria was used to compare models evaluating strain contributions at different spatial and temporal scales. The best performing models were the most complex models, suggesting that hatchery strain contributions to naturally produced lake trout varied spatially among management districts and temporally between time periods. Contributions of Seneca strain lake trout were consistently high across most management districts, with contributions increasing from early to late time periods (estimates ranged from 52-94% for the late period across eight of nine districts). Strain contributions deviated from expectations based on historical stocking levels, indicating strains differed with respect to survival, reproductive success, and/or dispersal. Knowledge of recruitment levels of strains stocked in different management districts, and how strain-specific recruitment varies temporally, spatially, and as a function of local or regional stocking is important to prioritize strains for future stocking and management of the transition process from primarily hatchery to naturally produced stocks.

EEG potentials associated with artificial grammar learning in the primate brain.

PubMed

Attaheri, Adam; Kikuchi, Yukiko; Milne, Alice E; Wilson, Benjamin; Alter, Kai; Petkov, Christopher I

2015-09-01

Electroencephalography (EEG) has identified human brain potentials elicited by Artificial Grammar (AG) learning paradigms, which present participants with rule-based sequences of stimuli. Nonhuman animals are sensitive to certain AGs; therefore, evaluating which EEG Event Related Potentials (ERPs) are associated with AG learning in nonhuman animals could identify evolutionarily conserved processes. We recorded EEG potentials during an auditory AG learning experiment in two Rhesus macaques. The animals were first exposed to sequences of nonsense words generated by the AG. Then surface-based ERPs were recorded in response to sequences that were 'consistent' with the AG and 'violation' sequences containing illegal transitions. The AG violations strongly modulated an early component, potentially homologous to the Mismatch Negativity (mMMN), a P200 and a late frontal positivity (P500). The macaque P500 is similar in polarity and time of occurrence to a late EEG positivity reported in human AG learning studies but might differ in functional role. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Aggregation of endosomal-vacuolar compartments in the Aovps24-deleted strain in the filamentous fungus Aspergillus oryzae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tatsumi, Akinori; Shoji, Jun-ya; Kikuma, Takashi

2007-10-19

Previously, we found that deletion of Aovps24, an ortholog of Saccharomyces cerevisiae VPS24, that encodes an ESCRT (endosomal sorting complex required for transport)-III component required for late endosomal function results in fragmented and aggregated vacuoles. Although defective late endosomal function is likely responsible for this phenotype, critical lack of our knowledge on late endosomes in filamentous fungi prevented us from further characterization. In this study, we identified late endosomes of Aspergillus oryzae, by expressing a series of fusion proteins of fluorescent proteins with orthologs of late endosomal proteins. Using these fusion proteins as markers, we observed late endosomes in themore » wild type strain and the Aovps24 disruptant and demonstrated that late endosomes are aberrantly aggregated in the Aovps24 disruptant. Moreover, we revealed that the aggregated late endosomes have features of vacuoles as well. As deletion of another ESCRT-III component-encoding gene, Aovps2, resulted in similar phenotypes to that in the Aovps24 disruptant, phenotypes of the Aovps24 disruptant are probably due to defective late endosomal function.« less

Complete Genome Sequence of Pseudomonas fluorescens LBUM636, a Strain with Biocontrol Capabilities against Late Blight of Potato

PubMed Central

Morrison, Christopher K.; Novinscak, Amy; Gadkar, Vijay J.; Joly, David L.

2016-01-01

Herein provided is the full-genome sequence of Pseudomonas fluorescens LBUM636. This strain is a plant growth-promoting rhizobacterium (PGPR) which produces phenazine-1-carboxylic acid, an antibiotic involved in the biocontrol of numerous plant pathogens, including late blight of potato caused by the plant pathogen Phytophthora infestans. PMID:27231373

Rhizobium symbiotic genes required for nodulation of legume and nonlegume hosts

PubMed Central

Marvel, Deborah J.; Torrey, John G.; Ausubel, Frederick M.

1987-01-01

Parasponia, a woody member of the elm family, is the only nonlegume genus whose members are known to form an effective nitrogen-fixing symbiosis with Bradyrhizobium or Rhizobium species. The Bradyrhizobium strain Rp501, isolated from Parasponia nodules, also nodulates the legumes siratro (Macroptilium atropurpureum) and cowpea (Vigna unguiculata). To test whether some of the same genes are involved in the early stages of legume and nonlegume nodulation, we generated transposon Tn5 insertions in the region of three evolutionarily conserved genes (nodA, nodB, and nodC) required for legume nodulation in several Rhizobium and Bradyrhizobium species. Assays of these mutant Rp501 strains on legume hosts and Parasponia seedlings established that nodABC are required for nodulation of legume and nonlegume hosts, indicating that nonlegumes and legumes can respond to the same bacterial signal(s). In addition, a strain carrying a Tn5 insertion adjacent to the nodABC genes vigorously nodulated Rp501 legume hosts but was incapable of nodulating Parasponia, possibly identifying a nonlegume-specific nodulation function. Images PMID:16593814

Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa)

USDA-ARS?s Scientific Manuscript database

Strain NRRL B-41902 and three closely related strains were isolated from iceberg lettuce. The strain was found to consist of strictly aerobic, gram-negative rods that formed cocci in late stationary phase. Subsequent to sequencing the 16S ribosomal RNA gene, it was found that strain NRRL B-41902 was...

Localization of an evolutionarily conserved protein proton pyrophosphatase in evolutionarily distant plants oryza sativa and physcomitrella patens

USDA-ARS?s Scientific Manuscript database

Proton Pyrophosphatase (H+-PPase) is a highly evolutionarily conserved protein that is prevalent in the plant kingdom. One of the salient features of H+-PPase expression pattern, at least in vascular plants like Arabidopsis, is its conspicuous localization in both actively dividing cells and the phl...

Multiple Memory Systems Are Unnecessary to Account for Infant Memory Development: An Ecological Model

PubMed Central

Rovee-Collier, Carolyn; Cuevas, Kimberly

2009-01-01

How the memory of adults evolves from the memory abilities of infants is a central problem in cognitive development. The popular solution holds that the multiple memory systems of adults mature at different rates during infancy. The early-maturing system (implicit or nondeclarative memory) functions automatically from birth, whereas the late-maturing system (explicit or declarative memory) functions intentionally, with awareness, from late in the first year. Data are presented from research on deferred imitation, sensory preconditioning, potentiation, and context for which this solution cannot account and present an alternative model that eschews the need for multiple memory systems. The ecological model of infant memory development (N. E. Spear, 1984) holds that members of all species are perfectly adapted to their niche at each point in ontogeny and exhibit effective, evolutionarily selected solutions to whatever challenges each new niche poses. Because adults and infants occupy different niches, what they perceive, learn, and remember about the same event differs, but their raw capacity to learn and remember does not. PMID:19209999

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales.

PubMed

Siddaramappa, Shivakumara; Viswanathan, Vandana; Thiyagarajan, Saravanamuthu; Narjala, Anushree

2018-04-05

The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C40 carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised.

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales

PubMed Central

Siddaramappa, Shivakumara; Viswanathan, Vandana; Thiyagarajan, Saravanamuthu; Narjala, Anushree

2018-01-01

The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C40 carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised. PMID:29620507

Sequence variations in RepMP2/3 and RepMP4 elements reveal intragenomic homologous DNA recombination events in Mycoplasma pneumoniae.

PubMed

Spuesens, Emiel B M; Oduber, Minoushka; Hoogenboezem, Theo; Sluijter, Marcel; Hartwig, Nico G; van Rossum, Annemarie M C; Vink, Cornelis

2009-07-01

The gene encoding major adhesin protein P1 of Mycoplasma pneumoniae, MPN141, contains two DNA sequence stretches, designated RepMP2/3 and RepMP4, which display variation among strains. This variation allows strains to be differentiated into two major P1 genotypes (1 and 2) and several variants. Interestingly, multiple versions of the RepMP2/3 and RepMP4 elements exist at other sites within the bacterial genome. Because these versions are closely related in sequence, but not identical, it has been hypothesized that they have the capacity to recombine with their counterparts within MPN141, and thereby serve as a source of sequence variation of the P1 protein. In order to determine the variation within the RepMP2/3 and RepMP4 elements, both within the bacterial genome and among strains, we analysed the DNA sequences of all RepMP2/3 and RepMP4 elements within the genomes of 23 M. pneumoniae strains. Our data demonstrate that: (i) recombination is likely to have occurred between two RepMP2/3 elements in four of the strains, and (ii) all previously described P1 genotypes can be explained by inter-RepMP recombination events. Moreover, the difference between the two major P1 genotypes was reflected in all RepMP elements, such that subtype 1 and 2 strains can be differentiated on the basis of sequence variation in each RepMP element. This implies that subtype 1 and subtype 2 strains represent evolutionarily diverged strain lineages. Finally, a classification scheme is proposed in which the P1 genotype of M. pneumoniae isolates can be described in a sequence-based, universal fashion.

Effects of age-related differences in femoral loading and bone mineral density on strains in the proximal femur during controlled walking.

PubMed

Anderson, Dennis E; Madigan, Michael L

2013-10-01

Maintenance of healthy bone mineral density (BMD) is important for preventing fractures in older adults. Strains experienced by bone in vivo stimulate remodeling processes, which can increase or decrease BMD. However, there has been little study of age differences in bone strains. This study examined the relative contributions of age-related differences in femoral loading and BMD to age-related differences in femoral strains during walking using gait analysis, static optimization, and finite element modeling. Strains in older adult models were similar or larger than in young adult models. Reduced BMD increased strains in a fairly uniform manner, whereas older adult loading increased strains in early stance but decreased strains in late stance. Peak ground reaction forces, hip joint contact forces, and hip flexor forces were lower in older adults in late stance phase, and this helped older adults maintain strains similar to those of young adults despite lower BMD. Because walking likely represents a "baseline" level of stimulus for bone remodeling processes, increased strains during walking in older adults might indicate the extent of age-related impairment in bone remodeling processes. Such a measure might be clinically useful if it could be accurately determined with age-appropriate patient-specific loading, geometry, and BMD.

Probiotic Bovamine fine-tunes the ruminal microbiome for enhanced fermentation and immunity

USDA-ARS?s Scientific Manuscript database

We evaluated the effect of Bovamine, Lactobacillus acidophilus strain NP51 and Propionibacterium freudenreichii strain strain NP24, feeding on the microbial composition of the digestive system microbiota of dairy cattle during late lactation (average DIM = 202 days on time 0). To examine the underly...

Phylogenetic constraints do not explain the rarity of nitrogen-fixing trees in late-successional temperate forests.

PubMed

Menge, Duncan N L; DeNoyer, Jeanne L; Lichstein, Jeremy W

2010-08-06

Symbiotic nitrogen (N)-fixing trees are rare in late-successional temperate forests, even though these forests are often N limited. Two hypotheses could explain this paradox. The 'phylogenetic constraints hypothesis' states that no late-successional tree taxa in temperate forests belong to clades that are predisposed to N fixation. Conversely, the 'selective constraints hypothesis' states that such taxa are present, but N-fixing symbioses would lower their fitness. Here we test the phylogenetic constraints hypothesis. Using U.S. forest inventory data, we derived successional indices related to shade tolerance and stand age for N-fixing trees, non-fixing trees in the 'potentially N-fixing clade' (smallest angiosperm clade that includes all N fixers), and non-fixing trees outside this clade. We then used phylogenetically independent contrasts (PICs) to test for associations between these successional indices and N fixation. Four results stand out from our analysis of U.S. trees. First, N fixers are less shade-tolerant than non-fixers both inside and outside of the potentially N-fixing clade. Second, N fixers tend to occur in younger stands in a given geographical region than non-fixers both inside and outside of the potentially N-fixing clade. Third, the potentially N-fixing clade contains numerous late-successional non-fixers. Fourth, although the N fixation trait is evolutionarily conserved, the successional traits are relatively labile. These results suggest that selective constraints, not phylogenetic constraints, explain the rarity of late-successional N-fixing trees in temperate forests. Because N-fixing trees could overcome N limitation to net primary production if they were abundant, this study helps to understand the maintenance of N limitation in temperate forests, and therefore the capacity of this biome to sequester carbon.

Phylogenetic Constraints Do Not Explain the Rarity of Nitrogen-Fixing Trees in Late-Successional Temperate Forests

PubMed Central

Menge, Duncan N. L.; DeNoyer, Jeanne L.; Lichstein, Jeremy W.

2010-01-01

Background Symbiotic nitrogen (N)-fixing trees are rare in late-successional temperate forests, even though these forests are often N limited. Two hypotheses could explain this paradox. The ‘phylogenetic constraints hypothesis’ states that no late-successional tree taxa in temperate forests belong to clades that are predisposed to N fixation. Conversely, the ‘selective constraints hypothesis’ states that such taxa are present, but N-fixing symbioses would lower their fitness. Here we test the phylogenetic constraints hypothesis. Methodology/Principal Findings Using U.S. forest inventory data, we derived successional indices related to shade tolerance and stand age for N-fixing trees, non-fixing trees in the ‘potentially N-fixing clade’ (smallest angiosperm clade that includes all N fixers), and non-fixing trees outside this clade. We then used phylogenetically independent contrasts (PICs) to test for associations between these successional indices and N fixation. Four results stand out from our analysis of U.S. trees. First, N fixers are less shade-tolerant than non-fixers both inside and outside of the potentially N-fixing clade. Second, N fixers tend to occur in younger stands in a given geographical region than non-fixers both inside and outside of the potentially N-fixing clade. Third, the potentially N-fixing clade contains numerous late-successional non-fixers. Fourth, although the N fixation trait is evolutionarily conserved, the successional traits are relatively labile. Conclusions/Significance These results suggest that selective constraints, not phylogenetic constraints, explain the rarity of late-successional N-fixing trees in temperate forests. Because N-fixing trees could overcome N limitation to net primary production if they were abundant, this study helps to understand the maintenance of N limitation in temperate forests, and therefore the capacity of this biome to sequester carbon. PMID:20700466

Initial orienting towards sexually relevant stimuli: preliminary evidence from eye movement measures.

PubMed

Fromberger, Peter; Jordan, Kirsten; von Herder, Jakob; Steinkrauss, Henrike; Nemetschek, Rebekka; Stolpmann, Georg; Müller, Jürgen Leo

2012-08-01

It has been proposed that sexual stimuli will be processed in a comparable manner to other evolutionarily meaningful stimuli (such as spiders or snakes) and therefore elicit an attentional bias and more attentional engagement (Spiering and Everaerd, In E. Janssen (Ed.), The psychophysiology of sex (pp. 166-183). Bloomington: Indiana University Press, 2007). To investigate early and late attentional processes while looking at sexual stimuli, heterosexual men (n = 12) viewed pairs of sexually preferred (images of women) and sexually non-preferred images (images of girls, boys or men), while eye movements were measured. Early attentional processing (initial orienting) was assessed by the number of first fixations and late attentional processing (maintenance of attention) was assessed by relative fixation time. Results showed that relative fixation time was significantly longer for sexually preferred stimuli than for sexually non-preferred stimuli. Furthermore, the first fixation was more often directed towards the preferred sexual stimulus, when simultaneously presented with a non-sexually preferred stimulus. Thus, the current study showed for the first time an attentional bias to sexually relevant stimuli when presented simultaneously with sexually irrelevant pictures. This finding, along with the discovery that heterosexual men maintained their attention to sexually relevant stimuli, highlights the importance of investigating early and late attentional processes while viewing sexual stimuli. Furthermore, the current study showed that sexually relevant stimuli are favored by the human attentional system.

Transient FTY720 treatment promotes immune-mediated clearance of a chronic viral infection.

PubMed

Premenko-Lanier, Mary; Moseley, Nelson B; Pruett, Sarah T; Romagnoli, Pablo A; Altman, John D

2008-08-14

For a wide variety of microbial pathogens, the outcome of the infection is indeterminate. In some individuals the microbe is cleared, but in others it establishes a chronic infection, and the factors that tip this balance are often unknown. In a widely used model of chronic viral infection, C57BL/6 mice clear the Armstrong strain of lymphocytic choriomeningitis virus (LCMV), but the clone 13 strain persists. Here we show that the Armstrong strain induces a profound lymphopenia at days 1-3 after infection, but the clone 13 strain does not. If we transiently augment lymphopenia by treating the clone-13-infected mice with the drug FTY720 at days 0-2 after infection, the mice successfully clear the infection by day 30. Clearance does not occur when CD4 T cells are absent at the time of treatment, indicating that the drug is not exerting direct antiviral effects. Notably, FTY720 treatment of an already established persistent infection also leads to viral clearance. In both models, FTY720 treatment preserves or augments LCMV-specific CD4 and CD8 T-cell responses, a result that is counter-intuitive because FTY720 is generally regarded as a new immunosuppressive agent. Because FTY720 targets host pathways that are completely evolutionarily conserved, our results may be translatable into new immunotherapies for the treatment of chronic microbial infections in humans.

In Vivo Fitness Adaptations of Colistin-Resistant Acinetobacter baumannii Isolates to Oxidative Stress.

PubMed

Jones, Crystal L; Singh, Shweta S; Alamneh, Yonas; Casella, Leila G; Ernst, Robert K; Lesho, Emil P; Waterman, Paige E; Zurawski, Daniel V

2017-03-01

The loss of fitness in colistin-resistant (CR) Acinetobacter baumannii was investigated using longitudinal isolates from the same patient. Early CR isolates were outcompeted by late CR isolates for growth in broth and survival in the lungs of mice. Fitness loss was associated with an increased susceptibility to oxidative stress since early CR strains had reduced in vitro survival in the presence of hydrogen peroxide and decreased catalase activity compared to that of late CR and colistin-susceptible (CS) strains. Copyright © 2017 Jones et al.

Position of human blood group O(H) and phenotype-determining enzymes in growth and infectious disease.

PubMed

Arend, Peter

2018-05-12

The human ABO(H) blood group phenotypes arise from the evolutionarily oldest genetic system found in primate populations. While the blood group antigen A is considered the ancestral primordial structure, under the selective pressure of life-threatening diseases blood group O(H) came to dominate as the most frequently occurring blood group worldwide. Non-O(H) phenotypes demonstrate impaired formation of adaptive and innate immunoglobulin specificities due to clonal selection and phenotype formation in plasma proteins. Compared with individuals with blood group O(H), blood group A individuals not only have a significantly higher risk of developing certain types of cancer but also exhibit high susceptibility to malaria tropica or infection by Plasmodium falciparum. The phenotype-determining blood group A glycotransferase(s), which affect the levels of anti-A/Tn cross-reactive immunoglobulins in phenotypic glycosidic accommodation, might also mediate adhesion and entry of the parasite to host cells via trans-species O-GalNAc glycosylation of abundantly expressed serine residues that arise throughout the parasite's life cycle, while excluding the possibility of antibody formation against the resulting hybrid Tn antigen. In contrast, human blood group O(H), lacking this enzyme, is indicated to confer a survival advantage regarding the overall risk of developing cancer, and individuals with this blood group rarely develop life-threatening infections involving evolutionarily selective malaria strains. © 2018 New York Academy of Sciences.

Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch Bordetella pertussis Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s

PubMed Central

Schouls, Leo M.; van der Heide, Han G. J.; Vauterin, Luc; Vauterin, Paul; Mooi, Frits R.

2004-01-01

Bordetella pertussis, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for B. pertussis. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of B. pertussis revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that B. pertussis is much more dynamic than expected. PMID:15292152

Sex-specific gene expression during asexual development of Neurospora crassa.

PubMed

Wang, Zheng; Kin, Koryu; López-Giráldez, Francesc; Johannesson, Hanna; Townsend, Jeffrey P

2012-07-01

The impact of loci that determine sexual identity upon the asexual, dominant stage of fungal life history has been well studied. To investigate their impact, expression differences between strains of different mating type during asexual development were assayed, with RNA sampled from otherwise largely isogenic mat A and mat a strains of Neurospora crassa at early, middle, and late clonal stages of development. We observed significant differences in overall gene expression between mating types across clonal development, especially at late development stages. The expression levels of mating-type genes and pheromone genes were assayed by reverse transcription and quantitative PCR, revealing expression of pheromone and receptor genes in strains of both mating types in all development stages, and revealing that mating type (mat) genes were increasingly expressed over the course of asexual development. Interestingly, among differentially expressed genes, the mat A genotype more frequently exhibited a higher expression level than mat a, and demonstrated greater transcriptional regulatory dynamism. Significant up-regulation of expression was observed for many late light-responsive genes at late asexual development stages. Further investigation of the impact of light and the roles of light response genes in asexual development of both mating types are warranted. Copyright © 2012 Elsevier Inc. All rights reserved.

The Late Oligocene to Early Miocene early evolution of rifting in the southwestern part of the Roer Valley Graben

NASA Astrophysics Data System (ADS)

Deckers, Jef

2016-06-01

The Roer Valley Graben is a Mesozoic continental rift basin that was reactivated during the Late Oligocene. The study area is located in the graben area of the southwestern part of the Roer Valley Graben. Rifting initiated in the study area with the development of a large number of faults in the prerift strata. Some of these faults were rooted in preexisting zones of weakness in the Mesozoic strata. Early in the Late Oligocene, several faults died out in the study area as strain became focused upon others, some of which were able to link into several-kilometer-long systems. Within the Late Oligocene to Early Miocene northwestward prograding shallow marine syn-rift deposits, the number of active faults further decreased with time. A relatively strong decrease was observed around the Oligocene/Miocene boundary and represents a further focus of strain onto the long fault systems. Miocene extensional strain was not accommodated by further growth, but predominantly by displacements along the long fault systems. Since the Oligocene/Miocene boundary coincides with a radical change in the European intraplate stress field, the latter might have contributed significantly to the simultaneous change of fault kinematics in the study area.

Nutrient depletion modifies cell wall adsorption activity of wine yeast.

PubMed

Sidari, R; Caridi, A

2016-06-01

Yeast cell wall is a structure that helps yeasts to manage and respond to many environmental stresses. The mannosylphosphorylation is a modification in response to stress that provides the cell wall with negative charges able to bind compounds present in the environment. Phenotypes related to the cell wall modification such as the filamentous growth in Saccharomyces cerevisiae are affected by nutrient depletion. The present work aimed at describing the effect of carbon and/or nitrogen limitation on the aptitude of S. cerevisiae strains to bind coloured polyphenols. Carbon- and nitrogen-rich or deficient media supplemented with grape polyphenols were used to simulate different grape juice conditions-early, mid, 'adjusted' for nitrogen, and late fermentations. In early fermentation condition, the R+G+B values range from 106 (high adsorption, strain Sc1128) to 192 (low adsorption, strain Σ1278b), in mid-fermentation the values range from 111 (high adsorption, strain Sc1321) to 258 (low adsorption, strain Sc2306), in 'adjusted' for nitrogen conditions the values range from 105 (high adsorption, strain Sc1321) to 194 (low adsorption, strain Sc2306) while in late fermentation conditions the values range from 101 (high adsorption, strain Sc384) to 293 (low adsorption, strain Sc2306). The effect of nutrient availability is not univocal for all the strains and the different media tested modified the strains behaviour. In all the media the strains show significant differences. Results demonstrate that wine yeasts decrease/increase their parietal adsorption activity according to the nutrient availability. The wide range of strain variability observed could be useful in selecting wine starters.

Evolutionary relevance facilitates visual information processing.

PubMed

Jackson, Russell E; Calvillo, Dusti P

2013-11-03

Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

Rif1 Binding and Control of Chromosome-Internal DNA Replication Origins Is Limited by Telomere Sequestration.

PubMed

Hafner, Lukas; Lezaja, Aleksandra; Zhang, Xu; Lemmens, Laure; Shyian, Maksym; Albert, Benjamin; Follonier, Cindy; Nunes, Jose Manuel; Lopes, Massimo; Shore, David; Mattarocci, Stefano

2018-04-24

The Saccharomyces cerevisiae telomere-binding protein Rif1 plays an evolutionarily conserved role in control of DNA replication timing by promoting PP1-dependent dephosphorylation of replication initiation factors. However, ScRif1 binding outside of telomeres has never been detected, and it has thus been unclear whether Rif1 acts directly on the replication origins that it controls. Here, we show that, in unperturbed yeast cells, Rif1 primarily regulates late-replicating origins within 100 kb of a telomere. Using the chromatin endogenous cleavage ChEC-seq technique, we robustly detect Rif1 at late-replicating origins that we show are targets of its inhibitory action. Interestingly, abrogation of Rif1 telomere association by mutation of its Rap1-binding module increases Rif1 binding and origin inhibition elsewhere in the genome. Our results indicate that Rif1 inhibits replication initiation by interacting directly with origins and suggest that Rap1-dependent sequestration of Rif1 increases its effective concentration near telomeres, while limiting its action at chromosome-internal sites. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Structure and expression of genes for a class of cysteine-rich proteins of the cuticle layers of differentiating wool and hair follicles

PubMed Central

1990-01-01

The major histological components of the hair follicle are the hair cortex and cuticle. The hair cuticle cells encase and protect the cortex and undergo a different developmental program to that of the cortex. We report the molecular characterization of a set of evolutionarily conserved hair genes which are transcribed in the hair cuticle late in follicle development. Two genes were isolated and characterized, one expressed in the human follicle and one in the sheep follicle. Each gene encodes a small protein of 16 kD, containing greater than 50 cysteine residues, ranging from 31 to 36 mol% cysteine. Their high cysteine content and in vitro expression data identify them as ultra-high-sulfur (UHS) keratin proteins. The predicted proteins are composed almost entirely of cysteine-rich and glycine-rich repeats. Genomic blots reveal that the UHS keratin proteins are encoded by related multigene families in both the human and sheep genomes. Tissue in situ hybridization demonstrates that the expression of both genes is localized to the hair fiber cuticle and occurs at a late stage in fiber morphogenesis. PMID:1703541

Left ventricular hypertrophy with strain and aortic stenosis.

PubMed

Shah, Anoop S V; Chin, Calvin W L; Vassiliou, Vassilis; Cowell, S Joanna; Doris, Mhairi; Kwok, T'ng Choong; Semple, Scott; Zamvar, Vipin; White, Audrey C; McKillop, Graham; Boon, Nicholas A; Prasad, Sanjay K; Mills, Nicholas L; Newby, David E; Dweck, Marc R

2014-10-28

ECG left ventricular hypertrophy with strain is associated with an adverse prognosis in aortic stenosis. We investigated the mechanisms and outcomes associated with ECG strain. One hundred and two patients (age, 70 years [range, 63-75 years]; male, 66%; aortic valve area, 0.9 cm(2) [range, 0.7-1.2 cm(2)]) underwent ECG, echocardiography, and cardiovascular magnetic resonance. They made up the mechanism cohort. Myocardial fibrosis was determined with late gadolinium enhancement (replacement fibrosis) and T1 mapping (diffuse fibrosis). The relationship between ECG strain and cardiovascular magnetic resonance was then assessed in an external validation cohort (n=64). The outcome cohort was made up of 140 patients from the Scottish Aortic Stenosis and Lipid Lowering Trial Impact on Regression (SALTIRE) study and was followed up for 10.6 years (1254 patient-years). Compared with those without left ventricular hypertrophy (n=51) and left ventricular hypertrophy without ECG strain (n=30), patients with ECG strain (n=21) had more severe aortic stenosis, increased left ventricular mass index, more myocardial injury (high-sensitivity plasma cardiac troponin I concentration, 4.3 ng/L [interquartile range, 2.5-7.3 ng/L] versus 7.3 ng/L [interquartile range, 3.2-20.8 ng/L] versus 18.6 ng/L [interquartile range, 9.0-45.2 ng/L], respectively; P<0.001) and increased diffuse fibrosis (extracellular volume fraction, 27.4±2.2% versus 27.2±2.9% versus 30.9±1.9%, respectively; P<0.001). All patients with ECG strain had midwall late gadolinium enhancement (positive and negative predictive values of 100% and 86%, respectively). Indeed, late gadolinium enhancement was independently associated with ECG strain (odds ratio, 1.73; 95% confidence interval, 1.08-2.77; P=0.02), a finding confirmed in the validation cohort. In the outcome cohort, ECG strain was an independent predictor of aortic valve replacement or cardiovascular death (hazard ratio, 2.67; 95% confidence interval, 1.35-5.27; P<0.01). ECG strain is a specific marker of midwall myocardial fibrosis and predicts adverse clinical outcomes in aortic stenosis. © 2014 American Heart Association, Inc.

Evolution of pathogen virulence across space during an epidemic

USGS Publications Warehouse

Osnas, Erik; Hurtado, Paul J.; Dobson, Andrew P.

2015-01-01

We explore pathogen virulence evolution during the spatial expansion of an infectious disease epidemic in the presence of a novel host movement trade-off, using a simple, spatially explicit mathematical model. This work is motivated by empirical observations of the Mycoplasma gallisepticum invasion into North American house finch (Haemorhous mexicanus) populations; however, our results likely have important applications to other emerging infectious diseases in mobile hosts. We assume that infection reduces host movement and survival and that across pathogen strains the severity of these reductions increases with pathogen infectiousness. Assuming these trade-offs between pathogen virulence (host mortality), pathogen transmission, and host movement, we find that pathogen virulence levels near the epidemic front (that maximize wave speed) are lower than those that have a short-term growth rate advantage or that ultimately prevail (i.e., are evolutionarily stable) near the epicenter and where infection becomes endemic (i.e., that maximize the pathogen basic reproductive ratio). We predict that, under these trade-offs, less virulent pathogen strains will dominate the periphery of an epidemic and that more virulent strains will increase in frequency after invasion where disease is endemic. These results have important implications for observing and interpreting spatiotemporal epidemic data and may help explain transient virulence dynamics of emerging infectious diseases.

Unexpected photoreactivation of Vibrio harveyi bacteria living in ionization environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alifano, P.; Tala, A.; Tredici, S. M.

2011-05-15

Bacteria undergoing environmental effects is extremely interesting for structural, mechanistic, and evolutionary implications. Luminescent bacteria that have evolved in a specific ambient have developed particular responses and their behavior can give us new suggestions on the task and production of luciferina proteins. To analyze the UV interaction under controlled laboratory conditions, we used photoluminescent bacterial strains belonging to a new species evolutionarily close to Vibrio harveyi sampled from a coastal cave with a high radon content that generates ionizing radiation. The survival of the bacterial strains was analyzed, in the light and in the dark, following a variety of genotoxicmore » treatments including UV radiation exposure. The strains were irradiated by a germicide lamp. The results demonstrated that most of the strains exhibited a low rate of survival after the UV exposure. After irradiation by visible light following the UV exposure, all strains showed a high capability of photoreactivation when grown. This capability was quite unexpected because these bacteria were sampled from a dark ambient without UV radiation. This leads us to hypothesize that the photoreactivation in these bacteria might have been evolved to repair DNA lesions also induced by different radiation sources other than UV (e.g., x-ray) and that the luminescent bacteria might use their own light emission to carry out the photoreactivation. The high capability of photoreactivation of these bacteria was also justified by the results of deconvolution. The deconvolution was applied to the emission spectra and it was able to show evidence of different light peaks. The presence of the visible peak could control the photolysis enzyme.« less

Inhibitory activity of reuterin, nisin, lysozyme and nitrite against vegetative cells and spores of dairy-related Clostridium species.

PubMed

Avila, Marta; Gómez-Torres, Natalia; Hernández, Marta; Garde, Sonia

2014-02-17

The butyric acid fermentation, responsible for late blowing of cheese, is caused by the outgrowth in cheese of some species of Clostridium, resulting in texture and flavor defects and economical losses. The aim of this study was to evaluate the effectiveness of different antimicrobial compounds against vegetative cells and spores of C. tyrobutyricum, C. butyricum, C. beijerinckii and C. sporogenes strains isolated from cheeses with late blowing defect. Minimal inhibitory concentration (MIC) for reuterin, nisin, lysozyme and sodium nitrite were determined against Clostridium strains in milk and modified RCM (mRCM) after 7d exposure. Although the sensitivity of Clostridium to the tested antimicrobials was strain-dependent, C. sporogenes and C. beijerinckii generally had higher MIC values than the rest of Clostridium species. The majority of Clostridium strains were more resistant to antimicrobials in milk than in mRCM, and vegetative cells exhibited higher sensitivity than spores. Reuterin (MIC values 0.51-32.5 mM) and nisin (MIC values 0.05-12.5 μg/ml) were able to inhibit the growth of vegetative cells and spores of all assayed Clostridium strains in milk and mRCM. Strains of C. tyrobutyricum exhibited the highest sensitivity to lysozyme (MIC values<0.20-400 μg/ml) and sodium nitrite (MIC values 18.75-150 μg/ml). These results suggest that reuterin and nisin, with a broad inhibitory activity spectrum against Clostridium spp. spores and vegetative cells, may be the best options to control Clostridium growth in dairy products and to prevent associated spoilage, such as late blowing defect of cheese. However, further studies in cheese would be necessary to validate this hypothesis. Copyright © 2013 Elsevier B.V. All rights reserved.

Paleaostress/strain study and its implications for the geodynamic history of the Jabal Akhdar Dome (Oman)

NASA Astrophysics Data System (ADS)

Scharf, Andreas; Amrouch, Khalid; Mattern, Frank

2016-04-01

Field observations, including oolite-, styolite, fracture analyses combined with laboratory measurements using calcite twin analysis show a ductile-to-brittle multiple-phase deformation history of the Arabian carbonate platform, ranging from Late Cretaceous to Neogene times. The Arabian carbonate platform, belonging to a passive continental margin since the Late Permian, was the site of the obduction of Tethyan oceanic lithosphere (Semail Ophiolite) during the Late Cretaceous, caused by the northward drift of Africa (Hanna, 1995). After or during the obduction, large parts of the entire nape pile composed of the Arabian platform and the Hawasina/Semail nappes, where folded and exhumed. This led to the exhumation of the Jabal Akhdar Dome. Our oolite samples from the Jabal Akhdar Dome and from below the ophiolite thrust reveal the strain ellipsoid related to the obduction. This strain ellipsoid shows components of pure and simple shear. In the latter case the longest axes of the strain ellipsoid are parallelly oriented to the direction of obduction (NE to SW), which is in good agreement with the direction of obduction as depicted by Hacker et al. (1996) for the study area. The pure-shear component (flattening) is interpreted to be a result of the overburden of the up to 7 km thick oceanic lithosphere. The oolites that are located approximately 200 m below the ophiolite thrust contact provide evidence for ductile deformation during the Late Cretaceous. These results are compared with strain and stress tensors obtained from styolites, calcite twins and fracture analyses, derived from the uppermost part of the Arabian platform of the Jabal Akhdar Dome. Our results show a complex and detailed structural deformation of the post-obduction history of the Jabal Akhdar Dome, including its folding and exhumation. Hanna, S. (1995) Field guide to the Geology of Oman. Ruwi (Historical Association of Oman. 178 pp. Hacker, B.R., Mosenfelder, J.L. & Gnos, E. (1996) Rapid emplacement of the Oman ophiolite: Thermal and geochronological constraints. Tectonics, 15(6), 1230-1247.

Endogenous Retrovirus ev21 Dose Not Recombine with ALV-J and Induces the Expression of ISGs in the Host.

PubMed

Feng, Min; Tan, Yan; Dai, Manman; Li, Yuanfang; Xie, Tingting; Li, Hongmei; Shi, Meiqing; Zhang, Xiquan

2016-01-01

Avian leukosis virus subgroup J (ALV-J) infection can cause tumors and immunosuppression. Endogenous viruses integrate into host genomes and can recombine with exogenous avian leukosis virus (ALV). In this study, we analyzed the interaction of endogenous retrovirus 21 ( ev21 ) with the ALV-J in late-feathering Chinese yellow chicken. Two ALV-J strains M180 and K243 were isolated from late-feathering and fast-feathering Chinese yellow chicken flocks, respectively. The env gene of the two strains showed 94.2-94.8% nucleotide identity with reference ALV-J strains. Compared with the env gene and the LTR of ev21 and M180, the nucleotide identity of LTR was 69.7% and env gene was 58.4%, respectively, especially the amino acid identity of env gene as low as 14.2%. Phylogenetic analysis of the nucleotide sequence of the env gene and the 3'LTR showed that M180 was closely related to ALV-J, and was located in a distinct group with ev21 in the phylogenetic tree. Using co-immunoprecipitation (co-IP), we next demonstrate that the envelope protein of ev21 does not interact with the M180 envelope protein. We further show that the envelope protein of ev21 cannot activate ALV-J LTR promoter activity using luciferase-reporter assays. qPCR and western blot analysis revealed that envelope protein of endogenous ev21 can facilitate the expression of PKR at 6h post ALV-J infection (hpi) and facilitate the expression of ISG12 and CH25H at 24 hpi. However, the expression of the env gene of M180 strain was not significantly at 6 and 24 hpi. We conclude that there is no evidence of recombination between endogenous retrovirus ev21 and ALV-J strain M180 in late-feathering Chinese yellow chicken, and envelope protein of ev21 can affect the expression of host ISGs, but appears not to influence the replication of ALV-J strain M180. This is the first report of interaction among the endogenous retrovirus ev21, ALV-J and the late-feathering chicken.

IF1, a natural inhibitor of mitochondrial ATP synthase, is not essential for the normal growth and breeding of mice.

PubMed

Nakamura, Junji; Fujikawa, Makoto; Yoshida, Masasuke

2013-09-17

IF1 is an endogenous inhibitor protein of mitochondrial ATP synthase. It is evolutionarily conserved throughout all eukaryotes and it has been proposed to play crucial roles in prevention of the wasteful reverse reaction of ATP synthase, in the metabolic shift from oxidative phosphorylation to glycolysis, in the suppression of ROS (reactive oxygen species) generation, in mitochondria morphology and in haem biosynthesis in mitochondria, which leads to anaemia. Here, we report the phenotype of a mouse strain in which IF1 gene was destroyed. Unexpectedly, individuals of this IF1-KO (knockout) mouse strain grew and bred without defect. The general behaviours, blood test results and responses to starvation of the IF1-KO mice were apparently normal. There were no abnormalities in the tissue anatomy or the autophagy. Mitochondria of the IF1-KO mice were normal in morphology, in the content of ATP synthase molecules and in ATP synthesis activity. Thus, IF1 is not an essential protein for mice despite its ubiquitous presence in eukaryotes.

Diversity in copy number and structure of a silkworm morphogenetic gene as a result of domestication.

PubMed

Sakudoh, Takashi; Nakashima, Takeharu; Kuroki, Yoko; Fujiyama, Asao; Kohara, Yuji; Honda, Naoko; Fujimoto, Hirofumi; Shimada, Toru; Nakagaki, Masao; Banno, Yutaka; Tsuchida, Kozo

2011-03-01

The carotenoid-binding protein (CBP) of the domesticated silkworm, Bombyx mori, a major determinant of cocoon color, is likely to have been substantially influenced by domestication of this species. We analyzed the structure of the CBP gene in multiple strains of B. mori, in multiple individuals of the wild silkworm, B. mandarina (the putative wild ancestor of B. mori), and in a number of other lepidopterans. We found the CBP gene copy number in genomic DNA to vary widely among B. mori strains, ranging from 1 to 20. The copies of CBP are of several types, based on the presence of a retrotransposon or partial deletion of the coding sequence. In contrast to B. mori, B. mandarina was found to possess a single copy of CBP without the retrotransposon insertion, regardless of habitat. Several other lepidopterans were found to contain sequences homologous to CBP, revealing that this gene is evolutionarily conserved in the lepidopteran lineage. Thus, domestication can generate significant diversity of gene copy number and structure over a relatively short evolutionary time. © 2011 by the Genetics Society of America

Diversity in Copy Number and Structure of a Silkworm Morphogenetic Gene as a Result of Domestication

PubMed Central

Sakudoh, Takashi; Nakashima, Takeharu; Kuroki, Yoko; Fujiyama, Asao; Kohara, Yuji; Honda, Naoko; Fujimoto, Hirofumi; Shimada, Toru; Nakagaki, Masao; Banno, Yutaka; Tsuchida, Kozo

2011-01-01

The carotenoid-binding protein (CBP) of the domesticated silkworm, Bombyx mori, a major determinant of cocoon color, is likely to have been substantially influenced by domestication of this species. We analyzed the structure of the CBP gene in multiple strains of B. mori, in multiple individuals of the wild silkworm, B. mandarina (the putative wild ancestor of B. mori), and in a number of other lepidopterans. We found the CBP gene copy number in genomic DNA to vary widely among B. mori strains, ranging from 1 to 20. The copies of CBP are of several types, based on the presence of a retrotransposon or partial deletion of the coding sequence. In contrast to B. mori, B. mandarina was found to possess a single copy of CBP without the retrotransposon insertion, regardless of habitat. Several other lepidopterans were found to contain sequences homologous to CBP, revealing that this gene is evolutionarily conserved in the lepidopteran lineage. Thus, domestication can generate significant diversity of gene copy number and structure over a relatively short evolutionary time. PMID:21242537

Spata6 is required for normal assembly of the sperm connecting piece and tight head–tail conjunction

PubMed Central

Yuan, Shuiqiao; Stratton, Clifford J.; Bao, Jianqiang; Zheng, Huili; Bhetwal, Bhupal P.; Yanagimachi, Ryuzo; Yan, Wei

2015-01-01

“Pinhead sperm,” or “acephalic sperm,” a type of human teratozoospermia, refers to the condition in which ejaculate contains mostly sperm flagella without heads. Family clustering and homogeneity of this syndrome suggests a genetic basis, but the causative genes remain largely unknown. Here we report that Spata6, an evolutionarily conserved testis-specific gene, encodes a protein required for formation of the segmented columns and the capitulum, two major structures of the sperm connecting piece essential for linking the developing flagellum to the head during late spermiogenesis. Inactivation of Spata6 in mice leads to acephalic spermatozoa and male sterility. Our proteomic analyses reveal that SPATA6 is involved in myosin-based microfilament transport through interaction with myosin subunits (e.g., MYL6). PMID:25605924

Multicellularity makes somatic differentiation evolutionarily stable

PubMed Central

Wahl, Mary E.; Murray, Andrew W.

2016-01-01

Many multicellular organisms produce two cell lineages: germ cells, whose descendants produce the next generation, and somatic cells, which support, protect, and disperse the germ cells. This germ-soma demarcation has evolved independently in dozens of multicellular taxa but is absent in unicellular species. A common explanation holds that in these organisms, inefficient intercellular nutrient exchange compels the fitness cost of producing nonreproductive somatic cells to outweigh any potential benefits. We propose instead that the absence of unicellular, soma-producing populations reflects their susceptibility to invasion by nondifferentiating mutants that ultimately eradicate the soma-producing lineage. We argue that multicellularity can prevent the victory of such mutants by giving germ cells preferential access to the benefits conferred by somatic cells. The absence of natural unicellular, soma-producing species previously prevented these hypotheses from being directly tested in vivo: to overcome this obstacle, we engineered strains of the budding yeast Saccharomyces cerevisiae that differ only in the presence or absence of multicellularity and somatic differentiation, permitting direct comparisons between organisms with different lifestyles. Our strains implement the essential features of irreversible conversion from germ line to soma, reproductive division of labor, and clonal multicellularity while maintaining sufficient generality to permit broad extension of our conclusions. Our somatic cells can provide fitness benefits that exceed the reproductive costs of their production, even in unicellular strains. We find that nondifferentiating mutants overtake unicellular populations but are outcompeted by multicellular, soma-producing strains, suggesting that multicellularity confers evolutionary stability to somatic differentiation. PMID:27402737

Genetic Diversity and Evolution of Salmonella enterica Serovar Enteritidis Strains with Different Phage Types

PubMed Central

Pettengill, James; Strain, Errol; Allard, Marc W.; Ahmed, Rafiq; Zhao, Shaohua; Brown, Eric W.

2014-01-01

Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis for over 2 decades. However, knowledge of the genetic and evolutionary relationships between phage types is very limited, making differences difficult to interpret. Here, single nucleotide polymorphisms (SNPs) identified from whole-genome comparisons were used to determine the relationships between some S. Enteritidis phage types (PTs) commonly associated with food-borne outbreaks in the United States. Emphasis was placed on the predominant phage types PT8, PT13a, and PT13 in North America. With >89,400 bp surveyed across 98 S. Enteritidis isolates representing 14 distinct phage types, 55 informative SNPs were discovered within 23 chromosomally anchored loci. To maximize the discriminatory and evolutionary partitioning of these highly homogeneous strains, sequences comprising informative SNPs were concatenated into a single combined data matrix and subjected to phylogenetic analysis. The resultant phylogeny allocated most S. Enteritidis isolates into two distinct clades (clades I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs capable of distinguishing individual clades/subclades were identified. However, individual phage types appeared to be evolutionarily disjunct when mapped to this phylogeny, suggesting that phage typing may not be valid for making phylogenetic inferences. Furthermore, the set of SNPs identified here represents useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provides core genotypic markers for future development of a SNP typing scheme with S. Enteritidis. PMID:24574287

Evolutionary and structural analyses of alpha-papillomavirus capsid proteins yields novel insights into L2 structure and interaction with L1

PubMed Central

Lowe, John; Panda, Debasis; Rose, Suzanne; Jensen, Ty; Hughes, Willie A; Tso, For Yue; Angeletti, Peter C

2008-01-01

Background PVs (PV) are small, non-enveloped, double-stranded DNA viruses that have been identified as the primary etiological agent for cervical cancer and their potential for malignant transformation in mucosal tissue has a large impact on public health. The PV family Papillomaviridae is organized into multiple genus based on sequential parsimony, host range, tissue tropism, and histology. We focused this analysis on the late gene products, major (L1) and minor (L2) capsid proteins from the family Papillomaviridae genus Alpha-papillomavirus. Alpha-PVs preferentially infect oral and anogenital mucosa of humans and primates with varied risk of oncogenic transformation. Development of evolutionary associations between PVs will likely provide novel information to assist in clarifying the currently elusive relationship between PV and its microenvironment (i.e., the single infected cell) and macro environment (i.e., the skin tissue). We attempt to identify the regions of the major capsid proteins as well as minor capsid proteins of alpha-papillomavirus that have been evolutionarily conserved, and define regions that are under constant selective pressure with respect to the entire family of viruses. Results This analysis shows the loops of L1 are in fact the most variable regions among the alpha-PVs. We also identify regions of L2, involved in interaction with L1, as evolutionarily conserved among the members of alpha- PVs. Finally, a predicted three-dimensional model was generated to further elucidate probable aspects of the L1 and L2 interaction. PMID:19087355

Avoidance of fisheries-induced evolution: management implications for catch selectivity and limit reference points.

PubMed

Hutchings, Jeffrey A

2009-08-01

I examined how the fitness (r) associated with early- and late-maturing genotypes varies with fishing mortality (F) and age-/size-specific probability of capture. Life-history data on Newfoundland's northern Atlantic cod (Gadus morhua) allowed for the estimation of r for individuals maturing at 4 and 7 year in the absence of fishing. Catch selectivity data associated with four types of fishing gear (trap, gillnet, handline, otter trawl) were then incorporated to examine how r varied with gear type and with F. The resulting fitness functions were then used to estimate the F above which selection would favour early (4 year) rather than delayed (7 year) maturity. This evolutionarily-sensitive threshold, F evol, identifies a limit reference point somewhat similar to those used to define overfishing (e.g., F msy, F 0.1). Over-exploitation of northern cod resulted in fishing mortalities considerably greater than those required to effect evolutionary change. Selection for early maturity is reduced by the dome-shaped selectivities characteristic of fixed gears such as handlines (the greater the leptokurtosis, the lower the probability of a selection response) and enhanced by the knife-edged selectivities of bottom trawls. Strategies to minimize genetic change are consistent with traditional management objectives (e.g., yield maximization, population increase). Compliance with harvest control rules guided by evolutionarily-sensitive limit reference points, which may be achieved by adherence to traditional reference points such as F msy and F 0.1, should be sufficient to minimize the probability of fisheries-induced evolution for commercially exploited species.

Promoter engineering of the Saccharomyces cerevisiae RIM15 gene for improvement of alcoholic fermentation rates under stress conditions.

PubMed

Watanabe, Daisuke; Kaneko, Akie; Sugimoto, Yukiko; Ohnuki, Shinsuke; Takagi, Hiroshi; Ohya, Yoshikazu

2017-02-01

A loss-of-function mutation in the RIM15 gene, which encodes a Greatwall-like protein kinase, is one of the major causes of the high alcoholic fermentation rates in Saccharomyces cerevisiae sake strains closely related to Kyokai no. 7 (K7). However, impairment of Rim15p may not be beneficial under more severe fermentation conditions, such as in the late fermentation stage, as it negatively affects stress responses. To balance stress tolerance and fermentation performance, we inserted the promoter of a gluconeogenic gene, PCK1, into the 5'-untranslated region (5'-UTR) of the RIM15 gene in a laboratory strain to achieve repression of RIM15 gene expression in the glucose-rich early stage with its induction in the stressful late stage of alcoholic fermentation. The promoter-engineered strain exhibited a fermentation rate comparable to that of the RIM15-deleted strain with no decrease in cell viability. The engineered strain achieved better alcoholic fermentation performance than the RIM15-deleted strain under repetitive and high-glucose fermentation conditions. These data demonstrated the validity of promoter engineering of the RIM15 gene that governs inhibitory control of alcoholic fermentation. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A Developmental Test of Mertonian Anomie Theory.

ERIC Educational Resources Information Center

Menard, Scott

1995-01-01

Carefully reviewed Merton's writings on anomie theory to construct a more complete and rigorous test of the theory for respondents in early, middle, and late adolescence. Concluded that misspecified models of strain theory have underestimated the predictive power of strain theory in general and of anomie theory in particular. (JBJ)

The Modes of Evolutionary Emergence of Primal and Late Pandemic Influenza Virus Strains from Viral Reservoir in Animals: An Interdisciplinary Analysis

PubMed Central

Shoham, Dany

2011-01-01

Based on a wealth of recent findings, in conjunction with earliest chronologies pertaining to evolutionary emergences of ancestral RNA viruses, ducks, Influenzavirus A (assumingly within ducks), and hominids, as well as to the initial domestication of mallard duck (Anas platyrhynchos), jungle fowl (Gallus gallus), wild turkey (Meleagris gallopavo), wild boar (Sus scrofa), and wild horse (Equus ferus), presumed genesis modes of primordial pandemic influenza strains have multidisciplinarily been configured. The virological fundamentality of domestication and farming of those various avian and mammalian species has thereby been demonstrated and broadly elucidated, within distinctive coevolutionary paradigms. The mentioned viral genesis modes were then analyzed, compatibly with common denominators and flexibility that mark the geographic profile of the last 18 pandemic strains, which reputedly emerged since 1510, the antigenic profile of the last 10 pandemic strains since 1847, and the genomic profile of the last 5 pandemic strains since 1918, until present. Related ecophylogenetic and biogeographic aspects have been enlightened, alongside with the crucial role of spatial virus gene dissemination by avian hosts. A fairly coherent picture of primary and late evolutionary and genomic courses of pandemic strains has thus been attained, tentatively. Specific patterns underlying complexes prone to generate past and future pandemic strains from viral reservoir in animals are consequentially derived. PMID:23074663

From grazing resistance to pathogenesis: the coincidental evolution of virulence factors.

PubMed

Adiba, Sandrine; Nizak, Clément; van Baalen, Minus; Denamur, Erick; Depaulis, Frantz

2010-08-11

To many pathogenic bacteria, human hosts are an evolutionary dead end. This begs the question what evolutionary forces have shaped their virulence traits. Why are these bacteria so virulent? The coincidental evolution hypothesis suggests that such virulence factors result from adaptation to other ecological niches. In particular, virulence traits in bacteria might result from selective pressure exerted by protozoan predator. Thus, grazing resistance may be an evolutionarily exaptation for bacterial pathogenicity. This hypothesis was tested by subjecting a well characterized collection of 31 Escherichia coli strains (human commensal or extra-intestinal pathogenic) to grazing by the social haploid amoeba Dictyostelium discoideum. We then assessed how resistance to grazing correlates with some bacterial traits, such as the presence of virulence genes. Whatever the relative population size (bacteria/amoeba) for a non-pathogenic bacteria strain, D. discoideum was able to phagocytise, digest and grow. In contrast, a pathogenic bacterium strain killed D. discoideum above a certain bacteria/amoeba population size. A plating assay was then carried out using the E. coli collection faced to the grazing of D. discoideum. E. coli strains carrying virulence genes such as iroN, irp2, fyuA involved in iron uptake, belonging to the B2 phylogenetic group and being virulent in a mouse model of septicaemia were resistant to the grazing from D. discoideum. Experimental proof of the key role of the irp gene in the grazing resistance was evidenced with a mutant strain lacking this gene. Such determinant of virulence may well be originally selected and (or) further maintained for their role in natural habitat: resistance to digestion by free-living protozoa, rather than for virulence per se.

Identification and characterization of new members of the SXT/R391 family of integrative and conjugative elements (ICEs) in Proteus mirabilis.

PubMed

Bie, Luyao; Wu, Hao; Wang, Xin-Hua; Wang, Mingyu; Xu, Hai

2017-08-01

Integrative and conjugative elements (ICEs) are self-transmissible chromosomal mobile elements that play significant roles in the dissemination of antimicrobial resistance genes. Identification of the structures and functions of ICEs, particularly those in pathogens, improves understanding of the dissemination of antimicrobial resistance. This study identified new members of the sulfamethoxazole-trimethoprim (SXT)/R391 family of ICEs that could confer multi-drug resistance in the opportunistic pathogen Proteus mirabilis, characterized their genetic structures, and explored their evolutionary connection with other members of this family of ICEs. Three new members of the SXT/R391 family of ICEs were detected in six of 77 P. mirabilis strains isolated in China: ICEPmiChn2 (one strain), ICEPmiChn3 (one strain) and ICEPmiChn4 (three strains). All three new ICEs harbour antimicrobial resistance genes from diverse origins, suggesting their capability in acquiring foreign genes and serving as important carriers for antimicrobial resistance genes. Structural analysis showed that ICEPmiChn3 is a particularly interesting and unique ICE that has lost core genes involved in conjugation, and could not transfer to other cells via conjugation. This finding confirmed the key roles of these missing genes in conjugation. Further phylogenetic analysis suggested that ICEs in geographically close strains are also connected evolutionarily, and ICEPmiChn3 lost its conjugation cassette from a former mobile ICE. The identification and characterization of the three new members of the SXT/R391 family of ICEs in this work leads to suggestions of core ICE genes essential for conjugation, and extends understanding on the structures of ICEs, evolutionary relationships between ICEs, and the antimicrobial resistance mechanisms of P. mirabilis. Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

Apes are intuitive statisticians.

PubMed

Rakoczy, Hannes; Clüver, Annette; Saucke, Liane; Stoffregen, Nicole; Gräbener, Alice; Migura, Judith; Call, Josep

2014-04-01

Inductive learning and reasoning, as we use it both in everyday life and in science, is characterized by flexible inferences based on statistical information: inferences from populations to samples and vice versa. Many forms of such statistical reasoning have been found to develop late in human ontogeny, depending on formal education and language, and to be fragile even in adults. New revolutionary research, however, suggests that even preverbal human infants make use of intuitive statistics. Here, we conducted the first investigation of such intuitive statistical reasoning with non-human primates. In a series of 7 experiments, Bonobos, Chimpanzees, Gorillas and Orangutans drew flexible statistical inferences from populations to samples. These inferences, furthermore, were truly based on statistical information regarding the relative frequency distributions in a population, and not on absolute frequencies. Intuitive statistics in its most basic form is thus an evolutionarily more ancient rather than a uniquely human capacity. Copyright © 2014 Elsevier B.V. All rights reserved.

Cyber Victimization and Perceived Stress: Linkages to Late Adolescents' Cyber Aggression and Psychological Functioning

ERIC Educational Resources Information Center

Wright, Michelle F.

2015-01-01

The present study examined multiple sources of strain, particular cyber victimization, and perceived stress from parents, peers, and academics, in relation to late adolescents' (ages 16-18; N = 423) cyber aggression, anxiety, and depression, each assessed 1 year later (Time 2). Three-way interactions revealed that the relationship between Time 1…

Pego do Diabo (Loures, Portugal): Dating the Emergence of Anatomical Modernity in Westernmost Eurasia

PubMed Central

Zilhão, João; Davis, Simon J. M.; Duarte, Cidália; Soares, António M. M.; Steier, Peter; Wild, Eva

2010-01-01

Background Neandertals and the Middle Paleolithic persisted in the Iberian Peninsula south of the Ebro drainage system for several millennia beyond their assimilation/replacement elsewhere in Europe. As only modern humans are associated with the later stages of the Aurignacian, the duration of this persistence pattern can be assessed via the dating of diagnostic occurrences of such stages. Methodology/Principal Findings Using AMS radiocarbon and advanced pretreatment techniques, we dated a set of stratigraphically associated faunal samples from an Aurignacian III–IV context excavated at the Portuguese cave site of Pego do Diabo. Our results establish a secure terminus ante quem of ca.34,500 calendar years ago for the assimilation/replacement process in westernmost Eurasia. Combined with the chronology of the regional Late Mousterian and with less precise dating evidence for the Aurignacian II, they place the denouement of that process in the 37th millennium before present. Conclusions/Significance These findings have implications for the understanding of the emergence of anatomical modernity in the Old World as a whole, support explanations of the archaic features of the Lagar Velho child's anatomy that invoke evolutionarily significant Neandertal/modern admixture at the time of contact, and counter suggestions that Neandertals could have survived in southwest Iberia until as late as the Last Glacial Maximum. PMID:20111705

The genetic origin of minor histocompatibility antigens.

PubMed

Roopenian, D C; Christianson, G J; Davis, A P; Zuberi, A R; Mobraaten, L E

1993-01-01

The purpose of this study was to elucidate the genetic origin of minor histocompatibility (H) antigens. Toward this end common inbred mouse strains, distinct subspecies, and species of the subgenus Mus were examined for expression of various minor H antigens. These antigens were encoded by the classical minor H loci H-3 and H-4 or by newly identified minor H antigens detected as a consequence of mutation. Both minor H antigens that stimulate MHC class I-restricted cytotoxic T cells (Tc) and antigens that stimulate MHC class II-restricted helper T cells (Th) were monitored. The results suggested that strains of distinct ancestry commonly express identical or cross-reactive antigens. Moreover, a correlation between the lack of expression of minor H antigens and ancestral heritage was observed. To address whether the antigens found on unrelated strains were allelic with the sensitizing minor H antigens or a consequence of antigen cross-reactivity, classical genetic segregation analysis was carried out. Even in distinct subspecies and species, the minor H antigens always mapped to the site of the appropriate minor H locus. Together the results suggest: 1) minor H antigen sequences are evolutionarily stable in that their pace of antigenic change is slow enough to predate subspeciation and speciation; 2) the minor H antigens originated in the inbred strains as a consequence of a rare polymorphism or loss mutation carried in a founder mouse stock that caused the mouse to perceive the wild-type protein as foreign; 3) there is a remarkable lack of antigenic cross-reactivity between the defined minor H antigens and other gene products.

Temperature influence on the development and loss of seawater tolerance in two fast-growing strains of Atlantic salmon

USGS Publications Warehouse

Handeland, S.O.; Wilkinson, E.; Sveinsbo, B.; McCormick, S.D.; Stefansson, S.O.

2004-01-01

Development of hypo-osmoregulatory ability, gill Na+,K +-ATPase activity, condition factor and growth in Atlantic salmon during parr-smolt transformation was studied in a 2??3 factorial design with three temperatures (12.0, 8.9??C and ambient, 2.4-11.9??C, mean: 6.0??C) and two farmed strains of smolts (Mowi and AquaGen). The development of hypo-osmoregulatory ability and gill Na+,K+-ATPase activity were significantly influenced by freshwater temperature. In smolts raised at 12.0??C, maximum gill Na+,K+-ATPase activity was reached in late April, compared with late May and mid-June in the 8.9??C and ambient groups, respectively. In all groups, peak gill Na+,K +-ATPase activity was seen 350 degree days (d??C) after the onset of the smolt-related increase in enzyme activity (30 March) The period of high enzyme activity (>90% of maximum) lasted approximately 250 d??C. No distinct peak level in gill Na+,K+-ATPase activity was seen in the AquaGen strain at ambient temperature. Elevated temperatures also accelerated the loss of hypo-osmoregulatory capacity. In all groups, gill Na+,K+-ATPase activity reached pre-smolt levels approximately 500 d??C after the calculated peak level. Growth rate in freshwater was influenced by strain, temperature and their interaction, with the Mowi strain showing a higher growth rate than the AquaGen strain at 8.9??C and ambient temperatures. Following transfer to seawater, a higher growth rate was recorded in smolts from the Mowi strain than the AquaGen strain from the ambient temperature regime. Temperature influences the development and loss of smolt characteristics in both strains, and has long-term effects on post-smolt performance in seawater. ?? 2004 Elsevier B.V. All rights reserved.

Microbial competition in porous environments can select against rapid biofilm growth

PubMed Central

Coyte, Katharine Z.; Tabuteau, Hervé; Gaffney, Eamonn A.; Durham, William M.

2017-01-01

Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow–biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live. PMID:28007984

Functional drug screening reveals anticonvulsants as enhancers of mTOR-independent autophagic killing of Mycobacterium tuberculosis through inositol depletion

PubMed Central

Schiebler, Mark; Brown, Karen; Hegyi, Krisztina; Newton, Sandra M; Renna, Maurizio; Hepburn, Lucy; Klapholz, Catherine; Coulter, Sarah; Obregón-Henao, Andres; Henao Tamayo, Marcela; Basaraba, Randall; Kampmann, Beate; Henry, Katherine M; Burgon, Joseph; Renshaw, Stephen A; Fleming, Angeleen; Kay, Robert R; Anderson, Karen E; Hawkins, Phillip T; Ordway, Diane J; Rubinsztein, David C; Floto, Rodrigo Andres

2015-01-01

Mycobacterium tuberculosis (MTB) remains a major challenge to global health made worse by the spread of multidrug resistance. We therefore examined whether stimulating intracellular killing of mycobacteria through pharmacological enhancement of macroautophagy might provide a novel therapeutic strategy. Despite the resistance of MTB to killing by basal autophagy, cell-based screening of FDA-approved drugs revealed two anticonvulsants, carbamazepine and valproic acid, that were able to stimulate autophagic killing of intracellular M. tuberculosis within primary human macrophages at concentrations achievable in humans. Using a zebrafish model, we show that carbamazepine can stimulate autophagy in vivo and enhance clearance of M. marinum, while in mice infected with a highly virulent multidrug-resistant MTB strain, carbamazepine treatment reduced bacterial burden, improved lung pathology and stimulated adaptive immunity. We show that carbamazepine induces antimicrobial autophagy through a novel, evolutionarily conserved, mTOR-independent pathway controlled by cellular depletion of myo-inositol. While strain-specific differences in susceptibility to in vivo carbamazepine treatment may exist, autophagy enhancement by repurposed drugs provides an easily implementable potential therapy for the treatment of multidrug-resistant mycobacterial infection. PMID:25535254

Functional drug screening reveals anticonvulsants as enhancers of mTOR-independent autophagic killing of Mycobacterium tuberculosis through inositol depletion.

PubMed

Schiebler, Mark; Brown, Karen; Hegyi, Krisztina; Newton, Sandra M; Renna, Maurizio; Hepburn, Lucy; Klapholz, Catherine; Coulter, Sarah; Obregón-Henao, Andres; Henao Tamayo, Marcela; Basaraba, Randall; Kampmann, Beate; Henry, Katherine M; Burgon, Joseph; Renshaw, Stephen A; Fleming, Angeleen; Kay, Robert R; Anderson, Karen E; Hawkins, Phillip T; Ordway, Diane J; Rubinsztein, David C; Floto, Rodrigo Andres

2015-02-01

Mycobacterium tuberculosis (MTB) remains a major challenge to global health made worse by the spread of multidrug resistance. We therefore examined whether stimulating intracellular killing of mycobacteria through pharmacological enhancement of macroautophagy might provide a novel therapeutic strategy. Despite the resistance of MTB to killing by basal autophagy, cell-based screening of FDA-approved drugs revealed two anticonvulsants, carbamazepine and valproic acid, that were able to stimulate autophagic killing of intracellular M. tuberculosis within primary human macrophages at concentrations achievable in humans. Using a zebrafish model, we show that carbamazepine can stimulate autophagy in vivo and enhance clearance of M. marinum, while in mice infected with a highly virulent multidrug-resistant MTB strain, carbamazepine treatment reduced bacterial burden, improved lung pathology and stimulated adaptive immunity. We show that carbamazepine induces antimicrobial autophagy through a novel, evolutionarily conserved, mTOR-independent pathway controlled by cellular depletion of myo-inositol. While strain-specific differences in susceptibility to in vivo carbamazepine treatment may exist, autophagy enhancement by repurposed drugs provides an easily implementable potential therapy for the treatment of multidrug-resistant mycobacterial infection. © 2014 The Authors. Published under the terms of the CC BY 4.0 license.

Evolutionary Instability of Symbiotic Function in Bradyrhizobium japonicum

PubMed Central

Sachs, Joel L.; Russell, James E.; Hollowell, Amanda C.

2011-01-01

Bacterial mutualists are often acquired from the environment by eukaryotic hosts. However, both theory and empirical work suggest that this bacterial lifestyle is evolutionarily unstable. Bacterial evolution outside of the host is predicted to favor traits that promote an independent lifestyle in the environment at a cost to symbiotic function. Consistent with these predictions, environmentally-acquired bacterial mutualists often lose symbiotic function over evolutionary time. Here, we investigate the evolutionary erosion of symbiotic traits in Bradyrhizobium japonicum, a nodulating root symbiont of legumes. Building on a previous published phylogeny we infer loss events of nodulation capability in a natural population of Bradyrhizobium, potentially driven by mutation or deletion of symbiosis loci. Subsequently, we experimentally evolved representative strains from the symbiont population under host-free in vitro conditions to examine potential drivers of these loss events. Among Bradyrhizobium genotypes that evolved significant increases in fitness in vitro, two exhibited reduced symbiotic quality, but no experimentally evolved strain lost nodulation capability or evolved any fixed changes at six sequenced loci. Our results are consistent with trade-offs between symbiotic quality and fitness in a host free environment. However, the drivers of loss-of-nodulation events in natural Bradyrhizobium populations remain unknown. PMID:22073160

Development of dry gram-negative bacteria biocontrol products and small pilot tests against dry rot

USDA-ARS?s Scientific Manuscript database

Pseudomonas fluorescens strains S11:P:12, P22:Y:05, and S22:T:04 suppress four important storage potato maladies; dry rot, late blight, pink rot, and sprouting. Studies were designed to identify methods for producing a dried, efficacious biological control product. The strains were evaluated individ...

Late sampling for automated culture to extend the platelet shelf life to 5 days in Germany.

PubMed

Vollmer, Tanja; Dabisch-Ruthe, Mareike; Weinstock, Melanie; Knabbe, Cornelius; Dreier, Jens

2018-04-15

Bacterial contamination of platelet concentrates (PCs) is still a major challenge in transfusion medicine. Different methodologic concepts and screening strategies have been developed and investigated concerning their usability. We evaluated the feasibility of BacT/ALERT automated culture (BacT/A, bioMérieux) with late sampling after 3 days at the earliest. Twenty-four bacterial strains isolated from PCs and six relevant strains from reference stocks were spiked into apheresis-derived PCs (10-60 colony-forming units [CFU]/bag). Sampling was performed after 3 days, and bacterial detection was investigated using the two detection methods (BacT/A and BactiFlow [BF], bioMérieux). The maximum time-to-result of BacT/A was set to less than 12 hours. All medium- or high-pathogenic strains are capable of proliferating to high titers, and 100% of contaminated samples were detected by BF and BacT/A (6 to ≤12 h incubation); lower detection rates of BacT/A were obtained within 6 hours of incubation (≤6 h: 76.2-93.4%). The majority of low-pathogenic isolates are also capable of growing in PCs (89.7%), showing a detection rate of 74.3% for BF versus 54.3% for BacT/A (6 to ≤12 h incubation). BacT/A failed to detect bacteria within 6 hours of incubation. Certainly, a small number of strains did not grow under PC storage conditions and were detectable by BacT/A only with increased detection times. Late sampling after 3 days at the earliest, combined with reduced BacT/A incubation following the negative-to-date concept, offer an alternative opportunity to extend the shelf life of PCs from 4 to 5 days in Germany. The sensitivity of BacT/A with late sampling is nearly comparable to BF; the time-to-result is considerably longer. © 2018 AABB.

Phylogeny and toxicology of Lyngbya wollei (Cyanobacteria, Oscillatoriales) from north-eastern Australia, with a description of Microseira gen. nov.

PubMed

McGregor, Glenn B; Sendall, Barbara C

2015-02-01

Three populations of the freshwater filamentous cyanobacterium Lyngbya wollei (Farlow ex Gomont) Speziale and Dyck have been putatively identified from north-eastern Australia and found to produce the potent cyanotoxin cylindrospermopsin (CYN) and its analog deoxy-cylindrospermopsin (deoxy-CYN). We investigated the phylogeny and toxicology of strains and mats isolated from two of these populations using a combination of molecular and morphological techniques. Morphologically the strains corresponded to the type description, however, the frequency of false-branching was low, and variable over time. Strains and mat samples from both sites were positive for the cyrF and cyrJ genes associated with CYN biosynthesis. Phylogenetic analysis of these genes from Australian L. wollei sequences and comparable cyanobacterial sequences revealed that the genes in L. wollei were more closely related to homologous genes in Oscillatoria sp. PCC 6506 than to homologs in Nostocalean CYN-producers. These data suggest a common evolutionary origin of CYN biosynthesis in L. wollei and Oscillatoria. In both the 16S rRNA and nifH phylogenies, the Australian L. wollei strains formed well-supported clades with United States L. wollei (= Plectonema wollei) strains. Pair-wise sequence similarities within the 16S rRNA clade containing all eleven L. wollei strains were high, ranging from 97% to 100%. This group was distantly related (<92% nucleotide similarity) to other taxa within the group previously considered under the genus Lyngbya sensu lato (C. Agardh ex Gomont). Collectively, these results suggest that this toxigenic group is evolutionarily distinct and sufficiently distant as to be considered a separate genus, which we have described as Microseira gen. nov. and hence transfer to it the type M. wollei comb. nov. © 2014 State of Queensland. Journal of Phycology © 2014 Phycological Society of America.

Streptomyces pini sp. nov., an actinomycete isolated from phylloplane of pine (Pinus sylvestris L.) needle-like leaves.

PubMed

Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Saravanan, Venkatakrishnan Sivaraj; Duraipandiyan, Veeramuthu; Al-Dhabi, Naif Abdullah; Pragatheswari, Dhandapani; Santhanakrishnan, Palani; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo

2016-10-01

A novel siderophore-producing actinomycete, designated PL19T, was isolated from the Scots-pine needle-like leaves collected from TNAU campus, Coimbatore, India. The isolate was chemoorganotrophic in nutrition and able to grow at 30 °C, and the optimum pH and NaCl facilitated the growth pH 6-11 and 0-8 % (w/v), respectively. The cells are filamentous and the mycelia formed are basically of wide and intricately branched substrate mycelium from which aerial mycelia arises, later gets differentiated into spores that are warty and arranged spirally. The 16S rRNA gene of strain PL19T was sequenced and was highly similar to the type strains of species of the genus Streptomyces, including Streptomyces barkulensis RC1831T (98.8 % pairwise similarity), Streptomyces fenghuangensis GIMN4.003T (98.2 %), Streptomyces nanhaiensis SCSIO 01248T (98.0 %), Streptomyces radiopugnans R97T (97.9 %), Streptomyces atacamensis C60T (97.8 %) and Streptomyces macrosporus NBRC 14749T (97.2 %), all of which were subjected to taxonomical characterization using a polyphasic approach. The strains showed unique carbon utilization patterns, and it possesses iso-C16 : 0 anteiso-C15 : 0 and anteiso-C17 : 0 as a major cellular fatty acids. The cell-wall was dominated with ll-type diaminopimelic acid, and the menaquinone type was MK-9(H6, H8). These chemotaxonomic evidences placed strain PL19T within the genus Streptomyces. The determination of G+C ratio (69.5 mol%) and DNA-DNA hybridization values (13.4-31.8 % with the phylogenetically related species) helped in further hierarchical classification of strain PL19T. Based on morphological, physiological and chemotaxonomic data as well as DNA-DNA hybridization values, strain PL19T could be distinguished from the evolutionarily closest species currently available. All these collective data show that strain PL19T represents a novel species of the genus Streptomyces, for which the name Streptomyces pini sp. nov. is proposed. The type strain is PL19T (=NRRL B-24728T=ICMP 17783T).

Commentary: Should Gender Differences Be Included in the Evolutionary Upgrade to Cognitive Load Theory?

ERIC Educational Resources Information Center

Bevilacqua, Andy

2017-01-01

Recent upgrades to cognitive load theory suggest that evolutionary processes have shaped the way that working memory processes cultural and social information. According to evolutionarily educational psychologists, some forms of information are processed with lower working memory loads than other forms. The former are evolutionarily salient and…

76 FR 50448 - Endangered and Threatened Species; 5-Year Reviews for 17 Evolutionarily Significant Units and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-15

... 11 evolutionarily significant units (ESUs) of Pacific salmon (Oncorhynchus sp.) and 6 distinct... and 6 DPSs of steelhead in Oregon, Washington, and Idaho shall remain listed as determined in 2005... Sound Chinook salmon; (4) Lower Columbia River Chinook salmon; (5) Upper Willamette Chinook salmon; (6...

Frequent premature atrial contractions impair left atrial contractile function and promote adverse left atrial remodeling.

PubMed

John, Anub G; Hirsch, Glenn A; Stoddard, Marcus F

2018-06-10

This study assessed if frequent premature atrial contractions (PACs) were associated with decreased left atrial (LA) strain and adverse remodeling. Left atrial dysfunction and enlargement increases risk of stroke. If frequent PACs cause LA dysfunction and remodeling, PAC suppressive therapy may be beneficial. Inclusion criteria were age ≥18 years and sinus rhythm. Exclusion criteria were atrial fibrillation or any etiology for LA enlargement. Hundred and thirty-two patients with frequent PACs (≥100/24 hours) by Holter were matched to controls. Speckle tracking strain of the left atrium was performed from the 4-chamber view. Strain measurements were LA peak contractile, reservoir and conduit strain and strain rates. In the frequent PAC vs control group, PACs were more frequent (1959 ± 3796 vs 28 ± 25/24 hours, P < .0001). LA peak contractile strain was reduced in the group with frequent PACs vs controls (-7.85 ± 4.12% vs -9.33 ± 4.45%, P = .006). LA peak late negative contractile strain rate was less negative in the frequent PAC vs control group (-0.63 ± 0.27 s -1 vs -0.69 ± 0.32 s -1 , P = .051). LA reservoir and conduit strain and strain rates did not differ. LA volume index (LAVI) was larger in the frequent PAC vs control group (26.6 ± 7.8 vs 24.6 ± 8.8 mL/m 2 , P < .05). Frequent PACs were an independent predictor of reduced LA peak contractile strain and reduced LA peak late negative contractile strain rate. Patients with frequent PACs have reduced LA peak contractile strain and strain rates and larger LAVI compared to controls. Frequent PACs are an independent predictor of reduced LA peak contractile strain and strain rate. These findings support the hypothesis that frequent PACs impair LA contractile function and promote adverse LA remodeling. © 2018 Wiley Periodicals, Inc.

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

PubMed Central

Long, Hannah K.; King, Hamish W.; Patient, Roger K.; Odom, Duncan T.; Klose, Robert J.

2016-01-01

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. PMID:27084945

Modeling lateral circulation and its influence on the along-channel flow in a branched estuary

NASA Astrophysics Data System (ADS)

Zhu, Lei; He, Qing; Shen, Jian

2018-02-01

A numerical modeling study of the influence of the lateral flow on the estuarine exchange flow was conducted in the north passage of the Changjiang estuary. The lateral flows show substantial variabilities within a flood-ebb tidal cycle. The strong lateral flow occurring during flood tide is caused primarily by the unique cross-shoal flow that induces a strong northward (looking upstream) barotropic force near the surface and advects saltier water toward the northern part of the channel, resulting in a southward baroclinic force caused by the lateral density gradient. Thus, a two-layer structure of lateral flows is produced during the flood tide. The lateral flows are vigorous near the flood slack and the magnitude can exceed that of the along-channel tidal flow during that period. The strong vertical shear of the lateral flows and the salinity gradient in lateral direction generate lateral tidal straining, which are out of phase with the along-channel tidal straining. Consequently, stratification is enhanced at the early stage of the ebb tide. In contrast, strong along-channel straining is apparent during the late ebb tide. The vertical mixing disrupts the vertical density gradient, thus suppressing stratification. The impact of lateral straining on stratification during spring tide is more pronounced than that of along-channel straining during late flood and early ebb tides. The momentum balance along the estuary suggests that lateral flow can augment the residual exchange flow. The advection of lateral flows brings low-energy water from the shoal to the deep channel during the flood tide, whereas the energetic water is moved to the shoal via lateral advection during the ebb tide. The impact of lateral flow on estuarine circulation of this multiple-channel estuary is different from single-channel estuary. A model simulation by blocking the cross-shoal flow shows that the magnitudes of lateral flows and tidal straining are reduced. Moreover, the reduced lateral tidal straining results in a decrease in vertical stratification from the late flood to early ebb tides during the spring tide. By contrast, the along-channel tidal straining becomes dominant. The model results illustrate the important dynamic linkage between lateral flows and estuarine dynamics in the Changjiang estuary.

Clonal relationship among Vibrio cholerae O1 El Tor strains isolated in Somalia.

PubMed

Scrascia, Maria; Pugliese, Nicola; Maimone, Francesco; Mohamud, Kadigia A; Grimont, Patrick A D; Materu, Sadiki F; Pazzani, Carlo

2009-03-01

One hundred and three Vibrio cholerae O1 strains, selected to represent the cholera outbreaks which occurred in Somalia in 1998-1999, were characterized by random amplified polymorphic DNA patterns, ribotyping, and antimicrobial susceptibility. All strains showed a unique amplified DNA pattern and 2 closely related ribotypes (B5a and B8a), among which B5a was the more frequently identified. Ninety-one strains were resistant to ampicillin, chloramphenicol, spectinomycin, streptomycin, sulfamethoxazole, and trimethoprim, conferred, except for spectinomycin, by a conjugative plasmid IncC. These findings indicated that the group of strains active in Somalia in the late 1990s had a clonal origin.

Survey, Culture, and Genome Analysis of Ocular Chlamydia trachomatis in Tibetan Boarding Primary Schools in Qinghai Province, China

PubMed Central

Feng, Le; Lu, Xinxin; Yu, Yonghui; Wang, Tao; Luo, Shengdong; Sun, Zhihui; Duan, Qing; Wang, Ningli; Song, Lihua

2017-01-01

Trachoma, the leading infectious cause of blindness worldwide, is an ancient human disease. Its existence in China can be traced back to as early as the twenty-seventh century BC. In modern China, the overall prevalence of trachoma has dramatically reduced, but trachoma is still endemic in many areas of the country. Here, we report that 26 (8%) of 322 students from two rural boarding schools of Qinghai province, west China, were identified as having ocular C. trachomatis infection; and 15 ocular C. trachomatis strains were isolated from these trachoma patients. Chlamydiae in 37 clinical samples were genotyped as type B based on ompA gene analyses. Three ompA variants with one or two in-between SNP differences in the second or fourth variable domain were found. C. trachomatis strains QH111L and QH111R were from the same patient's left and right conjunctival swabs, respectively, but their ompA genes have a non-synonymous base difference in the second variable domain. Moreover, this SNP only exists in this single sample, suggesting QH111L is a newly emerged ompA variant. Interestingly, chromosomal phylogeny analysis found QH111L clusters between a branch of two type B strains and a branch of both A and C strains, but is significantly divergent from both branches. Comparative chromosome analysis found that compared to sequences of reference B/TZ1A828/OT strain, 12 of 22 QH111L's chromosomal genes exhibiting more than nine SNPs have the best homology with reciprocal genes of UGT strains while 9 of 22 genes are closest to those of type C strains. Consistent with findings of UGT-type genetic features in the chromosome, the QH111L plasmid appears to be intermediate between UGT and classical ocular plasmids due to the existence of UGT-type SNPs in the QH111L plasmid. Moreover, the QH111L strain has a unique evolutionarily older cytotoxin region compared to cytotoxin regions of other C. trachomatis strains. The genome analyses suggest that the QH111L strain is derived from recombinations between UGT and classical ocular ancestors. This is the first study of culture and characterization of ocular C. trachomatis in Qinghai Tibetan areas. PMID:28119858

Unleashing Natural Competence in Lactococcus lactis by Induction of the Competence Regulator ComX

PubMed Central

Mulder, Joyce; Wels, Michiel; Kuipers, Oscar P.; Bron, Peter A.

2017-01-01

ABSTRACT In biotechnological workhorses like Streptococcus thermophilus and Bacillus subtilis, natural competence can be induced, which facilitates genetic manipulation of these microbes. However, in strains of the important dairy starter Lactococcus lactis, natural competence has not been established to date. However, in silico analysis of the complete genome sequences of 43 L. lactis strains revealed complete late competence gene sets in 2 L. lactis subsp. cremoris strains (KW2 and KW10) and at least 10 L. lactis subsp. lactis strains, including the model strain IL1403 and the plant-derived strain KF147. The remainder of the strains, including all dairy isolates, displayed genomic decay in one or more of the late competence genes. Nisin-controlled expression of the competence regulator comX in L. lactis subsp. lactis KF147 resulted in the induction of expression of the canonical competence regulon and elicited a state of natural competence in this strain. In contrast, comX expression in L. lactis NZ9000, which was predicted to encode an incomplete competence gene set, failed to induce natural competence. Moreover, mutagenesis of the comEA-EC operon in strain KF147 abolished the comX-driven natural competence, underlining the involvement of the competence machinery. Finally, introduction of nisin-inducible comX expression into nisRK-harboring derivatives of strains IL1403 and KW2 allowed the induction of natural competence in these strains also, expanding this phenotype to other L. lactis strains of both subspecies. IMPORTANCE Specific bacterial species are able to enter a state of natural competence in which DNA is taken up from the environment, allowing the introduction of novel traits. Strains of the species Lactococcus lactis are very important starter cultures for the fermentation of milk in the cheese production process, where these bacteria contribute to the flavor and texture of the end product. The activation of natural competence in this industrially relevant organism can accelerate research aiming to understand industrially relevant traits of these bacteria and can facilitate engineering strategies to harness the natural biodiversity of the species in optimized starter strains. PMID:28778888

Development of regional liquefaction-induced deformation hazard maps

USGS Publications Warehouse

Rosinski, A.; Knudsen, K.-L.; Wu, J.; Seed, R.B.; Real, C.R.; ,

2004-01-01

This paper describes part of a project to assess the feasibility of producing regional (1:24,000-scale) liquefaction hazard maps that are based-on potential liquefaction-induced deformation. The study area is the central Santa Clara Valley, at the south end of San Francisco Bay in Central California. The information collected and used includes: a) detailed Quaternary geological mapping, b) over 650 geotechnical borings, c) probabilistic earthquake shaking information, and d) ground-water levels. Predictions of strain can be made using either empirical formulations or numerical simulations. In this project lateral spread displacements are estimated and new empirical relations to estimate future volumetric and shear strain are used. Geotechnical boring data to are used to: (a) develop isopach maps showing the thickness of sediment thatis likely to liquefy and deform under earthquake shaking; and (b) assess the variability in engineering properties within and between geologic map units. Preliminary results reveal that late Holocene deposits are likely to experience the greatest liquefaction-induced strains, while Holocene and late Pleistocene deposits are likely to experience significantly less horizontal and vertical strain in future earthquakes. Development of maps based on these analyses is feasible.

Characterization of Clostridium perfringens TpeL Toxin Gene Carriage, Production, Cytotoxic Contributions, and Trypsin Sensitivity

PubMed Central

Chen, Jianming

2015-01-01

Large clostridial toxins (LCTs) are produced by at least four pathogenic clostridial species, and several LCTs are proven pivotal virulence factors for both human and veterinary diseases. TpeL is a recently identified LCT produced by Clostridium perfringens that has received relatively limited study. In response, the current study surveyed carriage of the tpeL gene among different C. perfringens strains, detecting this toxin gene in some type A, B, and C strains but not in any type D or E strains. This study also determined that all tested strains maximally produce, and extracellularly release, TpeL at the late-log or early-stationary growth stage during in vitro culture, which is different from the maximal late-stationary-phase production reported previously for other LCTs and for TpeL production by C. perfringens strain JIR12688. In addition, the present study found that TpeL levels in culture supernatants can be repressed by either glucose or sucrose. It was also shown that, at natural production levels, TpeL is a significant contributor to the cytotoxic activity of supernatants from cultures of tpeL-positive strain CN3685. Lastly, this study identified TpeL, which presumably is produced in the intestines during diseases caused by TpeL-positive type B and C strains, as a toxin whose cytotoxicity decreases after treatment with trypsin; this finding may have pathophysiologic relevance by suggesting that, like beta toxin, TpeL contributes to type B and C infections in hosts with decreased trypsin levels due to disease, diet, or age. PMID:25824828

Landscape-level model to predict spawning habitat for Lower Columbia River fall Chinook salmon (Oncorhynchus tshawytscha)

Treesearch

D. Shallin Busch; Mindi Sheer; Kelly Burnett; Paul McElhany; Tom Cooney

2013-01-01

We developed an intrinsic potential (IP) model to estimate the potential of streams to provide habitat for spawning fall Chinook salmon (Oncorhynchus tshawytscha) in the Lower Columbia River evolutionarily significant unit. This evolutionarily significant unit is a threatened species, and both fish abundance and distribution are reduced from...

Stochastic stability in three-player games.

PubMed

Kamiński, Dominik; Miekisz, Jacek; Zaborowski, Marcin

2005-11-01

Animal behavior and evolution can often be described by game-theoretic models. Although in many situations the number of players is very large, their strategic interactions are usually decomposed into a sum of two-player games. Only recently were evolutionarily stable strategies defined for multi-player games and their properties analyzed [Broom, M., Cannings, C., Vickers, G.T., 1997. Multi-player matrix games. Bull. Math. Biol. 59, 931-952]. Here we study the long-run behavior of stochastic dynamics of populations of randomly matched individuals playing symmetric three-player games. We analyze the stochastic stability of equilibria in games with multiple evolutionarily stable strategies. We also show that, in some games, a population may not evolve in the long run to an evolutionarily stable equilibrium.

Wolbachia as a bacteriocyte-associated nutritional mutualist

PubMed Central

Hosokawa, Takahiro; Koga, Ryuichi; Kikuchi, Yoshitomo; Meng, Xian-Ying; Fukatsu, Takema

2009-01-01

Many insects are dependent on bacterial symbionts that provide essential nutrients (ex. aphid–Buchnera and tsetse–Wiglesworthia associations), wherein the symbionts are harbored in specific cells called bacteriocytes that constitute a symbiotic organ bacteriome. Facultative and parasitic bacterial symbionts like Wolbachia have been regarded as evolutionarily distinct from such obligate nutritional mutualists. However, we discovered that, in the bedbug Cimex lectularius, Wolbachia resides in a bacteriome and appears to be an obligate nutritional mutualist. Two bacterial symbionts, a Wolbachia strain and an unnamed γ-proteobacterium, were identified from different strains of the bedbug. The Wolbachia symbiont was detected from all of the insects examined whereas the γ-proteobacterium was found in a part of them. The Wolbachia symbiont was specifically localized in the bacteriomes and vertically transmitted via the somatic stem cell niche of germalia to oocytes, infecting the incipient symbiotic organ at an early stage of the embryogenesis. Elimination of the Wolbachia symbiont resulted in retarded growth and sterility of the host insect. These deficiencies were rescued by oral supplementation of B vitamins, confirming the essential nutritional role of the symbiont for the host. The estimated genome size of the Wolbachia symbiont was around 1.3 Mb, which was almost equivalent to the genome sizes of parasitic Wolbachia strains of other insects. These results indicate that bacteriocyte-associated nutritional mutualism can evolve from facultative and prevalent microbial associates like Wolbachia, highlighting a previously unknown aspect of the parasitism-mutualism evolutionary continuum. PMID:20080750

Right ventricular diastolic performance in children with pulmonary arterial hypertension associated with congenital heart disease: correlation of echocardiographic parameters with invasive reference standards by high-fidelity micromanometer catheter.

PubMed

Okumura, Kenichi; Slorach, Cameron; Mroczek, Dariusz; Dragulescu, Andreea; Mertens, Luc; Redington, Andrew N; Friedberg, Mark K

2014-05-01

Right ventricular diastolic dysfunction influences outcomes in pulmonary arterial hypertension (PAH), but echocardiographic parameters have not been investigated in relation to invasive reference standards in pediatric PAH. We investigated echocardiographic parameters of right ventricular diastolic function in children with PAH in relation to simultaneously measured invasive reference measures. We prospectively recruited children undergoing a clinically indicated cardiac catheterization for evaluation of PAH and pulmonary vasoreactivity testing. Echocardiography was performed simultaneously with invasive reference measurements by high-fidelity micromanometer catheter. For analysis, patients were divided into shunt and nonshunt groups. Sixteen children were studied. In the group as a whole, significant correlations were found among τ and tricuspid deceleration time, E', E/E', TimeE-E', A wave velocity, and global early and late diastolic strain rate. dp/dt minimum correlated significantly with late diastolic tricuspid annular velocity (A'), tissue Doppler imaging-derived systolic:diastolic duration ratio, and global late diastolic strain rate. End-diastolic pressure correlated significantly with tissue Doppler imaging-derived systolic:diastolic duration ratio. On multivariate analysis, tricuspid deceleration time, TimeE-E', and global early diastolic strain rate were independent predictors of τ, whereas tissue Doppler imaging-derived systolic:diastolic duration ratio was an independent predictor of dp/dt minimum. In general, correlations between echocardiographic and invasive parameters were better in the shunt group than in the nonshunt group. Echocardiography correlates with invasive reference measures of right ventricular diastolic function in children with PAH, although it does not differentiate between early versus late diastolic abnormalities. Newer echocardiographic techniques may have added value to assess right ventricular diastolic dysfunction in this population. © 2014 American Heart Association, Inc.

Role of Caenorhabditis elegans AKT-1/2 and SGK-1 in Manganese Toxicity.

PubMed

Peres, Tanara V; Arantes, Leticia P; Miah, Mahfuzur R; Bornhorst, Julia; Schwerdtle, Tanja; Bowman, Aaron B; Leal, Rodrigo B; Aschner, Michael

2018-06-07

Excessive levels of the essential metal manganese (Mn) may cause a syndrome similar to Parkinson's disease. The model organism Caenorhabditis elegans mimics some of Mn effects in mammals, including dopaminergic neurodegeneration, oxidative stress, and increased levels of AKT. The evolutionarily conserved insulin/insulin-like growth factor-1 signaling pathway (IIS) modulates worm longevity, metabolism, and antioxidant responses by antagonizing the transcription factors DAF-16/FOXO and SKN-1/Nrf-2. AKT-1, AKT-2, and SGK-1 act upstream of these transcription factors. To study the role of these proteins in C. elegans response to Mn intoxication, wild-type N2 and loss-of-function mutants were exposed to Mn (2.5 to 100 mM) for 1 h at the L1 larval stage. Strains with loss-of-function in akt-1, akt-2, and sgk-1 had higher resistance to Mn compared to N2 in the survival test. All strains tested accumulated Mn similarly, as shown by ICP-MS. DAF-16 nuclear translocation was observed by fluorescence microscopy in WT and loss-of-function strains exposed to Mn. qRT-PCR data indicate increased expression of γ-glutamyl cysteine synthetase (GCS-1) antioxidant enzyme in akt-1 mutants. The expression of sod-3 (superoxide dismutase homologue) was increased in the akt-1 mutant worms, independent of Mn treatment. However, dopaminergic neurons degenerated even in the more resistant strains. Dopaminergic function was evaluated with the basal slowing response behavioral test and dopaminergic neuron integrity was evaluated using worms expressing green fluorescent protein (GFP) under the dopamine transporter (DAT-1) promoter. These results suggest that AKT-1/2 and SGK-1 play a role in C. elegans response to Mn intoxication. However, tissue-specific responses may occur in dopaminergic neurons, contributing to degeneration.

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Casjens S. R.; Dunn J.; Mongodin, E. F.

2012-03-14

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so aremore » informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33-40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi {approx}900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short {le}20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant.« less

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

PubMed Central

Casjens, Sherwood R.; Mongodin, Emmanuel F.; Qiu, Wei-Gang; Luft, Benjamin J.; Schutzer, Steven E.; Gilcrease, Eddie B.; Huang, Wai Mun; Vujadinovic, Marija; Aron, John K.; Vargas, Levy C.; Freeman, Sam; Radune, Diana; Weidman, Janice F.; Dimitrov, George I.; Khouri, Hoda M.; Sosa, Julia E.; Halpin, Rebecca A.; Dunn, John J.; Fraser, Claire M.

2012-01-01

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33–40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi ∼900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short ≤20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant. PMID:22432010

Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection

PubMed Central

Chen, Swaine L.; Wu, Meng; Henderson, Jeffrey P.; Hooton, Thomas M.; Hibbing, Michael E.; Hultgren, Scott J.; Gordon, Jeffrey I.

2013-01-01

Urinary tract infections (UTIs) are common in women and recurrence is a major clinical problem. Most UTIs are caused by uropathogenic Escherichia coli (UPEC). UPEC are generally thought to migrate from the gut to the bladder to cause UTI. UPEC strains form specialized intracellular bacterial communities (IBCs) in the bladder urothelium as part of a pathogenic mechanism to establish a foothold during acute stages of infection. Evolutionarily, such a specific adaptation to the bladder environment would be predicted to result in decreased fitness in other habitats, such as the gut. To examine this concept, we characterized 45 E. coli strains isolated from the feces and urine of four otherwise healthy women with recurrent UTIs. Multi-locus sequence typing revealed that two of the patients maintained a clonal population in both of these body habitats throughout their recurrent UTIs, whereas the other two manifested a wholesale shift in the dominant UPEC strain colonizing their urinary tract and gut between UTIs. These results were confirmed when we subjected 26 isolates from two patients, one representing the persistent clonal pattern and the other representing the dynamic population shift, to whole genome sequencing. In vivo competition studies conducted in mouse models of bladder and gut colonization, using isolates taken from one of the patients with a wholesale population shift, and a newly developed SNP-based method for quantifying strains, revealed that the strain that dominated in her last UTI episode had increased fitness in both body habitats relative to the one that dominated in the preceding episodes. Furthermore, increased fitness was correlated with differences in the strains’ gene repertoires and their in vitro carbohydrate and amino acid utilization profiles. Thus, UPEC appear capable of persisting in both the gut and urinary tract without a fitness tradeoff. Determination of all of the potential reservoirs for UPEC strains that cause recurrent UTI will require additional longitudinal studies of the type described in this report, with sampling of multiple body habitats during and between episodes. PMID:23658245

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved.

PubMed

Long, Hannah K; King, Hamish W; Patient, Roger K; Odom, Duncan T; Klose, Robert J

2016-08-19

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil

PubMed Central

Battenberg, Kai; Wren, Jannah A.; Hillman, Janell; Edwards, Joseph; Huang, Liujing

2016-01-01

ABSTRACT The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia, cluster I, II, and III strains are capable of forming effective nitrogen-fixing symbiotic associations, while cluster IV strains generally do not. Cluster II Frankia strains have rarely been detected in soil devoid of host plants, unlike cluster I or III strains, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the cluster II Frankia strain distribution in rhizosphere soil in three locations in northern California. The presence/absence of cluster II Frankia strains at a given site correlated significantly with the presence/absence of host plants on the site, as determined by glutamine synthetase (glnA) gene sequence analysis, and by microbiome analysis (16S rRNA gene) of a subset of host/nonhost rhizosphere soils. However, the distribution of cluster II Frankia strains was not significantly affected by other potential determinants such as host-plant species, geographical location, climate, soil pH, or soil type. Rhizosphere soil microbiome analysis showed that cluster II Frankia strains occupied only a minute fraction of the microbiome even in the host-plant-present site and further revealed no statistically significant difference in the α-diversity or in the microbiome composition between the host-plant-present or -absent sites. Taken together, these data suggest that host plants provide a factor that is specific for cluster II Frankia strains, not a general growth-promoting factor. Further, the factor accumulates or is transported at the site level, i.e., beyond the host rhizosphere. IMPORTANCE Biological nitrogen fixation is a bacterial process that accounts for a major fraction of net new nitrogen input in terrestrial ecosystems. Transfer of fixed nitrogen to plant biomass is especially efficient via root nodule symbioses, which represent evolutionarily and ecologically specialized mutualistic associations. Frankia spp. (Actinobacteria), especially cluster II Frankia spp., have an extremely broad host range, yet comparatively little is known about the soil ecology of these organisms in relation to the host plants and their rhizosphere microbiomes. This study reveals a strong influence of the host plant on soil distribution of cluster II Frankia spp. PMID:27795313

Delayed Disease Progression in Cynomolgus Macaques Infected with Ebola Virus Makona Strain.

PubMed

Marzi, Andrea; Feldmann, Friederike; Hanley, Patrick W; Scott, Dana P; Günther, Stephan; Feldmann, Heinz

2015-10-01

In late 2013, the largest documented outbreak of Ebola hemorrhagic fever started in Guinea and has since spread to neighboring countries, resulting in almost 27,000 cases and >11,000 deaths in humans. In March 2014, Ebola virus (EBOV) was identified as the causative agent. This study compares the pathogenesis of a new EBOV strain, Makona, which was isolated in Guinea in 2014 with the prototype strain from the 1976 EBOV outbreak in the former Zaire. Both strains cause lethal disease in cynomolgus macaques with similar pathologic changes and hallmark features of Ebola hemorrhagic fever. However, disease progression was delayed in EBOV-Makona-infected animals, suggesting decreased rather than increased virulence of this most recent EBOV strain.

Involvement of Clostridium botulinum ATCC 3502 Sigma Factor K in Early-Stage Sporulation

PubMed Central

Kirk, David G.; Dahlsten, Elias; Zhang, Zhen; Korkeala, Hannu

2012-01-01

A key survival mechanism of Clostridium botulinum, the notorious neurotoxic food pathogen, is the ability to form heat-resistant spores. While the genetic mechanisms of sporulation are well understood in the model organism Bacillus subtilis, nothing is known about these mechanisms in C. botulinum. Using the ClosTron gene-knockout tool, sigK, encoding late-stage (stage IV) sporulation sigma factor K in B. subtilis, was disrupted in C. botulinum ATCC 3502 to produce two different mutants with distinct insertion sites and orientations. Both mutants were unable to form spores, and their elongated cell morphology suggested that the sporulation pathway was blocked at an early stage. In contrast, sigK-complemented mutants sporulated successfully. Quantitative real-time PCR analysis of sigK in the parent strain revealed expression at the late log growth phase in the parent strain. Analysis of spo0A, encoding the sporulation master switch, in the sigK mutant and the parent showed significantly reduced relative levels of spo0A expression in the sigK mutant compared to the parent strain. Similarly, sigF showed significantly lower relative transcription levels in the sigK mutant than the parent strain, suggesting that the sporulation pathway was blocked in the sigK mutant at an early stage. We conclude that σK is essential for early-stage sporulation in C. botulinum ATCC 3502, rather than being involved in late-stage sporulation, as reported for the sporulation model organism B. subtilis. Understanding the sporulation mechanism of C. botulinum provides keys to control the public health risks that the spores of this dangerous pathogen cause through foods. PMID:22544236

Involvement of Clostridium botulinum ATCC 3502 sigma factor K in early-stage sporulation.

PubMed

Kirk, David G; Dahlsten, Elias; Zhang, Zhen; Korkeala, Hannu; Lindström, Miia

2012-07-01

A key survival mechanism of Clostridium botulinum, the notorious neurotoxic food pathogen, is the ability to form heat-resistant spores. While the genetic mechanisms of sporulation are well understood in the model organism Bacillus subtilis, nothing is known about these mechanisms in C. botulinum. Using the ClosTron gene-knockout tool, sigK, encoding late-stage (stage IV) sporulation sigma factor K in B. subtilis, was disrupted in C. botulinum ATCC 3502 to produce two different mutants with distinct insertion sites and orientations. Both mutants were unable to form spores, and their elongated cell morphology suggested that the sporulation pathway was blocked at an early stage. In contrast, sigK-complemented mutants sporulated successfully. Quantitative real-time PCR analysis of sigK in the parent strain revealed expression at the late log growth phase in the parent strain. Analysis of spo0A, encoding the sporulation master switch, in the sigK mutant and the parent showed significantly reduced relative levels of spo0A expression in the sigK mutant compared to the parent strain. Similarly, sigF showed significantly lower relative transcription levels in the sigK mutant than the parent strain, suggesting that the sporulation pathway was blocked in the sigK mutant at an early stage. We conclude that σ(K) is essential for early-stage sporulation in C. botulinum ATCC 3502, rather than being involved in late-stage sporulation, as reported for the sporulation model organism B. subtilis. Understanding the sporulation mechanism of C. botulinum provides keys to control the public health risks that the spores of this dangerous pathogen cause through foods.

Assessment of Late Quaternary strain partitioning in the Afar Triple Junction: Dobe and Hanle grabens, Ethiopia and Djibouti

NASA Astrophysics Data System (ADS)

Polun, S. G.; Stockman, M. B.; Hickcox, K.; Horrell, D.; Tesfaye, S.; Gomez, F. G.

2015-12-01

As the only subaerial exposure of a ridge - ridge - ridge triple junction, the Afar region of Ethiopia and Djibouti offers a rare opportunity to assess strain partitioning within this type of triple junction. Here, the plate boundaries do not link discretely, but rather the East African rift meets the Red Sea and Gulf of Aden rifts in a zone of diffuse normal faulting characterized by a lack of magmatic activity, referred to as the central Afar. An initial assessment of Late Quaternary strain partitioning is based on faulted landforms in the Dobe - Hanle graben system in Ethiopia and Djibouti. These two extensional basins are connected by an imbricated accommodation zone. Several fault scarps occur within terraces formed during the last highstand of Lake Dobe, around 5 ka - they provide a means of calibrating a numerical model of fault scarp degradation. Additional timing constraints will be provided by pending exposure ages. The spreading rates of both grabens are equivalent, however in Dobe graben, extension is partitioned 2:1 between northern, south dipping faults and the southern, north dipping fault. Extension in Hanle graben is primarily focused on the north dipping Hanle fault. On the north margin of Dobe graben, the boundary fault bifurcates, where the basin-bordering fault displays a significantly higher modeled uplift rate than the more distal fault, suggesting a basinward propagation of faulting. On the southern Dobe fault, surveyed fault scarps have ages ranging from 30 - 5 ka with uplift rates of 0.71, 0.47, and 0.68 mm/yr, suggesting no secular variation in slip rates from the late Plestocene through the Holocene. These rates are converted into horizontal stretching estimates, which are compared with regional strain estimated from velocities of relatively sparse GPS data.

A new giraffid (Mammalia, Ruminantia, Pecora) from the late Miocene of Spain, and the evolution of the sivathere-samothere lineage

PubMed Central

Morales, Jorge

2017-01-01

Giraffids include the only living giraffomorph ruminants and are diagnosed by the presence of bi-lobed canines and a special type of epiphyseal cranial appendages called ossicones. The family Giraffidae ranges from the latest early Miocene until today. However they are currently extant relics with only two living representatives, the African genera Okapia and Giraffa. Giraffids were much more diverse and widespread in the past, with more than 30 fossil species described. For the past decades a number of studies intended to resolve the phylogenetic relationships of the family, but due to the lack of really good cranial material no clear consensus was reached regarding the phylogenetic relationships amongst the different members of the group. The exceptionally complete remains of a new large giraffid from the late Miocene of Spain, Decennatherium rex sp. nov., allows us to improve and reassess giraffid systematics, offering a lot of new data, both anatomic and phylogenetic, on the large late Miocene giraffids of Eurasia. The results of our cladistic analysis show Decennatherium as a basal offshoot of a clade containing the gigantic samotheres and sivatheres, characterized by the presence of a Sivatherium-like ossicone-plan among other features. Decennatherium thus offers the most ancient evidence of this Sivatherium-plan and firmly establishes the early morphological patterns of evolution of a sivathere / samothere-clade that is defined as the less inclusive clade that contains Decennatherium and Sivatherium. Finally, this large group of four-ossiconed giraffids evolutionarily links Miocene Europe and Africa indicating vicariance / migration processes among the giraffid genetic pools separated by the Mediterranean Sea. PMID:29091914

Late Pliocene paleoeco­logic reconstructions based on ostracode assemblages from the Sagavanirktok and Gubik formations, Alaskan North Slope

USGS Publications Warehouse

Brouwers, Elisabeth M.

1994-01-01

Shallow-marine ostracode assemblages from upper Pliocene sediments of the upper part of the Sagavanirktok Formation and lower part of the Gubik Formation record the last warm period that occurred before the onset of significant cooling of the Arctic Ocean and the initiation of Northern Hemisphere continental glaciation. The informally named Colvillian and Bigbendian transgressions represent the oldest deposits of the Gubik Formation and are dated, based on various lines of evidence, between 2.48 and 3 Ma. Ostracode faunas from the lower part of the Gubik Formation indicate a cold-temperate to subfrigid marine climate with summer bottom temperatures 1-4 C warmer than today. Deposits of the upper part of the Sagavanirktok Formation at Manning Point and Barter Island are older than Colvillian sediments but are believed to be late Pliocene in age and contain an ostracode fauna that has many species in common with the lower part of the Gubik Formation. The Sagavanirktok ostracode faunas indicate a cold-temperature to subfrigid marine climate, similar to that inferred for the lower part of the Gubik Formation, with summer bottom temperatures 1-3 C warmer than today. The opening of Bering Strait at about 3 Ma altered Arctic Ocean assemblage composition as Pacific species migrated into the Arctic and North Atlantic oceans. The admixture of evolutionarily distinct faunas from the Atlantic and Pacific oceans identifies Colvillian (and younger) faunas and provides a convenient reference horizon in the Alaskan fossil record. The marine climatic deterioration that followed the Bigbendian appears to have been abrupt and is documented by biotic turnover, with large numbers of species extinctions and first appearances of new species. The change in species composition can be attributed to the cooling of the Arctic Ocean during the late Pliocene.

No strategy is evolutionarily stable in the repeated prisoner's dilemma.

PubMed

Lorberbaum, J

1994-05-21

Following the influential work of Axelrod, the repeated Prisoner's Dilemma game has become the theoretical gold standard for understanding the evolution of co-operative behavior among unrelated individuals. Using the game, several authors have found that a reciprocal strategy known as Tit for Tat (TFT) has done quite well in a wide range of environments. TFT strategists start out co-operating and then do what the other player did on the previous move. Despite the success of TFT and similar strategies in experimental studies of the game, Boyd & Lorberbaum (1987, Nature, Lond. 327, 58) have shown that no pure strategy, including TFT, is evolutionarily stable in the sense that each can be invaded by the joint effect of two invading strategies when long-term interaction occurs in the repeated game and future moves are discounted. Farrell & Ware (1989, Theor. Popul. Biol. 36, 161) have since extended these results to include finite mixes of pure strategies as well. Here, it is proven that no strategy is evolutionarily stable when long-term relationships are maintained in the repeated Prisoner's Dilemma and future moves are discounted. Namely, it is shown each completely probabilistic strategy (i.e. one that both co-operates and defects with positive probability after every sequence of behavior) may be invaded by a single deviant strategy. This completes the proof started by Boyd and Lorberbaum and extended by Farrell and Ware. This paper goes on to prove that no reactive strategy with a memory restricted to the opponent's preceding move is evolutionarily stable when there is no discounting of future moves. This is true despite the success of a more forgiving variant of TFT called GTFT in a recent tournament among reactive strategies conducted by Nowak & Sigmund (1992, Nature 355, 250) where future moves were not discounted. GTFT, for example, may be invaded by a pair of reactive mutants. Since no strategy is evolutionarily stable when future moves are discounted in the repeated game, the restriction of strategy types to those actually maintained by mutation and phenotypic and environmental variability in natural populations may be the key to understanding the evolution of co-operation. However, the result presented here that the somewhat realistic reactive strategies are also not evolutionarily stable at least in the non-discounted game suggests something else may be going on. For one, the proof that no reactive strategy is evolutionarily stable ironically shows the robustness of TFT-like strategies.(ABSTRACT TRUNCATED AT 400 WORDS)

Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa).

PubMed

Rooney, Alejandro P; Dunlap, Christopher A; Flor-Weiler, Lina B

2016-09-01

Strain NRRL B-41902T and three closely related strains were isolated from iceberg lettuce. The strain was found to consist of strictly aerobic, Gram-stain-negative rods that formed cocci in late stationary phase. 16S rRNA gene sequence analysis showed that strain NRRL B-41902T was most closely related to species within the genera Acinetobacter, and that a grouping of it and the three other closely related strains was most closely related to the type strain of Acinetobacter pittii, which was also confirmed through a phylogenomic analysis. Moreover, in silico DNA-DNA hybridization analysis revealed a substantial amount of genomic divergence (39.1 %) between strain NRRL B-41902T and the type strain of A. pittii, which is expected if the strains represent distinct species. Further phenotypic analysis revealed that strain NRRL B-41902T was able to utilize a combination of l-serine, citraconic acid and citramalic acid, which differentiated it from other, closely related Acinetobacter species. Therefore, strain NRRL B-41902T (=CCUG 68785T) is proposed as the type strain of a novel species, Acinetobacter lactucae sp. nov.

Strains and stressors: an analysis of touchscreen learning in genetically diverse mouse strains.

PubMed

Graybeal, Carolyn; Bachu, Munisa; Mozhui, Khyobeni; Saksida, Lisa M; Bussey, Timothy J; Sagalyn, Erica; Williams, Robert W; Holmes, Andrew

2014-01-01

Touchscreen-based systems are growing in popularity as a tractable, translational approach for studying learning and cognition in rodents. However, while mouse strains are well known to differ in learning across various settings, performance variation between strains in touchscreen learning has not been well described. The selection of appropriate genetic strains and backgrounds is critical to the design of touchscreen-based studies and provides a basis for elucidating genetic factors moderating behavior. Here we provide a quantitative foundation for visual discrimination and reversal learning using touchscreen assays across a total of 35 genotypes. We found significant differences in operant performance and learning, including faster reversal learning in DBA/2J compared to C57BL/6J mice. We then assessed DBA/2J and C57BL/6J for differential sensitivity to an environmental insult by testing for alterations in reversal learning following exposure to repeated swim stress. Stress facilitated reversal learning (selectively during the late stage of reversal) in C57BL/6J, but did not affect learning in DBA/2J. To dissect genetic factors underlying these differences, we phenotyped a family of 27 BXD strains generated by crossing C57BL/6J and DBA/2J. There was marked variation in discrimination, reversal and extinction learning across the BXD strains, suggesting this task may be useful for identifying underlying genetic differences. Moreover, different measures of touchscreen learning were only modestly correlated in the BXD strains, indicating that these processes are comparatively independent at both genetic and phenotypic levels. Finally, we examined the behavioral structure of learning via principal component analysis of the current data, plus an archival dataset, totaling 765 mice. This revealed 5 independent factors suggestive of "reversal learning," "motivation-related late reversal learning," "discrimination learning," "speed to respond," and "motivation during discrimination." Together, these findings provide a valuable reference to inform the choice of strains and genetic backgrounds in future studies using touchscreen-based tasks.

Speckle-Tracking Layer-Specific Analysis of Myocardial Deformation and Evaluation of Scar Transmurality in Chronic Ischemic Heart Disease.

PubMed

Tarascio, Michela; Leo, Laura Anna; Klersy, Catherine; Murzilli, Romina; Moccetti, Tiziano; Faletra, Francesco Fulvio

2017-07-01

Identification of the extent of scar transmurality in chronic ischemic heart disease is important because it correlates with viability. The aim of this retrospective study was to evaluate whether layer-specific two-dimensional speckle-tracking echocardiography allows distinction of scar presence and transmurality. A total of 70 subjects, 49 with chronic ischemic cardiomyopathy and 21 healthy subjects, underwent two-dimensional speckle-tracking echocardiography and late gadolinium-enhanced cardiac magnetic resonance. Scar extent was determined as the relative amount of hyperenhancement using late gadolinium-enhanced cardiac magnetic resonance in an 18-segment model (0% hyperenhancement = normal; 1%-50% = subendocardial scar; 51%-100% = transmural scar). In the same 18-segment model, peak systolic circumferential strain and longitudinal strain were calculated separately for the endocardial and epicardial layers as well as the full-wall myocardial thickness. All strain parameters showed cutoff values (area under the curve > 0.69) that allowed the discrimination of normal versus scar segments but not of transmural versus subendocardial scars. This was true for all strain parameters analyzed, without differences in efficacy between longitudinal and circumferential strain and subendocardial, subepicardial, and full-wall-thickness strain values. Circumferential and longitudinal strain in normal segments showed transmural and basoapical gradients (greatest values at the subendocardial layer and apex). In segments with scar, transmural gradient was maintained, whereas basoapical gradient was lost because the reduction of strain values in the presence of the scar was greater at the apex. The two-dimensional speckle-tracking echocardiographic values distinguish scar presence but not transmurality; thus, they are not useful predictors of scar segment viability. It remains unclear why there is a greater strain value reduction in the presence of a scar at the apical level. Copyright © 2017 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Virulent strain of African swine fever virus eclipses its attenuated derivative after challenge.

PubMed

Titov, Ilya; Burmakina, Galina; Morgunov, Yuriy; Morgunov, Sergey; Koltsov, Andrey; Malogolovkin, Alexander; Kolbasov, Denis

2017-10-01

African swine fever (ASF) is one of the most devastating diseases affecting the swine industry worldwide. No effective vaccine is currently available for disease prevention and control. Although live attenuated vaccines (LAV) have demonstrated great potential for immunizing against homologous strains of African swine fever virus (ASFV), adverse reactions from LAV remain a concern. Here, by using a homologous ASFV Congo strain system, we show passage-attenuated Congo LAV to induce an efficient protective immune response against challenge with the virulent parental Congo strain. Notably, only the parental challenge Congo strain was identified in blood and organs of recovered pigs through B602L gene PCR, long-range PCR, nucleotide sequencing and virus isolation. Thus, despite the great protective potential of homologous attenuated ASFV strain, the challenge Congo strain can persist for weeks in recovered pigs and a recrudescence of virulent virus at late time post-challenge may occur.

Adaptation of A-to-I RNA editing in Drosophila

PubMed Central

Zhang, Hong

2017-01-01

Adenosine-to-inosine (A-to-I) editing is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach. However, it is challenging to provide evidences to support this hypothesis at the whole editome level. In this study, we systematically characterized 2,114 A-to-I RNA editing sites in female and male brains of D. melanogaster, and nearly half of these sites had events evolutionarily conserved across Drosophila species. We detected strong signatures of positive selection on the nonsynonymous editing sites in Drosophila brains, and the beneficial editing sites were significantly enriched in genes related to chemical and electrical neurotransmission. The signal of adaptation was even more pronounced for the editing sites located in X chromosome or for those commonly observed across Drosophila species. We identified a set of gene candidates (termed “PSEB” genes) that had nonsynonymous editing events favored by natural selection. We presented evidence that editing preferentially increased mutation sequence space of evolutionarily conserved genes, which supported the adaptive evolution hypothesis of editing. We found prevalent nonsynonymous editing sites that were favored by natural selection in female and male adults from five strains of D. melanogaster. We showed that temperature played a more important role than gender effect in shaping the editing levels, although the effect of temperature is relatively weaker compared to that of species effect. We also explored the relevant factors that shape the selective patterns of the global editomes. Altogether we demonstrated that abundant nonsynonymous editing sites in Drosophila brains were adaptive and maintained by natural selection during evolution. Our results shed new light on the evolutionary principles and functional consequences of RNA editing. PMID:28282384

Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses

PubMed Central

Silva, Fernanda D.F.; Gregori, F.; McDonald, Sarah M.

2016-01-01

Group A rotaviruses (RVAs) are 11-segmented, double-stranded RNA viruses and important causes of gastroenteritis in the young of many animal species. Previous studies have suggested that human Wa-like RVAs share a close evolutionary relationship with porcine RVAs. Specifically, the VP1-VP3 and NSP2-5/6 genes of these viruses are usually classified as genotype 1 with >81% nucleotide sequence identity. Yet, it remains unknown whether the genotype 1 genes and proteins of human Wa-like strains are distinguishable from those of porcine strains. To investigate this, we performed comprehensive bioinformatic analyses using all known genotype 1 gene sequences. The RVAs analyzed represent wildtype strains isolated from humans or pigs at various geographical locations during the years of 2004–2013, including 11 newly-sequenced porcine RVAs from Brazil. We also analyzed archival strains that were isolated during the years of 1977–1992 as well as atypical strains involved in inter-species transmission between humans and pigs. We found that, in general, the genotype 1 genes of typical modern human Wa-like RVAs clustered together in phylogenetic trees and were separate from those of typical modern porcine RVAs. The only exception was for the NSP5/6 gene, which showed no host-specific phylogenetic clustering. Using amino acid sequence alignments, we identified 34 positions that differentiated the VP1-VP3, NSP2, and NSP3 genotype 1 proteins of typical modern human Wa-like RVAs versus typical modern porcine RVAs and documented how these positions vary in the archival/unusual isolates. No host-specific amino acid positions were identified for NSP4, NSP5, or NSP6. Altogether, the results of this study support the notion that human Wa-like RVAs and porcine RVAs are evolutionarily related, but indicate that some of their genotype 1 genes and proteins have diverged over time possibly as a reflection of sequestered replication and protein co-adaptation in their respective hosts. PMID:27180895

A new long-necked ‘sauropod-mimic’ stegosaur and the evolution of the plated dinosaurs

PubMed Central

Mateus, Octávio; Maidment, Susannah C.R.; Christiansen, Nicolai A.

2009-01-01

Stegosaurian dinosaurs have a quadrupedal stance, short forelimbs, short necks, and are generally considered to be low browsers. A new stegosaur, Miragaia longicollum gen. et sp. nov., from the Late Jurassic of Portugal, has a neck comprising at least 17 cervical vertebrae. This is eight additional cervical vertebrae when compared with the ancestral condition seen in basal ornithischians such as Scutellosaurus. Miragaia has a higher cervical count than most of the iconically long-necked sauropod dinosaurs. Long neck length has been achieved by ‘cervicalization’ of anterior dorsal vertebrae and probable lengthening of centra. All these anatomical features are evolutionarily convergent with those exhibited in the necks of sauropod dinosaurs. Miragaia longicollum is based upon a partial articulated skeleton, and includes the only known cranial remains from any European stegosaur. A well-resolved phylogeny supports a new clade that unites Miragaia and Dacentrurus as the sister group to Stegosaurus; this new topology challenges the common view of Dacentrurus as a basal stegosaur. PMID:19324778

Population Distribution Analyses Reveal a Hierarchy of Molecular Players Underlying Parallel Endocytic Pathways

PubMed Central

Gupta, Gagan D.; Howes, Mark T.; Chandran, Ruma; Das, Anupam; Menon, Sindhu; Parton, Robert G.; Sowdhamini, R.; Thattai, Mukund; Mayor, Satyajit

2014-01-01

Single-cell-resolved measurements reveal heterogeneous distributions of clathrin-dependent (CD) and -independent (CLIC/GEEC: CG) endocytic activity in Drosophila cell populations. dsRNA-mediated knockdown of core versus peripheral endocytic machinery induces strong changes in the mean, or subtle changes in the shapes of these distributions, respectively. By quantifying these subtle shape changes for 27 single-cell features which report on endocytic activity and cell morphology, we organize 1072 Drosophila genes into a tree-like hierarchy. We find that tree nodes contain gene sets enriched in functional classes and protein complexes, providing a portrait of core and peripheral control of CD and CG endocytosis. For 470 genes we obtain additional features from separate assays and classify them into early- or late-acting genes of the endocytic pathways. Detailed analyses of specific genes at intermediate levels of the tree suggest that Vacuolar ATPase and lysosomal genes involved in vacuolar biogenesis play an evolutionarily conserved role in CG endocytosis. PMID:24971745

Beyond pleasure and arousal: appetitive erotic stimuli modulate electrophysiological brain correlates of early attentional processing.

PubMed

Kuhr, Benjamin; Schomberg, Jessica; Gruber, Thomas; Quirin, Markus

2013-03-27

Previous studies investigating affective reactions to pictures that elicit a specific effect have mainly focused on the dimensions valence and arousal. Using an event-related picture-viewing paradigm in electroencephalography, we investigated whether erotica - that is appetitive, evolutionarily relevant stimuli - have effects on early stages of attentional processing that are distinct from those of other positive and arousing stimuli. Seventeen male students viewed arousing photos of erotic, nude women or pictures of extreme sport scenes, as well as control pictures of attractive, dressed women or daily activities. Erotic pictures differed from extreme sport pictures not only in late but also in early attentional processes, as indicated by event-related potentials appearing from 130 ms after stimulus onset (P1). The findings suggest (a) that the dimension of appetence should be considered in addition to valence and arousal when investigating psychophysiological reactions to affective-motivational stimuli and (b) that early attentional processing as mirrored by the P1 can be influenced by motivational systems.

Multiple transcription factor codes activate epidermal wound–response genes in Drosophila

PubMed Central

Pearson, Joseph C.; Juarez, Michelle T.; Kim, Myungjin; Drivenes, Øyvind; McGinnis, William

2009-01-01

Wounds in Drosophila and mouse embryos induce similar genetic pathways to repair epidermal barriers. However, the transcription factors that transduce wound signals to repair epidermal barriers are largely unknown. We characterize the transcriptional regulatory enhancers of 4 genes—Ddc, ple, msn, and kkv—that are rapidly activated in epidermal cells surrounding wounds in late Drosophila embryos and early larvae. These epidermal wound enhancers all contain evolutionarily conserved sequences matching binding sites for JUN/FOS and GRH transcription factors, but vary widely in trans- and cis-requirements for these inputs and their binding sites. We propose that the combination of GRH and FOS is part of an ancient wound–response pathway still used in vertebrates and invertebrates, but that other mechanisms have evolved that result in similar transcriptional output. A common, but largely untested assumption of bioinformatic analyses of gene regulatory networks is that transcription units activated in the same spatial and temporal patterns will require the same cis-regulatory codes. Our results indicate that this is an overly simplistic view. PMID:19168633

Test of Von Baer's law of the conservation of early development.

PubMed

Poe, Steven

2006-11-01

One of the oldest and most pervasive ideas in comparative embryology is the perceived evolutionary conservation of early ontogeny relative to late ontogeny. Karl Von Baer first noted the similarity of early ontogeny across taxa, and Ernst Haeckel and Charles Darwin gave evolutionary interpretation to this phenomenon. In spite of a resurgence of interest in comparative embryology and the development of mechanistic explanations for Von Baer's law, the pattern itself has been largely untested. Here, I use statistical phylogenetic approaches to show that Von Baer's law is an unnecessarily complex explanation of the patterns of ontogenetic timing in several clades of vertebrates. Von Baer's law suggests a positive correlation between ontogenetic time and amount of evolutionary change. I compare ranked position in ontogeny to frequency of evolutionary change in rank for developmental events and find that these measures are not correlated, thus failing to support Von Baer's model. An alternative model that postulates that small changes in ontogenetic rank are evolutionarily easier than large changes is tentatively supported.

ISCA1 is essential for mitochondrial Fe4S4 biogenesis in vivo.

PubMed

Beilschmidt, Lena Kristina; Ollagnier de Choudens, Sandrine; Fournier, Marjorie; Sanakis, Ioannis; Hograindleur, Marc-André; Clémancey, Martin; Blondin, Geneviève; Schmucker, Stéphane; Eisenmann, Aurélie; Weiss, Amélie; Koebel, Pascale; Messaddeq, Nadia; Puccio, Hélène; Martelli, Alain

2017-05-11

Mammalian A-type proteins, ISCA1 and ISCA2, are evolutionarily conserved proteins involved in iron-sulfur cluster (Fe-S) biogenesis. Recently, it was shown that ISCA1 and ISCA2 form a heterocomplex that is implicated in the maturation of mitochondrial Fe 4 S 4 proteins. Here we report that mouse ISCA1 and ISCA2 are Fe 2 S 2 -containing proteins that combine all features of Fe-S carrier proteins. We use biochemical, spectroscopic and in vivo approaches to demonstrate that despite forming a complex, ISCA1 and ISCA2 establish discrete interactions with components of the late Fe-S machinery. Surprisingly, knockdown experiments in mouse skeletal muscle and in primary cultures of neurons suggest that ISCA1, but not ISCA2, is required for mitochondrial Fe 4 S 4 proteins biogenesis. Collectively, our data suggest that cellular processes with different requirements for ISCA1, ISCA2 and ISCA1-ISCA2 complex seem to exist.

ISCA1 is essential for mitochondrial Fe4S4 biogenesis in vivo

PubMed Central

Beilschmidt, Lena Kristina; Ollagnier de Choudens, Sandrine; Fournier, Marjorie; Sanakis, Ioannis; Hograindleur, Marc-André; Clémancey, Martin; Blondin, Geneviève; Schmucker, Stéphane; Eisenmann, Aurélie; Weiss, Amélie; Koebel, Pascale; Messaddeq, Nadia; Puccio, Hélène; Martelli, Alain

2017-01-01

Mammalian A-type proteins, ISCA1 and ISCA2, are evolutionarily conserved proteins involved in iron–sulfur cluster (Fe–S) biogenesis. Recently, it was shown that ISCA1 and ISCA2 form a heterocomplex that is implicated in the maturation of mitochondrial Fe4S4 proteins. Here we report that mouse ISCA1 and ISCA2 are Fe2S2-containing proteins that combine all features of Fe–S carrier proteins. We use biochemical, spectroscopic and in vivo approaches to demonstrate that despite forming a complex, ISCA1 and ISCA2 establish discrete interactions with components of the late Fe–S machinery. Surprisingly, knockdown experiments in mouse skeletal muscle and in primary cultures of neurons suggest that ISCA1, but not ISCA2, is required for mitochondrial Fe4S4 proteins biogenesis. Collectively, our data suggest that cellular processes with different requirements for ISCA1, ISCA2 and ISCA1–ISCA2 complex seem to exist. PMID:28492233

A disturbance-based ecosystem approach to maintaining and restoring freshwater habitats of evolutionarily significant units of anadromous salmonids in the Pacific Northwest.

Treesearch

G.H. Reeves; L.E. Benda; K.M. Burnett; P.A. Bisson; J.R. Sedell

1995-01-01

To preserve and recover evolutionarily significant units (ESUs) of anadromous salmonids Oncorhynchus spp. in the Pacific Northwest, long-term and short-term ecological processes that create and maintain freshwater habitats must be restored and protected. Aquatic ecosystems through- out the region are dynamic in space and time, and lack of...

Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese

PubMed Central

Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

2015-01-01

Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. PMID:25767226

Whole Genome Shotgun Sequencing Shows Selection on Leptospira Regulatory Proteins during in vitro Culture Attenuation

PubMed Central

Lehmann, Jason S.; Corey, Victoria C.; Ricaldi, Jessica N.; Vinetz, Joseph M.; Winzeler, Elizabeth A.; Matthias, Michael A.

2016-01-01

Leptospirosis is the most common zoonotic disease worldwide with an estimated 500,000 severe cases reported annually, and case fatality rates of 12–25%, due primarily to acute kidney and lung injuries. Despite its prevalence, the molecular mechanisms underlying leptospirosis pathogenesis remain poorly understood. To identify virulence-related genes in Leptospira interrogans, we delineated cumulative genome changes that occurred during serial in vitro passage of a highly virulent strain of L. interrogans serovar Lai into a nearly avirulent isogenic derivative. Comparison of protein coding and computationally predicted noncoding RNA (ncRNA) genes between these two polyclonal strains identified 15 nonsynonymous single nucleotide variant (nsSNV) alleles that increased in frequency and 19 that decreased, whereas no changes in allelic frequency were observed among the ncRNA genes. Some of the nsSNV alleles were in six genes shown previously to be transcriptionally upregulated during exposure to in vivo-like conditions. Five of these nsSNVs were in evolutionarily conserved positions in genes related to signal transduction and metabolism. Frequency changes of minor nsSNV alleles identified in this study likely contributed to the loss of virulence during serial in vitro culture. The identification of new virulence-associated genes should spur additional experimental inquiry into their potential role in Leptospira pathogenesis. PMID:26711524

Evidence for Multiple Mediator Complexes in Yeast Independently Recruited by Activated Heat Shock Factor

PubMed Central

Anandhakumar, Jayamani; Moustafa, Yara W.; Chowdhary, Surabhi; Kainth, Amoldeep S.

2016-01-01

Mediator is an evolutionarily conserved coactivator complex essential for RNA polymerase II transcription. Although it has been generally assumed that in Saccharomyces cerevisiae, Mediator is a stable trimodular complex, its structural state in vivo remains unclear. Using the “anchor away” (AA) technique to conditionally deplete select subunits within Mediator and its reversibly associated Cdk8 kinase module (CKM), we provide evidence that Mediator's tail module is highly dynamic and that a subcomplex consisting of Med2, Med3, and Med15 can be independently recruited to the regulatory regions of heat shock factor 1 (Hsf1)-activated genes. Fluorescence microscopy of a scaffold subunit (Med14)-anchored strain confirmed parallel cytoplasmic sequestration of core subunits located outside the tail triad. In addition, and contrary to current models, we provide evidence that Hsf1 can recruit the CKM independently of core Mediator and that core Mediator has a role in regulating postinitiation events. Collectively, our results suggest that yeast Mediator is not monolithic but potentially has a dynamic complexity heretofore unappreciated. Multiple species, including CKM-Mediator, the 21-subunit core complex, the Med2-Med3-Med15 tail triad, and the four-subunit CKM, can be independently recruited by activated Hsf1 to its target genes in AA strains. PMID:27185874

Eavesdropping and crosstalk between secreted quorum sensing peptide signals that regulate bacteriocin production in Streptococcus pneumoniae.

PubMed

Miller, Eric L; Kjos, Morten; Abrudan, Monica I; Roberts, Ian S; Veening, Jan-Willem; Rozen, Daniel E

2018-06-13

Quorum sensing (QS), where bacteria secrete and respond to chemical signals to coordinate population-wide behaviors, has revealed that bacteria are highly social. Here, we investigate how diversity in QS signals and receptors can modify social interactions controlled by the QS system regulating bacteriocin secretion in Streptococcus pneumoniae, encoded by the blp operon (bacteriocin-like peptide). Analysis of 4096 pneumococcal genomes detected nine blp QS signals (BlpC) and five QS receptor groups (BlpH). Imperfect concordance between signals and receptors suggested widespread social interactions between cells, specifically eavesdropping (where cells respond to signals that they do not produce) and crosstalk (where cells produce signals that non-clones detect). This was confirmed in vitro by measuring the response of reporter strains containing six different blp QS receptors to cognate and non-cognate peptides. Assays between pneumococcal colonies grown adjacent to one another provided further evidence that crosstalk and eavesdropping occur at endogenous levels of signal secretion. Finally, simulations of QS strains producing bacteriocins revealed that eavesdropping can be evolutionarily beneficial even when the affinity for non-cognate signals is very weak. Our results highlight that social interactions can mediate intraspecific competition among bacteria and reveal that competitive interactions can be modified by polymorphic QS systems.

Rapid depletion of budding yeast proteins by fusion to a heat-inducible degron.

PubMed

Sanchez-Diaz, Alberto; Kanemaki, Masato; Marchesi, Vanessa; Labib, Karim

2004-03-02

One effective way to study the biological function of a protein in vivo is to inactivate it and see what happens to the cell. For proteins that are dispensable for cell viability, the corresponding gene can simply be deleted from its chromosomal locus. The study of essential proteins is more challenging, however, because the function of the protein must be inactivated conditionally. Here, we describe a method that allows the target protein to be depleted rapidly and conditionally, so that the immediate effects on the cell can be examined. The chromosomal locus of a budding yeast gene is modified so that a "heat-inducible degron cassette" is added to the N terminus of the encoded protein, causing it to be degraded by a specific ubiquitin-mediated pathway when cells are shifted from 24 degrees to 37 degrees C. Degradation requires recognition of the degron cassette by the evolutionarily conserved Ubr1 protein, which is associated with a ubiquitin-conjugating enzyme. To promote rapid and conditional depletion of the target protein, we use a yeast strain in which expression of the UBR1 gene can be either repressed or strongly induced. Degron strains are constructed by a simple "one-step" approach using the polymerase chain reaction.

Evolutionarily stable learning schedules and cumulative culture in discrete generation models.

PubMed

Aoki, Kenichi; Wakano, Joe Yuichiro; Lehmann, Laurent

2012-06-01

Individual learning (e.g., trial-and-error) and social learning (e.g., imitation) are alternative ways of acquiring and expressing the appropriate phenotype in an environment. The optimal choice between using individual learning and/or social learning may be dictated by the life-stage or age of an organism. Of special interest is a learning schedule in which social learning precedes individual learning, because such a schedule is apparently a necessary condition for cumulative culture. Assuming two obligatory learning stages per discrete generation, we obtain the evolutionarily stable learning schedules for the three situations where the environment is constant, fluctuates between generations, or fluctuates within generations. During each learning stage, we assume that an organism may target the optimal phenotype in the current environment by individual learning, and/or the mature phenotype of the previous generation by oblique social learning. In the absence of exogenous costs to learning, the evolutionarily stable learning schedules are predicted to be either pure social learning followed by pure individual learning ("bang-bang" control) or pure individual learning at both stages ("flat" control). Moreover, we find for each situation that the evolutionarily stable learning schedule is also the one that optimizes the learned phenotype at equilibrium. Copyright © 2012 Elsevier Inc. All rights reserved.

Epidemiological dynamics of norovirus GII.4 variant New Orleans 2009.

PubMed

Medici, Maria Cristina; Tummolo, Fabio; De Grazia, Simona; Calderaro, Adriana; De Conto, Flora; Terio, Valentina; Chironna, Maria; Bonura, Floriana; Pucci, Marzia; Bányai, Kristián; Martella, Vito; Giammanco, Giovanni Maurizio

2015-09-01

Norovirus (NoV) is one of the major causes of diarrhoeal disease with epidemic, outbreak and sporadic patterns in humans of all ages worldwide. NoVs of genotype GII.4 cause nearly 80-90 % of all NoV infections in humans. Periodically, some GII.4 strains become predominant, generating major pandemic variants. Retrospective analysis of the GII.4 NoV strains detected in Italy between 2007 and 2013 indicated that the pandemic variant New Orleans 2009 emerged in Italy in the late 2009, became predominant in 2010-2011 and continued to circulate in a sporadic fashion until April 2013. Upon phylogenetic analysis based on the small diagnostic regions A and C, the late New Orleans 2009 NoVs circulating during 2011-2013 appeared to be genetically different from the early New Orleans 2009 strains that circulated in 2010. For a selection of strains, a 3.2 kb genome portion at the 3' end was sequenced. In the partial ORF1 and in the full-length ORF2 and ORF3, the 2011-2013 New Orleans NoVs comprised at least three distinct genetic subclusters. By comparison with sequences retrieved from the databases, these subclusters were also found to circulate globally, suggesting that the local circulation reflected repeated introductions of different strains, rather than local selection of novel viruses. Phylogenetic subclustering did not correlate with changes in residues located in predicted putative capsid epitopes, although several changes affected the P2 domain in epitopes A, C, D and E.

Horizontal transmission of group B streptococcus in a neonatal intensive care unit

PubMed Central

Morinis, Julia; Shah, Jay; Murthy, Prashanth; Fulford, Martha

2011-01-01

The incidence of early-onset group B streptococcal (GBS) sepsis in the neonatal population has decreased substantially since the introduction of maternal intrapartum antibiotic prophylaxis and routine prenatal screening. However, these strategies have not reduced the incidence of late-onset GBS infections. Additional research pertaining to the transmission of late-onset GBS infections is required to develop effective preventive methods. The present report describes probable horizontal transmission of late-onset GBS infection among three infants in a neonatal intensive care unit. GBS strain confirmation was based on the microbiological picture, antibiogram and pulsed-field gel electrophoresis. These cases highlight the morbidity associated with late-onset GBS disease and the importance of considering horizontal transmission as an etiological factor in GBS infection in the newborn period. Further studies assessing horizontal transmission in late-onset GBS disease may improve prevention and early intervention. PMID:22654550

Horizontal transmission of group B streptococcus in a neonatal intensive care unit.

PubMed

Morinis, Julia; Shah, Jay; Murthy, Prashanth; Fulford, Martha

2011-06-01

The incidence of early-onset group B streptococcal (GBS) sepsis in the neonatal population has decreased substantially since the introduction of maternal intrapartum antibiotic prophylaxis and routine prenatal screening. However, these strategies have not reduced the incidence of late-onset GBS infections. Additional research pertaining to the transmission of late-onset GBS infections is required to develop effective preventive methods. The present report describes probable horizontal transmission of late-onset GBS infection among three infants in a neonatal intensive care unit. GBS strain confirmation was based on the microbiological picture, antibiogram and pulsed-field gel electrophoresis. These cases highlight the morbidity associated with late-onset GBS disease and the importance of considering horizontal transmission as an etiological factor in GBS infection in the newborn period. Further studies assessing horizontal transmission in late-onset GBS disease may improve prevention and early intervention.

Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese.

PubMed

Storari, Michelangelo; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

2015-03-12

Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. Copyright © 2015 Storari et al.

Genomic Location of the Major Ribosomal Protein Gene Locus Determines Vibrio cholerae Global Growth and Infectivity

PubMed Central

Soler-Bistué, Alfonso; Mondotte, Juan A.; Bland, Michael Jason; Val, Marie-Eve; Saleh, María-Carla; Mazel, Didier

2015-01-01

The effects on cell physiology of gene order within the bacterial chromosome are poorly understood. In silico approaches have shown that genes involved in transcription and translation processes, in particular ribosomal protein (RP) genes, localize near the replication origin (oriC) in fast-growing bacteria suggesting that such a positional bias is an evolutionarily conserved growth-optimization strategy. Such genomic localization could either provide a higher dosage of these genes during fast growth or facilitate the assembly of ribosomes and transcription foci by keeping physically close the many components of these macromolecular machines. To explore this, we used novel recombineering tools to create a set of Vibrio cholerae strains in which S10-spec-α (S10), a locus bearing half of the ribosomal protein genes, was systematically relocated to alternative genomic positions. We show that the relative distance of S10 to the origin of replication tightly correlated with a reduction of S10 dosage, mRNA abundance and growth rate within these otherwise isogenic strains. Furthermore, this was accompanied by a significant reduction in the host-invasion capacity in Drosophila melanogaster. Both phenotypes were rescued in strains bearing two S10 copies highly distal to oriC, demonstrating that replication-dependent gene dosage reduction is the main mechanism behind these alterations. Hence, S10 positioning connects genome structure to cell physiology in Vibrio cholerae. Our results show experimentally for the first time that genomic positioning of genes involved in the flux of genetic information conditions global growth control and hence bacterial physiology and potentially its evolution. PMID:25875621

How Does Subclinical Hyperthyroidism Affect Right Heart Function and Mechanics?

PubMed

Tadic, Marijana; Celic, Vera; Cuspidi, Cesare; Ilic, Sanja; Zivanovic, Vladimir; Marjanovic, Tamara

2016-02-01

Right heart function and mechanics have not been investigated in patients with subclinical hyperthyroidism. Our aim was to investigate right ventricular (RV) and right atrial (RA) function and deformation as evaluated by 3-dimensional echocardiography (3DE) and speckle-tracking 2-dimensional echocardiography (2DE) in these individuals. We included 39 untreated women with endogenous subclinical hyperthyroidism and 39 healthy women matched by age. All participants underwent laboratory analyses that included thyroid hormone levels and comprehensive 2DE and 3DE examinations. Three-dimensional echocardiographic RV volumes were significantly elevated in the patients with subclinical hyperthyroidism (P < .05), whereas the 3DE RV ejection fraction was reduced in this group, but with borderline significance. Two-dimensional echocardiographic longitudinal RV and RA strain were significantly reduced in the patients with subclinical hyperthyroidism. Two-dimensional echocardiographic RV systolic and early diastolic strain rates were reduced, whereas late diastolic strain rates were increased in the patients with subclinical hyperthyroidism. The same changes were detected in RA mechanics among the patients with subclinical hyperthyroidism. The thyrotropin (TSH) level correlated with the left ventricular mass index, transmitral early diastolic peak flow velocity (E)/late diastolic flow velocity (A) ratio, tricuspid E/A ratio, 2DE RV global strain, 2DE RA, strain, and 3DE RV end-diastolic volume. A multivariate regression analysis showed that the mitral E/A ratio, 2DE RV global strain, and 3DE RV end-diastolic volume were independently associated with the TSH level. Right ventricular and RA function as evaluated by 3DE and speckle-tracking 2DE is significantly impaired in patients with subclinical hyperthyroidism. The TSH level correlated with parameters for RV function and mechanics in the whole study population. © 2016 by the American Institute of Ultrasound in Medicine.

Isolation of a new heterolobosean amoeba from a rice field soil: Vrihiamoeba italica gen. nov., sp. nov.

PubMed

Murase, Jun; Kawasaki, Michio; De Jonckheere, Johan F

2010-08-01

A heterolobosean amoeba strain 6_5F was isolated from an Italian rice field soil. Although 18S rRNA gene sequence analysis demonstrated that the new isolate was closely related to Stachyamoeba sp. ATCC 50324, further molecular analysis and morphological observation showed distinct differences amongst the two. The 5.8S rRNA gene was successfully amplified and sequenced for strain 6_5F but not for strain ATCC 50324. Trophozoites of strain ATCC 50324 transform into flagellate forms in the late stage of incubation before encystment, while strain 6_5F do not show flagellate forms under different conditions of the flagellation test. Light and electron microscopic observation showed the structural difference of cysts of strain 6_5F from strain ATCC 50324 and also from the type strain Stachyamoeba lipophora. The results show that the strain 6_5F is distinct from Stachyamoeba spp. and we propose a new genus and species for this isolate, Vrihiamoeba italica gen. nov., sp. nov. Copyright (c) 2010 Elsevier GmbH. All rights reserved.

Mechanical work makes important contributions to surface chemistry at steps.

PubMed

Francis, M F; Curtin, W A

2015-02-13

The effect of mechanical strain on the binding energy of adsorbates to late transition metals is believed to be entirely controlled by electronic factors, with tensile stress inducing stronger binding. Here we show, via computation, that mechanical strain of late transition metals can modify binding at stepped surfaces opposite to well-established trends on flat surfaces. The mechanism driving the trend is mechanical, arising from the relaxation of stored mechanical energy. The mechanical energy change can be larger than, and of opposite sign than, the energy changes due to electronic effects and leads to a violation of trends predicted by the widely accepted electronic 'd-band' model. This trend has a direct impact on catalytic activity, which is demonstrated here for methanation, where biaxial tension is predicted to shift the activity of nickel significantly, reaching the peak of the volcano plot and comparable to cobalt and ruthenium.

Evaluation of left ventricular function by tissue Doppler and speckle-derived strain rate echocardiography after percutaneous ductus closure.

PubMed

Amoogzar, Hamid; Shakiba, Ali Mohammad; Derakhshan, Dorna; Ajami, Gholamhossein; Cheriki, Sirous; Borzouee, Mohammad; Edraki, Mohammad Reza; Mehdizadegan, Nima

2015-01-01

The aim of this study was to evaluate the left ventricular systolic and diastolic function before and after transcatheter percutaneous patent ductus arteriosus (PDA) closure. 21 children (age >6 months old) diagnosed with hemodynamically significant PDA underwent percutaneous PDA closure. Conventional, Doppler and tissue Doppler imaging and speckled-derived strain rate echocardiography were done at pre-closure, 1 day (early) and 1 month (late) post-closure. Mean age of the patients (female/male: 1.3) was 17.54 ± 24.7 months with the mean PDA diameter of 3.6 ± 0.8 mm. Systolic measures (ejection fraction, shortening fraction) reduced significantly early after PDA closure (P < 0.05). After 1 month, both improved significantly; ultimately, after 1 month no change was observed in systolic function measures compared with the pre-closure status. Early and late diastolic flow velocities of mitral (E M and A M) reduced considerably in early and late post-closure time (P < 0.05). Both early tissue Doppler early velocity of lateral mitral annulus (E'M) and early to late velocity ratio (E'M/A'M) of lateral mitral annulus decreased significantly (P = 0.02) in early post-closure. After 1 month, E'M increased considerably. (P = 0.01) but E'M/A'M had an insignificant rise (P > 0.05). E M/E'M ratio did not change in early post-closure but it had a considerable reduction in the subsequent month compared with the pre- and early post-closure (P < 0.001 for both occasions). Global and segmental longitudinal strain measures reduced significantly early after PDA closure (P < 0.05) but it improved remarkably in the subsequent month. Transcatheter PDA closure causes a significant decrease in left ventricular performance early after PDA closure which recovers completely within 1 month. Also PDA size can affect post-closure left ventricular function.

Physiological and Biochemical Changes Reveal Differential Patterns of Docosahexaenoic Acid Partitioning in Two Marine Algal Strains of Isochrysis

PubMed Central

Chen, Yong; Mao, Xuemei; Liu, Jin

2017-01-01

The marine microalgae Isochrysis are a good producer of natural docosahexaenoic acid (DHA). To better understand the patterns of DHA accumulation and distribution, two Isochrysis strains, CL153180 and CCMP462, were evaluated in this study. In a batch culture, CL153180 showed a decline in DHA content while CCMP462 exhibited a progressive increase during the late growth period when nitrogen was almost exhausted. In response to nitrogen deficiency (ND), both strains showed a considerable increase in neutral lipids (NL) at the expense of glycolipids (GL) but had little variation in phospholipids (PL). In CL153180, the DHA percentage of NL decreased gradually upon ND, while that in CCMP462 increased progressively to 21.4% after 4 days of ND, which is around 5-fold higher than CL153180. Accordingly, in contrast to CL153180 that stored DHA predominantly in GL, CCMP462 accumulated DHA mainly in NL in late days of ND. Taken together, we proposed a working model for the differential DHA partitioning patterns between two Isochrysis strains: for CCMP462, the degradation of GL released free fatty acids including DHA, which was incorporated into NL upon ND; whereas for CL153180, the released DHA from GL might not be incorporated into NL, and, consequently, might be subject to β-oxidation for degradation. PMID:29137149

C. elegans MCM-4 is a general DNA replication and checkpoint component with an epidermis-specific requirement for growth and viability.

PubMed

Korzelius, Jerome; The, Inge; Ruijtenberg, Suzan; Portegijs, Vincent; Xu, Huihong; Horvitz, H Robert; van den Heuvel, Sander

2011-02-15

DNA replication and its connection to M phase restraint are studied extensively at the level of single cells but rarely in the context of a developing animal. C. elegans lin-6 mutants lack DNA synthesis in postembryonic somatic cell lineages, while entry into mitosis continues. These mutants grow slowly and either die during larval development or develop into sterile adults. We found that lin-6 corresponds to mcm-4 and encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex. The MCM-4 protein is expressed in all dividing cells during embryonic and postembryonic development and associates with chromatin in late anaphase. Induction of cell cycle entry and differentiation continues in developing mcm-4 larvae, even in cells that went through abortive division. In contrast to somatic cells in mcm-4 mutants, the gonad continues DNA replication and cell division until late larval development. Expression of MCM-4 in the epidermis (also known as hypodermis) is sufficient to rescue the growth retardation and lethality of mcm-4 mutants. While the somatic gonad and germline show substantial ability to cope with lack of zygotic mcm-4 function, mcm-4 is specifically required in the epidermis for growth and survival of the whole organism. Thus, C. elegans mcm-4 has conserved functions in DNA replication and replication checkpoint control but also shows unexpected tissue-specific requirements. Copyright © 2010 Elsevier Inc. All rights reserved.

C. elegans MCM-4 is a general DNA replication and checkpoint component with an epidermis-specific requirement for growth and viability

PubMed Central

Korzelius, Jerome; The, Inge; Ruijtenberg, Suzan; Portegijs, Vincent; Xu, Huihong; Horvitz, H. Robert; van den Heuvel, Sander

2012-01-01

DNA replication and its connection to M phase restraint are studied extensively at the level of single cells but rarely in the context of a developing animal. C. elegans lin-6 mutants lack DNA synthesis in postembryonic somatic cell lineages, while entry into mitosis continues. These mutants grow slowly and either die during larval development or develop into sterile adults. We found that lin-6 corresponds to mcm-4 and encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex. The MCM-4 protein is expressed in all dividing cells during embryonic and postembryonic development and associates with chromatin in late anaphase. Induction of cell-cycle entry and differentiation continues in developing mcm-4 larvae, even in cells that went through abortive division. In contrast to somatic cells in mcm-4 mutants, the gonad continues DNA replication and cell division until late larval development. Expression of MCM-4 in the epidermis (also known as hypodermis) is sufficient to rescue the growth retardation and lethality of mcm-4 mutants. While the somatic gonad and germline show substantial ability to cope with lack of zygotic mcm-4 function, mcm-4 is specifically required in the epidermis for growth and survival of the whole organism. Thus, C. elegans mcm-4 has conserved functions in DNA replication and replication checkpoint control but also shows unexpected tissue-specific requirements. PMID:21146520

YB-1 Is Important for Late-Stage Embryonic Development, Optimal Cellular Stress Responses, and the Prevention of Premature Senescence

PubMed Central

Lu, Zhi Hong; Books, Jason T.; Ley, Timothy J.

2005-01-01

Proteins containing “cold shock” domains belong to the most evolutionarily conserved family of nucleic acid-binding proteins known among bacteria, plants, and animals. One of these proteins, YB-1, is widely expressed throughout development and has been implicated as a cell survival factor that regulates the transcription and/or translation of many cellular growth and death-related genes. For these reasons, YB-1 deficiency has been predicted to be incompatible with cell survival. However, the majority of YB-1−/− embryos develop normally up to embryonic day 13.5 (E13.5). After E13.5, YB-1−/− embryos exhibit severe growth retardation and progressive mortality, revealing a nonredundant role of YB-1 in late embryonic development. Fibroblasts derived from YB-1−/− embryos displayed a normal rate of protein synthesis and minimal alterations in the transcriptome and proteome but demonstrated reduced abilities to respond to oxidative, genotoxic, and oncogene-induced stresses. YB-1−/− cells under oxidative stress expressed high levels of the G1-specific CDK inhibitors p16Ink4a and p21Cip1 and senesced prematurely; this defect was corrected by knocking down CDK inhibitor levels with specific small interfering RNAs. These data suggest that YB-1 normally represses the transcription of CDK inhibitors, making it an important component of the cellular stress response signaling pathway. PMID:15899865

Combinatorial Wnt control of zebrafish midbrain-hindbrain boundary formation.

PubMed

Buckles, Gerri R; Thorpe, Christopher J; Ramel, Marie-Christine; Lekven, Arne C

2004-05-01

Wnt signaling is known to be required for the normal development of the vertebrate midbrain and hindbrain, but genetic loss of function analyses in the mouse and zebrafish yield differing results regarding the relative importance of specific Wnt loci. In the zebrafish, Wnt1 and Wnt10b functionally overlap in their control of gene expression in the ventral midbrain-hindbrain boundary (MHB), but they are not required for the formation of the MHB constriction. Whether other wnt loci are involved in zebrafish MHB development is unclear, although the expression of at least two wnts, wnt3a and wnt8b, is maintained in wnt1/wnt10b mutants. In order to address the role of wnt3a in zebrafish, we have isolated a full length cDNA and examined its expression and function via knockdown by morpholino antisense oligonucleotide (MO)-mediated knockdown. The expression pattern of wnt3a appears to be evolutionarily conserved between zebrafish and mouse, and MO knockdown shows that Wnt3a, while not uniquely required for MHB development, is required in the absence of Wnt1 and Wnt10b for the formation of the MHB constriction. In zebrafish embryos lacking Wnt3a, Wnt1 and Wnt10b, the expression of engrailed orthologs, pax2a and fgf8 is not maintained after mid-somitogenesis. In contrast to acerebellar and no isthmus mutants, in which midbrain and hindbrain cells acquire new fates but cell number is not significantly affected until late in embryogenesis, zebrafish embryos lacking Wnt3a, Wnt1 and Wnt10b undergo extensive apoptosis in the midbrain and cerebellum anlagen beginning in mid-somitogenesis, which results in the absence of a significant portion of the midbrain and cerebellum. Thus, the requirement for Wnt signaling in forming the MHB constriction is evolutionarily conserved in vertebrates and it is possible in zebrafish to dissect the relative impact of multiple Wnt loci in midbrain and hindbrain development.

Spiroplasma infection causes either early or late male killing in Drosophila, depending on maternal host age

NASA Astrophysics Data System (ADS)

Kageyama, Daisuke; Anbutsu, Hisashi; Shimada, Masakazu; Fukatsu, Takema

2007-04-01

Symbiont-induced male-killing phenotypes have been found in a variety of insects. Conventionally, these phenotypes have been divided into two categories according to the timing of action: early male killing at embryonic stages and late male killing at late larval stages. In Drosophila species, endosymbiotic bacteria of the genus Spiroplasma have been known to cause early male killing. Here, we report that a spiroplasma strain normally causing early male killing also induces late male killing depending on the maternal host age: male-specific mortality of larvae and pupae was more frequently observed in the offspring of young females. As the lowest spiroplasma density and occasional male production were also associated with newly emerged females, we proposed the density-dependent hypothesis for the expression of early and late male-killing phenotypes. Our finding suggested that (1) early and late male-killing phenotypes can be caused by the same symbiont and probably by the same mechanism; (2) late male killing may occur as an attenuated expression of early male killing; (3) expression of early and late male-killing phenotypes may be dependent on the symbiont density, and thus, could potentially be affected by the host immunity and regulation; and (4) early male killing and late male killing could be alternative strategies adopted by microbial reproductive manipulators.

Strains and Stressors: An Analysis of Touchscreen Learning in Genetically Diverse Mouse Strains

PubMed Central

Graybeal, Carolyn; Bachu, Munisa; Mozhui, Khyobeni; Saksida, Lisa M.; Bussey, Timothy J.; Sagalyn, Erica; Williams, Robert W.; Holmes, Andrew

2014-01-01

Touchscreen-based systems are growing in popularity as a tractable, translational approach for studying learning and cognition in rodents. However, while mouse strains are well known to differ in learning across various settings, performance variation between strains in touchscreen learning has not been well described. The selection of appropriate genetic strains and backgrounds is critical to the design of touchscreen-based studies and provides a basis for elucidating genetic factors moderating behavior. Here we provide a quantitative foundation for visual discrimination and reversal learning using touchscreen assays across a total of 35 genotypes. We found significant differences in operant performance and learning, including faster reversal learning in DBA/2J compared to C57BL/6J mice. We then assessed DBA/2J and C57BL/6J for differential sensitivity to an environmental insult by testing for alterations in reversal learning following exposure to repeated swim stress. Stress facilitated reversal learning (selectively during the late stage of reversal) in C57BL/6J, but did not affect learning in DBA/2J. To dissect genetic factors underlying these differences, we phenotyped a family of 27 BXD strains generated by crossing C57BL/6J and DBA/2J. There was marked variation in discrimination, reversal and extinction learning across the BXD strains, suggesting this task may be useful for identifying underlying genetic differences. Moreover, different measures of touchscreen learning were only modestly correlated in the BXD strains, indicating that these processes are comparatively independent at both genetic and phenotypic levels. Finally, we examined the behavioral structure of learning via principal component analysis of the current data, plus an archival dataset, totaling 765 mice. This revealed 5 independent factors suggestive of “reversal learning,” “motivation-related late reversal learning,” “discrimination learning,” “speed to respond,” and “motivation during discrimination.” Together, these findings provide a valuable reference to inform the choice of strains and genetic backgrounds in future studies using touchscreen-based tasks. PMID:24586288

Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae▿ †

PubMed Central

Urbanczyk, Henryk; Ast, Jennifer C.; Kaeding, Allison J.; Oliver, James D.; Dunlap, Paul V.

2008-01-01

Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib2 operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib2 operon of P. leiognathi. In none of these cases of apparent HGT, however, did acquisition of the lux genes correlate with phylogenetic divergence of the recipient strain from other members of its species. The results indicate that horizontal transfer of the lux genes in nature is rare and that horizontal acquisition of the lux genes apparently has not contributed to speciation in recipient taxa. PMID:18359809

CRUSTAL FAILURE DURING BINARY INSPIRAL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Penner, A. J.; Andersson, N.; Jones, D. I.

2012-04-20

We present the first fully relativistic calculations of the crustal strain induced in a neutron star by a binary companion at the late stages of inspiral, employing realistic equations of state for the fluid core and the solid crust. We show that while the deep crust is likely to fail only shortly before coalescence, there is a large variation in elastic strain, with the outermost layers failing relatively early on in the inspiral. We discuss the significance of the results for both electromagnetic and gravitational-wave astronomy.

Identifying the seasonal origins of human campylobacteriosis

PubMed Central

STRACHAN, N. J. C.; ROTARIU, O.; SMITH-PALMER, A.; COWDEN, J.; SHEPPARD, S. K.; O’BRIEN, S. J.; MAIDEN, M. C. J.; MACRAE, M.; BESSELL, P. R.; MATTHEWS, L.; REID, S. W. J.; INNOCENT, G. T.; OGDEN, I. D.; FORBES, K. J.

2014-01-01

SUMMARY Human campylobacteriosis exhibits a distinctive seasonality in temperate regions. This paper aims to identify the origins of this seasonality. Clinical isolates [typed by multi-locus sequence typing (MLST)] and epidemiological data were collected from Scotland. Young rural children were found to have an increased burden of disease in the late spring due to strains of non-chicken origin (e.g. ruminant and wild bird strains from environmental sources). In contrast the adult population had an extended summer peak associated with chicken strains. Travel abroad and UK mainland travel were associated with up to 17% and 18% of cases, respectively. International strains were associated with chicken, had a higher diversity than indigenous strains and a different spectrum of MLST types representative of these countries. Integrating empirical epidemiology and molecular subtyping can successfully elucidate the seasonal components of human campylobacteriosis. The findings will enable public health officials to focus strategies to reduce the disease burden. PMID:22989449

Simultaneous imaging of strain waves and induced magnetization dynamics at the nanometer scale

NASA Astrophysics Data System (ADS)

Macia, Ferran; Foerster, Michael; Statuto, Nahuel; Finizio, Simone; Hernandez-Minguez, Alberto; Lendinez, Sergi; Santos, Paulo V.; Fontcuberta, Josep; Hernandez, Joan Manel; Klaui, Mathias; Aballe, Lucia

The magnetoelastic effect or inverse magnetostriction-the change of magnetic properties by elastic deformation or strain-is often a key coupling mechanism in multiferroic heterostructures and nanocomposites. It has lately attracted considerable interest as a possible approach for controlling magnetization by electric fields (instead of current) in future devices with low power consumption. However, many experiments addressing the magnetoelastic effect are performed at slow speeds, often using materials and conditions which are impractical or too expensive for device integration. Here, we have studied the effect of the dynamic strain accompanying a surface acoustic wave on magnetic nanostructures. We have simultaneously imaged the temporal evolution of both strain waves and magnetization dynamics of nanostructures at the picosecond timescale. Our experimental technique, based on X-ray microscopy, is versatile and provides a pathway to the study of strain-induced effects at the nanoscale.

A Search for a General Phenomenon of Adaptive Mutability

PubMed Central

Galitski, T.; Roth, J. R.

1996-01-01

The most prominent systems for the study of adaptive mutability depend on the specialized activities of genetic elements like bacteriophage Mu and the F plasmid. Searching for general adaptive mutability, we have investigated the behavior of Salmonella typhimurium strains with chromosomal lacZ mutations. We have studied 30 revertible nonsense, missense, frameshift, and insertion alleles. One-third of the mutants produced >=10 late revertant colonies (appearing three to seven days after plating on selective medium). For the prolific mutants, the number of late revertants showed rank correlation with the residual β-galactosidase activity; for the same mutants, revertant number showed no correlation with the nonselective reversion rate (from fluctuation tests). Leaky mutants, which grew slowly on selective medium, produced late revertants whereas tight nongrowing mutants generally did not produce late revertants. However, the number of late revertants was not proportional to residual growth. Using total residual growth and the nonselective reversion rate, the expected number of late revertants was calculated. For several leaky mutants, the observed revertant number exceeded the expected number. We suggest that excess late revertants from these mutants arise from general adaptive mutability available to any chromosomal gene. PMID:8725216

Increased survival of experimentally evolved antimicrobial peptide-resistant Staphylococcus aureus in an animal host

PubMed Central

Dobson, Adam J; Purves, Joanne; Rolff, Jens

2014-01-01

Antimicrobial peptides (AMPs) have been proposed as new class of antimicrobial drugs, following the increasing prevalence of bacteria resistant to antibiotics. Synthetic AMPs are functional analogues of highly evolutionarily conserved immune effectors in animals and plants, produced in response to microbial infection. Therefore, the proposed therapeutic use of AMPs bears the risk of ‘arming the enemy’: bacteria that evolve resistance to AMPs may be cross-resistant to immune effectors (AMPs) in their hosts. We used a panel of populations of Staphylococcus aureus that were experimentally selected for resistance to a suite of individual AMPs and antibiotics to investigate the ‘arming the enemy’ hypothesis. We tested whether the selected strains showed higher survival in an insect model (Tenebrio molitor) and cross-resistance against other antimicrobials in vitro. A population selected for resistance to the antimicrobial peptide iseganan showed increased in vivo survival, but was not more virulent. We suggest that increased survival of AMP-resistant bacteria almost certainly poses problems to immune-compromised hosts. PMID:25469169

Whole Genome Shotgun Sequencing Shows Selection on Leptospira Regulatory Proteins During in vitro Culture Attenuation.

PubMed

Lehmann, Jason S; Corey, Victoria C; Ricaldi, Jessica N; Vinetz, Joseph M; Winzeler, Elizabeth A; Matthias, Michael A

2016-02-01

Leptospirosis is the most common zoonotic disease worldwide with an estimated 500,000 severe cases reported annually, and case fatality rates of 12-25%, due primarily to acute kidney and lung injuries. Despite its prevalence, the molecular mechanisms underlying leptospirosis pathogenesis remain poorly understood. To identify virulence-related genes in Leptospira interrogans, we delineated cumulative genome changes that occurred during serial in vitro passage of a highly virulent strain of L. interrogans serovar Lai into a nearly avirulent isogenic derivative. Comparison of protein coding and computationally predicted noncoding RNA (ncRNA) genes between these two polyclonal strains identified 15 nonsynonymous single nucleotide variant (nsSNV) alleles that increased in frequency and 19 that decreased, whereas no changes in allelic frequency were observed among the ncRNA genes. Some of the nsSNV alleles were in six genes shown previously to be transcriptionally upregulated during exposure to in vivo-like conditions. Five of these nsSNVs were in evolutionarily conserved positions in genes related to signal transduction and metabolism. Frequency changes of minor nsSNV alleles identified in this study likely contributed to the loss of virulence during serial in vitro culture. The identification of new virulence-associated genes should spur additional experimental inquiry into their potential role in Leptospira pathogenesis. © The American Society of Tropical Medicine and Hygiene.

The role of mycelium production and a MAPK-mediated immune response in the C. elegans-Fusarium model system

PubMed Central

Muhammed, Maged; Fuchs, Beth Burgwyn; WU, Michael P.; Breger, Julia; Coleman, Jeffrey J.; Mylonakis, Eleftherios

2013-01-01

Fusariosis is an emerging infectious complication of immune deficiency, but models to study this infection are lacking. The use of the soil nematode Caenorhabditis elegans as a model host to study the pathogenesis of Fusarium spp. was investigated. We observed that Fusarium conidia consumed by C. elegans can cause a lethal infection and result in more than 90% killing of the host within 120 hours, and the nematode had a significantly longer survival when challenged with Fusarium proliferatum compared to other species. Interestingly, mycelium production appears to be a major contributor in nematode killing in this model system, and C. elegans mutant strains with the immune response genes, tir-1 (encoding a protein containing a TIR domain that functions upstream of PMK-1) and pmk-1 (the homolog of the mammalian p38 MAPK) lived significantly shorter when challenged with Fusarium compared to the wild type strain. Furthermore, we used the C. elegans model to assess the efficacy and toxicity of various compounds against Fusarium. We demonstrated that amphotericin B, voriconazole, mancozeb, and phenyl mercury acetate significantly prolonged the survival of Fusarium-infected C. elegans, although mancozeb was toxic at higher concentrations. In conclusion, we describe a new model system for the study of Fusarium pathogenesis and evolutionarily preserved host responses to this important fungal pathogen. PMID:22225407

Evidence for Multiple Mediator Complexes in Yeast Independently Recruited by Activated Heat Shock Factor.

PubMed

Anandhakumar, Jayamani; Moustafa, Yara W; Chowdhary, Surabhi; Kainth, Amoldeep S; Gross, David S

2016-07-15

Mediator is an evolutionarily conserved coactivator complex essential for RNA polymerase II transcription. Although it has been generally assumed that in Saccharomyces cerevisiae, Mediator is a stable trimodular complex, its structural state in vivo remains unclear. Using the "anchor away" (AA) technique to conditionally deplete select subunits within Mediator and its reversibly associated Cdk8 kinase module (CKM), we provide evidence that Mediator's tail module is highly dynamic and that a subcomplex consisting of Med2, Med3, and Med15 can be independently recruited to the regulatory regions of heat shock factor 1 (Hsf1)-activated genes. Fluorescence microscopy of a scaffold subunit (Med14)-anchored strain confirmed parallel cytoplasmic sequestration of core subunits located outside the tail triad. In addition, and contrary to current models, we provide evidence that Hsf1 can recruit the CKM independently of core Mediator and that core Mediator has a role in regulating postinitiation events. Collectively, our results suggest that yeast Mediator is not monolithic but potentially has a dynamic complexity heretofore unappreciated. Multiple species, including CKM-Mediator, the 21-subunit core complex, the Med2-Med3-Med15 tail triad, and the four-subunit CKM, can be independently recruited by activated Hsf1 to its target genes in AA strains. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Comparative Analysis of the Complete Genome of Lactobacillus plantarum GB-LP2 and Potential Candidate Genes for Host Immune System Enhancement.

PubMed

Kwak, Woori; Kim, Kwondo; Lee, Chul; Lee, Chanho; Kang, Jungsun; Cho, Kyungjin; Yoon, Sook Hee; Kang, Dae-Kyung; Kim, Heebal; Heo, Jaeyoung; Cho, Seoae

2016-04-28

Acute respiratory virus infectious diseases are a growing health problem, particularly among children and the elderly. Much effort has been made to develop probiotics that prevent influenza virus infections by enhancing innate immunity in the respiratory tract until vaccines are available. Lactobacillus plantarum GB-LP2, isolated from a traditional Korean fermented vegetable, has exhibited preventive effects on influenza virus infection in mice. To identify the molecular basis of this strain, we conducted a whole-genome assembly study. The single circular DNA chromosome of 3,284,304 bp was completely assembled and 3,250 proteinencoding genes were predicted. Evolutionarily accelerated genes related to the phenotypic trait of anti-infective activities for influenza virus were identified. These genes encode three integral membrane proteins, a teichoic acid export ATP-binding protein and a glucosamine - fructose-6-phosphate aminotransferase involved in host innate immunity, the nonspecific DNA-binding protein Dps, which protects bacteria from oxidative damage, and the response regulator of the three-component quorum-sensing regulatory system, which is related to the capacity of adhesion to the surface of the respiratory tract and competition with pathogens. This is the first study to identify the genetic backgrounds of the antiviral activity in L. plantarum strains. These findings provide insight into the anti-infective activities of L. plantarum and the development of preventive probiotics.

Pathogenicity and molecular analysis of an infectious bursal disease virus isolated from Malaysian village chickens.

PubMed

Tan, D Y; Hair-Bejo, M; Omar, A R; Aini, I

2004-01-01

The characteristics of the pathogenic infectious bursal disease virus (IBDV) that infected avian species other than commercial chickens were largely unknown. In this study, by using in vivo and molecular methods, we had characterized an IBDV isolate (named 94268) isolated from an infectious bursal disease (IBD) outbreak in Malaysian village chickens--the adulterated descendant of the Southeast Asian jungle fowl (Gallus bankiva) that were commonly reared in the backyard. The 94268 isolate was grouped as the very virulent IBDV (vvIBDV) strain because it caused severe lesions and a high mortality rate in village chickens (>88%) and experimentally infected specific-pathogen-free chickens (>66%). In addition, it possessed all of the vvIBDV molecular markers in its VP2 gene. Phylogenetic analysis using distance, maximum parsimony, and maximum likelihood methods revealed that 94268 was monophyletic with other vvIBDV isolates and closely related to the Malaysian vvIBDV isolates. Given that the VP2 gene of 94268 isolate was almost identical and evolutionarily closely related to other field IBDV isolates that affected the commercial chickens, we therefore concluded that IBD infections had spread across the farm boundary. IBD infection in the village chicken may represent an important part of the IBD epidemiology because these birds could harbor the vvIBDV strain and should not be overlooked in the control and prevention of the disease.

An Evolutionarily Conserved Role for the Aryl Hydrocarbon Receptor in the Regulation of Movement

PubMed Central

Williams, Evan G.; Mouchiroud, Laurent; Frochaux, Michael; Pandey, Ashutosh; Andreux, Pénélope A.; Deplancke, Bart; Auwerx, Johan

2014-01-01

The BXD genetic reference population is a recombinant inbred panel descended from crosses between the C57BL/6 (B6) and DBA/2 (D2) strains of mice, which segregate for about 5 million sequence variants. Recently, some of these variants have been established with effects on general metabolic phenotypes such as glucose response and bone strength. Here we phenotype 43 BXD strains and observe they have large variation (∼5-fold) in their spontaneous activity during waking hours. QTL analyses indicate that ∼40% of this variance is attributable to a narrow locus containing the aryl hydrocarbon receptor (Ahr), a basic helix-loop-helix transcription factor with well-established roles in development and xenobiotic metabolism. Strains with the D2 allele of Ahr have reduced gene expression compared to those with the B6 allele, and have significantly higher spontaneous activity. This effect was also observed in B6 mice with a congenic D2 Ahr interval, and in B6 mice with a humanized AHR allele which, like the D2 allele, is expressed much less and has less enzymatic activity than the B6 allele. Ahr is highly conserved in invertebrates, and strikingly inhibition of its orthologs in D. melanogaster and C. elegans (spineless and ahr-1) leads to marked increases in basal activity. In mammals, Ahr has numerous ligands, but most are either non-selective (e.g. resveratrol) or highly toxic (e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)). Thus, we chose to examine a major environmental influence—long term feeding with high fat diet (HFD)—to see if the effects of Ahr are dependent on major metabolic differences. Interestingly, while HFD robustly halved movement across all strains, the QTL position and effects of Ahr remained unchanged, indicating that the effects are independent. The highly consistent effects of Ahr on movement indicate that changes in its constitutive activity have a role on spontaneous movement and may influence human behavior. PMID:25255223

Comparative analysis of growth-phase-dependent gene expression in virulent and avirulent Streptococcus pneumoniae using a high-density DNA microarray.

PubMed

Ko, Kwan Soo; Park, Sulhee; Oh, Won Sup; Suh, Ji-Yoeun; Oh, Taejeong; Ahn, Sungwhan; Chun, Jongsik; Song, Jae-Hoon

2006-02-28

The global pattern of growth-dependent gene expres-sion in Streptococcus pneumoniae strains was evalu-ated using a high-density DNA microarray. Total RNAs obtained from an avirulent S. pneumoniae strain R6 and a virulent strain AMC96-6 were used to compare the expression patterns at seven time points (2.5, 3.5, 4.5, 5.5, 6.0, 6.5, and 8.0 h). The expression profile of strain R6 changed between log and station-ary growth (the Log-Stat switch). There were clear differences between the growth-dependent gene ex-pression profiles of the virulent and avirulent pneumo-coccal strains in 367 of 1,112 genes. Transcripts of genes associated with bacterial competence and capsular polysaccharide formation, as well as clpP and cbpA, were higher in the virulent strain. Our data suggest that late log or early stationary phase may be the most virulent phase of S. pneumoniae.

Influence of red wine fermentation oenological additives on inoculated strain implantation.

PubMed

Duarte, Filomena L; Alves, Ana Claudia; Alemão, Maria Filomena; Baleiras-Couto, M Margarida

2013-06-01

Pure selected cultures of Saccharomyces cerevisiae starters are regularly used in the wine industry. A survey of S. cerevisiae populations during red wine fermentations was performed in order to evaluate the influence of oenological additives on the implantation of the inoculated strain. Pilot scale fermentations (500 L) were conducted with active dry yeast (ADY) and other commercial oenological additives, namely two commercial fermentation activators and two commercial tannins. Six microsatellite markers were used to type S. cerevisiae strains. The methodology proved to be very discriminating as a great diversity of wild strains (48 genotypes) was detected. Statistical analysis confirmed a high detection of the inoculated commercial strain, and for half the samples an effective implantation of ADY (over 80 %) was achieved. At late fermentation time, ADY strain implantation in fermentations conducted with commercial additives was lower than in the control. These results question the efficacy of ADY addition in the presence of other additives, indicating that further studies are needed to improve knowledge on oenological additives' use.

On Nash Equilibrium and Evolutionarily Stable States That Are Not Characterised by the Folk Theorem

PubMed Central

Li, Jiawei; Kendall, Graham

2015-01-01

In evolutionary game theory, evolutionarily stable states are characterised by the folk theorem because exact solutions to the replicator equation are difficult to obtain. It is generally assumed that the folk theorem, which is the fundamental theory for non-cooperative games, defines all Nash equilibria in infinitely repeated games. Here, we prove that Nash equilibria that are not characterised by the folk theorem do exist. By adopting specific reactive strategies, a group of players can be better off by coordinating their actions in repeated games. We call it a type-k equilibrium when a group of k players coordinate their actions and they have no incentive to deviate from their strategies simultaneously. The existence and stability of the type-k equilibrium in general games is discussed. This study shows that the sets of Nash equilibria and evolutionarily stable states have greater cardinality than classic game theory has predicted in many repeated games. PMID:26288088

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing

PubMed Central

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-01-01

ABSTRACT Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure. PMID:28277933

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing.

PubMed

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-10-03

Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.

Novel Insights into the Role of Neurospora crassa NDUFAF2, an Evolutionarily Conserved Mitochondrial Complex I Assembly Factor

PubMed Central

Pereira, Bruno; Videira, Arnaldo

2013-01-01

Complex I deficiency is commonly associated with mitochondrial oxidative phosphorylation diseases. Mutations in nuclear genes encoding structural subunits or assembly factors of complex I have been increasingly identified as the cause of the diseases. One such factor, NDUFAF2, is a paralog of the NDUFA12 structural subunit of the enzyme, but the mechanism by which it exerts its function remains unknown. Herein, we demonstrate that the Neurospora crassa NDUFAF2 homologue, the 13.4L protein, is a late assembly factor that associates with complex I assembly intermediates containing the membrane arm and the connecting part but lacking the N module of the enzyme. Furthermore, we provide evidence that dissociation of the assembly factor is dependent on the incorporation of the putative regulatory module composed of the subunits of 13.4 (NDUFA12), 18.4 (NDUFS6), and 21 (NDUFS4) kDa. Our results demonstrate that the 13.4L protein is a complex I assembly factor functionally conserved from fungi to mammals. PMID:23648483

ZNF750 is a p63 Target Gene that Induces KLF4 to Drive Terminal Epidermal Differentiation

PubMed Central

Sen, George L.; Boxer, Lisa D.; Webster, Dan E.; Bussat, Rose T.; Qu, Kun; Zarnegar, Brian J.; Johnston, Danielle; Siprashvili, Zurab; Khavari, Paul A.

2012-01-01

SUMMARY Disrupted epidermal differentiation characterizes numerous diseases that impact >25% of the population. In a search for dominant mediators of differentiation, we defined a requirement for ZNF750 in terminal epidermal differentiation. ZNF750 controlled genes mutated in numerous human skin diseases, including FLG, LOR, LCE3B, ALOXE3, and SPINK5. ZNF750 induced progenitor differentiation via an evolutionarily conserved C2H2 zinc finger motif. The epidermal master regulator, p63, bound the ZNF750 promoter and was necessary for its induction. ZNF750 restored differentiation to p63-deficient tissue, suggesting it acts downstream of p63. A search for functionally important ZNF750 targets via analysis of ZNF750-regulated genes identified KLF4, a transcription factor that activates late epidermal differentiation. ZNF750 binds to KLF4 at multiple sites flanking the transcriptional start site and controls its expression. ZNF750 thus directly links a tissue-specifying factor, p63, to an effector of terminal differentiation, KLF4, and represents a potential future target for disorders of this process. PMID:22364861

Mechanisms of lipase maturation

PubMed Central

Péterfy, Miklós

2010-01-01

Lipases are acyl hydrolases that represent a diverse group of enzymes present in organisms ranging from prokaryotes to humans. This article focuses on an evolutionarily related family of extracellular lipases that include lipoprotein lipase, hepatic lipase and endothelial lipase. As newly synthesized proteins, these lipases undergo a series of co- and post-translational maturation steps occurring in the endoplasmic reticulum, including glycosylation and glycan processing, and protein folding and subunit assembly. This article identifies and discusses mechanisms that direct early and late events in lipase folding and assembly. Lipase maturation employs the two general chaperone systems operating in the endoplasmic reticulum, as well as a recently identified lipase-specific chaperone termed lipase maturation factor 1. We propose that the two general chaperone systems act in a coordinated manner early in lipase maturation in order to help create partially folded monomers; lipase maturation factor 1 then facilitates final monomer folding and subunit assembly into fully functional homodimers. Once maturation is complete, the lipases exit the endoplasmic reticulum and are secreted to extracellular sites, where they carry out a number of functions related to lipoprotein and lipid metabolism. PMID:20543905

Regulatory functions of SnRK1 in stress-responsive gene expression and in plant growth and development.

PubMed

Cho, Young-Hee; Hong, Jung-Woo; Kim, Eun-Chul; Yoo, Sang-Dong

2012-04-01

Sucrose-nonfermentation1-related protein kinase1 (SnRK1) is an evolutionarily conserved energy sensor protein that regulates gene expression in response to energy depletion in plants. Efforts to elucidate the functions and mechanisms of this protein kinase are hampered, however, by inherent growth defects of snrk1-null mutant plants. To overcome these limitations and study SnRK1 functions in vivo, we applied a method combining transient expression in leaf mesophyll protoplasts and stable expression in transgenic plants. We found that both rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) SnRK1 activities critically influence stress-inducible gene expression and the induction of stress tolerance. Genetic, molecular, and chromatin immunoprecipitation analyses further revealed that the nuclear SnRK1 modulated target gene transcription in a submergence-dependent manner. From early seedling development through late senescence, SnRK1 activities appeared to modulate developmental processes in the plants. Our findings offer insight into the regulatory functions of plant SnRK1 in stress-responsive gene regulation and in plant growth and development throughout the life cycle.

Drosophila melanogaster cellular repressor of E1A-stimulated genes is a lysosomal protein essential for fly development

PubMed Central

Kowalewski-Nimmerfall, Elisabeth; Schähs, Philipp; Maresch, Daniel; Rendic, Dubravko; Krämer, Helmut; Mach, Lukas

2014-01-01

Mammalian cellular repressor of E1A-stimulated genes is a lysosomal glycoprotein implicated in cellular growth and differentiation. The genome of the fruit fly Drosophila melanogaster encodes a putative orthologue (dCREG), suggesting evolutionarily conserved physiological functions of this protein. In D. melanogaster S2 cells, dCREG was found to localize in lysosomes. Further studies revealed that intracellular dCREG is subject of proteolytic maturation. Processing and turnover could be substantially reduced by RNAi-mediated silencing of cathepsin L. In contrast to mammalian cells, lysosomal delivery of dCREG does not depend on its carbohydrate moiety. Furthermore, depletion of the putative D. melanogaster lysosomal sorting receptor lysosomal enzyme receptor protein did not compromise cellular retention of dCREG. We also investigated the developmental consequences of dCREG ablation in whole D. melanogaster flies. Ubiquitous depletion of dCREG proved lethal at the late pupal stage once a knock-down efficiency of > 95% was achieved. These results demonstrate that dCREG is essential for proper completion of fly development. PMID:25173815

Drosophila melanogaster cellular repressor of E1A-stimulated genes is a lysosomal protein essential for fly development.

PubMed

Kowalewski-Nimmerfall, Elisabeth; Schähs, Philipp; Maresch, Daniel; Rendic, Dubravko; Krämer, Helmut; Mach, Lukas

2014-12-01

Mammalian cellular repressor of E1A-stimulated genes is a lysosomal glycoprotein implicated in cellular growth and differentiation. The genome of the fruit fly Drosophila melanogaster encodes a putative orthologue (dCREG), suggesting evolutionarily conserved physiological functions of this protein. In D. melanogaster S2 cells, dCREG was found to localize in lysosomes. Further studies revealed that intracellular dCREG is subject of proteolytic maturation. Processing and turnover could be substantially reduced by RNAi-mediated silencing of cathepsin L. In contrast to mammalian cells, lysosomal delivery of dCREG does not depend on its carbohydrate moiety. Furthermore, depletion of the putative D. melanogaster lysosomal sorting receptor lysosomal enzyme receptor protein did not compromise cellular retention of dCREG. We also investigated the developmental consequences of dCREG ablation in whole D. melanogaster flies. Ubiquitous depletion of dCREG proved lethal at the late pupal stage once a knock-down efficiency of >95% was achieved. These results demonstrate that dCREG is essential for proper completion of fly development. Copyright © 2014. Published by Elsevier B.V.

Euryhaline ecology of early tetrapods revealed by stable isotopes.

PubMed

Goedert, Jean; Lécuyer, Christophe; Amiot, Romain; Arnaud-Godet, Florent; Wang, Xu; Cui, Linlin; Cuny, Gilles; Douay, Guillaume; Fourel, François; Panczer, Gérard; Simon, Laurent; Steyer, J-Sébastien; Zhu, Min

2018-06-01

The fish-to-tetrapod transition-followed later by terrestrialization-represented a major step in vertebrate evolution that gave rise to a successful clade that today contains more than 30,000 tetrapod species. The early tetrapod Ichthyostega was discovered in 1929 in the Devonian Old Red Sandstone sediments of East Greenland (dated to approximately 365 million years ago). Since then, our understanding of the fish-to-tetrapod transition has increased considerably, owing to the discovery of additional Devonian taxa that represent early tetrapods or groups evolutionarily close to them. However, the aquatic environment of early tetrapods and the vertebrate fauna associated with them has remained elusive and highly debated. Here we use a multi-stable isotope approach (δ 13 C, δ 18 O and δ 34 S) to show that some Devonian vertebrates, including early tetrapods, were euryhaline and inhabited transitional aquatic environments subject to high-magnitude, rapid changes in salinity, such as estuaries or deltas. Euryhalinity may have predisposed the early tetrapod clade to be able to survive Late Devonian biotic crises and then successfully colonize terrestrial environments.

Food deprivation increases the low-dose locomotor stimulant response to ethanol in Drosophila melanogaster.

PubMed

Kliethermes, Christopher L

2013-10-01

Acute and chronic states of food deprivation result in increased sensitivity to a variety of natural reinforcers as well as to drugs of abuse. Food deprived animals show increased locomotor activity during periods of food deprivation, as well as increased locomotor stimulant responses to drugs of abuse, including cocaine, amphetamine, morphine, and ethanol, implying that drugs of abuse act in part on neural systems that underlie responses towards food. To determine whether this effect extends to an invertebrate, highly genetically tractable animal, the locomotor stimulant effects of low dose ethanol were assessed under a variety of feeding conditions in the fruit fly, Drosophila melanogaster. Food deprivation resulted in strain specific increases in ethanol-stimulated locomotor activity in most strains tested, although elevated baseline activity confounded interpretation in some strains. Experiments conducted with Canton S flies found that the effects of food deprivation on the locomotor stimulant response to ethanol increased with the duration of deprivation, and could be blocked by refeeding the flies with standard food or sucrose, but not yeast, immediately prior to the ethanol exposure. Life-span extending dietary depletion procedures or previous periods of food deprivation did not affect the response to ethanol, indicating that only animals in an acutely food deprived state are more sensitive to the stimulant effects of ethanol. These results suggest that increased sensitivity to the stimulant effects of some drugs of abuse might reflect an evolutionarily conserved neural mechanism that underlies behavioral responses to natural reinforcers and drugs of abuse. The identification of this mechanism, and the genes that underlie its development and function, will constitute a novel approach towards the study of alcohol abuse and dependence. © 2013.

Strain accumulation in southern California, 1973-1980.

USGS Publications Warehouse

Savage, J.C.; Prescott, W.H.; Lisowski, M.; King, N.E.

1981-01-01

Frequent surveys of seven trilateration networks in southern California over the interval 1973-1980 suggest that a regional increment in strain may have occurred in 1978-1979. Prior to 1978 and after late 1979 the strain accumulation has been predominantly a uniaxial north-south compression. This secular trend was interrupted sometime in 1978-1979 by an increment in both north-south and east-west extension in five of the seven networks. The onset of this change appears to have occurred first in the networks farthest south. The changes occurred without any unusual seismicity within the networks, but the overall seismicity in southern California was unusually low prior to and has been unusually high since the occurrence. The average principal strain rates for the seven networks in the 1973-1980 interval are 0.17 mu strain/yr north- south contraction and 0.08 mu strain/yr east-west extension. Although the observed increment in strain could be related to unidentified systematic error in the measuring system, a careful review of the measurements and comparisons with three other measuring systems reveal no appreciable cumulative systematic error. -Authors

Identification of the anti-terminator qO111:H)- gene in Norwegian sorbitol-fermenting Escherichia coli O157:NM.

PubMed

Haugum, Kjersti; Lindstedt, Bjørn-Arne; Løbersli, Inger; Kapperud, Georg; Brandal, Lin Thorstensen

2012-04-01

Sorbitol-fermenting Escherichia coli O157:NM (SF O157) is an emerging pathogen suggested to be more virulent than nonsorbitol-fermenting Escherichia coli O157:H7 (NSF O157). Important virulence factors are the Shiga toxins (stx), encoded by stx1 and/or stx2 located within prophages integrated in the bacterial genome. The stx genes are expressed from p(R) (') as a late protein, and anti-terminator activity from the Q protein is necessary for read through of the late terminator t(R) (') and activation of p(R) (') . We investigated the regulation of stx2(EDL933) expression at the genomic level in 17 Norwegian SF O157. Sequencing of three selected SF O157 strains revealed that the anti-terminator q gene and genes upstream of stx2(EDL933) were identical or similar to the ones observed in the E. coli O111:H- strain AP010960, but different from the ones observed in the NSF O157 strain EDL933 (AE005174). This suggested divergent stx2(EDL933) -encoding bacteriophages between NSF O157 and the SF O157 strains (FR874039-41). Furthermore, different DNA structures were detected in the SF O157 strains, suggesting diversity among bacteriophages also within the SF O157 group. Further investigations are needed to elucidate whether the q(O111:H) (-) gene observed in all our SF O157 contributes to the increased virulence seen in SF O157 compared to NSF O157. An assay for detecting q(O111:H) (-) was developed. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Assessment of Right Atrium Function in Patients With Systemic Lupus Erythematosus With Different Pulmonary Artery Systolic Pressures by 2-Dimensional Speckle-Tracking Echocardiography.

PubMed

Sun, Lihua; Wang, Ying; Dong, Yu; Song, Shengda; Luo, Runlan; Li, Guangsen

2018-02-26

To assess right atrium (RA) function of patients with systemic lupus erythematosus (SLE) and pulmonary artery hypertension (PAH) by 2-dimensional speckle-tracking echocardiography. Thirty matched healthy adults were selected as group A. Then, 102 patients with SLE were divided into 3 groups according to the severity of PAH. Group B included 37 patients without PAH (pulmonary artery [PA] systolic pressure ≤ 30 mm Hg); group C included 34 patients with PAH (PA systolic pressure of 30-50 mm Hg); and group D included 31 patients with PAH (PA systolic pressure ≥ 50 mm Hg). Parameters evaluated included RA maximum volume, minimum volume, preatrial contraction volume, passive ejection fraction (EF), and active EF. The global peak longitudinal systolic strain rate and early and late diastolic strain rates of the RA were obtained by 2-dimensional speckle-tracking echocardiography. No significant differences were found in all parameters between groups B and A (P > .05). The RA maximum volume, minimum volume, preatrial contraction volume, active EF, and late diastolic strain rate in groups C and D were significantly increased compared with those in groups A and B, and the parameters in group D were significantly higher than those in group C (P < .05). Although the RA passive EF, early diastolic strain rate, and systolic strain rate in groups C and D were significantly decreased compared with those in groups A and B, those in group D were significantly lower than those in group C (P < .05). Two-dimensional speckle-tracking echocardiography could effectively assess RA function in patients with SLE who have different severities of PAH. © 2018 by the American Institute of Ultrasound in Medicine.

History of the First-Generation Marek's Disease Vaccines: The Science and Little-Known Facts.

PubMed

Schat, Karel A

2016-12-01

Shortly after the isolation of Marek's disease (MD) herpesvirus (MDV) in the late 1960s vaccines were developed in England, the United States, and The Netherlands. Biggs and associates at the Houghton Poultry Research Station (HPRS) in England attenuated HPRS-16, the first cell-culture-isolated MDV strain, by passaging HPRS-16 in chick kidney cells. Although HPRS-16/Att was the first commercially available vaccine, it never became widely used and was soon replaced by the FC126 strain of herpesvirus of turkeys (HVT) vaccine developed by Witter and associates at the Regional Poultry Research Laboratory (now Avian Disease and Oncology Laboratory [ADOL]) in East Lansing, MI. Ironically, Kawamura et al. isolated a herpesvirus from kidney cell cultures from turkeys in 1969 but never realized its potential as a vaccine against MD. Rispens of the Central Veterinary Institute (CVI) developed the third vaccine. His associate, Maas, had found commercial flocks of chickens with MDV antibodies but without MD. Subsequently, Rispens isolated a very low pathogenic strain from hen number 988 from his MD antibody-positive flock, which was free of avian leukosis virus and clinical MD. This isolate became the CVI-988 vaccine used mostly in The Netherlands. During the late 1970s, HVT was no longer fully protective against some new emerging field strains. The addition of SB-1, isolated by Schat and Calnek, to HVT improved protection against the emerging very virulent strains. In the 1990s CVI-988 became the worldwide vaccine gold standard. This review will present data from published papers and personal communications providing additional information about the exciting 15-yr period after the isolation of MDV to the development of the different vaccines.

Outbreak Caused by Escherichia coli O18: K1: H7 Sequence Type 95 in a Neonatal Intensive Care Unit in Barcelona, Spain.

PubMed

Sáez-López, Emma; Bosch, Jordi; Salvia, Maria Dolors; Fernández-Orth, Dietmar; Cepas, Virginio; Ferrer-Navarro, Mario; Figueras-Aloy, Josep; Vila, Jordi; Soto, Sara M

2017-11-01

Escherichia coli is one of the most frequent causes of late-onset neonatal sepsis. The aim of this study was to characterize an outbreak of neonatal sepsis occurring in the neonatal intensive care unit of the Hospital Clinic of Barcelona from April to August 2013. After presentation of the index case, all E. coli isolates from previously hospitalized neonates, health-care workers and neonates admitted to the neonatal intensive care unit from April to October 2013 were tested for K1 antigen positivity and epidemiologically compared by pulse-field gel electrophoresis. Furthermore, the E. coli K1 strains collected from neonates during this period were analyzed by different methods (serotyping, phylotyping, polymerase chain reaction of virulence factors, antimicrobial resistance and "in vitro" assays in Human Brain Microvascular Endothelial Cells (HBMEC)). An E. coli O18:K1:H7 sequence type 95 and phylogenetic group B2 strain was the cause of the outbreak involving 6 preterm neonates: 1 with late septicemia because of a urinary focus and 5 with late-onset septicemia and meningitis, 3 of whom died. All showed the same pulsotype, full resistance to ampicillin and intermediate resistance to gentamicin. The outbreak strain carried the pathogenicity island (PAI) IIJ96-like domain that could explain the high-grade bacteremia necessary to develop meningitis. All the E. coli isolates responsible for this outbreak belonged to a single clone suggesting a common source of infection, and it was categorized as O18:K1:H7. Despite the bacteria's pathogenicity has an important role in the severity of infection, the host-associated factors were crucial for the fatal outcomes.

Response of Methylocystis sp. Strain SC2 to Salt Stress: Physiology, Global Transcriptome, and Amino Acid Profiles.

PubMed

Han, Dongfei; Link, Hannes; Liesack, Werner

2017-08-11

Soil microorganisms have to rapidly respond to salt-induced osmotic stress. Type II methanotrophs of the genus Methylocystis are widely distributed in upland soils, but are known to have a low salt tolerance. Here, we tested the ability of Methylocystis sp. strain SC2 to adapt to increased salinity. When exposed to 0.75% NaCl, methane oxidation was completely inhibited for 2.25 h and fully recovered within 6 h. Growth was inhibited for 23.5 h and then fully recovered. Its transcriptome was profiled after 0 min (control), 45 min (early response) and 14 h (late response) of stress exposure. Physiological and transcriptomic stress response corresponded well. Salt stress induced differential expression of 301 genes, with sigma factor σ 32 being a major controller of the transcriptional stress response. The transcript levels of nearly all the genes involved in oxidizing CH 4 to CO 2 remained unaffected, while gene expression involved in energy-yielding reactions ( nuoEFGHI ) recovered concomitantly with methane oxidation from salt stress shock. Glutamate acted as an osmoprotectant. Its accumulation in late response corresponded to increased production of glutamate dehydrogenase 1. Chromosomal genes whose products (stress-induced protein, DNA-binding protein from starved cells, and CsbD family protein) are known to confer stress tolerance showed increased expression. On plasmid pBSC2-1, genes encoding type IV secretion system and single-strand DNA-binding protein were upregulated in late response, suggesting stress-induced activation of the plasmid-borne conjugation machinery. Collectively, our results show that Methylocystis sp. strain SC2 is able to adapt to salt stress, but only within a narrow range of salinities. Importance Besides the oxic interface of methanogenic environments, Methylocystis spp. are widely distributed in upland soils where they may contribute to the oxidation of atmospheric methane. However, little is known about their ability to cope with changes in moisture content and soil salinity. Growth and methane oxidation of Methylocystis sp. strain SC2 was not affected by the presence of 0.5% NaCl, while 1% NaCl completely inhibited its activities. This places strain SC2 into the low salt tolerance range reported for other Methylocystis spp. Our results show that, albeit in a narrow range, strain SC2 is able to respond and adapt to salinity changes. It possesses various stress-response mechanisms, which allows for a full resumption of its activities within 23.5 hours when exposed to 0.75% NaCl. Presumably, these mechanisms allow Methylocystis spp., such as strain SC2, to thrive in upland soils and to adapt to certain fluctuations in soil salinity. Copyright © 2017 American Society for Microbiology.

Neuroinvasive influenza virus A(H5N8) in fattening ducks, Hungary, 2015.

PubMed

Bányai, Krisztián; Bistyák, Andrea Tóthné; Thuma, Ákos; Gyuris, Éva; Ursu, Krisztina; Marton, Szilvia; Farkas, Szilvia L; Hortobágyi, Eleonóra; Bacsadi, Árpád; Dán, Ádám

2016-09-01

Highly pathogenic avian influenza (HPAI) A virus H5N8 was detected in far east Asian countries during 2014 and emerged in late 2014 in European countries. Hungary reported a HPAI A(H5N8) outbreak during late winter of 2015 at a Pekin duck fattening facility. Epidemiologic monitoring was extended to holdings in neighboring areas and nearby habitats used by wild birds but failed to identify the source of infection. In addition to respiratory symptoms, the affected birds showed lethargy and neuronal signs, including torticollis. Consistent with this finding, influenza A virus antigen was detected in large quantity in the brain. Molecular analysis of the identified strain showed very close genetic relationship (and >99% nucleotide sequence identity) with co-circulating HPAI A(H5N8) strains. A number of unique or rarely detected amino acid changes was detected in the HA (T220I, R512G), the M2 (I39M), the NA (T211I), the NS1 (P85T), and the PB2 (I261V) proteins of the Hungarian strain. Further studies are needed to demonstrate whether any of these mutations can be linked to neuroinvasiveness and neurovirulence in ducks. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of different Sinorhizobium meliloti inocula on abundance of genes involved in nitrogen transformations in the rhizosphere of alfalfa (Medicago sativa L.).

PubMed

Babić, Katarina Huić; Schauss, Kristina; Hai, Brigitte; Sikora, Sanja; Redzepović, Sulejman; Radl, Viviane; Schloter, Michael

2008-11-01

Inoculation of leguminous seeds with selected rhizobial strains is practised in agriculture to ameliorate the plant yield by enhanced root nodulation and nitrogen uptake of the plant. However, effective symbiosis between legumes and rhizobia does not only depend on the capacity of nitrogen fixation but also on the entire nitrogen turnover in the rhizosphere. We investigated the influence of seed inoculation with two indigenous Sinorhizobium meliloti strains exhibiting different efficiency concerning plant growth promotion on nitrogen turnover processes in the rhizosphere during the growth of alfalfa. Quantification of six target genes (bacterial amoA, nirK, nirS, nosZ, nifH and archaeal amoA) within the nitrogen cycle was performed in rhizosphere samples before nodule formation, at bud development and at the late flowering stage. The results clearly demonstrated that effectiveness of rhizobial inocula is related to abundance of nifH genes in the late flowering phase of alfalfa. Moreover, other genes involved in nitrogen turnover had been affected by the inocula, e.g. higher numbers of amoA copies were observed during flowering when the more effective strain had been inoculated. However, the respective gene abundances differed overall to a greater extent between the three plant development stages than between the inoculation variants.

Neonatal streptococcal infections.

PubMed Central

Parker, M. T.

1977-01-01

Most serious neonatal streptococcal infections are caused by group-B streptococci. The pattern of serious group-B neonatal disease in Britain resembles that described in other countries; both "early-onset" and "late-onset" forms are seen, but reliable incidence rates have not yet been determined. Serological-type III strains predominate in neonatal meningitis in Britain, but not so markedly as in some parts of the U.S.A. A deficiency of group-II strains in meningitis is, however, apparent in both countries. Present information about the carriage of group-B streptococci suggests that antibiotic prophylaxis administered to mothers or infants is unlikely to reduce greatly the frequency of "early-onset" disease. The continuous presence of a suitable chemical disinfectant in the vagina during labour might be more effective. Insufficient is known about the epidemiology of "late-onset" neonatal disease for rational preventive measures to be designed. More information is required about the postnatal acquisition of group-B streptococci by neonates and its sources, and about passive transfer of type-specific antibody from the mother to her child. PMID:339212

Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague.

PubMed

Spyrou, Maria A; Tukhbatova, Rezeda I; Wang, Chuan-Chao; Valtueña, Aida Andrades; Lankapalli, Aditya K; Kondrashin, Vitaly V; Tsybin, Victor A; Khokhlov, Aleksandr; Kühnert, Denise; Herbig, Alexander; Bos, Kirsten I; Krause, Johannes

2018-06-08

The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics. Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000-3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear. Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia. We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested. Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day.

IFN-Dependent and -Independent Reduction in West Nile Virus Infectivity in Human Dermal Fibroblasts

PubMed Central

Hoover, Lisa I.; Fredericksen, Brenda L.

2014-01-01

Although dermal fibroblasts are one of the first cell types exposed to West Nile virus (WNV) during a blood meal by an infected mosquito, little is known about WNV replication within this cell type. Here, we demonstrate that neuroinvasive, WNV-New York (WNV-NY), and nonneuroinvasive, WNV-Australia (WNV-AUS60) strains are able to infect and replicate in primary human dermal fibroblasts (HDFs). However, WNV-AUS60 replication and spread within HDFs was reduced compared to that of WNV-NY due to an interferon (IFN)-independent reduction in viral infectivity early in infection. Additionally, replication of both strains was constrained late in infection by an IFN-β-dependent reduction in particle infectivity. Overall, our data indicates that human dermal fibroblasts are capable of supporting WNV replication; however, the low infectivity of particles produced from HDFs late in infection suggests that this cell type likely plays a limited role as a viral reservoir in vivo. PMID:24662674

Identification of Plasmodium falciparum DNA Repair Protein Mre11 with an Evolutionarily Conserved Nuclease Function

PubMed Central

Badugu, Sugith Babu; Nabi, Shaik Abdul; Vaidyam, Pratap; Laskar, Shyamasree; Bhattacharyya, Sunanda; Bhattacharyya, Mrinal Kanti

2015-01-01

The eukaryotic Meiotic Recombination protein 11 (Mre11) plays pivotal roles in the DNA damage response (DDR). Specifically, Mre11 senses and signals DNA double strand breaks (DSB) and facilitates their repair through effector proteins belonging to either homologous recombination (HR) or non-homologous end joining (NHEJ) repair mechanisms. In the human malaria parasite Plasmodium falciparum, HR and alternative-NHEJ have been identified; however, little is known about the upstream factors involved in the DDR of this organism. In this report, we identify a putative ortholog of Mre11 in P. falciparum (PfalMre11) that shares 22% sequence similarity to human Mre11. Homology modeling reveals striking structural resemblance of the predicted PfalMre11 nuclease domain to the nuclease domain of Saccharomyces cerevisiae Mre11 (ScMre11). Complementation analyses reveal functional conservation of PfalMre11 nuclease activity as demonstrated by the ability of the PfalMre11 nuclease domain, in conjunction with the C-terminal domain of ScMre11, to functionally complement an mre11 deficient yeast strain. Functional complementation was virtually abrogated by an amino acid substitution in the PfalMre11 nuclease domain (D398N). PfalMre11 is abundant in the mitotically active trophozoite and schizont stages of P. falciparum and is up-regulated in response to DNA damage, suggesting a role in the DDR. PfalMre11 exhibits physical interaction with PfalRad50. In addition, yeast 2-hybrid studies show that PfalMre11 interacts with ScRad50 and ScXrs2, two important components of the well characterized Mre11-Rad50-Xrs2 complex which is involved in DDR signaling and repair in S. cerevisiae, further supporting a role for PfalMre11 in the DDR. Taken together, these findings provide evidence that PfalMre11 is an evolutionarily conserved component of the DDR in Plasmodium. PMID:25938776

A new comprehensive 12-segment approach to right ventricular systolic and diastolic functions by 2D speckle tracking echocardiography in healthy individuals.

PubMed

Rimbaş, Roxana C; Mihăilă, Sorina; Enescu, Oana A; Vinereanu, Dragoş

2016-12-01

2D speckle tracking echocardiography (2DSTE) was proved to be accurate for the assessment of the RV function. However, normal values for RV strain refer mostly to 3- or 6-segment models, excluding the contribution of other RV walls to RV function. We analyze RV function by 2DSTE in a normal population, using parasternal two-(2C) and apical four-chamber (4C) RV views, and creating a new 12-segment model for a potential better definition of RV function. We prospectively evaluated 100 normals using 2DE and STE. We assessed the RV systolic function from regional strain (basal, mid, and apical), and at the level of each wall: lateral (LS), septal (SS), inferior (IS), and anterior (AS), and also global strain for 4C (4CGS), and 2C (2CGS). Global systolic strain rate (SRs) was measured from 2C and 4C views. Diastolic function was assessed from early (SRe) and late global strain rate (SRl), for both views. A total of 70 healthy individuals (48±15 years, 34 men) were suitable for concomitant 4C and 2CRV analysis. Feasibility of the STE analysis was 87.8%. We found significantly lower SS by comparison with LS, AS, and IS (P<.001). All S/SR parameters (GS, SRs, and SRe) were higher in 2C view than in 4C view (P<.001). All systolic S/SR parameters did not change with age. The early diastolic SR decreased, while the late diastolic SR increased with age. Our 12-segment RV strain model is feasible. Moreover, 2DSTE analysis using 2C and 4C views of the RV does not provide similar information. Rather, they offer complementary data. This might be of particularly clinical interest in diseases with regional RV dysfunction. © 2016, Wiley Periodicals, Inc.

The Effect of Vaccination on the Evolution and Population Dynamics of Avian Paramyxovirus-1

PubMed Central

Hudson, Peter J.; Poss, Mary

2010-01-01

Newcastle Disease Virus (NDV) is a pathogenic strain of avian paramyxovirus (aPMV-1) that is among the most serious of disease threats to the poultry industry worldwide. Viral diversity is high in aPMV-1; eight genotypes are recognized based on phylogenetic reconstruction of gene sequences. Modified live vaccines have been developed to decrease the economic losses caused by this virus. Vaccines derived from avirulent genotype II strains were developed in the 1950s and are in use globally, whereas Australian strains belonging to genotype I were developed as vaccines in the 1970s and are used mainly in Asia. In this study, we evaluated the consequences of attenuated live virus vaccination on the evolution of aPMV-1 genotypes. There was phylogenetic incongruence among trees based on individual genes and complete coding region of 54 full length aPMV-1 genomes, suggesting that recombinant sequences were present in the data set. Subsequently, five recombinant genomes were identified, four of which contained sequences from either genotype I or II. The population history of vaccine-related genotype II strains was distinct from other aPMV-1 genotypes; genotype II emerged in the late 19th century and is evolving more slowly than other genotypes, which emerged in the 1960s. Despite vaccination efforts, genotype II viruses have experienced constant population growth to the present. In contrast, other contemporary genotypes showed population declines in the late 1990s. Additionally, genotype I and II viruses, which are circulating in the presence of homotypic vaccine pressure, have unique selection profiles compared to nonvaccine-related strains. Collectively, these data show that vaccination with live attenuated viruses has changed the evolution of aPMV-1 by maintaining a large effective population size of a vaccine-related genotype, allowing for coinfection and recombination of vaccine and wild type strains, and by applying unique selective pressures on viral glycoproteins. PMID:20421950

Adipose tissue conditioned media support macrophage lipid-droplet biogenesis by interfering with autophagic flux.

PubMed

Bechor, Sapir; Nachmias, Dikla; Elia, Natalie; Haim, Yulia; Vatarescu, Maayan; Leikin-Frenkel, Alicia; Gericke, Martin; Tarnovscki, Tanya; Las, Guy; Rudich, Assaf

2017-09-01

Obesity promotes the biogenesis of adipose tissue (AT) foam cells (FC), which contribute to AT insulin resistance. Autophagy, an evolutionarily-conserved house-keeping process, was implicated in cellular lipid handling by either feeding and/or degrading lipid-droplets (LDs). We hypothesized that beyond phagocytosis of dead adipocytes, AT-FC biogenesis is supported by the AT microenvironment by regulating autophagy. Non-polarized ("M0") RAW264.7 macrophages exposed to AT conditioned media (AT-CM) exhibited a markedly enhanced LDs biogenesis rate compared to control cells (8.3 Vs 0.3 LDs/cells/h, p<0.005). Autophagic flux was decreased by AT-CM, and fluorescently following autophagosomes over time revealed ~20% decline in new autophagic vesicles' formation rate, and 60-70% decrease in autophagosomal growth rate, without marked alternations in the acidic lysosomal compartment. Suppressing autophagy by either targeting autophagosome formation (pharmacologically, with 3-methyladenine or genetically, with Atg12±Atg7-siRNA), decreased the rate of LD formation induced by oleic acid. Conversely, interfering with late autophago-lysosomal function, either pharmacologically with bafilomycin-A1, chloroquine or leupeptin, enhanced LD formation in macrophages without affecting LD degradation rate. Similarly enhanced LD biogenesis rate was induced by siRNA targeting Lamp-1 or the V-ATPase. Collectively, we propose that secreted products from AT interrupt late autophagosome maturation in macrophages, supporting enhanced LDs biogenesis and AT-FC formation, thereby contributing to AT dysfunction in obesity. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Mcm3 replicative helicase mutation impairs neuroblast proliferation and memory in Drosophila.

PubMed

Blumröder, R; Glunz, A; Dunkelberger, B S; Serway, C N; Berger, C; Mentzel, B; de Belle, J S; Raabe, T

2016-09-01

In the developing Drosophila brain, a small number of neural progenitor cells (neuroblasts) generate in a co-ordinated manner a high variety of neuronal cells by integration of temporal, spatial and cell-intrinsic information. In this study, we performed the molecular and phenotypic characterization of a structural brain mutant called small mushroom bodies (smu), which was isolated in a screen for mutants with altered brain structure. Focusing on the mushroom body neuroblast lineages we show that failure of neuroblasts to generate the normal number of mushroom body neurons (Kenyon cells) is the major cause of the smu phenotype. In particular, the premature loss of mushroom body neuroblasts caused a pronounced effect on the number of late-born Kenyon cells. Neuroblasts showed no obvious defects in processes controlling asymmetric cell division, but generated less ganglion mother cells. Cloning of smu uncovered a single amino acid substitution in an evolutionarily conserved protein interaction domain of the Minichromosome maintenance 3 (Mcm3) protein. Mcm3 is part of the multimeric Cdc45/Mcm/GINS (CMG) complex, which functions as a helicase during DNA replication. We propose that at least in the case of mushroom body neuroblasts, timely replication is not only required for continuous proliferation but also for their survival. The absence of Kenyon cells in smu reduced learning and early phases of conditioned olfactory memory. Corresponding to the absence of late-born Kenyon cells projecting to α'/β' and α/β lobes, smu is profoundly defective in later phases of persistent memory. © 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Estimate the contribution of incubation parameters influence egg hatchability using multiple linear regression analysis

PubMed Central

Khalil, Mohamed H.; Shebl, Mostafa K.; Kosba, Mohamed A.; El-Sabrout, Karim; Zaki, Nesma

2016-01-01

Aim: This research was conducted to determine the most affecting parameters on hatchability of indigenous and improved local chickens’ eggs. Materials and Methods: Five parameters were studied (fertility, early and late embryonic mortalities, shape index, egg weight, and egg weight loss) on four strains, namely Fayoumi, Alexandria, Matrouh, and Montazah. Multiple linear regression was performed on the studied parameters to determine the most influencing one on hatchability. Results: The results showed significant differences in commercial and scientific hatchability among strains. Alexandria strain has the highest significant commercial hatchability (80.70%). Regarding the studied strains, highly significant differences in hatching chick weight among strains were observed. Using multiple linear regression analysis, fertility made the greatest percent contribution (71.31%) to hatchability, and the lowest percent contributions were made by shape index and egg weight loss. Conclusion: A prediction of hatchability using multiple regression analysis could be a good tool to improve hatchability percentage in chickens. PMID:27651666

Total lipid and fatty acid composition of eight strains of marine diatoms

NASA Astrophysics Data System (ADS)

Liang, Ying; Mai, Kang-Sen; Sun, Shi-Chun

2000-12-01

Fatty acid composition and total lipid content of 8 strains of marine diatoms ( Nitzschia frustrula, Nitzschia closterium, Nitzschia incerta, Navicula pelliculosa, Phaeodactylum tricornutum, Synedra fragilaroides) were examined. The microalgae were grown under defined conditions and harvested at the late exponential phase. The major fatty acids in most strains were 14∶0 (1.0% 6.3%), 16∶0 (13.5 26.4%), 16∶1n-7 (21.1% 46.3%) and 20∶5n-3 (6.5% 19.5%). The polyunsaturated fatty acids 16∶2n-4, 16∶3n-4, 16∶4n-1 and 20∶4n-6 also comprised a significant proportion of the total fatty acids in some strains. The characteristic fatty acid composition of diatoms is readily distinguishable from those of other microalgal groups. Significant concentration of the polyunsaturated fatty acid 20∶5n-3 (eicosapentaenoic acid) was present in each strain, with the highest proportion in B222 (19.5%).

Mechanisms of stable lipid loss in a social insect

PubMed Central

Ament, Seth A.; Chan, Queenie W.; Wheeler, Marsha M.; Nixon, Scott E.; Johnson, S. Peir; Rodriguez-Zas, Sandra L.; Foster, Leonard J.; Robinson, Gene E.

2011-01-01

SUMMARY Worker honey bees undergo a socially regulated, highly stable lipid loss as part of their behavioral maturation. We used large-scale transcriptomic and proteomic experiments, physiological experiments and RNA interference to explore the mechanistic basis for this lipid loss. Lipid loss was associated with thousands of gene expression changes in abdominal fat bodies. Many of these genes were also regulated in young bees by nutrition during an initial period of lipid gain. Surprisingly, in older bees, which is when maximum lipid loss occurs, diet played less of a role in regulating fat body gene expression for components of evolutionarily conserved nutrition-related endocrine systems involving insulin and juvenile hormone signaling. By contrast, fat body gene expression in older bees was regulated more strongly by evolutionarily novel regulatory factors, queen mandibular pheromone (a honey bee-specific social signal) and vitellogenin (a conserved yolk protein that has evolved novel, maturation-related functions in the bee), independent of nutrition. These results demonstrate that conserved molecular pathways can be manipulated to achieve stable lipid loss through evolutionarily novel regulatory processes. PMID:22031746

Mechanisms of stable lipid loss in a social insect.

PubMed

Ament, Seth A; Chan, Queenie W; Wheeler, Marsha M; Nixon, Scott E; Johnson, S Peir; Rodriguez-Zas, Sandra L; Foster, Leonard J; Robinson, Gene E

2011-11-15

Worker honey bees undergo a socially regulated, highly stable lipid loss as part of their behavioral maturation. We used large-scale transcriptomic and proteomic experiments, physiological experiments and RNA interference to explore the mechanistic basis for this lipid loss. Lipid loss was associated with thousands of gene expression changes in abdominal fat bodies. Many of these genes were also regulated in young bees by nutrition during an initial period of lipid gain. Surprisingly, in older bees, which is when maximum lipid loss occurs, diet played less of a role in regulating fat body gene expression for components of evolutionarily conserved nutrition-related endocrine systems involving insulin and juvenile hormone signaling. By contrast, fat body gene expression in older bees was regulated more strongly by evolutionarily novel regulatory factors, queen mandibular pheromone (a honey bee-specific social signal) and vitellogenin (a conserved yolk protein that has evolved novel, maturation-related functions in the bee), independent of nutrition. These results demonstrate that conserved molecular pathways can be manipulated to achieve stable lipid loss through evolutionarily novel regulatory processes.

Kinetics of force recovery following length changes in active skinned single fibres from rabbit psoas muscle

PubMed Central

Burton, Kevin; Simmons, Robert M; Sleep, John; Smith, David A

2006-01-01

Redevelopment of isometric force following shortening of skeletal muscle is thought to result from a redistribution of cross-bridge states. We varied the initial force and cross-bridge distribution by applying various length-change protocols to active skinned single fibres from rabbit psoas muscle, and observed the effect on the slowest phase of recovery (‘late recovery’) that follows transient changes. In response to step releases that reduced force to near zero (∼8 nm (half sarcomere)−1) or prolonged shortening at high velocity, late recovery was well described by two exponentials of approximately equal amplitude and rate constants of ∼2 s−1 and ∼9 s−1 at 5°C. When a large restretch was applied at the end of rapid shortening, recovery was accelerated by (1) the introduction of a slow falling component that truncated the rise in force, and (2) a relative increase in the contribution of the fast exponential component. The rate of the slow fall was similar to that observed after a small isometric step stretch, with a rate of 0.4–0.8 s−1, and its effects could be reversed by reducing force to near zero immediately after the stretch. Force at the start of late recovery was varied in a series of shortening steps or ramps in order to probe the effect of cross-bridge strain on force redevelopment. The rate constants of the two components fell by 40–50% as initial force was raised to 75–80% of steady isometric force. As initial force increased, the relative contribution of the fast component decreased, and this was associated with a length constant of about 2 nm. The results are consistent with a two-state strain-dependent cross-bridge model. In the model there is a continuous distribution of recovery rate constants, but two-exponential fits show that the fast component results from cross-bridges initially at moderate positive strain and the slow component from cross-bridges at high positive strain. PMID:16497718

Quaternary deformation in the central Neuquén basin (35°-37°S), Argentina: evidences for active strain partitioning.

NASA Astrophysics Data System (ADS)

Niviere, B.; Backé, G.

2006-12-01

The tectonic evolution of the Central Andes is a consequence of the relative convergence between the Nazca and the South American plates. The Neuquén basin is located in the southernmost part of the Central Andes, between latitudes 32°S and 40°S. The present day geometry of the basin has been inherited from different compressive pulses, separated by times of relative tectonic quiescence since the late Cretaceous. The complex tectonic evolution of the area has often been explained by changes in the geometry of the subducted plate. The last broad scale tectonic event in the Neuquén basin is the Miocene compressive stage referred to as the Quechua phase. The tectonic evolution of the outer part of the Neuquén Basin from the late Miocene onwards is still a matter of debate. For instance, strain partitioning has been described in the inner part of the basin, which corresponds to the modern arc area close to the Chile Argentina border. The strain regime in the foreland between 35°S and 37°S is more uncertain. Extensional tectonic features have been described in different areas of the basin, leading to the formulation of a possible orogenic collapse in response to the steepening of the oceanic slab that followed a late Miocene shallow subduction. This model accounts for the occurrence of large Pleistocene to Quaternary back-arc volcanism in the Neuquén basin. However, field structural data and borehole breakout analysis strongly support on-going compression in the basin. Our study is based on the morphostructural analysis of remote sensing data (satellite and digital elevation model images) complemented by field work. Here we show that strike-slip faulting and localized extension in the outer zone of the basin is coeval with active thrusting and folding. This can be explained by strain partitioning or segmentation processes due to the oblique convergence between the Nazca and the South American plates.

Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.

PubMed

Brody, Thomas; Yavatkar, Amarendra S; Park, Dong Sun; Kuzin, Alexander; Ross, Jermaine; Odenwald, Ward F

2017-06-01

Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome comparative analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the comparative analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest. We have adapted EvoPrinter alignment algorithms for the rapid comparative analysis of Flavivirus or Filovirus sequences including Zika and Ebola strains. The user can input a full genome or partial viral sequence and then view either individual comparisons or generate color-coded readouts that superimpose hundreds of one-on-one alignments to identify unique or shared identity SNPs that reveal ancestral relationships between strains. The user can also opt to select a database genome in order to access a library of pre-aligned genomes of either 1,094 Flaviviruses or 460 Filoviruses for rapid comparative analysis with all database entries or a select subset. Using EvoPrinter search and alignment programs, we show the following: 1) superimposing alignment data from many related strains identifies lineage identity SNPs, which enable the assessment of sublineage complexity within viral outbreaks; 2) whole-genome SNP profile screens uncover novel Dengue2 and Zika recombinant strains and their parental lineages; 3) differential SNP profiling identifies host cell A-to-I hyper-editing within Ebola and Marburg viruses, and 4) hundreds of superimposed one-on-one Ebola genome alignments highlight ultra-conserved regulatory sequences, invariant amino acid codons and evolutionarily variable protein-encoding domains within a single genome. EvoPrinter allows for the assessment of lineage complexity within Flavivirus or Filovirus outbreaks, identification of recombinant strains, highlights sequences that have undergone host cell A-to-I editing, and identifies unique input and database SNPs within highly conserved sequences. EvoPrinter's ability to superimpose alignment data from hundreds of strains onto a single genome has allowed us to identify unique Zika virus sublineages that are currently spreading in South, Central and North America, the Caribbean, and in China. This new set of integrated alignment programs should serve as a useful addition to existing tools for the comparative analysis of these viruses.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryo, H.; Yoo, M.A.; Fujikawa, K.

Somatic reversion of strains with the ivory (wi) allele, a mutation associated with a tandem duplication of a DNA sequence at the white locus, increased with the age of larvae at the time of X-irradiation as expected from the increase in the number of target cells. In contrast, two independently isolated strains with unstable w+ loci associated with insertion of transposable elements showed higher reversion frequencies after treatment with X rays or ethyl methanesulfonate (EMS) at early larval stages than at late stages. Nevertheless, both the wi strain and the two unstable w+ strains reverted at nearly equal rates aftermore » treatment with X rays or EMS at early larval stages. Possible similarity in hot spot structure for the high reversibility of the two types of mutations is discussed in relation to production of presumed mutator-type cofactors specific to the transposon-caused mutations at early larval stages.« less

Acetic acid fermentation of acetobacter pasteurianus: relationship between acetic acid resistance and pellicle polysaccharide formation.

PubMed

Kanchanarach, Watchara; Theeragool, Gunjana; Inoue, Taketo; Yakushi, Toshiharu; Adachi, Osao; Matsushita, Kazunobu

2010-01-01

Acetobacter pasteurianus strains IFO3283, SKU1108, and MSU10 were grown under acetic acid fermentation conditions, and their growth behavior was examined together with their capacity for acetic acid resistance and pellicle formation. In the fermentation process, the cells became aggregated and covered by amorphous materials in the late-log and stationary phases, but dispersed again in the second growth phase (due to overoxidation). The morphological change in the cells was accompanied by changes in sugar contents, which might be related to pellicle polysaccharide formation. To determine the relationship between pellicle formation and acetic acid resistance, a pellicle-forming R strain and a non-forming S strain were isolated, and their fermentation ability and acetic acid diffusion activity were compared. The results suggest that pellicle formation is directly related to acetic acid resistance ability, and thus is important to acetic acid fermentation in these A. pasteurianus strains.

Modification of digestive system microbiome of lactating dairy cows by feeding Bovamine: effect on ruminal fermentation

USDA-ARS?s Scientific Manuscript database

We evaluated the immune modulatory effects as well as effects on productivity of Bovamine® (Lactobacillus acidophilus strain NP51 and Probionibacterium freudenreichii) on the digestive system microbiome of dairy cattle during late lactation (average DIM = 202). To unveil the underlying mechanisms, ...

Graduation Certification--Too Late to Graduate!

ERIC Educational Resources Information Center

Doman, Mark S.

2017-01-01

Oakland University (OU) in Rochester, Michigan, was experiencing growing pains. The good news was that OU had experienced 23 years of continuous enrollment growth, with student enrollment exceeding 20,000 in 2015 for the first time ever. The downside was that various administrative processes throughout the university were straining to keep up. One…

Understanding the molecular basis of the resistance of Phytophthora infestans to fungicides by functional genomics

USDA-ARS?s Scientific Manuscript database

Development of resistance to fungicides is a major concern in managing potato late blight disease caused by Phytophthora infestans. The problem is P. infestans is capable of sexual recombination contributing to increased strain variability and high adaptability that hastens the development of resis...

Coaggregation between Rhodococcus and Acinetobacter strains isolated from the food industry.

PubMed

Møretrø, Trond; Sharifzadeh, Shahab; Langsrud, Solveig; Heir, Even; Rickard, Alexander H

2015-07-01

In this study, coaggregation interactions between Rhodococcus and Acinetobacter strains isolated from food-processing surfaces were characterized. Rhodococcus sp. strain MF3727 formed intrageneric coaggregates with Rhodococcus sp. strain MF3803 and intergeneric coaggregates with 2 strains of Acinetobacter calcoaceticus (MF3293, MF3627). Stronger coaggregation between A. calcoaceticus MF3727 and Rhodococcus sp. MF3293 was observed after growth in batch culture at 30 °C than at 20 °C, after growth in tryptic soy broth than in liquid R2A medium, and between cells in exponential and early stationary phases than cells in late stationary phase. The coaggregation ability of Rhodococcus sp. MF3727 was maintained even after heat and Proteinase K treatment, suggesting its ability to coaggregate was protein independent whereas the coaggregation determinants of the other strains involved proteinaceous cell-surface-associated polymers. Coaggregation was stable at pH 5-9. The mechanisms of coaggregation among Acinetobacter and Rhodococcus strains bare similarity to those displayed by coaggregating bacteria of oral and freshwater origin, with respect to binding between proteinaceous and nonproteinaceous determinants and the effect of environmental factors on coaggregation. Coaggregation may contribute to biofilm formation on industrial food surfaces, protecting bacteria against cleaning and disinfection.

Orogenic inheritance in Death Valley region, western US Basin and Range: implications for Neogene crustal extension.

NASA Astrophysics Data System (ADS)

Lima, R. D.; Hayman, N. W.; Prior, M. G.; Stockli, D. F.; Kelly, E. D.

2016-12-01

Deformation and temperature evolution during orogenic stages may influence later fabric development, thus controlling large-scale extensional processes that can occur millions of years later. Here, we describe pressure-temperature and fabric evolution from the Death Valley (DV) region and show how inherited fabrics, formed in late orogenic stages during Late Cretaceous time, influenced later Neogene age Basin and Range (BR) extension. The DV region is one of the most extended and thinned regions in the western US BR province, and the two of the ranges that bound the eastern valley expose basement rocks exhumed during the Neogene extension. In the Funeral range, it has been established that older (Precambrian) basement underwent Mesozoic age syn-deformational metamorphism during the Sevier-Laramide orogeny. In contrast, the Black Mountains record widespread tectonic stretching and magmatism of Miocene age on Precambrian basement, and have, overall, been lacking previous evidence of Mesozoic metamorphism and fabric development. In the Funeral Range Late Cretaceous migmatitic fabrics were overprinted by zones of high-strain fabrics formed due to melt-consuming reaction that define an overall P-T cooling path likely during late- to post-orogenesis. These fabrics form interconnected layers of quartz + biotite aggregates, in which individual quartz grains lack evidence of intracrystalline plastic deformation and show consistently random [c]-axis microfabrics. This suggests coupled reaction-diffusion processes that favored diffusion-assisted creep. New geochronometric results of melt products in the Black Mountains show evidence of partial melting of Late Cretaceous age. Contrasting with the neighboring Funeral Range, overprinting by extensional fabrics of Miocene age is widespread, and consists of high-strain, anastomosing foliation composed of retrograde products from preexisting, higher-temperature fabrics. These include interconnected fine-grained chlorite + quartz and sericite aggregates showing [c]-axis quartz microfabrics consistent with diffusion-assisted creep. In both ranges, the formation of new-over-old fabric due to the extensional deformation is favored by local heterogeneities in bulk composition due previous melt segregation during late- to post-orogenic stages.

Comparative genome analysis of Lactobacillus plantarum GB-LP3 provides candidates of survival-related genetic factors.

PubMed

Jeon, Soomin; Jung, Jaehoon; Kim, Kwondo; Yoo, DongAhn; Lee, Chanho; Kang, Jungsun; Cho, Kyungjin; Kang, Dae-Kyung; Kwak, Woori; Yoon, Sook Hee; Kim, Heebal; Cho, Seoae

2017-09-01

Lactobacillus plantarum is found in various environmental niches such as in the gastrointestinal tract of an animal host or a fermented food. This species isolated from a certain environment is known to possess a variety of properties according to inhabited environment's adaptation. However, a causal relationship of a genetic factor and phenotype affected by a specific environment has not been systematically comprehended. L. plantarum GB-LP3 strain was isolated from Korean traditional fermented vegetable and the whole genome of GB-LP3 was sequenced. Comparative genome analysis of GB-LP3, with other 14 L. plantarum strains, was conducted. In addition, genomic island regions were investigated. The assembled whole GB-LP3 genome contained a single circular chromosome of 3,206,111bp with the GC content of 44.7%. In the phylogenetic tree analysis, GB-LP3 was in the closest distance from ZJ316. The genomes of GB-LP3 and ZJ316 have the high level of synteny. Functional genes that are related to prophage, bacteriocin, and quorum sensing were found through comparative genomic analysis with ZJ316 and investigation of genomic islands. dN/dS analysis identified that the gene coding for phosphonate ABC transporter ATP-binding protein is evolutionarily accelerated in GB-LP3. Our study found that potential candidate genes that are affected by environmental adaptation in Korea traditional fermented vegetable. Copyright © 2017. Published by Elsevier B.V.

High level expression and characterization of the cyclophilin B gene from the anaerobic fungus Orpinomyces sp. strain PC-2.

PubMed

Chen, Huizhong; Li, Xin-Liang; Xu, Haiyan; Ljungdahl, Lars G; Cerniglia, Carl E

2006-01-01

Cyclophilins are an evolutionarily conserved family of peptidyl-prolyl cis-trans isomerases (PPIases). A cyclophilin B (cypB) gene from the anaerobic fungus Orpinomyces sp. strain PC-2 was cloned and overexpressed in Escherichia coli. It was expressed as an amino-terminal 6 x His-tagged recombinant protein to facilitate purification. Highly purified protein (26.5 kDa) was isolated by two chromatographic steps involving affinity and gel filtration for biochemical studies of the enzyme. The recombinant CypB displayed PPIase activity with a k(cat)/K(m) of 8.9 x 10(6) M(-1) s(-1) at 10 degrees C and pH 7.8. It was inhibited by cyclosporin A (CsA) with an IC(50) of 23.5 nM, similar to those of the native protein and other cyclophilin B enzymes from animals. Genomic DNA analysis of cypB revealed that it was present as a single copy in Orpinomyces PC-2 and contained two introns, indicating it has a eukaryotic origin. It is one of the most heavily interrupted genes with intron sequences found in anaerobic fungi. The three-dimensional model of Orpinomyces PC-2 CypB was predicted with a homology modeling approach using the Swiss-Model Protein Modeling Server and three dimensional structure of human CypB as a template. The overall architecture of the CypB molecule is very similar to that of human CypB.

The taxonomic status of "Halobacterium marismortui" from the Dead Sea: a comparison with Halobacterium vallismortis

NASA Technical Reports Server (NTRS)

Oren, A.; Lau, P. P.; Fox, G. E.

1988-01-01

A Halobacterium strain, isolated by Ginzburg et al. from the Dead Sea in the late 1960's, often referred to as "Halobacterium marismortui" or "Halobacterium of the Dead Sea" (deposited in the American Type Culture Collection as ATCC 43049) was compared with Halobacterium (Haloarcula) vallismortis ATCC 29715. The strains appeared to be very closely related, as shown by the near identity of their 5S and 16S ribosomal RNA's, and a large number of other common properties. Distinct differences exist, however, in cell morphology, and in their potency to utilize different sugars and other compounds.

Strain Release Amination

PubMed Central

Gianatassio, Ryan; Lopchuk, Justin M.; Wang, Jie; Pan, Chung-Mao; Malins, Lara R.; Prieto, Liher; Brandt, Thomas A.; Collins, Michael R.; Gallego, Gary M.; Sach, Neal W.; Spangler, Jillian E.; Zhu, Huichin; Zhu, Jinjiang; Baran, Phil S.

2015-01-01

To optimize drug candidates, modern medicinal chemists are increasingly turning to an unconventional structural motif: small, strained ring systems. However, the difficulty of introducing substituents such as bicyclo[1.1.1]pentanes, azetidines, or cyclobutanes often outweighs the challenge of synthesizing the parent scaffold itself. Thus, there is an urgent need for general methods to rapidly and directly append such groups onto core scaffolds. Here we report a general strategy to harness the embedded potential energy of effectively spring-loaded C–C and C–N bonds with the most oft-encountered nucleophiles in pharmaceutical chemistry, amines. Strain release amination can diversify a range of substrates with a multitude of desirable bioisosteres at both the early and late-stages of a synthesis. The technique has also been applied to peptide labeling and bioconjugation. PMID:26816372

Phosphoproteomic analysis reveals Smad protein family activation following Rift Valley fever virus infection.

PubMed

de la Fuente, Cynthia; Pinkham, Chelsea; Dabbagh, Deemah; Beitzel, Brett; Garrison, Aura; Palacios, Gustavo; Hodge, Kimberley Alex; Petricoin, Emanuel F; Schmaljohn, Connie; Campbell, Catherine E; Narayanan, Aarthi; Kehn-Hall, Kylene

2018-01-01

Rift Valley fever virus (RVFV) infects both ruminants and humans leading to a wide variance of pathologies dependent on host background and age. Utilizing a targeted reverse phase protein array (RPPA) to define changes in signaling cascades after in vitro infection of human cells with virulent and attenuated RVFV strains, we observed high phosphorylation of Smad transcription factors. This evolutionarily conserved family is phosphorylated by and transduces the activation of TGF-β superfamily receptors. Moreover, we observed that phosphorylation of Smad proteins required active RVFV replication and loss of NSs impaired this activation, further corroborating the RPPA results. Gene promoter analysis of transcripts altered after RVFV infection identified 913 genes that contained a Smad-response element. Functional annotation of these potential Smad-regulated genes clustered in axonal guidance, hepatic fibrosis and cell signaling pathways involved in cellular adhesion/migration, calcium influx, and cytoskeletal reorganization. Furthermore, chromatin immunoprecipitation confirmed the presence of a Smad complex on the interleukin 1 receptor type 2 (IL1R2) promoter, which acts as a decoy receptor for IL-1 activation.

Modification of immune responses and digestive system microbiota of lactating dairy cows by feeding Bovamine(R)

USDA-ARS?s Scientific Manuscript database

We evaluated the immune modulatory effects as well as effects on productivity of Bovamine® (Lactobacillus acidophilus strain NP51 and Probionibacterium freudenreichii) fed to Holstein and Jersey dairy cows during late lactation (average DIM = 202.44 days on wk-0). Cows were randomized to treatment g...

Strain Differences in Dimethylbenz[a]anthracene-Induced Mammary Tumor Incidence in Long Evans and Sprague Dawley Rat Offspring Following Prenatal Atrazine Exposure

EPA Science Inventory

It has been shown that prenatal exposure to the chlorotriazine herbicide atrazine (ATR) during mammary bud outgrowth (late gestation) delays postnatal mammary epithelial progression in Long Evans (LE) rats. Our laboratory has recently found that prenatal exposure to ATR also effe...

Scare Tactics

ERIC Educational Resources Information Center

Hua, Vanessa

2010-01-01

This article discusses how the H1N1 flu pandemic served notice to districts to get their disaster readiness strategies in order and how technology played an important part in schools effort. In late April 2010, as public fears about a mysterious new strain of flu grew, the Los Angeles Unified School District (LAUSD) moved to forestall a panic. On…

Frequency-dependent selection can lead to evolution of high mutation rates.

PubMed

Rosenbloom, Daniel I S; Allen, Benjamin

2014-05-01

Theoretical and experimental studies have shown that high mutation rates can be advantageous, especially in novel or fluctuating environments. Here we examine how frequency-dependent competition may lead to fluctuations in trait frequencies that exert upward selective pressure on mutation rates. We use a mathematical model to show that cyclical trait dynamics generated by "rock-paper-scissors" competition can cause the mutation rate in a population to converge to a high evolutionarily stable mutation rate, reflecting a trade-off between generating novelty and reproducing past success. Introducing recombination lowers the evolutionarily stable mutation rate but allows stable coexistence between mutation rates above and below the evolutionarily stable rate. Even considering strong mutational load and ignoring the costs of faithful replication, evolution favors positive mutation rates if the selective advantage of prevailing in competition exceeds the ratio of recombining to nonrecombining offspring. We discuss a number of genomic mechanisms that may meet our theoretical requirements for the adaptive evolution of mutation. Overall, our results suggest that local mutation rates may be higher on genes influencing cyclical competition and that global mutation rates in asexual species may be higher in populations subject to strong cyclical competition.

Evolutionary stability of egg trading and parceling in simultaneous hermaphrodites: the chalk bass revisited.

PubMed

Crowley, Philip H; Hart, Mary K

2007-06-07

Several species of simultaneously hermaphroditic seabasses living on coral reefs mate by alternating male and female roles with a partner. This is known as egg trading, one of the classic and most widely cited examples of social reciprocity among animals. Some of the egg-trading seabass species, including the chalk bass, Serranus tortugarum, switch mating roles repeatedly, having subdivided their clutch of eggs into parcels offered to the partner for fertilization. Here we attempt to understand these dynamics as a pair of evolutionary games, modifying some previous approaches to better reflect the biological system. We find that the trading of egg clutches is evolutionarily stable via byproduct mutualism and resistant to invasion by rare individuals that take the male role exclusively. We note why and how parceling may reflect sexual conflict between individuals in the mating pair. We estimate evolutionarily stable parcel numbers and show how they depend on parameter values. Typically, two or more sequential parcel numbers are evolutionarily stable, though the lowest of these yields the highest fitness. Assuming that parcel numbers are adjusted to local conditions, we predict that parcel numbers in nature are inversely related both to mating group density (except at low density) and predation risk.

Evolutionarily diverse SYP1 Qa-SNAREs jointly sustain pollen tube growth in Arabidopsis.

PubMed

Slane, Daniel; Reichardt, Ilka; El Kasmi, Farid; Bayer, Martin; Jürgens, Gerd

2017-11-01

Intracellular membrane fusion is effected by SNARE proteins that reside on adjacent membranes and form bridging trans-SNARE complexes. Qa-SNARE members of the Arabidopsis SYP1 family are involved in membrane fusion at the plasma membrane or during cell plate formation. Three SYP1 family members have been classified as pollen-specific as inferred from gene expression profiling studies, and two of them, SYP124 and SYP125, are confined to angiosperms. The SYP124 gene appears genetically unstable, whereas its sister gene SYP125 shows essentially no variation among Arabidopsis accessions. The third pollen-specific member SYP131 is sister to SYP132, which appears evolutionarily conserved in the plant lineage. Although evolutionarily diverse, the three SYP1 proteins are functionally overlapping in that only the triple mutant syp124 syp125 syp131 shows a specific and severe male gametophytic defect. While pollen development and germination appear normal, pollen tube growth is arrested during passage through the style. Our results suggest that angiosperm pollen tubes employ a combination of ancient and modern Qa-SNARE proteins to sustain their growth-promoting membrane dynamics during the reproductive process. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Mammalian monogamy is not controlled by a single gene

PubMed Central

Fink, Sabine; Excoffier, Laurent; Heckel, Gerald

2006-01-01

Complex social behavior in Microtus voles and other mammals has been postulated to be under the direct genetic control of a single locus: the arginine vasopressin 1a receptor (avpr1a) gene. Using a phylogenetic approach, we show that a repetitive element in the promoter region of avpr1a, which reportedly causes social monogamy, is actually widespread in nonmonogamous Microtus and other rodents. There was no evidence for intraspecific polymorphism in regard to the presence or absence of the repetitive element. Among 25 rodent species studied, the element was absent in only two closely related nonmonogamous species, indicating that this absence is certainly the result of an evolutionarily recent loss. Our analyses further demonstrate that the repetitive structures upstream of the avpr1a gene in humans and primates, which have been associated with social bonding, are evolutionarily distinct from those in rodents. Our evolutionary approach reveals that monogamy in rodents is not controlled by a single polymorphism in the promoter region of the avpr1a gene. We thus resolve the contradiction between the claims for an evolutionarily conserved genetic programming of social behavior in mammals and the vast evidence for highly complex and flexible mating systems. PMID:16832060

Structural phylogenetic analysis of activation-induced deaminase function.

PubMed

Ichikawa, H Travis; Sowden, Mark P; Torelli, Andrew T; Bachl, Jürgen; Huang, Pinwei; Dance, Geoffrey S C; Marr, Shauna H; Robert, Jacques; Wedekind, Joseph E; Smith, Harold C; Bottaro, Andrea

2006-07-01

In mammals, activation-induced deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of Ig genes. SHM and CSR activities require separate regions within AID. A chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES) at the AID C terminus is necessary for CSR, and has been suggested to associate with CSR-specific cofactors. CSR appeared late in AID evolution, during the emergence of land vertebrates from bony fish, which only display SHM. Here, we show that AID from African clawed frog (Xenopus laevis), but not pufferfish (Takifugu rubripes), can induce CSR in AID-deficient mouse B cells, although both are catalytically active in bacteria and mammalian cell systems, albeit at decreased level. Like mammalian AID, Takifugu AID is actively exported from the cell nucleus by CRM1, and the Takifugu NES can substitute for the equivalent region in human AID, indicating that all the CSR-essential NES motif functions evolutionarily predated CSR activity. We also show that fusion of the Takifugu AID catalytic domain to the entire human noncatalytic domain restores activity in mammalian cells, suggesting that AID features mapping within the noncatalytic domain, but outside the NES, influence its function.

Evidence of an evolutionary hourglass pattern in herbivory-induced transcriptomic responses.

PubMed

Durrant, Matthew; Boyer, Justin; Zhou, Wenwu; Baldwin, Ian T; Xu, Shuqing

2017-08-01

Herbivory-induced defenses are specific and activated in plants when elicitors, frequently found in the herbivores' oral secretions, are introduced into wounds during attack. While complex signaling cascades are known to be involved, it remains largely unclear how natural selection has shaped the evolution of these induced defenses. We analyzed herbivory-induced transcriptomic responses in wild tobacco, Nicotiana attenuata, using a phylotranscriptomic approach that measures the origin and sequence divergence of herbivory-induced genes. Highly conserved and evolutionarily ancient genes of primary metabolism were activated at intermediate time points (2-6 h) after elicitation, while less constrained and young genes associated with defense signaling and biosynthesis of specialized metabolites were activated at early (before 2 h) and late (after 6 h) stages of the induced response, respectively - a pattern resembling the evolutionary hourglass pattern observed during embryogenesis in animals and the developmental process in plants and fungi. The hourglass patterns found in herbivory-induced defense responses and developmental process are both likely to be a result of signaling modularization and differential evolutionary constraints on the modules involved in the signaling cascade. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

An amphioxus nodal gene (AmphiNodal) with early symmetrical expression in the organizer and mesoderm and later asymmetrical expression associated with left-right axis formation

NASA Technical Reports Server (NTRS)

Yu, Jr-Kai; Holland, Linda Z.; Holland, Nicholas D.

2002-01-01

The full-length sequence and zygotic expression of an amphioxus nodal gene are described. Expression is first detected in the early gastrula just within the dorsal lip of the blastopore in a region of hypoblast that is probably comparable with the vertebrate Spemann's organizer. In the late gastrula and early neurula, expression remains bilaterally symmetrical, limited to paraxial mesoderm and immediately overlying regions of the neural plate. Later in the neurula stage, all neural expression disappears, and mesodermal expression disappears from the right side. All along the left side of the neurula, mesodermal expression spreads into the left side of the gut endoderm. Soon thereafter, all expression is down-regulated except near the anterior and posterior ends of the animal, where transcripts are still found in the mesoderm and endoderm on the left side. At this time, expression also begins in the ectoderm on the left side of the head, in the region where the mouth later forms. These results suggest that amphioxus and vertebrate nodal genes play evolutionarily conserved roles in establishing Spemann's organizer, patterning the mesoderm rostrocaudally and setting up the asymmetrical left-right axis of the body.

Human papillomavirus type 18 chimeras containing the L2/L1 capsid genes from evolutionarily diverse papillomavirus types generate infectious virus

PubMed Central

Bowser, Brian S.; Chen, Horng-Shen; Conway, Michael J.; Christensen, Neil D.; Meyers, Craig

2011-01-01

Papillomaviruses (PVs) comprise a large family of viruses infecting nearly all vertebrate species, with more than 100 human PVs identified. Our previous studies showed that a mutant chimera HPV18/16 genome, consisting of the upper regulatory region and early ORFs of HPV18 and the late ORFs of HPV16, was capable of producing infectious virus in organotypic raft cultures. We were interested in determining whether the ability of this chimeric genome to produce infectious virus was the result of HPV18 and HPV16 being similarly oncogenic, anogenital types and whether more disparate PV types could also interact functionally. To test this we created a series of HPV18 chimeric genomes where the ORFs for the HPV18 capsid genes were replaced with the capsid genes of HPV45, HPV39, HPV33, HPV31, HPV11, HPV6b, HPV1a, CRPV, and BPV1. All chimeras were able to produce infectious chimeric viral particles, although with lower infectivity than wild-type HPV18. Steps in the viral life cycle and characteristics of the viral particles were examined to identify potential causes for the decrease in infectivity. PMID:21762735

The Murine Ortholog of Notchless, a Direct Regulator of the Notch Pathway in Drosophila melanogaster, Is Essential for Survival of Inner Cell Mass Cells

PubMed Central

Cormier, Sarah; Le Bras, Stéphanie; Souilhol, Céline; Vandormael-Pournin, Sandrine; Durand, Béatrice; Babinet, Charles; Baldacci, Patricia; Cohen-Tannoudji, Michel

2006-01-01

Notch signaling is an evolutionarily conserved pathway involved in intercellular communication and is essential for proper cell fate choices. Numerous genes participate in the modulation of the Notch signaling pathway activity. Among them, Notchless (Nle) is a direct regulator of the Notch activity identified in Drosophila melanogaster. Here, we characterized the murine ortholog of Nle and demonstrated that it has conserved the ability to modulate Notch signaling. We also generated mice deficient for mouse Nle (mNle) and showed that its disruption resulted in embryonic lethality shortly after implantation. In late mNle−/− blastocysts, inner cell mass (ICM) cells died through a caspase 3-dependent apoptotic process. Most deficient embryos exhibited a delay in the temporal down-regulation of Oct4 expression in the trophectoderm (TE). However, mNle-deficient TE was able to induce decidual swelling in vivo and properly differentiated in vitro. Hence, our results indicate that mNle is mainly required in ICM cells, being instrumental for their survival, and raise the possibility that the death of mNle-deficient embryos might result from abnormal Notch signaling during the first steps of development. PMID:16611995

The murine ortholog of notchless, a direct regulator of the notch pathway in Drosophila melanogaster, is essential for survival of inner cell mass cells.

PubMed

Cormier, Sarah; Le Bras, Stéphanie; Souilhol, Céline; Vandormael-Pournin, Sandrine; Durand, Béatrice; Babinet, Charles; Baldacci, Patricia; Cohen-Tannoudji, Michel

2006-05-01

Notch signaling is an evolutionarily conserved pathway involved in intercellular communication and is essential for proper cell fate choices. Numerous genes participate in the modulation of the Notch signaling pathway activity. Among them, Notchless (Nle) is a direct regulator of the Notch activity identified in Drosophila melanogaster. Here, we characterized the murine ortholog of Nle and demonstrated that it has conserved the ability to modulate Notch signaling. We also generated mice deficient for mouse Nle (mNle) and showed that its disruption resulted in embryonic lethality shortly after implantation. In late mNle(-/-) blastocysts, inner cell mass (ICM) cells died through a caspase 3-dependent apoptotic process. Most deficient embryos exhibited a delay in the temporal down-regulation of Oct4 expression in the trophectoderm (TE). However, mNle-deficient TE was able to induce decidual swelling in vivo and properly differentiated in vitro. Hence, our results indicate that mNle is mainly required in ICM cells, being instrumental for their survival, and raise the possibility that the death of mNle-deficient embryos might result from abnormal Notch signaling during the first steps of development.

A Presynaptic Regulatory System Acts Transsynaptically via Mon1 to Regulate Glutamate Receptor Levels in Drosophila.

PubMed

Deivasigamani, Senthilkumar; Basargekar, Anagha; Shweta, Kumari; Sonavane, Pooja; Ratnaparkhi, Girish S; Ratnaparkhi, Anuradha

2015-10-01

Mon1 is an evolutionarily conserved protein involved in the conversion of Rab5 positive early endosomes to late endosomes through the recruitment of Rab7. We have identified a role for Drosophila Mon1 in regulating glutamate receptor levels at the larval neuromuscular junction. We generated mutants in Dmon1 through P-element excision. These mutants are short-lived with strong motor defects. At the synapse, the mutants show altered bouton morphology with several small supernumerary or satellite boutons surrounding a mature bouton; a significant increase in expression of GluRIIA and reduced expression of Bruchpilot. Neuronal knockdown of Dmon1 is sufficient to increase GluRIIA levels, suggesting its involvement in a presynaptic mechanism that regulates postsynaptic receptor levels. Ultrastructural analysis of mutant synapses reveals significantly smaller synaptic vesicles. Overexpression of vglut suppresses the defects in synaptic morphology and also downregulates GluRIIA levels in Dmon1 mutants, suggesting that homeostatic mechanisms are not affected in these mutants. We propose that DMon1 is part of a presynaptically regulated transsynaptic mechanism that regulates GluRIIA levels at the larval neuromuscular junction. Copyright © 2015 by the Genetics Society of America.

Diversity of HIV-1 subtype C strains isolated in Romania.

PubMed

Paraschiv, Simona; Foley, Brian; Otelea, Dan

2011-03-01

Two unique aspects particularities of the HIV-1 epidemics in Romania are the high prevalence of subtype F1 strains and the large pediatric population infected in the late 1980s and early 1990s. During recent years, more infections with other subtypes have been seen in newly diagnosed patients. After subtype B, subtype C was the most frequent one. This subtype is prevalent in countries from sub-Saharan Africa and India, being responsible for half of the total HIV-1 infections in the world. We have identified 37 patients infected with subtype C, sequenced the reverse transcriptase and protease regions of their pol genes, and applied phylogenetic analyses to the sequences. We have also included 20 subtype F1 strains isolated from both teenagers (children at the time of diagnosis) and adults. The phylogenetic analysis was performed by using the PhyML method, the GTR (general time reversible) model of evolution and gamma distribution of variability of rates between sites, empirically calculated from the data. The epidemiological data indicates that the main route of transmission for the adult subjects was by heterosexual contact and a relatively small number of patients were possibly infected abroad. In three cases, blood transfusion prior to 1989 or surgical procedures at early ages were suspected to be the cause of the HIV infection and three other patients were most probably parenterally infected. The phylogenetic analyses showed that the Romanian C strains are very diverse overall, clustered in several groups characterized by common transmission route (transfusion/surgical procedures) or local geographical relatedness. The HIV-1 epidemics in Romania apparently followed different patterns for subtypes F and C. While subtype F1 seems to have been monoclonally introduced and extensively spread in the 80s, the subtype C strains, although present in the late 80s, failed to spread to the same extent. Copyright © 2010 Elsevier B.V. All rights reserved.

Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis.

PubMed

Baby, Vincent; Lachance, Jean-Christophe; Gagnon, Jules; Lucier, Jean-François; Matteau, Dominick; Knight, Tom; Rodrigue, Sébastien

2018-01-01

The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. IMPORTANCE The last years have witnessed the development of whole-genome cloning and transplantation methods and the complete synthesis of entire chromosomes. Recently, the first minimal cell, Mycoplasma mycoides JCVI-syn3.0, was created. Despite these milestone achievements, several questions remain to be answered. For example, is the composition of minimal genomes virtually identical in phylogenetically related species? On the basis of comparative genomics and transposon mutagenesis, we investigated this question by using an alternative model, Mesoplasma florum, that is also amenable to genome reduction efforts. Our results suggest that the creation of additional minimal genomes could help reveal different gene compositions and strategies that can support life, even within closely related species.

Extension of platelet shelf life from 4 to 5 days by implementation of a new screening strategy in Germany.

PubMed

Sireis, W; Rüster, B; Daiss, C; Hourfar, M K; Capalbo, G; Pfeiffer, H-U; Janetzko, K; Goebel, M; Kempf, V A J; Seifried, E; Schmidt, M

2011-10-01

The Paul-Ehrlich-Institute analysed all fatalities due to bacterial infections between 1997 and 2007. Thereafter, the platelet shelf life was reduced to a maximum of 4 days after blood donation because the majority of all cases of severe transfusion-transmitted bacterial infections occurred with day 5 platelets. The current study compares the analytical sensitivity and the diagnostic specificity of four rapid bacterial detection procedures. Nine transfusion-relevant bacterial strains were spiked in pooled platelets or apheresis platelets at a low concentration (10 CFU/bag). Samples were collected after day 3, day 4 and day 5 and investigated by four rapid bacterial detection methods (modified BacT/ALERT, Bactiflow, FACS method and 16s DNA PCR methods). Seven out of nine bacterial strains were adequately detected by BacT/ALERT, Bactiflow and PCR in apheresis platelets and pooled platelets after sample collection at day 3, day 4 and day 5. For three bacterial strains, analytical sensitivity was reduced for the FACS method. Two bacterial strains did not grow under the storage conditions in either pooled or apheresis platelets. A late sample collection on day 3, day 4 or day 5 after blood donation in combination with a rapid bacterial detection method offers a new opportunity to improve blood safety and reduce errors due to sampling., BacT/ALERT, Bactiflow or 16s ID-NAT are feasible for late bacterial screening in platelets may provide data which support the extension of platelet shelf life in Germany to 5 days. © 2011 The Author(s). Vox Sanguinis © 2011 International Society of Blood Transfusion.

Phylogenies of Microcystin-Producing Cyanobacteria in the Lower Laurentian Great Lakes Suggest Extensive Genetic Connectivity

PubMed Central

Davis, Timothy W.; Watson, Susan B.; Rozmarynowycz, Mark J.; Ciborowski, Jan J. H.; McKay, Robert Michael; Bullerjahn, George S.

2014-01-01

Lake St. Clair is the smallest lake in the Laurentian Great Lakes system. MODIS satellite imagery suggests that high algal biomass events have occurred annually along the southern shore during late summer. In this study, we evaluated these events and tested the hypothesis that summer bloom material derived from Lake St. Clair may enter Lake Erie via the Detroit River and represent an overlooked source of potentially toxic Microcystis biomass to the western basin of Lake Erie. We conducted a seasonally and spatially resolved study carried out in the summer of 2013. Our goals were to: 1) track the development of the 2013 summer south-east shore bloom 2) conduct a spatial survey to characterize the extent of toxicity, taxonomic diversity of the total phytoplankton population and the phylogenetic diversity of potential MC-producing cyanobacteria (Microcystis, Planktothrix and Anabaena) during a high biomass event, and 3) compare the strains of potential MC-producers in Lake St. Clair with strains from Lake Erie and Lake Ontario. Our results demonstrated a clear predominance of cyanobacteria during a late August bloom event, primarily dominated by Microcystis, which we traced along the Lake St. Clair coastline downstream to the Detroit River's outflow at Lake Erie. Microcystin levels exceeded the Province of Ontario Drinking Water Quality Standard (1.5 µg L−1) for safe drinking water at most sites, reaching up to five times this level in some areas. Microcystis was the predominant microcystin producer, and all toxic Microcystis strains found in Lake St. Clair were genetically similar to toxic Microcystis strains found in lakes Erie and Ontario. These findings suggest extensive genetic connectivity among the three systems. PMID:25207941

Toward a consistent model for strain accrual and release for the New Madrid Seismic Zone, central United States

USGS Publications Warehouse

Hough, S.E.; Page, M.

2011-01-01

At the heart of the conundrum of seismogenesis in the New Madrid Seismic Zone is the apparently substantial discrepancy between low strain rate and high recent seismic moment release. In this study we revisit the magnitudes of the four principal 1811–1812 earthquakes using intensity values determined from individual assessments from four experts. Using these values and the grid search method of Bakun and Wentworth (1997), we estimate magnitudes around 7.0 for all four events, values that are significantly lower than previously published magnitude estimates based on macroseismic intensities. We further show that the strain rate predicted from postglacial rebound is sufficient to produce a sequence with the moment release of one Mmax6.8 every 500 years, a rate that is much lower than previous estimates of late Holocene moment release. However, Mw6.8 is at the low end of the uncertainty range inferred from analysis of intensities for the largest 1811–1812 event. We show that Mw6.8 is also a reasonable value for the largest main shock given a plausible rupture scenario. One can also construct a range of consistent models that permit a somewhat higher Mmax, with a longer average recurrence rate. It is thus possible to reconcile predicted strain and seismic moment release rates with alternative models: one in which 1811–1812 sequences occur every 500 years, with the largest events being Mmax∼6.8, or one in which sequences occur, on average, less frequently, with Mmax of ∼7.0. Both models predict that the late Holocene rate of activity will continue for the next few to 10 thousand years.

Insights on Structure and Function of a Late Embryogenesis Abundant Protein from Amaranthus cruentus: An Intrinsically Disordered Protein Involved in Protection against Desiccation, Oxidant Conditions, and Osmotic Stress

PubMed Central

Saucedo, Alma L.; Hernández-Domínguez, Eric E.; de Luna-Valdez, Luis A.; Guevara-García, Angel A.; Escobedo-Moratilla, Abraham; Bojorquéz-Velázquez, Esaú; del Río-Portilla, Federico; Fernández-Velasco, Daniel A.; Barba de la Rosa, Ana P.

2017-01-01

Late embryogenesis abundant (LEA) proteins are part of a large protein family that protect other proteins from aggregation due to desiccation or osmotic stresses. Recently, the Amaranthus cruentus seed proteome was characterized by 2D-PAGE and one highly accumulated protein spot was identified as a LEA protein and was named AcLEA. In this work, AcLEA cDNA was cloned into an expression vector and the recombinant protein was purified and characterized. AcLEA encodes a 172 amino acid polypeptide with a predicted molecular mass of 18.34 kDa and estimated pI of 8.58. Phylogenetic analysis revealed that AcLEA is evolutionarily close to the LEA3 group. Structural characteristics were revealed by nuclear magnetic resonance and circular dichroism methods. We have shown that recombinant AcLEA is an intrinsically disordered protein in solution even at high salinity and osmotic pressures, but it has a strong tendency to take a secondary structure, mainly folded as α-helix, when an inductive additive is present. Recombinant AcLEA function was evaluated using Escherichia coli as in vivo model showing the important protection role against desiccation, oxidant conditions, and osmotic stress. AcLEA recombinant protein was localized in cytoplasm of Nicotiana benthamiana protoplasts and orthologs were detected in seeds of wild and domesticated amaranth species. Interestingly AcLEA was detected in leaves, stems, and roots but only in plants subjected to salt stress. This fact could indicate the important role of AcLEA protection during plant stress in all amaranth species studied. PMID:28439280

An ESS treatment of the pattern of female arrival at the mating site in the yellow dung fly scathophaga stercoraria (L.)

PubMed

Reuter; Ward; Blanckenhorn

1998-12-07

In most previous work on the yellow dung fly Scathophaga stercoraria (L.), as on other species, adaptive explanations have been sought for male behaviour whereas female behaviour has not been examined in similar detail. Here, the arrival of females at the mating site, fresh cattle droppings, is investigated. While almost all males are present shortly after pat deposition females arrive at a low, decreasing rate over an interval of about 5 hours. We propose that the distribution of female arrival times represents a mixed Evolutionarily Stable Strategy (ESS), formed by different trade-offs between costs and benefits of early and late arrival. Early arrival could be favoured by advantages due to better conditions for oviposition, faster egg development of reduced larval competition. Late arrival could be favoured by negative effects on females of male-male competition being weaker later after deposition. Computer simulations with distributions of arrival times deviating from the natural one were performed to "measure" the costs for females arriving at different times. These costs were compared with estimated benefits corresponding to the females' arrival times. This procedure revealed that females coming to the pat later in a population of females arriving shortly after deposition would be favoured. In a population arriving according to a uniform distribution, early females would have fitness advantages. Thus, evolution should lead to an intermediate distribution of arrival times, as in nature, i.e. female arrival behaviour is probably adaptive. The simulations also revealed that the intensity of sexual selection though male-male competition is highest with the natural pattern of female arrival. Therefore, natural selection generating this pattern amplifies the intensity of male-male interaction as a by-product. Copyright 1998 Academic Press

An iron-deficient diet during development induces oxidative stress in relation to age and gender in Wistar rats.

PubMed

Vieyra-Reyes, Patricia; Millán-Aldaco, Diana; Palomero-Rivero, Marcela; Jiménez-Garcés, Clementina; Hernández-González, Margarita; Caballero-Villarraso, Javier

2017-02-01

Iron is a trace element and a structural part of antioxidant enzymes, and its requirements vary according to age and gender. We hypothesized that iron deficiency (ID) leads to an increase in free radicals which mainly affect the brain, and the severity of damage would therefore be dependent on age and gender. Two groups of Wistar rats were evaluated evolutionarily: 100 rats (50 males; 50 females) with ID diet and 100 rats (50 males; 50 females) with standard diet. Both groups were offspring from mothers who were previously under the same dietary intervention. The ages studied roughly correspond to stages of human development: birth (0 postnatal day "PND" in rats), childhood (21 PND), early adolescence (42 PND), late adolescence (56 PND), and adulthood (70 PND). The following biomarkers in the brain, blood, and liver were analyzed: lipid peroxidation products (LPO), protein carbonyl content and activity of the antioxidant enzymes, superoxide dismutase, catalase, and glutathione peroxidase. It was demonstrated that ID subjects are born with high levels of LPO in the brain and low antioxidant activity, the damage being more severe in males. After birth, antioxidant defense focuses on the central level (brain) in ID females and on the peripheral level (blood and liver) in ID males. In two critical stages of development, birth and late adolescence, antioxidant protection is insufficient to counteract oxidative damage in ID subjects. Moreover, we observed that the variability of results in the literature on oxidative stress and ID comes from gender and age of the subjects under study. With this, we can establish patterns and exact moments to carry out studies or treatments.

Bounds on strain in large Tertiary shear zones of SE Asia from boudinage restoration

NASA Astrophysics Data System (ADS)

Lacassin, R.; Leloup, P. H.; Tapponnier, P.

1993-06-01

We have used surface-balanced restoration of stretched, boudinaged layers to estimate minimum amounts of finite strain in the mylonitic gneisses of the Oligo-Miocene Red River-Ailao Shan shear zone (Yunnan, China) and of the Wang Chao shear zone (Thailand). The layer-parallel extension values thus obtained range between 250 and 870%. We discuss how to use such extension values to place bounds on amounts of finite shear strain in these large crustal shear zones. Assuming simple shear, these values imply minimum total and late shear strains of, respectively, 33 ± 6 and 7 ± 3 at several sites along the Red River-Ailao Shan shear zone. For the Wang Chao shear zone a minimum shear strain of 7 ± 4 is deduced. Assuming homogeneous shear would imply that minimum strike-slip displacements along these two left-lateral shear zones, which have been interpreted to result from the India-Asia collision, have been of the order of 330 ± 60 km (Red River-Ailao Shan) and 35 ± 20 km (Wang Chao).

Pulsed-field gel electrophoresis of chromosomal DNA of methicillin-resistant Staphylococcus aureus associated with nosocomial infections.

PubMed

Hanifah, Y A; Hiramatsu, K

1994-12-01

Methicillin-resistant Staphylococcus aureus (MRSA) infection has been endemic in the University Hospital, Kuala Lumpur since the late 1970s. Fifty isolates of MRSA obtained from clinical specimens of patients with nosocomial infections associated with this organism have been studied by pulsed-field gel electrophoresis (PFGE) of its chromosomal DNA fragments to discrimate between strains and to identify the predominant strain. Twenty-one chromosomal patterns were observed which could be further grouped into nine types. The predominant strain was Type 9-b (40% of isolates) found mainly in the Orthopaedic and Surgical Units. Outbreak strains found in the Special Care Nursery were of Type 1, entirely different from those of the surgical ward S2, which were of Type 9-b. Type 8 strains were found mainly at one end of the hospital building where the maternity, paediatric and orthopaedic units were situated. Genomic DNA fingerprinting by PFGE is recommended as a useful and effective tool for the purpose of epidemiological studies of MSRA infections, particularly for nosocomial infections.

The complete genomic sequence of egg drop syndrome virus strain AAV-2.

PubMed

Jin, Q; Zeng, L; Yang, F; Li, M; Hou, Y

1999-12-01

In the search for the genome of egg drop syndrome virus (EDSV-76) Chinese strain AAV-2, part of restriction endonuclease physical map is analyzed, the complete genomic library is organized. On basis of this, the complete genome nucleotide sequences (32 838 bp in length, including terminal structures) are determined. The data analysis shows: compared with the other Adenoviruses, strain AAV-2 has more disparity on genomic structure and the distribution of open reading frame (ORF). There are no clear E1, E3 and E4 regions in AAV-2 genome. Two segments located at both ends of genome (1.1 kb and 8.3 kb in length respectively) have no homology with the other adenovirus genomes. In addition, strain AAV-2 genome lacks ORFs encoding ElA, pV and pIX, which are common ORFs encoding early, lately proteins in Adenovirus. This reveals differences between EDSA-76, the sole standard strain of group III Avian Adenoviruses, and the other Avian Adenoviruses for the first time. It will help the search for Avian Adenovirus and will also help the search of all Adenoviruses.

Strain-specific protective immunity following vaccination against experimental Trypanosoma cruzi infection.

PubMed

Haolla, Filipe A; Claser, Carla; de Alencar, Bruna C G; Tzelepis, Fanny; de Vasconcelos, José Ronnie; de Oliveira, Gabriel; Silvério, Jaline C; Machado, Alexandre V; Lannes-Vieira, Joseli; Bruna-Romero, Oscar; Gazzinelli, Ricardo T; dos Santos, Ricardo Ribeiro; Soares, Milena B P; Rodrigues, Mauricio M

2009-09-18

Immunisation with Amastigote Surface Protein 2 (asp-2) and trans-sialidase (ts) genes induces protective immunity in highly susceptible A/Sn mice, against infection with parasites of the Y strain of Trypanosoma cruzi. Based on immunological and biological strain variations in T. cruzi parasites, our goal was to validate our vaccination results using different parasite strains. Due to the importance of the CD8(+) T cells in protective immunity, we initially determined which strains expressed the immunodominant H-2K(k)-restricted epitope TEWETGQI. We tested eight strains, four of which elicited immune responses to this epitope (Y, G, Colombian and Colombia). We selected the Colombian and Colombia strains for our studies. A/Sn mice were immunised with different regimens using both T. cruzi genes (asp-2 and ts) simultaneously and subsequently challenged with blood trypomastigotes. Immune responses before the challenge were confirmed by the presence of specific antibodies and peptide-specific T cells. Genetic vaccination did not confer protective immunity against acute infection with a lethal dose of the Colombian strain. In contrast, we observed a drastic reduction in parasitemia and a significant increase in survival, following challenge with an otherwise lethal dose of the Colombia strain. In many surviving animals with late-stage chronic infection, we observed alterations in the heart's electrical conductivity, compared to naive mice. In summary, we concluded that immunity against T. cruzi antigens, similar to viruses and bacteria, may be strain-specific and have a negative impact on vaccine development.

Assessment of left atrial mechanical function and synchrony in paroxysmal atrial fibrillation with two-dimensional speckle tracking echocardiography.

PubMed

Shang, Zhijuan; Su, Dechun; Cong, Tao; Sun, Yinghui; Liu, Yan; Chen, Na; Yang, Jun

2017-02-01

The aim of this study was to investigate left atrial (LA) function and synchrony in paroxysmal atrial fibrillation (PAF) patients using two-dimensional speckle tracking echocardiography (STE). Forty-five PAF patients and 30 healthy controls were enrolled. LA peak ventricular systolic longitudinal strain (LA S -S ) and strain rate (LA SR -S ) and left atrial longitudinal strain (LA S -A ) and strain rate (LA SR -A ) during late diastole were determined using STE, and the standard deviation of the time to peak (TPSD) of the regional strains was calculated to quantify LA dyssynchrony. TPSD during ventricular systole and late diastole were named SDs and SDa, respectively. Left atrial peak longitudinal strain during ventricular systole (LA S -S ) (29.34±8.57 vs 36.73±6.13), LA SR -S (1.27±0.311 vs 1.57±0.25), LA S -A (13.11±4.91 vs 17.86±3.57), and LA SR -A (-1.51±0.58 vs -1.90±0.30) were reduced in the PAF group compared with the controls (P<.05 for all). SDs (8.11±3.00% vs 4.67±1.48%) and SDa (5.57±2.26% vs 3.11±1.13%) were greater in PAF patients than in the controls (P<.05 for both). Furthermore, PAF patients with normal LA sizes exhibited lower LA S -S (P<.05), LA SR -S (P<.05), LA S -A (P<.05), and LA SR -A (P<.05) values and increased SDs (P<.05) and SDa (P<.05) values compared with the controls. Multivariate regression confirmed that SDs and SDa were powerful parameters for differentiating PAF patients from controls (SDs: sensitivity, 83%; specificity, 72%; SDa: sensitivity, 81%; specificity, 76%). Left atrial (LA) dysfunction and dyssynchrony in PAF patients can be detected with STE even in the absence of LA enlargement. STE-derived SDs and SDa were powerful parameters for identifying PAF patients. © 2017, Wiley Periodicals, Inc.

Novel L-amino acid oxidase with algicidal activity against toxic cyanobacterium Microcystis aeruginosa synthesized by a bacterium Aquimarina sp.

PubMed

Chen, Wen Ming; Sheu, Fu Sian; Sheu, Shih Yi

2011-09-10

A brownish yellow pigmented bacterial strain, designated antisso-27, was recently isolated from a water area of saltpan in Southern Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences indicate that strain antisso-27 belongs the genus Aquimarina in the family Flavobacteriacea and its only closest neighbor is Aquimarina spongiae (96.6%). Based on screening for algicidal activity, strain antisso-27 exhibits potent activity against the toxic cyanobacterium Microcystis aeruginosa. Both the strain antisso-27 bacterial culture and its culture filtrate show algicidal activity against the toxic cyanobacterium, indicating that an algicidal substance is released from strain antisso-27. The algicidal activity of strain antisso-27 occurs during the late stationary phase of bacterial growth. Strain antisso-27 can synthesize an algicidal protein with a molecular mass of 190 kDa, and its isoelectric point is approximately 9.4. This study explores the nature of this algicidal protein such as L-amino acid oxidase with broad substrate specificity. The enzyme is most active with L-leucine, L-isoleucine, L-methionine and L-valine and the hydrogen peroxide generated by its catalysis mediates algicidal activity. This is the first report on an Aquimarina strain algicidal to the toxic M. aeruginosa and the algicidal activity is generated through its enzymatic activity of L-amino acid oxidase. Copyright © 2011 Elsevier Inc. All rights reserved.

Deletion and Complementation of the Mating Type (MAT) Locus of the Wheat Head Blight Pathogen Gibberella zeae

PubMed Central

Desjardins, A. E.; Brown, D. W.; Yun, S.-H.; Proctor, R. H.; Lee, T.; Plattner, R. D.; Lu, S.-W.; Turgeon, B. G.

2004-01-01

Gibberella zeae, a self-fertile, haploid filamentous ascomycete, causes serious epidemics of wheat (Triticum aestivum) head blight worldwide and contaminates grain with trichothecene mycotoxins. Anecdotal evidence dating back to the late 19th century indicates that G. zeae ascospores (sexual spores) are a more important inoculum source than are macroconidia (asexual spores), although the fungus can produce both during wheat head blight epidemics. To develop fungal strains to test this hypothesis, the entire mating type (MAT1) locus was deleted from a self-fertile (MAT1-1/MAT1-2), virulent, trichothecene-producing wild-type strain of G. zeae. The resulting MAT deletion (mat1-1/mat1-2) strains were unable to produce perithecia or ascospores and appeared to be unable to mate with the fertile strain from which they were derived. Complementation of a MAT deletion strain by transformation with a copy of the entire MAT locus resulted in recovery of production of perithecia and ascospores. MAT deletion strains and MAT-complemented strains retained the ability to produce macroconidia that could cause head blight, as assessed by direct injection into wheat heads in greenhouse tests. Availability of MAT-null and MAT-complemented strains provides a means to determine the importance of ascospores in the biology of G. zeae and perhaps to identify novel approaches to control wheat head blight. PMID:15066842

Strain heating in process zones; implications for metamorphism and partial melting in the lithosphere

NASA Astrophysics Data System (ADS)

Devès, Maud H.; Tait, Stephen R.; King, Geoffrey C. P.; Grandin, Raphaël

2014-05-01

Since the late 1970s, most earth scientists have discounted the plausibility of melting by shear-strain heating because temperature-dependent creep rheology leads to negative feedback and self-regulation. This paper presents a new model of distributed shear-strain heating that can account for the genesis of large volumes of magmas in both the crust and the mantle of the lithosphere. The kinematic (geometry and rates) frustration associated with incompatible fault junctions (e.g. triple-junction) prevents localisation of all strain on the major faults. Instead, deformation distributes off the main faults forming a large process zone that deforms still at high rates under both brittle and ductile conditions. The increased size of the shear-heated region minimises conductive heat loss, compared with that commonly associated with narrow shear zones, thus promoting strong heating and melting under reasonable rheological assumptions. Given the large volume of the heated zone, large volumes of melt can be generated even at small melt fractions.

S5 Lipase: an organic solvent tolerant enzyme.

PubMed

Rahman, Raja Noor Zaliha Abdul; Baharum, Syarul Nataqain; Salleh, Abu Bakar; Basri, Mahiran

2006-12-01

In this study, an organic solvent tolerant bacterial strain was isolated. This strain was identified as Pseudomonas sp. strain S5, and was shown to degrade BTEX (Benzene, Toluene, Ethyl-Benzene, and Xylene). Strain S5 generates an organic solvent-tolerant lipase in the late logarithmic phase of growth. Maximum lipase production was exhibited when peptone was utilized as the sole nitrogen source. Addition of any of the selected carbon sources to the medium resulted in a significant reduction of enzyme production. Lower lipase generation was noted when an inorganic nitrogen source was used as the sole nitrogen source. This bacterium hydrolyzed all tested triglycerides and the highest levels of production were observed when olive oil was used as a natural triglyceride. Basal medium containing Tween 60 enhanced lipase production to the most significant degree. The absence of magnesium ions (Mg2+) in the basal medium was also shown to stimulate lipase production. Meanwhile, an alkaline earth metal ion, Na+, was found to stimulate the production of S5 lipase.

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen

PubMed Central

Martin, Michael D.; Cappellini, Enrico; Samaniego, Jose A.; Zepeda, M. Lisandra; Campos, Paula F.; Seguin-Orlando, Andaine; Wales, Nathan; Orlando, Ludovic; Ho, Simon Y. W.; Dietrich, Fred S.; Mieczkowski, Piotr A.; Heitman, Joseph; Willerslev, Eske; Krogh, Anders; Ristaino, Jean B.; Gilbert, M. Thomas P.

2013-01-01

Responsible for the Irish potato famine of 1845–49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era strain remains entirely unknown. Here we characterize temporal genomic changes in introduced P. infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples—including the oldest known European specimen, collected in 1845 from the first reported source of introduction. We then compare their genomes to those of extant isolates. We report multiple distinct genotypes in historical Europe and a suite of infection-related genes different from modern strains. At virulence-related loci, several now-ubiquitous genotypes were absent from the historical gene pool. At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century’s episodic replacements of European P. infestans lineages. PMID:23863894

Regional Variation in Geniohyoid Muscle Strain During Suckling in the Infant Pig

PubMed Central

HOLMAN, SHAINA DEVI; KONOW, NICOLAI; LUKASIK, STACEY L.; GERMAN, REBECCA Z.

2014-01-01

The geniohyoid muscle (GH) is a critical suprahyoid muscle in most mammalian oropharyngeal motor activities. We used sonomicrometry to evaluate regional strain (i.e., changes in length) in the muscle origin, belly, and insertion during suckling in infant pigs, and compared the results to existing information on strain heterogeneity in the hyoid musculature. We tested the hypothesis that during rhythmic activity, the GH shows regional variation in muscle strain. We used sonomicrometry transducer pairs to divide the muscle into three regions from anterior to posterior. The results showed differences in strain among the regions within a feeding cycle; however, no region consistently shortened or lengthened over the course of a cycle. Moreover, regional strain patterns were not correlated with timing of the suck cycles, neither (1) relative to a swallow cycle (before or after) nor (2) to the time in feeding sequence (early or late). We also found a tight relationship between muscle activity and muscle strain, however, the relative timing of muscle activity and muscle strain was different in some muscle regions and between individuals. A dissection of the C1 innervations of the geniohyoid showed that there are between one and three branches entering the muscle, possibly explaining the variation seen in regional activity and strain. In combination, our findings suggest that regional heterogeneity in muscle strain during patterned suckling behavior functions to stabilize the hyoid bone, whereas the predictable regional strain differences in reflexive behaviors may be necessary for faster and higher amplitude movements of the hyoid bone. PMID:22549885

New insight into the epidemiology of rabbit hemorrhagic disease viruses in Portugal: retrospective study reveals the circulation of genogroup 5 (G5) in Azores and discloses the circulation of G1 and G6 strains in mainland until 2008.

PubMed

Duarte, Margarida Dias; Henriques, Ana Margarida; Barros, Sílvia; Luís, Tiago; Fagulha, Teresa; Ramos, Fernanda; Fevereiro, Miguel

2014-10-01

The genetic relationships between 10 rabbit hemorrhagic disease strains collected in Portugal between 2006 and 2013, originated in the mainland and Azorean islands, were investigated based on the vp60 gene variability. A genetic diversity ranging from 2% to 13% was determined among the 10-vp60 complete sequences revealing a significant level of genetic heterogeneity between same strains. Phylogenetic Bayesian analysis showed that the Portuguese RHDV strains fell within different genogroups, namely G1, G5 and G6. Interestingly, all strains obtained from Azores, where RHDV was first detected in 1988, belong to G5 genogroup. G5 strains, that were not identified in the continent so far, seem to be the dominant group in these Atlantic islands. G1-related strains belonging to the Iberian group 3 (n=3) and G6 (RHDVa) strains (n=2) were identified among the samples originated in mainland which were collected between 2006 and 2008. Although the presence of G1 and G6 in Portugal had been shown before, our data refines the time of circulation of these strains until at least 2008. In summary, this study revises the epidemiological information of RHDV in Portugal since it reports for the first time the presence of G5 strains in Azores and demonstrates the circulation of G1 and G6 strains in mainland Portugal until the late 2000s. Copyright © 2014 Elsevier B.V. All rights reserved.

The Stress-Strain State of Recent Structures in the Northeastern Sector of the Russian Arctic Region

NASA Astrophysics Data System (ADS)

Imaeva, L. P.; Imaev, V. S.; Mel'nikova, V. I.

2018-03-01

Complex research to determine the stress-strain state of the Earth's crust and the types of seismotectonic destruction for the northeastern sector of the Russian Arctic was conducted. The principles of regional ranking of neotectonic structures were developed according to the activity of geodynamic processes, and argumentation for their class differentiation is presented. The structural-tectonic position, the parameters of the deep structure, the system of active faults, and the tectonic stress fields, calculated on the basis of both tectonophysical analysis of discontinuous and folded late Cenozoic deformations and seismological data, were analyzed. This complex of investigations made it possible to determine the directions of the main axes of deformations of the stress-strain state of the Earth's crust and to reveal the regularity in the change of tectonic regimes.

Late or Lack of Vaccination Linked to Importation of Yellow Fever from Angola to China.

PubMed

Song, Rui; Guan, Shengcan; Lee, Shui Shan; Chen, Zhihai; Chen, Chen; Han, Lifen; Xu, Yanli; Li, Ang; Zeng, Hui; Ye, Hanhui; Zhang, Fujie

2018-07-17

During March and April 2016, 11 yellow fever cases were identified in China. We report epidemic and viral information for 10 of these patients, 6 of whom had been vaccinated before travel. Phylogenetic analyses suggest these viruses nested within the diversity of strains endemic to Angola, where an outbreak began in 2015.

Formation of dry gram-negative bacteria biocontrol products and small pilot tests against potato dry rot

USDA-ARS?s Scientific Manuscript database

Pseudomonas fluorescens strains S11:P:12, P22:Y:05, and S22:T:04 reduce important potato maladies in storage including dry rot, late blight, pink rot, and sprouting. Experiments were conducted to identify methods for producing a dried, efficacious biological control product from one or more of these...

Characterization of shiga toxin subtypes and virulence genes in Porcine shiga toxin-producing Escherichia coli

USDA-ARS?s Scientific Manuscript database

Similar to ruminants, swine have been shown to be a reservoir for Shiga toxin-producing Escherichia coli (STEC), and pork products have been linked with outbreaks associated with STEC O157 and O111:H-. STEC strains, isolated in a previous study from fecal samples of late-finisher pigs, belonged to a...

Evolutionary landscape of the Mycobacterium tuberculosis complex from the viewpoint of PhoPR: implications for virulence regulation and application to vaccine development.

PubMed

Broset, Esther; Martín, Carlos; Gonzalo-Asensio, Jesús

2015-10-20

Different members of the Mycobacterium genus have evolved to cause tuberculosis in diverse human populations and in a variety of animal species. Our cumulative knowledge of mycobacterial genomes indicates that mutations in the PhoPR two-component virulence system were acquired not only during the natural evolution of mycobacterial species but also during in vitro subculture, which has given rise to the attenuated reference strain H37Ra or to different daughter strains of Mycobacterium bovis BCG. PhoPR is a well-known regulator of pathogenic phenotypes, including secretion of the virulence factor ESAT-6, biosynthesis of acyltrehalose-based lipids, and modulation of antigen export, in members of the Mycobacterium tuberculosis complex (MTBC). Evolutionarily conserved polymorphisms in PhoPR from Mycobacterium africanum, M. bovis, or M. tuberculosis H37Ra result in loss of functional phenotypes. Interestingly, some members of the MTBC have acquired compensatory mutations to counteract these polymorphisms and, probably, to maintain their pathogenic potential. Some of these compensatory mutations include the insertion of the IS6110 element upstream from phoPR in a particular M. bovis strain that is able to transmit between humans or polymorphisms in M. africanum and M. bovis that affect the regulatory region of the espACD operon, allowing PhoPR-independent ESAT-6 secretion. This review highlights the increasing knowledge of the significance of PhoPR in the evolution of the MTBC and its potential application in the construction of new attenuated vaccines based on phoPR inactivation. In this context, the live attenuated vaccine MTBVAC, based on a phoP fadD26 deletion mutant of M. tuberculosis, is the first vaccine of this kind to successfully enter into clinical development, representing a historic milestone in the field of human vaccinology. Copyright © 2015 Broset et al.

Evolutionary Landscape of the Mycobacterium tuberculosis Complex from the Viewpoint of PhoPR: Implications for Virulence Regulation and Application to Vaccine Development

PubMed Central

Broset, Esther

2015-01-01

ABSTRACT Different members of the Mycobacterium genus have evolved to cause tuberculosis in diverse human populations and in a variety of animal species. Our cumulative knowledge of mycobacterial genomes indicates that mutations in the PhoPR two-component virulence system were acquired not only during the natural evolution of mycobacterial species but also during in vitro subculture, which has given rise to the attenuated reference strain H37Ra or to different daughter strains of Mycobacterium bovis BCG. PhoPR is a well-known regulator of pathogenic phenotypes, including secretion of the virulence factor ESAT-6, biosynthesis of acyltrehalose-based lipids, and modulation of antigen export, in members of the Mycobacterium tuberculosis complex (MTBC). Evolutionarily conserved polymorphisms in PhoPR from Mycobacterium africanum, M. bovis, or M. tuberculosis H37Ra result in loss of functional phenotypes. Interestingly, some members of the MTBC have acquired compensatory mutations to counteract these polymorphisms and, probably, to maintain their pathogenic potential. Some of these compensatory mutations include the insertion of the IS6110 element upstream from phoPR in a particular M. bovis strain that is able to transmit between humans or polymorphisms in M. africanum and M. bovis that affect the regulatory region of the espACD operon, allowing PhoPR-independent ESAT-6 secretion. This review highlights the increasing knowledge of the significance of PhoPR in the evolution of the MTBC and its potential application in the construction of new attenuated vaccines based on phoPR inactivation. In this context, the live attenuated vaccine MTBVAC, based on a phoP fadD26 deletion mutant of M. tuberculosis, is the first vaccine of this kind to successfully enter into clinical development, representing a historic milestone in the field of human vaccinology. PMID:26489860

A T-DNA gene required for agropine biosynthesis by transformed plants is functionally and evolutionarily related to a Ti plasmid gene required for catabolism of agropine by Agrobacterium strains.

PubMed Central

Hong, S B; Hwang, I; Dessaux, Y; Guyon, P; Kim, K S; Farrand, S K

1997-01-01

The mechanisms that ensure that Ti plasmid T-DNA genes encoding proteins involved in the biosynthesis of opines in crown gall tumors are always matched by Ti plasmid genes conferring the ability to catabolize that set of opines on the inducing Agrobacterium strains are unknown. The pathway for the biosynthesis of the opine agropine is thought to require an enzyme, mannopine cyclase, coded for by the ags gene located in the T(R) region of octopine-type Ti plasmids. Extracts prepared from agropine-type tumors contained an activity that cyclized mannopine to agropine. Tumor cells containing a T region in which ags was mutated lacked this activity and did not contain agropine. Expression of ags from the lac promoter conferred mannopine-lactonizing activity on Escherichia coli. Agrobacterium tumefaciens strains harboring an octopine-type Ti plasmid exhibit a similar activity which is not coded for by ags. Analysis of the DNA sequence of the gene encoding this activity, called agcA, showed it to be about 60% identical to T-DNA ags genes. Relatedness decreased abruptly in the 5' and 3' untranslated regions of the genes. ags is preceded by a promoter that functions only in the plant. Expression analysis showed that agcA also is preceded by its own promoter, which is active in the bacterium. Translation of agcA yielded a protein of about 45 kDa, consistent with the size predicted from the DNA sequence. Antibodies raised against the agcA product cross-reacted with the anabolic enzyme. These results indicate that the agropine system arose by a duplication of a progenitor gene, one copy of which became associated with the T-DNA and the other copy of which remained associated with the bacterium. PMID:9244272

The stress-regulatory transcription factors Msn2 and Msn4 regulate fatty acid oxidation in budding yeast.

PubMed

Rajvanshi, Praveen Kumar; Arya, Madhuri; Rajasekharan, Ram

2017-11-10

The transcription factors Msn2 and Msn4 (multicopy suppressor of SNF1 mutation proteins 2 and 4) bind the stress-response element in gene promoters in the yeast Saccharomyces cerevisiae However, the roles of Msn2/4 in primary metabolic pathways such as fatty acid β-oxidation are unclear. Here, in silico analysis revealed that the promoters of most genes involved in the biogenesis, function, and regulation of the peroxisome contain Msn2/4-binding sites. We also found that transcript levels of MSN2/MSN4 are increased in glucose-depletion conditions and that during growth in nonpreferred carbon sources, Msn2 is constantly localized to the nucleus in wild-type cells. Of note, the double mutant msn2 Δ msn4 Δ exhibited a severe growth defect when grown with oleic acid as the sole carbon source and had reduced transcript levels of major β-oxidation genes. ChIP indicated that Msn2 has increased occupancy on the promoters of β-oxidation genes in glucose-depleted conditions, and in vivo reporter gene analysis indicated reduced expression of these genes in msn2 Δ msn4 Δ cells. Moreover, mobility shift assays revealed that Msn4 binds β-oxidation gene promoters. Immunofluorescence microscopy with anti-peroxisome membrane protein antibodies disclosed that the msn2 Δ msn4 Δ strain had fewer peroxisomes than the wild type, and lipid analysis indicated that the msn2 Δ msn4 Δ strain had increased triacylglycerol and steryl ester levels. Collectively, our data suggest that Msn2/Msn4 transcription factors activate expression of the genes involved in fatty acid oxidation. Because glucose sensing, signaling, and fatty acid β-oxidation pathways are evolutionarily conserved throughout eukaryotes, the msn2 Δ msn4 Δ strain could therefore be a good model system for further study of these critical processes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Increased longitudinal contractility and diastolic function at rest in well-trained amateur Marathon runners: a speckle tracking echocardiography study

PubMed Central

2014-01-01

Background Regular physical activity reduces cardiovascular risk. There is concern that Marathon running might acutely damage the heart. It is unknown to what extent intensive physical endurance activity influences the cardiac mechanics at resting condition. Methods Eighty-four amateur marathon runners (43 women and 41 men) from Berlin-Brandenburg area who had completed at least one marathon previously underwent clinical examination and echocardiography at least 10 days before the Berlin Marathon at rest. Standard transthoracic echocardiography and 2D strain and strain rate analysis were performed. The 2D Strain and strain rate values were compared to previous published data of healthy untrained individuals. Results The average global longitudinal peak systolic strain of the left ventricle was -23 +/- 2% with peak systolic strain rate -1.39 +/- 0.21/s, early diastolic strain rate 2.0 +/- 0.40/s and late diastolic strain rate 1.21 +/- 0.31/s. These values are significantly higher compared to the previous published values of normal age-adjusted individuals. In addition, no age-related decline of longitudinal contractility in well-trained athletes was observed. Conclusions There is increased overall longitudinal myocardial contractility at rest in experienced endurance athletes compared to the published normal values in the literature indicating a preserved and even supra-normal contractility in the athletes. There is no age dependent decline of the longitudinal 2D Strain values. This underlines the beneficial effects of regular physical exercise even in advanced age. PMID:24571726

A retrospective: Use of Escherichia coli as a vehicle to study phospholipid synthesis and function

PubMed Central

Dowhan, William

2012-01-01

Although the study of individual phospholipids and their synthesis began in the 1920’s first in plants and then mammals, it was not until the early 1960’s that Eugene Kennedy using Escherichia coli initiated studies of bacterial phospholipid metabolism. With the base of information already available from studies of mammalian tissue, the basic blueprint of phospholipid biosynthesis in E. coli was worked out by the late 1960’s. In 1970’s and 1980’s most of the enzymes responsible for phospholipid biosynthesis were purified and many of the genes encoding these enzymes were identified. By the late 1990’s conditional and null mutants were available along with clones of the genes for every step of phospholipid biosynthesis. Most of these genes had been sequenced before the complete E. coli genome sequence was available. Strains of E. coli were developed in which phospholipid composition could be changed in a systematic manner while maintaining cell viability. Null mutants, strains in which phospholipid metabolism was artificially regulated, and strains synthesizing foreign lipids not found in E. coli have been used to this day to define specific roles for individual phospholipid. This review will trace the findings that have led to the development of E. coli as an excellent model system to study mechanisms underlying the synthesis and function of phospholipids that are widely applicable to other prokaryotic and eukaryotic systems. PMID:22925633

Temporal variations in extension rate on the Lone Mountain fault and strain distribution in the eastern California shear zone-Walker Lane

NASA Astrophysics Data System (ADS)

Hoeft, J. S.; Frankel, K. L.

2010-12-01

The eastern California shear zone (ECSZ) and Walker Lane represent an evolving segment of the Pacific-North America plate boundary. Understanding temporal variations in strain accumulation and release along plate boundary structures is critical to assessing how deformation is accommodated throughout the lithosphere. Late Pleistocene displacement along the Lone Mountain fault suggests the Silver Peak-Lone Mountain (SPLM) extensional complex is an important structure in accommodating and transferring strain within the ECSZ and Walker Lane. Using geologic and geomorphic mapping, differential global positioning system surveys, and terrestrial cosmogenic nuclide (TCN) geochronology, we determined rates of extension across the Lone Mountain fault in western Nevada. The Lone Mountain fault displaces the northwestern Lone Mountain and Weepah Hills piedmonts and is the northeastern component of the SPLM extensional complex, a series of down-to-the-northwest normal faults. We mapped seven distinct alluvial fan deposits and dated three of the surfaces using 10Be TCN geochronology, yielding ages of 16.5 ± 1.2 ka, 92 ± 9 ka, and 137 ± 25 ka for the Q3b, Q2c, and Q2b deposits, respectively. The ages were combined with scarp profile measurements across the displaced fans to obtain minimum rates of extension; the Q2b and Q2c surfaces yield an extension rate between 0.1 ± 0.1 and 0.2 ± 01 mm/yr and the Q3b surface yields a rate of 0.2 ± 0.1 to 0.4 ± 0.1 mm/yr, depending on the dip of the fault. Active extension on the Lone Mountain fault suggests that it helps partition strain off of the major strike-slip faults in the northern ECSZ and transfers deformation to the east around the Mina Deflection and northward into the Walker Lane. Combining our results with estimates from other faults accommodating dextral shear in the northern ECSZ reveals an apparent discrepancy between short- and long-term rates of strain accumulation and release. If strain rates have remained constant since the late Pleistocene, this could reflect transient strain accumulation, similar to the Mojave segment of the ECSZ. However, our data also suggest a potential increase in strain rates between ~92 ka and ~17 ka, and possibly to present day, which may also help explain the mismatch between long- and short-term rates of deformation in the region.

Changes in Central Walker Lane Strain Accommodation near Bridgeport, California; as told by the Stanislaus Group

NASA Astrophysics Data System (ADS)

Carlson, C. W.; Pluhar, C. J.; Glen, J. M.; Farner, M. J.

2012-12-01

Accommodating ~20-25% of the dextral-motion between the Pacific and North American plates the Walker Lane is represented as an elongate, NW oriented, region of active tectonics positioned between the northwesterly-translating Sierra Nevada microplate and the east-west extension of the Basin and Range. This region of transtension is being variably accommodated on regional-scale systems of predominantly strike-slip faulting. At the western edge of the central Walker Lane (ca. 38°-39°N latitude) is a region of crustal-scale blocks bounded by wedge-shaped depositional-basins and normal-fault systems, here defined as the west-central Walker Lane (WCWL). Devoid of obvious strike-slip faulting, the presence of tectonic-block vertical-axis rotations in the WCWL represents unrecognized components of dextral-shearing and/or changes of strain-accommodation over time. We use paleomagnetic reference directions for Eureka Valley Tuff (EVT) members of the late Miocene Stanislaus Group as spatial and temporal markers for documentation of tectonic-block vertical-axis rotations near Bridgeport, CA. Study-site rotations revealed discrete rotational domains of mean vertical-axis rotation ranging from ~10°-30° with heterogeneous regional distribution. Additionally, the highest measured magnitudes of vertical-axis rotation (~50°-60° CW) define a 'Region of High Strain' that includes the wedge-shaped Bridgeport Valley (Basin). This study revealed previously-unrecognized tectonic rotation of reference direction sites from prior studies for two (By-Day and Upper) of the three members of the EVT, resulting in under-estimates of regional strain accommodation by these studies. Mean remanent directions and virtual geomagnetic poles utilized in our study yielded a recalculated reference direction for the By-Day member of: Dec.=353.2°; Inc.= 43.7°; α95=10.1, in agreement with new measurements in the stable Sierra Nevada. This recalculated direction confirmed the presence of previously unrecognized reference site rotations, and provided an additional reference direction for determining vertical-axis rotation magnitudes. We present a kinematic model based on mean rotation magnitudes of ~30° CW for the Sweetwater Mountains and Bodie Hills that accounts for rotational-strain accommodation of dextral shear in the WCWL since the late Miocene. This model considers rotational magnitudes, paleostrain indicators, edge-effects, and strain-accommodating structures of rotating crustal blocks to represent changes in regional strain accommodation over time. The results and models presented here elucidate the complicated and evolving nature of the WCWL, and further understanding of variations in strain accommodation for the Walker Lane.

Sost, independent of the non-coding enhancer ECR5, is required for bone mechanoadaptation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robling, Alexander G.; Kang, Kyung Shin; Bullock, Whitney A.

Here, sclerostin ( Sost) is a negative regulator of bone formation that acts upon the Wnt signaling pathway. Sost is mechanically regulated at both mRNA and protein level such that loading represses and unloading enhances Sost expression, in osteocytes and in circulation. The non-coding evolutionarily conserved enhancer ECR5 has been previously reported as a transcriptional regulatory element required for modulating Sost expression in osteocytes. Here we explored the mechanisms by which ECR5, or several other putative transcriptional enhancers regulate Sost expression, in response to mechanical stimulation. We found that in vivo ulna loading is equally osteoanabolic in wildtype and Sostmore » –/– mice, although Sost is required for proper distribution of load-induced bone formation to regions of high strain. Using Luciferase reporters carrying the ECR5 non-coding enhancer and heterologous or homologous h SOST promoters, we found that ECR5 is mechanosensitive in vitro and that ECR5-driven Luciferase activity decreases in osteoblasts exposed to oscillatory fluid flow. Yet, ECR5–/– mice showed similar magnitude of load-induced bone formation and similar periosteal distribution of bone formation to high-strain regions compared to wildtype mice. Further, we found that in contrast to Sost–/– mice, which are resistant to disuse-induced bone loss, ECR5–/– mice lose bone upon unloading to a degree similar to wildtype control mice. ECR5 deletion did not abrogate positive effects of unloading on Sost, suggesting that additional transcriptional regulators and regulatory elements contribute to load-induced regulation of Sost.« less

Multilocus sequence typing (MLST) of leptospiral strains isolated from two geographic locations of Tamil Nadu, India.

PubMed

Kanagavel, Murugesan; Princy Margreat, Alphonse Asirvatham; Arunkumar, Manivel; Prabhakaran, Shanmugarajan Gnanasekaran; Shanmughapriya, Santhanam; Natarajaseenivasan, Kalimuthusamy

2016-01-01

Here the rodent carrier status for the transmission of human leptospirosis in Tiruchirappalli, district, Tamil Nadu, India was assessed. The predominantly circulating leptospiral STs were recognized by multilocus sequence typing (MLST). A total of 113 rodents were trapped from different provinces of the Tiruchirappalli district. The most prevalent rodent was Bandicota bengalensis (37.2%), and of the total, 52.2% (n=59) rodents were found to be positive for leptospiral 16S rRNA. These results were validated with a leptospiral culture positivity of 45.8% (n=27). Three isolates from Chennai (2 rodents and 1 human) and 1 human isolate from Tiruchirappalli were included to understand the spatial variations and to track the source of human leptospirosis. The serogroup, serovar, and species level identification of all 31 isolates identified 28 to be Leptospira borgpetersenii serovar Javanica and three as Leptospira interrogans serovar Autumnalis. MLST analysis defined all isolates to the existing ST profiles (ST145 and ST27) with the exception of 6 L. borgpetersenii (ST DR) isolates that showed variations in the sucA and pfkB loci. The DR ST was locally confined to Chatram province of Tiruchirappalli suggesting an epidemiological link. The predominant STs, ST145 and ST-DR form a group, indicating the presence of original strain that subsequently diverged evolutionarily into two STs. The variations between L. borgpetersenii in sucA and pfkB loci may be an indication that evolutionary changes transpired in Tiruchirappalli. Copyright © 2015 Elsevier B.V. All rights reserved.

Sost, independent of the non-coding enhancer ECR5, is required for bone mechanoadaptation

DOE PAGES

Robling, Alexander G.; Kang, Kyung Shin; Bullock, Whitney A.; ...

2016-09-04

Here, sclerostin ( Sost) is a negative regulator of bone formation that acts upon the Wnt signaling pathway. Sost is mechanically regulated at both mRNA and protein level such that loading represses and unloading enhances Sost expression, in osteocytes and in circulation. The non-coding evolutionarily conserved enhancer ECR5 has been previously reported as a transcriptional regulatory element required for modulating Sost expression in osteocytes. Here we explored the mechanisms by which ECR5, or several other putative transcriptional enhancers regulate Sost expression, in response to mechanical stimulation. We found that in vivo ulna loading is equally osteoanabolic in wildtype and Sostmore » –/– mice, although Sost is required for proper distribution of load-induced bone formation to regions of high strain. Using Luciferase reporters carrying the ECR5 non-coding enhancer and heterologous or homologous h SOST promoters, we found that ECR5 is mechanosensitive in vitro and that ECR5-driven Luciferase activity decreases in osteoblasts exposed to oscillatory fluid flow. Yet, ECR5–/– mice showed similar magnitude of load-induced bone formation and similar periosteal distribution of bone formation to high-strain regions compared to wildtype mice. Further, we found that in contrast to Sost–/– mice, which are resistant to disuse-induced bone loss, ECR5–/– mice lose bone upon unloading to a degree similar to wildtype control mice. ECR5 deletion did not abrogate positive effects of unloading on Sost, suggesting that additional transcriptional regulators and regulatory elements contribute to load-induced regulation of Sost.« less

A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes

PubMed Central

2014-01-01

Background Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes. PMID:24898731

The presence of a mycangium in European Sinodendron cylindricum (Coleoptera: Lucanidae) and the associated yeast symbionts

PubMed Central

Tanahashi, Masahiko; Hawes, Colin J.

2016-01-01

Part of the exoskeleton of some wood-inhabiting insects is modified to form a mycangium, which is a specialized organ used to convey fungal spores or yeasts to their offspring. Although most stag beetles (Coleoptera: Lucanidae) are known to have female-specific mycangia and associated yeast symbionts, the evolutionary origin of the mycangium in this group remains unresolved. Here, we report the presence of a mycangium and associated yeast symbionts in the European horned stag beetle Sinodendron cylindricum (L.), which belongs to an ancestral clade of the Lucanidae. The mycangium of S. cylindricum is shown to be female-specific and have the same developmental origin as that of other stag beetles. A total of five yeast strains were isolated from adult mycangia and larval gut of S. cylindricum. Of these, we suggest that SICYAM1 is an undescribed yeast with taxonomic novelty, and have identified SICYLG3 as the xylose-fermenting yeast Scheffersomyces insectosa using nuclear ribosomal RNA and ITS sequences. The remaining three yeast strains, SICYAM2, SICYLG1, and SICYLG2, were assigned to the genus Sugiyamaella. Yeast density in the adult mycangium was lower than that of the more evolutionarily advanced stag beetles, the European Lucanus cervus (L.) and Dorcus parallelipipedus (L.), which were also examined in this study. No living yeasts were isolated from the adult guts. However, a third instar larva of S. cylindricum harbored 104–106 living yeasts in each gut region, which suggests that gut yeasts play an important role in these wood-feeding larvae. PMID:27432353

A Mutation in PGM2 Causing Inefficient Galactose Metabolism in the Probiotic Yeast Saccharomyces boulardii.

PubMed

Liu, Jing-Jing; Zhang, Guo-Chang; Kong, In Iok; Yun, Eun Ju; Zheng, Jia-Qi; Kweon, Dae-Hyuk; Jin, Yong-Su

2018-05-15

The probiotic yeast Saccharomyces boulardii has been extensively studied for the prevention and treatment of diarrheal diseases, and it is now commercially available in some countries. S. boulardii displays notable phenotypic characteristics, such as a high optimal growth temperature, high tolerance against acidic conditions, and the inability to form ascospores, which differentiate S. boulardii from Saccharomyces cerevisiae The majority of prior studies stated that S. boulardii exhibits sluggish or halted galactose utilization. Nonetheless, the molecular mechanisms underlying inefficient galactose uptake have yet to be elucidated. When the galactose utilization of a widely used S. boulardii strain, ATCC MYA-796, was examined under various culture conditions, the S. boulardii strain could consume galactose, but at a much lower rate than that of S. cerevisiae While all GAL genes were present in the S. boulardii genome, according to analysis of genomic sequencing data in a previous study, a point mutation (G1278A) in PGM2 , which codes for phosphoglucomutase, was identified in the genome of the S. boulardii strain. As the point mutation resulted in the truncation of the Pgm2 protein, which is known to play a pivotal role in galactose utilization, we hypothesized that the truncated Pgm2 might be associated with inefficient galactose metabolism. Indeed, complementation of S. cerevisiae PGM2 in S. boulardii restored galactose utilization. After reverting the point mutation to a full-length PGM2 in S. boulardii by Cas9-based genome editing, the growth rates of wild-type (with a truncated PGM2 gene) and mutant (with a full-length PGM2 ) strains with glucose or galactose as the carbon source were examined. As expected, the mutant (with a full-length PGM2 ) was able to ferment galactose faster than the wild-type strain. Interestingly, the mutant showed a lower growth rate than that of the wild-type strain on glucose at 37°C. Also, the wild-type strain was enriched in the mixed culture of wild-type and mutant strains on glucose at 37°C, suggesting that the truncated PGM2 might offer better growth on glucose at a higher temperature in return for inefficient galactose utilization. Our results suggest that the point mutation in PGM2 might be involved in multiple phenotypes with different effects. IMPORTANCE Saccharomyces boulardii is a probiotic yeast strain capable of preventing and treating diarrheal diseases. However, the genetics and metabolism of this yeast are largely unexplored. In particular, molecular mechanisms underlying the inefficient galactose metabolism of S. boulardii remain unknown. Our study reports that a point mutation in PGM2 , which codes for phosphoglucomutase, is responsible for inferior galactose utilization by S. boulardii After correction of the mutated PGM2 via genome editing, the resulting strain was able to use galactose faster than a parental strain. While the PGM2 mutation made the yeast use galactose slowly, investigation of the genomic sequencing data of other S. boulardii strains revealed that the PGM2 mutation is evolutionarily conserved. Interestingly, the PGM2 mutation was beneficial for growth at a higher temperature on glucose. We speculate that the PGM2 mutation was enriched due to selection of S. boulardii in the natural habitat (sugar-rich fruits in tropical areas). Copyright © 2018 American Society for Microbiology.

Impact of revascularization of coronary chronic total occlusion on left ventricular function and electrical stability: analysis by speckle tracking echocardiography and signal-averaged electrocardiogram.

PubMed

Sotomi, Yohei; Okamura, Atsunori; Iwakura, Katsuomi; Date, Motoo; Nagai, Hiroyuki; Yamasaki, Tomohiro; Koyama, Yasushi; Inoue, Koichi; Sakata, Yasushi; Fujii, Kenshi

2017-06-01

The present study aimed to assess the mechanisms of effects of percutaneous coronary intervention (PCI) for chronic total occlusion (CTO) from two different aspects: left ventricular (LV) systolic function assessed by two-dimensional speckle tracking echocardiography (2D-STE) and electrical stability evaluated by late potential on signal-averaged electrocardiogram (SAECG). We conducted a prospective observational study with consecutive CTO-PCI patients. 2D-STE and SAECG were performed before PCI, and after 1-day and 3-months of procedure. 2D-STE computed global longitudinal strain (GLS) and regional longitudinal strain (RLS) in CTO area, collateral blood-supplying donor artery area, and non-CTO/non-donor area. A total of 37 patients (66 ± 11 years, 78% male) were analyzed. RLS in CTO and donor areas and GLS were significantly improved 1-day after the procedure, but these improvements diminished during 3 months. The improvement of RLS in donor area remained significant after 3-months the index procedure (pre-PCI -13.4 ± 4.8% vs. post-3M -15.1 ± 4.5%, P = 0.034). RLS in non-CTO/non-donor area and LV ejection fraction were not influenced. Mitral annulus velocity was improved at 3-month follow-up (5.0 ± 1.4 vs. 5.6 ± 1.7 cm/s, P = 0.049). Before the procedure, 12 patients (35%) had a late potential. All components of the late potential (filtered QRS duration, root-mean-square voltage in the terminal 40 ms, and duration of the low amplitude signal <40 μV) were not improved. CTO-PCI improved RLS in the donor area at 3-month follow-up without changes of LV ejection fraction. Although higher prevalence of late potential in the current population compared to healthy population was observed, late potential as a surrogate of arrhythmogenic substrate was not influenced by CTO-PCI.

Popular culture and sporting life in the rural margins of late eighteenth-century England: the world of Robert Anderson, "The Cumberland Bard".

PubMed

Huggins, Mike

2012-01-01

This study sets out to extend and challenge existing historiography on late eighteenth century British popular culture, customary sports, class and cultural identity, focusing upon the rural geo-political borderland of England. It suggests that prevailing class-based and more London-biased studies need to be balanced with more regionalist-based work, and shows the importance of northern regional leisure variants. The textual and historical analysis draws largely on the published works of a neglected working-class dialect poet, Robert Anderson, living and working in Cumberland, arguing that he represented a strain of ''bardic regionalism,'' a variant of Katie Trumpener’s ''bardic nationalism.''

An evolutionarily conserved gene, FUWA, plays a role in determining panicle architecture, grain shape and grain weight in rice.

PubMed

Chen, Jun; Gao, He; Zheng, Xiao-Ming; Jin, Mingna; Weng, Jian-Feng; Ma, Jin; Ren, Yulong; Zhou, Kunneng; Wang, Qi; Wang, Jie; Wang, Jiu-Lin; Zhang, Xin; Cheng, Zhijun; Wu, Chuanyin; Wang, Haiyang; Wan, Jian-Min

2015-08-01

Plant breeding relies on creation of novel allelic combinations for desired traits. Identification and utilization of beneficial alleles, rare alleles and evolutionarily conserved genes in the germplasm (referred to as 'hidden' genes) provide an effective approach to achieve this goal. Here we show that a chemically induced null mutation in an evolutionarily conserved gene, FUWA, alters multiple important agronomic traits in rice, including panicle architecture, grain shape and grain weight. FUWA encodes an NHL domain-containing protein, with preferential expression in the root meristem, shoot apical meristem and inflorescences, where it restricts excessive cell division. Sequence analysis revealed that FUWA has undergone a bottleneck effect, and become fixed in landraces and modern cultivars during domestication and breeding. We further confirm a highly conserved role of FUWA homologs in determining panicle architecture and grain development in rice, maize and sorghum through genetic transformation. Strikingly, knockdown of the FUWA transcription level by RNA interference results in an erect panicle and increased grain size in both indica and japonica genetic backgrounds. This study illustrates an approach to create new germplasm with improved agronomic traits for crop breeding by tapping into evolutionary conserved genes. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Success of cuckoo catfish brood parasitism reflects coevolutionary history and individual experience of their cichlid hosts

PubMed Central

Polačik, Matej; Smith, Carl; Honza, Marcel; Reichard, Martin

2018-01-01

Obligate brood parasites manipulate other species into raising their offspring. Avian and insect brood parasitic systems demonstrate how interacting species engage in reciprocal coevolutionary arms races through behavioral and morphological adaptations and counteradaptations. Mouthbrooding cichlid fishes are renowned for their remarkable evolutionary radiations and complex behaviors. In Lake Tanganyika, mouthbrooding cichlids are exploited by the only obligate nonavian vertebrate brood parasite, the cuckoo catfish Synodontis multipunctatus. We show that coevolutionary history and individual learning both have a major impact on the success of cuckoo catfish parasitism between coevolved sympatric and evolutionarily naïve allopatric cichlid species. The rate of cuckoo catfish parasitism in coevolved Tanganyikan hosts was 3 to 11 times lower than in evolutionarily naïve cichlids. Moreover, using experimental infections, we demonstrate that parasite egg rejection in sympatric hosts was much higher, leading to seven times greater parasite survival in evolutionarily naïve than sympatric hosts. However, a high rejection frequency of parasitic catfish eggs by coevolved sympatric hosts came at a cost of increased rejection of their own eggs. A significant cost of catfish parasitism was universal, except for coevolved sympatric cichlid species with previous experience of catfish parasitism, demonstrating that learning and individual experience both contribute to a successful host response. PMID:29732407

The evolutionarily conserved interaction between LC3 and p62 selectively mediates autophagy-dependent degradation of mutant huntingtin.

PubMed

Tung, Ying-Tsen; Hsu, Wen-Ming; Lee, Hsinyu; Huang, Wei-Pang; Liao, Yung-Feng

2010-07-01

Mammalian p62/sequestosome-1 protein binds to both LC3, the mammalian homologue of yeast Atg8, and polyubiquitinated cargo proteins destined to undergo autophagy-mediated degradation. We previously identified a cargo receptor-binding domain in Atg8 that is essential for its interaction with the cargo receptor Atg19 in selective autophagic processes in yeast. We, thus, sought to determine whether this interaction is evolutionally conserved from yeast to mammals. Using an amino acid replacement approach, we demonstrate that cells expressing mutant LC3 (LC3-K30D, LC3-K51A, or LC3-L53A) all exhibit defective lipidation of LC3, a disrupted LC3-p62 interaction, and impaired autophagic degradation of p62, suggesting that the p62-binding site of LC3 is localized within an evolutionarily conserved domain. Importantly, whereas cells expressing these LC3 mutants exhibited similar overall autophagic activity comparable to that of cells expressing wild-type LC3, autophagy-mediated clearance of the aggregation-prone mutant Huntingtin was defective in the mutant-expressing cells. Together, these results suggest that p62 directly binds to the evolutionarily conserved cargo receptor-binding domain of Atg8/LC3 and selectively mediates the clearance of mutant Huntingtin.

[Amphioxus ortholog of ECSIT, an evolutionarily conserved adaptor in the Toll and BMP signaling pathways].

PubMed

Lin, Y H; Zhang, W; Li, J W; Zhang, H W; Chen, D Y

2017-01-01

In vertebrates, evolutionarily conserved signaling intermediate in the Toll pathway (ECSIT) interacts with the TNF-receptor associated factor 6 (TRAF6) to regulate the processing of MEKK1, activate NF-κB, and also control BMP target genes. However, the role of ECSIT in invertebrates remains largely unexplored. We performed comparative investigations of the expression, gene structure, and phylogeny of ECSIT, Toll-like receptor (TLR), and Smad4 in the cephalochordate Branchiostoma belcheri. Phylogenetic analysis indicated that, in amphioxus, ECSIT, TLR, and Smad4 form independent clusters at the base of Chordate   clusters. Interestingly, overall gene structures were comparable to those in vertebrate orthologs. Transcripts of AmphiECSIT were detectable at the mid-neural stage, and continued to be expressed in the epithelium of the pharyngeal region at later stages. In adult animals, strong expression was observed in the nerve cord, endostyle, epithelial cells of the gut and wheel organ, genital membrane of the testis, and coelom and lymphoid cavities, what is highly similar to AmphiTLR and AmphiSmad4 expression patterns during development and in adult organisms. Our data suggests that ECSIT is evolutionarily conserved. Its amphioxus ortholog functions during embryonic development and as part of the innate immune system and may be involved in TLR/BMP signaling.

Evolutionarily stable range limits set by interspecific competition.

PubMed

Price, Trevor D; Kirkpatrick, Mark

2009-04-22

A combination of abiotic and biotic factors probably restricts the range of many species. Recent evolutionary models and tests of those models have asked how a gradual change in environmental conditions can set the range limit, with a prominent idea being that gene flow disrupts local adaptation. We investigate how biotic factors, explicitly competition for limited resources, result in evolutionarily stable range limits even in the absence of the disruptive effect of gene flow. We model two competing species occupying different segments of the resource spectrum. If one segment of the resource spectrum declines across space, a species that specializes on that segment can be driven to extinction, even though in the absence of competition it would evolve to exploit other abundant resources and so be saved. The result is that a species range limit is set in both evolutionary and ecological time, as the resources associated with its niche decline. Factors promoting this outcome include: (i) inherent gaps in the resource distribution, (ii) relatively high fitness of the species when in its own niche, and low fitness in the alternative niche, even when resource abundances are similar in each niche, (iii) strong interspecific competition, and (iv) asymmetric interspecific competition. We suggest that these features are likely to be common in multispecies communities, thereby setting evolutionarily stable range limits.

Evolutionarily stable range limits set by interspecific competition

PubMed Central

Price, Trevor D.; Kirkpatrick, Mark

2009-01-01

A combination of abiotic and biotic factors probably restricts the range of many species. Recent evolutionary models and tests of those models have asked how a gradual change in environmental conditions can set the range limit, with a prominent idea being that gene flow disrupts local adaptation. We investigate how biotic factors, explicitly competition for limited resources, result in evolutionarily stable range limits even in the absence of the disruptive effect of gene flow. We model two competing species occupying different segments of the resource spectrum. If one segment of the resource spectrum declines across space, a species that specializes on that segment can be driven to extinction, even though in the absence of competition it would evolve to exploit other abundant resources and so be saved. The result is that a species range limit is set in both evolutionary and ecological time, as the resources associated with its niche decline. Factors promoting this outcome include: (i) inherent gaps in the resource distribution, (ii) relatively high fitness of the species when in its own niche, and low fitness in the alternative niche, even when resource abundances are similar in each niche, (iii) strong interspecific competition, and (iv) asymmetric interspecific competition. We suggest that these features are likely to be common in multispecies communities, thereby setting evolutionarily stable range limits. PMID:19324813

Characterization of a C—C Bond Hydrolase from Sphingomonas wittichii RW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites▿

PubMed Central

Seah, Stephen Y. K.; Ke, Jiyuan; Denis, Geoffroy; Horsman, Geoff P.; Fortin, Pascal D.; Whiting, Cheryl J.; Eltis, Lindsay D.

2007-01-01

Sphingomonas wittichii RW1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. We used inverse PCR to amplify dxnB2, a gene encoding one of three meta-cleavage product (MCP) hydrolases identified in the organism that are homologues of BphD involved in biphenyl catabolism. Purified DxnB2 catalyzed the hydrolysis of 8-OH 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) approximately six times faster than for HOPDA at saturating substrate concentrations. Moreover, the specificity of DxnB2 for HOPDA (kcat/Km = 1.2 × 107 M−1 s−1) was about half that of the BphDs of Burkholderia xenovorans LB400 and Rhodococcus globerulus P6, two potent polychlorinated biphenyl (PCB)-degrading strains. Interestingly, DxnB2 transformed 3-Cl and 4-OH HOPDAs, compounds that inhibit the BphDs and limit PCB degradation. DxnB2 had a higher specificity for 9-Cl HOPDA than for HOPDA but a lower specificity for 8-Cl HOPDA (kcat/Km = 1.7 × 106 M−1 s−1), the chlorinated analog of 8-OH HOPDA produced during dibenzofuran catabolism. Phylogenetic analyses based on structure-guided sequence alignment revealed that DxnB2 belongs to a previously unrecognized class of MCP hydrolases, evolutionarily divergent from the BphDs although the physiological substrates of both enzyme types are HOPDAs. However, both classes of enzymes have mainly small hydrophobic residues lining the subsite that binds the C-6 phenyl of HOPDA, in contrast to the bulky hydrophobic residues (Phe106, Phe135, Trp150, and Phe197) found in the class II enzymes that prefer substrates possessing a C-6 alkyl. Thr196 and/or Asn203 appears to be an important determinant of specificity for DxnB2, potentially forming hydrogen bonds with the 8-OH substituent. This study demonstrates that the substrate specificities of evolutionarily divergent hydrolases may be useful for degrading mixtures of pollutants, such as PCBs. PMID:17416660

Feasibility and reproducibility of feature-tracking-based strain and strain rate measures of the left ventricle in different diseases and genders.

PubMed

Maceira, Alicia M; Tuset-Sanchis, Luis; López-Garrido, Miguel; San Andres, Marta; López-Lereu, M Pilar; Monmeneu, Jose V; García-González, M Pilar; Higueras, Laura

2018-05-01

The measurement of myocardial deformation by strain analysis is an evolving tool to quantify regional and global myocardial function. To assess the feasibility and reproducibility of myocardial strain/strain rate measurements with magnetic resonance feature tracking (MR-FT) in healthy subjects and in patient groups. Prospective study. Sixty patients (20 hypertensives with left ventricular (LV) hypertrophy (H); 20 nonischemic dilated cardiomyopathy (D); 20 ischemic heart disease (I); as well as 20 controls (C) were included, 10 men and 10 women in each group. A 1.5T MR protocol including steady-state free precession (SSFP) cine sequences in the standard views and late enhancement sequences. LV volumes, mass, global and regional radial, circumferential, and longitudinal strain/strain rate were measured using CVI42 software. The analysis time was recorded. Intraobserver and interobserver agreement and intraclass correlation coefficients (ICC) were obtained for reproducibility assessment as well as differences according to gender and group of pertinence. Strain/strain rate analysis could be achieved in all subjects. The average analysis time was 14 ± 3 minutes. The average intraobserver ICC was excellent (ICC >0.90) for strain and good (ICC >0.75) for strain rate. Reproducibility of strain measurements was good to excellent (ICC >0.75) for all groups of subjects and both genders. Reproducibility of strain measurements was good for basal segments (ICC >0.75) and excellent for middle and apical segments (ICC >0.90). Reproducibility of strain rate measurements was moderate for basal segments (ICC >0.50) and good for middle and apical segments. MR-FT for strain/strain rate analysis is a feasible and highly reproducible technique. CVI42 FT analysis was equally feasible and reproducible in various pathologies and between genders. Better reproducibility was seen globally for middle and apical segments, which needs further clarification. 3 Technical Efficacy Stage 2 J. Magn. Reson. Imaging 2018;47:1415-1425. © 2017 International Society for Magnetic Resonance in Medicine.

Some fungal endophytes from vegetable crops and their anti-oomycete activities against tomato late blight.

PubMed

Kim, H-Y; Choi, G J; Lee, H B; Lee, S-W; Lim, H K; Jang, K S; Son, S W; Lee, S O; Cho, K Y; Sung, N D; Kim, J-C

2007-03-01

To isolate endophytic fungi from vegetable plants and examine their in vivo anti-oomycete activity against Phytophthora infestans in tomato plants. Endophytic fungi were isolated from surface-sterilized plant tissues and anti-oomycete activity was measured by in vivo assay using tomato seedlings. Endophytic fungi showing potent anti-oomycete activity were identified by morphological characteristics and nuclear ribosomal ITS1-5.8S-ITS2 sequence analysis. A total of 152 isolates were obtained from 66 healthy tissue samples of cucumber, red pepper, tomato, pumpkin and Chinese cabbage and the fermentation broths of 23 isolates showed potent in vivo anti-oomycete activity against tomato late blight with control values over 90%. The Fusarium oxysporum strain EF119, which was isolated from roots of red pepper, showed the most potent disease control efficacy against tomato late blight. In dual-culture tests, it inhibited the growth of Pythium ultimum, P. infestans and Phytophthora capsici. Among endophytic fungi isolated from healthy tissues of vegetable plants, F. oxysporum EF119 showed the most potent in vivo anti-oomycete activity against tomato late blight and in vitro anti-oomycete activity against several oomycete pathogens. Endophytic fungi showing anti-oomycete activity in vitro and in vivo may be used as biocontrol agents particularly of tomato late blight.

Silencing of six susceptibility genes results in potato late blight resistance.

PubMed

Sun, Kaile; Wolters, Anne-Marie A; Vossen, Jack H; Rouwet, Maarten E; Loonen, Annelies E H M; Jacobsen, Evert; Visser, Richard G F; Bai, Yuling

2016-10-01

Phytophthora infestans, the causal agent of late blight, is a major threat to commercial potato production worldwide. Significant costs are required for crop protection to secure yield. Many dominant genes for resistance (R-genes) to potato late blight have been identified, and some of these R-genes have been applied in potato breeding. However, the P. infestans population rapidly accumulates new virulent strains that render R-genes ineffective. Here we introduce a new class of resistance which is based on the loss-of-function of a susceptibility gene (S-gene) encoding a product exploited by pathogens during infection and colonization. Impaired S-genes primarily result in recessive resistance traits in contrast to recognition-based resistance that is governed by dominant R-genes. In Arabidopsis thaliana, many S-genes have been detected in screens of mutant populations. In the present study, we selected 11 A. thaliana S-genes and silenced orthologous genes in the potato cultivar Desiree, which is highly susceptible to late blight. The silencing of five genes resulted in complete resistance to the P. infestans isolate Pic99189, and the silencing of a sixth S-gene resulted in reduced susceptibility. The application of S-genes to potato breeding for resistance to late blight is further discussed.

Evolutionarily Conserved Epitopes on Human Immunodeficiency Virus Type 1 (HIV-1) and Feline Immunodeficiency Virus Reverse Transcriptases Detected by HIV-1-Infected Subjects

PubMed Central

Sanou, Missa P.; Roff, Shannon R.; Mennella, Antony; Sleasman, John W.; Rathore, Mobeen H.; Levy, Jay A.

2013-01-01

Anti-human immunodeficiency virus (HIV) cytotoxic T lymphocyte (CTL)-associated epitopes, evolutionarily conserved on both HIV type 1 (HIV-1) and feline immunodeficiency virus (FIV) reverse transcriptases (RT), were identified using gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) and carboxyfluorescein diacetate succinimide ester (CFSE) proliferation assays followed by CTL-associated cytotoxin analysis. The peripheral blood mononuclear cells (PBMC) or T cells from HIV-1-seropositive (HIV+) subjects were stimulated with overlapping RT peptide pools. The PBMC from the HIV+ subjects had more robust IFN-γ responses to the HIV-1 peptide pools than to the FIV peptide pools, except for peptide-pool F3. In contrast, much higher and more frequent CD8+ T-cell proliferation responses were observed with the FIV peptide pools than with the HIV peptide pools. HIV-1-seronegative subjects had no proliferation or IFN-γ responses to the HIV and FIV peptide pools. A total of 24% (40 of 166) of the IFN-γ responses to HIV pools and 43% (23 of 53) of the CD8+ T-cell proliferation responses also correlated to responses to their counterpart FIV pools. Thus, more evolutionarily conserved functional epitopes were identified by T-cell proliferation than by IFN-γ responses. In the HIV+ subjects, peptide-pool F3, but not the HIV H3 counterpart, induced the most IFN-γ and proliferation responses. These reactions to peptide-pool F3 were highly reproducible and persisted over the 1 to 2 years of testing. All five individual peptides and epitopes of peptide-pool F3 induced IFN-γ and/or proliferation responses in addition to inducing CTL-associated cytotoxin responses (perforin, granzyme A, granzyme B). The epitopes inducing polyfunctional T-cell activities were highly conserved among human, simian, feline, and ungulate lentiviruses, which indicated that these epitopes are evolutionarily conserved. These results suggest that FIV peptides could be used in an HIV-1 vaccine. PMID:23824804

Analysis of Dibenzothiophene Desulfurization in a Recombinant Pseudomonas putida Strain▿

PubMed Central

Calzada, Javier; Zamarro, María T.; Alcón, Almudena; Santos, Victoria E.; Díaz, Eduardo; García, José L.; Garcia-Ochoa, Felix

2009-01-01

Biodesulfurization was monitored in a recombinant Pseudomonas putida CECT5279 strain. DszB desulfinase activity reached a sharp maximum at the early exponential phase, but it rapidly decreased at later growth phases. A model two-step resting-cell process combining sequentially P. putida cells from the late and early exponential growth phases was designed to significantly increase biodesulfurization. PMID:19047400

Hearts of Darkness and Hot Zones: The Ideologeme of Imperial Contagion in Recent Accounts of Viral Outbreaks.

ERIC Educational Resources Information Center

Bass, Jeff D.

1998-01-01

Examines three recent popularized accounts of emerging lethal viral strains within the context of a late 19th-century rationale for imperialism: the ideologeme of scenic contamination, which justifies imperialism as a defensive measure. Notes how the three texts present ideologically charged images of the Third World and its relationship to the…

Early Assessment of Right Ventricular Function in Systemic Lupus Erythematosus Patients using Strain and Strain Rate Imaging.

PubMed

Luo, Runlan; Cui, Hongyan; Huang, Dongmei; Sun, Lihua; Song, Shengda; Sun, Mengyao; Li, Guangsen

2018-06-11

Right ventricular function is a crucial factor of the prognosis of systemic lupus erythematosus (SLE). To evaluate the right ventricular function in SLE patients with different degrees of pulmonary hypertension (PH) by strain and strain rate imaging. A total of 102 SLE patients and 30 healthy volunteers were studied between October 2015 and May 2016. Patients were divided into three groups according to pulmonary artery systolic pressure (PASP) estimated by echocardiography: group control (A); PASP ≤ 30 mmHg (group B, n = 37); PASP 30-50 mmHg (mild PH; group C, n = 34); and PASP ≥ 50 mmHg (moderate-to-severe PH; group D, n = 31). Longitudinal peak systolic strain (ε) and strain rate (SR), including systolic strain rate (SRs), early diastolic strain rate (SRe) and late diastolic strain rate (SRa) were measured in the basal, middle and apical segments of the right ventricular free wall in participants by two-dimensional speckle tracking echocardiography (2D-STE) from the apical four-chamber view. A p < 0.05 was set for statistical significance. The parameters of ε, SRs, SRe, and SRa were significantly decreased in groups C and D compared with groups A and B. The ε of each segments was significantly lower in group D than in group C, while there were no differences in SRs, SRe and SRa between groups C and D. Strain and strain rate imaging could early detect the right ventricular dysfunction in SLE patients with PH, and provide important value for clinical therapy and prognosis of these patients. (Arq Bras Cardiol. 2018; [online].ahead print, PP.0-0).

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum.

PubMed

Porter, Ashleigh F; Duggan, Ana T; Poinar, Hendrik N; Holmes, Edward C

2017-09-28

The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.

[Activating effect of adrenaline, prednisolone and vincristine in the late periods of tick-borne encephalitis virus persistence].

PubMed

Frolova, T V; Pogodina, V V

1984-01-01

The activating effect of adrenalin (A), prednisolone (P), and vincristine (V) on persistent infection caused by subcutaneous inoculation of Syrian hamsters with the Vasilchenko and B-383 strains of tick-borne encephalitis virus (TBE) was studied. The drugs were administered once, twice, or three times 250-270 days after virus inoculation. Complement-fixing antigen was found in the organs of the infected animals given no A, P, or V; in the organ explants synthesis of hemagglutinin was observed but no infectious virus could be isolated. After treatment of the infected hamsters with A, P, or V organ explants yielded TBE virus strains which showed either high or low virulence for white mice. The activated TBE virus strains were obtained from explants of hamster brains and spleens but not liver. V produced the most marked activating effect, A the least.

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum

PubMed Central

Porter, Ashleigh F.; Duggan, Ana T.

2017-01-01

The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD. PMID:28956829

Intelligence and homosexuality.

PubMed

Kanazawa, Satoshi

2012-09-01

The origin of preferences and values is an unresolved theoretical problem in behavioural sciences. The Savanna-IQ Interaction Hypothesis, derived from the Savanna Principle and a theory of the evolution of general intelligence, suggests that more intelligent individuals are more likely to acquire and espouse evolutionarily novel preferences and values than less intelligent individuals, but general intelligence has no effect on the acquisition and espousal of evolutionarily familiar preferences and values. Ethnographies of traditional societies suggest that exclusively homosexual behaviour was probably rare in the ancestral environment, so the Hypothesis would predict that more intelligent individuals are more likely to identify themselves as homosexual and engage in homosexual behaviour. Analyses of three large, nationally representative samples (two of which are prospectively longitudinal) from two different nations confirm the prediction.

[Seasonal changes of steroid levels in blood plasma of three Phodopus species (Mammalia, Cricetinae)].

PubMed

Feoktistova, N Iu; Kropotkina, M V; Naĭĭdenko, S V

2010-01-01

Seasonal change of the base plasma level of testosterone and cortisol in males and progesterone, estradiol, and cortisol levels in females were analyzed in three Phodopus species: Ph. campbelli (Campbell's dwarf hamster), Ph. sungorus (Russian dwarf hamster), and Ph. roborovskii (Roborovski's dwarf hamster). Our results showed a significant difference in the seasonal plasma level of testosterone and cortisol in males and cortisol in females of all Phodopus species, though the rhythms of breeding activity were similar. The results are discussed in the context of adaptive differences between hormonal patterns of evolutionarily young species (Campbell's dwarf hamster and Russian dwarf hamster) and the evolutionarily old Roborovski's dwarf hamster, the phylogenic position of which is currently under discussion.

Essential oil composition and antibacterial activity of Origanum vulgare subsp. glandulosum Desf. at different phenological stages.

PubMed

Béjaoui, Afef; Chaabane, Hédia; Jemli, Maroua; Boulila, Abdennacer; Boussaid, Mohamed

2013-12-01

Variation in the quantity and quality of the essential oil (EO) of wild population of Origanum vulgare at different phenological stages, including vegetative, late vegetative, and flowering set, is reported. The oils of air-dried samples were obtained by hydrodistillation. The yield of oils (w/w%) at different stages were in the order of late vegetative (2.0%), early vegetative (1.7%), and flowering (0.6%) set. The oils were analyzed by gas chromatography (GC) and GC-mass spectrometry (GC-MS). In total, 36, 33, and 16 components were identified and quantified in vegetative, late vegetative, and flowering set, representing 94.47%, 95.91%, and 99.62% of the oil, respectively. Carvacrol was the major compound in all samples. The ranges of major constituents were as follows: carvacrol (61.08-83.37%), p-cymene (3.02-9.87%), and γ-terpinene (4.13-6.34%). Antibacterial activity of the oils was tested against three Gram-positive and two Gram-negative bacteria by the disc diffusion method and determining their diameter of inhibition and the minimum inhibitory concentration (MIC) values. The inhibition zones and MIC values for bacterial strains, which were sensitive to the EO of O. vulgare subsp. glandulosum, were in the range of 9-36 mm and 125-600 μg/mL, respectively. The oils of various phenological stages showed high activity against all tested bacteria, of which Bacillus subtilis was the most sensitive and resistant strain, respectively. Thus, they represent an inexpensive source of natural antibacterial substances that exhibited potential for use in pathogenic systems.

Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changes

PubMed Central

Flores, Anthony R.; Galloway-Peña, Jessica; Sahasrabhojane, Pranoti; Saldaña, Miguel; Yao, Hui; Su, Xiaoping; Ajami, Nadim J.; Holder, Michael E.; Petrosino, Joseph F.; Thompson, Erika; Margarit Y Ros, Immaculada; Rosini, Roberto; Grandi, Guido; Horstmann, Nicola; Teatero, Sarah; McGeer, Allison; Fittipaldi, Nahuel; Rappuoli, Rino; Baker, Carol J.; Shelburne, Samuel A.

2015-01-01

The molecular mechanisms underlying pathogen emergence in humans is a critical but poorly understood area of microbiologic investigation. Serotype V group B Streptococcus (GBS) was first isolated from humans in 1975, and rates of invasive serotype V GBS disease significantly increased starting in the early 1990s. We found that 210 of 229 serotype V GBS strains (92%) isolated from the bloodstream of nonpregnant adults in the United States and Canada between 1992 and 2013 were multilocus sequence type (ST) 1. Elucidation of the complete genome of a 1992 ST-1 strain revealed that this strain had the highest homology with a GBS strain causing cow mastitis and that the 1992 ST-1 strain differed from serotype V strains isolated in the late 1970s by acquisition of cell surface proteins and antimicrobial resistance determinants. Whole-genome comparison of 202 invasive ST-1 strains detected significant recombination in only eight strains. The remaining 194 strains differed by an average of 97 SNPs. Phylogenetic analysis revealed a temporally dependent mode of genetic diversification consistent with the emergence in the 1990s of ST-1 GBS as major agents of human disease. Thirty-one loci were identified as being under positive selective pressure, and mutations at loci encoding polysaccharide capsule production proteins, regulators of pilus expression, and two-component gene regulatory systems were shown to affect the bacterial phenotype. These data reveal that phenotypic diversity among ST-1 GBS is mainly driven by small genetic changes rather than extensive recombination, thereby extending knowledge into how pathogens adapt to humans. PMID:25941374

Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changes.

PubMed

Flores, Anthony R; Galloway-Peña, Jessica; Sahasrabhojane, Pranoti; Saldaña, Miguel; Yao, Hui; Su, Xiaoping; Ajami, Nadim J; Holder, Michael E; Petrosino, Joseph F; Thompson, Erika; Margarit Y Ros, Immaculada; Rosini, Roberto; Grandi, Guido; Horstmann, Nicola; Teatero, Sarah; McGeer, Allison; Fittipaldi, Nahuel; Rappuoli, Rino; Baker, Carol J; Shelburne, Samuel A

2015-05-19

The molecular mechanisms underlying pathogen emergence in humans is a critical but poorly understood area of microbiologic investigation. Serotype V group B Streptococcus (GBS) was first isolated from humans in 1975, and rates of invasive serotype V GBS disease significantly increased starting in the early 1990s. We found that 210 of 229 serotype V GBS strains (92%) isolated from the bloodstream of nonpregnant adults in the United States and Canada between 1992 and 2013 were multilocus sequence type (ST) 1. Elucidation of the complete genome of a 1992 ST-1 strain revealed that this strain had the highest homology with a GBS strain causing cow mastitis and that the 1992 ST-1 strain differed from serotype V strains isolated in the late 1970s by acquisition of cell surface proteins and antimicrobial resistance determinants. Whole-genome comparison of 202 invasive ST-1 strains detected significant recombination in only eight strains. The remaining 194 strains differed by an average of 97 SNPs. Phylogenetic analysis revealed a temporally dependent mode of genetic diversification consistent with the emergence in the 1990s of ST-1 GBS as major agents of human disease. Thirty-one loci were identified as being under positive selective pressure, and mutations at loci encoding polysaccharide capsule production proteins, regulators of pilus expression, and two-component gene regulatory systems were shown to affect the bacterial phenotype. These data reveal that phenotypic diversity among ST-1 GBS is mainly driven by small genetic changes rather than extensive recombination, thereby extending knowledge into how pathogens adapt to humans.

Exploration of a novel object in late adolescence predicts novelty-seeking behavior in adulthood: Associations among behavioral responses in four novelty-seeking tests.

PubMed

Cuenya, Lucas; Sabariego, Marta; Donaire, Rocío; Callejas-Aguilera, José Enrique; Torres, Carmen; Fernández-Teruel, Alberto

2016-04-01

The sensation/novelty seeking behavioral trait refers to the exploration/preference for a novel environment. Novelty seeking increases during late adolescence and it has been associated with several neurobehavioral disorders. In this experiment, we asked whether inbred Roman high- and low-avoidance (RHA-I, RLA-I) rats (1) differ in novelty seeking in late adolescence and (2) whether late adolescent novelty seeking predicts this trait in adulthood. Thirty six male RHA-I and 36 RLA-I rats were exposed to a novel object exploration (NOE) test during late adolescence (pnd: 52-59; contact latency, contact time, contact frequency). Head-dipping (hole-board, HB), time and visits to a novel-arm (Y-maze), and latency-in and emergence latency (emergence test) were registered in adulthood (pnd: 83-105). The results showed strain differences in all these tests (RHA-I>RLA-I). Factor analysis (RHA-I+RLA-I) revealed two clusters. The first one grouped HB and emergence test measures. The second one grouped NOE and Y-maze variables. Time exploring a novel object (NOE) was a significant predictor of novel arm time (RHA-I+RLA, RHA-I); contact latency was a significant predictor of novel arm frequency (RLA-I). Present results show consistent behavioral associations across four novelty-seeking tests and suggest that late adolescent novelty seeking predicts this genetically-influenced temperamental trait in adult Roman rats. Copyright © 2016 Elsevier B.V. All rights reserved.

Sickness-Associated Anorexia: Mother Nature's Idea of Immunonutrition?

PubMed

van Niekerk, Gustav; Isaacs, Ashwin W; Nell, Theo; Engelbrecht, Anna-Mart

2016-01-01

During an infection, expansion of immune cells, assembly of antibodies, and the induction of a febrile response collectively place continual metabolic strain on the host. These considerations also provide a rationale for nutritional support in critically ill patients. Yet, results from clinical and preclinical studies indicate that aggressive nutritional support does not always benefit patients and may occasionally be detrimental. Moreover, both vertebrates and invertebrates exhibit a decrease in appetite during an infection, indicating that such sickness-associated anorexia (SAA) is evolutionarily conserved. It also suggests that SAA performs a vital function during an infection. We review evidence signifying that SAA may present a mechanism by which autophagic flux is upregulated systemically. A decrease in serum amino acids during an infection promotes autophagy not only in immune cells, but also in nonimmune cells. Similarly, bile acids reabsorbed postprandially inhibit hepatic autophagy by binding to farnesoid X receptors, indicating that SAA may be an attempt to conserve autophagy. In addition, augmented autophagic responses may play a critical role in clearing pathogens (xenophagy), in the presentation of epitopes in nonprovisional antigen presenting cells and the removal of damaged proteins and organelles. Collectively, these observations suggest that some patients might benefit from permissive underfeeding.

Mycobacterium tuberculosis TlyA Protein Negatively Regulates T Helper (Th) 1 and Th17 Differentiation and Promotes Tuberculosis Pathogenesis*

PubMed Central

Rahman, Md. Aejazur; Sobia, Parveen; Dwivedi, Ved Prakash; Bhawsar, Aakansha; Singh, Dhiraj Kumar; Sharma, Pawan; Moodley, Prashini; Van Kaer, Luc; Bishai, William R; Das, Gobardhan

2015-01-01

Mycobacterium tuberculosis, the causative agent of tuberculosis, is an ancient pathogen and a major cause of death worldwide. Although various virulence factors of M. tuberculosis have been identified, its pathogenesis remains incompletely understood. TlyA is a virulence factor in several bacterial infections and is evolutionarily conserved in many Gram-positive bacteria, but its function in M. tuberculosis pathogenesis has not been elucidated. Here, we report that TlyA significantly contributes to the pathogenesis of M. tuberculosis. We show that a TlyA mutant M. tuberculosis strain induces increased IL-12 and reduced IL-1β and IL-10 cytokine responses, which sharply contrasts with the immune responses induced by wild type M. tuberculosis. Furthermore, compared with wild type M. tuberculosis, TlyA-deficient M. tuberculosis bacteria are more susceptible to autophagy in macrophages. Consequently, animals infected with the TlyA mutant M. tuberculosis organisms exhibited increased host-protective immune responses, reduced bacillary load, and increased survival compared with animals infected with wild type M. tuberculosis. Thus, M. tuberculosis employs TlyA as a host evasion factor, thereby contributing to its virulence. PMID:25847237

Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion.

PubMed

Tse, Longping Victor; Klinc, Kelli A; Madigan, Victoria J; Castellanos Rivera, Ruth M; Wells, Lindsey F; Havlik, L Patrick; Smith, J Kennon; Agbandje-McKenna, Mavis; Asokan, Aravind

2017-06-13

Preexisting neutralizing antibodies (NAbs) against adeno-associated viruses (AAVs) pose a major, unresolved challenge that restricts patient enrollment in gene therapy clinical trials using recombinant AAV vectors. Structural studies suggest that despite a high degree of sequence variability, antibody recognition sites or antigenic hotspots on AAVs and other related parvoviruses might be evolutionarily conserved. To test this hypothesis, we developed a structure-guided evolution approach that does not require selective pressure exerted by NAbs. This strategy yielded highly divergent antigenic footprints that do not exist in natural AAV isolates. Specifically, synthetic variants obtained by evolving murine antigenic epitopes on an AAV serotype 1 capsid template can evade NAbs without compromising titer, transduction efficiency, or tissue tropism. One lead AAV variant generated by combining multiple evolved antigenic sites effectively evades polyclonal anti-AAV1 neutralizing sera from immunized mice and rhesus macaques. Furthermore, this variant displays robust immune evasion in nonhuman primate and human serum samples at dilution factors as high as 1:5, currently mandated by several clinical trials. Our results provide evidence that antibody recognition of AAV capsids is conserved across species. This approach can be applied to any AAV strain to evade NAbs in prospective patients for human gene therapy.

SERIAL ULTRASOUND EVALUATION OF INTRAMYOCARDIAL STRAIN AFTER REPERFUSED MYOCARDIAL INFARCTION REVEALS THAT REMOTE ZONE DYSSYNCHRONY DEVELOPS IN CONCERT WITH LEFT VENTRICULAR REMODELING

PubMed Central

Li, Yinbo; Garson, Christopher D.; Xu, Yaqin; Helm, Patrick A.; Hossack, John A.; French, Brent A.

2011-01-01

This study noninvasively evaluated the development of left ventricular (LV) dyssynchrony following reperfused myocardial infarction (MI) in mice using an ultrasonic speckle-tracking method. Eight C57BL/6J mice were assessed by high-resolution echocardiography at baseline and at eight time-points following MI. Images were acquired at 1mm elevational intervals encompassing the entire LV to determine chamber volumes and radial strain. Receiver-operating characteristic (ROC) analysis of regional radial strain was used to segment the three-dimensional (3-D) LV into infarct, adjacent and remote zones. This in vivo segmentation was correlated to histologic infarct size (R = 0.89, p < 0.01) in a short-axis, slice-by-slice comparison. The onset of dyssynchrony during LV remodeling was assessed by standard deviation of time to peak radial strain in the infarct, adjacent and remote zones. It was discovered that the form of LV dyssynchrony that develops in the remote zone late after MI does so in concert with the progression of LV remodeling (R = 0.70, p < 0.05). PMID:21640480

Importance of confirming data on the in vivo efficacy of novel antibacterial drug regimens against various strains of Mycobacterium tuberculosis.

PubMed

De Groote, Mary A; Gruppo, Veronica; Woolhiser, Lisa K; Orme, Ian M; Gilliland, Janet C; Lenaerts, Anne J

2012-02-01

In preclinical testing of antituberculosis drugs, laboratory-adapted strains of Mycobacterium tuberculosis are usually used both for in vitro and in vivo studies. However, it is unknown whether the heterogeneity of M. tuberculosis stocks used by various laboratories can result in different outcomes in tests of antituberculosis drug regimens in animal infection models. In head-to-head studies, we investigated whether bactericidal efficacy results in BALB/c mice infected by inhalation with the laboratory-adapted strains H37Rv and Erdman differ from each other and from those obtained with clinical tuberculosis strains. Treatment of mice consisted of dual and triple drug combinations of isoniazid (H), rifampin (R), and pyrazinamide (Z). The results showed that not all strains gave the same in vivo efficacy results for the drug combinations tested. Moreover, the ranking of HRZ and RZ efficacy results was not the same for the two H37Rv strains evaluated. The magnitude of this strain difference also varied between experiments, emphasizing the risk of drawing firm conclusions for human trials based on single animal studies. The results also confirmed that the antagonism seen within the standard HRZ regimen by some investigators appears to be an M. tuberculosis strain-specific phenomenon. In conclusion, the specific identity of M. tuberculosis strain used was found to be an important variable that can change the apparent outcome of in vivo efficacy studies in mice. We highly recommend confirmation of efficacy results in late preclinical testing against a different M. tuberculosis strain than the one used in the initial mouse efficacy study, thereby increasing confidence to advance potent drug regimens to clinical trials.

Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence.

PubMed

Beres, Stephen B; Sylva, Gail L; Barbian, Kent D; Lei, Benfang; Hoff, Jessica S; Mammarella, Nicole D; Liu, Meng-Yao; Smoot, James C; Porcella, Stephen F; Parkins, Larye D; Campbell, David S; Smith, Todd M; McCormick, John K; Leung, Donald Y M; Schlievert, Patrick M; Musser, James M

2002-07-23

Genome sequences are available for many bacterial strains, but there has been little progress in using these data to understand the molecular basis of pathogen emergence and differences in strain virulence. Serotype M3 strains of group A Streptococcus (GAS) are a common cause of severe invasive infections with unusually high rates of morbidity and mortality. To gain insight into the molecular basis of this high-virulence phenotype, we sequenced the genome of strain MGAS315, an organism isolated from a patient with streptococcal toxic shock syndrome. The genome is composed of 1,900,521 bp, and it shares approximately 1.7 Mb of related genetic material with genomes of serotype M1 and M18 strains. Phage-like elements account for the great majority of variation in gene content relative to the sequenced M1 and M18 strains. Recombination produces chimeric phages and strains with previously uncharacterized arrays of virulence factor genes. Strain MGAS315 has phage genes that encode proteins likely to contribute to pathogenesis, such as streptococcal pyrogenic exotoxin A (SpeA) and SpeK, streptococcal superantigen (SSA), and a previously uncharacterized phospholipase A(2) (designated Sla). Infected humans had anti-SpeK, -SSA, and -Sla antibodies, indicating that these GAS proteins are made in vivo. SpeK and SSA were pyrogenic and toxic for rabbits. Serotype M3 strains with the phage-encoded speK and sla genes increased dramatically in frequency late in the 20th century, commensurate with the rise in invasive disease caused by M3 organisms. Taken together, the results show that phage-mediated recombination has played a critical role in the emergence of a new, unusually virulent clone of serotype M3 GAS.

Natural hybrid of Leishmania infantum/L. donovani: development in Phlebotomus tobbi, P. perniciosus and Lutzomyia longipalpis and comparison with non-hybrid strains differing in tissue tropism.

PubMed

Seblova, Veronika; Myskova, Jitka; Hlavacova, Jana; Votypka, Jan; Antoniou, Maria; Volf, Petr

2015-11-25

Infection caused by parasites from L. donovani complex can manifest as a serious visceral disease or a self-healing milder cutaneous form. The different tropism and pathology in humans is caused by the interaction between parasites, host and vector determinants but the mechanisms are not well understood. In Cukurova region in Turkey we previously identified a major focus of cutaneous leishmaniasis caused by L. donovani/infantum hybrids (CUK strain) and isolated this parasite from the locally abundant sand fly, Phlebotomus tobbi. Here, we present the first experimental study with P. tobbi. We tested the susceptibility of this species to various Leishmania under laboratory conditions, characterized glycoproteins in the P. tobbi midgut putatively involved in parasite-vector interaction and compared the development of the CUK strain in the sand fly with one other dermotropic and three viscerotropic strains belonging to the L. donovani complex. Females of laboratory reared P. tobbi, P. perniciosus and Lutzomyia longipalpis were infected using membrane feeding on rabbit blood containing promastigotes of various Leishmania species with different tropisms. The individual guts were checked microscopically for presence and localization of Leishmania parasites; the number of parasites was assessed more precisely by qPCR. In addition, glycosylation of midgut proteins of P. tobbi was studied by lectin blotting of midgut lysate with lectins specific for terminal sugars of N-type and O-type glycans. High infection rates, heavy parasite loads and late-stage infection with colonization of the stomodeal valve were observed in P. tobbi infected by Leishmania major or L. infantum CUK hybrid. In parallel, lectin blotting revealed the presence of O-glycosylated proteins in the P. tobbi midgut. In P. perniciosus and L. longipalpis all five Leishmania strains tested developed well. In both vectors, significantly higher parasite numbers were detected by qPCR for dermotropic L. donovani from Cyprus, however, in all other parameters studied, including localization of infection and colonization of stomodeal valve, dermotropic and viscerotropic strains were not significantly different. We showed high susceptibility of P. tobbi to various Leishmania spp. This, together with the presence of O-glycosylated midgut proteins in their midguts demonstrate that P. tobbi is a permissive vector. Two dermotropic and three viscerotropic strains from the L. donovani complex developed late-stage infections in natural L. infantum vectors, P. perniciosus and L. longipalpis and none of the parameters studied seem to be linked with different tropism of parasites in the vertebrate host.

Recent Basal Melting of a Mid-Latitude Glacier on Mars

NASA Astrophysics Data System (ADS)

Butcher, Frances E. G.; Balme, M. R.; Gallagher, C.; Arnold, N. S.; Conway, S. J.; Hagermann, A.; Lewis, S. R.

2017-12-01

Evidence for past basal melting of young (late Amazonian-aged), debris-covered glaciers in Mars' mid-latitudes is extremely rare. Thus, it is widely thought that these viscous flow features (VFFs) have been perennially frozen to their beds. We identify an instance of recent, localized wet-based mid-latitude glaciation, evidenced by a candidate esker emerging from a VFF in a tectonic rift in Tempe Terra. Eskers are sedimentary ridges deposited in ice-walled meltwater conduits and are indicative of glacial melting. We compare the candidate esker to terrestrial analogues, present a geomorphic map of landforms in the rift, and develop a landsystem model to explain their formation. We propose that the candidate esker formed during a transient phase of wet-based glaciation. We then consider the similarity between the geologic setting of the new candidate esker and that of the only other candidate esker to be identified in association with an existing mid-latitude VFF; both are within tectonic graben/rifts proximal to volcanic provinces. Finally, we calculate potential basal temperatures for a range of VFF thicknesses, driving stresses, mean annual surface temperatures, and geothermal heat fluxes, which unlike previous studies, include the possible role of internal strain heating. Strain heating can form an important additional heat source, especially in flow convergence zones, or where ice is warmer due to elevated surface temperatures or geothermal heat flux. Elevated geothermal heat flux within rifts, perhaps combined with locally-elevated strain heating, may have permitted wet-based glaciation during the late Amazonian, when cold climates precluded more extensive wet-based glaciation on Mars.

Acid-Catalyzed Algal Biomass Pretreatment for Integrated Lipid and Carbohydrate-Based Biofuels Production

DOE PAGES

Laurens, L. M. L.; Nagle, N.; Davis, R.; ...

2014-11-12

One of the major challenges associated with algal biofuels production in a biorefinery-type setting is improving biomass utilization in its entirety, increasing the process energetic yields and providing economically viable and scalable co-product concepts. We demonstrate the effectiveness of a novel, integrated technology based on moderate temperatures and low pH to convert the carbohydrates in wet algal biomass to soluble sugars for fermentation, while making lipids more accessible for downstream extraction and leaving a protein-enriched fraction behind. We studied the effect of harvest timing on the conversion yields, using two algal strains; Chlorella and Scenedesmus, generating biomass with distinctive compositionalmore » ratios of protein, carbohydrate, and lipids. We found that the late harvest Scenedesmus biomass had the maximum theoretical biofuel potential at 143 gasoline gallon equivalent (GGE) combined fuel yield per dry ton biomass, followed by late harvest Chlorella at 128 GGE per ton. Our experimental data show a clear difference between the two strains, as Scenedesmus was more successfully converted in this process with a demonstrated 97 GGE per ton. Our measurements indicated a release of >90% of the available glucose in the hydrolysate liquors and an extraction and recovery of up to 97% of the fatty acids from wet biomass. Techno-economic analysis for the combined product yields indicates that this process exhibits the potential to improve per-gallon fuel costs by up to 33% compared to a lipids-only process for one strain, Scenedesmus, grown to the mid-point harvest condition.« less

Siblings in Kars, Turkey, with Uner Tan syndrome (quadrupedal locomotion, severe mental retardation, and no speech): a novel theory for the evolution of human bipedalism.

PubMed

Tan, Uner

2015-02-01

To investigate siblings from Kars (n  =  2), Turkey, with diagonal-sequence quadrupedal locomotion (QL), severe mental retardation, and no speech (Uner Tan syndrome, UTS), in relation to the evolutionary emergence of human bipedal locomotion (BL). Video recordings were made to assess gaits. Brain MRI scanning was performed to visualize the cerebro-cerebellar malformations. Genome-wide association analyses were performed in venous blood samples. One of the two men with UTS showed early-onset QL and late-onset BL without infantile hypotonia, the other consistent QL with infantile hypotonia. No homozygosity was found in the genetic analysis. The family lived under extremely poor socioeconomic conditions. Low socioeconomic status may be a triggering factor for the epigenetic emergence of UTS. The neural networks responsible for the ancestral diagonal-sequence QL, evolutionarily preserved since about 400 MYA, may be selected during locomotor development, under the influence of self-organizing processes during pre- and postnatal periods. The diagonal-sequence QL induced ipsilateral limb interference in UTS cases as in nonhuman primates. To overcome this condition, our ancestors would prefer the attractor BL. This novel theory for the evolution of human bipedalism was evaluated in light of dynamical systems theory.

Mitochondrial CHCHD-Containing Proteins: Physiologic Functions and Link with Neurodegenerative Diseases.

PubMed

Zhou, Zhi-Dong; Saw, Wuan-Ting; Tan, Eng-King

2017-09-01

The coiled-coil-helix-coiled-coil-helix domain (CHCHD)-containing proteins are evolutionarily conserved nucleus-encoded small mitochondrial proteins with important functions. So far, nine members have been identified in this protein family. All CHCHD proteins have at least one functional coiled-coil-helix-coiled-coil-helix (CHCH) domain, which is stabilized by two pairs of disulfide bonds between two helices. CHCHD proteins have various important pathophysiological roles in mitochondria and other key cellular processes. Mutations of CHCHD proteins have been associated with various human neurodegenerative diseases. Mutations of CHCHD10 are associated with amyotrophic lateral sclerosis (ALS) and/or frontotemporal lobe dementia (FTD), motor neuron disease, and late-onset spinal muscular atrophy and autosomal dominant mitochondrial myopathy. CHCHD10 stabilizes mitochondrial crista ultrastructure and maintains its integrity. In patients with CHCHD10 mutations, there are abnormal mitochondrial crista structure, deficiencies of respiratory chain complexes, impaired mitochondrial respiration, and multiple mitochondrial DNA (mtDNA) deletions. Recently, CHCHD2 mutations are linked with autosomal dominant and sporadic Parkinson's disease (PD). The CHCHD2 is a multifunctional protein and plays roles in regulation of mitochondrial metabolism, synthesis of respiratory chain components, and modulation of cell apoptosis. With a better understanding of the pathophysiologic roles of CHCHD proteins, they may be potential novel therapeutic targets for human neurodegenerative diseases.

Retromer Ensures the Degradation of Autophagic Cargo by Maintaining Lysosome Function in Drosophila.

PubMed

Maruzs, Tamás; Lőrincz, Péter; Szatmári, Zsuzsanna; Széplaki, Szilvia; Sándor, Zoltán; Lakatos, Zsolt; Puska, Gina; Juhász, Gábor; Sass, Miklós

2015-10-01

The retromer is an evolutionarily conserved coat complex that consists of Vps26, Vps29, Vps35 and a heterodimer of sorting nexin (Snx) proteins in yeast. Retromer mediates the recycling of transmembrane proteins from endosomes to the trans-Golgi network, including receptors that are essential for the delivery of hydrolytic enzymes to lysosomes. Besides its function in lysosomal enzyme receptor recycling, involvement of retromer has also been proposed in a variety of vesicular trafficking events, including early steps of autophagy and endocytosis. Here we show that the late stages of autophagy and endocytosis are impaired in Vps26 and Vps35 deficient Drosophila larval fat body cells, but formation of autophagosomes and endosomes is not compromised. Accumulation of aberrant autolysosomes and amphisomes in the absence of retromer function appears to be the consequence of decreased degradative capacity, as they contain undigested cytoplasmic material. Accordingly, we show that retromer is required for proper cathepsin L trafficking mainly independent of LERP, the Drosophila homolog of the cation-independent mannose 6-phosphate receptor. Finally, we find that Snx3 and Snx6 are also required for proper autolysosomal degradation in Drosophila larval fat body cells. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Atmospheric oxygen level and the evolution of insect body size.

PubMed

Harrison, Jon F; Kaiser, Alexander; VandenBrooks, John M

2010-07-07

Insects are small relative to vertebrates, possibly owing to limitations or costs associated with their blind-ended tracheal respiratory system. The giant insects of the late Palaeozoic occurred when atmospheric PO(2) (aPO(2)) was hyperoxic, supporting a role for oxygen in the evolution of insect body size. The paucity of the insect fossil record and the complex interactions between atmospheric oxygen level, organisms and their communities makes it impossible to definitively accept or reject the historical oxygen-size link, and multiple alternative hypotheses exist. However, a variety of recent empirical findings support a link between oxygen and insect size, including: (i) most insects develop smaller body sizes in hypoxia, and some develop and evolve larger sizes in hyperoxia; (ii) insects developmentally and evolutionarily reduce their proportional investment in the tracheal system when living in higher aPO(2), suggesting that there are significant costs associated with tracheal system structure and function; and (iii) larger insects invest more of their body in the tracheal system, potentially leading to greater effects of aPO(2) on larger insects. Together, these provide a wealth of plausible mechanisms by which tracheal oxygen delivery may be centrally involved in setting the relatively small size of insects and for hyperoxia-enabled Palaeozoic gigantism.

Knowledge Management to Exploit Agrarian Resources as Part of Late-Eighteenth-Century Cultures of Innovation: Friedrich Casimir Medicus and Franz Von Paula Schrank

ERIC Educational Resources Information Center

Popplow, Marcus

2012-01-01

This essay contributes to a recent strain of research that questions clear-cut dichotomies between "scientists" and "artisans" in the early modern period. With a focus on the exploitation of agrarian resources, it argues for the appreciation of a more complex panorama of intersecting knowledge systems spanning from botany as…

Activation of PI3K, Akt, and ERK during early rotavirus infection leads to V-ATPase-dependent endosomal acidification required for uncoating

PubMed Central

Kim, Deok-Song; Kim, Ji-Yun; Park, Jun-Gyu; Alfajaro, Mia Madel; Baek, Yeong-Bin; Cho, Eun-Hyo; Kwon, Joseph; Choi, Jong-Soon; Kang, Mun-Il; Park, Sang-Ik; Cho, Kyoung-Oh

2018-01-01

The cellular PI3K/Akt and/or MEK/ERK signaling pathways mediate the entry process or endosomal acidification during infection of many viruses. However, their roles in the early infection events of group A rotaviruses (RVAs) have remained elusive. Here, we show that late-penetration (L-P) human DS-1 and bovine NCDV RVA strains stimulate these signaling pathways very early in the infection. Inhibition of both signaling pathways significantly reduced production of viral progeny due to blockage of virus particles in the late endosome, indicating that neither of the two signaling pathways is involved in virus trafficking. However, immunoprecipitation assays using antibodies specific for pPI3K, pAkt, pERK and the subunit E of the V-ATPase co-immunoprecipitated the V-ATPase in complex with pPI3K, pAkt, and pERK. Moreover, Duolink proximity ligation assay revealed direct association of the subunit E of the V-ATPase with the molecules pPI3K, pAkt, and pERK, indicating that both signaling pathways are involved in V-ATPase-dependent endosomal acidification. Acidic replenishment of the medium restored uncoating of the RVA strains in cells pretreated with inhibitors specific for both signaling pathways, confirming the above results. Isolated components of the outer capsid proteins, expressed as VP4-VP8* and VP4-VP5* domains, and VP7, activated the PI3K/Akt and MEK/ERK pathways. Furthermore, psoralen-UV-inactivated RVA and CsCl-purified RVA triple-layered particles triggered activation of the PI3K/Akt and MEK/ERK pathways, confirming the above results. Our data demonstrate that multistep binding of outer capsid proteins of L-P RVA strains with cell surface receptors phosphorylates PI3K, Akt, and ERK, which in turn directly interact with the subunit E of the V-ATPase to acidify the late endosome for uncoating of RVAs. This study provides a better understanding of the RVA-host interaction during viral uncoating, which is of importance for the development of strategies aiming at controlling or preventing RVA infections. PMID:29352319

Mind the gap... in intelligence: re-examining the relationship between inequality and health.

PubMed

Kanazawa, Satoshi

2006-11-01

Wilkinson contends that economic inequality reduces the health and life expectancy of the whole population but his argument does not make sense within its own evolutionary framework. Recent evolutionary psychological theory suggests that the human brain, adapted to the ancestral environment, has difficulty comprehending and dealing with entities and situations that did not exist in the ancestral environment and that general intelligence evolved as a domain-specific adaptation to solve evolutionarily novel problems. Since most dangers to health in the contemporary society are evolutionarily novel, it follows that more intelligent individuals are better able to recognize and deal with such dangers and live longer. Consistent with the theory, the macro-level analyses show that income inequality and economic development have no effect on life expectancy at birth, infant mortality and age-specific mortality net of average intelligence quotient (IQ) in 126 countries. They also show that an average IQ has a very large and significant effect on population health but not in the evolutionarily familiar sub-Saharan Africa. At the micro level, the General Social Survey data show that, while both income and intelligence have independent positive effects on self-reported health, intelligence has a stronger effect than income. The data collectively suggest that individuals in wealthier and more egalitarian societies live longer and stay healthier, not because they are wealthier or more egalitarian but because they are more intelligent.

The relative roles of cultural drift and acoustic adaptation in shaping syllable repertoires of island bird populations change with time since colonization.

PubMed

Potvin, Dominique A; Clegg, Sonya M

2015-02-01

In birds, song divergence often precedes and facilitates divergence of other traits. We assessed the relative roles of cultural drift, innovation, and acoustic adaptation in divergence of island bird dialects, using silvereyes (Zosterops lateralis). In recently colonized populations, syllable diversity was not significantly lower than source populations, shared syllables between populations decreased with increasing number of founder events, and dialect variation displayed contributions from both habitat features and drift. The breadth of multivariate space occupied by recently colonized Z. l. lateralis populations was comparable to evolutionarily old forms that have diverged over thousands to hundreds of thousands of years. In evolutionarily old subspecies, syllable diversity was comparable to the mainland and the amount of variation in syllable composition explained by habitat features increased by two- to threefold compared to recently colonized populations. Together these results suggest that cultural drift influences syllable repertoires in recently colonized populations, but innovation likely counters syllable loss from colonization. In evolutionarily older populations, the influence of acoustic adaptation increases, possibly favoring a high diversity of syllables. These results suggest that the relative importance of cultural drift and acoustic adaptation changes with time since colonization in island bird populations, highlighting the value of considering multiple mechanisms and timescale of divergence when investigating island song divergence. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Evolutionary stability of mutualism: interspecific population regulation as an evolutionarily stable strategy.

PubMed

Holland, J Nathaniel; DeAngelis, Donald L; Schultz, Stewart T

2004-09-07

Interspecific mutualisms are often vulnerable to instability because low benefit : cost ratios can rapidly lead to extinction or to the conversion of mutualism to parasite-host or predator-prey interactions. We hypothesize that the evolutionary stability of mutualism can depend on how benefits and costs to one mutualist vary with the population density of its partner, and that stability can be maintained if a mutualist can influence demographic rates and regulate the population density of its partner. We test this hypothesis in a model of mutualism with key features of senita cactus (Pachycereus schottii)-senita moth (Upiga virescens) interactions, in which benefits of pollination and costs of larval seed consumption to plant fitness depend on pollinator density. We show that plants can maximize their fitness by allocating resources to the production of excess flowers at the expense of fruit. Fruit abortion resulting from excess flower production reduces pre-adult survival of the pollinating seed-consumer, and maintains its density beneath a threshold that would destabilize the mutualism. Such a strategy of excess flower production and fruit abortion is convergent and evolutionarily stable against invasion by cheater plants that produce few flowers and abort few to no fruit. This novel mechanism of achieving evolutionarily stable mutualism, namely interspecific population regulation, is qualitatively different from other mechanisms invoking partner choice or selective rewards, and may be a general process that helps to preserve mutualistic interactions in nature.

Effect of strain of layer and age at photostimulation on egg production, egg quality, and bone strength.

PubMed

Silversides, F G; Korver, D R; Budgell, K L

2006-07-01

Bone strength in layers is a concern for economic reasons and animal welfare concerns. Bone characteristics were investigated in 3 strains of hens: Babcock B-300, a small-bodied commercial white-egg layer; ISA-Brown, a commercial brown-egg layer; and an unselected Brown Leghorn line (BL). After being reared together in a single pen with 8 h of light per day, hens were caged with 14 h of light per day. Half of the hens were caged at 18 wk of age and the other half at 20 wk of age, resulting in a 2-wk difference in the age at photostimulation. Body weights, egg production, feed efficiency, and egg quality were measured throughout production. At 15, 25, 50, and 74 wk of age, hens were euthanized for sampling of the radius and the humerus. Breaking strength of the radius and humerus was measured, and the area and density of trabecular (largely medullary bone) and cortical bone were measured using quantitative computed tomography. Egg production and feed conversion of ISA-Brown hens was as good as or better than that of Babcock B-300 hens, and both commercial strains had higher production than the BL. Photostimulation late delayed sexual maturity and improved albumen and shell characteristics but had only minor effects on egg production and did not affect the yolk weight. The delayed photostimulation resulting from caging 2 wk later affected the radius by increasing the area of the trabecular space at 50 wk of age and the density of the bone in the trabecular space at 74 wk of age. Breaking strength of the humerus at 25 wk of age was greater for the birds that were photostimulated late but was not different later in the trial. The humerus, but not the radius, of the BL had a greater breaking strength than that of the commercial strains, suggesting that selection has decreased humeral breaking strength.

Ductile to Brittle Shear Localization in the Upper Crust During Thermal Anomaly: the Calamita Complex (Elba Island, Italy)

NASA Astrophysics Data System (ADS)

Papeschi, S.

2016-12-01

A field and microstructural study of contemporaneous pluton-related thermal anomaly and thrust faulting highlights the mutual interaction between active regional tectonics, magma emplacement and contact metamorphism. The Calamita Complex is composed of highly strained HT/LP schists, metarenites and metacarbonates. HT metamorphism was caused by the emplacement of the buried Porto Azzurro intrusion occurred at pressures below 0.2 GPa. Thermal anomaly was associated to top-to-NE shearing that produced multiple mylonitic shear zones, a HT/LP W-dipping foliation and E-W trending lineations. Strain markers provided by metaconglomerates suggest that deformation occurred in a constrictional regime, independent from the geometry of the magmatic system. Pluton emplacement and shearing were not caused by each other but they interacted producing an entirely new fabric that transposed the previous regional features. Deformation outlasted cooling causing the progressive localization of shearing along a main cataclastic zone localized at the contact between mylonitic metacarbonates and schists. The interaction between shearing and the emplacement of late leucogranitic sills caused also the development of mylonitic to cataclastic fabrics within the sills, depending on temperature and strain rate at the time of emplacement. At the microscale synkinematic blastesis of andalusite plus cordierite and the progressive switch from GBM- to SGR- to BLG- microstructures of quartz, locally overprinted by cataclastic fabrics. The analysis of microstructures suggest that in the Calamita Complex regional deformation affected the host rocks and the late magmatic products of the pluton that registered the switch from ductile to brittle conditions. This switch was generally due to the progressive cooling of the system; however multiple microstructures suggest that deformation in the Calamita was heterogeneous in time and space and possibly subject to different strain rates in different portions that may have produced coeval ductile and brittle deformation.

Persistence, population dynamics and competitiveness for nodulation of marker gene-tagged Rhizobium galegae strains in field lysimeters in the boreal climatic zone.

PubMed

Pitkäjärvi, Jyrki; Räsänen, Leena A; Langenskiöld, Jenny; Wallenius, Kaisa; Niemi, Maarit; Lindström, Kristina

2003-10-01

Abstract A non-indigenous wild-type strain Rhizobium galegae HAMBI 540, which specifically nodulates perennial goat's rue (Galega orientalis), and its marker gene-tagged derivatives R. galegae HAMBI 2363(luc), R. galegae HAMBI 2368(gusA21) and R. galegae HAMBI 2364(gusA30) were used to evaluate the persistence, population dynamics and competitiveness for nodulation of rhizobia under field conditions in Finland. The lysimeters were filled with clean or diesel oil-polluted (3000 mug g(-1)) agricultural soil. During the first 2 years of the field release luc- and gusA21-tagged strains could be effectively detected by cultivation, reinforced with colony polymerase chain reaction. The population densities remained relatively stable from 10(4) to 10(5) cfu g(-1) dry soil from spring until late autumn. Replicate limiting dilution polymerase chain reaction analysis gave comparable results with cultivation with strain HAMBI 2363 until 49 weeks after inoculation. GUS activity of strain HAMBI 2368 could be stably detected in nodules and soil. On the other hand, luc activity weakened clearly in cold conditions along with decreased metabolic activity of rhizobia. The competitive ability for nodulation of the gusA30-tagged strain decreased slowly with time compared to the wild-type strain. Moderate soil pollution did not have significant effects on target bacteria or plant growth. Limited vertical movement of target bacteria outside the rhizosphere was detected from percolated water.

Assessment of Liver Fibrosis Using Fast Strain-Encoded (FSENC) MRI Driven by Inherent Cardiac Motion

PubMed Central

Harouni, Ahmed A.; Gharib, Ahmed M.; Osman, Nael F.; Morse, Caryn; Heller, Theo; Abd-Elmoniem, Khaled Z.

2014-01-01

Purpose An external driver-free MRI method for assessment of liver fibrosis offers a promising non-invasive tool for diagnosis and monitoring of liver disease. Lately, the heart’s intrinsic motion and MR tagging have been utilized for the quantification of liver strain. However, MR tagging requires multiple breath-hold acquisitions and substantial post-processing. This work proposes a fast strain-encoded (FSENC) MRI methodology to measure the peak strain (Sp) in the liver’s left lobe, which is in close proximity and caudal to the heart. Additionally, a new method is introduced to measure heart-induced shear wave velocity (SWV) inside the liver. Methods Phantom and in-vivo experiments (11 healthy subjects, and 11 patients with liver fibrosis) were conducted. Reproducibility experiments were performed in seven healthy subjects. Results Peak liver strain Sp significantly decreased in fibrotic liver compared healthy liver (6.46%±2.27% vs. 12.49%±1.76%, P<0.05). Heart-induced SWV significantly increased in patients compared to healthy subjects (0.15±0.04 m/s vs. 0.63±0.32 m/s, P<0.05). Reproducibility analysis yielded no significant difference in Sp (P=0.47) or SWV (P=0.56). Conclusion Accelerated external driver-free noninvasive assessment of left liver lobe strain and shear wave velocity is feasible using strain-encoded MRI. The two measures significantly separate healthy subjects from patients with fibrotic liver. PMID:25081734

Comparative Analysis of Four Calypogeia Species Revealed Unexpected Change in Evolutionarily-Stable Liverwort Mitogenomes

PubMed Central

Ślipiko, Monika; Buczkowska-Chmielewska, Katarzyna; Bączkiewicz, Alina; Szczecińska, Monika; Sawicki, Jakub

2017-01-01

Liverwort mitogenomes are considered to be evolutionarily stable. A comparative analysis of four Calypogeia species revealed differences compared to previously sequenced liverwort mitogenomes. Such differences involve unexpected structural changes in the two genes, cox1 and atp1, which have lost three and two introns, respectively. The group I introns in the cox1 gene are proposed to have been lost by two-step localized retroprocessing, whereas one-step retroprocessing could be responsible for the disappearance of the group II introns in the atp1 gene. These cases represent the first identified losses of introns in mitogenomes of leafy liverworts (Jungermanniopsida) contrasting the stability of mitochondrial gene order with certain changes in the gene content and intron set in liverworts. PMID:29257096

Evolutionary instability of zero-determinant strategies demonstrates that winning is not everything.

PubMed

Adami, Christoph; Hintze, Arend

2013-01-01

Zero-determinant strategies are a new class of probabilistic and conditional strategies that are able to unilaterally set the expected payoff of an opponent in iterated plays of the Prisoner's Dilemma irrespective of the opponent's strategy (coercive strategies), or else to set the ratio between the player's and their opponent's expected payoff (extortionate strategies). Here we show that zero-determinant strategies are at most weakly dominant, are not evolutionarily stable, and will instead evolve into less coercive strategies. We show that zero-determinant strategies with an informational advantage over other players that allows them to recognize each other can be evolutionarily stable (and able to exploit other players). However, such an advantage is bound to be short-lived as opposing strategies evolve to counteract the recognition.

Nuclear autophagy: An evolutionarily conserved mechanism of nuclear degradation in the cytoplasm.

PubMed

Luo, Majing; Zhao, Xueya; Song, Ying; Cheng, Hanhua; Zhou, Rongjia

2016-11-01

Macroautophagy/autophagy is a catabolic process that is essential for cellular homeostasis. Studies on autophagic degradation of cytoplasmic components have generated interest in nuclear autophagy. Although its mechanisms and roles have remained elusive, tremendous progress has been made toward understanding nuclear autophagy. Nuclear autophagy is evolutionarily conserved in eukaryotes that may target various nuclear components through a series of processes, including nuclear sensing, nuclear export, autophagic substrate encapsulation and autophagic degradation in the cytoplasm. However, the molecular processes and regulatory mechanisms involved in nuclear autophagy remain largely unknown. Numerous studies have highlighted the importance of nuclear autophagy in physiological and pathological processes such as cancer. This review focuses on current advances in nuclear autophagy and provides a summary of its research history and landmark discoveries to offer new perspectives.

Pathogenic outcome following experimental infection of sheep with Chlamydia abortus variant strains LLG and POS.

PubMed

Livingstone, Morag; Wheelhouse, Nicholas; Ensor, Hannah; Rocchi, Mara; Maley, Stephen; Aitchison, Kevin; Wattegedera, Sean; Wilson, Kim; Sait, Michelle; Siarkou, Victoria; Vretou, Evangelia; Entrican, Gary; Dagleish, Mark; Longbottom, David

2017-01-01

This study investigated the pathogenesis of two variant strains (LLG and POS) of Chlamydia abortus, in comparison to a typical wild-type strain (S26/3) which is known to be responsible for late term abortion in small ruminants. Challenge with the three strains at mid-gestation resulted in similar pregnancy outcomes, with abortion occurring in approximately 50-60% of ewes with the mean gestational lengths also being similar. However, differences were observed in the severity of placental pathology, with infection appearing milder for strain LLG, which was reflected in the lower number of organisms shed in vaginal swabs post-partum and less gross pathology and organisms present in placental smears. Results for strain POS were somewhat different than LLG with a more focal restriction of infection observed. Post-abortion antibody responses revealed prominent differences in seropositivity to the major outer membrane protein (MOMP) present in elementary body (EB) preparations under denaturing conditions, most notably with anti-LLG and anti-POS convalescent sera where there was no or reduced detection of MOMP present in EBs derived from the three strains. These results and additional analysis of whole EB and chlamydial outer membrane complex preparations suggest that there are conformational differences in MOMP for the three strains. Overall, the results suggest that gross placental pathology and clinical outcome is not indicative of bacterial colonization and the severity of infection. The results also highlight potential conformational differences in MOMP epitopes that perhaps impact on disease diagnosis and the development of new vaccines.

Left ventricular longitudinal myocardial function in overt hypothyroidism: a tissue Doppler echocardiographic study.

PubMed

Tiryakioglu, Selma Kenar; Tiryakioglu, Osman; Ari, Hasan; Basel, Mehmet Cem; Ozkan, Hakan; Bozat, Tahsin

2010-05-01

The aim of this study was to assess left ventricular (LV) myocardial regional function in overt hypothyroidism by use of tissue Doppler imaging and to compare the results to the hormonal profile and standard Doppler echocardiographic examination. Hypothyroidic (Group 1, n = 25) and euthyroidic patients (Group 2, n = 25) underwent transthorasic echocardiography, strain and strain rate imaging. Standard echocardiography showed that patients with overt hypothyroidism had significantly longer isovolumic contraction time (IVCT) (P < 0.05), deceleration time (DT) (P = 0.014) and isovolumic relaxation time (IVRT) (P = 0.022). Tissue Doppler imaging showed that the mean peak systolic strain (SI) (16.47 + or - 1.45 vs. 20.63 + or - 1.51, P < 0.001), the mean peak systolic strain rate (SSR) (1.05 + or - 0.13 vs. 1.47 + or - 0.11, P < 0.001), the mean peak early diastolic strain rate (ESr) (1.72 + or - 0.38 vs. 2.03 + or - 0.25, P < 0.05) and the mean peak late diastolic strain rate (ASr) (1.22 + or - 0.31 vs. 1.46 + or - 0.32, P < 0.05) were significantly lower in Group 1 compared to Group 2. For all patients, the systolic strain and systolic strain rate parameters negatively correlated with thyroid stimulating hormone levels and positively correlated with the levels of free triiodothyronine (fT(3)) and free tetraiodothyronine (fT(4)). These results indicate that overt hypothyroidism is associated with early impairment in LV longitudinal myocardial function, and that tissue Doppler echocardiography is useful for the grading of disease and detection of early impairment. (ECHOCARDIOGRAPHY 2010;27:505-511).

Phylogenetic Analysis of the Spike (S) Gene of the New Variants of Porcine Epidemic Diarrhoea Virus in Taiwan.

PubMed

Chiou, H-Y; Huang, Y-L; Deng, M-C; Chang, C-Y; Jeng, C-R; Tsai, P-S; Yang, C; Pang, V F; Chang, H-W

2017-02-01

New variants of porcine epidemic diarrhoea virus (PEDV), which emerged in Taiwan in late 2013, have caused a high morbidity and mortality in neonatal piglets. To investigate the molecular characteristics of the spike (S) gene of the emerging Taiwan PEDV strains for a better understanding of the genetic diversity and relationship among the Taiwan new variants and the global PEDVs, full-length S genes of PEDVs from nine 1-7 day-old piglets from three pig farms in the central and southern Taiwan were sequenced and analysed. The result of phylogenetic analysis of the S gene showed that all the Taiwan PEDV strains were closely related to the non-S INDEL strains from US, Canada and China, suggesting a common ancestor for these strains. As compared with the historic PEDVs and CV777-based vaccine strains, the nine Taiwan PEDV variants shared almost the same genetic signatures as the global non-S INDEL strains, including a series of insertions, deletions and mutations in the amino terminal as well as identical mutations in the neutralizing epitopes of the S gene. The high similarity of the S protein among the Taiwan and the globally emerged non-S INDEL PEDV strains suggests that the Taiwan new variants may share similar pathogenesis and immunogenicity as the global outbreak variants. The development of a novel vaccine based on the Taiwan or the global non-S INDEL strains may be contributive to the control of the current global porcine epidemic diarrhoea outbreaks. © 2015 Blackwell Verlag GmbH.

Burkholderia cepacia complex in cystic fibrosis in the post-epidemic period: multilocus sequence typing-based approach.

PubMed

Fila, Libor; Dřevínek, Pavel

2017-11-01

Cystic fibrosis (CF) patients in the Czech Republic suffered in the late 1990s from an epidemic with ST32 strain of Burkholderia cepacia complex (Bcc). Cohort segregation of Bcc and of ST32 positive patients was introduced in 1999 and 2002, respectively. We performed a study to evaluate the molecular epidemiology of Bcc infection after implementation of these infection control measures. Patients attending the Prague CF adult Centre from 2000 to 2015 were included in the present study. Demographic data and microbial statuses were collected from patient records. All Bcc isolates were analyzed using multilocus sequence typing (MLST). The prevalences of epidemic strain ST32 and of other Bcc strains were calculated. Ninety out of 227 CF patients were infected with Bcc during the study period. The prevalence of ST32 cases significantly decreased from 46.5% in 2000-2001 to 10.4% in 2014-2015 (P < 0.001) due to occurrence of only one new case in 2003, as well as to the death of 72% of ST32-infected patients. Conversely, there was a significant increase in prevalence of other Bcc strains, which rose from 0 to 14.9% (P = 0.015) and of transient infections. A micro-epidemic of infection with ST630 strain was observed in 2014 in lung transplant patients hospitalized in intensive care unit. The prevalence of epidemic strain ST32 decreased, whereas that of non-clonal strains of Bcc increased. Routine use of MLST allowed early detection of new and potentially epidemic strains.

Functional role of the MrpA- and MrpD-homologous protein subunits in enzyme complexes evolutionary related to respiratory chain complex I.

PubMed

Moparthi, Vamsi K; Kumar, Brijesh; Al-Eryani, Yusra; Sperling, Eva; Górecki, Kamil; Drakenberg, Torbjörn; Hägerhäll, Cecilia

2014-01-01

NADH:quinone oxidoreductase or complex I is a large membrane bound enzyme complex that has evolved from the combination of smaller functional building blocks. Intermediate size enzyme complexes exist in nature that comprise some, but not all of the protein subunits in full size 14-subunit complex I. The membrane spanning complex I subunits NuoL, NuoM and NuoN are homologous to each other and to two proteins from one particular class of Na(+)/H(+) antiporters, denoted MrpA and MrpD. In complex I, these ion transporter protein subunits are prime candidates for harboring important parts of the proton pumping machinery. Using a model system, consisting of Bacillus subtilis MrpA and MrpD deletion strains and a low copy expression plasmid, it was recently demonstrated that NuoN can rescue the strain deleted for MrpD but not that deleted for MrpA, whereas the opposite tendency was seen for NuoL. This demonstrated that the MrpA-type and MrpD-type proteins have unique functional specializations. In this work, the corresponding antiporter-like protein subunits from the smaller enzymes evolutionarily related to complex I were tested in the same model system. The subunits from 11-subunit complex I from Bacillus cereus behaved essentially as those from full size complex I, corroborating that this enzyme should be regarded as a bona fide complex I. The hydrogenase-3 and hydrogenase-4 antiporter-like proteins on the other hand, could substitute equally well for MrpA or MrpD at pH7.4, suggesting that these enzymes have intermediate forms of the antiporter-like proteins, which seemingly lack the functional specificity. © 2013. Published by Elsevier B.V. All rights reserved.

The bacterial type III-secreted protein AvrRps4 is a bipartite effector

PubMed Central

Spears, Benjamin J.; Garner, Christopher M.; Rogan, Conner J.; Su, Jianbin; Bhattacharjee, Saikat

2018-01-01

Bacterial effector proteins secreted into host plant cells manipulate those cells to the benefit of the pathogen, but effector-triggered immunity (ETI) occurs when effectors are recognized by host resistance proteins. The RPS4/RRS1 pair recognizes the Pseudomonas syringae pv. pisi effector AvrRps4. AvrRps4 is processed in planta into AvrRps4N (133 amino acids), homologous to the N-termini of other effectors including the native P. syringae pv. tomato strain DC3000 effector HopK1, and AvrRps4C (88 amino acids). Previous data suggested that AvrRps4C alone is necessary and sufficient for resistance when overexpressed in heterologous systems. We show that delivering AvrRps4C from DC3000, but not from a DC3000 hopK1- strain, triggers resistance in the Arabidopsis accession Col-0. Delivering AvrRps4C in tandem with AvrRps4N, or as a chimera with HopK1N, fully complements AvrRps4-triggered immunity. AvrRps4N in the absence of AvrRps4C enhances virulence in Col-0. In addition, AvrRps4N triggers a hypersensitive response in lettuce that is attenuated by coexpression of AvrRps4C, further supporting the role of AvrRps4N as a bona fide effector domain. Based on these results we propose that evolutionarily, fusion of AvrRps4C to AvrRps4N may have counteracted recognition of AvrRps4N, and that the plant RPS4/RRS1 resistance gene pair was selected as a countermeasure. We conclude that AvrRps4 represents an unusual chimeric effector, with recognition in Arabidopsis by RPS4/RRS1 requiring the presence of both processed effector moieties. PMID:29601603

Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways

PubMed Central

Ma, Menggen; Song, Mingzhou

2010-01-01

Lignocellulosic biomass conversion inhibitors, furfural and HMF, inhibit microbial growth and interfere with subsequent fermentation of ethanol, posing significant challenges for a sustainable cellulosic ethanol conversion industry. Numerous yeast genes were found to be associated with the inhibitor tolerance. However, limited knowledge is available about mechanisms of the tolerance and the detoxification of the biomass conversion inhibitors. Using a robust standard for absolute mRNA quantification assay and a recently developed tolerant ethanologenic yeast Saccharomyces cerevisiae NRRL Y-50049, we investigate pathway-based transcription profiles relevant to the yeast tolerance and the inhibitor detoxification. Under the synergistic inhibitory challenges by furfural and HMF, Y-50049 was able to withstand the inhibitor stress, in situ detoxify furfural and HMF, and produce ethanol, while its parental control Y-12632 failed to function till 65 h after incubation. The tolerant strain Y-50049 displayed enriched genetic background with significantly higher abundant of transcripts for at least 16 genes than a non-tolerant parental strain Y-12632. The enhanced expression of ZWF1 appeared to drive glucose metabolism in favor of pentose phosphate pathway over glycolysis at earlier steps of glucose metabolisms. Cofactor NAD(P)H generation steps were likely accelerated by enzymes encoded by ZWF1, GND1, GND2, TDH1, and ALD4. NAD(P)H-dependent aldehyde reductions including conversion of furfural and HMF, in return, provided sufficient NAD(P)+ for NAD(P)H regeneration in the yeast detoxification pathways. Enriched genetic background and a well maintained redox balance through reprogrammed expression responses of Y-50049 were accountable for the acquired tolerance and detoxification of furfural to furan methanol and HMF to furan dimethanol. We present significant gene interactions and regulatory networks involved in NAD(P)H regenerations and functional aldehyde reductions under the inhibitor stress. PMID:19517136

Function of the evolutionarily conserved plant methionine-S-sulfoxide reductase without the catalytic residue.

PubMed

Le, Dung Tien; Nguyen, Kim-Lien; Chu, Ha Duc; Vu, Nam Tuan; Pham, Thu Thi Ly; Tran, Lam-Son Phan

2018-05-28

In plants, two types of methionine sulfoxide reductase (MSR) exist, namely methionine-S-sulfoxide reductase (MSRA) and methionine-R-sulfoxide reductase (MSRB). These enzymes catalyze the reduction of methionine sulfoxides (MetO) back to methionine (Met) by a catalytic cysteine (Cys) and one or two resolving Cys residues. Interestingly, a group of MSRA encoded by plant genomes does not have a catalytic residue. We asked that if this group of MSRA did not have any function (as fitness), why it was not lost during the evolutionary process. To challenge this question, we analyzed the gene family encoding MSRA in soybean (GmMSRAs). We found seven genes encoding GmMSRAs, which included three segmental duplicated pairs. Among them, a pair of duplicated genes, namely GmMSRA1 and GmMSRA6, was without a catalytic Cys residue. Pseudogenes were ruled out as their transcripts were detected in various tissues and their Ka/Ks ratio indicated a negative selection pressure. In vivo analysis in Δ3MSR yeast strain indicated that the GmMSRA6 did not have activity toward MetO, contrasting to GmMSRA3 which had catalytic Cys and had activity. When exposed to H 2 O 2 -induced oxidative stress, GmMSRA6 did not confer any protection to the Δ3MSR yeast strain. Overexpression of GmMSRA6 in Arabidopsis thaliana did not alter the plant's phenotype under physiological conditions. However, the transgenic plants exhibited slightly higher sensitivity toward salinity-induced stress. Taken together, this data suggested that the plant MSRAs without the catalytic Cys are not enzymatically active and their existence may be explained by a role in regulating plant MSR activity via dominant-negative substrate competition mechanism.

Reconstruction of the High-Osmolarity Glycerol (HOG) Signaling Pathway from the Halophilic Fungus Wallemia ichthyophaga in Saccharomyces cerevisiae.

PubMed

Konte, Tilen; Terpitz, Ulrich; Plemenitaš, Ana

2016-01-01

The basidiomycetous fungus Wallemia ichthyophaga grows between 1.7 and 5.1 M NaCl and is the most halophilic eukaryote described to date. Like other fungi, W. ichthyophaga detects changes in environmental salinity mainly by the evolutionarily conserved high-osmolarity glycerol (HOG) signaling pathway. In Saccharomyces cerevisiae, the HOG pathway has been extensively studied in connection to osmotic regulation, with a valuable knock-out strain collection established. In the present study, we reconstructed the architecture of the HOG pathway of W. ichthyophaga in suitable S. cerevisiae knock-out strains, through heterologous expression of the W. ichthyophaga HOG pathway proteins. Compared to S. cerevisiae, where the Pbs2 (ScPbs2) kinase of the HOG pathway is activated via the SHO1 and SLN1 branches, the interactions between the W. ichthyophaga Pbs2 (WiPbs2) kinase and the W. ichthyophaga SHO1 branch orthologs are not conserved: as well as evidence of poor interactions between the WiSho1 Src-homology 3 (SH3) domain and the WiPbs2 proline-rich motif, the absence of a considerable part of the osmosensing apparatus in the genome of W. ichthyophaga suggests that the SHO1 branch components are not involved in HOG signaling in this halophilic fungus. In contrast, the conserved activation of WiPbs2 by the S. cerevisiae ScSsk2/ScSsk22 kinase and the sensitivity of W. ichthyophaga cells to fludioxonil, emphasize the significance of two-component (SLN1-like) signaling via Group III histidine kinase. Combined with protein modeling data, our study reveals conserved and non-conserved protein interactions in the HOG signaling pathway of W. ichthyophaga and therefore significantly improves the knowledge of hyperosmotic signal processing in this halophilic fungus.

Larval excretory-secretory products from the parasite Schistosoma mansoni modulate HSP70 protein expression in defence cells of its snail host, Biomphalaria glabrata

PubMed Central

Zahoor, Zahida; Davies, Angela J.; Kirk, Ruth S.; Rollinson, David

2010-01-01

Synthesis of heat shock proteins (HSPs) following cellular stress is a response shared by many organisms. Amongst the HSP family, the ∼70 kDa HSPs are the most evolutionarily conserved with intracellular chaperone and extracellular immunoregulatory functions. This study focused on the effects of larval excretory-secretory products (ESPs) from the parasite Schistosoma mansoni on HSP70 protein expression levels in haemocytes (defence cells) from its snail intermediate host Biomphalaria glabrata. S. mansoni larval stage ESPs are known to interfere with haemocyte physiology and behaviour. Haemocytes from two different B. glabrata strains, one which is susceptible to S. mansoni infection and one which is resistant, both showed reduced HSP70 protein levels following 1 h challenge with S. mansoni ESPs when compared to unchallenged controls; however, the reduction observed in the resistant strain was less marked. The decline in intracellular HSP70 protein persisted for at least 5 h in resistant snail haemocytes only. Furthermore, in schistosome-susceptible snails infected by S. mansoni for 35 days, haemocytes possessed approximately 70% less HSP70. The proteasome inhibitor, MG132, partially restored HSP70 protein levels in ESP-challenged haemocytes, demonstrating that the decrease in HSP70 was in part due to intracellular degradation. The extracellular signal-regulated kinase (ERK) signalling pathway appears to regulate HSP70 protein expression in these cells, as the mitogen-activated protein-ERK kinase 1/2 (MEK1/2) inhibitor, U0126, significantly reduced HSP70 protein levels. Disruption of intracellular HSP70 protein expression in B. glabrata haemocytes by S. mansoni ESPs may be a strategy employed by the parasite to manipulate the immune response of the intermediate snail host. PMID:20182834

Larval excretory-secretory products from the parasite Schistosoma mansoni modulate HSP70 protein expression in defence cells of its snail host, Biomphalaria glabrata.

PubMed

Zahoor, Zahida; Davies, Angela J; Kirk, Ruth S; Rollinson, David; Walker, Anthony John

2010-09-01

Synthesis of heat shock proteins (HSPs) following cellular stress is a response shared by many organisms. Amongst the HSP family, the approximately 70 kDa HSPs are the most evolutionarily conserved with intracellular chaperone and extracellular immunoregulatory functions. This study focused on the effects of larval excretory-secretory products (ESPs) from the parasite Schistosoma mansoni on HSP70 protein expression levels in haemocytes (defence cells) from its snail intermediate host Biomphalaria glabrata. S. mansoni larval stage ESPs are known to interfere with haemocyte physiology and behaviour. Haemocytes from two different B. glabrata strains, one which is susceptible to S. mansoni infection and one which is resistant, both showed reduced HSP70 protein levels following 1 h challenge with S. mansoni ESPs when compared to unchallenged controls; however, the reduction observed in the resistant strain was less marked. The decline in intracellular HSP70 protein persisted for at least 5 h in resistant snail haemocytes only. Furthermore, in schistosome-susceptible snails infected by S. mansoni for 35 days, haemocytes possessed approximately 70% less HSP70. The proteasome inhibitor, MG132, partially restored HSP70 protein levels in ESP-challenged haemocytes, demonstrating that the decrease in HSP70 was in part due to intracellular degradation. The extracellular signal-regulated kinase (ERK) signalling pathway appears to regulate HSP70 protein expression in these cells, as the mitogen-activated protein-ERK kinase 1/2 (MEK1/2) inhibitor, U0126, significantly reduced HSP70 protein levels. Disruption of intracellular HSP70 protein expression in B. glabrata haemocytes by S. mansoni ESPs may be a strategy employed by the parasite to manipulate the immune response of the intermediate snail host.

Ecological perspectives on synthetic biology: insights from microbial population biology

PubMed Central

Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

2015-01-01

The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID:25767468

Precipitation of Phosphate Minerals by Microorganisms Isolated from a Fixed-Biofilm Reactor Used for the Treatment of Domestic Wastewater

PubMed Central

Rivadeneyra, Almudena; Gonzalez-Martinez, Alejandro; Gonzalez-Lopez, Jesus; Martin-Ramos, Daniel; Martinez-Toledo, Maria Victoria; Rivadeneyra, Maria Angustias

2014-01-01

The ability of bacteria isolated from a fixed-film bioreactor to precipitate phosphate crystals for the treatment of domestic wastewater in both artificial and natural media was studied. When this was demonstrated in artificial solid media for crystal formation, precipitation took place rapidly, and crystal formation began 3 days after inoculation. The percentage of phosphate-forming bacteria was slightly higher than 75%. Twelve major colonies with phosphate precipitation capacity were the dominant heterotrophic platable bacteria growing aerobically in artificial media. According to their taxonomic affiliations (based on partial sequencing of the 16S rRNA), the 12 strains belonged to the following genera of Gram-negative bacteria: Rhodobacter, Pseudoxanthobacter, Escherichia, Alcaligenes, Roseobacter, Ochrobactrum, Agromyce, Sphingomonas and Paracoccus. The phylogenetic tree shows that most of the identified populations were evolutionarily related to the Alphaproteobacteria (91.66% of sequences). The minerals formed were studied by X-ray diffraction, scanning electron microscopy (SEM), and energy dispersive X-ray microanalysis (EDX). All of these strains formed phosphate crystals and precipitated struvite (MgNH4PO4·6H2O), bobierrite [Mg3(PO4)2·8H2O] and baricite [(MgFe)3(PO4)2·8H2O]. The results obtained in this study show that struvite and spherulite crystals did not show any cell marks. Moreover, phosphate precipitation was observed in the bacterial mass but also near the colonies. Our results suggest that the microbial population contributed to phosphate precipitation by changing the media as a consequence of their metabolic activity. Moreover, the results of this research suggest that bacteria play an active role in the mineral precipitation of soluble phosphate from urban wastewater in submerged fixed-film bioreactors. PMID:24699031

The bacterial type III-secreted protein AvrRps4 is a bipartite effector.

PubMed

Halane, Morgan K; Kim, Sang Hee; Spears, Benjamin J; Garner, Christopher M; Rogan, Conner J; Okafor, Elizabeth C; Su, Jianbin; Bhattacharjee, Saikat; Gassmann, Walter

2018-03-01

Bacterial effector proteins secreted into host plant cells manipulate those cells to the benefit of the pathogen, but effector-triggered immunity (ETI) occurs when effectors are recognized by host resistance proteins. The RPS4/RRS1 pair recognizes the Pseudomonas syringae pv. pisi effector AvrRps4. AvrRps4 is processed in planta into AvrRps4N (133 amino acids), homologous to the N-termini of other effectors including the native P. syringae pv. tomato strain DC3000 effector HopK1, and AvrRps4C (88 amino acids). Previous data suggested that AvrRps4C alone is necessary and sufficient for resistance when overexpressed in heterologous systems. We show that delivering AvrRps4C from DC3000, but not from a DC3000 hopK1- strain, triggers resistance in the Arabidopsis accession Col-0. Delivering AvrRps4C in tandem with AvrRps4N, or as a chimera with HopK1N, fully complements AvrRps4-triggered immunity. AvrRps4N in the absence of AvrRps4C enhances virulence in Col-0. In addition, AvrRps4N triggers a hypersensitive response in lettuce that is attenuated by coexpression of AvrRps4C, further supporting the role of AvrRps4N as a bona fide effector domain. Based on these results we propose that evolutionarily, fusion of AvrRps4C to AvrRps4N may have counteracted recognition of AvrRps4N, and that the plant RPS4/RRS1 resistance gene pair was selected as a countermeasure. We conclude that AvrRps4 represents an unusual chimeric effector, with recognition in Arabidopsis by RPS4/RRS1 requiring the presence of both processed effector moieties.

Upsurge and spread of G3 rotaviruses in Eastern India (2014-2016): Full genome analyses reveals heterogeneity within Wa-like genomic constellation.

PubMed

Banerjee, Anindita; Lo, Mahadeb; Indwar, Pallavi; Deb, Alok K; Das, Santasabuj; Manna, Byomkesh; Dutta, Shanta; Bhadra, Uchhal K; Bhattacharya, Mala; Okamoto, Keinosuke; Chawla-Sarkar, Mamta

2018-05-26

Advent of new strains and shift in predominantly circulating genotypes are characteristics of group- A rotavirus (RVA), one of the major causes of childhood gastroenteritis. During diarrheal disease surveillance at Kolkata, India (2014-2016), a shift in circulating RVA strains from G1P[8] to G3P[8] was seen. Stool samples from children (n = 3048) with acute gastroenteritis were tested of which 38.7% were RVA positive. G1 was the predominant strain (65.3%) in 2014-2015 whereas in late 2015 and 2016, G3 became the preponderant strain (44.6%). In the past decade G3 strains were not observed in this region, we conducted whole genome sequencing of representative strains to gain insight into the phenomenon of emergence and genetic constellation of these circulating human G3 strains. The analyses revealed intergenogroup reassortment in G3P[4] strains (among Wa and DS-1-like genogroup) whereas G3P[8] strains were authentic Wa-like. Phylogenetic analysis revealed Kolkata G3 strains as polymorphic and thus they formed two sub-clusters due to antigenic differences in their VP7 protein. One of the sub-clusters had the wild-type threonine at 87 amino acid position while another sub-cluster had an isoleucine mutation. Presence of additional N-linked glycosylation site at amino acid 283 of VP7 glycoprotein suggests that the major neutralizing epitope on the VP7 (G3) of RotaTeq vaccine differs from the currently circulating G3 strains. The study is important as efficiency of rotavirus vaccine depends on the circulating heterogeneous genotype constellations. Continuous monitoring of circulating RVA strains in endemic settings like India is therefore important in pre- and post-vaccination period to monitor the emergence of new reassortant genotypes in addition to assessing vaccine efficacy. Copyright © 2018. Published by Elsevier B.V.

Normal values for myocardial deformation within the right heart measured by feature-tracking cardiovascular magnetic resonance imaging.

PubMed

Liu, Boyang; Dardeer, Ahmed M; Moody, William E; Edwards, Nicola C; Hudsmith, Lucy E; Steeds, Richard P

2018-02-01

Reproducible and repeatable assessment of right heart function is vital for monitoring congenital and acquired heart disease. There is increasing evidence for the additional value of myocardial deformation (strain and strain rate) in determining prognosis. This study aims to determine the reproducibility of deformation analyses in the right heart using cardiovascular magnetic resonance feature tracking (FT-CMR); and to establish normal ranges within an adult population. A cohort of 100 healthy subjects containing 10 males and 10 females from each decade of life between the ages of 20 and 70 without known congenital or acquired cardiovascular disease, hypertension, diabetes, dyslipidaemia or renal, hepatic, haematologic and systemic inflammatory disorders underwent FT-CMR assessment of right ventricular (RV) and right atrial (RA) myocardial strain and strain rate. RV longitudinal strain (Ell) was -21.9±3.24% (FW+S Ell) and -24.2±3.59% (FW-Ell). Peak systolic strain rate (S') was -1.45±0.39s -1 (FW+S) and -1.54±0.41s -1 (FW). Early diastolic strain rate (E') was 1.04±0.26s -1 (FW+S) and 1.04±0.33s -1 (FW). Late diastolic strain rate (A') was 0.94±0.33s -1 (FW+S) and 1.08±0.33s -1 (FW). RA peak strain was -21.1±3.76%. The intra- and inter-observer ICC for RV Ell (FW+S) was 0.92 and 0.80 respectively, while for RA peak strain was 0.92 and 0.89 respectively. Normal values of RV & RA deformation for healthy individuals using FT-CMR are provided with good RV Ell and RA peak strain reproducibility. Strain rate suffered from sub-optimal reproducibility and may not be satisfactory for clinical use. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Degradation of 1,2-dichloroethane by Ancylobacter aquaticus and other facultative methylotrophs.

PubMed Central

van den Wijngaard, A J; van der Kamp, K W; van der Ploeg, J; Pries, F; Kazemier, B; Janssen, D B

1992-01-01

Cultures of the newly isolated bacterial strains AD20, AD25, and AD27, identified as strains of Ancylobacter aquaticus, were capable of growth on 1,2-dichloroethane (DCE) as the sole carbon and energy source. These strains, as well as two other new DCE utilizers, were facultative methylotrophs and were also able to grow on 2-chloroethanol, chloroacetate, and 2-chloropropionate. In all strains tested, DCE was degraded by initial hydrolytic dehalogenation to 2-chloroethanol, followed by oxidation by a phenazine methosulfate-dependent alcohol dehydrogenase and an NAD-dependent aldehyde dehydrogenase. The resulting chloroacetic acid was converted to glycolate by chloroacetate dehalogenase. The alcohol dehydrogenase was induced during growth on methanol or DCE in strain AD20, but no activity was found during growth on glucose. However, in strain AD25 the enzyme was synthesized to a higher level during growth on glucose than on methanol, and it reached levels of around 2 U/mg of protein in late-exponential-phase cultures growing on glucose. The haloalkane dehalogenase was constitutively produced in all strains tested, but strain AD25 synthesized the enzyme at a level of 30 to 40% of the total cellular protein, which is much higher than that found in other DCE degraders. The nucleotide sequences of the haloalkane dehalogenase (dhlA) genes of strains AD20 and AD25 were the same as the sequence of dhlA from Xanthobacter autotrophicus GJ10 and GJ11. Hybridization experiments showed that the dhlA genes of six different DCE utilizers were all located on an 8.3-kb EcoRI restriction fragment, indicating that the organisms may have obtained the dhlA gene by horizontal gene transmission. Images PMID:1575500

Diffusible and Volatile Antifungal Compounds Produced by an Antagonistic Bacillus velezensis G341 against Various Phytopathogenic Fungi.

PubMed

Lim, Seong Mi; Yoon, Mi-Young; Choi, Gyung Ja; Choi, Yong Ho; Jang, Kyoung Soo; Shin, Teak Soo; Park, Hae Woong; Yu, Nan Hee; Kim, Young Ho; Kim, Jin-Cheol

2017-10-01

The aim of this study was to identify volatile and agar-diffusible antifungal metabolites produced by Bacillus sp. G341 with strong antifungal activity against various phytopathogenic fungi. Strain G341 isolated from four-year-old roots of Korean ginseng with rot symptoms was identified as Bacillus velezensis based on 16S rDNA and gyrA sequences. Strain G341 inhibited mycelial growth of all phytopathogenic fungi tested. In vivo experiment results revealed that n -butanol extract of fermentation broth effectively controlled the development of rice sheath blight, tomato gray mold, tomato late blight, wheat leaf rust, barley powdery mildew, and red pepper anthracnose. Two antifungal compounds were isolated from strain G341 and identified as bacillomycin L and fengycin A by MS/MS analysis. Moreover, volatile compounds emitted from strain G341 were found to be able to inhibit mycelial growth of various phytopathogenic fungi. Based on volatile compound profiles of strain G341 obtained through headspace collection and analysis on GC-MS, dimethylsulfoxide, 1-butanol, and 3-hydroxy-2-butanone (acetoin) were identified. Taken together, these results suggest that B. valezensis G341 can be used as a biocontrol agent for various plant diseases caused by phytopathogenic fungi.

Coevolution of antibiotic production and counter-resistance in soil bacteria.

PubMed

Laskaris, Paris; Tolba, Sahar; Calvo-Bado, Leo; Wellington, Elizabeth M; Wellington, Liz

2010-03-01

We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.

Differential Requirements in Endocytic Trafficking for Penetration of Dengue Virus

PubMed Central

Acosta, Eliana G.; Castilla, Viviana; Damonte, Elsa B.

2012-01-01

The entry of DENV into the host cell appears to be a very complex process which has been started to be studied in detail. In this report, the route of functional intracellular trafficking after endocytic uptake of dengue virus serotype 1 (DENV-1) strain HW, DENV-2 strain NGC and DENV-2 strain 16681 into Vero cells was studied by using a susceptibility to ammonium chloride assay, dominant negative mutants of several members of the family of cellular Rab GTPases that participate in regulation of transport through endosome vesicles and immunofluorescence colocalization. Together, the results presented demonstrate that in spite of the different internalization route among viral serotypes in Vero cells and regardless of the viral strain, DENV particles are first transported to early endosomes in a Rab5-dependent manner. Then a Rab7-dependent pathway guides DENV-2 16681 to late endosomes, whereas a yet unknown sorting event controls the transport of DENV-2 NGC, and most probably DENV-1 HW, to the perinuclear recycling compartments where fusion membrane would take place releasing nucleocapsid into the cytoplasm. Besides the demonstration of a different intracellular trafficking for two DENV-2 strains that shared the initial clathrin-independent internalization route, these studies proved for the first time the involvement of the slow recycling pathway for DENV-2 productive infection. PMID:22970315

On the lag time between internal strain and basement involved thrust induced exhumation: The case of the Colombian Eastern Cordillera

NASA Astrophysics Data System (ADS)

Mora, Andrès; Blanco, Vladimir; Naranjo, Julian; Sanchez, Nelson; Ketcham, Richard A.; Rubiano, Jorge; Stockli, Daniel F.; Quintero, Isaid; Nemčok, Michal; Horton, Brian K.; Davila, Hamblet

2013-07-01

Thrust sheets accumulate internal strain before they start moving along discrete fault planes. However, there are no previous studies evaluating the time difference between initiation of strain and fault displacement. In this paper we use observations from the Eastern Cordillera of Colombia to evaluate this interval. We utilize multiple thermochronometers and paleothermometers to refine the timing of deformation. Based on these new data we build time-temperature path estimates that together with geometric outcrop-based structural analysis and fluid inclusions allow us to assign relative timing to features associated with strain, such as cleavage, veins and certain types of fractures, and compare that with the timing of thrusting. We find that cleavage was only formed close to maximum paleotemperatures, almost coeval with the onset of thrust-induced denudation by the Late Oligocene. The corresponding structural level of fold-related veins suggest that they were formed later but still when the country rocks were at temperatures higher than 160 °C, mostly during the Early Miocene and still coexisted with the latest stages of cleavage formation. Our data show that the main period of strain hardening was short (probably a few million years) and occurred before first-order basement thrusting was dominant, but was associated with second-order folding.

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

PubMed Central

Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita

2016-01-01

We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution. PMID:27803195

Characterization, production, and purification of carnocin H, a bacteriocin produced by Carnobacterium 377.

PubMed

Blom, H; Katla, T; Nissen, H; Holo, H

2001-10-01

Carnocin H, a bacteriocin produced by a Carnobacterium sp., inhibited lactic acid bacteria, clostridia, enterococci, and some Staphylococcus aureus strains. Some strains of Listeria and Pediococcus were also sensitive to carnocin H. The bacteriocin was produced during the late stationary growth phase. Carnocin H was purified by cation exchange chromatography and reverse phase chromatography. Amino acid sequence and composition indicate that carnocin H is a novel bacteriocin belonging to the class II bacteriocins. The bacteriocin consists of approximately 75 amino acid residues with a highly cationic N-terminal containing six succeeding lysines. Activity, as measured by agar diffusion zones, was reduced at increased pH values, levels of indicator bacteria, NaCl, agar, and soy oil.

Proteome profiling of virus-host interactions of wild type and attenuated measles virus strains.

PubMed

Billing, Anja M; Kessler, Julia R; Revets, Dominique; Sausy, Aurélie; Schmitz, Stephanie; Barra, Claire; Muller, Claude P

2014-08-28

Quantitative gel-based proteomics (2D DIGE coupled to MALDI-TOF/TOF MS) has been used to investigate the effects of different measles virus (MV) strains on the host cell proteome. A549/hSLAM cells were infected either with wild type MV strains, an attenuated vaccine or a multiple passaged Vero cell adapted strain. By including interferon beta treatment as a control it was possible to distinguish between the classical antiviral response and changes induced specifically by the different strains. Of 38 differentially expressed proteins in total (p-value ≤0.05, fold change ≥2), 18 proteins were uniquely modulated following MV infection with up to 9 proteins specific per individual strain. Interestingly, wt strains displayed distinct protein patterns particularly during the late phase of infection. Proteins were grouped into cytoskeleton, metabolism, transcription/translation, immune response and mitochondrial proteins. Bioinformatics analysis revealed mostly changes in proteins regulating cell death and apoptosis. Surprisingly, wt strains affected the cytokeratin system much stronger than the vaccine strain. To our knowledge, this is the first study on the MV-host proteome addressing interstrain differences. In the present study we investigated the host cell proteome upon measles virus (MV) infection. The novelty about this study is the side-by side comparison of different strains from the same virus, which has not been done at the proteome level for any other virus including MV. We used different virus strains including a vaccine strain, wild type isolates derived from MV-infected patients as well as a Vero cell adapted strain, which serves as an intermediate between vaccine and wild type strain. We observed differences between vaccine and wild type strains as well as common features between different wild type strains. Perhaps one of the most surprising findings was that differences did not only occur between wild type and vaccine or Vero cell adapted strains but also between different wild type strains. In fact our study suggests that besides the cytokeratin and the IFN system wild type viruses seem to differ as much among each other than from vaccine strains. Thus our results are suggestive of complex and diverse virus-host interactions which differ considerably between different wild type strains. Our data indicate that interstrain differences are prominent and have so far been neglected by proteomics studies. Copyright © 2014 Elsevier B.V. All rights reserved.

Essential Oil Composition and Antibacterial Activity of Origanum vulgare subsp. glandulosum Desf. at Different Phenological Stages

PubMed Central

Chaabane, Hédia; Jemli, Maroua; Boulila, Abdennacer; Boussaid, Mohamed

2013-01-01

Abstract Variation in the quantity and quality of the essential oil (EO) of wild population of Origanum vulgare at different phenological stages, including vegetative, late vegetative, and flowering set, is reported. The oils of air-dried samples were obtained by hydrodistillation. The yield of oils (w/w%) at different stages were in the order of late vegetative (2.0%), early vegetative (1.7%), and flowering (0.6%) set. The oils were analyzed by gas chromatography (GC) and GC–mass spectrometry (GC-MS). In total, 36, 33, and 16 components were identified and quantified in vegetative, late vegetative, and flowering set, representing 94.47%, 95.91%, and 99.62% of the oil, respectively. Carvacrol was the major compound in all samples. The ranges of major constituents were as follows: carvacrol (61.08–83.37%), p-cymene (3.02–9.87%), and γ-terpinene (4.13–6.34%). Antibacterial activity of the oils was tested against three Gram-positive and two Gram-negative bacteria by the disc diffusion method and determining their diameter of inhibition and the minimum inhibitory concentration (MIC) values. The inhibition zones and MIC values for bacterial strains, which were sensitive to the EO of O. vulgare subsp. glandulosum, were in the range of 9–36 mm and 125–600 μg/mL, respectively. The oils of various phenological stages showed high activity against all tested bacteria, of which Bacillus subtilis was the most sensitive and resistant strain, respectively. Thus, they represent an inexpensive source of natural antibacterial substances that exhibited potential for use in pathogenic systems. PMID:24320986

Passive recording of an active transform, an example from the Levant continental margin and the Dead Sea Fault

NASA Astrophysics Data System (ADS)

Lang, Guy; Lazar, Michael; Schattner, Uri

2017-04-01

Transform faults accommodate lateral motion between two adjacent plates. Records of plate motion and consequent boundary development on land is, at times, scarce and limited to structures along the fault axis. Investigation of a passive continental margin adjacent to the plate boundary might broaden the scope and provide estimates for its structural development. To examine this hypothesis, we analyzed depth and time migrated 3D seismic data together with four boreholes located along the southern Levant continental margin, ca. 100 Km from the continental Dead Sea fault (DSF). The analysis focus on the Plio-Pleistocene sequence, a key period in the development of the DSF. It includes formation of structural maps, stacking pattern investigation and calculation of sedimentation rates based on decompacted 3D depth data. These, in turn, enabled the reconstruction of margin development. This includes Messinian-earliest Zanclean NNE-SSW sinistral strike-slip faulting followed by Zanclean-Late Gelasian syn-depositional folding striking in the same direction. Abrupt change is marked by the Top Gelasian surface that shows indications of regional mass slumping. Successive Mid-Late Pleistocene progradation marks a basinward shift of the depocenter. Progradation controls margin sedimentation rates during the mid-late Pleistocene. These were found to increase throughout the whole Plio-Pleistocene, in contrast to reported sediment discharge from the Nile, which was shown to decrease after the Gelasian. Correlations to onshore findings, suggest that the continental margin records strain localization on the DSF during the Pliocene-Gelasian. This trend peaked at 1.8 Ma when short wavelength strain ceased along the margin, and differential subsidence commenced basinwards. This is attributed to consequent deepening of the DSF plate boundary.

Decarboxylative Trifluoromethylation of Aliphatic Carboxylic Acids.

PubMed

Kautzky, Jacob A; Wang, Tao; Evans, Ryan W; MacMillan, David W C

2018-05-14

Herein we disclose an efficient method for the conversion of carboxylic acids to trifluoromethyl groups via the combination of photoredox and copper catalysis. This transformation tolerates a wide range of functionality including heterocycles, olefins, alcohols, and strained ring systems. To demonstrate the broad potential of this new methodology for late-stage functionalization, we successfully converted a diverse array of carboxylic acid-bearing natural products and medicinal agents to the corresponding trifluoromethyl analogues.

First Case of Infant Botulism Caused by Clostridium baratii Type F in California

PubMed Central

Barash, Jason R.; Tang, Tania W. H.; Arnon, Stephen S.

2005-01-01

In late 2003 a severely hypotonic neonate, just 38 h old at onset of illness, was found to have infant botulism caused by neurotoxigenic Clostridium baratii type F. Environmental investigations failed to identify a source of this strain. This is the youngest patient reported to have infant botulism and the fifth instance of infant botulism caused by C. baratii type F. PMID:16082001

Late movement of basin-edge lobate scarps on Mercury

NASA Astrophysics Data System (ADS)

Fegan, E. R.; Rothery, D. A.; Marchi, S.; Massironi, M.; Conway, S. J.; Anand, M.

2017-05-01

Basin-edge lobate scarps are a sub-type of tectonic shortening structure on the surface of Mercury that have formed at the edge of volcanic units that fill or partly fill impact basins. We have performed a global survey of these features and find that they are widespread in basins across the planet. We obtained model ages from crater size-frequency distribution analysis for a subset of our surveyed basins, for both the smooth plains infill and for the last resolvable tectonic activity on the associated basin-edge scarps. Our results indicate that some of these lobate scarps were still accumulating strain in the late Mansurian (approximately 1 Ga). From a photogeological assessment, we find that the orientations of these basin-edge lobate scarps are similar to those reported for the global population of lobate scarps in earlier studies, appearing to align ∼north-south at low latitudes and ∼east-west at higher latitudes. However, reassessing these landforms' orientation with artificially illuminated topographic data does not allow us to rule out the effect of illumination bias. We propose that these landforms, the result of crustal shortening in response to global contraction, formed along the interface between the basin floor and the smooth plains unit, which acted as a mechanical discontinuity along which shortening strains were concentrated.

Late Eocene Inversion and Exhumation of the Sivas Basin (Central Anatolia) Based On Low-Temperature Thermochronometry: Implications for Diachronous Initiation of Arabia-Eurasia Collision

NASA Astrophysics Data System (ADS)

Darin, M. H.; Umhoefer, P. J.; Thomson, S. N.; Schleiffarth, W. K.

2017-12-01

The timing of initial Arabia-Eurasia collision along the Bitlis-Zagros suture is controversial, with widely varying estimates from middle Eocene to late Miocene ( 45-10 Ma). The Cenozoic Sivas Basin (central Anatolia) preserves a detailed record of the initial stages of Arabia collision directly north of the suture in the Eurasian foreland. New apatite fission track and (U-Th)/He thermochronology data from Late Cretaceous to Paleogene units indicate rapid basin inversion and initiation of the north-vergent Southern Sivas Fold and Thrust Belt (SSFTB) during the late Eocene to early Oligocene ( 40-30 Ma), consistent with the age of a basin-wide unconformity and switch from marine to nonmarine sedimentation. We interpret late Eocene exhumation and the predominantly north-vergent kinematics of the SSFTB to reflect northward propagation of contraction into the Sivas retro-foreland basin due to initial collision of the Arabian passive margin with the Anatolide-Tauride block along the southern Eurasian margin during the late middle Eocene. We test this hypothesis by comparing our new results with regional-scale compilations of both published thermochronology and geochronology data from the entire Arabia-Eurasia collision zone. Low-temperature thermochronology data from eastern Anatolia, the Caucasus, Zagros, and Alborz demonstrate that rapid cooling and intraplate deformation occurred across much of the Eurasian foreland during the middle Eocene to early Oligocene ( 45-30 Ma). Our regional compilation of published geochronology data from central and eastern Anatolia reveals a distinct magmatic lull during the latest Eocene, Oligocene, and earliest Miocene (ca. 38-20 Ma), slightly earlier than a diachronous magmatic lull initiating at 25-5 Ma from northwest to southeast in Iran (Chiu et al., 2013). These results support a tectonic model for diachronous collision in which initial collision of the Arabia promontory occurred in central-eastern Anatolia during the middle-late Eocene ( 45-35 Ma) followed by magmatic quiescence due to subduction termination. Collisional strain transferred into the Caucasus, Alborz, and northwestern Zagros by the late Eocene to early Oligocene and became progressively younger towards the southeast along the Zagros suture from the late Oligocene to late Miocene.

Usefulness of right ventricular and right atrial two-dimensional speckle tracking strain to predict late arrhythmic events in adult patients with repaired Tetralogy of Fallot.

PubMed

Timóteo, Ana T; Branco, Luísa M; Rosa, Sílvia A; Ramos, Ruben; Agapito, Ana F; Sousa, Lídia; Galrinho, Ana; Oliveira, José A; Oliveira, Mário M; Ferreira, Rui C

2017-01-01

To determine whether right ventricular and/or atrial speckle tracking strain is associated with previous arrhythmic events in patients with repaired tetralogy of Fallot. We studied right ventricular and atrial strain in 100 consecutive patients with repaired tetralogy of Fallot referred for routine echocardiographic evaluation. Patients were divided into two groups, one with previous documentation of arrhythmias (n=26) and one without arrhythmias, in a median follow-up of 22 years. Patients with arrhythmias were older (p<0.001) and had surgical repair at an older age (p=0.001). They also had significantly reduced right ventricular strain (-14.7±5.5 vs. -16.9±4.0%, p=0.029) and right atrial strain (19.1±7.7% vs. 25.8±11.4%, p=0.001). Neither right ventricular nor right atrial strain were independent predictors of the presence of a history of documented arrhythmias, which was associated with age at correction and with the presence of residual defects. In a subanalysis after excluding 23 patients who had had more than one corrective surgery, right ventricular strain was an independent predictor of the presence of previous arrhythmic events (OR 1.19, 95% CI 1.02-1.38, p=0.025). Right atrial strain was also an independent predictor after adjustment (OR 0.93, 95% CI 0.87-0.99, p=0.029). The ideal cut-off for right ventricular strain was -15.3% and for right atrial strain 23.0%. Compared with conventional echocardiographic parameters, strain measures of the right heart are associated with the presence of arrhythmic events, and may be useful for risk stratification of patients with repaired tetralogy of Fallot, although a prospective study is required. Copyright © 2016 Sociedade Portuguesa de Cardiologia. Publicado por Elsevier España, S.L.U. All rights reserved.

Characterization of Regional Left Ventricular Function in Nonhuman Primates Using Magnetic Resonance Imaging Biomarkers: A Test-Retest Repeatability and Inter-Subject Variability Study

PubMed Central

Sampath, Smita; Klimas, Michael; Feng, Dai; Baumgartner, Richard; Manigbas, Elaine; Liang, Ai-Leng; Evelhoch, Jeffrey L.; Chin, Chih-Liang

2015-01-01

Pre-clinical animal models are important to study the fundamental biological and functional mechanisms involved in the longitudinal evolution of heart failure (HF). Particularly, large animal models, like nonhuman primates (NHPs), that possess greater physiological, biochemical, and phylogenetic similarity to humans are gaining interest. To assess the translatability of these models into human diseases, imaging biomarkers play a significant role in non-invasive phenotyping, prediction of downstream remodeling, and evaluation of novel experimental therapeutics. This paper sheds insight into NHP cardiac function through the quantification of magnetic resonance (MR) imaging biomarkers that comprehensively characterize the spatiotemporal dynamics of left ventricular (LV) systolic pumping and LV diastolic relaxation. MR tagging and phase contrast (PC) imaging were used to quantify NHP cardiac strain and flow. Temporal inter-relationships between rotational mechanics, myocardial strain and LV chamber flow are presented, and functional biomarkers are evaluated through test-retest repeatability and inter subject variability analyses. The temporal trends observed in strain and flow was similar to published data in humans. Our results indicate a dominant dimension based pumping during early systole, followed by a torsion dominant pumping action during late systole. Early diastole is characterized by close to 65% of untwist, the remainder of which likely contributes to efficient filling during atrial kick. Our data reveal that moderate to good intra-subject repeatability was observed for peak strain, strain-rates, E/circumferential strain-rate (CSR) ratio, E/longitudinal strain-rate (LSR) ratio, and deceleration time. The inter-subject variability was high for strain dyssynchrony, diastolic strain-rates, peak torsion and peak untwist rate. We have successfully characterized cardiac function in NHPs using MR imaging. Peak strain, average systolic strain-rate, diastolic E/CSR and E/LSR ratios, and deceleration time were identified as robust biomarkers that could potentially be applied to future pre-clinical drug studies. PMID:26010607

Effects of the inoculant strain Sphingomonas paucimobilis 20006FA on soil bacterial community and biodegradation in phenanthrene-contaminated soil.

PubMed

Coppotelli, B M; Ibarrolaza, A; Del Panno, M T; Morelli, I S

2008-02-01

The effects of the inoculant strain Sphingomonas paucimobilis 20006FA (isolated from a phenanthrene-contaminated soil) on the dynamics and structure of microbial communities and phenanthrene elimination rate were studied in soil microcosms artificially contaminated with phenanthrene. The inoculant managed to be established from the first inoculation as it was evidenced by denaturing gradient gel electrophoresis analysis, increasing the number of cultivable heterotrophic and PAH-degrading cells and enhancing phenanthrene degradation. These effects were observed only during the inoculation period. Nevertheless, the soil biological activity (dehydrogenase activity and CO(2) production) showed a late increase. Whereas gradual and successive changes in bacterial community structures were caused by phenanthrene contamination, the inoculation provoked immediate, significant, and stable changes on soil bacterial community. In spite of the long-term establishment of the inoculated strain, at the end of the experiment, the bioaugmentation did not produce significant changes in the residual soil phenanthrene concentration and did not improve the residual effects on the microbial soil community.

Family Economic Stress and Academic Well-Being Among Chinese-American Youth: The Influence of Adolescents’ Perceptions of Economic Strain

PubMed Central

Mistry, Rashmita S.; Benner, Aprile D.; Tan, Connie S.; Kim, Su Yeong

2009-01-01

This study examined the pathways by which family economic stress influenced youth's educational outcomes in a sample of 444 Chinese American adolescents (Mages = 13.0, 17.1 years at waves 1 and 2, respectively). Using latent variable structural equation modeling, results across two waves of data, spanning early to late adolescence, demonstrated that the influence of parent report of economic stress on youth academic achievement (i.e., GPA), school engagement, and positive attitudes about education was mediated through youth's perceptions of family economic strain and self-reports of depressive symptoms. These relationships were observed to remain significant after accounting for selection bias using individual fixed-effects models. Finally, youth's perceptions of family economic strain were found to more strongly predict depressive symptoms during later, as compared to earlier, adolescence; all other modeled relationships were equivalent across the two time periods. Implications for expanding theoretical tenets of the Family Economic Stress Model are discussed. PMID:19586191

Proteomic Analysis of Bacillus thuringiensis Strain 4.0718 at Different Growth Phases

PubMed Central

Li, Xiaohui; Ding, Xuezhi; Xia, Liqiu; Sun, Yunjun; Yuan, Can; Yin, Jia

2012-01-01

The growth process of Bacillus thuringiensis Bt4.0718 strain was studied using proteomic technologies. The proteins of Bt whole cells at three phases—middle vegetative, early sporulation, and late sporulation—were extracted with lysis buffer, followed with separation by 2-DE and identified by MALDI-TOF/TOF MS. Bioactive factors such as insecticidal crystal proteins (ICPs) including Cry1Ac(3), Cry2Aa, and BTRX28, immune inhibitor (InhA), and InhA precursor were identified. InhA started to express at the middle vegetative phase, suggesting its contribution to the survival of Bt in the host body. At the early sporulation phase, ICPs started their expression. CotJC, OppA, ORF1, and SpoIVA related to the formation of crystals and spores were identified, the expression characteristics of which ensured the stable formation of crystals and spores. This study provides an important foundation for further exploration of the stable expression of ICPs, the smooth formation of crystals, and the construction of recombinant strains. PMID:22649324

Phylogeny and History of the Lost SIV from Crab-Eating Macaques: SIVmfa.

PubMed

McCarthy, Kevin R; Johnson, Welkin E; Kirmaier, Andrea

2016-01-01

In the 20th century, thirteen distinct human immunodeficiency viruses emerged following independent cross-species transmission events involving simian immunodeficiency viruses (SIV) from African primates. In the late 1900s, pathogenic SIV strains also emerged in the United Sates among captive Asian macaque species following their unintentional infection with SIV from African sooty mangabeys (SIVsmm). Since their discovery in the 1980s, SIVs from rhesus macaques (SIVmac) and pig-tailed macaques (SIVmne) have become invaluable models for studying HIV pathogenesis, vaccine design and the emergence of viruses. SIV isolates from captive crab-eating macaques (SIVmfa) were initially described but lost prior to any detailed molecular and genetic characterization. In order to infer the origins of the lost SIVmfa lineage, we located archived material and colony records, recovered its genomic sequence by PCR, and assessed its phylogenetic relationship to other SIV strains. We conclude that SIVmfa is the product of two cross-species transmission events. The first was the established transmission of SIVsmm to rhesus macaques, which occurred at the California National Primate Research Center in the late 1960s and the virus later emerged as SIVmac. In a second event, SIVmac was transmitted to crab-eating macaques, likely at the Laboratory for Experimental Medicine and Surgery in Primates in the early 1970s, and it was later spread to the New England Primate Research Center colony in 1973 and eventually isolated in 1986. Our analysis suggests that SIVmac had already emerged by the early 1970s and had begun to diverge into distinct lineages. Furthermore, our findings suggest that pathogenic SIV strains may have been more widely distributed than previously appreciated, raising the possibility that additional isolates may await discovery.

Bacterial rep- mutations that block development of small DNA bacteriophages late in infection.

PubMed Central

Tessman, E S; Peterson, P K

1976-01-01

Several related mutants of Escherichia coli C have been isolated that block the growth of the small icosahedral DNA phages phiX174 and S13 late in infection. Phage G6 is also blocked, at a stage not yet known. Growth of the filamentous phage M13, though not blocked, is affected in these strains. These host mutations co-transduce with ilv at high frequency, as do rep- mutations. However, the new mutants, designated groL-, differ from previously studied rep- mutants in that they permit synthesis of progeny replicative-form DNA. The groL- mutants are blocked in synthesis of stable single-stranded DNA of phiX174 and related phages. They are gro+ for P2. Evidence that groL- mutations and rep- mutations are in the same gene is presented. Spontaneous mutants (ogr) of phiX174, S13, and the G phages can grow on groL- strains. The ogr mutations are located in the phage's major capsid gene, F, as determined by complementation tests. There are numerous sites for mutation to ogr. Some mutations in genes A and F interfere with the ogr property when combined with an ogr mutation on the same genome. The ogr mutations are cis acting in a groL- cell; i.e., an ogr mutant gives very poor rescue of a non-ogr mutant. The wild-type form of each G phage appears to be naturally in the ogr mutant state for one or more groL- strains. It is suggested that a complex between F and rep proteins is involved in phage maturation. The A protein appears to interact with this complex. PMID:789914

Assessment of cardiac function in absence of congenital and acquired heart disease in patients with Down syndrome.

PubMed

Balli, Sevket; Yucel, Ilker Kemal; Kibar, Ayse Esin; Ece, Ibrahim; Dalkiran, Eylem Sen; Candan, Sukru

2016-11-01

Extra genetic material in patients with Down syndrome (DS) may affect the function of any organ system. We evaluated cardiac functions using conventional tissue Doppler and two-dimensional speckle tracking echocardiography in patients with DS in the absence of congenital and acquired heart disease in patients. A total of 115 patients with DS between 6 and 13 years of age with clinically and anatomically normal heart and 55 healthy children were included in this cross-sectional study. DS was diagnosed by a karyotype test. Patients with mosaic type were not included in this study. Systolic and diastolic functions were evaluated by echocardiography. Pulsed waved Doppler transmitral early/late inflow velocity (E/A), tissue Doppler mitral annular early/late diastolic peak velocity (Ea/Aa), transtricuspid E/A and tricuspid valve annulus Ea/Aa, pulmonary venous Doppler systolic/diastolic (S/D) wave ratio were lower in patients with Down syndrome than in the control group (P=0.04, P=0.001, P<0.05, P<0.001, P<0.001, respectively). Mitral and tricuspid annular Ea were lower in patients with DS (P<0.001). The right and left ventricular myocardial performance indexes were higher in patients with DS than in the controls (P<0.01). They had significantly higher left ventricular mass, ejection fraction, the mitral annular plane systolic excursion values. However, the Down syndrome group compared with the controls had a lower strain values examined by two-dimensional longitudinal speckle-tracking strain echocardiography. These findings suggest conventional tissue Doppler and two-dimensional longitudinal speckletracking strain echocardiography were useful methods of investigating ventricular function and identifying a higher incidence of biventricular dysfunction in patients with Down syndrome compared with the healthy controls.

Repeated large-magnitude earthquakes in a tectonically active, low-strain continental interior: The northern Tien Shan, Kyrgyzstan

NASA Astrophysics Data System (ADS)

Landgraf, A.; Dzhumabaeva, A.; Abdrakhmatov, K. E.; Strecker, M. R.; Macaulay, E. A.; Arrowsmith, Jr.; Sudhaus, H.; Preusser, F.; Rugel, G.; Merchel, S.

2016-05-01

The northern Tien Shan of Kyrgyzstan and Kazakhstan has been affected by a series of major earthquakes in the late 19th and early 20th centuries. To assess the significance of such a pulse of strain release in a continental interior, it is important to analyze and quantify strain release over multiple time scales. We have undertaken paleoseismological investigations at two geomorphically distinct sites (Panfilovkoe and Rot Front) near the Kyrgyz capital Bishkek. Although located near the historic epicenters, both sites were not affected by these earthquakes. Trenching was accompanied by dating stratigraphy and offset surfaces using luminescence, radiocarbon, and 10Be terrestrial cosmogenic nuclide methods. At Rot Front, trenching of a small scarp did not reveal evidence for surface rupture during the last 5000 years. The scarp rather resembles an extensive debris-flow lobe. At Panfilovkoe, we estimate a Late Pleistocene minimum slip rate of 0.2 ± 0.1 mm/a, averaged over at least two, probably three earthquake cycles. Dip-slip reverse motion along segmented, moderately steep faults resulted in hanging wall collapse scarps during different events. The most recent earthquake occurred around 3.6 ± 1.3 kyr ago (1σ), with dip-slip offsets between 1.2 and 1.4 m. We calculate a probabilistic paleomagnitude to be between 6.7 and 7.2, which is in agreement with regional data from the Kyrgyz range. The morphotectonic signals in the northern Tien Shan are a prime example of deformation in a tectonically active intracontinental mountain belt and as such can help understand the longer-term coevolution of topography and seismogenic processes in similar structural settings worldwide.

Non-Invasive In Vivo Study of the Trypanosoma vivax Infectious Process Consolidates the Brain Commitment in Late Infections

PubMed Central

D'Archivio, Simon; Cosson, Alain; Medina, Mathieu; Lang, Thierry; Minoprio, Paola; Goyard, Sophie

2013-01-01

Trypanosoma vivax, one of the leading parasites responsible for Animal African Trypanosomosis (Nagana), is generally cyclically transmitted by Glossina spp. but in areas devoid of the tsetse flies in Africa or in Latin American countries is mechanically transmitted across vertebrate hosts by other haematophagous insects, including tabanids. We followed on from our recent studies on the maintenance of this parasite in vivo and in vitro, and its genetic manipulation, by constructing a West African IL1392 T. vivax strain that stably expresses firefly luciferase and is fully virulent for immunocompetent mice. We report here on a study where murine infection with this strain was monitored in vivo using a non-invasive method. Study findings fully support the use of this strain in the assessment of parasite dynamics in vivo since a strong correlation was found between whole body light emission measured over the course of the infection and parasitemia determined microscopically. In addition, parasitemia and survival rates were very similar for mice infected by the intraperitoneal and sub-cutaneous routes, except for a longer prepatent period following sub-cutaneous inoculation with the parasite. Our results clearly show that when administered by the subcutaneous route, the parasite is retained few days in the skin close to the inoculation site where it multiplies before passing into the bloodstream. Ex vivo bioluminescence analyses of organs isolated from infected mice corroborated our previous histopathological observations with parasite infiltration into spleen, liver and lungs. Finally, our study reinforces previous observations on the presence of the parasite in the central nervous system and consequently the brain commitment in the very late phases of the experimental infection. PMID:23301112

Non-invasive in vivo study of the Trypanosoma vivax infectious process consolidates the brain commitment in late infections.

PubMed

D'Archivio, Simon; Cosson, Alain; Medina, Mathieu; Lang, Thierry; Minoprio, Paola; Goyard, Sophie

2013-01-01

Trypanosoma vivax, one of the leading parasites responsible for Animal African Trypanosomosis (Nagana), is generally cyclically transmitted by Glossina spp. but in areas devoid of the tsetse flies in Africa or in Latin American countries is mechanically transmitted across vertebrate hosts by other haematophagous insects, including tabanids. We followed on from our recent studies on the maintenance of this parasite in vivo and in vitro, and its genetic manipulation, by constructing a West African IL1392 T. vivax strain that stably expresses firefly luciferase and is fully virulent for immunocompetent mice. We report here on a study where murine infection with this strain was monitored in vivo using a non-invasive method. Study findings fully support the use of this strain in the assessment of parasite dynamics in vivo since a strong correlation was found between whole body light emission measured over the course of the infection and parasitemia determined microscopically. In addition, parasitemia and survival rates were very similar for mice infected by the intraperitoneal and sub-cutaneous routes, except for a longer prepatent period following sub-cutaneous inoculation with the parasite. Our results clearly show that when administered by the subcutaneous route, the parasite is retained few days in the skin close to the inoculation site where it multiplies before passing into the bloodstream. Ex vivo bioluminescence analyses of organs isolated from infected mice corroborated our previous histopathological observations with parasite infiltration into spleen, liver and lungs. Finally, our study reinforces previous observations on the presence of the parasite in the central nervous system and consequently the brain commitment in the very late phases of the experimental infection.

Association of Left Atrial Function and Left Atrial Enhancement in Patients with Atrial Fibrillation: A Cardiac Magnetic Resonance Study

PubMed Central

Habibi, Mohammadali; Lima, Joao A.C.; Khurram, Irfan M.; Zimmerman, Stefan L.; Zipunnikov, Vadim; Fukumoto, Kotaro; Spragg, David; Ashikaga, Hiroshi; Rickard, John; Marine, Joseph E.; Calkins, Hugh; Nazarian, Saman

2015-01-01

Background Atrial fibrillation (AF) is associated with left atrial (LA) structural and functional changes. Cardiac magnetic resonance (CMR) late gadolinium enhancement (LGE) and feature-tracking are capable of noninvasive quantification of LA fibrosis and myocardial motion, respectively. We sought to examine the association of phasic LA function with LA enhancement in patients with AF. Methods and Results LA structure and function was measured in 90 AF patients (age 61 ± 10 years, 76% male) referred for ablation and 14 healthy volunteers. Peak global longitudinal LA strain (PLAS), LA systolic strain rate (SR-s), and early (SR-ed) and late diastolic (SR-ld) strain rates were measured using cine-CMR images acquired during sinus rhythm. The degree of LGE was quantified. Compared to patients with paroxysmal AF (60% of cohort), those with persistent AF had larger maximum LA volume index (LAVImax, 56 ± 17ml/m2 versus 49 ± 13ml/m2 p=0.036), and increased LGE (27.1± 11.7% versus 36.8 ± 14.8% p<0.001). Aside from LA active emptying fraction, all LA parameters (passive emptying fraction, PLAS, SR-s, SR-ed and SR-ld) were lower in patients with persistent AF (p< 0.05 for all). Healthy volunteers had less LGE and higher LA functional parameters compared to AF patients (p<0.05 for all). In multivariable analysis, increased LGE was associated with lower LA passive emptying fraction, PLAS, SR-s, SR-ed, and SR-ld (p<0.05 for all). Conclusions Increased LA enhancement is associated with decreased LA reservoir, conduit, and booster pump functions. Phasic measurement of LA function using feature-tracking CMR may add important information regarding the physiological importance of LA fibrosis. PMID:25652181

Evolutionarily stable and convergent stable strategies in reaction-diffusion models for conditional dispersal.

PubMed

Lam, King-Yeung; Lou, Yuan

2014-02-01

We consider a mathematical model of two competing species for the evolution of conditional dispersal in a spatially varying, but temporally constant environment. Two species are different only in their dispersal strategies, which are a combination of random dispersal and biased movement upward along the resource gradient. In the absence of biased movement or advection, Hastings showed that the mutant can invade when rare if and only if it has smaller random dispersal rate than the resident. When there is a small amount of biased movement or advection, we show that there is a positive random dispersal rate that is both locally evolutionarily stable and convergent stable. Our analysis of the model suggests that a balanced combination of random and biased movement might be a better habitat selection strategy for populations.

Male secondary sexual structures and the systematics of the Thereus oppia species group (Lepidoptera, Lycaenidae, Eumaeini)

PubMed Central

Robbins, Robert K.; Heredia, María Dolores; Busby, Robert C.

2015-01-01

Abstract The Thereus oppia species group includes species with and without a scent pad, which is a histologically and morphologically characterized male secondary sexual structure on the dorsal surface of the forewing. To assess the hypothesis that these structures are lost evolutionarily, but not regained (Dollo’s Law), the taxonomy of this species group is revised. Thereus lomalarga sp. n., and Thereus brocki sp. n., are described. Diagnostic traits, especially male secondary structures, within the Thereus oppia species group are illustrated. Distributional and biological information is summarized for each species. Three species have been reared, and the caterpillars eat Loranthaceae. An inferred phylogeny is consistent with the hypothesis that scent pads in the Thereus oppia species group have been lost evolutionarily twice (in allopatry), and not re-gained. PMID:26448715

Evolutionary stability of mutualism: interspecific population regulation as an evolutionarily stable strategy

USGS Publications Warehouse

Holland, J. Nathaniel; DeAngelis, Donald L.; Schultz, Stewart T.

2004-01-01

Interspecific mutualisms are often vulnerable to instability because low benefit : cost ratios can rapidly lead to extinction or to the conversion of mutualism to parasite–host or predator–prey interactions. We hypothesize that the evolutionary stability of mutualism can depend on how benefits and costs to one mutualist vary with the population density of its partner, and that stability can be maintained if a mutualist can influence demographic rates and regulate the population density of its partner. We test this hypothesis in a model of mutualism with key features of senita cactus (Pachycereus schottii) – senita moth (Upiga virescens) interactions, in which benefits of pollination and costs of larval seed consumption to plant fitness depend on pollinator density. We show that plants can maximize their fitness by allocating resources to the production of excess flowers at the expense of fruit. Fruit abortion resulting from excess flower production reduces pre–adult survival of the pollinating seed–consumer, and maintains its density beneath a threshold that would destabilize the mutualism. Such a strategy of excess flower production and fruit abortion is convergent and evolutionarily stable against invasion by cheater plants that produce few flowers and abort few to no fruit. This novel mechanism of achieving evolutionarily stable mutualism, namely interspecific population regulation, is qualitatively different from other mechanisms invoking partner choice or selective rewards, and may be a general process that helps to preserve mutualistic interactions in nature.

Multi-target drugs to address multiple checkpoints in complex inflammatory pathologies: evolutionary cues for novel "first-in-class" anti-inflammatory drug candidates: a reviewer's perspective.

PubMed

Mathew, Geetha; Unnikrishnan, M K

2015-10-01

Inflammation is a complex, metabolically expensive process involving multiple signaling pathways and regulatory mechanisms which have evolved over evolutionary timescale. Addressing multiple targets of inflammation holistically, in moderation, is probably a more evolutionarily viable strategy, as compared to current therapy which addresses drug targets in isolation. Polypharmacology, addressing multiple targets, is commonly used in complex ailments, suggesting the superior safety and efficacy profile of multi-target (MT) drugs. Phenotypic drug discovery, which generated successful MT and first-in-class drugs in the past, is now re-emerging. A multi-pronged approach, which modulates the evolutionarily conserved, robust and pervasive cellular mechanisms of tissue repair, with AMPK at the helm, regulating the complex metabolic/immune/redox pathways underlying inflammation, is perhaps a more viable strategy than addressing single targets in isolation. Molecules that modulate multiple molecular mechanisms of inflammation in moderation (modulating TH cells toward the anti-inflammatory phenotype, activating AMPK, stimulating Nrf2 and inhibiting NFκB) might serve as a model for a novel Darwinian "first-in-class" therapeutic category that holistically addresses immune, redox and metabolic processes associated with inflammatory repair. Such a multimodal biological activity is supported by the fact that several non-calorific pleiotropic natural products with anti-inflammatory action have been incorporated into diet (chiefly guided by the adaptive development of olfacto-gustatory preferences over evolutionary timescales) rendering such molecules, endowed with evolutionarily privileged molecular scaffolds, naturally oriented toward multiple targets.

Dawn song in natural and artificial continuous day: Light pollution affects songbirds at high latitudes.

PubMed

Derryberry, Elizabeth P

2017-10-01

In Focus: Da Silva, A., & Kempenaers, B. (2017). Singing from North to South: Latitudinal variation in timing of dawn singing under natural and artificial light conditions. Journal of Animal Ecology, 86, 1286-1297. doi: 10.1111/1365-2656.12739 Satellite images of the world at night show bright dots connected by glowing lines crisscrossing the globe. As these connect-the-dots become brighter and expand into more and more remote regions, much of the flora and fauna of the world are experiencing evolutionarily unprecedented levels of light at night. Light cues are essential to most physiological and behavioural processes, and so the need to measure the effects of light pollution on these processes is critical. In this issue, Da Silva and Kempenaers take on this task using an important reproductive behaviour in songbirds-dawn song. The geographic, temporal and taxonomic breadth of sampling in this study allows for a close examination of a potentially complex interaction between light pollution and natural variation in the behaviour of dawn singing across latitude, season and species. Their extensive dataset highlights complexity in how songbirds respond to light pollution. Although light pollution has a strong effect on the timing of dawn song, not all songbirds respond the same way to light pollution, and the effects of light pollution vary with changes in natural light levels. Early dawn singers show more flexibility in the timing of dawn song across the season and across latitudes than late dawn singers, and also appear less affected by light pollution at high latitudes than are late dawn singers. These findings suggest that not all songbirds are responding to artificial continuous daylight as they do to natural continuous daylight, highlighting the general need to measure the fitness effects of light pollution. © 2017 The Author. Journal of Animal Ecology © 2017 British Ecological Society.

Organization of Human Papillomavirus Productive Cycle during Neoplastic Progression Provides a Basis for Selection of Diagnostic Markers

PubMed Central

Middleton, Kate; Peh, Woei; Southern, Shirley; Griffin, Heather; Sotlar, Karl; Nakahara, Tomomi; El-Sherif, Amira; Morris, Lesley; Seth, Rashmi; Hibma, Merilyn; Jenkins, David; Lambert, Paul; Coleman, Nicholas; Doorbar, John

2003-01-01

The productive cycle of human papillomaviruses (HPVs) can be divided into discrete phases. Cell proliferation and episomal maintenance in the lower epithelial layers are followed by genome amplification and the expression of capsid proteins. These events, which occur in all productive infections, can be distinguished by using antibodies to viral gene products or to surrogate markers of their expression. Here we have compared precancerous lesions caused by HPV type 16 (HPV16) with lesions caused by HPV types that are not generally associated with human cancer. These include HPV2 and HPV11, which are related to HPV16 (supergroup A), as well as HPV1 and HPV65, which are evolutionarily divergent (supergroups E and B). HPV16-induced low-grade squamous intraepithelial lesions (CIN1) are productive infections which resemble those caused by other HPV types. During progression to cancer, however, the activation of late events is delayed, and the thickness of the proliferative compartment is progressively increased. In many HPV16-induced high-grade squamous intraepithelial lesions (CIN3), late events are restricted to small areas close to the epithelial surface. Such heterogeneity in the organization of the productive cycle was seen only in lesions caused by HPV16 and was not apparent when lesions caused by other HPV types were compared. By contrast, the order in which events in the productive cycle were initiated was invariant and did not depend on the infecting HPV type or the severity of disease. The distribution of viral gene products in the infected cervix depends on the extent to which the virus can complete its productive cycle, which in turn reflects the severity of cervical neoplasia. It appears from our work that the presence of such proteins in cells at the epithelial surface allows the severity of the underlying disease to be predicted and that markers of viral gene expression may improve cervical screening. PMID:12970404

Cretaceous gastropods: contrasts between tethys and the temperate provinces.

USGS Publications Warehouse

Sohl, N.F.

1987-01-01

During the Cretaceous Period, gastropod faunas show considerable differences in their evolution between the Tethyan Realm (tropical) and the Temperate Realms to the north and south. Like Holocene faunas, prosobranch, gastropods constitute the dominant part of Cretaceous marine snail faunas. Entomotaeneata and opisthobranchs usually form all of the remainder. In Tethyan faunas the Archaeogastropoda form a consistent high proportion of total taxa but less than the Mesogastropoda throughout the period. In contrast, the Temperate faunas beginning in Albian times show a decline in percentages of archaeogastropod taxa and a significant increase in the Neogastropoda, until they constitute over 50 percent of the taxa in some faunas. The neogastropods never attain high diversity in the Cretaceous of the Tethyan Realm and are judged to be of Temperate Realm origin. Cretaceous Tethyan gastropod faunas are closely allied to those of the 'corallien facies' of the Jurassic and begin the period evolutionarily mature and well diversified. Three categories of Tethyan gastropods are analyzed. The first group consists of those of Jurassic ancestry. The second group orginates mainly during the Barremian and Aptian, reaches a climax in diversification during middle Cretaceous time, and usually declines during the latest Cretaceous. The third group originates late in the Cretaceous and consists of taxa that manage to either survive the Cretaceous-Tertiary crisis or give rise to forms of prominence among Tertiary warm water faunas. Temperate Realm gastropod faunas are less diverse than those of Tethys during the Early Cretaceous. They show a steady increase in diversity, primarily among the Mesogastropoda and Neogastropoda. This trend culminates in latest Cretaceous times when the gastropod assemblages of the clastic provinces of the inner shelf contain an abundance of taxa outstripping that of any other part of the Cretaceous of either realm. Extinction at the Cretaceous-Tertiary boundary is much less pronounced in the Temperate Realm than in the Tethys. In essence, by the late Maastrichtian, gastropod faunas of the Temperate Realm had attained a modern faunal aspect. - from Author

The temporal program of chromosome replication: genomewide replication in clb5{Delta} Saccharomyces cerevisiae.

PubMed

McCune, Heather J; Danielson, Laura S; Alvino, Gina M; Collingwood, David; Delrow, Jeffrey J; Fangman, Walton L; Brewer, Bonita J; Raghuraman, M K

2008-12-01

Temporal regulation of origin activation is widely thought to explain the pattern of early- and late-replicating domains in the Saccharomyces cerevisiae genome. Recently, single-molecule analysis of replication suggested that stochastic processes acting on origins with different probabilities of activation could generate the observed kinetics of replication without requiring an underlying temporal order. To distinguish between these possibilities, we examined a clb5Delta strain, where origin firing is largely limited to the first half of S phase, to ask whether all origins nonspecifically show decreased firing (as expected for disordered firing) or if only some origins ("late" origins) are affected. Approximately half the origins in the mutant genome show delayed replication while the remainder replicate largely on time. The delayed regions can encompass hundreds of kilobases and generally correspond to regions that replicate late in wild-type cells. Kinetic analysis of replication in wild-type cells reveals broad windows of origin firing for both early and late origins. Our results are consistent with a temporal model in which origins can show some heterogeneity in both time and probability of origin firing, but clustering of temporally like origins nevertheless yields a genome that is organized into blocks showing different replication times.

Control of poultry coccidiosis: changing trends.

PubMed

Tewari, A K; Maharana, B R

2011-06-01

Coccidiosis is the most important protozoan disease affecting the poultry industry worldwide. Control of poultry coccidiosis is presently based on managerial skills and the use of prophylactic coccidiostatic drugs. With the emergence of drug resistant Eimeria strains, emphasis has been laid on development and use of safer vaccines; some of them have been commercialized successfully. The present review deals with the various factors responsible for the development of clinical coccidiosis in poultry as well as an overview of the currently available inducers and boosters of immunity against coccidiosis. There are three groups of vaccines currently available against coccidiosis which can be distinguished on the basis of characteristics of the Eimeria species included in the respective products, viz. vaccines based on live virulent strains, vaccines based on live attenuated strains, and vaccines based on live strains that are relatively tolerant to the ionophore compounds. The latter vaccine combines the early chemotherapeutic effect of ionophores with the late prophylactic effect of vaccination. Although in the near future more varieties of oocyst based live vaccines are expected, identification of selective coccidian-specific immunoprotective molecules is likely to get more attention to facilitate the sustainable control of poultry coccidiosis.

Production of acyl-homoserine lactone quorum-sensing signals is widespread in gram-negative Methylobacterium.

PubMed

Poonguzhali, Selvaraj; Madhaiyan, Munusamy; Sa, Tongmin

2007-02-01

Members of Methylobacterium, referred as pink-pigmented facultative methylotrophic bacteria, are frequently associated with terrestrial and aquatic plants, tending to form aggregates on the phyllosphere. We report here that the production of autoinducer molecules involved in the cell-to-cell signaling process, which is known as quorum sensing, is common among Methylobacterium species. Several strains of Methylobacterium were tested for their ability to produce N-acyl-homoserine lactone (AHL) signal molecules using different indicators. Most strains of Methylobacterium tested could elicit a positive response in Agrobacterium tumefaciens harboring lacZ fused to a gene that is regulated by autoinduction. The synthesis of these compounds was cell-density dependent, and the maximal activity was reached during the late exponential to stationary phases. The bacterial extracts were separated by thin-layer chromatography and bioassayed with A. tumefaciens NT1 (traR, tra::lacZ749). They revealed the production of various patterns of the signal molecules, which are strain dependent. At least two signal molecules could be detected in most of the strains tested, and comparison of their relative mobilities suggested that they are homologs of N-octanoyl-DL-homoserine lactone (C8-HSL) and N-decanoyl-DL-homoserine lactone (C10-HSL).

Natural exopolysaccharides enhance survival of lactic acid bacteria in frozen dairy desserts.

PubMed

Hong, S H; Marshall, R T

2001-06-01

Viable lactic acid-producing bacteria in frozen dairy desserts can be a source of beta-galactosidase for persons who absorb lactose insufficiently. However, freezing kills many of the cells, causing loss of enzymatic activity. Cultures selected for high beta-galactosidase activities and high survival rates in the presence of bile were examined for survivability during freezing in reduced-fat ice cream. Encapsulated S. thermophilus strains survived better than their nonencapsulated mutants in reduced-fat ice cream after freezing and frozen storage at -29 degrees C for 16 d (28 vs. 19%). However, a small nonencapsulated strain of Lactobacillus delbrueckii sp. bulgaricus survived better than the large encapsulated strain in reduced-fat ice cream. Factors that improved survival of encapsulated S. thermophilus 1068 in ice cream were 1) harvest of cells in the late-log phase of growth at 37 degrees C rather than at 40, 42.5, or 45 degrees C; 2) overrun at 50% rather than 100%; and 3) storage at -17 degrees C rather than -23 or -29 degrees C. Survival of strain ST1068 was unaffected by 1) neutralization of acid during growth or 2) substitution of nitrogen for air in building overrun.

Lipophosphoglycan polymorphisms do not affect Leishmania amazonensis development in the permissive vectors Lutzomyia migonei and Lutzomyia longipalpis.

PubMed

Nogueira, Paula M; Guimarães, Agna C; Assis, Rafael R; Sadlova, Jovana; Myskova, Jitka; Pruzinova, Katerina; Hlavackova, Jana; Turco, Salvatore J; Torrecilhas, Ana C; Volf, Petr; Soares, Rodrigo P

2017-12-16

Lipophosphoglycan (LPG) is a dominant surface molecule of Leishmania promastigotes. Its species-specific polymorphisms are found mainly in the sugars that branch off the conserved Gal(β1,4)Man(α1)-PO 4 backbone of repeat units. Leishmania amazonensis is one of the most important species causing human cutaneous leishmaniasis in the New World. Here, we describe LPG intraspecific polymorphisms in two Le. amazonensis reference strains and their role during the development in three sand fly species. Strains isolated from Lutzomyia flaviscutellata (PH8) and from a human patient (Josefa) displayed structural polymorphism in the LPG repeat units, possessing side chains with 1 and 2 β-glucose or 1 to 3 β-galactose, respectively. Both strains successfully infected permissive vectors Lutzomyia longipalpis and Lutzomyia migonei and could colonize their stomodeal valve and differentiate into metacyclic forms. Despite bearing terminal galactose residues on LPG, Josefa could not sustain infection in the restrictive vector Phlebotomus papatasi. LPG polymorphisms did not affect the ability of Le. amazonensis to develop late-stage infections in permissive vectors. However, the non-establishment of infection in Ph. papatasi by Josefa strain suggested other LPG-independent factors in this restrictive vector.

Modeling of the ComRS Signaling Pathway Reveals the Limiting Factors Controlling Competence in Streptococcus thermophilus

PubMed Central

Haustenne, Laurie; Bastin, Georges; Hols, Pascal; Fontaine, Laetitia

2015-01-01

In streptococci, entry in competence is dictated by ComX abundance. In Streptococcus thermophilus, production of ComX is transient and tightly regulated during growth: it is positively regulated by the cell-cell communication system ComRS during the activation phase and negatively regulated during the shut-off phase by unidentified late competence gene(s). Interestingly, most S. thermophilus strains are not or weakly transformable in permissive growth conditions (i.e., chemically defined medium, CDM), suggesting that some players of the ComRS regulatory pathway are limiting. Here, we combined mathematical modeling and experimental approaches to identify the components of the ComRS system which are critical for both dynamics and amplitude of ComX production in S. thermophilus. We built a deterministic, population-scaled model of the time-course regulation of specific ComX production in CDM growth conditions. Strains LMD-9 and LMG18311 were respectively selected as representative of highly and weakly transformable strains. Results from in silico simulations and in vivo luciferase activities show that ComR concentration is the main limiting factor for the level of comX expression and controls the kinetics of spontaneous competence induction in strain LMD-9. In addition, the model predicts that the poor transformability of strain LMG18311 results from a 10-fold lower comR expression level compared to strain LMD-9. In agreement, comR overexpression in both strains was shown to induce higher competence levels with deregulated kinetics patterns during growth. In conclusion, we propose that the level of ComR production is one important factor that could explain competence heterogeneity among S. thermophilus strains. PMID:26733960

Geographic isolation of Escherichia coli genotypes in sediments and water of the Seven Mile Creek - A constructed riverine watershed.

PubMed

Chandrasekaran, Ramyavardhanee; Hamilton, Matthew J; Wang, Ping; Staley, Christopher; Matteson, Scott; Birr, Adam; Sadowsky, Michael J

2015-12-15

Escherichia coli is used to indicate fecal contamination in freshwater systems and is an indicator of the potential presence of human pathogens. However, naturalized E. coli strains that persist and grow in the environment confound the use of this bacterium as a fecal indicator. Here we examined the spatial and temporal distribution of E. coli in water and sediments of the Seven Mile Creek (SMC), a constructed, ephemeral watershed. E. coli concentrations showed variation by site and date, likely due to changes in temperature and rainfall. Horizontal fluorophore enhanced rep-PCR (HFERP) DNA fingerprint analyses indicated that E. coli populations were very diverse and consisted of transient and naturalized strains, which were especially prevalent in sediment. E. coli fingerprints from water and sediment collected in the same year clustered together with significant overlap, indicating exchange of strains between matrices. Isolates obtained during periods of flow, but not during non-flow conditions, clustered together regardless of sample site, indicating that transport between sites occurred. Naturalized E. coli strains were found in the SMC and strains become geographically isolated and distinct during non-flow conditions. Isolates collected during late spring to fall clustered together at each site, suggesting that temperature and growth of naturalized strains are likely factors affecting population dynamics. Results of this study show that newly introduced and naturalized E. coli strains are present in the SMC. Results of this study highlight an important concern for resource managers using this species for water quality monitoring. Copyright © 2015 Elsevier B.V. All rights reserved.

Abnormal biventricular performance in asymptomatic adolescents late after repaired Tetralogy of Fallot: Combined two-dimensional speckle tracking and three-dimensional echocardiography study.

PubMed

Weng, Ken-Pen; Hung, Yu-Chi; Huang, Shih-Hui; Wu, Huang-Wei; Chien, Kuang-Jen; Lin, Chu-Chuan; Peng, Hsu-Hsia; Wu, Ming-Ting

2018-02-01

The aim of this prospective study was to assess biventricular performance in asymptomatic adolescents with repaired tetralogy of Fallot (TOF) using 2D speckle tracking and real time 3D echocardiography simultaneously. We studied 31 patients with repaired TOF (M/F: 22/9, age: 16.1 ± 6.1 yrs) who had history of cardiac surgery with mean follow-up duration of 12.8 years, and 32 age- and sex-matched normal individuals (M/F: 23/9, age: 16.6 ± 5.1 yrs). All subjects underwent speckle tracking and 3D echocardiography, electrocardiogram, treadmill, and blood sampling for measurement of brain natriuretic peptide (BNP). Compared to the control group, the TOF group had higher BNP level (31.8 ± 21.4 vs 14.1 ± 12.4 pg/ml, p < 0.01), lower peak oxygen consumption (8.4 ± 1.7 vs 9.9 ± 1.6 ml/kg/min, p < 0.05), and longer QRS duration (126 ± 30 vs 82 ± 9 ms, p < 0.01). Patients with repaired TOF had significantly impaired right ventricle (RV) global and all six regional longitudinal strain and strain rate than normal controls. Left ventricle (LV) global and mainly apical regional longitudinal strain and strain rate were reduced in patients with repaired TOF. There was a significant correlation of global longitudinal strain (r = 0.456, p = 0.01) and global time to peak longitudinal strain (r = 0.484, p < 0.01) between LV and RV in patients with repaired TOF. In terms of 3D echo cardiographic volume data, patients with repaired TOF had lower LV stroke volume index (p < 0.05), but higher RV end diastolic volume index (p < 0.01), RV end systolic volume index (p < 0.01), RV stroke volume index (p < 0.01), and pulmonary regurgitation fraction (p < 0.01) than normal controls. Our results suggest asymptomatic adolescents with repaired TOF had abnormal biventricular myocardial performance, as demonstrated by combined 2D speckle-tracking and 3D echocardiography. The implications of these findings for management of adolescents late after repaired TOF remain to be determined. Copyright © 2017. Published by Elsevier Taiwan LLC.

Serologic Correlates of Protection against Enterotoxigenic Escherichia coli Diarrhea

DTIC Science & Technology

2005-01-14

strain expressed either LT, CFA/I, CFA/II, or CFA/IV. Episodes in which Shigella spe- cies, Campylobacter species, rotavirus , or astrovirus were iso- lated...serum antibody levels cor- relate with protection against diarrheal illness caused by cholera and rotavirus [29–33]. Serum vibriocidal antibodies...cholera. J Infect Dis 1991; 163:1235–42. 31. Clemens JD, Ward RL, Rao MR, et al. Seroepidemiologic evaluation of antibodies to rotavirus as correlates of

Regional Disease Vector Ecology Profile. Southeast Asia

DTIC Science & Technology

2009-06-01

strains of Escherichia coli, hepatitis A and E, rotaviruses, etc. Infection with pathogenic protozoa, such as Entamoeba histolytica, Giardia lamblia and...the genus Plasmodium that are transmitted by the bite of an infective female Anopheles mosquito. Clinical symptoms of malaria vary with the species...some feed only late at night or at dawn. Most anophelines feed on exposed legs, but some may feed on arms, ears or the neck. Infected females tend to

Les intrusions de Wirgane (Haut Atlas occidental, Maroc): témoins d'un magmatisme syn- à tardi-cinématique hercynien? (Intrusions of Wirgane [western High Atlas, Morocco]: evidence for a syn- to late kinematic magmatism of Variscan age?)

NASA Astrophysics Data System (ADS)

Eddif, A.; Gasquet, D.; Hoepffner, C.; Ayad, N. Ait

2000-11-01

The Wirgane intrusives were emplaced into the Late Neoproterozoic to Palæozoic series of the northeast of the Moroccan western High Atlas. The intrusions exhibit a large compositional range from monzogabbro to granite, and they have suffered, together with the country rocks, part of the Variscan tectonic evolution. In the immediate vicinity of the intrusions, thermal metamorphism developed in the country rocks. According to the mineral chemistry of igneous amphibole compositions of diorites and metamorphic minerals, the depth of intrusives was estimated to be less than 11 km. Strain patterns, mapped in both the plutons and the country rocks, and microtectonic data indicate that the intrusions were emplaced in a dextral transcurrent shearing context during the Variscan Orogen. When compared with other intrusions of the western High Atlas (Tichka, Azegour), the Wirgane intrusives are considered to be related to the late stages of the Variscan Belt of Morocco.

Dynamic measurement of surface strain distribution on the foot during walking.

PubMed

Ito, Kohta; Maeda, Kosuke; Fujiwara, Ikumi; Hosoda, Koh; Nagura, Takeo; Lee, Taeyong; Ogihara, Naomichi

2017-05-01

To clarify the mechanism underlying the development of foot disorders such as diabetic ulcers and deformities, it is important to understand how the foot surface elongates and contracts during gait. Such information is also helpful for improving the prevention and treatment of foot disorders. We therefore measured temporal changes in the strain distribution on the foot surface during human walking. Five adult male participants walked across a glass platform placed over an angled mirror set in a wooden walkway at a self-selected speed and the dorsolateral and plantar surfaces of the foot were filmed using two pairs of synchronized high-speed cameras. Three-dimensional (3D) digital image correlation was used to quantify the spatial strain distribution on the foot surface with respect to that during quiet standing. Using the proposed method, we observed the 3D patterns of foot surface strain distribution during walking. Large strain was generated around the ball on the plantar surface of the foot throughout the entire stance phase, due to the windlass mechanism. The dorsal surface around the cuboid was stretched in the late stance phase, possibly due to lateral protruding movement of the cuboid. It may be possible to use this technique to non-invasively estimate movements of the foot bones under the skin using the surface strain distribution. The proposed technique may be an effective tool with which to analyze foot deformation in the fields of diabetology, clinical orthopedics, and ergonomics. Copyright © 2017. Published by Elsevier Ltd.

High CD4(+) T-cell surface CXCR4 density as a risk factor for R5 to X4 switch in the course of HIV-1 infection.

PubMed

Fiser, Anne-Laure; Vincent, Thierry; Brieu, Natalie; Lin, Yea-Lih; Portalès, Pierre; Mettling, Clément; Reynes, Jacques; Corbeau, Pierre

2010-12-15

For unclear reasons, about 50% of HIV-infected subjects harbour CXCR4-using (X4) viral strains in addition of CCR5-using (R5) viral strains at late stages of the disease. One hypothesis is that a low CD4(+) T-cell surface CCR5 density could facilitate the emergence of X4 strains. Alternatively, one could argue that a high CD4(+) T-cell surface CXCR4 density that is observed in individuals presenting with X4 strains, could favour R5 to X4 switch. Here, we tested both hypotheses. In vivo, we observed by quantitative flow cytometry no difference in CD4(+) T-cell surface CCR5 densities between patients with or without X4 strains. In the course of an in vitro R5 infection, the delay of emergence of X4 mutants was similar between cells expressing 2 distinct cell surface CCR5 densities, but shorter (12 ± 0 days and 21 ± 0 days, respectively, P = 0.01) in cells expressing a high surface CXCR4 density as compared with cells with a low surface CXCR4 density. These data argue for a role of CXCR4 density, but not of CCR5 density, in the emergence of X4 strains. They are reassuring concerning the risk of inducing an R5 to X4 switch using CCR5 antagonists to treat HIV infection.

Phylogenetic lineages in Entomophthoromycota

USDA-ARS?s Scientific Manuscript database

Entomophthoromycota Humber is one of five major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular st...

Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir.

PubMed

Huy, Hangsak; Jin, Long; Lee, Keun Chul; Kim, Song-Gun; Lee, Jung-Sook; Ahn, Chi-Yong; Oh, Hee-Mock

2014-04-01

Strain CH15-11(T), isolated from a sediment sample taken from Daechung Reservoir, South Korea, during the late-blooming period of cyanobacteria, was found to be a Gram-stain-negative, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain CH15-11(T) grew optimally at pH 7 and 28-30 °C. According to a phylogenetic tree based on 16S rRNA gene sequences, strain CH15-11(T) belonged to the genus Sphingomonas and clustered with Sphingomonas sediminicola Dae 20(T), with which it shared the highest 16S rRNA gene sequence similarity (97.6 %). Chemotaxonomic analysis showed that strain CH15-11(T) had characteristics typical of members of the genus Sphingomonas, such as the presence of sphingoglycolipid, ubiquinone Q-10 and sym-homospermidine. Plus, strain CH15-11(T) included summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids. The genomic DNA G+C content was 65.6 mol%. Sequence data showed that strain CH15-11(T) was most closely related to Sphingomonas sediminicola Dae 20(T) (97.6 %), Sphingomonas ginsengisoli Gsoil 634(T) (97.2 %) and http://www.genebank.go.kr/eng/microbe/microbe_search_view.jsp?sStrainsn=4602Sphingomonas jaspi TDMA-16(T) (97.0 %). However, the DNA-DNA relatedness values between strain CH15-11(T) and the most closely related type strains were within a range of 35-59 %. Thus, based on the phylogenetic, phenotypic and genetic data, strain CH15-11(T) was classified as a member of the genus Sphingomonas as a representative of a novel species, for which the name Sphingomonas daechungensis sp. nov. is proposed. The type strain is CH15-11(T) ( = KCTC 23718(T) = JCM 17887(T)).

Cyclic stressing and seismicity at strongly coupled subduction zones

USGS Publications Warehouse

Taylor, M.A.J.; Zheng, G.; Rice, J.R.; Stuart, W.D.; Dmowska, R.

1996-01-01

We use the finite element method to analyze stress variations in and near a strongly coupled subduction zone during an earthquake cycle. Deformation is assumed to be uniform along strike (plane strain on a cross section normal to the trench axis), and periodic earthquake slip is imposed consistent with the long-term rate of plate convergence and degree of coupling. Simulations of stress and displacement rate fields represent periodic fluctuations in time superimposed on an average field. The oceanic plate, descending slab, and continental lithosphere are assumed here to respond elastically to these fluctuations, and the remaining mantle under and between plates is assumed to respond as Maxwell viscoelastic. In the first part of the analysis we find that computed stress fluctuations in space and time are generally consistent with observed earthquake mechanism variations with time since a great thrust event. In particular, trench-normal extensional earthquakes tend to occur early in the earthquake cycle toward the outer rise but occur more abundantly late in the cycle in the subducting slab downdip of the main thrust zone. Compressional earthquakes, when they occur at all, have the opposite pattern. Our results suggest also that the actual timing of extensional outer rise events is controlled by the rheology of the shallow aseismic portion of the thrust interface. The second part of the analysis shows the effects of mantle relaxation on the rate of ground surface deformation during the earthquake cycle. Models without relaxation predict a strong overall compressional strain rate in the continental plate above the main thrust zone, with the strain rate constant between mainshocks. However with significant relaxation present, a localized region of unusually low compressional, or even slightly extensional, strain rate develops along the surface of the continental plate above and somewhat inland from the downdip edge of the locked main thrust zone. The low strain rate starts in the middle or late part of the cycle, depending on position. This result suggests that the negligible or small contraction measured on the Shumagin Islands, Alaska, during 1980 to 1991, may not invalidate an interpretation of that region as being a moderately coupled subduction zone. In contrast, mantle relaxation causes only modest temporal nonuniformity of uplift rates in the overriding plate and of extensional stress rates in the subducting plate, even when the Maxwell time is an order of magnitude less than the recurrence interval.

Natural DNA transformation is functional in Lactococcus lactis ssp. cremoris KW2.

PubMed

David, Blandine; Radziejwoski, Amandine; Toussaint, Frédéric; Fontaine, Laetitia; Henry de Frahan, Marie; Patout, Cédric; van Dillen, Sabine; Boyaval, Patrick; Horvath, Philippe; Fremaux, Christophe; Hols, Pascal

2017-06-16

Lactococcus lactis is one of the most commonly used lactic acid bacteria in the dairy industry. Activation of competence for natural DNA transformation in this species would greatly improve the selection of novel strains with desired genetic traits. Here, we investigated the activation of natural transformation in L. lactis ssp. cremoris KW2, a strain of plant origin whose genome encodes the master competence regulator ComX and the complete set of proteins usually required for natural transformation. In the absence of knowledge about competence regulation in this species, we constitutively overproduced ComX in a reporter strain of late competence phase activation and showed, by transcriptomic analyses, a ComX-dependent induction of all key competence genes. We further demonstrated that natural DNA transformation is functional in this strain and requires the competence DNA uptake machinery. Since constitutive ComX overproduction is unstable, we alternatively expressed comX under the control of an endogenous xylose-inducible promoter. This regulated system was used to successfully inactivate the adaptor protein MecA and subunits of the Clp proteolytic complex, which were previously shown to be involved in ComX degradation in streptococci. In the presence of a low amount of ComX, the deletion of mecA , clpC , or clpP genes markedly increased the activation of the late competence phase and transformability. Altogether, our results report the functionality of natural DNA transformation in L. lactis and pave the way for the identification of signaling mechanisms that trigger the competence state in this species. IMPORTANCE Lactococcus lactis is a lactic acid bacterium of major importance, which is used as a starter species for milk fermentation, a host for heterologous protein production, and a delivery platform for therapeutic molecules. Here, we report the functionality of natural transformation in L. lactis ssp. cremoris KW2 by the overproduction of the master competence regulator ComX. The developed procedure enables a flexible approach to modify the chromosome with single point mutation, sequence insertion, or sequence replacement. These results represent an important step for the genetic engineering of L. lactis that will facilitate the design of strains optimized for industrial applications. This will also help to discover natural regulatory mechanisms controlling competence in the genus Lactococcus . Copyright © 2017 American Society for Microbiology.

[Ototoxicity study of netilmicin in pregnant guinea pigs and the embryo].

PubMed

Kawasaki, H; Yamada, Y; Takei, T; Akiyoshi, M

1982-06-01

The ototoxicity of netilmicin (NTL) in pregnant guinea pigs (Hartley strain) and the newborn was examined and compared to that of gentamicin (GM). NTL was administered intramuscularly at dose of 90 mg/kg to pregnant guinea pigs from day 0 to day 35 of pregnancy (the early period of pregnancy) or from day 42 of pregnancy to 1 day prior to delivery (the late period of pregnancy). GM at dose of 45 mg/kg or physiological saline were administered intramuscularly to pregnant guinea pigs during the late period of pregnancy. Four of 5 dams given NTL during the early period of pregnancy, 4 of 7 dams given TNL during the late period of pregnancy, and 2 of 4 dams given GM during the late period of pregnancy died. No pinna reflex loss in frequency range from 2 to 20 KHz were detected in mother guinea pigs treated with NTL either during the early period of pregnancy or during the late period of pregnancy. GM caused a loss of pinna reflex at 20 KHz in mother guinea pigs treated during the late period of pregnancy. Histopathologically, no damages were detected in the cochlea of mother guinea pigs treated with NTL during the early or late period of pregnancy, whereas slight scattered loss of hair cells was seen in the vestibulum. However, GM at dose of 45 mg/kg, caused an incomplete scattered loss of outer hair cells in the spiral organ, moderate atrophy of the spiral ganglion cells and a partial loss of hair cells in the vestibular organs in mother guinea pigs treated during the late period of pregnancy. In newborn guinea pig from the pregnant one treated with NTL during the early period of pregnancy, there was no loss of pinna reflex. The same results were obtained in newborn guinea pigs from the pregnant ones treated with either NTL or GM during the late period of pregnancy. No histopathological damages were detected. The present study suggests that NTL has a minimal effect on the auditory and vestibular organs in pregnant guinea pigs and the newborn and is considered to be 1 of the aminoglycosides with low ototoxic potential.

Anaerosporomusa subterranea gen. nov., sp. nov., a spore-forming anaerobe belonging to the class Negativicutes isolated from saprolite.

PubMed

Choi, Jessica K; Shah, Madhavi; Yee, Nathan

2016-10-01

A Gram-stain-negative, spore-forming, anaerobic bacterium designated strain RU4T was isolated from a saprolite core collected from Oak Ridge, Tennessee, USA. Cells were slightly curved rods and exhibited an outer membrane exterior to a thin cell wall. Strain RU4T formed heat-resistant endospores in late-log phase and stationary phase cultures. Under anaerobic conditions, strain RU4T grew by fermenting fumarate and maleate, but did not grow on glucose, glycerol, pyruvate, lactate, succinate, citrate, formate, acetate, propionate, butyrate or valerate. Strain RU4T did not reduce sulfate or ferric iron. The main cellular fatty acids were C17 : 0 cyclo, C16 : 0 and C15 : 0. The DNA G+C content was 52 mol%. Analysis of the 16S rRNA, rpoB, recA, infB, gyrB and atpD gene sequences indicated that the isolate is related to members of the family Sporomusaceae. Based on 92 % sequence similarity of the 16S rRNA gene to its closest relatives in the family Sporomusaceae and divergent physiological traits, the newly-cultivated isolate was assigned to a novel species of a new genus, Anaerosporomusa subterranea gen. nov., sp. nov. The type strain of Anaerosporomusa subterranea is RU4T (=DSM 29728T=ATCC BAA-2723T).

Dyadic Configurations of Sexual Problems Among Older U.S. Adults: A National Study.

PubMed

Das, Aniruddha

2017-07-04

Using data from the 2010-2011 National Social Life Health and Aging Project (NSHAP)-a nationally representative probability sample of older U.S. adults as well as their partners-this study provides the first comprehensive, population-based analysis of dyadic configurations of sexual problems and their correlates among those aged 60 to 90 years. Results suggest the majority of late-life partnerships (N = 854) may not have a heavy burden of sexual difficulties. However, almost a fifth (18.21%) of partnered older women do not abstain from sex despite low sexual motivation and capacity. This relational "type" seems unlinked to demographic or health attributes, and may be driven more by partnership strains. In addition, an "at risk" group with consistent sexual problems, arguably due to age-related decline, comprises 27.16% of all late-life couples.

Genetic Engineering: A Promising Tool to Engender Physiological, Biochemical, and Molecular Stress Resilience in Green Microalgae

PubMed Central

Guihéneuf, Freddy; Khan, Asif; Tran, Lam-Son P.

2016-01-01

As we march into the 21st century, the prevailing scenario of depleting energy resources, global warming and ever increasing issues of human health and food security will quadruple. In this context, genetic and metabolic engineering of green microalgae complete the quest toward a continuum of environmentally clean fuel and food production. Evolutionarily related, but unlike land plants, microalgae need nominal land or water, and are best described as unicellular autotrophs using light energy to fix atmospheric carbon dioxide (CO2) into algal biomass, mitigating fossil CO2 pollution in the process. Remarkably, a feature innate to most microalgae is synthesis and accumulation of lipids (60–65% of dry weight), carbohydrates and secondary metabolites like pigments and vitamins, especially when grown under abiotic stress conditions. Particularly fruitful, such an application of abiotic stress factors such as nitrogen starvation, salinity, heat shock, etc., can be used in a biorefinery concept for production of multiple valuable products. The focus of this mini-review underlies metabolic reorientation practices and tolerance mechanisms as applied to green microalgae under specific stress stimuli for a sustainable pollution-free future. Moreover, we entail current progress on genetic engineering as a promising tool to grasp adaptive processes for improving strains with potential biotechnological interests. PMID:27066043

Molecular cloning and characterization of Aspergillus nidulans cyclophilin B.

PubMed

Joseph, J D; Heitman, J; Means, A R

1999-06-01

Cyclophilins are an evolutionarily conserved family of proteins which serve as the intracellular receptors for the immunosuppressive drug cyclosporin A. Here we report the characterization of the first cyclophilin cloned from the filamentous fungus Aspergillus nidulans (CYPB). Sequence analysis of the cypB gene predicts an encoded protein with highest homology to the murine cyclophilin B protein. The sequence similarity includes an N-terminal sequence predicted to target the protein to the endoplasmic reticulum (ER) as well as a C-terminal sequence predicted to retain the mature protein in the ER. The bacterially expressed hexa-histidine tagged protein displays peptidyl-prolyl isomerase activity which is inhibited by cyclosporin A. In the presence of cyclosporin A, the expressed protein also inhibits purified calcineurin. When the endogenous cypB gene was disrupted and placed under the control of the regulatable alcohol dehydrogenase promoter, the strain demonstrated no detectable growth phenotype under conditions which induce or repress cypB transcription. Induction or repression of the cypB gene also did not effect sensitivity of A. nidulans to cyclosporin A. cypB mRNA levels were significantly elevated under severe heat shock conditions, indicating a possible role for the A. nidulans cyclophilin B protein during growth in high stress environments. Copyright 1999 Academic Press.

The Thoc1 Encoded Ribonucleoprotein Is Required for Myeloid Progenitor Cell Homeostasis in the Adult Mouse

PubMed Central

Chinnam, Meenalakshmi; Povinelli, Benjamin J.; Fisher, Daniel T.; Golding, Michelle; Appenheimer, Michelle M.; Nemeth, Michael J.; Evans, Sharon; Goodrich, David W.

2014-01-01

Co-transcriptionally assembled ribonucleoprotein (RNP) complexes are critical for RNA processing and nuclear export. RNPs have been hypothesized to contribute to the regulation of coordinated gene expression, and defects in RNP biogenesis contribute to genome instability and disease. Despite the large number of RNPs and the importance of the molecular processes they mediate, the requirements for individual RNP complexes in mammalian development and tissue homeostasis are not well characterized. THO is an evolutionarily conserved, nuclear RNP complex that physically links nascent transcripts with the nuclear export apparatus. THO is essential for early mouse embryonic development, limiting characterization of the requirements for THO in adult tissues. To address this shortcoming, a mouse strain has been generated allowing inducible deletion of the Thoc1 gene which encodes an essential protein subunit of THO. Bone marrow reconstitution was used to generate mice in which Thoc1 deletion could be induced specifically in the hematopoietic system. We find that granulocyte macrophage progenitors have a cell autonomous requirement for Thoc1 to maintain cell growth and viability. Lymphoid lineages are not detectably affected by Thoc1 loss under the homeostatic conditions tested. Myeloid lineages may be more sensitive to Thoc1 loss due to their relatively high rate of proliferation and turnover. PMID:24830368

The Thoc1 encoded ribonucleoprotein is required for myeloid progenitor cell homeostasis in the adult mouse.

PubMed

Pitzonka, Laura; Ullas, Sumana; Chinnam, Meenalakshmi; Povinelli, Benjamin J; Fisher, Daniel T; Golding, Michelle; Appenheimer, Michelle M; Nemeth, Michael J; Evans, Sharon; Goodrich, David W

2014-01-01

Co-transcriptionally assembled ribonucleoprotein (RNP) complexes are critical for RNA processing and nuclear export. RNPs have been hypothesized to contribute to the regulation of coordinated gene expression, and defects in RNP biogenesis contribute to genome instability and disease. Despite the large number of RNPs and the importance of the molecular processes they mediate, the requirements for individual RNP complexes in mammalian development and tissue homeostasis are not well characterized. THO is an evolutionarily conserved, nuclear RNP complex that physically links nascent transcripts with the nuclear export apparatus. THO is essential for early mouse embryonic development, limiting characterization of the requirements for THO in adult tissues. To address this shortcoming, a mouse strain has been generated allowing inducible deletion of the Thoc1 gene which encodes an essential protein subunit of THO. Bone marrow reconstitution was used to generate mice in which Thoc1 deletion could be induced specifically in the hematopoietic system. We find that granulocyte macrophage progenitors have a cell autonomous requirement for Thoc1 to maintain cell growth and viability. Lymphoid lineages are not detectably affected by Thoc1 loss under the homeostatic conditions tested. Myeloid lineages may be more sensitive to Thoc1 loss due to their relatively high rate of proliferation and turnover.

Physical and Functional Interaction between the Eukaryotic Orthologs of Prokaryotic Translation Initiation Factors IF1 and IF2

PubMed Central

Choi, Sang Ki; Olsen, DeAnne S.; Roll-Mecak, Antonina; Martung, Agnes; Remo, Keith L.; Burley, Stephen K.; Hinnebusch, Alan G.; Dever, Thomas E.

2000-01-01

To initiate protein synthesis, a ribosome with bound initiator methionyl-tRNA must be assembled at the start codon of an mRNA. This process requires the coordinated activities of three translation initiation factors (IF) in prokaryotes and at least 12 translation initiation factors in eukaryotes (eIF). The factors eIF1A and eIF5B from eukaryotes show extensive amino acid sequence similarity to the factors IF1 and IF2 from prokaryotes. By a combination of two-hybrid, coimmunoprecipitation, and in vitro binding assays eIF1A and eIF5B were found to interact directly, and the eIF1A binding site was mapped to the C-terminal region of eIF5B. This portion of eIF5B was found to be critical for growth in vivo and for translation in vitro. Overexpression of eIF1A exacerbated the slow-growth phenotype of yeast strains expressing C-terminally truncated eIF5B. These findings indicate that the physical interaction between the evolutionarily conserved factors eIF1A and eIF5B plays an important role in translation initiation, perhaps to direct or stabilize the binding of methionyl-tRNA to the ribosomal P site. PMID:10982835

The filamentous ascomycete Sordaria macrospora can survive in ambient air without carbonic anhydrases.

PubMed

Lehneck, Ronny; Elleuche, Skander; Pöggeler, Stefanie

2014-06-01

The rapid interconversion of carbon dioxide and bicarbonate (hydrogen carbonate) is catalysed by metalloenzymes termed carbonic anhydrases (CAs). CAs have been identified in all three domains of life and can be divided into five evolutionarily unrelated classes (α, β, γ, δ and ζ) that do not share significant sequence similarities. The function of the mammalian, prokaryotic and plant α-CAs has been intensively studied but the function of CAs in filamentous ascomycetes is mostly unknown. The filamentous ascomycete Sordaria macrospora codes for four CAs, three of the β-class and one of the α-class. Here, we present a functional analysis of CAS4, the S. macrospora α-class CA. The CAS4 protein was post-translationally glycosylated and secreted. The knockout strain Δcas4 had a significantly reduced rate of ascospore germination. To determine the cas genes required for S. macrospora growth under ambient air conditions, we constructed double and triple mutations of the four cas genes in all possible combinations and a quadruple mutant. Vegetative growth rate of the quadruple mutant lacking all cas genes was drastically reduced compared to the wild type and invaded the agar under normal air conditions. Likewise the fruiting bodies were embedded in the agar and completely devoid of mature ascospores. © 2014 John Wiley & Sons Ltd.

The evolution of plant virus transmission pathways.

PubMed

Hamelin, Frédéric M; Allen, Linda J S; Prendeville, Holly R; Hajimorad, M Reza; Jeger, Michael J

2016-05-07

The evolution of plant virus transmission pathways is studied through transmission via seed, pollen, or a vector. We address the questions: under what circumstances does vector transmission make pollen transmission redundant? Can evolution lead to the coexistence of multiple virus transmission pathways? We restrict the analysis to an annual plant population in which reproduction through seed is obligatory. A semi-discrete model with pollen, seed, and vector transmission is formulated to investigate these questions. We assume vector and pollen transmission rates are frequency-dependent and density-dependent, respectively. An ecological stability analysis is performed for the semi-discrete model and used to inform an evolutionary study of trade-offs between pollen and seed versus vector transmission. Evolutionary dynamics critically depend on the shape of the trade-off functions. Assuming a trade-off between pollen and vector transmission, evolution either leads to an evolutionarily stable mix of pollen and vector transmission (concave trade-off) or there is evolutionary bi-stability (convex trade-off); the presence of pollen transmission may prevent evolution of vector transmission. Considering a trade-off between seed and vector transmission, evolutionary branching and the subsequent coexistence of pollen-borne and vector-borne strains is possible. This study contributes to the theory behind the diversity of plant-virus transmission patterns observed in nature. Copyright © 2016 Elsevier Ltd. All rights reserved.

Recombinational DSBs-intersected genes converge on specific disease- and adaptability-related pathways.

PubMed

Yang, Zhi-Kai; Luo, Hao; Zhang, Yanming; Wang, Baijing; Gao, Feng

2018-05-03

The budding yeast Saccharomyces cerevisiae is a model species powerful for studying the recombination of eukaryotes. Although many recombination studies have been performed for this species by experimental methods, the population genomic study based on bioinformatics analyses is urgently needed to greatly increase the range and accuracy of recombination detection. Here, we carry out the population genomic analysis of recombination in S. cerevisiae to reveal the potential rules between recombination and evolution in eukaryotes. By population genomic analysis, we discover significantly more and longer recombination events in clinical strains, which indicates that adverse environmental conditions create an obviously wider range of genetic combination in response to the selective pressure. Based on the analysis of recombinational DSBs-intersected genes (RDIGs), we find that RDIGs significantly converge on specific disease- and adaptability-related pathways, indicating that recombination plays a biologically key role in the repair of DSBs related to diseases and environmental adaptability, especially the human neurological disorders (NDs). By evolutionary analysis of RDIGs, we find that the RDIGs highly prevailing in populations of yeast tend to be more evolutionarily conserved, indicating the accurate repair of DSBs in these RDIGs is critical to ensure the eukaryotic survival or fitness. fgao@tju.edu.cn. Supplementary data are available at Bioinformatics online.

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

PubMed Central

Dujon, Bernard

2012-01-01

Summary: Forced interspecific hybridization has been used in yeasts for many years to study speciation or to construct artificial strains with novel fermentative and metabolic properties. Recent genome analyses indicate that natural hybrids are also generated spontaneously between yeasts belonging to distinct species, creating lineages with novel phenotypes, varied genetic stability, or altered virulence in the case of pathogens. Large segmental introgressions from evolutionarily distant species are also visible in some yeast genomes, suggesting that interspecific genetic exchanges occur during evolution. The origin of this phenomenon remains unclear, but it is likely based on weak prezygotic barriers, limited Dobzhansky-Muller (DM) incompatibilities, and rapid clonal expansions. Newly formed interspecies hybrids suffer rapid changes in the genetic contribution of each parent, including chromosome loss or aneuploidy, translocations, and loss of heterozygosity, that, except in a few recently studied cases, remain to be characterized more precisely at the genomic level by use of modern technologies. We review here known cases of natural or artificially formed interspecies hybrids between yeasts and discuss their potential importance in terms of genome evolution. Problems of meiotic fertility, ploidy constraint, gene and gene product compatibility, and nucleomitochondrial interactions are discussed and placed in the context of other known mechanisms of yeast genome evolution as a model for eukaryotes. PMID:23204364

Evolutionarily conserved coupling of adaptive and excitable networks mediates eukaryotic chemotaxis

NASA Astrophysics Data System (ADS)

Tang, Ming; Wang, Mingjie; Shi, Changji; Iglesias, Pablo A.; Devreotes, Peter N.; Huang, Chuan-Hsiang

2014-10-01

Numerous models explain how cells sense and migrate towards shallow chemoattractant gradients. Studies show that an excitable signal transduction network acts as a pacemaker that controls the cytoskeleton to drive motility. Here we show that this network is required to link stimuli to actin polymerization and chemotactic motility and we distinguish the various models of chemotaxis. First, signalling activity is suppressed towards the low side in a gradient or following removal of uniform chemoattractant. Second, signalling activities display a rapid shut off and a slower adaptation during which responsiveness to subsequent test stimuli decline. Simulations of various models indicate that these properties require coupled adaptive and excitable networks. Adaptation involves a G-protein-independent inhibitor, as stimulation of cells lacking G-protein function suppresses basal activities. The salient features of the coupled networks were observed for different chemoattractants in Dictyostelium and in human neutrophils, suggesting an evolutionarily conserved mechanism for eukaryotic chemotaxis.

Apology and forgiveness evolve to resolve failures in cooperative agreements.

PubMed

Martinez-Vaquero, Luis A; Han, The Anh; Pereira, Luís Moniz; Lenaerts, Tom

2015-06-09

Making agreements on how to behave has been shown to be an evolutionarily viable strategy in one-shot social dilemmas. However, in many situations agreements aim to establish long-term mutually beneficial interactions. Our analytical and numerical results reveal for the first time under which conditions revenge, apology and forgiveness can evolve and deal with mistakes within ongoing agreements in the context of the Iterated Prisoners Dilemma. We show that, when the agreement fails, participants prefer to take revenge by defecting in the subsisting encounters. Incorporating costly apology and forgiveness reveals that, even when mistakes are frequent, there exists a sincerity threshold for which mistakes will not lead to the destruction of the agreement, inducing even higher levels of cooperation. In short, even when to err is human, revenge, apology and forgiveness are evolutionarily viable strategies which play an important role in inducing cooperation in repeated dilemmas.

Apology and forgiveness evolve to resolve failures in cooperative agreements

PubMed Central

Martinez-Vaquero, Luis A.; Han, The Anh; Pereira, Luís Moniz; Lenaerts, Tom

2015-01-01

Making agreements on how to behave has been shown to be an evolutionarily viable strategy in one-shot social dilemmas. However, in many situations agreements aim to establish long-term mutually beneficial interactions. Our analytical and numerical results reveal for the first time under which conditions revenge, apology and forgiveness can evolve and deal with mistakes within ongoing agreements in the context of the Iterated Prisoners Dilemma. We show that, when the agreement fails, participants prefer to take revenge by defecting in the subsisting encounters. Incorporating costly apology and forgiveness reveals that, even when mistakes are frequent, there exists a sincerity threshold for which mistakes will not lead to the destruction of the agreement, inducing even higher levels of cooperation. In short, even when to err is human, revenge, apology and forgiveness are evolutionarily viable strategies which play an important role in inducing cooperation in repeated dilemmas. PMID:26057819

The presence of the ancestral insect telomeric motif in kissing bugs (Triatominae) rules out the hypothesis of its loss in evolutionarily advanced Heteroptera (Cimicomorpha)

PubMed Central

Pita, Sebastián; Panzera, Francisco; Mora, Pablo; Vela, Jesús; Palomeque, Teresa; Lorite, Pedro

2016-01-01

Abstract Next-generation sequencing data analysis on Triatoma infestans Klug, 1834 (Heteroptera, Cimicomorpha, Reduviidae) revealed the presence of the ancestral insect (TTAGG)n telomeric motif in its genome. Fluorescence in situ hybridization confirms that chromosomes bear this telomeric sequence in their chromosomal ends. Furthermore, motif amount estimation was about 0.03% of the total genome, so that the average telomere length in each chromosomal end is almost 18 kb long. We also detected the presence of (TTAGG)n telomeric repeat in mitotic and meiotic chromosomes in other three species of Triatominae: Triatoma dimidiata Latreille, 1811, Dipetalogaster maxima Uhler, 1894, and Rhodnius prolixus Ståhl, 1859. This is the first report of the (TTAGG)n telomeric repeat in the infraorder Cimicomorpha, contradicting the currently accepted hypothesis that evolutionarily recent heteropterans lack this ancestral insect telomeric sequence. PMID:27830050

Global priorities for conserving the evolutionary history of sharks, rays and chimaeras.

PubMed

Stein, R William; Mull, Christopher G; Kuhn, Tyler S; Aschliman, Neil C; Davidson, Lindsay N K; Joy, Jeffrey B; Smith, Gordon J; Dulvy, Nicholas K; Mooers, Arne O

2018-02-01

In an era of accelerated biodiversity loss and limited conservation resources, systematic prioritization of species and places is essential. In terrestrial vertebrates, evolutionary distinctness has been used to identify species and locations that embody the greatest share of evolutionary history. We estimate evolutionary distinctness for a large marine vertebrate radiation on a dated taxon-complete tree for all 1,192 chondrichthyan fishes (sharks, rays and chimaeras) by augmenting a new 610-species molecular phylogeny using taxonomic constraints. Chondrichthyans are by far the most evolutionarily distinct of all major radiations of jawed vertebrates-the average species embodies 26 million years of unique evolutionary history. With this metric, we identify 21 countries with the highest richness, endemism and evolutionary distinctness of threatened species as targets for conservation prioritization. On average, threatened chondrichthyans are more evolutionarily distinct-further motivating improved conservation, fisheries management and trade regulation to avoid significant pruning of the chondrichthyan tree of life.

IQ and the values of nations.

PubMed

Kanazawa, Satoshi

2009-07-01

The origin of values and preferences is an unresolved theoretical question in behavioural and social sciences. The Savanna-IQ Interaction Hypothesis, derived from the Savanna Principle and a theory of the evolution of general intelligence, suggests that more intelligent individuals may be more likely to acquire and espouse evolutionarily novel values and preferences (such as liberalism and atheism and, for men, sexual exclusivity) than less intelligent individuals, but that general intelligence may have no effect on the acquisition and espousal of evolutionarily familiar values. Macro-level analyses show that nations with higher average intelligence are more liberal (have greater highest marginal individual tax rate and, as a result, lower income inequality), less religious (a smaller proportion of the population believes in God or considers themselves religious) and more monogamous. The average intelligence of a population appears to be the strongest predictor of its level of liberalism, atheism and monogamy.

H2B ubiquitination: Conserved molecular mechanism, diverse physiologic functions of the E3 ligase during meiosis.

PubMed

Wang, Liying; Cao, Chunwei; Wang, Fang; Zhao, Jianguo; Li, Wei

2017-09-03

RNF20/Bre1 mediated H2B ubiquitination (H2Bub) has various physiologic functions. Recently, we found that H2Bub participates in meiotic recombination by promoting chromatin relaxation during meiosis. We then analyzed the phylogenetic relationships among the E3 ligase for H2Bub, its E2 Rad6 and their partner WW domain-containing adaptor with a coiled-coil (WAC) or Lge1, and found that the molecular mechanism underlying H2Bub is evolutionarily conserved from yeast to mammals. However, RNF20 has diverse physiologic functions in different organisms, which might be caused by the evolutionary divergency of their domain/motif architectures. In the current extra view, we not only elucidate the evolutionarily conserved molecular mechanism underlying H2Bub, but also discuss the diverse physiologic functions of RNF20 during meiosis.

A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein.

PubMed

Agrawal, Neeraj J; Helk, Bernhard; Trout, Bernhardt L

2014-01-21

Identifying hot-spot residues - residues that are critical to protein-protein binding - can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein-protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36-57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein-protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily Conserved

PubMed Central

Meng, Hao; Agbagwa, Ikechukwu O.; Wang, Ling-Xiang; Wang, Yingzhi; Yan, Shi; Ren, Shancheng; Sun, Yinghao; Pei, Gang; Liu, Xin; Liu, Jiang; Jin, Li; Li, Hui; Sun, Yingli

2016-01-01

DNA methylation plays an important role for mammalian development. However, it is unclear whether the DNA methylation pattern is evolutionarily conserved. The Y chromosome serves as a powerful tool for the study of human evolution because it is transferred between males. In this study, based on deep-rooted pedigrees and the latest Y chromosome phylogenetic tree, we performed epigenetic pattern analysis of the Y chromosome from 72 donors. By comparing their respective DNA methylation level, we found that the DNA methylation pattern on the Y chromosome was stable among family members and haplogroups. Interestingly, two haplogroup-specific methylation sites were found, which were both genotype-dependent. Moreover, the African and Asian samples also had similar DNA methylation pattern with a remote divergence time. Our findings indicated that the DNA methylation pattern on the Y chromosome was conservative during human male history. PMID:26760298

Body-enlarging effect of royal jelly in a non-holometabolous insect species, Gryllus bimaculatus

PubMed Central

Miyashita, Atsushi; Kizaki, Hayato; Sekimizu, Kazuhisa; Kaito, Chikara

2016-01-01

ABSTRACT Honeybee royal jelly is reported to have body-enlarging effects in holometabolous insects such as the honeybee, fly and silkmoth, but its effect in non-holometabolous insect species has not yet been examined. The present study confirmed the body-enlarging effect in silkmoths fed an artificial diet instead of mulberry leaves used in the previous literature. Administration of honeybee royal jelly to silkmoth from early larval stage increased the size of female pupae and adult moths, but not larvae (at the late larval stage) or male pupae. We further examined the body-enlarging effect of royal jelly in a non-holometabolous species, the two-spotted cricket Gryllus bimaculatus, which belongs to the evolutionarily primitive group Polyneoptera. Administration of royal jelly to G. bimaculatus from its early nymph stage enlarged both males and females at the mid-nymph and adult stages. In the cricket, the body parts were uniformly enlarged in both males and females; whereas the enlarged female silkmoths had swollen abdomens. Administration of royal jelly increased the number, but not the size, of eggs loaded in the abdomen of silkmoth females. In addition, fat body cells were enlarged by royal jelly in the silkmoth, but not in the cricket. These findings suggest that the body-enlarging effect of royal jelly is common in non-holometabolous species, G. bimaculatus, but it acts in a different manner than in holometabolous species. PMID:27185266

An ERP Study on Decisions between Attractive Females and Money

PubMed Central

Zhang, Qinglin

2012-01-01

To investigate the neural processes of decision-makings between attractive females and money, we recorded 18 male participants' brain event-related potentials (ERPs) when they performed a novel task of deciding between viewing an attractive female's fuzzy picture in clear and gaining a certain amount of money. Two types of attractive females were included: sexy females and beautiful females. Several new electrophysiological discoveries were obtained as following. First, the beautiful females vs. money task (task B) elicited a larger positive ERP deflection (P2) than the sexy females vs. money task (task S) between 290 and 340 ms, and this probably related to the perception matching process between a visual input and an internal representation or expectation. Second, task S evoked greater negative ERP waves (N2) than task B during the time window of 340–390 ms, and this might relate to response conflict and cognitive monitoring for impulsive tendency. Third, the ERP positivity in task S was larger than task B in the time interval of 550–1000 ms, reflecting that sexy female images may have higher decision value for males than beautiful female images. Fourth, compared with choosing to gain money, choosing to view an attractive female evoked a larger late positive component (LPC) during the same time window, possibly because attractive females are more direct and evolutionarily earlier rewards for males than money amounts. PMID:23077499

Evidence of a Pivotal Role for the Distal Part of the Complement Cascade in the Diurnal Release of Hematopoietic Stem Cells Into Peripheral Blood.

PubMed

Borkowska, Sylwia; Suszynska, Malwina; Ratajczak, Janina; Ratajczak, Mariusz Z

2016-01-01

We found that diurnal activation of the three evolutionarily ancient proteolytic cascades in peripheral blood (PB), namely, the complement, coagulation, and fibrinolytic cascades, late at night or in the early morning hours, precedes the diurnal release of hematopoietic stem/progenitor cells (HSPCs) from bone marrow (BM) into PB in wild-type mice. Moreover, activation of the distal part of the complement cascade (ComC), involving cleavage of the fifth component (C5), seems to play a crucial role in pharmacological mobilization of HSPCs. In order to shed more light on the role of diurnal rhythms in the egress of HSPCs, we studied diurnal changes in the number of circulating HSPCs in C5-deficient mice and did not observe diurnal changes in the number of these cells circulating in PB in C5(-/-) animals. Based on this finding, we conclude that activation of the distal part of the ComC, C5 cleavage, and release of C5a and desArgC5a are required in executing the diurnal release of HSPCs from BM into PB. Moreover, the fact that C5(-/-) mice still displayed normal activation of the coagulation and fibrinolytic cascades indicates that, of all the proteolytic cascades, the ComC is the dominant player regulating diurnal egress of HSPCs.

An ERP study on decisions between attractive females and money.

PubMed

Zeng, Jianmin; Wang, Yujiao; Zhang, Qinglin

2012-01-01

To investigate the neural processes of decision-makings between attractive females and money, we recorded 18 male participants' brain event-related potentials (ERPs) when they performed a novel task of deciding between viewing an attractive female's fuzzy picture in clear and gaining a certain amount of money. Two types of attractive females were included: sexy females and beautiful females. Several new electrophysiological discoveries were obtained as following. First, the beautiful females vs. money task (task B) elicited a larger positive ERP deflection (P2) than the sexy females vs. money task (task S) between 290 and 340 ms, and this probably related to the perception matching process between a visual input and an internal representation or expectation. Second, task S evoked greater negative ERP waves (N2) than task B during the time window of 340-390 ms, and this might relate to response conflict and cognitive monitoring for impulsive tendency. Third, the ERP positivity in task S was larger than task B in the time interval of 550-1000 ms, reflecting that sexy female images may have higher decision value for males than beautiful female images. Fourth, compared with choosing to gain money, choosing to view an attractive female evoked a larger late positive component (LPC) during the same time window, possibly because attractive females are more direct and evolutionarily earlier rewards for males than money amounts.

A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration

PubMed Central

Petersen, Hendrik O.; Höger, Stefanie K.; Looso, Mario; Lengfeld, Tobias; Kuhn, Anne; Warnken, Uwe; Nishimiya-Fujisawa, Chiemi; Schnölzer, Martina; Krüger, Marcus; Özbek, Suat; Simakov, Oleg; Holstein, Thomas W.

2015-01-01

The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct molecular cascades: an early injury response and a subsequent, signaling driven patterning of the regenerating tissue. A key factor of the initial injury response is a general stabilization of proteins and a net upregulation of transcripts, which is followed by a subsequent activation cascade of signaling molecules including Wnts and transforming growth factor (TGF) beta-related factors. We observed moderate overlap between the factors contributing to proteomic and transcriptomic responses suggesting a decoupled regulation between the transcriptional and translational levels. Our data also indicate that interstitial stem cells and their derivatives (e.g., neurons) have no major role in Hydra head regeneration. Remarkably, we found an enrichment of evolutionarily more recent genes in the early regeneration response, whereas conserved genes are more enriched in the late phase. In addition, genes specific to the early injury response were enriched in transposon insertions. Genetic dynamicity and taxon-specific factors might therefore play a hitherto underestimated role in Hydra regeneration. PMID:25841488

A role for autophagic protein beclin 1 early in lymphocyte development.

PubMed

Arsov, Ivica; Adebayo, Adeola; Kucerova-Levisohn, Martina; Haye, Joanna; MacNeil, Margaret; Papavasiliou, F Nina; Yue, Zhenyu; Ortiz, Benjamin D

2011-02-15

Autophagy is a highly regulated and evolutionarily conserved process of cellular self-digestion. Recent evidence suggests that this process plays an important role in regulating T cell homeostasis. In this study, we used Rag1(-/-) (recombination activating gene 1(-/-)) blastocyst complementation and in vitro embryonic stem cell differentiation to address the role of Beclin 1, one of the key autophagic proteins, in lymphocyte development. Beclin 1-deficient Rag1(-/-) chimeras displayed a dramatic reduction in thymic cellularity compared with control mice. Using embryonic stem cell differentiation in vitro, we found that the inability to maintain normal thymic cellularity is likely caused by impaired maintenance of thymocyte progenitors. Interestingly, despite drastically reduced thymocyte numbers, the peripheral T cell compartment of Beclin 1-deficient Rag1(-/-) chimeras is largely normal. Peripheral T cells displayed normal in vitro proliferation despite significantly reduced numbers of autophagosomes. In addition, these chimeras had greatly reduced numbers of early B cells in the bone marrow compared with controls. However, the peripheral B cell compartment was not dramatically impacted by Beclin 1 deficiency. Collectively, our results suggest that Beclin 1 is required for maintenance of undifferentiated/early lymphocyte progenitor populations. In contrast, Beclin 1 is largely dispensable for the initial generation and function of the peripheral T and B cell compartments. This indicates that normal lymphocyte development involves Beclin 1-dependent, early-stage and distinct, Beclin 1-independent, late-stage processes.

Prolonged myelination in human neocortical evolution.

PubMed

Miller, Daniel J; Duka, Tetyana; Stimpson, Cheryl D; Schapiro, Steven J; Baze, Wallace B; McArthur, Mark J; Fobbs, Archibald J; Sousa, André M M; Sestan, Nenad; Wildman, Derek E; Lipovich, Leonard; Kuzawa, Christopher W; Hof, Patrick R; Sherwood, Chet C

2012-10-09

Nerve myelination facilitates saltatory action potential conduction and exhibits spatiotemporal variation during development associated with the acquisition of behavioral and cognitive maturity. Although human cognitive development is unique, it is not known whether the ontogenetic progression of myelination in the human neocortex is evolutionarily exceptional. In this study, we quantified myelinated axon fiber length density and the expression of myelin-related proteins throughout postnatal life in the somatosensory (areas 3b/3a/1/2), motor (area 4), frontopolar (prefrontal area 10), and visual (areas 17/18) neocortex of chimpanzees (N = 20) and humans (N = 33). Our examination revealed that neocortical myelination is developmentally protracted in humans compared with chimpanzees. In chimpanzees, the density of myelinated axons increased steadily until adult-like levels were achieved at approximately the time of sexual maturity. In contrast, humans displayed slower myelination during childhood, characterized by a delayed period of maturation that extended beyond late adolescence. This comparative research contributes evidence crucial to understanding the evolution of human cognition and behavior, which arises from the unfolding of nervous system development within the context of an enriched cultural environment. Perturbations of normal developmental processes and the decreased expression of myelin-related molecules have been related to psychiatric disorders such as schizophrenia. Thus, these species differences suggest that the human-specific shift in the timing of cortical maturation during adolescence may have implications for vulnerability to certain psychiatric disorders.

Characterization of a Bacteriocin-Like Substance Produced by a Vaginal Lactobacillus salivarius Strain

PubMed Central

Ocaña, Virginia S.; Pesce de Ruiz Holgado, Aída A.; Nader-Macías, María Elena

1999-01-01

A novel bacteriocin-like substance produced by vaginal Lactobacillus salivarius subsp. salivarius CRL 1328 with activity against Enterococcus faecalis, Enterococcus faecium, and Neisseria gonorrhoeae was characterized. The highest level of production of this heat-resistant peptide or protein occurred during the late exponential phase. Its mode of action was shown to be bactericidal. L. salivarius subsp. salivarius CRL 1328 could be used for the design of a probiotic to prevent urogenital infections. PMID:10584033

Late Tharsis tectonic activity and implications for Early Mars

NASA Astrophysics Data System (ADS)

Bouley, S.; Baratoux, D.; Paulien, N.; Missenard, Y.; Saint-Bezar, B.

2017-12-01

Constraining the timing of Tharsis volcanism is critical to understanding the planet's evolution including its climate, surface environment and mantle dynamics. The tectonic history of the Tharsis bulge was previously documented from the distribution and ages of related tectonic features [1]. Here we revisit the ages of 7493 Tharsis-related tectonic features based on their relationship with stratigraphic units defined in the new geological map [2]. Conversely to previous tectonic mapping [1], which suggested that Tharsis growth was nearly achieved during the Noachian, we find a protracted growth of Tharsis during the Hesperian. Faulting at Tempe Terra, Claritas and Coracis Fossae and Thaumasia Planum confirms that tectonic deformation started during the Noachian. Accumulated tectonic deformation was maximum in the Early Hesperian for compressional strain (Solis, Lunae and Ascuris Planum) and extended over time from Noachian to Amazonian for extensional strain (Noctis Labyrinthus and Fossae, Sinai Planum and Tractus, Ulysses and Fortuna fossae, Alba Patera). This new scenario is consistent with a protracted growth of Tharsis dome during the Hesperian and with the timing a large Tharsis-driven true polar wander post-dating the incision of Late Noachian/Hesperian valley networks[3]. References:[1] Anderson et al. JGR-Planets 106, E9, 20,563-20,585 (2001).[2] Tanaka, K.L. et al. Geologic map of Mars (2014). [3] Bouley et al. Nature doi:10.1038 (2016)

A simple fitness proxy for structured populations with continuous traits, with case studies on the evolution of haplo-diploids and genetic dimorphisms.

PubMed

Metz, J A J; Leimar, O

2011-03-01

For structured populations in equilibrium with everybody born equal, ln(R (0)) is a useful fitness proxy for evolutionarily steady strategy (ESS) and most adaptive dynamics calculations, with R (0) the average lifetime number of offspring in the clonal and haploid cases, and half the average lifetime number of offspring fathered or mothered for Mendelian diploids. When individuals have variable birth states, as is, for example, the case in spatial models, R (0) is itself an eigenvalue, which usually cannot be expressed explicitly in the trait vectors under consideration. In that case, Q(Y| X):=-det (I-L(Y| X)) can often be used as fitness proxy, with L the next-generation matrix for a potential mutant characterized by the trait vector Y in the (constant) environment engendered by a resident characterized by X. If the trait space is connected, global uninvadability can be determined from it. Moreover, it can be used in all the usual local calculations like the determination of evolutionarily singular trait vectors and their local invadability and attractivity. We conclude with three extended case studies demonstrating the usefulness of Q: the calculation of ESSs under haplo-diploid genetics (I), of evolutionarily steady genetic dimorphisms (ESDs) with a priori proportionality of macro- and micro-gametic outputs (an assumption that is generally made but the fulfilment of which is a priori highly exceptional) (II), and of ESDs without such proportionality (III). These case studies should also have some interest in their own right for the spelled out calculation recipes and their underlying modelling methodology.

The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages

PubMed Central

Imanian, Behzad; Keeling, Patrick J

2007-01-01

Background The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully integrated with the host cell cycle and is so altered in structure as to be difficult to recognize it as a diatom, and yet it retains a number of features normally lost in tertiary and secondary endosymbionts, most notably mitochondria. The dinoflagellate host is also reported to retain mitochondrion-like structures, making these cells unique in retaining two evolutionarily distinct mitochondria. This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them. Results We show that both host and endosymbiont mitochondrial genomes encode genes for electron transport proteins. We have characterized cytochrome c oxidase 1 (cox1), cytochrome oxidase 2 (cox2), cytochrome oxidase 3 (cox3), cytochrome b (cob), and large subunit of ribosomal RNA (LSUrRNA) of endosymbiont mitochondrial ancestry, and cox1 and cob of host mitochondrial ancestry. We show that all genes are transcribed and that those ascribed to the host mitochondrial genome are extensively edited at the RNA level, as expected for a dinoflagellate mitochondrion-encoded gene. We also found evidence for extensive recombination in the host mitochondrial genes and that recombination products are also transcribed, as expected for a dinoflagellate. Conclusion Durinskia baltica and K. foliaceum retain two mitochondria from evolutionarily distinct lineages, and the functions of these organelles are at least partially overlapping, since both express genes for proteins in electron transport. PMID:17892581

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCEPost-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

Differential sensitivity of Chironomus and human hemoglobin to gamma radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaikwad, Pallavi S.; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085; Panicker, Lata

Chironomus ramosus is known to tolerate high doses of gamma radiation exposure. Larvae of this insect possess more than 95% of hemoglobin (Hb) in its circulatory hemolymph. This is a comparative study to see effect of gamma radiation on Hb of Chironomus and humans, two evolutionarily diverse organisms one having extracellular and the other intracellular Hb respectively. Stability and integrity of Chironomus and human Hb to gamma radiation was compared using biophysical techniques like Dynamic Light Scattering (DLS), UV-visible spectroscopy, fluorescence spectrometry and CD spectroscopy after exposure of whole larvae, larval hemolymph, human peripheral blood, purified Chironomus and human Hb.more » Sequence- and structure-based bioinformatics methods were used to analyze the sequence and structural similarities or differences in the heme pockets of respective Hbs. Resistivity of Chironomus Hb to gamma radiation is remarkably higher than human Hb. Human Hb exhibited loss of heme iron at a relatively low dose of gamma radiation exposure as compared to Chironomus Hb. Unlike human Hb, the heme pocket of Chironomus Hb is rich in aromatic amino acids. Higher hydophobicity around heme pocket confers stability of Chironomus Hb compared to human Hb. Previously reported gamma radiation tolerance of Chironomus can be largely attributed to its evolutionarily ancient form of extracellular Hb as evident from the present study. -- Highlights: •Comparison of radiation tolerant Chironomus Hb and radiation sensitive Human Hb. •Amino acid composition of midge and human heme confer differential hydrophobicity. •Heme pocket of evolutionarily ancient midge Hb provide gamma radiation resistivity.« less

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

DOE PAGES

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.; ...

2017-11-28

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

The anatomy of a major late-stage thrust and implications for models of late-stage collisional orogenesis in the Caledonian crust of northern Scandinavia

NASA Astrophysics Data System (ADS)

Anderson, Mark; Hames, Willis; Stokes, Alison

2010-05-01

Within the stack of Caledonian crystalline thrust sheets of northern Scandinavia, a single amphibolite facies lithotectonic unit, the Småtinden nappe, is identified as a major, basement-coupled ("stretching") shear zone. This dominantly pelitic unit achieved peak metamorphic conditions of 535-550°C and 8-9kbars, and the stretching geometry suggests that this most likely occurred in response to overthrusting of a hot, pre-assembled Caledonian thrust stack. Along-strike variations in microstructural geometries and patterns of mineral zoning in widely developed porphyroblast phases suggest, however, subsequent strain partitioning within the zone during late-stage decoupling of the thrust stack from the basement along major out-of-sequence thrusts. Large parts of the nappe are characterised by relatively late, static growth preserving concordant Si-Se relationships, and typically symmetrical external fabrics consistent with formation under dominantly pure shear conditions. In the Salangen area, however, the nappe is characterised by early garnet growth, with discordant Si-Se relationships and asymmetric external fabric geometries consistent with formation during ESE-directed simple shear. Remarkably consistent thermometric estimates from chlorites in both regimes (post- and syn-shearing) suggest that out-of-sequence ramping occurred at temperatures in the range 370-400 ̊C, within the typical range of blocking temperatures for argon retention in muscovite. 40Ar-39Ar dating of muscovites from S-C fabrics in the out-of-sequence shear zone suggest that late-stage thrusting occurred during the middle-late Devonian (ca. 395-375 Ma). Hanging-wall and footwall geometries coupled with these radiometric dates indicate that the development of these late thrusts closely relates to reactivation of pre-Caledonian Baltic basement during the Devonian (400-370 Ma). East-west contraction during the upper end of this time frame is peculiar considering that this was the period of large magnitude and rapid extension in western Norway.

Identification of genes associated with prophage-like gene transfer agents in the pathogenic intestinal spirochaetes Brachyspira hyodysenteriae, Brachyspira pilosicoli and Brachyspira intermedia.

PubMed

Motro, Yair; La, Tom; Bellgard, Matthew I; Dunn, David S; Phillips, Nyree D; Hampson, David J

2009-03-02

VSH-1 is an unusual prophage-like gene transfer agent (GTA) that has been described in the intestinal spirochaete Brachyspira hyodysenteriae. The GTA does not self-propagate, but it assembles into a virus-like particle and transfers random 7.5kb fragments of host DNA to other B. hyodysenteriae cells. To date the GTA VSH-1 has only been analysed in B. hyodysenteriae strain B204, in which 11 late function genes encoding prophage capsid, tail and lysis elements have been described. The aim of the current study was to look for these 11 genes in the near-complete genomes of B. hyodysenteriae WA1, B. pilosicoli 95/1000 and B. intermedia HB60. All 11 genes were found in the three new strains. The GTA genes in WA1 and 95/1000 were contiguous, whilst some of those in HB60 were not-although in all three strains some gene rearrangements were present. A new predicted open reading frame with potential functional importance was found in a consistent position associated with all four GTAs, located between the genes for head protein Hvp24 and tail protein Hvp53, overlapping with the hvp24 sequence. Differences in the nucleotide and predicted amino acid sequences of the GTA genes in the spirochaete strains were consistent with the overall genetic distances between the strains. Hence the GTAs in the two B. hyodysenteriae strains were considered to be strain specific variants, and were designated GTA/Bh-B204 and GTA/Bh-WA1 respectively. The GTAs in the strains of B. intermedia and B. pilosicoli were designated GTA/Bint-HB60 and GTA/Bp-95/1000 respectively. Further work is required to determine the extent to which these GTAs can transfer host genes between different Brachyspira species and strains.

Different evolutionary trends of swine H1N2 influenza viruses in Italy compared to European viruses

PubMed Central

2013-01-01

European H1N2 swine influenza viruses (EU H1N2SIVs) arose from multiple reassortment events among human H1N1, human H3N2, and avian influenza viruses. We investigated the evolutionary dynamics of 53 Italian H1N2 strains by comparing them with EU H1N2 SIVs. Hemagglutinin (HA) phylogeny revealed Italian strains fell into four groups: Group A and B (41 strains) had a human H1 similar to EU H1N2SIVs, which probably originated in 1986. However Group B (38 strains) formed a subgroup that had a two-amino acid deletion at positions 146/147 in HA. Group C (11 strains) contained an avian H1 that probably originated in 1996, and Group D (1 strain) had an H1 characteristic of the 2009 pandemic strain. Neuraminidase (NA) phylogeny suggested a series of genomic reassortments had occurred. Group A had an N2 that originated from human H3N2 in the late 1970s. Group B had different human N2 that most likely arose from a reassortment with the more recent human H3N2 virus, which probably occurred in 2000. Group C had an avian-like H1 combined with an N2 gene from one of EU H1N2SIVs, EU H3N2SIVs or Human H3N2. Group D was part of the EU H3N2SIVs clade. Although selection pressure for HA and NA was low, several positively selected sites were identified in both proteins, some of which were antigenic, suggesting selection influenced the evolution of SIV. The data highlight different evolutionary trends between European viruses and currently circulating Italian B strains and show the establishment of reassortant strains involving human viruses in Italian pigs. PMID:24289094

Different evolutionary trends of swine H1N2 influenza viruses in Italy compared to European viruses.

PubMed

Moreno, Ana; Gabanelli, Elena; Sozzi, Enrica; Lelli, Davide; Chiapponi, Chiara; Ciccozzi, Massimo; Zehender, Gianguglielmo; Cordioli, Paolo

2013-12-01

European H1N2 swine influenza viruses (EU H1N2SIVs) arose from multiple reassortment events among human H1N1, human H3N2, and avian influenza viruses. We investigated the evolutionary dynamics of 53 Italian H1N2 strains by comparing them with EU H1N2 SIVs. Hemagglutinin (HA) phylogeny revealed Italian strains fell into four groups: Group A and B (41 strains) had a human H1 similar to EU H1N2SIVs, which probably originated in 1986. However Group B (38 strains) formed a subgroup that had a two-amino acid deletion at positions 146/147 in HA. Group C (11 strains) contained an avian H1 that probably originated in 1996, and Group D (1 strain) had an H1 characteristic of the 2009 pandemic strain. Neuraminidase (NA) phylogeny suggested a series of genomic reassortments had occurred. Group A had an N2 that originated from human H3N2 in the late 1970s. Group B had different human N2 that most likely arose from a reassortment with the more recent human H3N2 virus, which probably occurred in 2000. Group C had an avian-like H1 combined with an N2 gene from one of EU H1N2SIVs, EU H3N2SIVs or Human H3N2. Group D was part of the EU H3N2SIVs clade. Although selection pressure for HA and NA was low, several positively selected sites were identified in both proteins, some of which were antigenic, suggesting selection influenced the evolution of SIV. The data highlight different evolutionary trends between European viruses and currently circulating Italian B strains and show the establishment of reassortant strains involving human viruses in Italian pigs.

Inactivation and Gene Expression of a Virulent Wastewater Escherichia coli Strain and the Nonvirulent Commensal Escherichia coli DSM1103 Strain upon Solar Irradiation.

PubMed

Al-Jassim, Nada; Mantilla-Calderon, David; Wang, Tiannyu; Hong, Pei-Ying

2017-04-04

This study examined the decay kinetics and molecular responses of two Escherichia coli strains upon solar irradiation. The first is E. coli PI-7, a virulent and antibiotic-resistant strain that was isolated from wastewater and carries the emerging NDM-1 antibiotic resistance gene. The other strain, E. coli DSM1103, displayed lower virulence and antibiotic resistance than E. coli PI-7. In a buffer solution, E. coli PI-7 displayed a longer lag phase prior to decay and a longer half-life compared with E. coli DSM1103 (6.64 ± 0.63 h and 2.85 ± 0.46 min vs 1.33 ± 0.52 h and 2.04 ± 0.36 min). In wastewater, both E. coli strains decayed slower than they did in buffer. Although solar irradiation remained effective in reducing the numbers of both strains by more than 5-log 10 in <24 h, comparative genomics and transcriptomics revealed differences in the genomes and overall regulation of genes between the two E. coli strains. A wider arsenal of genes related to oxidative stress, cellular repair and protective mechanisms were upregulated in E. coli PI-7. Subpopulations of E. coli PI-7 expressed genes related to dormancy and persister cell formation during the late decay phase, which may have accounted for its prolonged persistence. Upon prolonged solar irradiation, both E. coli strains displayed upregulation of genes related to horizontal gene transfer and antibiotic resistance. Virulence functions unique to E. coli PI-7 were also upregulated. Our findings collectively indicated that, whereas solar irradiation is able to reduce total cell numbers, viable E. coli remained and expressed genes that enable survival despite solar treatment. There remains a need for heightened levels of concern regarding risks arising from the dissemination of E. coli that may remain viable in wastewater after solar irradiation.

Influence of loading and unloading velocity of confining pressure on strength and permeability characteristics of crystalline sandstone

NASA Astrophysics Data System (ADS)

Zhang, Dong-ming; Yang, Yu-shun; Chu, Ya-pei; Zhang, Xiang; Xue, Yan-guang

2018-06-01

The triaxial compression test of crystalline sandstone under different loading and unloading velocity of confining pressure is carried out by using the self-made "THM coupled with servo-controlled seepage apparatus for containing-gas coal", analyzed the strength, deformation and permeability characteristics of the sample, the results show that: with the increase of confining pressures loading-unloading velocity, Mohr's stress circle center of the specimen shift to the right, and the ultimate intensity, peak strain and residual stress of the specimens increase gradually. With the decrease of unloading velocity of confining pressure, the axial strain, the radial strain and the volumetric strain of the sample decrease first and then increases, but the radial strain decreases more greatly. The loading and unloading of confining pressure has greater influence on axial strain of specimens. The deformation modulus decreases rapidly with the increase of axial strain and the Poisson's ratio decreases gradually at the initial stage of loading. When the confining pressure is loaded, the deformation modulus decrease gradually, and the Poisson's ratio increases gradually. When the confining pressure is unloaded, the deformation modulus increase gradually, and the Poisson's ratio decreases gradually. When the specimen reaches the ultimate intensity, the deformation modulus decreases rapidly, while the Poisson's ratio increases rapidly. The fitting curve of the confining pressure and the deformation modulus and the Poisson's ratio in accordance with the distribution of quadratic polynomial function in the loading-unloading confining pressure. There is a corresponding relationship between the evolution of rock permeability and damage deformation during the process of loading and unloading. In the late stage of yielding, the permeability increases slowly, and the permeability increases sharply after the rock sample is destroyed. Fitting the permeability and confining pressure conform to the variation law of the exponential function.

Lactobacillus wasatchensis sp. nov., a non-starter lactic acid bacteria isolated from aged Cheddar cheese.

PubMed

Oberg, Craig J; Oberg, Taylor S; Culumber, Michele D; Ortakci, Fatih; Broadbent, Jeffery R; McMahon, Donald J

2016-01-01

A Gram-stain positive, rod-shaped, non-spore-forming strain (WDC04T), which may be associated with late gas production in cheese, was isolated from aged Cheddar cheese following incubation on MRS agar (pH 5.2) at 6 °C for 35 days. Strain WDC04T had 97 % 16S rRNA gene sequence similarity with Lactobacillus hokkaidonensis DSM 26202T, Lactobacillus oligofermentans 533, 'Lactobacillus danicus' 9M3, Lactobacillus suebicus CCUG 32233T and Lactobacillus vaccinostercus DSM 20634T. API 50 CH carbohydrate fermentation panels indicated strain WDC04T could only utilize one of the 50 substrates tested, ribose, although it does slowly utilize galactose. In the API ZYM system, strain WDC04T was positive for leucine arylamidase, valine arylamidase, cysteine arylamidase (weakly), naphthol-AS-BI-phosphohydrolase and β-galactosidase activities. Total genomic DNA was sequenced from strain WDC04T using a whole-genome shotgun strategy on a 454 GS Titanium pyrosequencer. The sequence was assembled into a 1.90 Mbp draft genome consisting of 105 contigs with preliminary genome annotation performed using the RAST algorithm (rast.nmpdr.org). Genome analysis confirmed the pentose phosphate pathway for ribose metabolism as well as galactose, N-acetylglucosamine, and glycerol fermentation pathways. Genomic analysis places strain WDC04T in the obligately heterofermentative group of lactobacilli and metabolic results confirm this conclusion. The result of genome sequencing, along with 16S rRNA gene sequence analysis, indicates WDC04T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus wasatchensis sp. nov. is proposed. The type strain is WDC04T ( = DSM 29958T = LMG 28678T).

Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts.

PubMed

Okuda, Yoshihiro; Sasaki, Daisuke; Nogami, Satoru; Kaneko, Yoshinobu; Ohya, Yoshikazu; Anraku, Yasuhiro

2003-05-01

VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of Saccharomyces cerevisiae. There have been two independent subfamilies of VDE, one from S. cerevisiae strain X2180-1A and the other from Saccharomyces sp. DH1-1A in the host VMA1 gene, and they share the identity of 96.3%. In order to search the occurrence, intra/interspecies transfer and molecular degeneration of VDE, complete sequences of VMA1 in 10 strains of S. cerevisiae, eight species of saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were determined. We found that six of 10 S. cerevisiae strains contain VDEs 99.7-100% identical to that of the strain X2180-1A, one has no VDE, whereas the other three harbour VDEs 100% identical to that of the strain DH1-1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that of the strain X2180-1A with VDE 100% identical to that of the strain DH1-1A and the other containing the same VMA1 in S. pastorianus with no VDE. This and other evidence indicates that intra/interspecies transmissions of VDEs have occurred among saccharomycete yeasts. Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs had branched earlier than other VDEs from an ancestral VDE and had invaded into the host loci as relatively late events. The two VDEs seemed to degenerate in individual host loci, retaining their splicing capacity intact. The degeneration of the endonuclease domains was distinct and, if compared, its apparent rate was much faster than that of the protein-splicing domains. Copyright 2003 John Wiley & Sons, Ltd.

Immunochemical characterization of the O antigens of two Proteus strains, O8-related antigen of Proteus mirabilis 12 B-r and O2-related antigen of Proteus genomospecies 5/6 12 B-k, infecting a hospitalized patient in Poland.

PubMed

Drzewiecka, Dominika; Shashkov, Alexander S; Arbatsky, Nikolay P; Knirel, Yuriy A

2016-05-01

A hospitalized 73-year-old woman was infected with a Proteus mirabilis strain, 12 B-r, isolated from the place of injection of a blood catheter. Another strain, 12 B-k, recognized as Proteus genomospecies 5 or 6, was isolated from the patient's faeces, which was an example of a nosocomial infection rather than an auto-infection. Serological investigation using ELISA and Western blotting showed that strain 12 B-k from faeces belonged to the Proteus O2 serogroup. Strain 12 B-r from the wound displayed cross-reactions with several Proteus O serogroups due to common epitopes on the core or O-specific parts of the lipopolysaccharide. Studies of the isolated 12 B-r O-specific polysaccharide by NMR spectroscopy revealed its close structural similarity to that of Proteus O8. The only difference in 12 B-r was the presence of an additional GlcNAc-linked phosphoethanolamine residue, which creates a putative epitope responsible for the cross-reactivity with Pt. mirabilis O16. The new O-antigen form could appear as a result of adaptation of the bacterium to a changing environment. On the basis of the data obtained, we suggest division of the O8 serogroup into two subgroups: O8a for strains of various Proteus species that have been previously classified into the O8 serogroup, and O8a,b for Pt. mirabilis 12 B-r, where 'a' is a common epitope and 'b' is a phosphoethanolamine-associated epitope. These findings further confirm serological and structural heterogeneity of O antigens of Proteus strains isolated lately from patients in Poland.

[A biomechanical study on the fracture treatment--intravital measurement of the strain on an intramedullary nail in the healing process of the femoral fracture in goats (author's transl)].

PubMed

Obara, T

1979-02-01

There have been many biomechanical studies throughout the world on the fracture treatment. However, only a few were performed under intravital condition. The purpose of the present study is to measure the successive strength changes of the callus after a fracture, in vivo in an animal. Specifically designed Küntscher nails were made to meet the anterior convexity and the size of the medullary canal of the femora of goats. Three self-temperature-compensating semi-conductor strain-gauges were glued on the inner surface of the nail and coated with epoxy-resin and silicone rubber. The nail was inserted into the intact femur, and the initial measurement of the strains was performed using a specially designed wooden three point bending jig. Then the femur was transected at the middle. Periodical measurements of the strains were done, first, during walking and, then, with the three point bending jig under general anesthesia. Ten goats were used for the experiments. The measurement was undertaken every two to three weeks. Serial x-rays were taken. The femur was studied histopathologically after the death of the animal. 1. Although the nail with the strain-gauges presented some foreign body reaction and certain difficulties in sterilization, it was well tolerated by the animal, permitting the strain measurement for as long as 18 weeks after the fracture. 2. There was a tendency that the less loosening is found between the nail and the bone, the larger is the strain and the smaller becomes the dispersion of the strains. 3. On the three point bending test, the post-fracture strain changes were not directly proportional to the lapse of time. In the early phase, the strains remained large for about four weeks and tended to rapidly decrease in the middle and late phases in accordance with the development of callus formation on x-ray. 4. A similar strain change was observed on the walking test, although the animal presented with some painful limp. The results suggest that early excessive exercise to be avoided when an intramedullary fixation is not sufficiently rigid.

Microstructural and strain rate effects on plastic deformation in aluminum 2219-T87

NASA Astrophysics Data System (ADS)

Rincon, Carlos D.

A fundamental investigation has been conducted on the effects of microstructure and strain rate on the plastic deformation of theta-prime-strengthened 2219 aluminum. The motivation for this work is based upon a previous study which showed inhomogeneous and locally extreme work hardening in the HAZ regions in VPPA 2219-T87 butt welds. This strongly suggests that the HAZ microstructure plays a major role in the deformation and fracture process in precipitation hardened aluminum alloy 2219. Tensile specimens of the weld joint exhibited more rapid work hardening in the heat-affected-zone (HAZ) at higher strain levels. Microhardness contour maps for these welds illustrated that late stage deformation was concentrated in two crossing bands at about 45sp° to the tensile axis. The width of the deformation bands and the ultimate tensile strength seemed to be dictated by the amount of work hardening in the HAZ. In this study, three different heat treatments were used to produce samples with different particle sizes and particle spacings, but all hardened by copper aluminide precipitates of the thetasp' structure. The heat treatments were categorized as being (A) as-received T87 condition, (B) T87 condition aged at approximately 204sp°C for 3 hours and (C) T87 over-aged at 204sp°C for 7 days. Uniaxial tensile tests consisted of two sets of experiments: (1) three heat treatments (A, B, and C) at two strain rates (0.02 minsp{-1} and 0.2 minsp{-1}) and (2) three heat treatments that were interrupted at select stress-strain levels (0.8% and 2% total strain) during the tensile tests at strain rate equal to 0.02 minsp{-1} at room temperature. Furthermore, a detailed transmission electron microscopy (TEM) study demonstrates the microstructural development during tensile deformation. The Voce equation of strain-hardening provides a slightly better fit to the tensile curves than the Ludwik-Hollomon equation. At higher strains, localized areas showed strain fields around thetasp' platelets had diminished. Lastly, in every treatment, both the yield and tensile strength were slightly higher for the higher strain rate, but only by 0.5 to 2.0 ksi.

Effect of different photoperiods on the growth, infectivity and colonization of Trinidadian strains of Paecilomyces fumosoroseus on the greenhouse whitefly, Trialeurodes vaporariorum, using a glass slide bioassay.

PubMed

Avery, Pasco B; Faull, Jane; Simmonds, Monique S J

2004-01-01

Growth, infectivity and colonization rates for blastospores and conidia of Trinidadian strains T, T10, and T11 of Paecilomyces fumosoroseus (Wize) Brown and Smith were assessed for activity against late fourth-instar nymphs of Trialeurodes vaporariorum (Westwood) (Homoptera:Aleyrodidae) under two different photoperiods (24 and 16 hour photophase). A glass-slide bioassay and a fungal development index, modified for both blastospores and conidia, were used to compare the development rates of the fungal strains on the insect hosts. Fewer adult whiteflies emerged from nymphs treated with blastospores and reared under a 16:8 hour light:dark photoperiod than a 24:0 hour photoperiod. Eclosion times of whitefly adults that emerged from nymphs treated with the different strains of conidia were similar over the 8 day experimental period at both light regimes. The percent eclosion of adult whiteflies seems to be directly correlated with the speed of infection of the blastospore or conidial treatment and the photoperiod regime. The longer photophase had a significant positive effect on development index for blastospores; however, a lesser effect was observed for the conidia at either light regime. Blastospore strain T11 offered the most potential of the three Trinidadian strains against T. vaporariorum fourth-instar nymphs, especially under constant light. The glass-slide bioassay was successfully used to compare both blastospores and conidia of P. fumosoroseus. It can be used to determine the pathogenicity and the efficacy of various fungal preparations against aleyrodid pests.

Genetic, antigenic and pathogenic characterization of four infectious bursal disease virus isolates from China suggests continued evolution of very virulent viruses.

PubMed

Li, Kai; Courtillon, Céline; Guionie, Olivier; Allée, Chantal; Amelot, Michel; Qi, Xiaole; Gao, Yulong; Wang, Xiaomei; Eterradossi, Nicolas

2015-03-01

Infectious bursal disease virus (IBDV) causes an economically significant disease of young chickens worldwide. The emergence of very virulent IBDV (vvIBDV) strains has brought more challenges for effective prevention and control of this disease. The aim of the present study was to characterize four IBDV isolates from various regions of China between late 1990s and recent years and to compare them with previously isolated European IBDV strains. In this study, one Chinese vvIBDV strain isolated in 1999 and three strains isolated between 2005 and 2011 were analyzed at the genetic, antigenic and pathogenic levels. Strain SH99 was closely related and clustered in the same genetic lineage as the typical vvIBDV based on the genomic sequences of segments A and B. However, the three more recent Chinese vvIBDV (HLJ0504, HeB10 and HuN11) showed several genetic changes in both segments and clustered in a distinct lineage from the typical vvIBDV and the previously known Chinese vvIBDV. Based on the binding to a panel of neutralizing monoclonal antibodies in antigen capture enzyme-linked immunosorbent assays, all Chinese vvIBDVs exhibited similar antigenicity with the European typical vvIBDV strains. Nonetheless, the pathogenicity caused by the recent Chinese vvIBDV was higher than that induced by the European typical vvIBDV. This study calls for a sustained surveillance of IBD situation in China in order to support a better prevention and control of the disease. Copyright © 2014 Elsevier B.V. All rights reserved.

Gas gun driven dynamic fracture and fragmentation of Ti-6Al-4V cylinders

NASA Astrophysics Data System (ADS)

Jones, D. R.; Chapman, D. J.; Eakins, D. E.

2014-05-01

The dynamic fracture and fragmentation of a material is a complex late stage phenomenon occurring in many shock loading scenarios. Improving our predictive capability depends upon exercising our current failure models against new loading schemes and data. We present axially-symmetric high strain rate (104 s-1) expansion of Ti-6Al-4V cylinders using a single stage light gas gun technique. A steel ogive insert was located inside the target cylinder, into which a polycarbonate rod was launched. Deformation of this rod around the insert drives the cylinder into rapid expansion. This technique we have developed facilitates repeatable loading, independent of the temperature of the sample cylinder, with straightforward adjustment of the radial strain rate. Expansion velocity was measured with multiple channels of photon Doppler velocimetry. High speed imaging was used to track the overall expansion process and record strain to failure and crack growth. Results from a cylinder at a temperature of 150 K are compared with work at room temperature, examining the deformation, failure mechanisms and differences in fragmentation.

Competitive exclusion by autologous antibodies can prevent broad HIV-1 antibodies from arising

DOE PAGES

Luo, Shishi; Perelson, Alan S.

2015-08-31

The past decade has seen the discovery of numerous broad and potent monoclonal antibodies against HIV type 1 (HIV-1). Eliciting these antibodies via vaccination appears to be remarkably difficult, not least because they arise late in infection and are highly mutated relative to germline antibody sequences. Here, using a computational model, we show that broad antibodies could in fact emerge earlier and be less mutated, but that they may be prevented from doing so as a result of competitive exclusion by the autologous antibody response. We further find that this competitive exclusion is weaker in infections founded by multiple distinctmore » strains, with broadly neutralizing antibodies emerging earlier than in infections founded by a single strain. Our computational model simulates coevolving multitype virus and antibody populations. Broadly neutralizing antibodies may therefore be easier for the adaptive immune system to generate than previously thought. As a result, if less mutated broad antibodies exist, it may be possible to elicit them with a vaccine containing a mixture of diverse virus strains.« less

Multilinear stress-strain and failure calibrations for Ti-6Al-4V.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corona, Edmundo

This memo concerns calibration of an elastic-plastic J 2 material model for Ti-6Al-4V (grade 5) alloy based on tensile uniaxial stress-strain data obtained in the laboratory. In addition, tension tests on notched specimens provided data to calibrate two ductile failure models: Johnson-Cook and Wellman's tearing parameter. The tests were conducted by Kim Haulen- beek and Dave Johnson (1528) in the Structural Mechanics Laboratory (SML) during late March and early April, 2017. The SML EWP number was 4162. The stock material was a TIMETALR® 6-4 Titanium billet with 9 in. by 9 in. square section and length of 137 in. Themore » product description indicates that it was a forging delivered in annealed condition (2 hours @ 1300oF, AC at the mill). The tensile mechanical properties reported in the material certi cation are given in Table 1, where σ o represents the 0.2% strain offset yield stress, σ u the ultimate stress, ε f the elongation at failure and R.A. the reduction in area.« less

The Streptococcus sanguinis competence regulon is not required for infective endocarditis virulence in a rabbit model.

PubMed

Callahan, Jill E; Munro, Cindy L; Kitten, Todd

2011-01-01

Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility in S. sanguinis. Strains deleted for the comCDE or comX master regulatory genes were created. Using a rabbit endocarditis model in conjunction with a variety of virulence assays, we determined that both mutants possessed infectivity equivalent to that of a virulent control strain, and that measures of disease were similar in rabbits infected with each strain. These results suggest that the com regulon is not required for S. sanguinis infective endocarditis virulence in this model. We propose that the different roles of the S. sanguinis, S. pneumoniae, and S. mutans com regulons in virulence can be understood in relation to the pathogenic mechanisms employed by each species.

[Development of the influenza epidemic in season 2011-2012 in some areas of Russia: results of activity of the Influenza Etiology and Epidemiology Center of the Ivanovsky Institute of Virology].

PubMed

L'vov, D K; Burtseva, E I; Kolobukhina, L V; Feodoritova, E L; Shevchenko, E S; Ivanova, V T; Lavrishcheva, V V; Breslav, N V; Trushakova, S V; Merkulova, L N; Vartanian, R V; Kisteneva, L B; Oskerko, T A; Al'khovskiĭ, S V; Siluianova, É V; Mukasheva, E A; Krasnoslobodtsev, K G; Prilipov, A G; Beliaev, A L; Samokhvalov, E I; Shchelkanov, M Iu; Malyshev, N A

2013-01-01

The results of analysis of the peculiarities of the epidemic 2011-2012 development in the areas of 10 cities of Russia obtained by basic laboratories of IEES on the base of D.I. Ivanovsky Research Institute of Virology, Ministry of Public Health and Social Development of Russia, are presented. The increasing ARD morbidity caused by the influenza viruses was detected rather late--in February-March 2012. The highest indices of the morbidity were detected during weeks 10-13 followed by decreasing to threshold levels by week 27. Children 0-2 and 3-6 years old were involved the most, meantime the high rate of hospitalization was found for 15-64 years old aged group (25%). Influenza A(H3N2) and B viruses were the cause of the epidemic. The results of studies of the antigenic and genetic properties of the influenza strains showed most of them to be close relatives to the vaccine strains. Some heterogeneity of circulating strains and their drift variants were found as well. All tested strains were sensitive to arbidol, oseltamivir and zanamivir, and saved resistance to rimantadine. The ratio of ARD viruses was comparable with the last epidemic seasons.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liolios, Konstantinos; Abt, Birte; Scheuner, Carmen

Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacte- rium that is motile via periplasmic flagella. The type strain of the species, Z-7692T, was iso- lated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second 'true' member of the genus Spirochaeta with a genome-sequenced type strainmore » to be pub- lished. The 3,285,855 bp long genome of strain Z-7692T with its 2,817 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

The synthesis, antimalarial activity and CoMFA analysis of novel aminoalkylated quercetin analogs.

PubMed

Helgren, Travis R; Sciotti, Richard J; Lee, Patricia; Duffy, Sandra; Avery, Vicky M; Igbinoba, Osayawemwen; Akoto, Matthew; Hagen, Timothy J

2015-01-15

A series of novel aminoalkylated quercetin analogs, prepared via the Mannich reaction of various primary and secondary amines with formaldehyde, were tested for antimalarial activity. The compounds were screened against three drug resistant malarial strains (D6, C235 and W2) and were found to exhibit sub-micromolar activity across all three strains (0.065-13.0μM). The structure-activity relationship determined from the antimalarial activity data suggests the inclusion of phenethyl amine sidechains on the quercetin scaffolding is necessary for potent activity. Additionally, the most active compounds ((5) and (6)) were tested for both early and late stage anti-gametocytocidal activity. Finally, the antimalarial activity data were utilized to construct comparative molecular field analysis (CoMFA) models to be used for further compound refinement. Copyright © 2014 Elqsevier Ltd. All rights reserved.

Investigating Extreme Lifestyles through Mangrove Transcriptomics

ERIC Educational Resources Information Center

Dassanayake, Maheshi

2009-01-01

Mangroves represent phylogenetically diverse taxa in tropical coastal terrestrial habitats. They are extremophiles, evolutionarily adapted to tolerate flooding, anoxia, high temperatures, wind, and high and extremely variable salt conditions in typically resource-poor environments. The genetic basis for these adaptations is, however, virtually…

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2014 CFR

2014-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2014 CFR

2014-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2011 CFR

2011-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2013 CFR

2013-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2012 CFR

2012-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2011 CFR

2011-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2013 CFR

2013-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2012 CFR

2012-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2010 CFR

2010-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2010 CFR

2010-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

Lactation Biology Symposium: Lactocrine signaling and developmental programming

USDA-ARS?s Scientific Manuscript database

Lactocrine signaling is defined as transmission of bioactive factors from mother to offspring as a consequence of nursing. Lactocrine transmission of signaling molecules may be an evolutionarily conserved process through which bioactive factors necessary for support of neonatal development are deliv...

Phylogenetic conservatism in plant phenology

USGS Publications Warehouse

Davies, T. Jonathan; Wolkovich, Elizabeth M.; Kraft, Nathan J. B.; Salamin, Nicolas; Allen, Jenica M.; Ault, Toby R.; Betancourt, Julio L.; Bolmgren, Kjell; Cleland, Elsa E.; Cook, Benjamin I.; Crimmins, Theresa M.; Mazer, Susan J.; McCabe, Gregory J.; Pau, Stephanie; Regetz, Jim; Schwartz, Mark D.; Travers, Steven E.

2013-01-01

Synthesis. Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conser ved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species’ shared evolutionary histories.

Drug Development and Conversion of Biodiversity in West and Central Africa

DTIC Science & Technology

2002-05-01

and Tri-trichomonas foetus ). An additional 68 extracts were received from WRAIR in late February and are now entering preliminary screening. For the...two strains of T. vaginalis and 22 were tested vs. T foetus . For trypanosome studies, 21 of the WRAIR extracts and 4 of 8 of the AP#2 extracts had IC50...while 2 of 22 tested vs. T foetus had similarly high activity. Extracts active vs. trypanosomes were tested in a mouse model infection of T brucei at a

On the Correlation Between the Self-Organized Island Pattern and Substrate Elastic Anisotropy

DTIC Science & Technology

2007-04-01

eters would be most useful to experimentalists. The kinetic Monte Carlo KMC has been proposed re- cently to study QD island self-organization by many...time ti. 21,25 Based on a proposed coupled KMC , the authors simu- lated the island ordering and narrow size distribution in two dimensions and further...100, 013527 2006pattern has not been studied so far within the coupled KMC algorithm where the long-range strain energy field is in- cluded

Pili in Microspheres Protect Rabbits From Diarrhoea Induced by E. Coli Strain RDEC-1

DTIC Science & Technology

1993-01-01

tested whether pilus proteins of rabbit diarrhoeagenic Escherichia coi (RDEC- F,~ incorporated into biodegradable microspheres. could function as safe...McQueen t",’E.C. Boedekert’, R. Reidt’, D. Jarboet, M. Wolfr, M. Le+ /1 1 and W.R. Brown+ We tested whether pilus proteins of rabbit diarrhoeagenic...that has early and late phases’. posed of biodegradable, biocompatible lactide/glycolide The AF/RI pilus adhesin is a well described virulence polymers

Detection of a chikungunya outbreak in Central Italy, August to September 2017.

PubMed

Venturi, Giulietta; Di Luca, Marco; Fortuna, Claudia; Remoli, Maria Elena; Riccardo, Flavia; Severini, Francesco; Toma, Luciano; Del Manso, Martina; Benedetti, Eleonora; Caporali, Maria Grazia; Amendola, Antonello; Fiorentini, Cristiano; De Liberato, Claudio; Giammattei, Roberto; Romi, Roberto; Pezzotti, Patrizio; Rezza, Giovanni; Rizzo, Caterina

2017-09-01

An autochthonous chikungunya outbreak is ongoing near Anzio, a coastal town in the province of Rome. The virus isolated from one patient and mosquitoes lacks the A226V mutation and belongs to an East Central South African strain. As of 20 September, 86 cases are laboratory-confirmed. The outbreak proximity to the capital, its late summer occurrence, and diagnostic delays, are favouring transmission. Vector control, enhanced surveillance and restricted blood donations are being implemented in affected areas.

Lung Irradiation Increases Mortality After Influenza A Virus Challenge Occurring Late After Exposure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manning, Casey M.; Johnston, Carl J.; Department of Pediatrics, University of Rochester Medical Center, Rochester, New York

2013-05-01

Purpose: To address whether irradiation-induced changes in the lung environment alter responses to a viral challenge delivered late after exposure but before the appearance of late lung radiation injury. Methods and Materials: C57BL/6J mice received either lung alone or combined lung and whole-body irradiation (0-15 Gy). At 10 weeks after irradiation, animals were infected with 120 HAU influenza virus strain A/HKx31. Innate and adaptive immune cell recruitment was determined using flow cytometry. Cytokine and chemokine production and protein leakage into the lung after infection were assessed. Results: Prior irradiation led to a dose-dependent failure to regain body weight after infectionmore » and exacerbated mortality, but it did not affect virus-specific immune responses or virus clearance. Surviving irradiated animals displayed a persistent increase in total protein in bronchoalveolar lavage fluid and edema. Conclusions: Lung irradiation increased susceptibility to death after infection with influenza virus and impaired the ability to complete recovery. This altered response does not seem to be due to a radiation effect on the immune response, but it may possibly be an effect on epithelial repair.« less

Vertical-axis rotations and deformation along the active strike-slip El Tigre Fault (Precordillera of San Juan, Argentina) assessed through palaeomagnetism and anisotropy of magnetic susceptibility

NASA Astrophysics Data System (ADS)

Fazzito, Sabrina Y.; Rapalini, Augusto E.; Cortés, José M.; Terrizzano, Carla M.

2017-03-01

Palaeomagnetic data from poorly consolidated to non-consolidated late Cenozoic sediments along the central segment of the active El Tigre Fault (Central-Western Precordillera of the San Juan Province, Argentina) demonstrate broad cumulative deformation up to 450 m from the fault trace and reveal clockwise and anticlockwise vertical-axis rotations of variable magnitude. This deformation has affected in different amounts Miocene to late Pleistocene samples and indicates a complex kinematic pattern. Several inherited linear structures in the shear zone that are oblique to the El Tigre Fault may have acted as block boundary faults. Displacement along these faults may have resulted in a complex pattern of rotations. The maximum magnitude of rotation is a function of the age of the sediments sampled, with largest values corresponding to middle Miocene-lower Pliocene deposits and minimum values obtained from late Pleistocene deposits. The kinematic study is complemented by low-field anisotropy of magnetic susceptibility data to show that the local strain regime suggests a N-S stretching direction, subparallel to the strike of the main fault.

Associations between work-related stress in late midlife, educational attainment, and serious health problems in old age: a longitudinal study with over 20 years of follow-up.

PubMed

Nilsen, Charlotta; Andel, Ross; Fors, Stefan; Meinow, Bettina; Darin Mattsson, Alexander; Kåreholt, Ingemar

2014-08-27

People spend a considerable amount of time at work over the course of their lives, which makes the workplace important to health and aging. However, little is known about the potential long-term effects of work-related stress on late-life health. This study aims to examine work-related stress in late midlife and educational attainment in relation to serious health problems in old age. Data from nationally representative Swedish surveys were used in the analyses (n = 1,502). Follow-up time was 20-24 years. Logistic regressions were used to examine work-related stress (self-reported job demands, job control, and job strain) in relation to serious health problems measured as none, serious problems in one health domain, and serious problems in two or three health domains (complex health problems). While not all results were statistically significant, high job demands were associated with higher odds of serious health problems among women but lower odds of serious health problems among men. Job control was negatively associated with serious health problems. The strongest association in this study was between high job strain and complex health problems. After adjustment for educational attainment some of the associations became statistically nonsignificant. However, high job demands, remained related to lower odds of serious problems in one health domain among men, and low job control remained associated with higher odds of complex health problems among men. High job demands were associated with lower odds of complex health problems among men with low education, but not among men with high education, or among women regardless of level of education. The results underscore the importance of work-related stress for long-term health. Modification to work environment to reduce work stress (e.g., providing opportunities for self-direction/monitoring levels of psychological job demands) may serve as a springboard for the development of preventive strategies to improve public health both before and after retirement.

Late quaternary out-of-sequence deformation in the innermost Kangra Reentrant, NW Himalaya of India: Seismic potential appraisal from 10Be dated fluvial terraces

NASA Astrophysics Data System (ADS)

Cortés-Aranda, J.; Vassallo, R.; Jomard, H.; Pousse-Beltrán, L.; Astudillo, L.; Mugnier, J.-L.; Jouanne, F.; Malik, M.; Carcaillet, J.

2018-06-01

The Kangra Reentrant is a convex-to-the-northeast U-shaped structure in the NW Himalaya, where the Sub-Himalayan fold-and-thrust belt is ∼90 km wide. This region has not been struck by large earthquakes since the 1905 Mw 7.8 Kangra Earthquake. Out-of-sequence deformation has been reported at the millennial timescale along intracrustal thrusts within this reentrant, such as the Jawalamukhi Thrust. Up to now, the occurrence of out-of-sequence deformation along inner thrusts within the Kangra Reentrant, during the Late Quaternary, has not yet been addressed. In this study, the results of a neotectonic survey undertaken in this reentrant are presented; the studied zone is located between the Beas and the Neogad rivers, and encompasses from the Jawalamukhi Thrust to the Main Boundary Thrust. Two terraces that are deformed by branches of the Medlicott-Wadia Thrust, locally named the Palampur Thrust, are identified; this is evidenced in the field by metric-scale fault scarps. By using 10Be dating, the ages of these terraces were constrained to ca. 7.5 and ca. 6.2 ka. This is clear evidence of the Late Quaternary out-of-sequence deformation in the innermost part of this reentrant, implying that strain is distributed along all the arc-orthogonal extent of the local fold and thrust belt over this timespan. A cumulative slip rate of ca. 1 mm/yr along the studied thrusts, which represents 10% of the bulk-strain accommodated by the whole reentrant for this timespan, is calculated. In spite of the marginal appearance of this figure, this deformation rate is attributed to 7 < Mw < 8 earthquakes triggered along the brittle/ductile zone of Main Himalayan Thrust and emerging at the surface along crustal ramps, such as those represented by the Palampur Thrust in the study area. Earthquakes of this magnitude may severely impact the Kangra District, which currently hosts 1.5 million people.

Quantifying strain partitioning between magmatic and amagmatic portions of the Afar triple junction of Ethiopia and Djibouti through use of contemporary and late Quaternary extension rates

NASA Astrophysics Data System (ADS)

Polun, S. G.; Hickcox, K.; Tesfaye, S.; Gomez, F. G.

2016-12-01

The central Afar rift in Ethiopia and Djibouti is a zone of accommodation between the onshore propagations of the Gulf of Aden and Red Sea oceanic spreading centers forming part of the Afar triple junction that divides the Arabia, Nubia, and Somalia plates. While extension in the onshore magmatic propagators is accommodated through magmatism and associated faulting, extension in the central Afar is accommodated solely by large and small faults. The contributions of these major faults to the overall strain budget can be well characterized, but smaller faults are more difficult to quantify. Sparse GPS data covering the region constrain the total extension budget across the diffuse triple junction zone. Late Quaternary slip rates for major faults in Hanle, Dobe, Guma, and Immino grabens were estimated using the quantitative analysis of faulted landforms. This forms a nearly complete transect from the onshore propagation of the Red Sea rift in Tendaho graben and the onshore propagation of the Gulf of Aden rift at Manda Inakir. Field surveying was accomplished using a combination of electronic distance measurer profiling and low altitude aerial surveying. Age constraints are provided from the Holocene lacustrine history or through terrestrial cosmogenic nuclide (TCN) dating of the faulted geomorphic surface. Along this transect, late Quaternary slip rates of major faults appear to accommodate 25% of the total horizontal stretching rate between the southern margin of Tendaho graben and the Red Sea coast, as determined from published GPS velocities. This constrains the proportion of total extension between Nubia and Arabia that is accommodated through major faulting in the central Afar, compared to the magmatism and associated faulting of the magmatic propagators elsewhere in the triple junction. Along the transect, individual fault slip rates decrease from the southeast to the northwest, suggesting a `Crank-Arm' model may be more applicable to explain the regional kinematics and the evolution of the triple junction.

Temporal deformation pattern in acute and late phases of ST-elevation myocardial infarction: incremental value of longitudinal post-systolic strain to assess myocardial viability.

PubMed

Huttin, Olivier; Marie, Pierre-Yves; Benichou, Maxime; Bozec, Erwan; Lemoine, Simon; Mandry, Damien; Juillière, Yves; Sadoul, Nicolas; Micard, Emilien; Duarte, Kevin; Beaumont, Marine; Rossignol, Patrick; Girerd, Nicolas; Selton-Suty, Christine

2016-10-01

Identification of transmural extent and degree of non-viability after ST-segment elevation myocardial infarction (STEMI) is clinically important. The objective of the present study was to assess the regional mechanics and temporal deformation patterns using speckle tracking echocardiography (STE) in acute and later phases of STEMI to predict myocardial damage in these patients. Ninety-eight patients with first STEMI underwent both echocardiography and cardiac magnetic resonance imaging in acute phase and at 6 months follow-up with 2D STE-derived measurements of peak longitudinal strain (PLS), Pre-STretch index (PST) and post-systolic deformation index (PSI). For each segment, late gadolinium enhancement (LGE) was defined as transmural (LGE >66 %) or non-transmural (<66 %). Global deformation values were significantly correlated with LVEFCMR and infarct size at both visits. A significantly lower value of segmental PLS and higher PSI and PST in necrotic segments were observed comparatively to control, adjacent and remote segments. The best parameters to predict transmural extent in acute phase were PSI with a cutoff value of 8 % (AUC: 0.84) and PLS with a cutoff value of -13 % (AUC: 0.86). PST showed high specificity, but poor sensitivity in predicting transmural extent. More importantly, the addition of PSI and PST to PLS in acute phase was associated with improved prediction of viability at 6 months (integrated discrimination improvement 2.5 % p < 0.01; net reclassification improvement 27 %; p < 0.01). All systolic deformation values separated transmural from non-transmural scarring. PLS combined with additional information relative to post-systolic deformation appears to be the most informative parameters to predict the transmural extent of MI in the early and late phases of MI. http://clinicaltrials.gov/show/NCT01109225 ; NCT01109225.

2,4,6-Trinitrotoluene Reduction by an Fe-Only Hydrogenase in Clostridium acetobutylicum

PubMed Central

Watrous, Mary M.; Clark, Sandra; Kutty, Razia; Huang, Shouqin; Rudolph, Frederick B.; Hughes, Joseph B.; Bennett, George N.

2003-01-01

The role of hydrogenase on the reduction of 2,4,6-trinitrotoluene (TNT) in Clostridium acetobutylicum was evaluated. An Fe-only hydrogenase was isolated and identified by using TNT reduction activity as the selection basis. The formation of hydroxylamino intermediates by the purified enzyme corresponded to expected products for this reaction, and saturation kinetics were determined with a Km of 152 μM. Comparisons between the wild type and a mutant strain lacking the region encoding an alternative Fe-Ni hydrogenase determined that Fe-Ni hydrogenase activity did not significantly contribute to TNT reduction. Hydrogenase expression levels were altered in various strains, allowing study of the role of the enzyme in TNT reduction rates. The level of hydrogenase activity in a cell system correlated (R2 = 0.89) with the organism's ability to reduce TNT. A strain that overexpressed the hydrogenase activity resulted in maintained TNT reduction during late growth phases, which it is not typically observed in wild type strains. Strains exhibiting underexpression of hydrogenase produced slower TNT rates of reduction correlating with the determined level of expression. The isolated Fe-only hydrogenase is the primary catalyst for reducing TNT nitro substituents to the corresponding hydroxylamines in C. acetobutylicum in whole-cell systems. A mechanism for the reaction is proposed. Due to the prevalence of hydrogenase in soil microbes, this research may enhance the understanding of nitroaromatic compound transformation by common microbial communities. PMID:12620841

Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic

PubMed Central

Garza, Daniel Rios; Thompson, Cristiane C.; Loureiro, Edvaldo Carlos Brito; Dutilh, Bas E.; Inada, Davi Toshio; Junior, Edivaldo Costa Sousa; Cardoso, Jedson Ferreira; Nunes, Márcio Roberto T.; de Lima, Clayton Pereira Silva; Silvestre, Rodrigo Vellasco Duarte; Nunes, Keley Nascimento Barbosa; Santos, Elisabeth C. O.; Edwards, Robert A.; Vicente, Ana Carolina P.; de Sá Morais, Lena Lillian Canto

2012-01-01

The 7th cholera pandemic reached Latin America in 1991, spreading from Peru to virtually all Latin American countries. During the late epidemic period, a strain that failed to ferment sucrose dominated cholera outbreaks in the Northern Brazilian Amazon region. In order to understand the genomic characteristics and the determinants of this altered sucrose fermenting phenotype, the genome of the strain IEC224 was sequenced. This paper reports a broad genomic study of this strain, showing its correlation with the major epidemic lineage. The potentially mobile genomic regions are shown to possess GC content deviation, and harbor the main V. cholera virulence genes. A novel bioinformatic approach was applied in order to identify the putative functions of hypothetical proteins, and was compared with the automatic annotation by RAST. The genome of a large bacteriophage was found to be integrated to the IEC224's alanine aminopeptidase gene. The presence of this phage is shown to be a common characteristic of the El Tor strains from the Latin American epidemic, as well as its putative ancestor from Angola. The defective sucrose fermenting phenotype is shown to be due to a single nucleotide insertion in the V. cholerae sucrose-specific transportation gene. This frame-shift mutation truncated a membrane protein, altering its structural pore-like conformation. Further, the identification of a common bacteriophage reinforces both the monophyletic and African-Origin hypotheses for the main causative agent of the 1991 Latin America cholera epidemics. PMID:22662140

The nature of species interactions shifts profoundly between time periods

USDA-ARS?s Scientific Manuscript database

Species interactions change through time, for example ontogenetically, successionally, and evolutionarily. They also change as environmental conditions change, both within years (seasonally) and between years (year effects). The former are relatively well-studied, but the latter have received less a...

Evolutionarily Engineered Ethanologenic Yeast Detoxifies Lignocellulosic Biomass Conversion Inhibitors by Reprogrammed Pathways

USDA-ARS?s Scientific Manuscript database

Lignocellulosic biomass conversion inhibitors furfural and HMF inhibit microbial growth and interfere with subsequent fermentation of ethanol, posing significant challenges for a sustainable cellulosic ethanol conversion industry. Numerous yeast genes were found to be associated with the inhibitor ...

Species delimitation: A case study in a problematic ant taxon

USDA-ARS?s Scientific Manuscript database

Species delimitation has been invigorated as a discipline in systematics by an influx of new character sets, analytical methods, and conceptual advances. We use genetic data from 68 markers, combined with distributional, bioclimatic, and coloration information, to distinguish evolutionarily indepe...

Cyanobacteria, Toxins and Indicators: Field Monitoring, Treatment Facility Monitoring and Treatment Studies

EPA Science Inventory

Cyanobacteria, formerly known as blue green algae, are an evolutionarily ancient and ubiquitous class of micro-organisms. Under a combination of conditions that include nutrient availability, warm temperatures, stagnant water and high solar irradiance, these organisms have the p...

Rare but evolutionarily consequential outcrossing in a highly inbred zoonotic parasite

USDA-ARS?s Scientific Manuscript database

Recurrent self-mating can result in nearly clonal propagation of biological lineages, but even occasional outcrossing can serve to redistribute variation in future generations, providing cohesion among regional populations. The zoonotic parasite Trichinella spiralis has been suspected to undergo fr...

Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica.

PubMed

Fukuda, Wakao; Kimura, Tomomi; Araki, Shigeo; Miyoshi, Yuki; Atomi, Haruyuki; Imanaka, Tadayuki

2013-09-01

A Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium (strain 107-E2(T)) was isolated from freshwater samples containing microbial mats collected at a lake in Skarvsnes, Antarctica (temporary lake name, Lake Tanago Ike). Strain 107-E2(T) grew between 5 and 25 °C, with an optimum of 23 °C. Moreover, colony formation was observed on agar media even at -5 °C. The pH range for growth was between 6.0 and 9.0, with an optimum of pH 7.0-8.0. The range of NaCl concentration for growth was between 0.0 and 0.5% (w/v), with an optimum of 0.0%. No growth was observed in media containing organic compounds at high concentrations, which indicated that strain 107-E2(T) was an oligotroph. In the late stationary phase, strain 107-E2(T) produced a dark brown water-soluble pigment. Esterase, amylase and protease production was observed. Antimicrobial-lytic activities for Gram-negative bacteria and yeast were observed. Ubiquinone-8 was the major respiratory quinone. The major fatty acids were iso-C15:0, iso-C(17:1)ω9c and iso-C(15:1) at 5. The G+C content of genomic DNA was 66.1 mol%. Analysis of the 16S rRNA gene sequences revealed that strain 107-E2(T) belonged to the genus Lysobacter, and low DNA-DNA relatedness values with closely related species distinguished strain 107-E2(T) from recognized species of the genus Lysobacter. The phylogenetic situation and physiological characteristics indicated that strain 107-E2(T) should be classified as a representative of a novel species of the genus Lysobacter, for which the name Lysobacter oligotrophicus sp. nov. is proposed. The type strain is 107-E2(T) ( =JCM 18257(T) =ATCC BAA-2438(T)).

Pyrite deformation and connections to gold mobility: insight from micro-structural analysis and trace element mapping

NASA Astrophysics Data System (ADS)

Dubosq, Renelle; Rogowitz, Anna; Lawley, Christopher; Schneider, David; Jackson, Simon

2017-04-01

Pyrite is an important and ubiquitous gold-bearing phase in many orogenic gold deposits making the study of its deformation behaviour under metamorphic conditions crucial to the understanding of gold (re)mobilization. However, pyrite deformation mechanisms and their influence on the retention or release of trace elements during deformation and metamorphism remain poorly understood. We propose a syn- to post-peak metamorphic and deformation driven gold upgrading model where gold is remobilized through deformation-induced diffusion pathways in the form of substructures in pyrite. The middle amphibolite facies assemblage (actinolite-biotite-plagioclase-almandine) of the Detour Lake deposit (Canada) makes it an ideal study area due to maximum temperatures reaching 550°C, exceeding the conditions for plastic deformation in pyrite (450°C). The world-class Detour Lake deposit, containing 16.4 Moz of Au at 1 g/t, is a Neoarchean orogenic gold ore body located in the northern Abitibi district within the Superior Province. The mine is situated along the high strain, sub-vertical ductile-brittle Sunday Lake Deformation Zone (SLDZ) parallel to the broadly E-W trending Abitibi greenstone belt. Herein we combine orientation contrast (OC) forescatter imaging, electron backscatter diffraction (EBSD) and 2D laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) trace element pyrite mapping to evaluate the influence of pyrite brittle and plastic deformation on the release of trace elements during syn-metamorphic gold remobilization. Local misorientation patterns in pyrite exhibit parallel bands that can be described by continuous rotation around one of the <100> axes, whereas higher strain areas reveal more heterogeneous misorientation patterns and the development of low-angle grain boundaries with late fractures indicative of dislocation creep and strain hardening. These late fractures are an important micro-structural setting for gold and clusters of precious-metal mineral inclusions (telluride minerals). Minor recrystallization processes can also be observed along phase boundaries between pyrite and more competent amphibole crystals. LA-ICP-MS trace element maps document primary, syn-metamorphic oscillatory zoning of some chalcophile and siderophile elements during crystallization of pyrite porphyroblasts. These primary pyrite features are cut by late metal-rich fractures suggesting that remobilization of gold occurred with trace element enrichment of other chalcophile and siderophile elements (Cu, Pb, Zn, Ag, Bi, Te), which post-dates the main period of syn-metamorphic pyrite crystallization at the margins of pre- to syn-deformation, high-grade gold veins. Pyrite grain boundaries and subgrains are also base and precious metal rich, suggesting that late gold remobilization also occurred during pyrite recrystallization. Additional trace element mapping will help determine to what extent pyrite plastic deformation facilitates the diffusion of gold and other trace elements during gold precipitation and remobilization, which, in turn, will inform the source to sink pathways of ore deposition.

Elastic, not plastic species: frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms.

PubMed

Flegr, Jaroslav

2010-01-13

Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years. The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct. Frozen plasticity theory, which includes the Darwinian model of evolution as a special case--the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories. This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell).

Prophylaxis of acute respiratory infections via improving the immune system in late preterm newborns with E. coli strain Nissle 1917: a controlled pilot trial.

PubMed

Aryayev, Mykola L; Senkivska, Liudmyla I; Bredeleva, Nataliya K; Talashova, Irina V

2018-01-01

Acute respiratory infections (ARIs), caused by the high level of immaturity of the immune system, are a major cause of morbidity in preterm newborns. The probiotic Escherichia coli strain Nissle 1917 (EcN) is well known for its immuno-modulatory properties and may therefore enhance the immune competence. Thus, EcN administration may provide a promising possibility to decrease the risk of ARIs in this vulnerable group of children. However, clinical data supporting or refuting this hypothesis are, to our knowledge, not available. Therefore, the aim of the presented pilot trial was to collect first data on the efficacy and safety of EcN treatment to prevent ARIs in late preterm newborns. Right after birth, 62 late preterm newborns were included into an open-labeled, controlled 4-week trial with two parallel groups and a follow-up phase until the age of 1 year. All children of the treatment group received an EcN suspension orally for 3 weeks, whereas the control group was only observed. Primary efficacy variable was the number of participants with at least one ARI during the first 28 days of life. Secondary efficacy variables were the number of ARIs and the number and duration of hospitalizations caused by ARIs during the first year of life. The number of participants with at least one ARI during the first 28 days of life was significantly lower in the group treated with EcN compared to that in the control group. Although only of exploratory nature, analyses of secondary efficacy variables suggest that EcN treatment may also reduce the average number of ARIs, the average number of hospitalizations caused by ARIs, and the mean duration of such hospitalizations. There is also some evidence that early EcN treatment may have long-term benefits on newborns' health status. The present pilot trial provides first evidence that EcN is able to reduce the incidence of ARIs in the neonatal period of late preterm newborns. Additionally, EcN is characterized by an excellent individual biocompatibility in the absence of adverse drug reactions. Limitations of the current trial are discussed and recommendations for future confirmatory studies are made. ClinicalTrials.gov identifier: NCT01540162; retrospectively registered on 16 February 2012.

Deformation of the Roberts Mountains Allochthon in north-central Nevada

USGS Publications Warehouse

Evans, James George; Theodore, Ted G.

1978-01-01

During the Antler orogeny in Late Devonian and Early Mississippian time, early and middle Paleozoic siliceous rocks, largely chert and sha1e, were thrust eastward for 90 to 160 km over coexisting carbonate rocks. Minor and major structures of two small areas of the allochthon at Battle Mountain and in the southern Tuscarora Mountains were studied in order to characterize the deformation and test the consistency of the movement plan with respect to the large eastward displacement. In the Battle Mountain area, the lower Paleozoic Scott Canyon and Valmy Formations were deformed in the Antler orogeny but were unaffected by later tectonism during late Paleozoic or early Mesozoic. In the southern Tuscarora Mountains area, the Ordovician and Silurian siliceous rocks deformed in the Antler Orogeny were deformed by later, possibly Mesozoic, folding and thrusting. Most of the minor folding visible in the allochthon is in the cheret, but proportionally more of the strain was taken up in the shale and argillite, both poorly exposed but predominant rock types. Most minor folds, concentric in form, plunge at small angles to the north-northeast and south-southwest with steeply dipping or vertical axial planes. The b-fabric axis, parallel to these folds, is identical apparently to the B-kinematic axis. The horizontal component of tectonic shortening of the allochthon, N. 70?-75? W. both in the Battle Mountain area and in the southern Tuscarora Mountains area, is therefore consistent with an eastward direction of movement of the allochthon. Folds with west- northwest trends locally present in the allochthon, may have formed in the direction of tectonic transport. In the southern Tuscarora Mountains, local strain in and below the allochthon was different from the prevailing strain in the allochthon, and tectonic shortening was locally at large angles to the accepted direction of movement of the allochthon.

Typhoid fever in young children in Bangladesh: clinical findings, antibiotic susceptibility pattern and immune responses.

PubMed

Khanam, Farhana; Sayeed, Md Abu; Choudhury, Feroza Kaneez; Sheikh, Alaullah; Ahmed, Dilruba; Goswami, Doli; Hossain, Md Lokman; Brooks, Abdullah; Calderwood, Stephen B; Charles, Richelle C; Cravioto, Alejandro; Ryan, Edward T; Qadri, Firdausi

2015-04-01

Children bear a large burden of typhoid fever caused by Salmonella enterica serotype Typhi (S. Typhi) in endemic areas. However, immune responses and clinical findings in children are not well defined. Here, we describe clinical and immunological characteristics of young children with S. Typhi bacteremia, and antimicrobial susceptibility patterns of isolated strains. As a marker of recent infection, we have previously characterized antibody-in-lymphocyte secretion (TPTest) during acute typhoid fever in adults. We similarly assessed membrane preparation (MP) IgA responses in young children at clinical presentation, and then 7-10 days and 21-28 days later. We also assessed plasma IgA, IgG and IgM responses and T cell proliferation responses to MP at these time points. We compared responses in young children (1-5 years) with those seen in older children (6-17 years), adults (18-59 years), and age-matched healthy controls. We found that, compared to age-matched controls patients in all age cohorts had significantly more MP-IgA responses in lymphocyte secretion at clinical presentation, and the values fell in all groups by late convalescence. Similarly, plasma IgA responses in patients were elevated at presentation compared to controls, with acute and convalescent IgA and IgG responses being highest in adults. T cell proliferative responses increased in all age cohorts by late convalescence. Clinical characteristics were similar in all age cohorts, although younger children were more likely to present with loss of appetite, less likely to complain of headache compared to older cohorts, and adults were more likely to have ingested antibiotics. Multi-drug resistant strains were present in approximately 15% of each age cohort, and 97% strains had resistance to nalidixic acid. This study demonstrates that S. Typhi bacteremia is associated with comparable clinical courses, immunologic responses in various age cohorts, including in young children, and that TPTest can be used as marker of recent typhoid fever, even in young children.

Machine-Learning Algorithms to Automate Morphological and Functional Assessments in 2D Echocardiography.

PubMed

Narula, Sukrit; Shameer, Khader; Salem Omar, Alaa Mabrouk; Dudley, Joel T; Sengupta, Partho P

2016-11-29

Machine-learning models may aid cardiac phenotypic recognition by using features of cardiac tissue deformation. This study investigated the diagnostic value of a machine-learning framework that incorporates speckle-tracking echocardiographic data for automated discrimination of hypertrophic cardiomyopathy (HCM) from physiological hypertrophy seen in athletes (ATH). Expert-annotated speckle-tracking echocardiographic datasets obtained from 77 ATH and 62 HCM patients were used for developing an automated system. An ensemble machine-learning model with 3 different machine-learning algorithms (support vector machines, random forests, and artificial neural networks) was developed and a majority voting method was used for conclusive predictions with further K-fold cross-validation. Feature selection using an information gain (IG) algorithm revealed that volume was the best predictor for differentiating between HCM ands. ATH (IG = 0.24) followed by mid-left ventricular segmental (IG = 0.134) and average longitudinal strain (IG = 0.131). The ensemble machine-learning model showed increased sensitivity and specificity compared with early-to-late diastolic transmitral velocity ratio (p < 0.01), average early diastolic tissue velocity (e') (p < 0.01), and strain (p = 0.04). Because ATH were younger, adjusted analysis was undertaken in younger HCM patients and compared with ATH with left ventricular wall thickness >13 mm. In this subgroup analysis, the automated model continued to show equal sensitivity, but increased specificity relative to early-to-late diastolic transmitral velocity ratio, e', and strain. Our results suggested that machine-learning algorithms can assist in the discrimination of physiological versus pathological patterns of hypertrophic remodeling. This effort represents a step toward the development of a real-time, machine-learning-based system for automated interpretation of echocardiographic images, which may help novice readers with limited experience. Copyright © 2016 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Chicken bile Matrix metalloproteinase; its characterization and significance

USDA-ARS?s Scientific Manuscript database

Previous studies from our lab had shown that the avian bile was rich in matrix metalloproteinase (MMP), enzymes implicated in the degradation of extracellular matrices (ECM) such as collagens and proteoglycans. We hypothesized that bile MMP may be evolutionarily associated with the digestion of ECM ...

Haplogroups as Evolutionary Markers of Cognitive Ability

ERIC Educational Resources Information Center

Rindermann, Heiner; Woodley, Michael A.; Stratford, James

2012-01-01

Studies investigating evolutionary theories on the origins of national differences in intelligence have been criticized on the basis that both national cognitive ability measures and supposedly evolutionarily informative proxies (such as latitude and climate) are confounded with general developmental status. In this study 14 Y chromosomal…

77 FR 476 - Endangered and Threatened Species; Recovery Plan Southern Oregon/Northern California Coast Coho...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-05

... and Threatened Species; Recovery Plan Southern Oregon/ Northern California Coast Coho Salmon... Oregon/Northern California Coast (SONCC) Coho Salmon (Oncorhynchus kisutch) Evolutionarily Significant... 95521, Attn: Recovery Coordinator/SONCC Coho Salmon Public Draft Recovery Plan Comments. Hand delivered...

An evolutionarily young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway.

PubMed

Malinovsky, Frederikke Gro; Thomsen, Marie-Louise F; Nintemann, Sebastian J; Jagd, Lea Møller; Bourgine, Baptiste; Burow, Meike; Kliebenstein, Daniel J

2017-12-12

To optimize fitness a plant should monitor its metabolism to appropriately control growth and defense. Primary metabolism can be measured by the universally conserved TOR (Target of Rapamycin) pathway to balance growth and development with the available energy and nutrients. Recent work suggests that plants may measure defense metabolites to potentially provide a strategy ensuring fast reallocation of resources to coordinate plant growth and defense. There is little understanding of mechanisms enabling defense metabolite signaling. To identify mechanisms of defense metabolite signaling, we used glucosinolates, an important class of plant defense metabolites. We report novel signaling properties specific to one distinct glucosinolate, 3-hydroxypropylglucosinolate across plants and fungi. This defense metabolite, or derived compounds, reversibly inhibits root growth and development. 3-hydroxypropylglucosinolate signaling functions via genes in the ancient TOR pathway. If this event is not unique, this raises the possibility that other evolutionarily new plant metabolites may link to ancient signaling pathways.

Myosin1D is an evolutionarily conserved regulator of animal left-right asymmetry.

PubMed

Juan, Thomas; Géminard, Charles; Coutelis, Jean-Baptiste; Cerezo, Delphine; Polès, Sophie; Noselli, Stéphane; Fürthauer, Maximilian

2018-05-16

The establishment of left-right (LR) asymmetry is fundamental to animal development, but the identification of a unifying mechanism establishing laterality across different phyla has remained elusive. A cilia-driven, directional fluid flow is important for symmetry breaking in numerous vertebrates, including zebrafish. Alternatively, LR asymmetry can be established independently of cilia, notably through the intrinsic chirality of the acto-myosin cytoskeleton. Here, we show that Myosin1D (Myo1D), a previously identified regulator of Drosophila LR asymmetry, is essential for the formation and function of the zebrafish LR organizer (LRO), Kupffer's vesicle (KV). Myo1D controls the orientation of LRO cilia and interacts functionally with the planar cell polarity (PCP) pathway component VanGogh-like2 (Vangl2), to shape a productive LRO flow. Our findings identify Myo1D as an evolutionarily conserved regulator of animal LR asymmetry, and show that functional interactions between Myo1D and PCP are central to the establishment of animal LR asymmetry.

An evolutionarily young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway

PubMed Central

Malinovsky, Frederikke Gro; Thomsen, Marie-Louise F; Nintemann, Sebastian J; Jagd, Lea Møller; Bourgine, Baptiste; Burow, Meike

2017-01-01

To optimize fitness a plant should monitor its metabolism to appropriately control growth and defense. Primary metabolism can be measured by the universally conserved TOR (Target of Rapamycin) pathway to balance growth and development with the available energy and nutrients. Recent work suggests that plants may measure defense metabolites to potentially provide a strategy ensuring fast reallocation of resources to coordinate plant growth and defense. There is little understanding of mechanisms enabling defense metabolite signaling. To identify mechanisms of defense metabolite signaling, we used glucosinolates, an important class of plant defense metabolites. We report novel signaling properties specific to one distinct glucosinolate, 3-hydroxypropylglucosinolate across plants and fungi. This defense metabolite, or derived compounds, reversibly inhibits root growth and development. 3-hydroxypropylglucosinolate signaling functions via genes in the ancient TOR pathway. If this event is not unique, this raises the possibility that other evolutionarily new plant metabolites may link to ancient signaling pathways. PMID:29231169

Modality and morphology: what we write may not be what we say.

PubMed

Rapp, Brenda; Fischer-Baum, Simon; Miozzo, Michele

2015-06-01

Written language is an evolutionarily recent human invention; consequently, its neural substrates cannot be determined by the genetic code. How, then, does the brain incorporate skills of this type? One possibility is that written language is dependent on evolutionarily older skills, such as spoken language; another is that dedicated substrates develop with expertise. If written language does depend on spoken language, then acquired deficits of spoken and written language should necessarily co-occur. Alternatively, if at least some substrates are dedicated to written language, such deficits may doubly dissociate. We report on 5 individuals with aphasia, documenting a double dissociation in which the production of affixes (e.g., the -ing in jumping) is disrupted in writing but not speaking or vice versa. The findings reveal that written- and spoken-language systems are considerably independent from the standpoint of morpho-orthographic operations. Understanding this independence of the orthographic system in adults has implications for the education and rehabilitation of people with written-language deficits. © The Author(s) 2015.

Cellular microbiology and molecular ecology of Legionella-amoeba interaction.

PubMed

Richards, Ashley M; Von Dwingelo, Juanita E; Price, Christopher T; Abu Kwaik, Yousef

2013-05-15

Legionella pneumophila is an aquatic organism that interacts with amoebae and ciliated protozoa as the natural hosts, and this interaction plays a central role in bacterial ecology and infectivity. Upon transmission to humans, L. pneumophila infect and replicate within alveolar macrophages causing pneumonia. Intracellular proliferation of L. pneumophila within the two evolutionarily distant hosts is facilitated by bacterial exploitation of evolutionarily conserved host processes that are targeted by bacterial protein effectors injected into the host cell by the Dot/Icm type VIB translocation system. Although cysteine is semi-essential for humans and essential for amoeba, it is a metabolically favorable source of carbon and energy generation by L. pneumophila. To counteract host limitation of cysteine, L. pneumophila utilizes the AnkB Dot/Icm-translocated F-box effector to promote host proteasomal degradation of polyubiquitinated proteins within amoebae and human cells. Evidence indicates ankB and other Dot/Icm-translocated effector genes have been acquired through inter-kingdom horizontal gene transfer.

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

DOE PAGES

Hawkes, Emily J.; Hennelly, Scott P.; Novikova, Irina V.; ...

2016-09-20

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. Here, we investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probingmore » and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.« less

Quantifying male attractiveness.

PubMed Central

McNamara, John M; Houston, Alasdair I; Marques Dos Santos, Miguel; Kokko, Hanna; Brooks, Rob

2003-01-01

Genetic models of sexual selection are concerned with a dynamic process in which female preference and male trait values coevolve. We present a rigorous method for characterizing evolutionary endpoints of this process in phenotypic terms. In our phenotypic characterization the mate-choice strategy of female population members determines how attractive females should find each male, and a population is evolutionarily stable if population members are actually behaving in this way. This provides a justification of phenotypic explanations of sexual selection and the insights into sexual selection that they provide. Furthermore, the phenotypic approach also has enormous advantages over a genetic approach when computing evolutionarily stable mate-choice strategies, especially when strategies are allowed to be complex time-dependent preference rules. For simplicity and clarity our analysis deals with haploid mate-choice genetics and a male trait that is inherited phenotypically, for example by vertical cultural transmission. The method is, however, easily extendible to other cases. An example illustrates that the sexy son phenomenon can occur when there is phenotypic inheritance of the male trait. PMID:14561306

Rational Design of Evolutionarily Stable Microbial Kill Switches.

PubMed

Stirling, Finn; Bitzan, Lisa; O'Keefe, Samuel; Redfield, Elizabeth; Oliver, John W K; Way, Jeffrey; Silver, Pamela A

2017-11-16

The evolutionary stability of synthetic genetic circuits is key to both the understanding and application of genetic control elements. One useful but challenging situation is a switch between life and death depending on environment. Here are presented "essentializer" and "cryodeath" circuits, which act as kill switches in Escherichia coli. The essentializer element induces cell death upon the loss of a bi-stable cI/Cro memory switch. Cryodeath makes use of a cold-inducible promoter to express a toxin. We employ rational design and a toxin/antitoxin titering approach to produce and screen a small library of potential constructs, in order to select for constructs that are evolutionarily stable. Both kill switches were shown to maintain functionality in vitro for at least 140 generations. Additionally, cryodeath was shown to control the growth environment of a population, with an escape frequency of less than 1 in 10 5 after 10 days of growth in the mammalian gut. Copyright © 2017 Elsevier Inc. All rights reserved.

In silico discovery of terpenoid metabolism in Cannabis sativa.

PubMed

Massimino, Luca

2017-01-01

Due to their efficacy, cannabis based therapies are currently being prescribed for the treatment of many different medical conditions. Interestingly, treatments based on the use of cannabis flowers or their derivatives have been shown to be very effective, while therapies based on drugs containing THC alone lack therapeutic value and lead to increased side effects, likely resulting from the absence of other pivotal entourage compounds found in the Phyto-complex. Among these compounds are terpenoids, which are not produced exclusively by cannabis plants, so other plant species must share many of the enzymes involved in their metabolism. In the present work, 23,630 transcripts from the canSat3 reference transcriptome were scanned for evolutionarily conserved protein domains and annotated in accordance with their predicted molecular functions. A total of 215 evolutionarily conserved genes encoding enzymes presumably involved in terpenoid metabolism are described, together with their expression profiles in different cannabis plant tissues at different developmental stages. The resource presented here will aid future investigations on terpenoid metabolism in Cannabis sativa .

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hawkes, Emily J.; Hennelly, Scott P.; Novikova, Irina V.

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. Here, we investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probingmore » and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.« less

Evolutionarily Conserved, Multitasking TRP Channels: Lessons from Worms and Flies

PubMed Central

Venkatachalam, Kartik; Luo, Junjie; Montell, Craig

2015-01-01

The Transient Receptor Potential (TRP) channel family is comprised of a large group of cation-permeable channels, which display an extraordinary diversity of roles in sensory signaling. TRPs allow animals to detect chemicals, mechanical force, light, and changes in temperature. Consequently, these channels control a plethora of animal behaviors. Moreover, their functions are not limited to the classical senses, as they are cellular sensors, which are critical for ionic homeostasis and metabolism. Two genetically tractable invertebrate model organisms, Caenorhabditis elegans and Drosophila melanogaster, have led the way in revealing a wide array of sensory roles and behaviors that depend on TRP channels. Two overriding themes have emerged from these studies. First, TRPs are multitasking proteins, and second, many functions and modes of activation of these channels are evolutionarily conserved, including some that were formerly thought to be unique to invertebrates, such as phototransduction. Thus, worms and flies offer the potential to decipher roles for mammalian TRPs, which would otherwise not be suspected. PMID:24961975

Cellular microbiology and molecular ecology of Legionella–amoeba interaction

PubMed Central

Richards, Ashley M.; Von Dwingelo, Juanita E.; Price, Christopher T.; Abu Kwaik, Yousef

2013-01-01

Legionella pneumophila is an aquatic organism that interacts with amoebae and ciliated protozoa as the natural hosts, and this interaction plays a central role in bacterial ecology and infectivity. Upon transmission to humans, L. pneumophila infect and replicate within alveolar macrophages causing pneumonia. Intracellular proliferation of L. pneumophila within the two evolutionarily distant hosts is facilitated by bacterial exploitation of evolutionarily conserved host processes that are targeted by bacterial protein effectors injected into the host cell by the Dot/Icm type VIB translocation system. Although cysteine is semi-essential for humans and essential for amoeba, it is a metabolically favorable source of carbon and energy generation by L. pneumophila. To counteract host limitation of cysteine, L. pneumophila utilizes the AnkB Dot/Icm-translocated F-box effector to promote host proteasomal degradation of polyubiquitinated proteins within amoebae and human cells. Evidence indicates ankB and other Dot/Icm-translocated effector genes have been acquired through inter-kingdom horizontal gene transfer. PMID:23535283

The HMMER Web Server for Protein Sequence Similarity Search.

PubMed

Prakash, Ananth; Jeffryes, Matt; Bateman, Alex; Finn, Robert D

2017-12-08

Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis. The HMMER Web server provides a common platform by linking the HMMER algorithms to databases, thereby enabling the search for homologs, as well as providing sequence and functional annotation by linking external databases. This unit describes three basic protocols and two alternate protocols that explain how to use the HMMER Web server using various input formats and user defined parameters. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

The Story of a Yakima Fold and How It Informs Late Neogene and Quaternary Backarc Deformation in the Cascadia Subduction Zone, Manastash Anticline, Washington, USA

NASA Astrophysics Data System (ADS)

Kelsey, Harvey M.; Ladinsky, Tyler C.; Staisch, Lydia; Sherrod, Brian L.; Blakely, Richard J.; Pratt, Thomas L.; Stephenson, William J.; Odum, Jack K.; Wan, Elmira

2017-10-01

The Yakima folds of central Washington, USA, are prominent anticlines that are the primary tectonic features of the backarc of the northern Cascadia subduction zone. What accounts for their topographic expression and how much strain do they accommodate and over what time period? We investigate Manastash anticline, a north vergent fault propagation fold typical of structures in the fold province. From retrodeformation of line- and area-balanced cross sections, the crust has horizontally shortened by 11% (0.8-0.9 km). The fold, and by inference all other folds in the fold province, formed no earlier than 15.6 Ma as they developed on a landscape that was reset to negligible relief following voluminous outpouring of Grande Ronde Basalt. Deformation is accommodated on two fault sets including west-northwest striking frontal thrust faults and shorter north to northeast striking faults. The frontal thrust fault system is active with late Quaternary scarps at the base of the range front. The fault-cored Manastash anticline terminates to the east at the Naneum anticline and fault; activity on the north trending Naneum structures predates emplacement of the Grande Ronde Basalt. The west trending Yakima folds and west striking thrust faults, the shorter north to northeast striking faults, and the Naneum fault together constitute the tectonic structures that accommodate deformation in the low strain rate environment in the backarc of the Cascadia Subduction Zone.

Refined Modeling of Flexural Deformation of Layered Plates with a Regular Structure Made from Nonlinear Hereditary Materials

NASA Astrophysics Data System (ADS)

Yankovskii, A. P.

2018-01-01

On the basis of constitutive equations of the Rabotnov nonlinear hereditary theory of creep, the problem on the rheonomic flexural behavior of layered plates with a regular structure is formu-lated. Equations allowing one to describe, with different degrees of accuracy, the stress-strain state of such plates with account of their weakened resistance to transverse shear were ob-tained. From them, the relations of the nonclassical Reissner- and Reddytype theories can be found. For axially loaded annular plates clamped at one edge and loaded quasistatically on the other edge, a simplified version of the refined theory, whose complexity is comparable to that of the Reissner and Reddy theories, is developed. The flexural strains of such metal-composite annular plates in shortterm and long-term loadings at different levels of heat action are calcu-lated. It is shown that, for plates with a relative thickness of order of 1/10, neither the classical theory, nor the traditional nonclassical Reissner and Reddy theories guarantee reliable results for deflections even with the rough 10% accuracy. The accuracy of these theories decreases at elevated temperatures and with time under long-term loadings of structures. On the basic of relations of the refined theory, it is revealed that, in bending of layered metal-composite heat-sensitive plates under elevated temperatures, marked edge effects arise in the neighborhood of the supported edge, which characterize the shear of these structures in the transverse direction

The story of a Yakima fold and how it informs Late Neogene and Quaternary backarc deformation in the Cascadia subduction zone, Manastash anticline, Washington, USA

USGS Publications Warehouse

Kelsey, Harvey M.; Ladinsky, Tyler C.; Staisch, Lydia; Sherrod, Brian; Blakely, Richard J.; Pratt, Thomas; Stephenson, William; Odum, Jackson K.; Wan, Elmira

2017-01-01

The Yakima folds of central Washington, USA, are prominent anticlines that are the primary tectonic features of the backarc of the northern Cascadia subduction zone. What accounts for their topographic expression and how much strain do they accommodate and over what time period? We investigate Manastash anticline, a north vergent fault propagation fold typical of structures in the fold province. From retrodeformation of line- and area-balanced cross sections, the crust has horizontally shortened by 11% (0.8–0.9 km). The fold, and by inference all other folds in the fold province, formed no earlier than 15.6 Ma as they developed on a landscape that was reset to negligible relief following voluminous outpouring of Grande Ronde Basalt. Deformation is accommodated on two fault sets including west-northwest striking frontal thrust faults and shorter north to northeast striking faults. The frontal thrust fault system is active with late Quaternary scarps at the base of the range front. The fault-cored Manastash anticline terminates to the east at the Naneum anticline and fault; activity on the north trending Naneum structures predates emplacement of the Grande Ronde Basalt. The west trending Yakima folds and west striking thrust faults, the shorter north to northeast striking faults, and the Naneum fault together constitute the tectonic structures that accommodate deformation in the low strain rate environment in the backarc of the Cascadia Subduction Zone.

Structural and Biophysical Characterization of Bacillus thuringiensis Insecticidal Proteins Cry34Ab1 and Cry35Ab1

PubMed Central

Kelker, Matthew S.; Berry, Colin; Evans, Steven L.; Pai, Reetal; McCaskill, David G.; Wang, Nick X.; Russell, Joshua C.; Baker, Matthew D.; Yang, Cheng; Pflugrath, J. W.; Wade, Matthew; Wess, Tim J.; Narva, Kenneth E.

2014-01-01

Bacillus thuringiensis strains are well known for the production of insecticidal proteins upon sporulation and these proteins are deposited in parasporal crystalline inclusions. The majority of these insect-specific toxins exhibit three domains in the mature toxin sequence. However, other Cry toxins are structurally and evolutionarily unrelated to this three-domain family and little is known of their three dimensional structures, limiting our understanding of their mechanisms of action and our ability to engineer the proteins to enhance their function. Among the non-three domain Cry toxins, the Cry34Ab1 and Cry35Ab1 proteins from B. thuringiensis strain PS149B1 are required to act together to produce toxicity to the western corn rootworm (WCR) Diabrotica virgifera virgifera Le Conte via a pore forming mechanism of action. Cry34Ab1 is a protein of ∼14 kDa with features of the aegerolysin family (Pfam06355) of proteins that have known membrane disrupting activity, while Cry35Ab1 is a ∼44 kDa member of the toxin_10 family (Pfam05431) that includes other insecticidal proteins such as the binary toxin BinA/BinB. The Cry34Ab1/Cry35Ab1 proteins represent an important seed trait technology having been developed as insect resistance traits in commercialized corn hybrids for control of WCR. The structures of Cry34Ab1 and Cry35Ab1 have been elucidated to 2.15 Å and 1.80 Å resolution, respectively. The solution structures of the toxins were further studied by small angle X-ray scattering and native electrospray ion mobility mass spectrometry. We present here the first published structure from the aegerolysin protein domain family and the structural comparisons of Cry34Ab1 and Cry35Ab1 with other pore forming toxins. PMID:25390338

Vaccination potential of B and T epitope-enriched NP and M2 against Influenza A viruses from different clades and hosts

PubMed Central

Esmagambetov, Ilias; Bagaev, Alexander; Pichugin, Alexey; Lysenko, Andrey; Shcherbinin, Dmitry; Sedova, Elena; Logunov, Denis; Shmarov, Maxim; Ataullakhanov, Ravshan; Naroditsky, Boris; Gintsburg, Alexander

2018-01-01

To avoid outbreaks of influenza virus epidemics and pandemics among human populations, modern medicine requires the development of new universal vaccines that are able to provide protection from a wide range of influenza A virus strains. In the course of development of a universal vaccine, it is necessary to consider that immunity must be generated even against viruses from different hosts because new human epidemic virus strains have their origins in viruses of birds and other animals. We have enriched conserved viral proteins–nucleoprotein (NP) and matrix protein 2 (M2)—by B and T-cell epitopes not only human origin but also swine and avian origin. For this purpose, we analyzed M2 and NP sequences with respect to changes in the sequences of known T and B-cell epitopes and chose conserved and evolutionarily significant epitopes. Eventually, we found consensus sequences of M2 and NP that have the maximum quantity of epitopes that are 100% coincident with them. Consensus epitope-enriched amino acid sequences of M2 and NP proteins were included in a recombinant adenoviral vector. Immunization with Ad5-tet-M2NP induced strong CD8 and CD4 T cells responses, specific to each of the encoded antigens, i.e. M2 and NP. Eight months after immunization with Ad5-tet-M2NP, high numbers of M2- and NP-responding “effector memory” CD44posCD62neg T cells were found in the mouse spleens, which revealed a long-term T cell immune memory conferred by the immunization. In all, the challenge experiments showed an extraordinarily wide-ranging efficacy of protection by the Ad5-tet-M2NP vaccine, covering 5 different heterosubtypes of influenza A virus (2 human, 2 avian and 1 swine). PMID:29377916

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns.

PubMed

Zhou, Hao; Yan, Bing; Chen, Shun; Wang, Mingshu; Jia, Renyong; Cheng, Anchun

2015-10-01

Tembusu virus (TMUV) is a single-stranded, positive-sense RNA virus. As reported, TMUV infection has resulted in significant poultry losses, and the virus may also pose a threat to public health. To characterize TMUV evolutionarily and to understand the factors accounting for codon usage properties, we performed, for the first time, a comprehensive analysis of codon usage bias for the genomes of 60 TMUV strains. The most recently published TMUV strains were found to be widely distributed in coastal cities of southeastern China. Codon preference among TMUV genomes exhibits a low bias (effective number of codons (ENC)=53.287) and is maintained at a stable level. ENC-GC3 plots and the high correlation between composition constraints and principal component factor analysis of codon usage demonstrated that mutation pressure dominates over natural selection pressure in shaping the TMUV coding sequence composition. The high correlation between the major components of the codon usage pattern and hydrophobicity (Gravy) or aromaticity (Aromo) was obvious, indicating that properties of viral proteins also account for the observed variation in TMUV codon usage. Principal component analysis (PCA) showed that CQW1 isolated from Chongqing may have evolved from GX2013H or GX2013G isolated from Guangxi, thus indicating that TMUV likely disseminated from southeastern China to the mainland. Moreover, the preferred codons encoding eight amino acids were consistent with the optimal codons for human cells, indicating that TMUV may pose a threat to public health due to possible cross-species transmission (birds to birds or birds to humans). The results of this study not only have theoretical value for uncovering the characteristics of synonymous codon usage patterns in TMUV genomes but also have significant meaning with regard to the molecular evolutionary tendencies of TMUV. Copyright © 2015 Elsevier B.V. All rights reserved.

Siderophore production and the evolution of investment in a public good: An adaptive dynamics approach to kin selection.

PubMed

Lee, William; van Baalen, Minus; Jansen, Vincent A A

2016-01-07

Like many other bacteria, Pseudomonas aeruginosa sequesters iron from the environment through the secretion, and subsequent uptake, of iron-binding molecules. As these molecules can be taken up by other bacteria in the population than those who secreted them, this is a form of cooperation through a public good. Traditionally, this problem has been studied by comparing the relative fitnesses of siderophore-producing and non-producing strains, but this gives no information about the fate of strains that do produce intermediate amounts of siderophores. Here, we investigate theoretically how the amount invested in this form of cooperation evolves. We use a mechanistic description of the laboratory protocols used in experimental evolution studies to describe the competition and cooperation of the bacteria. From this dynamical model we derive the fitness following the adaptive dynamics method. The results show how selection is driven by local siderophore production and local competition. Because siderophore production reduces the growth rate, local competition decreases with the degree of relatedness (which is a dynamical variable in our model). Our model is not restricted to the analysis of small phenotypic differences and allows for theoretical exploration of the effects of large phenotypic differences between cooperators and cheats. We predict that an intermediate ESS level of cooperation (molecule production) should exist. The adaptive dynamics approach allows us to assess evolutionary stability, which is often not possible in other kin-selection models. We found that selection can lead to an intermediate strategy which in our model is always evolutionarily stable, yet can allow invasion of strategies that are much more cooperative. Our model describes the evolution of a public good in the context of the ecology of the microorganism, which allows us to relate the extent of production of the public good to the details of the interactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Age, Sex, and Blood Pressure-Related Influences on Reference Values of Left Atrial Deformation and Mechanics From a Large-Scale Asian Population.

PubMed

Liao, Jo-Nan; Chao, Tze-Fan; Kuo, Jen-Yuan; Sung, Kuo-Tzu; Tsai, Jui-Peng; Lo, Chi-In; Lai, Yau-Huei; Su, Cheng-Huang; Hung, Chung-Lieh; Yeh, Hung-I; Chen, Shih-Ann

2017-10-01

Left atrial (LA) function is tightly linked to several cardiovascular diseases and confers key prognostic information. Speckle tracking-based deformation as a feasible and sensitive LA mechanical assessment has proven its clinical significance beyond volume measures; however, the reference values remain largely unknown. We studied 4042 participants undergoing annual cardiovascular survey. Among them, 2812 healthy participants (65% men; mean age, 47.4±9.9 years) were eligible for speckle tracking analysis. Peak atrial longitudinal systolic strain and strain rate (SR) at systolic (SRs), early diastolic (SRe), and late diastolic atrial contraction phases (SRa) were analyzed by dedicated software (EchoPAC, GE) and compared in terms of age, sex, and blood pressure. Overall, women demonstrated higher peak atrial longitudinal systolic strain (39.34±7.99% versus 37.95±7.96%; P<0.001) and showed age-dependent more pronounced peak atrial longitudinal systolic strain functional decay than those of men (P value for interaction, <0.05), with men showing higher SRs and SRa, although lower SRe (all P<0.001). Both increasing age and higher blood pressure were independently associated with deteriorated peak atrial longitudinal systolic strain, SRs, and SRe, although augmented LA SRa, even after accounting for baseline clinical covariates in multivariable models that incorporated LA volume, NT-proBNP (N-terminal pro-B-type natriuretic peptide), or left ventricular E/e' (all P<0.001). Our findings suggest LA mechanical functional decays in association with increasing age and higher blood pressure, which seem to be compensated for by augmentation of atrial pump function. We have also provided age- and sex-stratified reference values for strain and SR based on a large-scale Asian population. © 2017 American Heart Association, Inc.

Avian influenza A (H7N9) virus infection in humans: epidemiology, evolution, and pathogenesis.

PubMed

Husain, Matloob

2014-12-01

New human influenza A virus strains regularly emerge causing seasonal epidemics and occasional pandemics. Lately, several zoonotic avian influenza A strains have been reported to directly infect humans. In early 2013, a novel avian influenza A virus (H7N9) strain was discovered in China to cause severe respiratory disease in humans. Since then, over 450 human cases of H7N9 infection have been discovered and 165 of them have died. Multiple epidemiological, phylogenetic, in vivo, and in vitro studies have been done to determine the origin and pathogenesis of novel H7N9 strain. This article reviews the literature related to the epidemiology, evolution, and pathogenesis of the H7N9 strain since its discovery in February 2013 till August 2014. The data available so far indicate that H7N9 was originated by a two-step reassortment process in birds and transmitted to humans through direct contact with live-bird markets. H7N9 is a low-pathogenic avian virus and contains several molecular signatures for adaptation in mammals. The severity of the respiratory disease caused by novel H7N9 virus in humans can be partly attributed to the age, sex, and underlying medical conditions of the patients. A universal influenza vaccine is not available, though several strain-specific H7N9 candidate vaccine viruses have been developed. Further, novel H7N9 virus is resistant to antiviral drug amantadine and some H7N9 isolates have acquired the resistance to neuraminidase-inhibitors. Therefore, constant surveillance and prompt control measures combined with novel research approaches to develop alternative and effective anti-influenza strategies are needed to overcome influenza A virus. Copyright © 2014 Elsevier B.V. All rights reserved.

Fermentation Temperature Modulates Phosphatidylethanolamine and Phosphatidylinositol Levels in the Cell Membrane of Saccharomyces cerevisiae

PubMed Central

Henderson, Clark M.; Zeno, Wade F.; Lerno, Larry A.; Longo, Marjorie L.

2013-01-01

During alcoholic fermentation, Saccharomyces cerevisiae is exposed to a host of environmental and physiological stresses. Extremes of fermentation temperature have previously been demonstrated to induce fermentation arrest under growth conditions that would otherwise result in complete sugar utilization at “normal” temperatures and nutrient levels. Fermentations were carried out at 15°C, 25°C, and 35°C in a defined high-sugar medium using three Saccharomyces cerevisiae strains with diverse fermentation characteristics. The lipid composition of these strains was analyzed at two fermentation stages, when ethanol levels were low early in stationary phase and in late stationary phase at high ethanol concentrations. Several lipids exhibited dramatic differences in membrane concentration in a temperature-dependent manner. Principal component analysis (PCA) was used as a tool to elucidate correlations between specific lipid species and fermentation temperature for each yeast strain. Fermentations carried out at 35°C exhibited very high concentrations of several phosphatidylinositol species, whereas at 15°C these yeast strains exhibited higher levels of phosphatidylethanolamine and phosphatidylcholine species with medium-chain fatty acids. Furthermore, membrane concentrations of ergosterol were highest in the yeast strain that experienced stuck fermentations at all three temperatures. Fluorescence anisotropy measurements of yeast cell membrane fluidity during fermentation were carried out using the lipophilic fluorophore diphenylhexatriene. These measurements demonstrate that the changes in the lipid composition of these yeast strains across the range of fermentation temperatures used in this study did not significantly affect cell membrane fluidity. However, the results from this study indicate that fermenting S. cerevisiae modulates its membrane lipid composition in a temperature-dependent manner. PMID:23811519

Signatures of adaptation in the weedy rice genome.

PubMed

Li, Lin-Feng; Li, Ya-Ling; Jia, Yulin; Caicedo, Ana L; Olsen, Kenneth M

2017-05-01

Crop domestication provided the calories that fueled the rise of civilization. For many crop species, domestication was accompanied by the evolution of weedy crop relatives, which aggressively outcompete crops and reduce harvests. Understanding the genetic mechanisms that underlie the evolution of weedy crop relatives is critical for agricultural weed management and food security. Here we use whole-genome sequences to examine the origin and adaptation of the two major strains of weedy rice found in the United States. We find that de-domestication from cultivated ancestors has had a major role in their evolution, with relatively few genetic changes required for the emergence of weediness traits. Weed strains likely evolved both early and late in the history of rice cultivation and represent an under-recognized component of the domestication process. Genomic regions identified here that show evidence of selection can be considered candidates for future genetic and functional analyses for rice improvement.

Fatty acid production in genetically modified cyanobacteria

PubMed Central

Liu, Xinyao; Sheng, Jie; Curtiss III, Roy

2011-01-01

To avoid costly biomass recovery in photosynthetic microbial biofuel production, we genetically modified cyanobacteria to produce and secrete fatty acids. Starting with introducing an acyl–acyl carrier protein thioesterase gene, we made six successive generations of genetic modifications of cyanobacterium Synechocystis sp. PCC6803 wild type (SD100). The fatty acid secretion yield was increased to 197 ± 14 mg/L of culture in one improved strain at a cell density of 1.0 × 109 cells/mL by adding codon-optimized thioesterase genes and weakening polar cell wall layers. Although these strains exhibited damaged cell membranes at low cell densities, they grew more rapidly at high cell densities in late exponential and stationary phase and exhibited less cell damage than cells in wild-type cultures. Our results suggest that fatty acid secreting cyanobacteria are a promising technology for renewable biofuel production. PMID:21482809

Design of a Sample Recovery Assembly for Magnetic Ramp-Wave Loading

NASA Astrophysics Data System (ADS)

Chantrenne, S.; Wise, J. L.; Asay, J. R.; Kipp, M. E.; Hall, C. A.

2009-06-01

Characterization of material behavior under dynamic loading requires studies at strain rates ranging from quasi-static to the limiting values of shock compression. For completeness, these studies involve complementary time-resolved data, which define the mechanical constitutive properties, and microstructural data, which reveal physical mechanisms underlying the observed mechanical response. Well-preserved specimens must be recovered for microstructural investigations. Magnetically generated ramp waves produce strain rates lower than those associated with shock waves, but recovery methods have been lacking for this type of loading. We adapted existing shock recovery techniques for application to magnetic ramp loading using 2-D and 3-D ALEGRA MHD code calculations to optimize the recovery design for mitigation of undesired late-time processing of the sample due to edge effects and secondary stress waves. To assess the validity of our simulations, measurements of sample deformation were compared to wavecode predictions.

Effect of timing of tracheostomy on changes in bacterial colonisation of the lower respiratory tract in burned children.

PubMed

Lipový, B; Brychta, P; Rihová, H; Suchanek, I; Hanslianová, M; Cvanová, M; Chaloupková, Z; Gregorova, N; Hufová, I

2013-03-01

The study aims to evaluate the impact of early and late tracheostomy on microbiological changes in the airways in severely burned children. Early tracheostomy is sometimes performed within 3 days after the start of mechanical ventilation regular microbiological surveillance of the respiratory tract was done in all patients. From each sputum, tracheobronchial aspirate and bronchoalveolar lavage (BAL), a microscopic slide was made and the material was seeded in a culture medium. The standard culture media used for the growth of respiratory pathogens are blood agar, McConkey agar, VL agar and chocolate agar. The obtained values were statistically analysed. In the observed period, a total of 68 children underwent mechanical ventilation in our department. A total of 31 (45.59%) children had undergone surgical tracheostomy (18 patients with early tracheostomy and 13 patients with late tracheostomy). The most common bacterium isolated from the lower respiratory tract in patients with early and late tracheostomy was Acinetobacter baumannii (31.53% resp. 44.30% of all bacterial strains). In patients with early tracheostomy, the ratio of G+/G- during the 6-7th day of mechanical ventilation was 1.29:1 and during the 8-10th day, 1:1.43. In patients with late tracheostomy the G+/G- ratio was 1:2.25 and during the 8-10th day, 1:2.25. There was not any statistically significant deviation in the G+/G- ratio in patients with early and late tracheostomy in any of the monitored periods. The main reasons for performing early tracheostomy are: extent, localisation and depth of the burn. Difficult weaning in an uncooperative patient, failure of extubation with subsequent reintubation and other complications may be an indication for late tracheostomy. The study confirms that the use of appropriately indicated early tracheostomy provides a microbiological benefit for burned children. Copyright © 2012 Elsevier Ltd and ISBI. All rights reserved.

Myocardial strain in healthy adults across a broad age range as revealed by cardiac magnetic resonance imaging at 1.5 and 3.0T: Associations of myocardial strain with myocardial region, age, and sex.

PubMed

Mangion, Kenneth; Clerfond, Guillaume; McComb, Christie; Carrick, David; Rauhalammi, Samuli M; McClure, John; Corcoran, David S; Woodward, Rosemary; Orchard, Vanessa; Radjenovic, Aleksandra; Zhong, Xiaodong; Berry, Colin

2016-11-01

To assess myocardial strain using cine displacement encoding with stimulated echoes (DENSE) using 1.5T and 3.0T MRI in healthy adults. Healthy adults without any history of cardiovascular disease underwent magnetic resonance imaging (MRI) at 1.5T and 3.0T within 2 days. The MRI protocol included balanced steady-state free-precession (b-SSFP), 2D cine-echo planar imaging (EPI)-DENSE, and late gadolinium enhancement in subjects >45 years. Acquisitions were divided into six segments; global and segmental peak longitudinal and circumferential strain were derived and analyzed by field strength, age, and gender. In all, 89 volunteers (mean age 44.8 ± 18.0 years, range: 18-87 years) underwent MRI at 1.5T, and 88 of these subjects underwent MRI at 3.0T (1.4 ± 1.4 days between the scans). Compared with 3.0T, the magnitudes of global circumferential (-19.5 ± 2.6% vs. -18.47 ± 2.6%; P = 0.001) and longitudinal (-12.47 ± 3.2% vs. -10.53 ± 3.1%; P = 0.004) strain were greater at 1.5T. At 1.5T, longitudinal strain was greater in females than in males: -10.17 ± 3.4% vs. -13.67 ± 2.4%; P = 0.001. Similar observations occurred for circumferential strain at 1.5T (-18.72 ± 2.2% vs. -20.10 ± 2.7%; P = 0.014) and at 3.0T (-17.92 ± 1.8% vs. -19.1 ± 3.1%; P = 0.047). At 1.5T, longitudinal and circumferential strain were not associated with age after accounting for sex (longitudinal strain P = 0.178, circumferential strain P = 0.733). At 3.0T, longitudinal and circumferential strain were associated with age (P < 0.05). Longitudinal strain values were greater in the apico-septal, basal-lateral, and mid-lateral segments and circumferential strain in the inferior, infero-lateral, and antero-lateral LV segments. Myocardial strain parameters as revealed by cine-DENSE at different MRI field strengths were associated with myocardial region, age, and sex. J. Magn. Reson. Imaging 2016;44:1197-1205. © 2016 The Authors Journal of Magnetic Resonance Imaging published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.