Pereira Gonçalo AG
Full Text Available Abstract Background For three decades the Mutator system was thought to be exclusive of plants, until the first homolog representatives were characterized in fungi and in early-diverging amoebas earlier in this decade. Results Here, we describe and characterize four families of Mutator-like elements in a new eukaryotic group, the Parabasalids. These Trichomonas vaginalis Mutator- like elements, or TvMULEs, are active in T. vaginalis and patchily distributed among 12 trichomonad species and isolates. Despite their relatively distinctive amino acid composition, the inclusion of the repeats TvMULE1, TvMULE2, TvMULE3 and TvMULE4 into the Mutator superfamily is justified by sequence, structural and phylogenetic analyses. In addition, we identified three new TvMULE-related sequences in the genome sequence of Candida albicans. While TvMULE1 is a member of the MuDR clade, predominantly from plants, the other three TvMULEs, together with the C. albicans elements, represent a new and quite distinct Mutator lineage, which we named TvCaMULEs. The finding of TvMULE1 sequence inserted into other putative repeat suggests the occurrence a novel TE family not yet described. Conclusion These findings expand the taxonomic distribution and the range of functional motif of MULEs among eukaryotes. The characterization of the dynamics of TvMULEs and other transposons in this organism is of particular interest because it is atypical for an asexual species to have such an extreme level of TE activity; this genetic landscape makes an interesting case study for causes and consequences of such activity. Finally, the extreme repetitiveness of the T. vaginalis genome and the remarkable degree of sequence identity within its repeat families highlights this species as an ideal system to characterize new transposable elements.
Involvement of multiple cell lineages in atherogenesis. ... PROMOTING ACCESS TO AFRICAN RESEARCH ... smooth muscle cells, fibroblasts, stem cells, pericytes, mast cells, dendritic cells, macrophages and immigrant cells usually found in ...
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our technique is statistically consistent under standard stochastic assumptions, that is, it returns the correct tree given sufficiently many unlinked loci. We also show that it can tolerate moderate estimation errors.
Bausch, D G; Nichol, S T; Muyembe-Tamfum, J J
A total of 154 cases (48 laboratory-confirmed and 106 suspected) were identified (case fatality rate, 83 percent); 52 percent of cases were in young male miners. Only 27 percent of these men reported having had contact with other affected persons, whereas 67 percent of patients who were not miners...... reported such contact (Pmultiple introductions of infection into the population was substantiated by the detection of at least nine...... genetically distinct lineages of virus in circulation during the outbreak. Conclusions Marburg hemorrhagic fever can have a very high case fatality rate. Since multiple genetic variants of virus were identified, ongoing introduction of virus into the population helped perpetuate this outbreak. The findings...
Bausch, D G; Nichol, S T; Muyembe-Tamfum, J J
chains of human-to-human transmission continued to occur until September 2000. Suspected cases were identified on the basis of a case definition; cases were confirmed by the detection of virus antigen and nucleic acid in blood, cell culture, antibody responses, and immunohistochemical analysis. Results...... genetically distinct lineages of virus in circulation during the outbreak. Conclusions Marburg hemorrhagic fever can have a very high case fatality rate. Since multiple genetic variants of virus were identified, ongoing introduction of virus into the population helped perpetuate this outbreak. The findings...
Salerno, Patricia E; Ron, Santiago R; Señaris, J Celsa; Rojas-Runjaic, Fernando J M; Noonan, Brice P; Cannatella, David C
The flattop mountains (tepuis) of South America are ancient remnants of the Precambrian Guiana Shield plateau. The tepui summits, isolated by their surrounding cliffs that can be up to 1000 m tall, are thought of as "islands in the sky," harboring relict flora and fauna that underwent vicariant speciation due to plateau fragmentation. High endemicity atop tepui summits support the idea of an ancient "Lost World" biota. However, recent work suggests that dispersal between lowlands and summits has occurred long after tepui formation indicating that tepui summits may not be as isolated from the lowlands as researchers have long suggested. Neither view of the origin of the tepui biota (i.e., ancient vicariance vs. recent dispersal) has strong empirical support owing to a lack of studies. We test diversification hypotheses of the Guiana Shield highlands by estimating divergence times of an endemic group of treefrogs, Tepuihyla. We find that diversification of this group does not support an ancient origin for this taxon; instead, divergence times among the highland species are 2-5 Ma. Our data indicate that most highland speciation occurred during the Pliocene. Thus, this unparalleled landscape known as "The Lost World" is inhabited, in part, not by Early Tertiary relicts but neoendemics.
Mahelka, Václav; Krak, Karol; Kopecký, David; Fehrer, Judith; Šafář, Jan; Bartoš, Jan; Hobza, Roman; Blavet, Nicolas; Blattner, Frank R.
The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral. PMID:28137844
Larribère, Lionel; Utikal, Jochen
NF1 is a tumour suppressor gene, germline mutations of which lead to neurofibromatosis type 1 syndrome. Patients develop benign tumours from several types of cells including neural crest-derived cells. NF1 somatic mutations also occur in 15% of sporadic melanoma, a cancer originating from melanocytes. Evidence now suggests the involvement of NF1 mutations in melanoma resistance to targeted therapies. Although NF1 is ubiquitously expressed, genetic links between NF1 and genes involved in melanocyte biology have been described, implying the lineage-specific mechanisms. In this review, we summarize and discuss the latest advances related to the roles of NF1 in melanocyte biology and in cutaneous melanoma.
O'Halloran Damien M
Full Text Available Abstract Background Guanylyl cyclases (GCs are responsible for the production of the secondary messenger cyclic guanosine monophosphate, which plays important roles in a variety of physiological responses such as vision, olfaction, muscle contraction, homeostatic regulation, cardiovascular and nervous function. There are two types of GCs in animals, soluble (sGCs which are found ubiquitously in cell cytoplasm, and receptor (rGC forms which span cell membranes. The complete genomes of several vertebrate and invertebrate species are now available. These data provide a platform to investigate the evolution of GCs across a diverse range of animal phyla. Results In this analysis we located GC genes from a broad spectrum of vertebrate and invertebrate animals and reconstructed molecular phylogenies for both sGC and rGC proteins. The most notable features of the resulting phylogenies are the number of lineage specific rGC and sGC expansions that have occurred during metazoan evolution. Among these expansions is a large nematode specific rGC clade comprising 21 genes in C. elegans alone; a vertebrate specific expansion in the natriuretic receptors GC-A and GC-B; a vertebrate specific expansion in the guanylyl GC-C receptors, an echinoderm specific expansion in the sperm rGC genes and a nematode specific sGC clade. Our phylogenetic reconstruction also shows the existence of a basal group of nitric oxide (NO insensitive insect and nematode sGCs which are regulated by O2. This suggests that the primordial eukaryotes probably utilized sGC as an O2 sensor, with the ligand specificity of sGC later switching to NO which provides a very effective local cell-to-cell signalling system. Phylogenetic analysis of the sGC and bacterial heme nitric oxide/oxygen binding protein domain supports the hypothesis that this domain originated from a cyanobacterial source. Conclusion The most salient feature of our phylogenies is the number of lineage specific expansions
Thornhill, Daniel J; Struck, Torsten H; Ebbe, Brigitte; Lee, Raymond W; Mendoza, Guillermo F; Levin, Lisa A; Halanych, Kenneth M
Metazoan inhabitants of extreme environments typically evolved from forms found in less extreme habitats. Understanding the prevalence with which animals move into and ultimately thrive in extreme environments is critical to elucidating how complex life adapts to extreme conditions. Methane seep sediments along the Oregon and California margins have low oxygen and very high hydrogen sulfide levels, rendering them inhospitable to many life forms. Nonetheless, several closely related lineages of dorvilleid annelids, including members of Ophryotrocha, Parougia, and Exallopus, thrive at these sites in association with bacterial mats and vesicomyid clam beds. These organisms are ideal for examining adaptive radiations in extreme environments. Did dorvilleid annelids invade these extreme environments once and then diversify? Alternatively, did multiple independent lineages adapt to seep conditions? To address these questions, we examined the evolutionary history of methane-seep dorvilleids using 16S and Cyt b genes in an ecological context. Our results indicate that dorvilleids invaded these extreme habitats at least four times, implying preadaptation to life at seeps. Additionally, we recovered considerably more dorvilleid diversity than is currently recognized. A total of 3 major clades (designated "Ophryotrocha," "Mixed Genera" and "Parougia") and 12 terminal lineages or species were encountered. Two of these lineages represented a known species, Parougia oregonensis, whereas the remaining 10 lineages were newly discovered species. Certain lineages exhibited affinity to geography, habitat, sediment depth, and/or diet, suggesting that dorvilleids at methane seeps radiated via specialization and resource partitioning.
Lazar, C S; Baker, B J; Seitz, K W; Teske, A P
Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H2, whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.
Hilty, Markus; Wüthrich, Daniel; Salter, Susannah J; Engel, Hansjürg; Campbell, Samuel; Sá-Leão, Raquel; de Lencastre, Hermínia; Hermans, Peter; Sadowy, Ewa; Turner, Paul; Chewapreecha, Claire; Diggle, Mathew; Pluschke, Gerd; McGee, Lesley; Köseoğlu Eser, Özgen; Low, Donald E; Smith-Vaughan, Heidi; Endimiani, Andrea; Küffer, Marianne; Dupasquier, Mélanie; Beaudoing, Emmanuel; Weber, Johann; Bruggmann, Rémy; Hanage, William P; Parkhill, Julian; Hathaway, Lucy J; Mühlemann, Kathrin; Bentley, Stephen D
The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve sporadically, if they have high antibiotic nonsusceptiblity rates and a unique, specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates sourced from 17 different locations around the world was performed. Results revealed a deep-branching classic lineage that is distinct from multiple sporadic lineages. The sporadic lineages clustered with a previously sequenced, global collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic lineage is comprised mainly of the frequently identified multilocus sequences types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates had high nonsusceptiblity rates to β-lactams and other antimicrobials. Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp. Performing adherence assays to human epithelial cells for selected classic and sporadic non-Ec-Sp revealed that the presence of a integrative conjugative element (ICE) results in increased adherence to human epithelial cells (P = 0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates from the classic lineage have evolved separately. They have spread globally, are well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due to continued use of PCV, non-Ec-Sp may become more prevalent.
Mahdian, Somayeh; Sadeghifard, Nourkhoda; Pakzad, Iraj; Ghanbari, Fatemeh; Soroush, Setareh; Azimi, Lila; Rastegar-Lari, Abdolaziz; Giannouli, Maria; Taherikalani, Morovat
The aim of this study was to analyze antimicrobial resistance patterns and their encoding genes and genotypic diversity of Acinetobacter baumannii isolated from burn patients in Tehran, Iran. The presence of extended-spectrum beta-lactamase- and blaOXA-encoding genes among 37 multidrug resistant (MDR) A. baumannii strains isolated from patients hospitalized in a teaching hospital in Tehran was evaluated. Susceptibility to 7 antibiotics was tested by disk agar diffusion and to polymyxin B and colistin was tested by E-test, according to CLSI guidelines. All isolates were then analyzed by PCR for the presence of blaIMP, blaVIM, blaSIMblaOXA-23, blaOXA-24, and blaOXA-58-like carbapenemase genes, and blaOXA-51-like, blaTEM, blaSHV, blaPER, blaVEB, and blaGIM genes. Genotyping of A. baumannii strains was performed by repetitive sequence-based (REP)-PCR and cluster analysis of REP-PCR profiles. A. baumannii isolates were assigned to international clones by multiplex PCR sequence group analysis. Twenty-five A. baumannii isolates were classified as MDR, and 12 were classified as extensively drug resistant. All isolates were susceptible to colistin and polymyxin B. Eighty-one percent of the isolates was resistant to imipenem or meropenem and harbored at least one or both of the blaOXA-23-like or blaOXA-24-like carbapenemase genes. Co-existence of different resistance genes was found among carbapenem-resistant isolates. Multiplex PCR sequence group analysis most commonly assigned A. baumannii isolates to international clones I (18/37; 48.6%) and II (18/37; 48.6%). An alarming increase in resistance to carbapenems and the spread of blaOXA-23-like and/or blaOXA-24-like carbapenemase genes was observed among A. baumannii strains belonging to clonal lineages I and II, isolated from burn patients in Tehran. Copyright © 2015 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.
Crigler, Lauren; Kazhanie, Amita; Yoon, Tae-Jin; Zakhari, Julia; Anders, Joanna; Taylor, Barbara; Virador, Victoria M
The skin contains two known subpopulations of stem cells/epidermal progenitors: a basal keratinocyte population found in the interfollicular epithelium and cells residing in the bulge region of the hair follicle. The major role of the interfollicular basal keratinocyte population may be epidermal renewal, whereas the bulge population may only be activated and recruited to form a cutaneous epithelium in case of trauma. Using 3-dimensional cultures of murine skin under stress conditions in which only reserve epithelial cells would be expected to survive and expand, we demonstrate that a mesenchymal population resident in neonatal murine dermis has the unique potential to develop an epidermis in vitro. In monolayer culture, this dermal subpopulation has long-term survival capabilities in restricted serum and an inducible capacity to evolve into multiple cell lineages, both epithelial and mesenchymal, depending on culture conditions. When grafted subcutaneously, this dermal subpopulation gave rise to fusiform structures, reminiscent of disorganized muscle, that stained positive for smooth muscle actin and desmin; on typical epidermal grafts, abundant melanocytes appeared throughout the dermis that were not associated with hair follicles. The multipotential cells can be repeatedly isolated from neonatal murine dermis by a sequence of differential centrifugation and selective culture conditions. These results suggest that progenitors capable of epidermal differentiation exist in the mesenchymal compartment of an abundant tissue source and may have a function in mesenchymal-epithelial transition upon insult. Moreover, these cells could be available in sufficient quantities for lineage determination or tissue engineering applications.
Kim, K S; Tsuda, Y
The ecology and geographical distribution of disease vectors are major determinants of spatial and temporal variations in the transmission dynamics of vector-borne pathogens. However, there are limited studies on the ecology of vectors that contribute to the natural transmission of most vector-borne pathogens. Avian Plasmodium parasites are multihost mosquito-borne pathogens transmitted by multiple mosquito species, which might regulate the diversity and persistence of these parasites. From 2007 to 2010, we conducted entomological surveys at Sakata wetland in central Japan, to investigate temporal variation in mosquito occurrence and prevalence of avian Plasmodium lineages in the mosquito populations. A polymerase chain reaction (PCR)-based method was used to detect Plasmodium parasites and identify the blood sources of mosquitoes. Culex inatomii and C. pipiens pallens represented 60.0% and 34.8% of 11 mosquito species collected, respectively. Our results showed that the two dominant mosquito species most likely serve as principal vectors of avian Plasmodium parasites during June, which coincides with the breeding season of bird species nesting in the wetland reed beds. Fourteen animal species were identified as blood sources of mosquitoes, with the oriental reed warbler (Acrocephalus orientalis) being the commonest blood source. Although there was significant temporal variation in the occurrence of mosquitoes and prevalence of Plasmodium lineages in the mosquitoes, the dominant Plasmodium lineages shared by the two dominant mosquito species were consistently found at the same time during transmission seasons. Because vector competence cannot be confirmed solely by PCR approaches, experimental demonstration is required to provide definitive evidence of transmission suggested in this study.
Kastelein, R.A.; Hoek, L.; Gransier, R.; Jong, C.A.F. de
Pile driving is presently the most common method used to attach wind turbines to the sea bed. To assess the impact of pile driving sounds on harbor porpoises, it is important to know at what distance these sounds can be detected. Using a psychophysical technique, a male porpoise’s hearing thresholds
Levin, I I; Zwiers, P; Deem, S L; Geest, E A; Higashiguchi, J M; Iezhova, T A; Jiménez-Uzcátegui, G; Kim, D H; Morton, J P; Perlut, N G; Renfrew, R B; Sari, E H R; Valkiunas, G; Parker, P G
Haemosporidian parasites in the genus Plasmodium were recently detected through molecular screening in the Galapagos Penguin (Spheniscus mendiculus). We summarized results of an archipelago-wide screen of 3726 endemic birds representing 22 species for Plasmodium spp. through a combination of molecular and microscopy techniques. Three additional Plasmodium lineages were present in Galapagos. Lineage A-infected penguins, Yellow Warblers (Setophaga petechia aureola), and one Medium Ground Finch (Geospiza fortis) and was detected at multiple sites in multiple years [corrected]. The other 3 lineages were each detected at one site and at one time; apparently, they were transient infections of parasites not established on the archipelago. No gametocytes were found in blood smears of infected individuals; thus, endemic Galapagos birds may be dead-end hosts for these Plasmodium lineages. Determining when and how parasites and pathogens arrive in Galapagos is key to developing conservation strategies to prevent and mitigate the effects of introduced diseases. To assess the potential for Plasmodium parasites to arrive via migratory birds, we analyzed blood samples from 438 North American breeding Bobolinks (Dolichonyx oryzivorus), the only songbird that regularly migrates through Galapagos. Two of the ephemeral Plasmodium lineages (B and C) found in Galapagos birds matched parasite sequences from Bobolinks. Although this is not confirmation that Bobolinks are responsible for introducing these lineages, evidence points to higher potential arrival rates of avian pathogens than previously thought. Linajes Múltiples de Parásitos de Malaria Aviar (Plasmodium) en las Islas Galápagos y Evidencia de su Arribo por Medio de Aves Migratorias. © 2013 Society for Conservation Biology.
Sabath, Niv; Goldberg, Emma E; Glick, Lior; Einhorn, Moshe; Ashman, Tia-Lynn; Ming, Ray; Otto, Sarah P; Vamosi, Jana C; Mayrose, Itay
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver.
Fregel, Rosa; Seetah, Krish; Betancor, Eva; Suárez, Nicolás M; Čaval, Diego; Caval, Saša; Janoo, Anwar; Pestano, Jose
This article reports on the first genetic assessment of the contemporary Mauritian population. Small island nodes such as Mauritius played a critical role in historic globalization processes and revealing high-resolution details of labour sourcing is crucial in order to better understand early-modern diaspora events. Mauritius is a particularly interesting case given detailed historic accounts attesting to European (Dutch, French and British), African and Asian points of origin. Ninety-seven samples were analysed for mitochondrial DNA to begin unravelling the complex dynamics of the island's modern population. In corroboration with general demographic information, the majority of maternal lineages were derived from South Asia (58.76%), with Malagasy (16.60%), East/Southeast Asian (11.34%) and Sub-Saharan African (10.21%) also making significant contributions. This study pinpoints specific regional origins for the South Asian genetic contribution, showing a greater influence on the contemporary population from northern and southeast India. Moreover, the analysis of lineages related to the slave trade demonstrated that Madagascar and East Asia were the main centres of origin, with less influence from West Africa.
Full Text Available Retrotransposons of the R2 superclade specifically insert within the 28S ribosomal gene. They have been isolated from a variety of metazoan genomes and were found vertically inherited even if their phylogeny does not always agree with that of the host species. This was explained with the diversification/extinction of paralogous lineages, being proved the absence of horizontal transfer. We here analyze the widest available collection of R2 sequences, either newly isolated from recently sequenced genomes or drawn from public databases, in a phylogenetic framework. Results are congruent with previous analyses, but new important issues emerge. First, the N-terminal end of the R2-B clade protein, so far unknown, presents a new zinc fingers configuration. Second, the phylogenetic pattern is consistent with an ancient, rapid radiation of R2 lineages: being the estimated time of R2 origin (850-600 Million years ago placed just before the metazoan Cambrian explosion, the wide element diversity and the incongruence with the host phylogeny could be attributable to the sudden expansion of available niches represented by host's 28S ribosomal genes. Finally, we detect instances of coexisting multiple R2 lineages showing a non-random phylogenetic pattern, strongly similar to that of the "library" model known for tandem repeats: a collection of R2s were present in the ancestral genome and then differentially activated/repressed in the derived species. Models for activation/repression as well as mechanisms for sequence maintenance are also discussed within this framework.
Nakajima, Yuichi; Nishikawa, Akira; Iguchi, Akira; Nagata, Tomofumi; Uyeno, Daisuke; Sakai, Kazuhiko; Mitarai, Satoshi
The elucidation of species diversity and connectivity is essential for conserving coral reef communities and for understanding the characteristics of coral populations. To assess the species diversity, intraspecific genetic diversity, and genetic differentiation among populations of the brooding coral Seriatopora spp., we conducted phylogenetic and population genetic analyses using a mitochondrial DNA control region and microsatellites at ten sites in the Ryukyu Archipelago, Japan. At least three genetic lineages of Seriatopora (Seriatopora-A, -B, and -C) were detected in our specimens. We collected colonies morphologically similar to Seriatopora hystrix, but these may have included multiple, genetically distinct species. Although sexual reproduction maintains the populations of all the genetic lineages, Seriatopora-A and Seriatopora-C had lower genetic diversity than Seriatopora-B. We detected significant genetic differentiation in Seriatopora-B among the three populations as follows: pairwise F ST = 0.064-0.116 (all P = 0.001), pairwise G''ST = 0.107-0.209 (all P = 0.001). Additionally, only one migrant from an unsampled population was genetically identified within Seriatopora-B. Because the peak of the settlement of Seriatopora larvae is within 1 d and almost all larvae are settled within 5 d of spawning, our observations may be related to low dispersal ability. Populations of Seriatopora in the Ryukyu Archipelago will probably not recover unless there is substantial new recruitment from distant populations.
Webby, R J; Rossow, K; Erickson, G; Sims, Y; Webster, R
Before the isolation of H3N2 viruses in 1998, swine influenza in the United States was an endemic disease caused exclusively by classical-swine H1N1 viruses. In this study we determined the antigenic and phylogenetic composition of a selection of currently circulating strains and revealed that, in contrast to the situation pre-1998, the swine population in the United States is now a dynamic viral reservoir containing multiple viral lineages. H3N2 viruses still circulate and representatives of each of two previously identified phylogenetic groups were isolated. H1N1 and H1N2 viruses were also identified. In addition to the genotypic diversity present, there was also considerable antigenic diversity seen. At least three antigenic profiles of H1 viruses were noted and all of the recent H3N2 viruses reacted poorly, if at all, to the index A/swine/Texas/4199-2/98 H3N2 antiserum in hemagglutination inhibition assays. The influenza reservoir in the United States swine population has thus gone from a stable single viral lineage to one where genetically and antigenically heterogenic viruses co-circulate. The growing complexity of influenza at this animal-human interface and the presence of viruses with a seemingly high affinity for reassortment makes the United States swine population an increasingly important reservoir of viruses with human pandemic potential.
Stöck, Matthias; Lampert, Kathrin P; Möller, Dirk; Schlupp, Ingo; Schartl, Manfred
Despite the advantage of avoiding the costs of sexual reproduction, asexual vertebrates are very rare and often considered evolutionarily disadvantaged when compared to sexual species. Asexual species, however, may have advantages when colonizing (new) habitats or competing with sexual counterparts. They are also evolutionary older than expected, leaving the question whether asexual vertebrates are not only rare because of their 'inferior' mode of reproduction but also because of other reasons. A paradigmatic model system is the unisexual Amazon molly, Poecilia formosa, that arose by hybridization of the Atlantic molly, Poecilia mexicana, as the maternal ancestor, and the sailfin molly, Poecilia latipinna, as the paternal ancestor. Our extensive crossing experiments failed to resynthesize asexually reproducing (gynogenetic) hybrids confirming results of previous studies. However, by producing diploid eggs, female F(1) -hybrids showed apparent preadaptation to gynogenesis. In a range-wide analysis of mitochondrial sequences, we examined the origin of P. formosa. Our analyses point to very few or even a single origin(s) of its lineage, which is estimated to be approximately 120,000 years old. A monophyletic origin was supported from nuclear microsatellite data. Furthermore, a considerable degree of genetic variation, apparent by high levels of clonal microsatellite diversity, was found. Our molecular phylogenetic evidence and the failure to resynthesize the gynogenetic P. formosa together with the old age of the species indicate that some unisexual vertebrates might be rare not because they suffer the long-term consequences of clonal reproduction but because they are only very rarely formed as a result of complex genetic preconditions necessary to produce viable and fertile clonal genomes and phenotypes ('rare formation hypothesis').
Jörger Katharina M
Full Text Available Abstract Background Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic and the success rate has never been explored on mesopsammic Mollusca. Results We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH. In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC, statistical parsimony, Bayesian Species Delineation (BPP and Automatic Barcode Gap Discovery (ABGD. The secondary species hypothesis (SSH is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’, resulting in the discovery of a radiation of (at least 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions. Conclusions Our study confirms extensive, morphologically
Sarkies, Peter; Selkirk, Murray E.; Jones, John T.; Blok, Vivian; Boothby, Thomas; Goldstein, Bob; Hanelt, Ben; Ardila-Garcia, Alex; Fast, Naomi M.; Schiffer, Phillip M.; Kraus, Christopher; Taylor, Mark J.; Koutsovoulos, Georgios; Blaxter, Mark L.; Miska, Eric A.
Small RNA pathways act at the front line of defence against transposable elements across the Eukaryota. In animals, Piwi interacting small RNAs (piRNAs) are a crucial arm of this defence. However, the evolutionary relationships among piRNAs and other small RNA pathways targeting transposable elements are poorly resolved. To address this question we sequenced small RNAs from multiple, diverse nematode species, producing the first phylum-wide analysis of how small RNA pathways evolve. Surprisingly, despite their prominence in Caenorhabditis elegans and closely related nematodes, piRNAs are absent in all other nematode lineages. We found that there are at least two evolutionarily distinct mechanisms that compensate for the absence of piRNAs, both involving RNA-dependent RNA polymerases (RdRPs). Whilst one pathway is unique to nematodes, the second involves Dicer-dependent RNA-directed DNA methylation, hitherto unknown in animals, and bears striking similarity to transposon-control mechanisms in fungi and plants. Our results highlight the rapid, context-dependent evolution of small RNA pathways and suggest piRNAs in animals may have replaced an ancient eukaryotic RNA-dependent RNA polymerase pathway to control transposable elements. PMID:25668728
Full Text Available Mechanisms for the evolution of convergent behavioral traits are largely unknown. Vocal learning is one such trait that evolved multiple times and is necessary in humans for the acquisition of spoken language. Among birds, vocal learning is evolved in songbirds, parrots, and hummingbirds. Each time similar forebrain song nuclei specialized for vocal learning and production have evolved. This finding led to the hypothesis that the behavioral and neuroanatomical convergences for vocal learning could be associated with molecular convergence. We previously found that the neural activity-induced gene dual specificity phosphatase 1 (dusp1 was up-regulated in non-vocal circuits, specifically in sensory-input neurons of the thalamus and telencephalon; however, dusp1 was not up-regulated in higher order sensory neurons or motor circuits. Here we show that song motor nuclei are an exception to this pattern. The song nuclei of species from all known vocal learning avian lineages showed motor-driven up-regulation of dusp1 expression induced by singing. There was no detectable motor-driven dusp1 expression throughout the rest of the forebrain after non-vocal motor performance. This pattern contrasts with expression of the commonly studied activity-induced gene egr1, which shows motor-driven expression in song nuclei induced by singing, but also motor-driven expression in adjacent brain regions after non-vocal motor behaviors. In the vocal non-learning avian species, we found no detectable vocalizing-driven dusp1 expression in the forebrain. These findings suggest that independent evolutions of neural systems for vocal learning were accompanied by selection for specialized motor-driven expression of the dusp1 gene in those circuits. This specialized expression of dusp1 could potentially lead to differential regulation of dusp1-modulated molecular cascades in vocal learning circuits.
Johnson, Jennifer, Ed.
This issue of "Loblolly Magazine" was written in observance of the 50th anniversary of the U.S. entrance into World War II. The publication features interviews conducted by East Texas high school students with Clarence Otterman, one of the few survivors of the crew of the USS Arizona, which was bombed during the attack on Pearl Harbor,…
Elmore, M Holly; McGary, Kriston L; Wisecaver, Jennifer H; Slot, Jason C; Geiser, David M; Sink, Stacy; O'Donnell, Kerry; Rokas, Antonis
Fungi that have the enzymes cyanase and carbonic anhydrase show a limited capacity to detoxify cyanate, a fungicide employed by both plants and humans. Here, we describe a novel two-gene cluster that comprises duplicated cyanase and carbonic anhydrase copies, which we name the CCA gene cluster, trace its evolution across Ascomycetes, and examine the evolutionary dynamics of its spread among lineages of the Fusarium oxysporum species complex (hereafter referred to as the FOSC), a cosmopolitan clade of purportedly clonal vascular wilt plant pathogens. Phylogenetic analysis of fungal cyanase and carbonic anhydrase genes reveals that the CCA gene cluster arose independently at least twice and is now present in three lineages, namely Cochliobolus lunatus, Oidiodendron maius, and the FOSC. Genome-wide surveys within the FOSC indicate that the CCA gene cluster varies in copy number across isolates, is always located on accessory chromosomes, and is absent in FOSC's closest relatives. Phylogenetic reconstruction of the CCA gene cluster in 163 FOSC strains from a wide variety of hosts suggests a recent history of rampant transfers between isolates. We hypothesize that the independent formation of the CCA gene cluster in different fungal lineages and its spread across FOSC strains may be associated with resistance to plant-produced cyanates or to use of cyanate fungicides in agriculture.
Quibod, Ian Lorenzo; Grande, Genelou; Oreiro, Eula Gems; Borja, Frances Nikki; Dossa, Gerbert Sylvestre; Mauleon, Ramil; Cruz, Casiana Vera; Oliva, Ricardo
Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.
Full Text Available Abstract Background All-trans retinoic acid (RA is one of the most important morphogens with pleiotropic actions. Its embryonic distribution correlates with neural differentiation in the developing central nervous system. To explore the precise effects of RA on neural differentiation of mouse embryonic stem cells (ESCs, we detected expression of RA nuclear receptors and RA-metabolizing enzymes in mouse ESCs and investigated the roles of RA in adherent monolayer culture. Results Upon addition of RA, cell differentiation was directed rapidly and exclusively into the neural lineage. Conversely, pharmacological interference with RA signaling suppressed this neural differentiation. Inhibition of fibroblast growth factor (FGF signaling did not suppress significantly neural differentiation in RA-treated cultures. Pharmacological interference with extracellular signal-regulated kinase (ERK pathway or activation of Wnt pathway effectively blocked the RA-promoted neural specification. ERK phosphorylation was enhanced in RA-treated cultures at the early stage of differentiation. Conclusion RA can promote neural lineage entry by ESCs in adherent monolayer culture systems. This effect depends on RA signaling and its crosstalk with the ERK and Wnt pathways.
Reddy, Anupama; Growney, Joseph D; Wilson, Nick S; Emery, Caroline M; Johnson, Jennifer A; Ward, Rebecca; Monaco, Kelli A; Korn, Joshua; Monahan, John E; Stump, Mark D; Mapa, Felipa A; Wilson, Christopher J; Steiger, Janine; Ledell, Jebediah; Rickles, Richard J; Myer, Vic E; Ettenberg, Seth A; Schlegel, Robert; Sellers, William R; Huet, Heather A; Lehár, Joseph
Death Receptor 5 (DR5) agonists demonstrate anti-tumor activity in preclinical models but have yet to demonstrate robust clinical responses. A key limitation may be the lack of patient selection strategies to identify those most likely to respond to treatment. To overcome this limitation, we screened a DR5 agonist Nanobody across >600 cell lines representing 21 tumor lineages and assessed molecular features associated with response. High expression of DR5 and Casp8 were significantly associated with sensitivity, but their expression thresholds were difficult to translate due to low dynamic ranges. To address the translational challenge of establishing thresholds of gene expression, we developed a classifier based on ratios of genes that predicted response across lineages. The ratio classifier outperformed the DR5+Casp8 classifier, as well as standard approaches for feature selection and classification using genes, instead of ratios. This classifier was independently validated using 11 primary patient-derived pancreatic xenograft models showing perfect predictions as well as a striking linearity between prediction probability and anti-tumor response. A network analysis of the genes in the ratio classifier captured important biological relationships mediating drug response, specifically identifying key positive and negative regulators of DR5 mediated apoptosis, including DR5, CASP8, BID, cFLIP, XIAP and PEA15. Importantly, the ratio classifier shows translatability across gene expression platforms (from Affymetrix microarrays to RNA-seq) and across model systems (in vitro to in vivo). Our approach of using gene expression ratios presents a robust and novel method for constructing translatable biomarkers of compound response, which can also probe the underlying biology of treatment response.
Vila, Marta; Vidal-Romaní, Juan R; Björklund, Mats
Evidence of four different Quaternary glacial stages has been found in NW Iberia. The different magnitude of these episodes probably conditioned the distribution of currently montane species. We examined if the population history of NW Iberian Erebia triaria butterflies reflected such an influence of different glacial stages. We also investigated whether these populations were post-glacially colonised from a single refugial area or several sources. For this, we performed phylogenetic analyses and coalescence simulations on mitochondrial DNA sequences of individuals from five NW Iberian locations. We analysed three additional populations as reference, i.e., Central Spain, the Pyrenees, and the Alps. One of the NW Iberian populations, a subspecies endemic to a particular mountain range (Xistral), showed a high level of genetic divergence from all other populations, regardless of their geographic distance. Isolation after an ancient glacial stage, and followed by allopatric differentiation, may account for such high differentiation. The genetic pattern shown by the rest of the NW Iberian population samples consisted of two lineages, likely reflecting that the ancestors of these populations sought for refuge in at least two different areas during a subsequent glacial stage. We showed evidence of both temporal and spatial divisions in the phylogeography of these butterflies. The congruence of this pattern with the geological history suggests that the Iberian Peninsula hosted several refugial areas that differed in area and location depending on the glacial stage.
Mutai, Collins; Njuguna, Joyce; Ghimire, Sita
Endophytic and plant-associated bacteria were isolated from plants and rhizoplane soil of naturally grown Brachiaria grasses at International Livestock Research Institute in Nairobi, Kenya. Eighty-four bacterial strains were isolated from leaf tissues, root tissues, and rhizoplane soil on nutrient agar and 869 media. All bacterial strains were identified to the lowest possible taxonomic unit using 16S rDNA primers and were characterized for the production of Indole-3-acetic acid, hydrogen cyanide, and ACC deaminase; phosphate solubilization; siderophore production; antifungal properties; and plant biomass production. The 16S rDNA-based identification grouped these 84 bacterial strains into 3 phyla, 5 classes, 8 orders, 12 families, 16 genera, and 50 unique taxa. The four most frequently isolated genera were Pseudomonas (23), Pantoea (17), Acinetobacter (9), and Enterobacter (8). The functional characterization of these strains revealed that 41 of 84 strains had a minimum of three plant beneficial properties. Inoculation of maize seedlings with Acinetobacter spp., Microbacterium spp., Pectobacterium spp., Pseudomonas spp., and Enterobacter spp. showed positive effects on seedling biomass production. The ability of Brachiaria grasses to host genetically diverse bacteria, many of them with multiple plant growth-promoting attributes, might have contributed to high biomass production and adaptation of Brachiaria grasses to drought and low fertility soils. © 2017 International Livestock Research Institute. MicrobiologyOpen published by John Wiley & Sons Ltd.
Full Text Available The epicardium is the mono-layered epithelium that covers the outer surface of the myocardium from early in cardiac development. Long thought to act merely passively to protect the myocardium from frictional forces in the pericardial cavity during the enduring contraction and expansion cycles of the heart, it is now considered to be a crucial source of cells and signals that direct myocardial growth and formation of the coronary vasculature during development and regeneration. Lineage tracing efforts in the chick, the mouse and the zebrafish unambiguously identified fibroblasts in interstitial and perivascular locations as well as coronary smooth muscle cells as the two major lineages that derive from epithelial-mesenchymal transition and subsequent differentiation from individual epicardial cells. However, controversies exist about an additional endothelial and myocardial fate of epicardial progenitor cells. Here, we review epicardial fate mapping efforts in three vertebrate model systems, describe their conceptual differences and discuss their methodological limitations to reach a consensus of the potential of (pro-epicardial cells in vitro and in vivo.
Full Text Available BACKGROUND: Human cryptococcal infections have been associated with bird droppings as a likely source of infection. Studies toward the local and global epidemiology of Cryptococcus spp. have been hampered by the lack of rapid, discriminatory, and exchangeable molecular typing methods. METHODOLOGY/PRINCIPAL FINDINGS: We selected nine microsatellite markers for high-resolution fingerprinting from the genome of C. neoformans var. grubii. This panel of markers was applied to a collection of clinical (n = 122 and environmental (n = 68; from pigeon guano C. neoformans var. grubii isolates from Cuba. All markers proved to be polymorphic. The average number of alleles per marker was 9 (range 5-51. A total of 104 genotypes could be distinguished. The discriminatory power of this panel of markers was 0.993. Multiple clusters of related genotypes could be discriminated that differed in only one or two microsatellite markers. These clusters were assigned as microsatellite complexes. The majority of environmental isolates (>70% fell into 1 microsatellite complex containing only few clinical isolates (49 environmental versus 2 clinical. Clinical isolates were segregated over multiple microsatellite complexes. CONCLUSIONS/SIGNIFICANCE: A large genotypic variation exists in C. neoformans var. grubii. The genotypic segregation between clinical and environmental isolates from pigeon guano suggests additional source(s of human cryptococcal infections. The selected panel of microsatellite markers is an excellent tool to study the epidemiology of C. neoformans var. grubii.
Full Text Available Abstract Background Dengue virus type 1 (DENV-1 have been mostly circulating silently with dominant serotypes DENV-2 and DENV-3 in India. However recent times have marked an increase in DENV-1 circulation in yearly outbreaks. Many studies have not been carried out on this virus type, leaving a lacunae pertaining to the circulating genotypes, since its earliest report in India. In the present study, we sequenced CprM gene junction of 13 DENV-1 isolated from Delhi and Gwalior (North India between 2001–2007 and one 1956 Vellore isolate as reference. For comparison, we retrieved 11 other Indian and 70 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis. Results The region was found to be AT rich with no insertion or deletion. Majority of the nucleotide substitutions were silent, except 3 non-conservative amino acid changes (I → T, A → T and L → S at amino acid positions 59,114 and 155 respectively in the Indian DENV-1 sequences, sequenced in this study. Except two 1997–98 Delhi isolates, which group in genotype I; all other Indian isolates group in genotype III. All Indian genotype III DENV-1 exhibited diversity among them, giving rise to at least 4 distinct lineages (India 1–4 showing proximity to isolates from diverse geographic locations. Conclusion The extensive phylogenetic analysis revealed consistent existence of multiple lineages of DENV-1 genotype III during the last 5 decades in India.
Federal Laboratory Consortium — The Coastal Harbors Modeling Facility is used to aid in the planning of harbor development and in the design and layout of breakwaters, absorbers, etc.. The goal is...
Baker, Ronald J.; Wieben, Christine M.; Lathrop, Richard G.; Nicholson, Robert S.
Concentrations, loads, and yields of nutrients (total nitrogen and total phosphorus) were calculated for the Barnegat Bay-Little Egg Harbor (BB-LEH) watershed for 1989–2011 at annual and seasonal (growing and nongrowing) time scales. Concentrations, loads, and yields were calculated at three spatial scales: for each of the 81 subbasins specified by 14-digit hydrologic unit codes (HUC-14s); for each of the three BB-LEH watershed segments, which coincide with segmentation of the BB-LEH estuary; and for the entire BB-LEH watershed. Base-flow and runoff values were calculated separately and were combined to provide total values. Available surface-water-quality data for all streams in the BB-LEH watershed for 1980–2011 were compiled from existing datasets and quality assured. Precipitation and streamflow data were used to distinguish between water-quality samples that were collected during base-flow conditions and those that were collected during runoff conditions. Base-flow separation of hydrographs of six streams in the BB-LEH watershed indicated that base flow accounts for about 72 to 94 percent of total flow in streams in the watershed. Base-flow mean concentrations (BMCs) of total nitrogen (TN) and total phosphorus (TP) for each HUC-14 subbasin were calculated from relations between land use and measured base-flow concentrations. These relations were developed from multiple linear regression models determined from water-quality data collected at sampling stations in the BB-LEH watershed under base-flow conditions and land-use percentages in the contributing drainage basins. The total watershed base-flow volume was estimated for each year and season from continuous streamflow records for 1989–2011 and relations between precipitation and streamflow during base-flow conditions. For each year and season, the base-flow load and yield were then calculated for each HUC-14 subbasin from the BMCs, total base-flow volume, and drainage area. The watershed
Multiple ESBL-Producing Escherichia coli Sequence Types Carrying Quinolone and Aminoglycoside Resistance Genes Circulating in Companion and Domestic Farm Animals in Mwanza, Tanzania, Harbor Commonly Occurring Plasmids.
Seni, Jeremiah; Falgenhauer, Linda; Simeo, Nabina; Mirambo, Mariam M; Imirzalioglu, Can; Matee, Mecky; Rweyemamu, Mark; Chakraborty, Trinad; Mshana, Stephen E
The increased presence of extended-spectrum beta-lactamase (ESBL)-producing bacteria in humans, animals, and their surrounding environments is of global concern. Currently there is limited information on ESBL presence in rural farming communities worldwide. We performed a cross-sectional study in Mwanza, Tanzania, involving 600 companion and domestic farm animals between August/September 2014. Rectal swab/cloaca specimens were processed to identify ESBL-producing Enterobacteriaceae. We detected 130 (21.7%) animals carrying ESBL-producing bacteria, the highest carriage being among dogs and pigs [39.2% (51/130) and 33.1% (43/130), respectively]. The majority of isolates were Escherichia coli [93.3% (125/134)] and exotic breed type [OR (95%CI) = 2.372 (1.460-3.854), p-value ESBL carriage among animals. Whole-genome sequences of 25 ESBL-producing E. coli were analyzed for phylogenetic relationships using multi-locus sequence typing (MLST) and core genome comparisons. Fourteen different sequence types were detected of which ST617 (7/25), ST2852 (3/25), ST1303 (3/25) were the most abundant. All isolates harbored the bla CTX-M-15 allele, 22/25 carried strA and strB, 12/25 aac(6')-lb-cr, and 11/25 qnrS1. Antibiotic resistance was associated with IncF, IncY, as well as non-typable plasmids. Eleven isolates carried pPGRT46-related plasmids, previously reported from isolates in Nigeria. Five isolates had plasmids exhibiting 85-99% homology to pCA28, previously detected in isolates from the US. Our findings indicate a pan-species distribution of ESBL-producing E. coli clonal groups in farming communities and provide evidence for plasmids harboring antibiotic resistances of regional and international impact.
Distribution of Porifera (Wet Weight in Grams) Collected in Piling Samples from Pearl Harbor, Oahu 2.4-26 2.4-7. Syllidae 2.4-28 2.4-8. Cirratulidae...COLLECTED FROM PEARL HARBOR m .-. Sped es/Group Porifera Demospongiae Cnidaria Hydrozoa Hydrdda Anthozoa Actlnarla Stolchactlnldae Radianthus...and abundance data for 113 taxa (species, genera and higher taxa) are provided in Table 2.4-4. Wet weights are listed for all sponges ( porifera ). The
Ken Daigoro Yokoyama
Full Text Available Changes in cis-regulatory element composition that result in novel patterns of gene expression are thought to be a major contributor to the evolution of lineage-specific traits. Although transcription factor binding events show substantial variation across species, most computational approaches to study regulatory elements focus primarily upon highly conserved sites, and rely heavily upon multiple sequence alignments. However, sequence conservation based approaches have limited ability to detect lineage-specific elements that could contribute to species-specific traits. In this paper, we describe a novel framework that utilizes a birth-death model to trace the evolution of lineage-specific binding sites without relying on detailed base-by-base cross-species alignments. Our model was applied to analyze the evolution of binding sites based on the ChIP-seq data for six transcription factors (GATA1, SOX2, CTCF, MYC, MAX, ETS1 along the lineage toward human after human-mouse common ancestor. We estimate that a substantial fraction of binding sites (∼58-79% for each factor in humans have origins since the divergence with mouse. Over 15% of all binding sites are unique to hominids. Such elements are often enriched near genes associated with specific pathways, and harbor more common SNPs than older binding sites in the human genome. These results support the ability of our method to identify lineage-specific regulatory elements and help understand their roles in shaping variation in gene regulation across species.
Agnes K M Weiner
Full Text Available Morphologically defined species of marine plankton often harbor a considerable level of cryptic diversity. Since many morphospecies show cosmopolitan distribution, an understanding of biogeographic and evolutionary processes at the level of genetic diversity requires global sampling. We use a database of 387 single-specimen sequences of the SSU rDNA of the planktonic foraminifera Globigerinella as a model to assess the biogeographic and phylogenetic distributions of cryptic diversity in marine microplankton on a global scale. Our data confirm the existence of multiple, well isolated genetic lineages. An analysis of their abundance and distribution indicates that our sampling is likely to approximate the actual total diversity. Unexpectedly, we observe an uneven allocation of cryptic diversity among the phylogenetic lineages. We show that this pattern is neither an artifact of sampling intensity nor a function of lineage age. Instead, we argue that it reflects an ongoing speciation process in one of the three major lineages. Surprisingly, four of the six genetic types in the hyperdiverse lineage are biogeographically restricted to the Indopacific. Their mutual co-occurrence and their hierarchical phylogenetic structure provide no evidence for an origin through sudden habitat fragmentation and their limitation to the Indopacific challenges the view of a global gene flow within the warm-water provinces. This phenomenon shows that passive dispersal is not sufficient to describe the distribution of plankton diversity. Rather, these organisms show differentiated distribution patterns shaped by species interactions and reflecting phylogenetic contingency with unique histories of diversification rates.
Horwitz, M.S.; Radich, J. [Fred Hutchinson Cancer Research Center, Seattle, WA (United States); Sabath, D.E. [Univ. of Washington, Seattle (United States)
The initial steps promoting carcinogenesis in the hematologic malignancies remain poorly understood. We report on a family with an incompletely penetrant, autosomal dominant syndrome of acute myelogenous leukemia, affecting at least eight adults from three generations. The affected individuals have developed leukemias differing in morphologic subtype, tumor cytogenetics, and abruptness of presentation. Within this family are found subtypes affecting the granulocytic, monocytic, and megakaryocytic lineages. At least one individual has a normal tumor karyotype while another has complex rearrangements including monsomy 7, trisomy 8 and translocation 1;7. Some have presented with acute onset and others with a protracted myelodysplasia syndrome. One person at fifty percent risk of inheriting this gene developed disseminated atypical mycobacterium infection in the absence of leukemia, but also without apparent causes for acquired deficiencies in cellular immunity. Features common to affected family members, including the individual with mycobacterium infection, are the early presence in bone marrow of red cell and platelet maturation defects. A search for mutations in diseased marrows fails to detect abnormalities of p53 exons 5, 6, 7 and 8 or N-ras codons 12, 13 and 61. We conclude that there is a gene in this family that probably acts early in hematopoetic differentiation and confers susceptibility to a wide range of leukemia subtypes spanning the maturation of the myeloid series.
Antibody producing B lineage cells invade the central nervous system predominantly at the time of and triggered by acute Epstein-Barr virus infection: A hypothesis on the origin of intrathecal immunoglobulin synthesis in multiple sclerosis.
Otto, Carolin; Hofmann, Jörg; Ruprecht, Klemens
Patients with multiple sclerosis (MS), a chronic inflammatory disease of the central nervous system (CNS), typically have an intrathecal synthesis of immunoglobulin (Ig)G. Intrathecal IgG is produced by B lineage cells that entered the CNS, but why and when these cells invade the CNS of patients with MS is unknown. The intrathecal IgG response in patients with MS is polyspecific and part of it is directed against different common viruses (e.g. measles virus, rubella virus, varicella zoster virus). Strong and consistent evidence suggests an association of MS and Epstein-Barr virus (EBV) infection and EBV seroprevalence in patients with MS is practically 100%. However, intriguingly, despite of the universal EBV seroprevalence, the frequency of intrathecally produced IgG to EBV in patients with MS is much lower than that of intrathecally produced IgG to other common viruses. The acute phase of primary EBV infection is characterized by a strong polyclonal B cell activation. As typical for humoral immune responses against viruses, EBV specific IgG is produced only with a temporal delay after acute EBV infection. Aiming to put the above facts into a logical structure, we here propose the hypothesis that in individuals going on to develop MS antibody producing B lineage cells invade the CNS predominantly at the time of and triggered by acute primary EBV infection. Because at the time of acute EBV infection EBV IgG producing B lineage cells have not yet occurred, the hypothesis could explain the universal EBV seroprevalence and the low frequency of intrathecally produced IgG to EBV in patients with MS. Evidence supporting the hypothesis could be provided by large prospective follow-up studies of individuals with symptomatic primary EBV infection (infectious mononucleosis). Furthermore, the clarification of the molecular mechanism underlying an EBV induced invasion of B lineage cells into the CNS of individuals going on to develop MS could corroborate it, too. If true, our
Full Text Available Aberrant pre-mRNA splice variants of hyaluronan synthase 1 (HAS1 have been identified in malignant cells from cancer patients. Bioinformatic analysis suggests that intronic sequence changes can underlie aberrant splicing. Deletions and mutations were introduced into HAS1 minigene constructs to identify regions that can influence aberrant intronic splicing, comparing the splicing pattern in transfectants with that in multiple myeloma (MM patients. Introduced genetic variations in introns 3 and 4 of HAS1 as shown here can promote aberrant splicing of the type detected in malignant cells from MM patients. HAS1Vd is a novel intronic splice variant first identified here. HAS1Vb, an intronic splice variant previously identified in patients, skips exon 4 and utilizes the same intron 4 alternative 3'splice site as HAS1Vd. For transfected constructs with unaltered introns 3 and 4, HAS1Vd transcripts are readily detectable, frequently to the exclusion of HAS1Vb. In contrast, in MM patients, HAS1Vb is more frequent than HAS1Vd. In the HAS1 minigene, combining deletion in intron 4 with mutations in intron 3 leads to a shift from HAS1Vd expression to HAS1Vb expression. The upregulation of aberrant splicing, exemplified here by the expression of HAS1Vb, is shown here to be influenced by multiple genetic changes in intronic sequences. For HAS1Vb, this includes enhanced exon 4 skipping and increased usage of alternative 3' splice sites. Thus, the combination of introduced mutations in HAS1 intron3 with introduced deletions in HAS1 intron 4 promoted a shift to an aberrant splicing pattern previously shown to be clinically significant. Most MM patients harbor genetic variations in intron 4, and as shown here, nearly half harbor recurrent mutations in HAS1 intron 3. Our work suggests that aberrant intronic HAS1 splicing in MM patients may rely on intronic HAS1 deletions and mutations that are frequent in MM patients but absent from healthy donors.
Saito, T; Guthmuller, H; DeWeert, M
Port and Harbor Security is a daunting task to which optics and photonics offers significant solutions. We are pleased to report that the 2005 Defense and Security Symposium (DSS, Orlando, FL) will include reports on active and passive photonic systems operating from both airborne and subsurface platforms. In addition to imaging techniques, there are various photonic applications, such as total internal reflection fluorescence (TIRF), which can be used to ''sniff'' for traces of explosives or contaminants in marine. These non-imaging technologies are beyond the scope of this article, but will also be represented at DSS 2005. We encourage colleagues to join our technical group to help us to make our ports and harbors safer and more secure.
Gryganskyi, A.P.; Humber, R.A.; Smith, M.E.; Hodge, K.; Huang, B.; Voigt, K.; Vilgalys, R.
Entomophthoromycota is one of six 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 studies ha
de Leeuw, Christiaan A.; Knegt, Bram; Maas, Diede L.; de Voogd, Nicole J.; Abdunnur; Suyatna, Iwan; Peijnenburg, Katja T.C.A.
Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago. PMID:27761314
Leontine E. Becking
Full Text Available Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI, and two nuclear markers (18S and 28S. In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence, two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%, we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present. Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago.
Chalfoun, Joe; Majurski, Michael; Dima, Alden; Halter, Michael; Bhadriraju, Kiran; Brady, Mary
The ability to accurately track cells and particles from images is critical to many biomedical problems. To address this, we developed Lineage Mapper, an open-source tracker for time-lapse images of biological cells, colonies, and particles. Lineage Mapper tracks objects independently of the segmentation method, detects mitosis in confluence, separates cell clumps mistakenly segmented as a single cell, provides accuracy and scalability even on terabyte-sized datasets, and creates division and/or fusion lineages. Lineage Mapper has been tested and validated on multiple biological and simulated problems. The software is available in ImageJ and Matlab at isg.nist.gov.
Xiao, Xiangwei; Guo, Ping; Prasadan, Krishna; Shiota, Chiyo; Peirish, Lauren; Fischbach, Shane; Song, Zewen; Gaffar, Iljana; Wiersch, John; El-Gohary, Yousef; Husain, Sohail Z; Gittes, George K
Genetic manipulations, with or without lineage tracing for specific pancreatic cell types, are very powerful tools for studying diabetes, pancreatitis and pancreatic cancer. Nevertheless, the use of Cre/loxP systems to conditionally activate or inactivate the expression of genes in a cell type- and/or temporal-specific manner is not applicable to cell tracing and/or gene manipulations in more than one lineage at a time. Here we report a technique that allows efficient delivery of dyes for cell tagging into the mouse pancreas through the duct system, and that also delivers viruses carrying transgenes or siRNA under a specific promoter. When this technique is applied in genetically modified mice, it enables the investigator to perform either double lineage tracing or cell lineage tracing combined with gene manipulation in a second lineage. The technique requires <40 min.
Miller, Lee; Verfuss, Ursula
The harbor porpoise (Phocoena phocoena) is a small toothed whale living mostly in coastal waters. There are large, but unknown, numbers in the inner Danish waters. Four are in captivity at Fjord & Bælt, Kerteminde, Denmark, one of which was born here in 2006. Harbor porpoises use their ultraso...
California Department of Resources — Harbor reciever sites from Everest (2009) 'Harbor Area Management Plan, In-Harbor Beach Replenishment Strategy', Technical Report. Prepared for Harbor Resources...
US Fish and Wildlife Service, Department of the Interior — Savannah Harbor, located near the mouth of the Savannah River, Georgia and South Carolina, is impacted by industrial and municipal effluents. Contaminants released...
National Oceanic and Atmospheric Administration, Department of Commerce — Floating glacial ice serves as a haul-out substrate for a significant number (10-15%) of Alaskan harbor seals, and thus surveying tidewater glacial fjords is an...
@@ 2007 China Harbor Ten People elected the entrepreneurs who contributed a lot to port economy and enterprises this year trough their talent management.These ten people embody their social responsibility,professional skills,creative ability,and charming personality.Bearing full confidence in China's port economy,the port entrepreneurs are brave enough to explore a brand new area,so as to promote harbor economic development.
Rodilla, Veronica; Dasti, Alessandro; Huyghe, Mathilde; Lafkas, Daniel; Laurent, Cécile; Reyal, Fabien; Fre, Silvia
The hierarchical relationships between stem cells and progenitors that guide mammary gland morphogenesis are still poorly defined. While multipotent basal stem cells have been found within the myoepithelial compartment, the in vivo lineage potential of luminal progenitors is unclear. Here we used the expression of the Notch1 receptor, previously implicated in mammary gland development and tumorigenesis, to elucidate the hierarchical organization of mammary stem/progenitor cells by lineage tracing. We found that Notch1 expression identifies multipotent stem cells in the embryonic mammary bud, which progressively restrict their lineage potential during mammary ductal morphogenesis to exclusively generate an ERαneg luminal lineage postnatally. Importantly, our results show that Notch1-labelled cells represent the alveolar progenitors that expand during pregnancy and survive multiple successive involutions. This study reveals that postnatal luminal epithelial cells derive from distinct self-sustained lineages that may represent the cells of origin of different breast cancer subtypes.
Full Text Available The hierarchical relationships between stem cells and progenitors that guide mammary gland morphogenesis are still poorly defined. While multipotent basal stem cells have been found within the myoepithelial compartment, the in vivo lineage potential of luminal progenitors is unclear. Here we used the expression of the Notch1 receptor, previously implicated in mammary gland development and tumorigenesis, to elucidate the hierarchical organization of mammary stem/progenitor cells by lineage tracing. We found that Notch1 expression identifies multipotent stem cells in the embryonic mammary bud, which progressively restrict their lineage potential during mammary ductal morphogenesis to exclusively generate an ERαneg luminal lineage postnatally. Importantly, our results show that Notch1-labelled cells represent the alveolar progenitors that expand during pregnancy and survive multiple successive involutions. This study reveals that postnatal luminal epithelial cells derive from distinct self-sustained lineages that may represent the cells of origin of different breast cancer subtypes.
Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee .
Shirafuji, Hiroaki; Yazaki, Ryu; Shuto, Yozo; Yanase, Tohru; Kato, Tomoko; Ishikura, Youji; Sakaguchi, Zenjiro; Suzuki, Moemi; Yamakawa, Makoto
TaqMan assays were developed for the broad-range detection of arboviruses belonging to Simbu serogroup lineage 1 in the genus Orthobunyavirus and also for the specific detection of three viruses in the lineage, Akabane, Aino and Peaton viruses (AKAV, AINOV and PEAV, respectively). A primer and probe set was designed for the broad-range detection of Simbu serogroup lineage 1 (Pan-Simbu1 set) mainly targeting AKAV, AINOV, PEAV, Sathuperi and Shamonda viruses (SATV and SHAV), and the forward and reverse primers of the Pan-Simbu1 set were also used for the specific detection of AKAV with another probe (AKAV-specific set). In addition, two more primer and probe sets were designed for AINOV- and PEAV-specific detection, respectively (AINOV- and PEAV-specific sets). All of the four primer and probe sets successfully detected targeted viruses, and thus broad-range and specific detection of all the targeted viruses can be achieved by using two multiplex assays and a single assay in a dual (two-color) assay format when another primer and probe set for a bovine β-actin control is also used. The assays had an analytical sensitivity of 10 copies/tube for AKAV, at least 100 copies/tube for AINOV, 100 copies/tube for PEAV, one copy/tube for SATV and at least 10 copies/tube for SHAV, respectively. Diagnostic sensitivity of the assays was tested with field-collected bovine samples, and the results suggested that the sensitivity was higher than that of a conventional RT-PCR. These data indicate that the newly developed TaqMan assays will be useful tools for the diagnosis and screening of field-collected samples for infections of AKAV and several other arboviruses belonging to the Simbu serogroup lineage 1.
Full Text Available In human leukemia, lineage-specific genes represent predominant targets of deletion, with lymphoid-specific genes frequently affected in lymphoid leukemia and myeloid-specific genes in myeloid leukemia. To investigate the basis of lineage-specific alterations, we analyzed global DNA damage in primary B cell precursors expressing leukemia-inducing oncogenes by ChIP-seq. We identified more than 1,000 sensitive regions, of which B lineage-specific genes constitute the most prominent targets. Identified hotspots at B lineage genes relate to DNA-DSBs, affect genes that harbor genomic lesions in human leukemia, and associate with ectopic deletion in successfully transformed cells. Furthermore, we show that most identified regions overlap with gene bodies of highly expressed genes and that induction of a myeloid lineage phenotype in transformed B cell precursors promotes de novo DNA damage at myeloid loci. Hence, we demonstrate that lineage-specific transcription predisposes lineage-specific genes in transformed B cell precursors to DNA damage, which is likely to promote the frequent alteration of lineage-specific genes in human leukemia.
Mark E. Samuels
Full Text Available Genetic mosaics provide information about cellular lineages that is otherwise difficult to obtain, especially in humans. De novo mutations act as cell markers, allowing the tracing of developmental trajectories of all descendants of the cell in which the new mutation arises. De novo mutations may arise at any time during development but are relatively rare. They have usually been observed through medical ascertainment, when the mutation causes unusual clinical signs or symptoms. Mutational events can include aneuploidies, large chromosomal rearrangements, copy number variants, or point mutations. In this review we focus primarily on the analysis of point mutations and their utility in addressing questions of germ line versus somatic lineages. Genetic mosaics demonstrate that the germ line and soma diverge early in development, since there are many examples of combined somatic and germ line mosaicism for de novo mutations. The occurrence of simultaneous mosaicism in both the germ line and soma also shows that the germ line is not strictly clonal but arises from at least two, and possibly multiple, cells in the embryo with different ancestries. Whole genome or exome DNA sequencing technologies promise to expand the range of studies of genetic mosaics, as de novo mutations can now be identified through sequencing alone in the absence of a medical ascertainment. These technologies have been used to study mutation patterns in nuclear families and in monozygotic twins, and in animal model developmental studies, but not yet for extensive cell lineage studies in humans.
Hopmans, R.; Van Kessel, L.; Lendering, K.; Oud, M.; Tromp, R.
The harbor of Surgidero de Batabano is a harbor that lies in the Gulf of Batabano in the South-Western part of Cuba. It serves as a connection between the main land of Cuba and the islands 'Isla de la Juventud' and Cayo Largo. The Batabano harbor suffers from sediment accretion. The accretion of sed
Hopmans, R.; Van Kessel, L.; Lendering, K.; Oud, M.; Tromp, R.
The harbor of Surgidero de Batabano is a harbor that lies in the Gulf of Batabano in the South-Western part of Cuba. It serves as a connection between the main land of Cuba and the islands 'Isla de la Juventud' and Cayo Largo. The Batabano harbor suffers from sediment accretion. The accretion of
@@ Douwei Harbor attracting petrochem investment Substantial progress has been made in the preliminary preparation of Douwei Harbor project in Hui'an, Fujian Province. It is one of the major four transfer ports in China planned by the Ministry of Transportation. A number of projects, with a total investment approaching 10 billion yuan,will come under construction in the harbor zone.
Levy, Carmit; Fisher, David E
Microphthalmia-associated Transcription Factor, MITF, is a master regulator of melanocyte development, differentiation, migration, and survival.(1) A broad collection of studies have indicated that MITF directly regulates the transcription of genes involved in pigmentation, which are selective to the melanocyte lineage. In addition, MITF controls expression of genes which are expressed in multiple cell lineages, and may also play differential roles in activating vs. maintaining gene expression patterns. In this Point of View article, we discuss lineage restricted transcription factor activation of both tissue-specific and ubiquitously expressed genes using melanocytes and MITF as a model system that may eventually provide insights into such processes in multiple cell lineages.
Full Text Available The phylogeographic structure and postglacial history of balsam fir (Abies balsamea, a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA and chloroplast DNA (cpDNA markers. Genetic structure among 107 populations (mtDNA data and 75 populations (cpDNA data was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only, but also for cpDNA (dispersed by seeds and pollen, indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.
Cinget, Benjamin; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean
The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.
Zhu Bing; Li Jinzong; Cheng Aijun
A fast knowledge based recognition method of the harbor target in large gray remote-sensing image is presented. First, the distributed features and the inherent feature are analyzed according to the knowledge of harbor targets; then, two methods for extracting the candidate region of harbor are devised in accordance with different sizes of the harbors; after that, thresholds are used to segment the land and the sea with strategies of the segmentation error control; finally, harbor recognition is implemented according to its inherent character (semi-closed region of seawater).
Nicolai Matthias Nürk
Full Text Available The páramos, high-elevation Andean grasslands ranging from ca. 2800 m to the snow line, harbor one of the fastest evolving biomes worldwide since their appearance in the northern Andes 3–5 million years (Ma ago. Hypericum (St. John’s wort, with over 65% of its Neotropical species, has a center of diversity in these high Mountain ecosystems. Using nuclear rDNA internal transcribed spacer (ITS sequences of a broad sample of New World Hypericum species we investigate phylogenetic patterns, estimate divergence times, and provide the first insights into diversification rates within the genus in the Neotropics. Two lineages appear to have independently dispersed into South America around 3.5 Ma ago, one of which has radiated in the páramos (Brathys. We find strong support for the polyphyly of section Trigynobrathys, several species of which group within Brathys, while others are found in temperate lowland South America (Trigynobrathys s.str.. All páramo species of Hypericum group in one clade. Within these páramo Hypericum species enormous phenotypic evolution has taken place (life forms from arborescent to prostrate shrubs evidently in a short time frame. We hypothesize multiple mechanisms to be responsible for the low differentiation in the ITS region contrary to the high morphological diversity found in Hypericum in the páramos. Amongst these may be ongoing hybridization and incomplete lineage sorting, as well as the putative adaptive radiation, which can explain the contrast between phenotypic diversity and the close phylogenetic relationships.
Nürk, Nicolai M; Scheriau, Charlotte; Madriñán, Santiago
The páramos, high-elevation Andean grasslands ranging from ca. 2800 m to the snow line, harbor one of the fastest evolving biomes worldwide since their appearance in the northern Andes 3-5 million years (Ma) ago. Hypericum (St. John's wort), with over 65% of its Neotropical species, has a center of diversity in these high Mountain ecosystems. Using nuclear rDNA internal transcribed spacer (ITS) sequences of a broad sample of New World Hypericum species we investigate phylogenetic patterns, estimate divergence times, and provide the first insights into diversification rates within the genus in the Neotropics. Two lineages appear to have independently dispersed into South America around 3.5 Ma ago, one of which has radiated in the páramos (Brathys). We find strong support for the polyphyly of section Trigynobrathys, several species of which group within Brathys, while others are found in temperate lowland South America (Trigynobrathys s.str.). All páramo species of Hypericum group in one clade. Within these páramo Hypericum species enormous phenotypic evolution has taken place (life forms from arborescent to prostrate shrubs) evidently in a short time frame. We hypothesize multiple mechanisms to be responsible for the low differentiation in the ITS region contrary to the high morphological diversity found in Hypericum in the páramos. Amongst these may be ongoing hybridization and incomplete lineage sorting, as well as the putative adaptive radiation, which can explain the contrast between phenotypic diversity and the close phylogenetic relationships.
Nürk, Nicolai M.; Scheriau, Charlotte; Madriñán, Santiago
The páramos, high-elevation Andean grasslands ranging from ca. 2800 m to the snow line, harbor one of the fastest evolving biomes worldwide since their appearance in the northern Andes 3–5 million years (Ma) ago. Hypericum (St. John's wort), with over 65% of its Neotropical species, has a center of diversity in these high Mountain ecosystems. Using nuclear rDNA internal transcribed spacer (ITS) sequences of a broad sample of New World Hypericum species we investigate phylogenetic patterns, estimate divergence times, and provide the first insights into diversification rates within the genus in the Neotropics. Two lineages appear to have independently dispersed into South America around 3.5 Ma ago, one of which has radiated in the páramos (Brathys). We find strong support for the polyphyly of section Trigynobrathys, several species of which group within Brathys, while others are found in temperate lowland South America (Trigynobrathys s.str.). All páramo species of Hypericum group in one clade. Within these páramo Hypericum species enormous phenotypic evolution has taken place (life forms from arborescent to prostrate shrubs) evidently in a short time frame. We hypothesize multiple mechanisms to be responsible for the low differentiation in the ITS region contrary to the high morphological diversity found in Hypericum in the páramos. Amongst these may be ongoing hybridization and incomplete lineage sorting, as well as the putative adaptive radiation, which can explain the contrast between phenotypic diversity and the close phylogenetic relationships. PMID:24062764
...) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater South Light 1. (b) A line drawn from Channel Islands Harbor Breakwater North Light to Channel Islands Harbor North Jetty Light 5....
Evelien M. Adriaenssens
Full Text Available Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.
Adriaenssens, Evelien M; van Zyl, Leonardo Joaquim; Cowan, Don A; Trindade, Marla I
Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.
Kang Hae Ji
Full Text Available Abstract Background Tanganya virus (TGNV, the only shrew-associated hantavirus reported to date from sub-Saharan Africa, is harbored by the Therese's shrew (Crocidura theresae, and is phylogenetically distinct from Thottapalayam virus (TPMV in the Asian house shrew (Suncus murinus and Imjin virus (MJNV in the Ussuri white-toothed shrew (Crocidura lasiura. The existence of myriad soricid-borne hantaviruses in Eurasia and North America would predict the presence of additional hantaviruses in sub-Saharan Africa, where multiple shrew lineages have evolved and diversified. Methods Lung tissues, collected in RNAlater®, from 39 Buettikofer's shrews (Crocidura buettikoferi, 5 Jouvenet's shrews (Crocidura jouvenetae, 9 West African pygmy shrews (Crocidura obscurior and 21 African giant shrews (Crocidura olivieri captured in Côte d'Ivoire during 2009, were systematically examined for hantavirus RNA by RT-PCR. Results A genetically distinct hantavirus, designated Azagny virus (AZGV, was detected in the West African pygmy shrew. Phylogenetic analysis of the S, M and L segments, using maximum-likelihood and Bayesian methods, under the GTR+I+Γ model of evolution, showed that AZGV shared a common ancestry with TGNV and was more closely related to hantaviruses harbored by soricine shrews than to TPMV and MJNV. That is, AZGV in the West African pygmy shrew, like TGNV in the Therese's shrew, did not form a monophyletic group with TPMV and MJNV, which were deeply divergent and basal to other rodent- and soricomorph-borne hantaviruses. Ancestral distributions of each hantavirus lineage, reconstructed using Mesquite 2.74, suggested that the common ancestor of all hantaviruses was most likely of Eurasian, not African, origin. Conclusions Genome-wide analysis of many more hantaviruses from sub-Saharan Africa are required to better understand how the biogeographic origin and radiation of African shrews might have contributed to, or have resulted from, the evolution
California Department of Resources — Harbor locations as identified originally in the California Shoreline Database compiled by Noble Consultants (Jon Moore) for California Department of Boating and...
their ultrasonic clicks as biosonar for orientation and detection of prey (mostly smaller pelagic and bottom dwelling fish), and for communication. For studying wild animals, hydrophone arrays [Villadsgaard et al. J.Exp.Biol. 210 (2007)] and acoustic (time/depth) tags [Akamatsu et al. Deep Sea Research II 54...... (2007)] have been used. For studying captive animals, arrays and video techniques [Verfuss et al. J.Exp.Biol. 208 (2005)] as well as miniature acoustic-behavioral tags [Deruiter et al. JASA 123 (2008)] have been used. While searching for prey, harbor porpoises use clicks at long intervals (~50 ms......) that progressively decrease when closing on an object. After detecting the prey, the click interval stabilizes and then becomes progressively shorter while approaching the prey. The sequence ends in a terminal, high repetition rate buzz (~500 clicks/s) just before capturing the prey (a video will be shown...
lwd. The authorized channel depth is -30 ft lwd at the entrance and -28 ft lwd in the Harbor. Original construction of Burns Harbor was completed in...and Burns Harbor North Breakwater, Indiana C oa st al a n d H yd ra u lic s La b or at or y Glenn B. Myrick, Jeffrey A. Melby, and...Breakwater, Ohio, and Burns Harbor North Breakwater, Indiana Glenn B. Myrick, Jeffrey A. Melby, and Elizabeth C. Burg Coastal and Hydraulics
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Winter Harbor Lobster Boat Race, Winter Harbor, ME. 100.109 Section 100.109 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Lobster Boat Race, Winter Harbor, ME. (a) Regulated area. The regulated area includes all waters of...
... Orleans Harbor, Inner Harbor Navigation Canal, New Orleans, Orleans Parish, LA AGENCY: Coast Guard, DHS... Seeber/Claiborne Avenue) ] vertical lift bridge across the Inner Harbor Navigational Canal, mile 0.9, (Gulf Intracoastal Waterway mile 6.7 East of Harvey Lock), at New Orleans, Orleans Parish,...
... Orleans Harbor, Inner Harbor Navigation Canal, New Orleans, Orleans Parish, LA AGENCY: Coast Guard, DHS... Seeber/Claiborne Avenue) vertical lift bridge across the Inner Harbor Navigational Canal, mile 0.9, (Gulf Intracoastal Waterway mile 6.7 East of Harvey Lock), at New Orleans, Orleans Parish, Louisiana. This...
Full Text Available Abstract Background Recent findings indicate that evolutionary breaks in the genome are not randomly distributed, and that certain regions, so-called fragile regions, are predisposed to breakages. Previous approaches to the study of genomic fragility have examined the distribution of breaks, as well as the coincidence of breaks with segmental duplications and repeats, within a single species. In contrast, we investigate whether this regional fragility is an inherent genomic characteristic and is thus conserved over multiple independent lineages. Results We do this by quantifying the extent to which certain genomic regions are disrupted repeatedly in independent lineages. Our investigation, based on Human, Chimp, Mouse, Rat, Dog and Chicken, suggests that the propensity of a chromosomal region to break is significantly correlated among independent lineages, even when covariates are considered. Furthermore, the fragile regions are enriched for segmental duplications. Conclusion Based on a novel methodology, our work provides additional support for the existence of fragile regions.
beamc. Tnis material will be re-deposited,, viaj troio it 1-apfro1inr ox prior location. j, MADAKET HARBOR NANTUCKET, MASSACHUSETTS FEASIBILITY...re- colonization of approximately 395 acres by scallops and quahogs. Also, barring any future disruption of the harbor area, the continued use of
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Cambridge Harbor. 117.549 Section... DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.549 Cambridge Harbor. The draw of the S342 bridge, mile 0.1 at Cambridge, shall open on signal from 6 a.m. to 8 p.m.; except that, from...
Odile B. Harrison
Interpretation: These data were inconsistent with a single point of origin followed by pandemic spread, rather suggesting that the sub-lineages had diversified and spread by asymptomatic transmission, with multiple distinct strains causing localised hyperendemic outbreaks.
ER D C/ CH L TR -1 4- 12 Inner Harbor Navigation Canal Basin Velocity Analysis Co as ta l a nd H yd ra ul ic s La bo ra to ry...library at http://acwc.sdp.sirsi.net/client/default. ERDC/CHL TR-14-12 October 2014 Inner Harbor Navigation Canal Basin Velocity Analysis...system of levees, gates, and drainage structures in the Inner Harbor Navigation Canal (IHNC) basin and the greater New Orleans, Louisiana, area. Two
Rossi, Flávia; Diaz, Lorena; Wollam, Aye; Panesso, Diana; Zhou, Yanjiao; Rincon, Sandra; Narechania, Apurva; Xing, Galen; Di Gioia, Thais S.R.; Doi, André; Tran, Truc T.; Reyes, Jinnethe; Munita, Jose M.; Carvajal, Lina P.; Hernandez-Roldan, Alejandra; Brandão, Denise; van der Heijden, Inneke Marie; Murray, Barbara E.; Planet, Paul J.; Weinstock, George M.; Arias, Cesar A.
SUMMARY We report the case of a patient from Brazil with a bloodstream infection caused by a strain of methicillin-resistant Staphylococcus aureus (MRSA) that was susceptible to vancomycin (designated BR-VSSA) but that acquired the vanA gene cluster during antibiotic therapy and became resistant to vancomycin (designated BR-VRSA). Both strains belong to the sequence type (ST) 8 community-associated genetic lineage that carries the staphylococcal chromosomal cassette mec (SCCmec) type IVa and the S. aureus protein A gene (spa) type t292 and are phylogenetically related to MRSA lineage USA300. A conjugative plasmid of 55,706 bp (pBRZ01) carrying the vanA cluster was identified and readily transferred to other staphylococci. The pBRZ01 plasmid harbors DNA sequences that are typical of the plasmid-associated replication genes rep24 or rep21 described in community-associated MRSA strains from Australia (pWBG745). The presence and dissemination of community-associated MRSA containing vanA could become a serious public health concern. PMID:24738669
US Fish and Wildlife Service, Department of the Interior — Unless additional salmon use data would indicate otherwise, harbor site 3 is considered the environmentally preferred alternative for construction of a small...
... child may have bones more typical of a child of 2. However, bone age is usually normal by age 6 to 12. Delay in speech development (expressive language delay) may be severe in Floating-Harbor syndrome , ...
Schupp James M
Full Text Available Abstract Background The global pattern of distribution of 1033 B. anthracis isolates has previously been defined by a set of 12 conserved canonical single nucleotide polymorphisms (canSNP. These studies reinforced the presence of three major lineages and 12 sub-lineages and sub-groups of this anthrax-causing pathogen. Isolates that form the A lineage (unlike the B and C lineages have become widely dispersed throughout the world and form the basis for the geographical disposition of "modern" anthrax. An archival collection of 191 different B. anthracis isolates from China provides a glimpse into the possible role of Chinese trade and commerce in the spread of certain sub-lineages of this pathogen. Canonical single nucleotide polymorphism (canSNP and multiple locus VNTR analysis (MLVA typing has been used to examine this archival collection of isolates. Results The canSNP study indicates that there are 5 different sub-lineages/sub-groups in China out of 12 previously described world-wide canSNP genotypes. Three of these canSNP genotypes were only found in the western-most province of China, Xinjiang. These genotypes were A.Br.008/009, a sub-group that is spread across most of Europe and Asia; A.Br.Aust 94, a sub-lineage that is present in Europe and India, and A.Br.Vollum, a lineage that is also present in Europe. The remaining two canSNP genotypes are spread across the whole of China and belong to sub-group A.Br.001/002 and the A.Br.Ames sub-lineage, two closely related genotypes. MLVA typing adds resolution to the isolates in each canSNP genotype and diversity indices for the A.Br.008/009 and A.Br.001/002 sub-groups suggest that these represent older and established clades in China. Conclusion B. anthracis isolates were recovered from three canSNP sub-groups (A.Br.008/009, A.Br.Aust94, and A.Br.Vollum in the western most portion of the large Chinese province of Xinjiang. The city of Kashi in this province appears to have served as a crossroads
Cieslak, Michael; Pruvost, Melanie; Benecke, Norbert; Hofreiter, Michael; Morales, Arturo; Reissmann, Monika; Ludwig, Arne
Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.
Full Text Available Neural crest cells are vertebrate-specific multipotent cells that contribute to a variety of tissues including the peripheral nervous system, melanocytes, and craniofacial bones and cartilage. Abnormal development of the neural crest is associated with several human maladies including cleft/lip palate, aggressive cancers such as melanoma and neuroblastoma, and rare syndromes, like Waardenburg syndrome, a complex disorder involving hearing loss and pigment defects. We previously identified the transcription factor Pax7 as an early marker, and required component for neural crest development in chick embryos. In mammals, Pax7 is also thought to play a role in neural crest development, yet the precise contribution of Pax7 progenitors to the neural crest lineage has not been determined.Here we use Cre/loxP technology in double transgenic mice to fate map the Pax7 lineage in neural crest derivates. We find that Pax7 descendants contribute to multiple tissues including the cranial, cardiac and trunk neural crest, which in the cranial cartilage form a distinct regional pattern. The Pax7 lineage, like the Pax3 lineage, is additionally detected in some non-neural crest tissues, including a subset of the epithelial cells in specific organs.These results demonstrate a previously unappreciated widespread distribution of Pax7 descendants within and beyond the neural crest. They shed light regarding the regionally distinct phenotypes observed in Pax3 and Pax7 mutants, and provide a unique perspective into the potential roles of Pax7 during disease and development.
Full Text Available Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times; 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.
This volume contains contributions by contributors to the 1985 Cold Springs Harbor Symposium on Quantitative Biology. This year's theme was Molecular Biology of Development. The volume consists of 104 articles organized by content into sections entitled Nuclear/Cytoplasmic Interactions in Early Development; Lineage and Segmentation/Pattern Formation; Homeotic Mutants; Homeo Boxes; Tissue Specificity/Position Effects; Expression of Genes Introduced into Transgenic Mice; Induced Developmental Defects; Control of Gene Expression; Sex Determination; Cell-cycle Effects; Pluripotent Cells/Oncogenes; Cellular Differentiation; and Developmental Neurobiology.
Multiple-locus variable-number tandem repeat fingerprinting as a method for rapid and cost-effective typing of animal-associated Staphylococcus aureus strains from lineages other than sequence type 398.
Kosecka-Strojek, Maja; Ilczyszyn, Weronika M; Buda, Aneta; Polakowska, Klaudia; Murzyn, Krzysztof; Panz, Tomasz; Bialecka, Anna; Kasprowicz, Andrzej; Jakubczak, Antoni; Krol, Jaroslaw; Wieliczko, Alina; Wladyka, Benedykt; Miedzobrodzki, Jacek
In veterinary medicine, Staphylococcus aureus is associated with a range of mild to severe infections. The high density of livestock in intensive farming systems increases the risk of disease spread and hampers its control and measures of prevention, making S. aureus one of the most important animal pathogens. Multiple-locus variable-number tandem repeat fingerprinting (MLVF) has been successfully applied to the characterization of livestock-associated meticillin-resistant Staphylococcus aureus (MRSA) ST398 but not to the characterization of a wide range of other animal isolates. The objective of the current study was to examine the effectiveness of MLVF for studying S. aureus strains isolated from households, farms and exotic animals in three regions of Poland. MLVF, random amplification of polymorphic DNA (RAPD), spa typing and diagnostic microarrays were compared to determine the most suitable combination of methods for veterinary purposes. MLVF generated results consistent with host and geographic origins, reflecting population structures with a high concordance to spa typing results. MLVF has been proven to be a rapid, highly discriminatory and cost-effective method suitable for molecular typing in veterinary settings.
Okolicsanyi, Rachel K; Griffiths, Lyn R; Haupt, Larisa M
Along with the tri-lineage of bone, cartilage and fat, human mesenchymal stem cells (hMSCs) retain neural lineage potential. Multiple factors have been described that influence lineage fate of hMSCs including the extracellular microenvironment or niche. The niche includes the extracellular matrix (ECM) providing structural composition, as well as other associated proteins and growth factors, which collectively influence hMSC stemness and lineage specification. As such, lineage specific differentiation of MSCs is mediated through interactions including cell-cell and cell-matrix, as well as through specific signalling pathways triggering downstream events. Proteoglycans (PGs) are ubiquitous within this microenvironment and can be localised to the cell surface or embedded within the ECM. In addition, the heparan sulfate (HS) and chondroitin sulfate (CS) families of PGs interact directly with a number of growth factors, signalling pathways and ECM components including FGFs, Wnts and fibronectin. With evidence supporting a role for HSPGs and CSPGs in the specification of hMSCs down the osteogenic, chondrogenic and adipogenic lineages, along with the localisation of PGs in development and regeneration, it is conceivable that these important proteins may also play a role in the differentiation of hMSCs toward the neuronal lineage. Here we summarise the current literature and highlight the potential for HSPG directed neural lineage fate specification in hMSCs, which may provide a new model for brain damage repair.
Lepper, G J; Swoboda, J
Investors and potential investors had hoped for meaningful guidance from the safe harbor regulations on appropriate structures for healthcare joint ventures. Unfortunately, the narrowly drawn final investment-interest safe harbor offers relatively little meaningful guidance or protection for the vast majority of such ventures. The Illegal Remuneration Statute (also known as the fraud and abuse statute) was first enacted in 1972 to prohibit members of the healthcare community from exchanging patient referrals for any kind of remuneration. In 1987 Congress instructed the secretary of Health and Human Services to create "safe harbors" for legitimate payment practices that, although they may violate the statute's strict prohibition, will be protected from prosecution. The investment-interest safe harbor has garnered the most attention. It provides two safe harbors, one for investments in large entities and one for investments in small entities. Both safe harbors contain onerous threshold requirements and other restrictions that diminish the usefulness of the safe harbor for all but a very few ventures. In addition, the Office of the Inspector General has created other obstacles to forming and preserving "safe" healthcare business ventures, including a refusal to "grandfather" or create a "safe harbor restructuring period" for existing business arrangements. Because most existing or planned joint ventures do not qualify for the investment-interest safe harbor, investors are forced to make their business decisions on the basis of the same factors used before publication of the safe harbor regulations. Such analysis will continue to focus on factors that demonstrate organizations' intent in making payments to investors as a return on investments.
Saelens, Joseph W; Lau-Bonilla, Dalia; Moller, Anneliese; Medina, Narda; Guzmán, Brenda; Calderón, Maylena; Herrera, Raúl; Sisk, Dana M; Xet-Mull, Ana M; Stout, Jason E; Arathoon, Eduardo; Samayoa, Blanca; Tobin, David M
Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased virulence and drug resistance, but there have been only a few cases reported in Central America. Here we report the first whole genome sequencing of Central American Beijing-lineage strains of Mtb. We find that multiple Beijing-lineage strains, derived from independent founding events, are currently circulating in Guatemala, but overall still represent a relatively small proportion of disease burden. Finally, we identify a specific Beijing-lineage outbreak centered on a poor neighborhood in Guatemala City.
Williams, June H; van Niekerk, Stephanie; Human, Stacey; van Wilpe, Erna; Venter, Marietjie
Since 2007, West Nile virus (WNV) has been reported in South African horses, causing severe neurological signs. All cases were of lineage 2, except for one case that clustered with lineage 1 viruses. In the present study, gross and microscopic lesions of six South African lineage 2-infected horses and the one lineage 1 case are described. Diagnoses were confirmed by real-time reverse-transcriptase polymerase chain reaction (RT-PCR) of central nervous system (CNS) tissue and one by RT-PCR of a brain virus isolate. The CNS of all cases was negative by RT-PCR or immunohistochemistry (IHC) for African horse sickness (AHS), equine encephalosis virus, equine herpes viruses 1 and 4, other zoonotic flaviviruses, alphaviruses, and shunivirus, and either by immunofluorescence or IHC for rabies. Gross visceral lesions were nonspecific but often mimicked those of AHS. The CNS histopathology of WNV lineage 2 cases resembled the nonsuppurative polioencephalomyelitis reported in the Northern Hemisphere lineage 1 and recent Hungarian lineage 2 cases. Occasional meningitis, focal spinal ventral horn poliomalacia, dorsal and lateral horn poliomyelitis, leucomyelitis, asymmetrical ventral motor spinal neuritis and frequent olfactory region involvement were also seen. Lineage 2 cases displayed marked variations in CNS lesion severity, type and distribution, and suggested various viral entry routes into the CNS, based on findings in experimental mice and hamsters. Lineage 1 lesions were comparable to the milder lineage 2 cases. West Nile virus IHC on CNS sections with marked lesions from all cases elicited only two antigen-positive cells in the olfactory cortex of one case. The presence in the CNS of T-lymphocytes, B-lymphocytes, plasma cells and macrophage-monocytes was confirmed by cluster of differentiation (CD) 3, CD20, multiple myeloma oncogene 1 (MUM1) and macrophage (MAC) 387 IHC.
June H. Williams
Full Text Available Since 2007, West Nile virus (WNV has been reported in South African horses, causing severe neurological signs. All cases were of lineage 2, except for one case that clustered with lineage 1 viruses. In the present study, gross and microscopic lesions of six South African lineage 2-infected horses and the one lineage 1 case are described. Diagnoses were confirmed by real-time reverse-transcriptase polymerase chain reaction (RT-PCR of central nervous system (CNS tissue and one by RT-PCR of a brain virus isolate. The CNS of all cases was negative by RT-PCR or immunohistochemistry (IHC for African horse sickness (AHS, equine encephalosis virus, equine herpes viruses 1 and 4, other zoonotic flaviviruses, alphaviruses, and shunivirus, and either by immunofluorescence or IHC for rabies. Gross visceral lesions were nonspecific but often mimicked those of AHS. The CNS histopathology of WNV lineage 2 cases resembled the nonsuppurative polioencephalomyelitis reported in the Northern Hemisphere lineage 1 and recent Hungarian lineage 2 cases. Occasional meningitis, focal spinal ventral horn poliomalacia, dorsal and lateral horn poliomyelitis, leucomyelitis, asymmetrical ventral motor spinal neuritis and frequent olfactory region involvement were also seen. Lineage 2 cases displayed marked variations in CNS lesion severity, type and distribution, and suggested various viral entry routes into the CNS, based on findings in experimental mice and hamsters. Lineage 1 lesions were comparable to the milder lineage 2 cases. West Nile virus IHC on CNS sections with marked lesions from all cases elicited only two antigen-positive cells in the olfactory cortex of one case. The presence in the CNS of T-lymphocytes, B-lymphocytes, plasma cells and macrophage-monocytes was confirmed by cluster of differentiation (CD 3, CD20, multiple myeloma oncogene 1 (MUM1 and macrophage (MAC 387 IHC.
Full Text Available Abstract Background Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the Indian populations has been characterized. In this study, we attempted to reconstruct and re-evaluate the phylogeny of Macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage, and to shed light on the origin of its deep rooting haplogroups. Results Using 11 whole mtDNA and 2231 partial coding sequence of Indian M lineage selected from 8670 HVS1 sequences across India, we have reconstructed the tree including Andamanese-specific lineage M31 and calculated the time depth of all the nodes. We defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31. Conclusion Our result indicates that the Indian mtDNA pool consists of several deep rooting lineages of macrohaplogroup 'M' suggesting in-situ origin of these haplogroups in South Asia, most likely in the India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of the Andamanese-specific lineage M31 suggests population specific two clear-cut subclades (M31a1 and M31a2. Onge and Jarwa share M31a1 branch while M31a2 clade is present in only Great Andamanese individuals. Overall our study supported the one wave, rapid dispersal theory of modern humans along the Asian coast.
Full Text Available Understanding of processes driving bacterial speciation requires examination of closely related, recently diversified lineages. To gain an insight into diversification of bacteria, we conducted comparative genomic analysis of two lineages of bioluminescent symbionts, Photobacterium leiognathi and 'P. mandapamensis'. The two lineages are evolutionary and ecologically closely related. Based on the methods used in bacterial taxonomy for classification of new species (DNA-DNA hybridization and ANI, genetic relatedness of the two lineages is at a cut-off point for species delineation. In this study, we obtained the whole genome sequence of a representative P. leiognathi strain lrivu.4.1, and compared it to the whole genome sequence of 'P. mandapamensis' svers.1.1. Results of the comparative genomic analysis suggest that P. leiognathi has a more plastic genome and acquired genes horizontally more frequently than 'P. mandapamensis'. We predict that different rates of recombination and gene acquisition contributed to diversification of the two lineages. Analysis of lineage-specific sequences in 25 strains of P. leiognathi and 'P. mandapamensis' found no evidence that bioluminescent symbioses with specific host animals have played a role in diversification of the two lineages.
Urbanczyk, Henryk; Urbanczyk, Yoshiko; Hayashi, Tetsuya; Ogura, Yoshitoshi
Understanding of processes driving bacterial speciation requires examination of closely related, recently diversified lineages. To gain an insight into diversification of bacteria, we conducted comparative genomic analysis of two lineages of bioluminescent symbionts, Photobacterium leiognathi and 'P. mandapamensis'. The two lineages are evolutionary and ecologically closely related. Based on the methods used in bacterial taxonomy for classification of new species (DNA-DNA hybridization and ANI), genetic relatedness of the two lineages is at a cut-off point for species delineation. In this study, we obtained the whole genome sequence of a representative P. leiognathi strain lrivu.4.1, and compared it to the whole genome sequence of 'P. mandapamensis' svers.1.1. Results of the comparative genomic analysis suggest that P. leiognathi has a more plastic genome and acquired genes horizontally more frequently than 'P. mandapamensis'. We predict that different rates of recombination and gene acquisition contributed to diversification of the two lineages. Analysis of lineage-specific sequences in 25 strains of P. leiognathi and 'P. mandapamensis' found no evidence that bioluminescent symbioses with specific host animals have played a role in diversification of the two lineages.
Volume 55 of the Cold Spring Harbor Symposium on Quantitative Biology is dedicated to the study of the brain. The symposium was subdivided into four major sections. Papers were presented in Molecular Mechanisms for Signalling; Neural Development; Sensory and Motor Systems; and Cognitive Neuroscience. Individual papers from the symposium are abstracted separately. (MHB)
This volume contains the first part of the proceeding of the 53rd Cold Springs Harbor Symposium on Quantitative Biology. This years topic was Immune Recognition. Part 1, this volume, contains papers prepared by presenters of the sessions entitled Introduction, Lymphocyte Development and Receptor Selection, and Recognition by Antibodies, Antigen Recognition by T cells. (DT)
This volume contains the second part of the proceedings of the 53rd Cold Springs Harbor Symposium on Quantitative Biology. This years topic was Immune Recognition. This volume, part 2, contains papers prepared by presenters for two sessions entitled Signals for Lymphocyte Activation, Proliferation, and Adhesion, and entitled Tolerance and Self Recognition. (DT)
... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Safe harbors. 312.10 Section 312.10 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS CHILDREN'S ONLINE... provide the same or greater protections for children as those contained in §§ 312.2 through 312.9; (2)...
Campana, Michael G; Robles García, Nelly M; Tuross, Noreen
Cultivated cochineal (Dactylopius coccus) produces carminic acid, a valuable red dye used to color textiles, cosmetics, and food. Extant native D. coccus is largely restricted to two populations in the Mexican and the Andean highlands, although the insect's ultimate center of domestication remains unclear. Moreover, due to Mexican D. coccus cultivation's near demise during the 19th century, the genetic diversity of current cochineal stock is unknown. Through genomic sequencing, we identified two divergent D. coccus populations in highland Mexico: one unique to Mexico and another that was more closely related to extant Andean cochineal. Relic diversity is preserved in the crops of small-scale Mexican cochineal farmers. Conversely, larger-scale commercial producers are cultivating the Andean-like cochineal, which may reflect clandestine 20th century importation.
Campana, Michael G; Robles García, Nelly M; Tuross, Noreen
Cultivated cochineal (Dactylopius coccus) produces carminic acid, a valuable red dye used to color textiles, cosmetics, and food. Extant native D. coccus is largely restricted to two populations in the Mexican and the Andean highlands, although the insect's ultimate center of domestication remains unclear. Moreover, due to Mexican D. coccus cultivation's near demise during the 19th century, the genetic diversity of current cochineal stock is unknown. Through genomic sequencing, we identified two divergent D. coccus populations in highland Mexico: one unique to Mexico and another that was more closely related to extant Andean cochineal. Relic diversity is preserved in the crops of small-scale Mexican cochineal farmers. Conversely, larger-scale commercial producers are cultivating the Andean-like cochineal, which may reflect clandestine 20th century importation. PMID:25691985
Tarkhnishvili, David; Gavashelishvili, Alexander; Murtskhvaladze, Marine; Gabelaia, Mariam; Tevzadze, Gigi
Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western
Zamoto-Niikura, Aya; Tsuji, Masayoshi; Qiang, Wei; Nakao, Minoru; Hirata, Haruyuki; Ishihara, Chiaki
The species Babesia microti, commonly found in rodents, demonstrates a high degree of genetic diversity. Three lineages, U.S., Kobe, and Hobetsu, are known to have zoonotic potential, but their tick vector(s) in Japan remains to be elucidated. We conducted a field investigation at Nemuro on Hokkaido Island and at Sumoto on Awaji Island, where up to two of the three lineages occur with similar frequencies in reservoirs. By flagging vegetation at these spots and surrounding areas, 4,010 ticks, comprising six species, were collected. A nested PCR that detects the 18S rRNA gene of Babesia species revealed that Ixodes ovatus and I. persulcatus alone were positive. Lineage-specific PCR for rRNA-positive samples demonstrated that I. ovatus and I. persulcatus carried, respectively, the Hobetsu and U.S. parasites. No Kobe-specific DNA was detected. Infected I. ovatus ticks were found at multiple sites, including Nemuro and Sumoto, with minimum infection rates (MIR) of ∼12.3%. However, all I. persulcatus ticks collected within the same regions, a total of 535, were negative for the Hobetsu lineage, indicating that I. ovatus, but not I. persulcatus, was the vector for the lineage. At Nemuro, U.S. lineage was detected in 2 of 139 adult I. persulcatus ticks (MIR, 1.4%), for the first time, while 48 of I. ovatus ticks were negative for that lineage. Laboratory experiments confirmed the transmission of Hobetsu and U.S. parasites to hamsters via I. ovatus and I. persulcatus, respectively. Differences in vector capacity shown by MIRs at Nemuro, where the two species were equally likely to acquire either lineage of parasite, may explain the difference in distribution of Hobetsu throughout Japan and U.S. taxa in Nemuro. These findings are of importance in the assessment of the regional risk for babesiosis in humans.
Evrony, Gilad D; Lee, Eunjung; Mehta, Bhaven K; Benjamini, Yuval; Johnson, Robert M; Cai, Xuyu; Yang, Lixing; Haseley, Psalm; Lehmann, Hillel S; Park, Peter J; Walsh, Christopher A
Somatic mutations occur during brain development and are increasingly implicated as a cause of neurogenetic disease. However, the patterns in which somatic mutations distribute in the human brain are unknown. We used high-coverage whole-genome sequencing of single neurons from a normal individual to identify spontaneous somatic mutations as clonal marks to track cell lineages in human brain. Somatic mutation analyses in >30 locations throughout the nervous system identified multiple lineages and sublineages of cells marked by different LINE-1 (L1) retrotransposition events and subsequent mutation of poly-A microsatellites within L1. One clone contained thousands of cells limited to the left middle frontal gyrus, whereas a second distinct clone contained millions of cells distributed over the entire left hemisphere. These patterns mirror known somatic mutation disorders of brain development and suggest that focally distributed mutations are also prevalent in normal brains. Single-cell analysis of somatic mutation enables tracing of cell lineage clones in human brain. Copyright © 2015 Elsevier Inc. All rights reserved.
US Fish and Wildlife Service, Department of the Interior — Six alternatives are presently being studied by the Corps of Engineers, in conjunction with facilitating construction of a bottomfish harbor at Akutan Harbor located...
National Oceanic and Atmospheric Administration, Department of Commerce — Aerial surveys of coastal Alaska are the primary method for estimating abundance of harbor seals. A particular challenge associated with aerial surveys of harbor...
Santamaria, Carlos A; Mateos, Mariana; DeWitt, Thomas J; Hurtado, Luis A
Multiple highly divergent lineages have been identified within Ligia occidentalis sensu lato, a rocky supralittoral isopod distributed along a ~3000 km latitudinal gradient that encompasses several proposed marine biogeographic provinces and ecoregions in the eastern Pacific. Highly divergent lineages have nonoverlapping geographic distributions, with distributional limits that generally correspond with sharp environmental changes. Crossbreeding experiments suggest postmating reproductive barriers exist among some of them, and surveys of mitochondrial and nuclear gene markers do not show evidence of hybridization. Populations are highly isolated, some of which appear to be very small; thus, the effects of drift are expected to reduce the efficiency of selection. Large genetic divergences among lineages, marked environmental differences in their ranges, reproductive isolation, and/or high isolation of populations may have resulted in morphological differences in L. occidentalis, not detected yet by traditional taxonomy. We used landmark-based geometric morphometric analyses to test for differences in body shape among highly divergent lineages of L. occidentalis, and among populations within these lineages. We analyzed a total of 492 individuals from 53 coastal localities from the southern California Bight to Central Mexico, including the Gulf of California. We conducted discriminant function analyses (DFAs) on body shape morphometrics to assess morphological variation among genetically differentiated lineages and their populations. We also tested for associations between phylogeny and morphological variation, and whether genetic divergence is correlated to multivariate morphological divergence. We detected significant differences in body shape among highly divergent lineages, and among populations within these lineages. Nonetheless, neither lineages nor populations can be discriminated on the basis of body shape, because correct classification rates of cross
Liehr, Patricia; Sopcheck, Janet; Milbrath, Gwyneth
: On December 7, 1941, the Sunday-morning quiet of the U.S. naval base in Pearl Harbor, Hawaii, was shattered by dive-bombing Japanese fighter planes. The planes came in two waves-and when it was all over, more than 2,400 were killed and more than 1,100 were injured.Nurses were stationed at U.S. Naval Hospital Pearl Harbor, Tripler General Hospital (now Tripler Army Medical Center), Hickam Field Hospital, Schofield Barracks Station Hospital, and aboard the USS Solace, and witnessed the devastation. But they also did what nurses do in emergencies-they responded and provided care to those in need. Here are the stories of a few of those nurses.
... 32 National Defense 5 2010-07-01 2010-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules and...
... Documents#0;#0; ] Proclamation 9068 of December 5, 2013 National Pearl Harbor Remembrance Day, 2013 By the... resolve. On National Pearl Harbor Remembrance Day, we honor the men and women who selflessly sacrificed... forces of tyranny and oppression in the Second World War. In remembrance of Pearl Harbor and to...
... Documents#0;#0; ] Proclamation 8614 of December 7, 2010 National Pearl Harbor Remembrance Day, 2010 By the... service members and civilians awoke on a quiet Sunday to a surprise attack on Pearl Harbor by Japanese... lives lost were forever seared into our national memory. The deadly attack on Pearl Harbor did...
Shields, Anna Marshall
These materials consist of sample lesson plans for teaching about the Japanese attack on Pearl Harbor on December 7, 1941, in both U.S. and world history classes. The lesson plans challenge students to examine how current attitudes toward the Japanese may be rooted in World War II and Pearl Harbor. Selected bibliographies on Pearl Harbor, World…
the finback whale (Balaenoptera physalus), humpback whale ( Megaptera novaeangliae ), sei whale (B. borealis), green sea turtle (Chelonia mydas...Environmental Policy Act, as amended, 42 USC 4321, et seq. Rivers and Harbors Act, 33 USC 401 et seq. Watershed Protection and Flood Prevention Act, 16...USC 1001, et seq. Wild and Scenic Rivers Act, as amended, 16 USC 1271, et seq. Uniform Relocation Assistance and Real Property Acquisition Policies Act
Hood, Rebecca L; Schenkel, Laila C; Nikkel, Sarah M; Ainsworth, Peter J; Pare, Guillaume; Boycott, Kym M; Bulman, Dennis E; Sadikovic, Bekim
Floating-Harbor syndrome (FHS) is an autosomal dominant genetic condition characterized by short stature, delayed osseous maturation, expressive language impairment, and unique facial dysmorphology. We previously identified mutations in the chromatin remodeling protein SRCAP (SNF2-related CBP Activator Protein) as the cause of FHS. SRCAP has multiple roles in chromatin and transcriptional regulation; however, specific epigenetic consequences of SRCAP mutations remain to be described. Using high resolution genome-wide DNA methylation analysis, we identified a unique and highly specific DNA methylation "epi-signature" in the peripheral blood of individuals with FHS. Both hyper and hypomethylated loci are distributed across the genome, preferentially occurring in CpG islands. Clonal bisulfite sequencing of two hypermethylated (FIGN and STPG2) and two hypomethylated (MYO1F and RASIP1) genes confirmed these findings. The identification of a unique methylation signature in FHS provides further insight into the biological function of SRCAP and provides a unique biomarker for this disorder.
Huynh, Thanh Canh; Lee, So Young; Nauyen, Khac Duy; Kim, Jeong Tae [Pukyong National Univ., Busan (Korea, Republic of)
The objective of this study is to monitor the health status of harbor caissons which have potential foundation damage. To obtain the objective, the following approaches are performed. Firstly, a structural damage monitoring(SDM) method is designed for interlocked multiple caisson structures. The SDM method utilizes the change in modal strain energy to monitor the foundation damage in a target caisson unit. Secondly, a finite element model of a caisson system which consists of three caisson units is established to verify the feasibility of the proposed method. In the finite element simulation, the caisson units are constrained each other by shear key connections. The health status of the caisson system against various levels of foundation damage is monitored by measuring relative modal displacements between the adjacent caissons.
Full Text Available Cellular barcoding and other single-cell lineage-tracing strategies form experimental methodologies for analysis of in vivo cell fate that have been instrumental in several significant recent discoveries. Due to the highly nonlinear nature of proliferation and differentiation, interrogation of the resulting data for evaluation of potential lineage pathways requires a new quantitative framework complete with appropriate statistical tests. Here, we develop such a framework, illustrating its utility by analyzing data from barcoded multipotent cells of the blood system. This application demonstrates that the data require additional paths beyond those found in the classical model, which leads us to propose that hematopoietic differentiation follows a loss of potential mechanism and to suggest further experiments to test this deduction. Our quantitative framework can evaluate the compatibility of lineage trees with barcoded data from any proliferating and differentiating cell system.
Catarina C F Homem
Full Text Available The developing Drosophila brain is a well-studied model system for neurogenesis and stem cell biology. In the Drosophila central brain, around 200 neural stem cells called neuroblasts undergo repeated rounds of asymmetric cell division. These divisions typically generate a larger self-renewing neuroblast and a smaller ganglion mother cell that undergoes one terminal division to create two differentiating neurons. Although single mitotic divisions of neuroblasts can easily be imaged in real time, the lack of long term imaging procedures has limited the use of neuroblast live imaging for lineage analysis. Here we describe a method that allows live imaging of cultured Drosophila neuroblasts over multiple cell cycles for up to 24 hours. We describe a 4D image analysis protocol that can be used to extract cell cycle times and growth rates from the resulting movies in an automated manner. We use it to perform lineage analysis in type II neuroblasts where clonal analysis has indicated the presence of a transit-amplifying population that potentiates the number of neurons. Indeed, our experiments verify type II lineages and provide quantitative parameters for all cell types in those lineages. As defects in type II neuroblast lineages can result in brain tumor formation, our lineage analysis method will allow more detailed and quantitative analysis of tumorigenesis and asymmetric cell division in the Drosophila brain.
Julia M Riehm
Full Text Available BACKGROUND: Whole genome sequencing allowed the development of a number of high resolution sequence based typing tools for Yersinia (Y. pestis. The application of these methods on isolates from most known foci worldwide and in particular from China and the Former Soviet Union has dramatically improved our understanding of the population structure of this species. In the current view, Y. pestis including the non or moderate human pathogen Y. pestis subspecies microtus emerged from Yersinia pseudotuberculosis about 2,600 to 28,600 years ago in central Asia. The majority of central Asia natural foci have been investigated. However these investigations included only few strains from Mongolia. METHODOLOGY/PRINCIPAL FINDINGS: Clustered Regularly Interspaced Short Prokaryotic Repeats (CRISPR analysis and Multiple-locus variable number of tandem repeats (VNTR analysis (MLVA with 25 loci was performed on 100 Y. pestis strains, isolated from 37 sampling areas in Mongolia. The resulting data were compared with previously published data from more than 500 plague strains, 130 of which had also been previously genotyped by single nucleotide polymorphism (SNP analysis. The comparison revealed six main clusters including the three microtus biovars Ulegeica, Altaica, and Xilingolensis. The largest cluster comprises 78 isolates, with unique and new genotypes seen so far in Mongolia only. Typing of selected isolates by key SNPs was used to robustly assign the corresponding clusters to previously defined SNP branches. CONCLUSIONS/SIGNIFICANCE: We show that Mongolia hosts the most recent microtus clade (Ulegeica. Interestingly no representatives of the ancestral Y. pestis subspecies pestis nodes previously identified in North-western China were identified in this study. This observation suggests that the subsequent evolution steps within Y. pestis pestis did not occur in Mongolia. Rather, Mongolia was most likely re-colonized by more recent clades coming back from
Mun-Fun, Hoo; Ferdaos, Nurfarhana; Hamzah, Siti Nurusaadah; Ridzuan, Noridzzaida; Hisham, Nurul Afiqah; Abdullah, Syahril; Ramasamy, Rajesh; Cheah, Pike See; Thilakavathy, Karrupiah; Yazid, Mohd Nazri; Nordin, Norshariza
Amniotic fluid stem cells (AFSCs) are commonly isolated from mid-term amniotic fluid (AF) of animals and human collected via an invasive technique, amniocentesis. Alternatively, AFSCs could be collected at full-term. However, it is unclear whether AFSCs are present in the AF at full term. Here, we aimed to isolate and characterize stem cells isolated from AF of full term pregnant rats. Three stem cell lines have been established following immuno-selection against the stem cell marker, c-kit. Two of the new lines expressed multiple markers of pluripotency until more than passage 90. Further, they spontaneously differentiated into derivatives of the three primary germ layers through the formation of good quality embryoid bodies (EBs), and can be directly differentiated into neural lineage. Their strong stemness and potent neurogenic properties highlight the presence of highly potent stem cells in AF of full-term pregnancies, which could serve as a potential source of stem cells for regenerative medicine.
Ohmura, Sakie; Mizuno, Seiya; Oishi, Hisashi; Ku, Chia-Jui; Hermann, Mary; Hosoya, Tomonori; Takahashi, Satoru; Engel, James Douglas
The transcription factor GATA3 is essential for the genesis and maturation of the T cell lineage, and GATA3 dysregulation has pathological consequences. Previous studies have shown that GATA3 function in T cell development is regulated by multiple signaling pathways and that the Notch nuclear effector, RBP-J, binds specifically to the Gata3 promoter. We previously identified a T cell-specific Gata3 enhancer (Tce1) lying 280 kb downstream from the structural gene and demonstrated in transgenic mice that Tce1 promoted T lymphocyte-specific transcription of reporter genes throughout T cell development; however, it was not clear if Tce1 is required for Gata3 transcription in vivo. Here, we determined that the canonical Gata3 promoter is insufficient for Gata3 transcriptional activation in T cells in vivo, precluding the possibility that promoter binding by a host of previously implicated transcription factors alone is responsible for Gata3 expression in T cells. Instead, we demonstrated that multiple lineage-affiliated transcription factors bind to Tce1 and that this enhancer confers T lymphocyte-specific Gata3 activation in vivo, as targeted deletion of Tce1 in a mouse model abrogated critical functions of this T cell-regulatory element. Together, our data show that Tce1 is both necessary and sufficient for critical aspects of Gata3 T cell-specific transcriptional activity.
Fábio P. Dornas
Full Text Available In 2003, Acanthamoeba polyphaga mimivirus (APMV was discovered as parasitizing Acanthamoeba. It was revealed to exhibit remarkable features, especially odd genomic characteristics, and founded viral family Mimiviridae. Subsequently, a second family of giant amoebal viruses was described, Marseilleviridae, whose prototype member is Marseillevirus, discovered in 2009. Currently, the genomes of seven different members of this family have been fully sequenced. Previous phylogenetic analysis suggested the existence of three Marseilleviridae lineages: A, B and C. Here, we describe a new member of this family, Brazilian Marseillevirus (BrMV, which was isolated from a Brazilian sample and whose genome was fully sequenced and analyzed. Surprisingly, data from phylogenetic analyses and comparative genomics, including mean amino acid identity between BrMV and other Marseilleviridae members and the analyses of the core genome and pan-genome of marseilleviruses, indicated that this virus can be assigned to a new Marseilleviridae lineage. Even if the BrMV genome is one of the smallest among Marseilleviridae members, it harbors the second largest gene content into this family. In addition, the BrMV genome encodes 29 ORFans. Here, we describe the isolation and genome analyses of the BrMV strain, and propose its classification as the prototype virus of a new lineage D within the family Marseilleviridae.
Dornas, Fábio P.; Assis, Felipe L.; Aherfi, Sarah; Arantes, Thalita; Abrahão, Jônatas S.; Colson, Philippe; La Scola, Bernard
In 2003, Acanthamoeba polyphaga mimivirus (APMV) was discovered as parasitizing Acanthamoeba. It was revealed to exhibit remarkable features, especially odd genomic characteristics, and founded viral family Mimiviridae. Subsequently, a second family of giant amoebal viruses was described, Marseilleviridae, whose prototype member is Marseillevirus, discovered in 2009. Currently, the genomes of seven different members of this family have been fully sequenced. Previous phylogenetic analysis suggested the existence of three Marseilleviridae lineages: A, B and C. Here, we describe a new member of this family, Brazilian Marseillevirus (BrMV), which was isolated from a Brazilian sample and whose genome was fully sequenced and analyzed. Surprisingly, data from phylogenetic analyses and comparative genomics, including mean amino acid identity between BrMV and other Marseilleviridae members and the analyses of the core genome and pan-genome of marseilleviruses, indicated that this virus can be assigned to a new Marseilleviridae lineage. Even if the BrMV genome is one of the smallest among Marseilleviridae members, it harbors the second largest gene content into this family. In addition, the BrMV genome encodes 29 ORFans. Here, we describe the isolation and genome analyses of the BrMV strain, and propose its classification as the prototype virus of a new lineage D within the family Marseilleviridae. PMID:26978387
Brandley, Matthew C; Wang, Yuezhao; Guo, Xianguang; Nieto Montes de Oca, Adrián; Fería Ortíz, Manuel; Hikida, Tsutomu; Ota, Hidetoshi
Oceanic islands are well known for harboring diverse species assemblages and are frequently the basis of research on adaptive radiation and neoendemism. However, a commonly overlooked role of some islands is their function in preserving ancient lineages that have become extinct everywhere else (paleoendemism). The island archipelago of Bermuda is home to a single species of extant terrestrial vertebrate, the endemic skink Plestiodon (formerly Eumeces) longirostris. The presence of this species is surprising because Bermuda is an isolated, relatively young oceanic island approximately 1000 km from the eastern United States. Here, we apply Bayesian phylogenetic analyses using a relaxed molecular clock to demonstrate that the island of Bermuda, although no older than two million years, is home to the only extant representative of one of the earliest mainland North American Plestiodon lineages, which diverged from its closest living relatives 11.5 to 19.8 million years ago. This implies that, within a short geological time frame, mainland North American ancestors of P. longirostris colonized the recently emergent Bermuda and the entire lineage subsequently vanished from the mainland. Thus, our analyses reveal that Bermuda is an example of a "life raft" preserving millions of years of unique evolutionary history, now at the brink of extinction. Threats such as habitat destruction, littering, and non-native species have severely reduced the population size of this highly endangered lizard.
Matthew C Brandley
Full Text Available Oceanic islands are well known for harboring diverse species assemblages and are frequently the basis of research on adaptive radiation and neoendemism. However, a commonly overlooked role of some islands is their function in preserving ancient lineages that have become extinct everywhere else (paleoendemism. The island archipelago of Bermuda is home to a single species of extant terrestrial vertebrate, the endemic skink Plestiodon (formerly Eumeces longirostris. The presence of this species is surprising because Bermuda is an isolated, relatively young oceanic island approximately 1000 km from the eastern United States. Here, we apply Bayesian phylogenetic analyses using a relaxed molecular clock to demonstrate that the island of Bermuda, although no older than two million years, is home to the only extant representative of one of the earliest mainland North American Plestiodon lineages, which diverged from its closest living relatives 11.5 to 19.8 million years ago. This implies that, within a short geological time frame, mainland North American ancestors of P. longirostris colonized the recently emergent Bermuda and the entire lineage subsequently vanished from the mainland. Thus, our analyses reveal that Bermuda is an example of a "life raft" preserving millions of years of unique evolutionary history, now at the brink of extinction. Threats such as habitat destruction, littering, and non-native species have severely reduced the population size of this highly endangered lizard.
Full Text Available West Nile virus (WNV has a complex eco-epidemiology with birds acting as reservoirs and hosts for the virus. Less well understood is the role of reptiles, especially in wild populations. The goal of our study was to determine whether a wild population of snakes in Pennsylvania harbored WNV. Six species of snakes were orally sampled in the summer of 2013 and were tested for the presence of WNV viral RNA using RT-PCR. Two Eastern Garter Snakes, Thamnophis sirtalis sirtalis tested positive for viral RNA (2/123, 1.62%. These results indicate a possible role for snakes in the complex transmission cycle of WNV.
For many decades, it has been clear that cells have a multitude of ways of sensing their environment and converting a plethora of external signals into measured intracellular responses. Now we realize that many first messengers do not act directly through second messengers, but instead work at the genetic level by binding to cytoplasmically located receptors, which can then bind to DNA and turn on or off the functioning of specific genes. Today, we refer to the way that external signals are passed through various cellular components as signal transduction processes, with receptors and their associated molecules known as biological transducers. Because most transducer molecules are present in very limited amounts, their study at the biochemical level until recently was at best difficult, and hypothesis as to how they functioned were almost impossible to test rigorously. Today, recombinant DNA techniques have dramatically changed the picture. Even very rare receptors are now open to analyses if their respective genes can be cloned, and virtually every month, the amino acid sequence of a new key biological transducer is established. The time was thus appropriate last June to hold a Cold Spring Harbor Symposium on the Molecular Biology of Signal Transduction. The final program consisted of 119 speakers, who spoke before an audience of 439, the largest ever yet to attend a Cold spring Harbor Symposium. This volume contains 61 papers. Individual papers are indexed separately on the energy data base.
For many decades, it has been clear that cells have a multitude of ways of sensing their environment and converting a plethora of external signals into measured intracellular responses. Now we realize that many first messengers do not act directly through second messengers, but instead work at the genetic level by binding to cytoplasmically located receptors, which can then bind to DNA and turn on or off the functioning of specific genes. Today, we refer to the way that external signals are passed through various cellular components as signal transduction processes, with receptors and their associated molecules known as biological transducers. Because most transducer molecules are present in very limited amounts, their study at the biochemical level until recently was at best difficult, and hypotheses as to how they functioned were almost impossible to test rigorously. Today, recombinant DNA techniques have dramatically changed the picture. Even very rare receptors are now open to analysis if their respective genes can be cloned, and virtually every month the amino acid sequence of a new key biological transducer is established. The time was thus appropriate last June to hold a Cold Spring Harbor Symposium on the Molecular Biology of Signal Transduction. The final program consisted of 119 speakers, who spoke before an audience of 439, the largest ever yet to attend a Cold Spring Harbor Symposium. This volume contains 54 papers. Individual papers are indexed separately on the energy data base.
It is generally accepted that nonlinear wave-wave interactions play an important role in harbor resonance. Nevertheless it is not clear how waves take part in those interactions. The aim of this paper is to investigate those processes for a rectangular harbor at transient phases. Long-period oscillations excited by bichromatic waves are simulated by the Boussinesq model. The simulations start from calm conditions for the purpose of studying the response process. The internal wavemaker stops working after the oscillations have reached a quasi-steady state, and it is used to simulate the damp process. In order to analyze temporary features of wave-wave interactions in different states, the wavelet-based bispectrum is employed. The influence of the short wave frequencies on long-period oscillations is investigated, and reasons are tried to be given from nonlinear triad interactions between different wave components and the interaction of short waves and the bay entrance. Finally, the response time and the damp time are estimated by a simple method.
Li, Kun; Lin, Xian-Dan; Wang, Wen; Shi, Mang; Guo, Wen-Ping; Zhang, Xiao-He; Xing, Jian-Guang; He, Jin-Rong; Wang, Ke; Li, Ming-Hui; Cao, Jian-Hai; Jiang, Mu-Liu; Holmes, Edward C; Zhang, Yong-Zhen
To determine the biodiversity of arenaviruses in China, we captured and screened rodents and shrews in Wenzhou city, Zhejiang province, a locality where hemorrhagic fever diseases are endemic in humans. Accordingly, arenaviruses were detected in 42 of 351 rodents from eight species, and in 12 of 272 Asian house shrews (Suncus murinus), by RT-PCR targeting the L segment. From these, a single arenavirus was successfully isolated in cell culture. The virion particles exhibited a typical arenavirus morphology under transmission electron microscopy. Comparison of the S and L segment sequences revealed high levels of nucleotide (>32.2% and >39.6%) and amino acid (>28.8% and >43.8%) sequence differences from known arenaviruses, suggesting that it represents a novel arenavirus, which we designated Wenzhou virus (WENV). Phylogenetic analysis revealed that all WENV strains harbored by both rodents and Asian house shrews formed a distinct lineage most closely related to Old World arenaviruses.
Marinelli, Carla; Bertalot, Thomas; Zusso, Morena; Skaper, Stephen D; Giusti, Pietro
Oligodendrogenesis and oligodendrocyte precursor maturation are essential processes during the course of central nervous system development, and lead to the myelination of axons. Cells of the oligodendrocyte lineage are generated in the germinal zone from migratory bipolar oligodendrocyte precursor cells (OPCs), and acquire cell surface markers as they mature and respond specifically to factors which regulate proliferation, migration, differentiation, and survival. Loss of myelin underlies a wide range of neurological disorders, some of an autoimmune nature-multiple sclerosis probably being the most prominent. Current therapies are based on the use of immunomodulatory agents which are likely to promote myelin repair (remyelination) indirectly by subverting the inflammatory response, aspects of which impair the differentiation of OPCs. Cells of the oligodendrocyte lineage express and are capable of responding to a diverse array of ligand-receptor pairs, including neurotransmitters and nuclear receptors such as γ-aminobutyric acid, glutamate, adenosine triphosphate, serotonin, acetylcholine, nitric oxide, opioids, prostaglandins, prolactin, and cannabinoids. The intent of this review is to provide the reader with a synopsis of our present state of knowledge concerning the pharmacological properties of the oligodendrocyte lineage, with particular attention to these receptor-ligand (i.e., neurotransmitters and nuclear receptor) interactions that can influence oligodendrocyte migration, proliferation, differentiation, and myelination, and an appraisal of their therapeutic potential. For example, many promising mediators work through Ca(2+) signaling, and the balance between Ca(2+) influx and efflux can determine the temporal and spatial properties of oligodendrocytes (OLs). Moreover, Ca(2+) signaling in OPCs can influence not only differentiation and myelination, but also process extension and migration, as well as cell death in mature mouse OLs. There is also evidence
2). BMT provides key engineering estimates for storms and non-storm waves, wave setup and wave-induced currents necessary for a risk-based design...Mississippi River Gulf Outlet, New Orleans Flood Control Gates, LA; Buffalo Harbor, NY; Tau Harbor, and Faleasao Harbor, American Samoa. BMT helps...innovative infrastructures design; probabilistic engineering design and rehabilitation estimates for jetties, breakwaters for coastal protection
of the harbor. A low- frequency surge problem occurs in the interior harbor, caused by waves that reach Piers 1 and 2. According to ship captains...present near the piers and at ADCP1. The amplitude and frequency of IG waves appeared to be more sensitive to dampers assigned to land boundaries...Results also showed the existence of wave energy in low frequencies near the harbor entrance far from the piers where the surge problem has been
Gabe, Todd; Lynch, Colleen; McConnon, James; Allen, Thomas
This report examines the economic impact of cruise ship passengers in Bar Harbor, Maine. In 2002, 64 cruise ships docked in Bar Harbor carrying about 120,000 passengers and crewmembers. The analysis presented in the report is based on 1,080 passenger surveys conducted between August and October of 2002. Economic impact figures are based on a total of 97,190 passengers, which is the capacity of the 64 cruise ships that were scheduled to visit Bar Harbor in 2002.
PIERS, *FOULING, *HARBORS, *MARINE BIOLOGY, CALIFORNIA, PACIFIC OCEAN, NAVAL RESEARCH, CRUSTACEA, ANIMALS, PERIODIC VARIATIONS, ENVIRONMENTAL TESTS, TIME, DISTRIBUTION, SEA WATER, PLATYHELMINTHES , OCEANOGRAPHIC DATA.
Stubberud, Stephen C.; Kramer, Kathleen A.
The process of ingress and egress of a United States Navy submarine is a human-intensive process that takes numerous individuals to monitor locations and for hazards. Sailors pass vocal information to bridge where it is processed manually. There is interest in using video imaging of the periscope view to more automatically provide navigation within harbors and other points of ingress and egress. In this paper, video-based navigation is examined as a target-tracking problem. While some image-processing methods claim to provide range information, the moving platform problem and weather concerns, such as fog, reduce the effectiveness of these range estimates. The video-navigation problem then becomes an angle-only tracking problem. Angle-only tracking is known to be fraught with difficulties, due to the fact that the unobservable space is not the null space. When using a Kalman filter estimator to perform the tracking, significant errors arise which could endanger the submarine. This work analyzes the performance of the Kalman filter when angle-only measurements are used to provide the target tracks. This paper addresses estimation unobservability and the minimal set of requirements that are needed to address it in this complex but real-world problem. Three major issues are addressed: the knowledge of navigation beacons/landmarks' locations, the minimal number of these beacons needed to maintain the course, and update rates of the angles of the landmarks as the periscope rotates and landmarks become obscured due to blockage and weather. The goal is to address the problem of navigation to and from the docks, while maintaining the traversing of the harbor channel based on maritime rules relying solely on the image-based data. The minimal number of beacons will be considered. For this effort, the image correlation from frame to frame is assumed to be achieved perfectly. Variation in the update rates and the dropping of data due to rotation and obscuration is considered
Hamann, Emmo; Gruber-Vodicka, Harald; Kleiner, Manuel; Tegetmeyer, Halina E.; Riedel, Dietmar; Littmann, Sten; Chen, Jianwei; Milucka, Jana; Viehweger, Bernhard; Becker, Kevin W.; Dong, Xiaoli; Stairs, Courtney W.; Hinrichs, Kai-Uwe; Brown, Matthew W.; Roger, Andrew J.; Strous, Marc
Summary Breviatea form a lineage of free living, unicellular protists, distantly related to animals and fungi1–3. This lineage emerged almost one billion years ago, when the oceanic oxygen content was low, and extant Breviatea have evolved or retained an anaerobic lifestyle4. Here we report the cultivation of Lenisia limosa, gen. et sp. nov., a newly discovered breviate colonized by relatives of animal-associated Arcobacter. Physiological experiments showed that the association of L. limosa with Arcobacter was driven by the transfer of hydrogen and was mutualistic, providing benefits to both partners. With whole genome sequencing and differential proteomics we show that an experimentally observed fitness gain of L. limosa could be explained by the activity of a so far unknown type of NAD(P)H accepting hydrogenase, which was expressed in the presence, but not in the absence of Arcobacter. Differential proteomics further revealed that the presence of Lenisia stimulated expression of known “virulence” factors by Arcobacter. These proteins typically enable colonization of animal cells during infection5, but may in the present case act for mutual benefit. Finally, re-investigation of two currently available transcriptomic datasets of other Breviatea4 revealed the presence and activity of related hydrogen-consuming Arcobacter, indicating that mutualistic interaction between these two groups of microbes might be pervasive. Our results support the notion that molecular mechanisms involved in virulence can also support mutualism6 as shown here for Arcobacter and Breviatea. PMID:27279223
Manna, Paul T; Obado, Samson O; Boehm, Cordula; Gadelha, Catarina; Sali, Andrej; Chait, Brian T; Rout, Michael P; Field, Mark C
Clathrin-mediated endocytosis (CME) is the most evolutionarily ancient endocytic mechanism known, and in many lineages the sole mechanism for internalisation. Significantly, in mammalian cells CME is responsible for the vast bulk of endocytic flux and has likely undergone multiple adaptations to accommodate specific requirements by individual species. In African trypanosomes, we previously demonstrated that CME is independent of the AP-2 adaptor protein complex, that orthologues to many of the animal and fungal CME protein cohort are absent, and that a novel, trypanosome-restricted protein cohort interacts with clathrin and drives CME. Here, we used a novel cryomilling affinity isolation strategy to preserve transient low-affinity interactions, giving the most comprehensive trypanosome clathrin interactome to date. We identified the trypanosome AP-1 complex, Trypanosoma brucei (Tb)EpsinR, several endosomal SNAREs plus orthologues of SMAP and the AP-2 associated kinase AAK1 as interacting with clathrin. Novel lineage-specific proteins were identified, which we designate TbCAP80 and TbCAP141. Their depletion produced extensive defects in endocytosis and endomembrane system organisation, revealing a novel molecular pathway subtending an early-branching and highly divergent form of CME, which is conserved and likely functionally important across the kinetoplastid parasites. © 2017. Published by The Company of Biologists Ltd.
Gregory Bonito; Matthew E. Smith; Michael Nowak; Rosanne A. Healy; Gonzalo Guevara; Efren Cazares; Akihiko Kinoshita; Eduardo R. Nouhra; Laura S. Dominguez; Leho Tedersoo; Claude Murat; Yun Wang; Baldomero Arroyo Moreno; Donald H. Pfister; Kazuhide Nara; Alessandra Zambonelli; James M. Trappe; Rytas. Vilgalys
In this study we reassessed the biogeography and origin of the Tuberaceae and their relatives using multiple loci and a global sampling of taxa. Multiple independent transitions from an aboveground to a belowground truffie fruiting body form have occurred in the Tuberaceae and in its newly recognized sister lineage...
Stenstad, Jaran Gjerlandj; Eppeland, Kjetil Grødal; Ingeman-Nielsen, Thomas
transported by rivers from the inland ice to the inner parts of the fjord. These sediment layers reduce the water depth and prevent container- and cruiseships to dock, imposing large additional maintenance costs, and inefficient operability. Through engineering geological field and lab investigations......The international airport of Greenland is located in Kangerlussuaq, making it an important connection point for tourists and transportation of goods. However, the existing harbor in Kangerlussuaq experiences major challenges in the form of extensive sedimentation of glaciofluvial sediments...... sediment deposits at the location are reusable as construction material and may reduce construction costs. Bathymetry investigations indicate however that measures must be taken to increase the water depth, and the offshore sediments were found not suitable as support for foundations....
Maes, Christa; Kobayashi, Tatsuya; Kronenberg, Henry M
Over the past few decades, osteoblast differentiation has been studied extensively in a variety of culture systems and findings from these experiments have shaped our understanding of the bone-forming cell lineage. However, in vitro assays are bound by intrinsic limitations and are unable to effectively mirror many aspects related to osteoblasts in vivo, including their origin, destiny, and life span. Therefore, these fundamental questions strongly advocate the need for novel models to characterize the osteoblast lineage in vivo. Here, we developed a transgenic mouse system to study stage-specific subsets of osteoblast lineage cells. We believe that this system will prove to be a helpful tool in deciphering multiple aspects of osteoblast biology in vivo.
Beshera, Kebede A; Harris, Phillip M; Mayden, Richard L
Phylogenetic relationships within Labeobarbus, the large-sized hexaploid cyprinids, were examined using cytochrome b gene sequences from a broad range of geographic localities and multiple taxa. Maximum likelihood and Bayesian methods revealed novel lineages from previously unsampled drainages in central (Congo River), eastern (Genale River) and southeastern (Revue and Mussapa Grande rivers) Africa. Relationships of some species of Varicorhinus in Africa (excluding 'V.' maroccanus) render Labeobarbus as paraphyletic. 'Varicorhinus' beso, 'V.' jubae, 'V.' mariae, 'V.' nelspruitensis, and 'V.' steindachneri are transferred to Labeobarbus. Bayesian estimation of time to most recent common ancestor suggested that Labeobarbus originated in the Late Miocene while lineage diversification began during the Late Miocene-Early Pliocene and continued to the late Pleistocene. The relationships presented herein provide phylogenetic resolution within Labeobarbus and advances our knowledge of genetic diversity within the lineage as well as provides some interesting insight into the hydrographic and geologic history of Africa.
Inderbitzin, Patrik; Davis, R. Michael; Bostock, Richard M.; Subbarao, Krishna V.
Accurate species identification is essential for effective plant disease management, but is challenging in fungi including Verticillium sensu stricto (Ascomycota, Sordariomycetes, Plectosphaerellaceae), a small genus of ten species that includes important plant pathogens. Here we present fifteen PCR assays for the identification of all recognized Verticillium species and the three lineages of the diploid hybrid V. longisporum. The assays were based on DNA sequence data from the ribosomal internal transcribed spacer region, and coding and non-coding regions of actin, elongation factor 1-alpha, glyceraldehyde-3-phosphate dehydrogenase and tryptophan synthase genes. The eleven single target (simplex) PCR assays resulted in amplicons of diagnostic size for V. alfalfae, V. albo-atrum, V. dahliae including V. longisporum lineage A1/D3, V. isaacii, V. klebahnii, V. nonalfalfae, V. nubilum, V. tricorpus, V. zaregamsianum, and Species A1 and Species D1, the two undescribed ancestors of V. longisporum. The four multiple target (multiplex) PCR assays simultaneously differentiated the species or lineages within the following four groups: Verticillium albo-atrum, V. alfalfae and V. nonalfalfae; Verticillium dahliae and V. longisporum lineages A1/D1, A1/D2 and A1/D3; Verticillium dahliae including V. longisporum lineage A1/D3, V. isaacii, V. klebahnii and V. tricorpus; Verticillium isaacii, V. klebahnii and V. tricorpus. Since V. dahliae is a parent of two of the three lineages of the diploid hybrid V. longisporum, no simplex PCR assay is able to differentiate V. dahliae from all V. longisporum lineages. PCR assays were tested with fungal DNA extracts from pure cultures, and were not evaluated for detection and quantification of Verticillium species from plant or soil samples. The DNA sequence alignments are provided and can be used for the design of additional primers. PMID:23823707
Prunier, Julien; Gérardi, Sébastien; Laroche, Jérôme; Beaulieu, Jean; Bousquet, Jean
In response to selective pressure, adaptation may follow different genetic pathways throughout the natural range of a species due to historical differentiation in standing genetic variation. Using 41 populations of black spruce (Picea mariana), the objectives of this study were to identify adaptive genetic polymorphisms related to temperature and precipitation variation across the transcontinental range of the species, and to evaluate the potential influence of historical events on their geographic distribution. Population structure was first inferred using 50 control nuclear markers. Then, 47 candidate gene SNPs identified in previous genome scans were tested for relationship with climatic factors using an F(ST) -based outlier method and regressions between allele frequencies and climatic variations. Two main intraspecific lineages related to glacial vicariance were detected at the transcontinental scale. Within-lineage analyses of allele frequencies allowed the identification of 23 candidate SNPs significantly related to precipitation and/or temperature variation, among which seven were common to both lineages, eight were specific to the eastern lineage and eight were specific to the western lineage. The implication of these candidate SNPs in adaptive processes was further supported by gene functional annotations. Multiple evidences indicated that the occurrence of lineage-specific adaptive SNPs was better explained by selection acting on historically differentiated gene pools rather than differential selection due to heterogeneity of interacting environmental factors and pleiotropic effects. Taken together, these findings suggest that standing genetic variation of potentially adaptive nature has been modified by historical events, hence affecting the outcome of recent selection and leading to different adaptive routes between intraspecific lineages. © 2012 Blackwell Publishing Ltd.
Matthews, Leanna P.
Harbor seals (Phoca vitulina) are a widely distributed pinniped species that mate underwater. Similar to other aquatically mating pinnipeds, male harbor seals produce vocalizations during the breeding season that function in male-male interactions and possibly as an attractant for females. I investigated multiple aspects of these reproductive advertisement displays in a population of harbor seals in Glacier Bay National Park and Preserve, Alaska. First, I looked at vocal production as a function of environmental variables, including season, daylight, and tidal state. Vocalizations were highly seasonal and detection of these vocalizations peaked in June and July, which correspond with the estimated time of breeding. Vocalizations also varied with light, with the lowest probability of detection during the day and the highest probability of detection at night. The high probability of detection corresponded to when females are known to forage. These results are similar to the vocal behavior of previously studied populations. However, unlike previously studied populations, the detection of harbor seal breeding vocalizations did not vary with tidal state. This is likely due to the location of the hydrophone, as it was not near the haul out and depth was therefore not significantly influenced by changes in tidal height. I also investigated the source levels and call parameters of vocalizations, as well as call rate and territoriality. The average source level of harbor seal breeding vocalizations was 144 dB re 1 ?Pa at 1 m and measurements ranged from 129 to 149 dB re 1 ?Pa. Analysis of call parameters indicated that vocalizations of harbor seals in Glacier Bay were similar in duration to other populations, but were much lower in frequency. During the breeding season, there were two discrete calling areas that likely represent two individual males; the average call rate in these display areas was approximately 1 call per minute. The harbor seal breeding season also
Ono, Noriaki; Kronenberg, Henry M
Mesenchymal progenitors of the osteogenic lineage provide the flexibility for bone to grow, maintain its function and homeostasis. Traditionally, colony-forming-unit fibroblasts (CFU-Fs) have been regarded as surrogates for mesenchymal progenitors; however, this definition cannot address the function of these progenitors in their native setting. Transgenic murine models including lineage-tracing technologies based on the cre-lox system have proven to be useful in delineating mesenchymal progenitors in their native environment. Although heterogeneity of cell populations of interest marked by a promoter-based approach complicates overall interpretation, an emerging complexity of mesenchymal progenitors has been revealed. Current literatures suggest two distinct types of bone progenitor cells; growth-associated mesenchymal progenitors contribute to explosive growth of bone in early life, whereas bone marrow mesenchymal progenitors contribute to the much slower remodeling process and response to injury that occurs mainly in adulthood. More detailed relationships of these progenitors need to be studied through further experimentation.
at Stanford) express membrane-targeted tandem dimer Tomato (mT) fluorescent protein in all cells prior to Cre-mediated excision, and membrane...Tie-2 Cre x mT/mG excises dTomato ( red ) and switches on GFP expression in endothelial cells. A. CD31 immunostaining (cyan). B. VE-Cadherin...the smooth muscle genetic lineage marking of some but not all, vascular lining cells (see red unrecombined cells adjacent to green cells in Figure 5A
Simon-Loriere, Etienne; Faye, Ousmane; Faye, Oumar; Koivogui, Lamine; Magassouba, Nfaly; Keita, Sakoba; Thiberge, Jean-Michel; Diancourt, Laure; Bouchier, Christiane; Vandenbogaert, Matthias; Caro, Valérie; Fall, Gamou; Buchmann, Jan P; Matranga, Christan B; Sabeti, Pardis C; Manuguerra, Jean-Claude; Holmes, Edward C; Sall, Amadou A
An epidemic of Ebola virus disease of unprecedented scale has been ongoing for more than a year in West Africa. As of 29 April 2015, there have been 26,277 reported total cases (of which 14,895 have been laboratory confirmed) resulting in 10,899 deaths. The source of the outbreak was traced to the prefecture of Guéckédou in the forested region of southeastern Guinea. The virus later spread to the capital, Conakry, and to the neighbouring countries of Sierra Leone, Liberia, Nigeria, Senegal and Mali. In March 2014, when the first cases were detected in Conakry, the Institut Pasteur of Dakar, Senegal, deployed a mobile laboratory in Donka hospital to provide diagnostic services to the greater Conakry urban area and other regions of Guinea. Through this process we sampled 85 Ebola viruses (EBOV) from patients infected from July to November 2014, and report their full genome sequences here. Phylogenetic analysis reveals the sustained transmission of three distinct viral lineages co-circulating in Guinea, including the urban setting of Conakry and its surroundings. One lineage is unique to Guinea and closely related to the earliest sampled viruses of the epidemic. A second lineage contains viruses probably reintroduced from neighbouring Sierra Leone on multiple occasions, while a third lineage later spread from Guinea to Mali. Each lineage is defined by multiple mutations, including non-synonymous changes in the virion protein 35 (VP35), glycoprotein (GP) and RNA-dependent RNA polymerase (L) proteins. The viral GP is characterized by a glycosylation site modification and mutations in the mucin-like domain that could modify the outer shape of the virion. These data illustrate the ongoing ability of EBOV to develop lineage-specific and potentially phenotypically important variation.
Vias, Maria; Ramos-Montoya, Antonio; Mills, Ian G
Tumour classification has traditionally focused on differentiation and cellular morphology, and latterly on the application of genomic approaches. By combining chromatin immunoprecipitation with expression array, it has been possible to identify direct gene targets for transcription factors for nuclear hormone receptors. At the same time, there have been great strides in deriving stem and progenitor cells from tissues. It is therefore timely to propose that pairing the isolation of these cell subpopulations from tissues and tumours with these genomics approaches will reveal conserved gene targets for transcription factors. By focusing on transcription factors (lineage-survival oncogenes) with roles in both organogenesis and tumourigenesis at multiple organ sites, we suggest that this comparative genomics approach will enable developmental biology to be used more fully in relation to understanding tumour progression and will reveal new cancer markers. We focus here on neurogenesis and neuroendocrine differentiation in tumours.
Full Text Available BACKGROUND: CRX is a homeobox transcription factor whose expression and function is critical to maintain retinal and pineal lineage cells and their progenitors. To determine the biologic and diagnostic potential of CRX in human tumors of the retina and pineal, we examined its expression in multiple settings. METHODOLOGY/PRINCIPAL FINDINGS: Using situ hybridization and immunohistochemistry we show that Crx RNA and protein expression are exquisitely lineage restricted to retinal and pineal cells during normal mouse and human development. Gene expression profiling analysis of a wide range of human cancers and cancer cell lines also supports that CRX RNA is highly lineage restricted in cancer. Immunohistochemical analysis of 22 retinoblastomas and 13 pineal parenchymal tumors demonstrated strong expression of CRX in over 95% of these tumors. Importantly, CRX was not detected in the majority of tumors considered in the differential diagnosis of pineal region tumors (n = 78. The notable exception was medulloblastoma, 40% of which exhibited CRX expression in a heterogeneous pattern readily distinguished from that seen in retino-pineal tumors. CONCLUSIONS/SIGNIFICANCE: These findings describe new potential roles for CRX in human cancers and highlight the general utility of lineage restricted transcription factors in cancer biology. They also identify CRX as a sensitive and specific clinical marker and a potential lineage dependent therapeutic target in retinoblastoma and pineoblastoma.
Li, Jiasi; Zhang, Lei; Chu, Yongxin; Namaka, Michael; Deng, Benqiang; Kong, Jiming; Bi, Xiaoying
White matter is primarily composed of myelin and myelinated axons. Structural and functional completeness of myelin is critical for the reliable and efficient transmission of information. White matter injury has been associated with the development of many demyelinating diseases. Despite a variety of scientific advances aimed at promoting re-myelination, their benefit has proven at best to be marginal. Research suggests that the failure of the re-myelination process may be the result of an unfavorable microenvironment. Astrocytes, are the most ample and diverse type of glial cells in central nervous system (CNS) which display multiple functions for the cells of the oligodendrocytes lineage. As such, much attention has recently been drawn to astrocyte function in terms of white matter myelin repair. They are different in white matter from those in gray matter in specific regards to development, morphology, location, protein expression and other supportive functions. During the process of demyelination and re-myelination, the functions of astrocytes are dynamic in that they are able to change functions in accordance to different time points, triggers or reactive pathways resulting in vastly different biologic effects. They have pivotal effects on oligodendrocytes and other cell types in the oligodendrocyte lineage by serving as an energy supplier, a participant of immunological and inflammatory functions, a source of trophic factors and iron and a sustainer of homeostasis. Astrocytic impairment has been shown to be directly linked to the development of neuromyelities optica (NMO). In addition, astroctyes have also been implicated in other white matter conditions such as psychiatric disorders and neurodegenerative diseases such as Alzheimer’s disease (AD), multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). Inhibiting specifically detrimental signaling pathways in astrocytes while preserving their beneficial functions may be a promising approach for
Full Text Available White matter is primarily composed of myelin and myelinated axons. Structural and functional completeness of myelin is critical for the reliable and efficient transmission of information. White matter injury has been associated with the development of many demyelinating diseases. Despite a variety of scientific advances aimed at promoting re-myelination, their benefit has proven at best to be marginal. Research suggests that the failure of the re-myelination process may be the result of an unfavorable microenvironment. Astrocytes, are the most ample and diverse type of glial cells in central nervous system which display multiple functions for the cells of the oligodendrocytes lineage. As such, much attention has recently been drawn to astrocyte function in terms of white matter myelin repair. They are different in white matter from those in grey matter in specific regards to development, morphology, location, protein expression and other supportive functions. During the process of demyelination and re-myelination, the functions of astrocytes are dynamic in that they are able to change functions in accordance to different time points, triggers or reactive pathways resulting in vastly different biologic effects. They have pivotal effects on oligodendrocytes and other cell types in the oligodendrocyte lineage by serving as an energy supplier, a participant of immunological and inflammatory functions, a source of trophic factors and iron and a sustainer of homeostasis. Astrocytic impairment has been shown to be directly linked to the development of neuromyelities optica. In addition, astroctyes have also been implicated in other white matter conditions such as psychiatric disorders and neurodegenerative diseases such as Alzheimer’s disease, multiple sclerosis and amyotrophic lateral sclerosis. Inhibiting specifically detrimental signaling pathways in astrocytes while preserving their beneficial functions may be a promising approach for
The Zygomycete lineages mark the major transition from zoosporic life histories of the common ancestors of Fungi and the earliest diverging chytrid lineages (Chytridiomycota and Blastocladiomycota). Genome comparisons from these lineages may reveal gene content changes that reflect the transition to...
More than 98% of reported human listeriosis cases are caused by Listeria monocytogenes serotypes within lineages I and II. Serotypes within lineage III (4a and 4c) are commonly isolated from environmental and food specimens. We report the first complete genome sequence of a lineage III isolate, HCC2...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Monterey Harbor, CA. 80.1134 Section 80.1134 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1134 Monterey Harbor, CA. A line drawn...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Dana Point Harbor, CA. 80.1110 Section 80.1110 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1110 Dana Point Harbor, CA. A line drawn...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Moss Landing Harbor, CA. 80.1136 Section 80.1136 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false San Diego Harbor, CA. 110.210... ANCHORAGE REGULATIONS Anchorage Grounds § 110.210 San Diego Harbor, CA. (a) The anchorage grounds. (1... Commander, Naval Base, San Diego, CA. The administration of these anchorages is exercised by the...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Crescent City Harbor, CA. 80.1152 Section 80.1152 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1152 Crescent City Harbor, CA. A line...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Santa Cruz Harbor, CA. 80.1138 Section 80.1138 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1138 Santa Cruz Harbor, CA. A line drawn...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Redondo Harbor, CA. 80.1116 Section 80.1116 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1116 Redondo Harbor, CA. A line drawn...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false San Francisco Harbor, CA. 80.1142 Section 80.1142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1142 San Francisco Harbor, CA. A straight...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Oceanside Harbor, CA. 80.1108 Section 80.1108 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1108 Oceanside Harbor, CA. A line drawn...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Santa Barbara Harbor, CA. 80.1126 Section 80.1126 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1126 Santa Barbara Harbor, CA. A line...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Pillar Point Harbor, CA. 80.1140 Section 80.1140 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1140 Pillar Point Harbor, CA. A line drawn...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false San Diego Harbor, CA. 80.1104 Section 80.1104 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1104 San Diego Harbor, CA. A line drawn...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Buffalo Harbor, N.Y. 110.208 Section 110.208 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.208 Buffalo Harbor, N.Y. (a) The anchorage...
defender will be used interchangeably throughout this paper. 2.2. Harbor System Architecture A high-level architecture of a harbor defence system is de...of a quadratic Lyapunov function. Let κ and μ2 be positive constants. Before defining the feedback laws for the agent dynamics (1), we intro - duce the
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Oakland Inner Harbor Tidal Canal. 117.181 Section 117.181 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements California § 117.181 Oakland Inner Harbor Tidal Canal. The draws of the...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Nawiliwili Harbor, Kauai, HI. 80.1450 Section 80.1450 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1450 Nawiliwili Harbor, Kauai,...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Hilo Harbor, Hawaii, HI. 80.1480 Section 80.1480 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1480 Hilo Harbor, Hawaii, HI. A line...
... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zones; Hawaiian Island Commercial Harbors, HI.... 14-1414 Safety Zones; Hawaiian Islands Commercial Harbors; HI. (a) Location. The following...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Kawaihae Harbor, Hawaii, HI. 80.1470 Section 80.1470 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1470 Kawaihae Harbor, Hawaii,...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Kahului Harbor, Maui, HI. 80.1460 Section 80.1460 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1460 Kahului Harbor, Maui, HI. A line...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Marina del Rey Harbor, Calif. 110.111 Section 110.111 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.111 Marina del Rey Harbor, Calif. An area in the main channel within the...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Marblehead Harbor, Marblehead, Mass. 110.26 Section 110.26 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND..., Mass. The area comprises that portion of the harbor lying between the extreme low water line...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Sesuit Harbor, Dennis, Mass. 110.37 Section 110.37 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.37 Sesuit Harbor, Dennis, Mass. All the...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Boston Inner Harbor, Mass. 110.29 Section 110.29 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.29 Boston Inner Harbor, Mass. (a) Vicinity of...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Nantucket Harbor, Mass. 110.142 Section 110.142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.142 Nantucket Harbor, Mass. (a) The anchorage grounds. In...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Hingham Harbor, Hingham, Mass. 110.32 Section 110.32 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.32 Hingham Harbor, Hingham, Mass. (a) Area...
... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY..., Prevention Department, Coast Guard Sector Lake Michigan, Milwaukee, WI at (414) 747-7188, email Jon.K.Grob....935, Safety Zone, Milwaukee Harbor, Milwaukee, WI, at the following time for the following events:...
... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY... Sector Lake Michigan, Milwaukee, WI at 414-747-7154, e-mail Adam.D.Kraft@uscg.mil . SUPPLEMENTARY... Harbor, Milwaukee, WI, for the following events: (1) Arab World Festival fireworks display on August...
... SECURITY Coast Guard 33 CFR Part 165 Safety Zone, Milwaukee Harbor, Milwaukee, WI AGENCY: Coast Guard, DHS..., call ] or e-mail BM1 Adam Kraft, Prevention Department, Coast Guard Sector Lake Michigan, Milwaukee, WI... enforce the safety zone listed in 33 CFR 165.935, Safety Zone, Milwaukee Harbor, Milwaukee, WI, for...
... SECURITY Coast Guard 33 CFR Part 165 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY: Coast Guard, DHS... Sector Lake Michigan, Milwaukee, WI at (414) 747-7148, email email@example.com . SUPPLEMENTARY... Harbor, Milwaukee, WI, at the following times for the following events: (1) Polish Fest fireworks...
... SECURITY Coast Guard 33 CFR Part 165 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY: Coast Guard, DHS... Sector Lake Michigan, Milwaukee, WI at (414) 747-7148, email firstname.lastname@example.org . SUPPLEMENTARY... Harbor, Milwaukee, WI, for the 2013 Pridefest fireworks. This zone will be enforced from 9:15 p.m....
... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY..., WI at 414-747-7154, e-mail Adam.D.Kraft@uscg.mil . SUPPLEMENTARY INFORMATION: The Coast Guard will enforce the safety zone listed in 33 CFR 165.935, Safety Zone, Milwaukee Harbor, Milwaukee, WI, for...
... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY... BM1 Adam Kraft, Prevention Department, Coast Guard Sector Lake Michigan, Milwaukee, WI at 414-747-7154... zone listed in 33 CFR 165.935, Safety Zones, Milwaukee Harbor, Milwaukee, WI, for the following...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Ponce Harbor, P.R. 110.255 Section 110.255 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...
... 32 National Defense 5 2010-07-01 2010-07-01 false USS Arizona Memorial, Pearl Harbor. 705.31... NAVY REGULATIONS AND OFFICIAL RECORDS PUBLIC AFFAIRS REGULATIONS § 705.31 USS Arizona Memorial, Pearl Harbor. (a) Limited space and the desirability of keeping the Memorial simple and dignified require...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Cos Cob Harbor, Greenwich, Conn. 110.58 Section 110.58 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.58 Cos Cob Harbor, Greenwich, Conn. (a) Area...
Kuhl, J; Stock, K F; Wulf, M; Aurich, C
Maternal lineage influences performance traits in horses. This is probably caused by differences in mitochondrial DNA (mtDNA) transferred to the offspring via the oocyte. In the present study, we investigated if reproductive traits with high variability-gestation length and fetal sex ratio-are influenced by maternal lineage. Data from 142 Warmblood mares from the Brandenburg State Stud at Neustadt (Dosse), Germany, were available for the study. Mares were grouped according to their maternal lineage. Influences on the reproduction parameters gestation length and sex ratio of offspring were analyzed by simple and multiple analyses of variance. A total of 786 cases were included. From the 142 mares, 119 were assigned to six maternal lineages with n≥10 mares per lineage, and 23 mares belonged to smaller maternal lineages. The mean number of live foals produced per mare was 4.6±3.6 (±SD). Live foal rate was 83.5%. Mean gestation length was 338.5±8.9 days (±SD) with a range of 313 to 370 days. Gestation length was affected by maternal lineage (pGestation length was also significantly influenced by the individual mare, age of the mare, year of breeding, month of breeding and sex of the foal (pgestation length and foal sex ratio in horses. In young primiparous and aged mares, the percentage of female offspring is higher than the expected 1:1 ratio.
Hauswaldt, J Susanne; Angelini, Claudio; Gehara, Marcelo; Benavides, Edgar; Polok, Andy; Steinfartz, Sebastian
The Apennine Peninsula is one of Europe's main glacial refugial areas and harbors a large number of lineages and species. Here, a pattern of higher genetic diversity in the south compared to that of the north is characteristic of most vertebrates; however, most studies that have produced these results have relied only on inferences based on mitochondrial DNA. The spectacled salamanders (genus Salamandrina) are endemic to the Apennine Peninsula and have diverged into two sibling species: S. terdigitata (in the south) and S. perspicillata (in the north), presumably in the late Miocene or early Pliocene. By sequencing one mitochondrial (cytb) and two nuclear genes (RAG1 and POMC) and genotyping 10 microsatellite loci, we traced the evolution of these sibling species from their divergence to their contemporary population structure at a fine scale. Using a multilocus coalescent-based approach, we estimated the temporal divergence of both species at approximately 2.25 mya (million years ago), which, hence, is much younger than previous estimates. The classical pattern of high genetic diversity in the south and lower diversity in the north was confirmed only for some markers, and the demographic histories of the two species differed substantially. Whereas S. perspicillata (north) expanded from a single major refugium in the center of the Apennine Peninsula, populations of S. terdigitata (south) persisted through cooler periods in multiple refugia. Further, the fine-scale population genetic structure of 16 S. perspicillata populations revealed significant genetic differentiation, even across short geographic distances. The results of our study stress that for a better understanding of phylogeographic patterns and past demographic processes, both mitochondrial and multiple nuclear loci should be analyzed to avoid gene-specific, and possibly biased results.
Jiao, J. J.
Tolo Harbor is an elongate and semi-enclosed bay in igneous rock areas in northeastern Hong Kong. It has an area of about 50 km2 and the groundwater catchment behind the harbor has an area of 160 km2, which is well-defined by ridges that reach a maximum elevation of 957 m above sea level. Over the last two decades, about half of the algal blooms reported in Hong Kong waters occurred in the harbor. Rivers and sewage are recognized as two key sources of nutrients. It is speculated that this harbor may have relatively high submarine groundwater discharge (SGD) due to its special topographical and hydrogeological setting and that the SGD may be another source of nutrients to the harbor. A research project is conduced to quantify the SGD into Tolo Harbor and to estimate the nutrient flux into the harbor through this pathway. The geochemical tracers of radon (222Rn) and radium (223Ra, 224Ra, 226Ra, and 228Ra) in groundwater and seawater are measured over the harbor and a seepage meter is deployed for direct and continuous SGD measurement for 72 hours. The study shows that the geochemical tracers fluctuate temporally in anti-phase with tidal height and that there is general trend for the geochemical tracers to decrease with distance offshore. Three sites with relatively high SGD are identified. The residence time estimated from 224Ra is around 30 days, which correlates well with previous studies. The flux of SGD to the harbor is estimated by three different approaches including radium and radon budget analyses and seepage meter. Finally, nutrient flux to the harbor through SGD is estimated, which shows that the nutrient loading through this pathway is significant. It is suggested that current practice for the management of algal blooms in Hong Kong, in which nutrient loading through SGD is ignored, should be reviewed and the control measures of groundwater contamination are obviously required.
Full Text Available Endogenous retroviruses (ERVs arise from retroviruses chromosomally integrated in the host germline. ERVs are common in vertebrate genomes and provide a valuable fossil record of past retroviral infections to investigate the biology and evolution of retroviruses over a deep time scale, including cross-species transmission events. Here we took advantage of a catalog of ERVs we recently produced for the bat Myotis lucifugus to seek evidence for infiltration of these retroviruses in other mammalian species (>100 currently represented in the genome sequence database. We provide multiple lines of evidence for the cross-ordinal transmission of a gammaretrovirus endogenized independently in the lineages of vespertilionid bats, felid cats and pangolin ~13-25 million years ago. Following its initial introduction, the ERV amplified extensively in parallel in both bat and cat lineages, generating hundreds of species-specific insertions throughout evolution. However, despite being derived from the same viral species, phylogenetic and selection analyses suggest that the ERV experienced different amplification dynamics in the two mammalian lineages. In the cat lineage, the ERV appears to have expanded primarily by retrotransposition of a single proviral progenitor that lost infectious capacity shortly after endogenization. In the bat lineage, the ERV followed a more complex path of germline invasion characterized by both retrotransposition and multiple infection events. The results also suggest that some of the bat ERVs have maintained infectious capacity for extended period of time and may be still infectious today. This study provides one of the most rigorously documented cases of cross-ordinal transmission of a mammalian retrovirus. It also illustrates how the same retrovirus species has transitioned multiple times from an infectious pathogen to a genomic parasite (i.e. retrotransposon, yet experiencing different invasion dynamics in different mammalian
Full Text Available Maternal lineage influences performance traits in horses. This is probably caused by differences in mitochondrial DNA (mtDNA transferred to the offspring via the oocyte. In the present study, we investigated if reproductive traits with high variability-gestation length and fetal sex ratio-are influenced by maternal lineage. Data from 142 Warmblood mares from the Brandenburg State Stud at Neustadt (Dosse, Germany, were available for the study. Mares were grouped according to their maternal lineage. Influences on the reproduction parameters gestation length and sex ratio of offspring were analyzed by simple and multiple analyses of variance. A total of 786 cases were included. From the 142 mares, 119 were assigned to six maternal lineages with n≥10 mares per lineage, and 23 mares belonged to smaller maternal lineages. The mean number of live foals produced per mare was 4.6±3.6 (±SD. Live foal rate was 83.5%. Mean gestation length was 338.5±8.9 days (±SD with a range of 313 to 370 days. Gestation length was affected by maternal lineage (p<0.001. Gestation length was also significantly influenced by the individual mare, age of the mare, year of breeding, month of breeding and sex of the foal (p<0.05. Of the 640 foals born alive at term, 48% were male and 52% female. Mare age group and maternal lineage significantly influenced the sex ratio of the foals (p<0.05. It is concluded that maternal lineage influences reproductive parameters with high variation such as gestation length and foal sex ratio in horses. In young primiparous and aged mares, the percentage of female offspring is higher than the expected 1:1 ratio.
Nightingale Kendra K
Full Text Available Abstract Background The bacterium Listeria monocytogenes is a saprotroph as well as an opportunistic human foodborne pathogen, which has previously been shown to consist of at least two widespread lineages (termed lineages I and II and an uncommon lineage (lineage III. While some L. monocytogenes strains show evidence for considerable diversification by homologous recombination, our understanding of the contribution of recombination to L. monocytogenes evolution is still limited. We therefore used STRUCTURE and ClonalFrame, two programs that model the effect of recombination, to make inferences about the population structure and different aspects of the recombination process in L. monocytogenes. Analyses were performed using sequences for seven loci (including the house-keeping genes gap, prs, purM and ribC, the stress response gene sigB, and the virulence genes actA and inlA for 195 L. monocytogenes isolates. Results Sequence analyses with ClonalFrame and the Sawyer's test showed that recombination is more prevalent in lineage II than lineage I and is most frequent in two house-keeping genes (ribC and purM and the two virulence genes (actA and inlA. The relative occurrence of recombination versus point mutation is about six times higher in lineage II than in lineage I, which causes a higher genetic variability in lineage II. Unlike lineage I, lineage II represents a genetically heterogeneous population with a relatively high proportion (30% average of genetic material imported from external sources. Phylograms, constructed with correcting for recombination, as well as Tajima's D data suggest that both lineages I and II have suffered a population bottleneck. Conclusion Our study shows that evolutionary lineages within a single bacterial species can differ considerably in the relative contributions of recombination to genetic diversification. Accounting for recombination in phylogenetic studies is critical, and new evolutionary models that
Wollrab, Cora; Heitkam, Tony; Holtgräwe, Daniela; Weisshaar, Bernd; Minoche, André E; Dohm, Juliane C; Himmelbauer, Heinz; Schmidt, Thomas
LTR retrotransposons and retroviruses are closely related. Although a viral envelope gene is found in some LTR retrotransposons and all retroviruses, only the latter show infectivity. The identification of Ty3-gypsy-like retrotransposons possessing putative envelope-like open reading frames blurred the taxonomical borders and led to the establishment of the Errantivirus, Metavirus and Chromovirus genera within the Metaviridae. Only a few plant Errantiviruses have been described, and their evolutionary history is not well understood. In this study, we investigated 27 retroelements of four abundant Elbe retrotransposon families belonging to the Errantiviruses in Beta vulgaris (sugar beet). Retroelements of the Elbe lineage integrated between 0.02 and 5.59 million years ago, and show family-specific variations in autonomy and degree of rearrangements: while Elbe3 members are highly fragmented, often truncated and present in a high number of solo LTRs, Elbe2 members are mainly autonomous. We observed extensive reshuffling of structural motifs across families, leading to the formation of new retrotransposon families. Elbe retrotransposons harbor a typical envelope-like gene, often encoding transmembrane domains. During the course of Elbe evolution, the additional open reading frames have been strongly modified or independently acquired. Taken together, the Elbe lineage serves as retrotransposon model reflecting the various stages in Errantivirus evolution, and allows a detailed analysis of retrotransposon family formation.
Dyballa, Sylvia; Savy, Thierry; Germann, Philipp; Mikula, Karol; Remesikova, Mariana; Špir, Róbert; Zecca, Andrea; Peyriéras, Nadine; Pujades, Cristina
Reconstructing the lineage of cells is central to understanding how the wide diversity of cell types develops. Here, we provide the neurosensory lineage reconstruction of a complex sensory organ, the inner ear, by imaging zebrafish embryos in vivo over an extended timespan, combining cell tracing and cell fate marker expression over time. We deliver the first dynamic map of early neuronal and sensory progenitor pools in the whole otic vesicle. It highlights the remodeling of the neuronal progenitor domain upon neuroblast delamination, and reveals that the order and place of neuroblasts’ delamination from the otic epithelium prefigure their position within the SAG. Sensory and non-sensory domains harbor different proliferative activity contributing distinctly to the overall growth of the structure. Therefore, the otic vesicle case exemplifies a generic morphogenetic process where spatial and temporal cues regulate cell fate and functional organization of the rudiment of the definitive organ. DOI: http://dx.doi.org/10.7554/eLife.22268.001 PMID:28051766
Full Text Available OOligodendrogenesis and oligodendrocyte precursor maturation are essential processes during the course of central nervous system development, and lead to the myelination of axons. Cells of the oligodendrocyte lineage are generated in the germinal zone from migratory bipolar oligodendrocyte precursor cells, and acquire cell surface markers as they mature and respond specifically to factors which regulate proliferation, migration, differentiation, and survival. Loss of myelin underlies a wide range of neurological disorders, some of an autoimmune nature – multiple sclerosis probably being the most prominent. Current therapies are based on the use of immunomodulatory agents which are likely to promote myelin repair (remyelination indirectly by subverting the inflammatory response, aspects of which impair the differentiation of oligodendrocyte precursor cells. Cells of the oligodendrocyte lineage express and are capable of responding to a diverse array of ligand-receptor pairs, including neurotransmitters and nuclear receptors such as gamma-aminobutyric acid, glutamate, ATP, serotonin, acetylcholine, nitric oxide, opioids, prostaglandins, prolactin, cannabinoids and nuclear receptors. The intent of this review is to provide the reader with a synopsis of our present state of knowledge concerning the pharmacological properties of the oligodendrocyte lineage, with particular attention to these receptor-ligand (i.e., neurotransmitters and nuclear receptor interactions that can influence oligodendrocyte migration, proliferation, differentiation, and myelination, and an appraisal of their therapeutic potential. For example, many promising mediators work through Ca2+ signalling, and the balance between Ca2+ influx and efflux can determine the temporal and spatial properties of oligodendrocytes. Moreover, Ca2+ signalling in oligodendrocyte precursor cells can influence not only differentiation and myelination, but also process extension and migration, as
Marinelli, Carla; Bertalot, Thomas; Zusso, Morena; Skaper, Stephen D.; Giusti, Pietro
Oligodendrogenesis and oligodendrocyte precursor maturation are essential processes during the course of central nervous system development, and lead to the myelination of axons. Cells of the oligodendrocyte lineage are generated in the germinal zone from migratory bipolar oligodendrocyte precursor cells (OPCs), and acquire cell surface markers as they mature and respond specifically to factors which regulate proliferation, migration, differentiation, and survival. Loss of myelin underlies a wide range of neurological disorders, some of an autoimmune nature—multiple sclerosis probably being the most prominent. Current therapies are based on the use of immunomodulatory agents which are likely to promote myelin repair (remyelination) indirectly by subverting the inflammatory response, aspects of which impair the differentiation of OPCs. Cells of the oligodendrocyte lineage express and are capable of responding to a diverse array of ligand-receptor pairs, including neurotransmitters and nuclear receptors such as γ-aminobutyric acid, glutamate, adenosine triphosphate, serotonin, acetylcholine, nitric oxide, opioids, prostaglandins, prolactin, and cannabinoids. The intent of this review is to provide the reader with a synopsis of our present state of knowledge concerning the pharmacological properties of the oligodendrocyte lineage, with particular attention to these receptor-ligand (i.e., neurotransmitters and nuclear receptor) interactions that can influence oligodendrocyte migration, proliferation, differentiation, and myelination, and an appraisal of their therapeutic potential. For example, many promising mediators work through Ca2+ signaling, and the balance between Ca2+ influx and efflux can determine the temporal and spatial properties of oligodendrocytes (OLs). Moreover, Ca2+ signaling in OPCs can influence not only differentiation and myelination, but also process extension and migration, as well as cell death in mature mouse OLs. There is also evidence
Huanping, Zhang; Tongming, Yin
Lineage-specific genes (LSGs) are defined as genes found in one particular taxonomic group but have no significant sequence similarity with genes from other lineages, which compose about 10%?20% of the total genes in the genome of a focal organism. LSGs were first uncovered in the yeast genome in 1996. The development of the whole genome sequencing leads to the emergence of studies on LSGs as a hot topic in comparative genomics. LSGs have been extensively studied on microbial species, lower marine organisms, plant (such as Arabidopsis thaliana, Oryza sativa, Populus), insects, primate, etc; the biological functions of LSGs are important to clarify the evolution and adaptability of a species. In this review, we summarize the progress of LSGs studies, including LSGs identification, gene characterization, origin and evolution of LSGs, biological function, and expression analysis of LSGs. In addition, we discuss the existing problems and future directions for studies in this area. Our purpose is to provide some unique insights into the researches of LSGs.
Lee, Paul; Morley, Gregory; Huang, Qian; Fischer, Avi; Seiler, Stephanie; Horner, James W.; Factor, Stephen; Vaidya, Dhananjay; Jalife, Jose; Fishman, Glenn I.
Cell loss contributes to the pathogenesis of many inherited and acquired human diseases. We have developed a system to conditionally ablate cells of any lineage and developmental stage in the mouse by regulated expression of the diphtheria toxin A (DTA) gene by using tetracycline-responsive promoters. As an example of this approach, we targeted expression of DTA to the hearts of adult mice to model structural abnormalities commonly observed in human cardiomyopathies. Induction of DTA expression resulted in cell loss, fibrosis, and chamber dilatation. As in many human cardiomyopathies, transgenic mice developed spontaneous arrhythmias in vivo, and programmed electrical stimulation of isolated-perfused transgenic hearts demonstrated a strikingly high incidence of spontaneous and inducible ventricular tachycardia. Affected mice showed marked perturbations of cardiac gap junction channel expression and localization, including a subset with disorganized epicardial activation patterns as revealed by optical action potential mapping. These studies provide important insights into mechanisms of arrhythmogenesis and suggest that conditional lineage ablation may have wide applicability for studies of disease pathogenesis.
Das, Sabyasachi; Li, Jianxu; Hirano, Masayuki; Sutoh, Yoichi; Herrin, Brantley R; Cooper, Max D
Jawless vertebrates, which occupy a unique position in chordate phylogeny, employ leucine-rich repeat (LRR)-based variable lymphocyte receptors (VLR) for antigen recognition. During the assembly of the VLR genes (VLRA, VLRB and VLRC), donor LRR-encoding sequences are copied in a step-wise manner into the incomplete germ-line genes. The assembled VLR genes are differentially expressed by discrete lymphocyte lineages: VLRA- and VLRC-producing cells are T-cell like, whereas VLRB-producing cells are B-cell like. VLRA(+) and VLRC(+) lymphocytes resemble the two principal T-cell lineages of jawed vertebrates that express the αβ or γδ T-cell receptors (TCR). Reminiscent of the interspersed nature of the TCRα/TCRδ locus in jawed vertebrates, the close proximity of the VLRA and VLRC loci facilitates sharing of donor LRR sequences during VLRA and VLRC assembly. Here we discuss the insight these findings provide into vertebrate T- and B-cell evolution, and the alternative types of anticipatory receptors they use for adaptive immunity.
Brinkmann, Melanie M; Dağ, Franziska; Hengel, Hartmut; Messerle, Martin; Kalinke, Ulrich; Čičin-Šain, Luka
Cytomegalovirus (CMV) evades the immune system in many different ways, allowing the virus to grow and its progeny to spread in the face of an adverse environment. Mounting evidence about the antiviral role of myeloid immune cells has prompted the research of CMV immune evasion mechanisms targeting these cells. Several cells of the myeloid lineage, such as monocytes, dendritic cells and macrophages, play a role in viral control, but are also permissive for CMV and are naturally infected by it. Therefore, CMV evasion of myeloid cells involves mechanisms that qualitatively differ from the evasion of non-CMV-permissive immune cells of the lymphoid lineage. The evasion of myeloid cells includes effects in cis, where the virus modulates the immune signaling pathways within the infected myeloid cell, and those in trans, where the virus affects somatic cells targeted by cytokines released from myeloid cells. This review presents an overview of CMV strategies to modulate and evade the antiviral activity of myeloid cells in cis and in trans.
Barbieri, Chiara; Vicente, Mário; Rocha, Jorge; Mpoloka, Sununguko W; Stoneking, Mark; Pakendorf, Brigitte
Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Zee, Peter C; Velicer, Gregory J
Epistatic interactions can greatly impact evolutionary phenomena, particularly the process of adaptation. Here, we leverage four parallel experimentally evolved lineages to study the emergence and trajectories of epistatic interactions in the social bacterium Myxococcus xanthus. A social gene (pilA) necessary for effective group swarming on soft agar had been deleted from the common ancestor of these lineages. During selection for competitiveness at the leading edge of growing colonies, two lineages evolved qualitatively novel mechanisms for greatly increased swarming on soft agar, whereas the other two lineages evolved relatively small increases in swarming. By reintroducing pilA into different genetic backgrounds along the four lineages, we tested whether parallel lineages showed similar patterns of epistasis. In particular, we tested whether a pattern of negative epistasis between accumulating mutations and pilA previously found in the fastest lineage would be found only in the two evolved lineages with the fastest and most striking swarming phenotypes, or rather was due to common epistatic structure across all lineages arising from the generic fixation of adaptive mutations. Our analysis reveals the emergence of negative epistasis across all four independent lineages. Further, we present results showing that the observed negative epistasis is not due exclusively to evolving populations approaching a maximum phenotypic value that inherently limits positive effects of pilA reintroduction, but rather involves direct antagonistic interactions between accumulating mutations and the reintroduced social gene.
US Fish and Wildlife Service, Department of the Interior — This Comprehensive Conservation Plan (CCP) was written to guide management on Pearl Harbor National Wildlife Refuge for the next 15 years. This plan outlines the...
U.S. Geological Survey, Department of the Interior — These data present oceanographic and water-quality observations made at 4 locations in West Falmouth Harbor and 3 in Buzzards Bay, Massachusetts. While both Buzzards...
...: September 11, 2013, 6:00 p.m. to 8:00 p.m. (Eastern). Location: Partnership Office, 15 State Street, 8th... recommendations to the Boston Harbor Islands Partnership with respect to the implementation of a management...
... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 117 Drawbridge Operation Regulations; Manchester Harbor, Manchester, MA AGENCY: Coast Guard, DHS. ACTION: Notice of temporary deviation from regulations. SUMMARY: The...
... receive all compensation benefits to which they are entitled. Agency: Office of Workers' Compensation... of Workers' Compensation Programs Division of Longshore and Harbor Workers' Compensation Proposed... Office of Workers' Compensation (OWCP) is soliciting comments concerning the proposed collection...
National Oceanic and Atmospheric Administration, Department of Commerce — The Pearl Harbor, Hawaii Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....
Soroos, Ronald L.; Ewart, Charles J.
Increasing demand for freshwater in Hawaii has placed heavy stress on many of the State 's basal aquifer systems. The most heavily stressed of these systems is the Pearl Harbor on Oahu. The Pearl Harbor basal aquifer supplies as much as 277 million gallons per day. Since early in this century, spring discharge has been declining while pumpage has been increasing. Total ground-water discharge has remained steady despite short-term fluctuations. Some wells show general increases in chloride concentration while others remain steady. Chloride concentrations throughout the area show no apparent increase since 1970. Basal water head maps of the Pearl Harbor area clearly reflect the natural discharge points, which are the springs located along the shore near the center of Pearl Harbor. Basal-water hydrographs show a general decline of about 0.09 foot per year. This implies depletion of storage at a rate of about 25 million gallons per day. (USGS).
National Oceanic and Atmospheric Administration, Department of Commerce — The 1/3-second Pearl Harbor Hawaii Elevation Grid provides bathymetric data in ASCII raster format of 1/3-second resolution in geographic coordinates. This grid is...
National Oceanic and Atmospheric Administration, Department of Commerce — The Apra Harbor, Guam Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model. MOST...
Yue, Xiang-Peng; Dechow, Chad; Liu, Wan-Sheng
Holsteins are the most numerous dairy cattle breed in North America and the breed has undergone intensive selection for improving milk production and conformation. Theoretically, this intensive selection could lead to a reduction of the effective population size and reduced genetic diversity. The objective of this study was to investigate the effective population size of the Holstein Y chromosome and the effects of limited Y chromosome lineages on male reproduction and the future of the breed. Paternal pedigree information of 62,897 Holstein bulls born between 1950 and 2013 in North America and 220,872 bulls evaluated by multiple-trait across-country genetic evaluations of Interbull (Uppsala, Sweden) were collected and analyzed. The results indicated that the number of Y chromosome lineages in Holsteins has undergone a dramatic decrease during the past 50 years because of artificial selection and the application of artificial insemination (AI) technology. All current Holstein AI bulls in North America are the descendants of only 2 ancestors (Hulleman and Neptune H) born in 1880. These 2 ancestral Y-lineages are continued through 3 dominant pedigrees from the 1960s; namely, Pawnee Farm Arlinda Chief, Round Oak Rag Apple Elevation, and Penstate Ivanhoe Star, with a contribution of 48.78, 51.06, and 0.16% to the Holstein bull population in the 2010s, respectively. The Y-lineage of Penstate Ivanhoe Star is almost eliminated from the breed. The genetic variations in the 2 ancestral Y-lineages were evaluated among 257 bulls by determining the copy number variations (CNV) of 3 Y-linked gene families: PRAMEY, HSFY, and ZNF280BY, which are spread along the majority (95%) of the bovine Y chromosome male-specific region (MSY). No significant difference was found between the 2 ancestral Y-lineages, although large CNV were observed within each lineage. This study suggests minimal genetic diversity on the Y chromosome in Holsteins and provides a starting point for investigating
Full Text Available The aim of the present study was to determine whether there is a correlation between phylogenetic relationship and inflammatory response amongst a panel of clinical isolates representative of the global diversity of the human Mycobacterium tuberculosis Complex (MTBC. Measurement of cytokines from infected human peripheral blood monocyte-derived macrophages revealed a wide variation in the response to different strains. The same pattern of high or low response to individual strains was observed for different pro-inflammatory cytokines and chemokines, and was conserved across multiple human donors. Although each major phylogenetic lineage of MTBC included strains inducing a range of cytokine responses, we found that overall inflammatory phenotypes differed significantly across lineages. In particular, comparison of evolutionarily modern lineages demonstrated a significant skewing towards lower early inflammatory response. The differential response to ancient and modern lineages observed using GM-CSF derived macrophages was also observed in autologous monocyte-derived dendritic cells and murine bone marrow-derived macrophages, but not in human unfractionated peripheral blood mononuclear cells. We hypothesize that the reduced immune responses to modern lineages contribute to more rapid disease progression and transmission, which might be a selective advantage in the context of expanding human populations. In addition to the lineage effects, the large strain-to-strain variation in innate immune responses elicited by MTBC will need to be considered in tuberculosis vaccine development.
Wilson, Jeremy D; Schmidt, Daniel J; Hughes, Jane M
In 1993, a population of freshwater glass shrimp (Paratya australiensis) was translocated from Kilcoy Creek to Branch Creek in the Conondale Range, Queensland. Subsequent genetic analysis revealed that the translocated and resident shrimp belonged to different mitochondrial DNA (mtDNA) lineages that were capable of hybridizing. Monitoring of the pools along Branch Creek up until 2002 suggested that the translocated lineage had an advantage in upstream pools and the resident lineage dominated downstream. Differential temperature tolerance and hybridization barriers such as hybrid inviability and mate selection were factors proposed to explain hybrid zone structure. The major objective of this study was to combine nuclear and mtDNA markers to identify the structure of the hybrid zone in 2013 and identify any changes that had occurred since 2002. Specifically, we used genetic data to test for evidence of hybrid zone movement and used the inbreeding coefficient (F IS) to investigate whether mating was random in the contact zone where hybridization barriers could be present. The results revealed that the hybrid zone center has shifted 510 m downstream since 2002. Increased rainfall in the region since 2010 could have facilitated this. Secondly, mating appears significantly nonrandom in the pools where both lineages occur, supporting the existence of partial hybridization barriers. This study reveals a complex and dynamic hybrid zone and exemplifies why multiple temporal studies are necessary to understand hybrid zone structure.
Yao, Zizhen; Mich, John K; Ku, Sherman; Menon, Vilas; Krostag, Anne-Rachel; Martinez, Refugio A; Furchtgott, Leon; Mulholland, Heather; Bort, Susan; Fuqua, Margaret A; Gregor, Ben W; Hodge, Rebecca D; Jayabalu, Anu; May, Ryan C; Melton, Samuel; Nelson, Angelique M; Ngo, N Kiet; Shapovalova, Nadiya V; Shehata, Soraya I; Smith, Michael W; Tait, Leah J; Thompson, Carol L; Thomsen, Elliot R; Ye, Chaoyang; Glass, Ian A; Kaykas, Ajamete; Yao, Shuyuan; Phillips, John W; Grimley, Joshua S; Levi, Boaz P; Wang, Yanling; Ramanathan, Sharad
During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development. Bayesian analyses inferred a unified cell-type lineage tree that bifurcates between cortical and mid/hindbrain cell types. Two methods of clonal analyses confirmed these findings and further revealed the importance of Wnt/β-catenin signaling in controlling this lineage decision. Together, these findings provide a rich transcriptome-based lineage map for studying human brain development and modeling developmental disorders. Copyright © 2017 Elsevier Inc. All rights reserved.
Matsuoka, Shinya; Armstrong, Alissa R; Sampson, Leesa L; Laws, Kaitlin M; Drummond-Barbosa, Daniela
Nutrients affect adult stem cells through complex mechanisms involving multiple organs. Adipocytes are highly sensitive to diet and have key metabolic roles, and obesity increases the risk for many cancers. How diet-regulated adipocyte metabolic pathways influence normal stem cell lineages, however, remains unclear. Drosophila melanogaster has highly conserved adipocyte metabolism and a well-characterized female germline stem cell (GSC) lineage response to diet. Here, we conducted an isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis to identify diet-regulated adipocyte metabolic pathways that control the female GSC lineage. On a rich (relative to poor) diet, adipocyte Hexokinase-C and metabolic enzymes involved in pyruvate/acetyl-CoA production are upregulated, promoting a shift of glucose metabolism toward macromolecule biosynthesis. Adipocyte-specific knockdown shows that these enzymes support early GSC progeny survival. Further, enzymes catalyzing fatty acid oxidation and phosphatidylethanolamine synthesis in adipocytes promote GSC maintenance, whereas lipid and iron transport from adipocytes controls vitellogenesis and GSC number, respectively. These results show a functional relationship between specific metabolic pathways in adipocytes and distinct processes in the GSC lineage, suggesting the adipocyte metabolism-stem cell link as an important area of investigation in other stem cell systems. Copyright © 2017 by the Genetics Society of America.
Jota, Marilza S; Lacerda, Daniela R; Sandoval, José R; Vieira, Pedro Paulo R; Ohasi, Dominique; Santos-Júnior, José E; Acosta, Oscar; Cuellar, Cinthia; Revollo, Susana; Paz-Y-Miño, Cesar; Fujita, Ricardo; Vallejo, Gustavo A; Schurr, Theodore G; Tarazona-Santos, Eduardo M; Pena, Sergio Dj; Ayub, Qasim; Tyler-Smith, Chris; Santos, Fabrício R
Many single-nucleotide polymorphisms (SNPs) in the non-recombining region of the human Y chromosome have been described in the last decade. High-coverage sequencing has helped to characterize new SNPs, which has in turn increased the level of detail in paternal phylogenies. However, these paternal lineages still provide insufficient information on population history and demography, especially for Native Americans. The present study aimed to identify informative paternal sublineages derived from the main founder lineage of the Americas-haplogroup Q-L54-in a sample of 1841 native South Americans. For this purpose, we used a Y-chromosomal genotyping multiplex platform and conventional genotyping methods to validate 34 new SNPs that were identified in the present study by sequencing, together with many Y-SNPs previously described in the literature. We updated the haplogroup Q phylogeny and identified two new Q-M3 and three new Q-L54*(xM3) sublineages defined by five informative SNPs, designated SA04, SA05, SA02, SA03 and SA29. Within the Q-M3, sublineage Q-SA04 was mostly found in individuals from ethnic groups belonging to the Tukanoan linguistic family in the northwest Amazon, whereas sublineage Q-SA05 was found in Peruvian and Bolivian Amazon ethnic groups. Within Q-L54*, the derived sublineages Q-SA03 and Q-SA02 were exclusively found among Coyaima individuals (Cariban linguistic family) from Colombia, while Q-SA29 was found only in Maxacali individuals (Jean linguistic family) from southeast Brazil. Furthermore, we validated the usefulness of several published SNPs among indigenous South Americans. This new Y chromosome haplogroup Q phylogeny offers an informative paternal genealogy to investigate the pre-Columbian history of South America.Journal of Human Genetics advance online publication, 31 March 2016; doi:10.1038/jhg.2016.26.
Full Text Available Abstract Background The genus Listeria includes two closely related pathogenic and non-pathogenic species, L. monocytogenes and L. innocua. L. monocytogenes is an opportunistic human foodborne and animal pathogen that includes two common lineages. While lineage I is more commonly found among human listeriosis cases, lineage II appears to be overrepresented among isolates from foods and environmental sources. This study used the genome sequences for one L. innocua strain and four L. monocytogenes strains representing lineages I and II, to characterize the contributions of positive selection and recombination to the evolution of the L. innocua/L. monocytogenes core genome. Results Among the 2267 genes in the L. monocytogenes/L. innocua core genome, 1097 genes showed evidence for recombination and 36 genes showed evidence for positive selection. Positive selection was strongly associated with recombination. Specifically, 29 of the 36 genes under positive selection also showed evidence for recombination. Recombination was more common among isolates in lineage II than lineage I; this trend was confirmed by sequencing five genes in a larger isolate set. Positive selection was more abundant in the ancestral branch of lineage II (20 genes as compared to the ancestral branch of lineage I (9 genes. Additional genes under positive selection were identified in the branch separating the two species; for this branch, genes in the role category "Cell wall and membrane biogenesis" were significantly more likely to have evidence for positive selection. Positive selection of three genes was confirmed in a larger isolate set, which also revealed occurrence of multiple premature stop codons in one positively selected gene involved in flagellar motility (flaR. Conclusion While recombination and positive selection both contribute to evolution of L. monocytogenes, the relative contributions of these evolutionary forces seem to differ by L. monocytogenes lineages and
M.H.C. Bakkus (Marleen)
textabstractMultiple myeloma (MM) is a malignant proliferating disorder of the B lymphocyte lineage, characterized by an increasing proportion of plasma cells in the bone marrow, a high and progressively increasing concentration of a homogeneous immunoglobulin in the blood and the occurrence of oste
Byron H. Hartman
Full Text Available Vertebrate embryogenesis gives rise to all cell types of an organism through the development of many unique lineages derived from the three primordial germ layers. The otic sensory lineage arises from the otic vesicle, a structure formed through invagination of placodal non-neural ectoderm. This developmental lineage possesses unique differentiation potential, giving rise to otic sensory cell populations including hair cells, supporting cells, and ganglion neurons of the auditory and vestibular organs. Here we present a systematic approach to identify transcriptional features that distinguish the otic sensory lineage (from early otic progenitors to otic sensory populations from other major lineages of vertebrate development. We used a microarray approach to analyze otic sensory lineage populations including microdissected otic vesicles (embryonic day 10.5 as well as isolated neonatal cochlear hair cells and supporting cells at postnatal day 3. Non-otic tissue samples including periotic tissues and whole embryos with otic regions removed were used as reference populations to evaluate otic specificity. Otic populations shared transcriptome-wide correlations in expression profiles that distinguish members of this lineage from non-otic populations. We further analyzed the microarray data using comparative and dimension reduction methods to identify individual genes that are specifically expressed in the otic sensory lineage. This analysis identified and ranked top otic sensory lineage-specific transcripts including Fbxo2, Col9a2, and Oc90, and additional novel otic lineage markers. To validate these results we performed expression analysis on select genes using immunohistochemistry and in situ hybridization. Fbxo2 showed the most striking pattern of specificity to the otic sensory lineage, including robust expression in the early otic vesicle and sustained expression in prosensory progenitors and auditory and vestibular hair cells and supporting
Imen BEL HADJ ALI; Zoubeir LAFHAJ; Mounir BOUASSIDA; Imen SAID
The objective of this article is to study the geotechnical and environmental characteristics of sediments dredged from two Tunisian harbors:Rades and Gabes. The first harbor represents the main facility place in the national transport chain. The second one is selected as its sediments present a serious ecological constraint caused by the discharge of wastes into the marine environment. These sediments are either discarded at sea or landfilled despite their harmful effects on the environment. The article is divided into three main sections. The first one presents the material that was carried for Rades and Gabes harbors. The conservation conditions and the used experimental tests are detailed. Geotechnical characterization includes the determination of the grain size distribution, the water content, the Atterberg limits, the methylene blue value, the specific area, the bulk density, the specific unit weight, the organic and carbonate contents. Environmental characterization is assessed by the determination of metals concentrations in a leaching solution. The second section deals with the description and analysis of geotechnical properties of Rades and Gabes harbors’ sediments. The results obtained show that Rades harbor sediments are slightly sandy clayey silts whereas Gabes harbor sediments are silty sands characterized by a highly plastic clay fraction. Both of the two sediments don’t exhibit a high organic content. Finally, chemical, mineralogical and environmental properties are presented and then analysed. The experimental results obtained show that Rades and Gabes sediments could be used as a sand substitute in the formulation of a new construction material. Gabes harbor sediments are more polluted than Rades harbor sediments.
... Foreign-Trade Zones Board Foreign-Trade Zone 152 - Burns Harbor, Indiana, Application for Reorganization...-purpose zone currently consists of six sites in the Burns Harbor/Gary, Indiana area: Site 1: (533,288 sq...); Site 2: (441 acres) within the Port of Indiana/Burns International Harbor, Burns Harbor (Porter...
Presents an annotated bibliography that provides Web sites about Pearl Harbor (Hawaii). Includes Web sites that cover Pearl Harbor history, a live view of Pearl Harbor, stories from people who remember where they were during the attack, information on the naval station at Pearl Harbor, and a virtual tour of the USS Arizona. (CMK)
W. Dontje; R. Schotte; T. Cupedo; M. Nagasawa; F. Scheeren; R. Gimeno; H. Spits; B. Blom
Human early thymic precursors have the potential to differentiate into multiple cell lineages, including T cells and plasmacytoid dendritic cells (pDCs). This decision is guided by the induction or silencing of lineage-specific transcription factors. The ETS family member Spi-B is a key regulator of
Loh, Kyle M; Ang, Lay Teng; Zhang, Jingyao; Kumar, Vibhor; Ang, Jasmin; Auyeong, Jun Qiang; Lee, Kian Leong; Choo, Siew Hua; Lim, Christina Y Y; Nichane, Massimo; Tan, Junru; Noghabi, Monireh Soroush; Azzola, Lisa; Ng, Elizabeth S; Durruthy-Durruthy, Jens; Sebastiano, Vittorio; Poellinger, Lorenz; Elefanty, Andrew G; Stanley, Edouard G; Chen, Qingfeng; Prabhakar, Shyam; Weissman, Irving L; Lim, Bing
Human pluripotent stem cell (hPSC) differentiation typically yields heterogeneous populations. Knowledge of signals controlling embryonic lineage bifurcations could efficiently yield desired cell types through exclusion of alternate fates. Therefore, we revisited signals driving induction and anterior-posterior patterning of definitive endoderm to generate a coherent roadmap for endoderm differentiation. With striking temporal dynamics, BMP and Wnt initially specified anterior primitive streak (progenitor to endoderm), yet, 24 hr later, suppressed endoderm and induced mesoderm. At lineage bifurcations, cross-repressive signals separated mutually exclusive fates; TGF-β and BMP/MAPK respectively induced pancreas versus liver from endoderm by suppressing the alternate lineage. We systematically blockaded alternate fates throughout multiple consecutive bifurcations, thereby efficiently differentiating multiple hPSC lines exclusively into endoderm and its derivatives. Comprehensive transcriptional and chromatin mapping of highly pure endodermal populations revealed that endodermal enhancers existed in a surprising diversity of "pre-enhancer" states before activation, reflecting the establishment of a permissive chromatin landscape as a prelude to differentiation.
Lanjuin, Anne; Claggett, Julia; Shibuya, Mayumi; Hunter, Craig P; Sengupta, Piali
Members of the HES subfamily of bHLH proteins play crucial roles in neural patterning via repression of neurogenesis. In C. elegans, loss-of-function mutations in ref-1, a distant nematode-specific member of this subfamily, were previously shown to cause ectopic neurogenesis from postembryonic lineages. However, while the vast majority of the nervous system in C. elegans is generated embryonically, the role of REF-1 in regulating these neural lineage decisions is unknown. Here, we show that mutations in ref-1 result in the generation of multiple ectopic neuron types derived from an embryonic neuroblast. In wild-type animals, neurons derived from this sublineage are present in a left/right symmetrical manner. However, in ref-1 mutants, while the ectopically generated neurons exhibit gene expression profiles characteristic of neurons on the left, they are present only on the right side. REF-1 functions in a Notch-independent manner to regulate this ectopic lineage decision. We also demonstrate that loss of REF-1 function results in defective differentiation of an embryonically generated serotonergic neuron type. These results indicate that REF-1 functions in both Notch-dependent and independent pathways to regulate multiple developmental decisions in different neuronal sublineages.
observations at the former collection stations, snorkeling surveys were conducted throughout Pearl Harbor and Ke’ehi Lagoon to estimate the abundance of introduced algae and in Pearl Harbor to document the occurrence of reef corals.
Full Text Available Recently, the Immunological Genome Project (ImmGen completed the first phase of the goal to understand the molecular circuitry underlying the immune cell lineage in mice. That milestone resulted in the creation of the most comprehensive collection of gene expression profiles in the immune cell lineage in any model organism of human disease. There is now a requisite to examine this resource using bioinformatics integration with other molecular information, with the aim of gaining deeper insights into the underlying processes that characterize this immune cell lineage. We present here a bioinformatics approach to study differential protein interaction mechanisms across the entire immune cell lineage, achieved using affinity propagation applied to a protein interaction network similarity matrix. We demonstrate that the integration of protein interaction networks with the most comprehensive database of gene expression profiles of the immune cells can be used to generate hypotheses into the underlying mechanisms governing the differentiation and the differential functional activity across the immune cell lineage. This approach may not only serve as a hypothesis engine to derive understanding of differentiation and mechanisms across the immune cell lineage, but also help identify possible immune lineage specific and common lineage mechanism in the cells protein networks.
Full Text Available BACKGROUND: Reduced expression of developmentally important genes and tumor suppressors due to haploinsufficiency or epigenetic suppression has been shown to contribute to the pathogenesis of various malignancies. However, methodology that allows spatio-temporally knockdown of gene expression in various model organisms such as zebrafish has not been well established, which largely limits the potential of zebrafish as a vertebrate model of human malignant disorders. PRINCIPAL FINDING: Here, we report that multiple copies of small hairpin RNA (shRNA are expressed from a single transcript that mimics the natural microRNA-30e precursor (mir-shRNA. The mir-shRNA, when microinjected into zebrafish embryos, induced an efficient knockdown of two developmentally essential genes chordin and alpha-catenin in a dose-controllable fashion. Furthermore, we designed a novel cassette vector to simultaneously express an intronic mir-shRNA and a chimeric red fluorescent protein driven by lineage-specific promoter, which efficiently reduced the expression of a chromosomally integrated reporter gene and an endogenously expressed gata-1 gene in the developing erythroid progenitors and hemangioblasts, respectively. SIGNIFICANCE: This methodology provides an invaluable tool to knockdown developmental important genes in a tissue-specific manner or to establish animal models, in which the gene dosage is critically important in the pathogenesis of human disorders. The strategy should be also applicable to other model organisms.
Serrano-Serrano, Martha L; Marcionetti, Anna; Perret, Mathieu; Salamin, Nicolas
Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic to the Brazilian Atlantic Forest. A total of 300 million reads were used to assemble the transcriptomes, with an average of 92,038 transcripts and 43,506 genes per species. The transcriptomes showed good quality metrics, with the presence of all eukaryotic core genes, and an equal representation of clusters of orthologous groups (COG) classifications between species. The orthologous search produced 8602 groups, with 15-20% of them annotated using BLAST tools. This study provides the first step toward a comprehensive multispecies transcriptome characterization of the Gesneriaceae family. These resources are the basis for comparative analyses in this species-rich Neotropical plant group; they will also allow the investigation of the evolutionary importance of multiple metabolic pathways and phenotypic diversity, as well as developmental programs in these nonmodel species.
Serrano-Serrano, Martha L.; Marcionetti, Anna; Perret, Mathieu; Salamin, Nicolas
Premise of the study: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. Methods and Results: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic to the Brazilian Atlantic Forest. A total of 300 million reads were used to assemble the transcriptomes, with an average of 92,038 transcripts and 43,506 genes per species. The transcriptomes showed good quality metrics, with the presence of all eukaryotic core genes, and an equal representation of clusters of orthologous groups (COG) classifications between species. The orthologous search produced 8602 groups, with 15–20% of them annotated using BLAST tools. Discussion: This study provides the first step toward a comprehensive multispecies transcriptome characterization of the Gesneriaceae family. These resources are the basis for comparative analyses in this species-rich Neotropical plant group; they will also allow the investigation of the evolutionary importance of multiple metabolic pathways and phenotypic diversity, as well as developmental programs in these nonmodel species. PMID:28439475
Darras, Hugo; Aron, Serge
We report a remarkable pattern of incongruence between nuclear and mitochondrial variations in a social insect, the desert ant Cataglyphis hispanica. This species reproduces by social hybridogenesis. In all populations, two distinct genetic lineages coexist; non-reproductive workers develop from hybrid crosses between the lineages, whereas reproductive offspring (males and new queens) are typically produced asexually by parthenogenesis. Genetic analyses based on nuclear markers revealed that the two lineages remain highly differentiated despite constant hybridization for worker production. Here, we show that, in contrast with nuclear DNA, mitochondrial DNA (mtDNA) does not recover the two lineages as monophyletic. Rather, mitochondrial haplotypes cluster according to their geographical origin. We argue that this cytonuclear incongruence stems from introgression of mtDNA among lineages, and review the mechanisms likely to explain this pattern under social hybridogenesis.
Pozniak, Christine D.; Langseth, Abraham J.; Dijkgraaf, Gerrit J. P.; Choe, Youngshik; Werb, Zena; Pleasure, Samuel J.
Oligodendrocyte precursor cells (OPCs) are lineage-restricted progenitors generally limited in vivo to producing oligodendrocytes. Mechanisms controlling genesis of OPCs are of interest because of their importance in myelin development and their potential for regenerative therapies in multiple sclerosis and dysmyelinating syndromes. We show here that the SoxE transcription factors (comprising Sox8, 9, and 10) induce multipotent neural precursor cells (NPCs) from the early postnatal subventricular zone (SVZ) to become OPCs in an autonomous manner. We performed a chromatin immunoprecipitation-based bioinformatic screen and identified Suppressor of Fused (Sufu) as a direct target of repression by Sox10. In vitro, overexpression of Sufu blocked OPC production, whereas RNAi-mediated inhibition augmented OPC production. Furthermore, mice heterozygous for Sufu have increased numbers of OPCs in the telencephalon during development. We conclude that Sox10 acts to restrict the potential of NPCs toward the oligodendrocyte lineage in part by regulating the expression of Sufu. PMID:21098272
Liu, Chang; Peng, Jia; Matzuk, Martin M.; Yao, Humphrey H-C
Organogenesis of the ovary is a highly orchestrated process involving multiple lineage determinations of ovarian surface epithelium, granulosa cells, and theca cells. While the sources of ovarian surface epithelium and granulosa cells are known, the origin(s) of theca progenitor cells have not been definitively identified. Here we show that theca cells derive from two sources: Wt1+ cells indigenous to the ovary and Gli1+ mesenchymal cells migrated from the mesonephros. These progenitors acquire theca lineage marker Gli1 in response to paracrine signals Desert hedgehog (Dhh) and Indian hedgehog (Ihh) from granulosa cells. Ovaries lacking Dhh/Ihh exhibit theca layer loss, blunted steroid production, arrested folliculogenesis, and failure to form corpora lutea. Production of Dhh/Ihh in granulosa cells requires Growth differentiation factor 9 (GDF9) from the oocyte. Our studies provide the first genetic evidence for the origins of theca cells and reveal a multicellular interaction critical for the formation of a functional theca. PMID:25917826
Behnaz Bakhshandeh; Masoud Soleimani; Seyed Hassan Paylakhi; Nasser Ghaemi
Generating appropriate cartilage for clinical applications to heal skeletal tissue loss is a major health concern. In this regard, cell-based approaches offer a potential therapeutic strategy for cartilage repair, although little is known about the precise mechanism of chondrogenesis. Unrestricted somatic stem cell (USSC) is considered as a suitable candidate because of its potential for differentiating into multiple cell types. Recent studies show that microRNAs (miRNAs) are involved in several biological processes including development and differentiation. To identify the chondro-specific miRNA signature, miRNA patterns of USSCs and differentiated chondrocytes were investigated using microarrays and validation by qPCR. Prior to these analyses, chondrogenic commitment of differentiated USSCs was verified by immunocytochemistry, specific staining and evaluation of some main chondrogenic marker genes. Various in silico explorations (for both putative targets and signalling pathways) and empirical analyses (miRNA transfections followed by qPCR of some chondrogenic indicators) were carried out to support our results. Transient modulation of multiple chondro-miRs (such as mir-630, mir-624 and mir-376) with chondrocyte targets (such as TGFbR, MAP3K, collagens, SMADs and cadherins) as mediators of chondrogenic signalling pathways including cell–cell interactions, TGF-beta, and MAPK signalling suggests a mechanism for genetic induction of chondrogenic differentiation. In conclusion, this research reveals more details about the allocation of USSCs into the chondrocytes through identification of miRNA signature which modulates targets and pathways required for chondrogenic lineage and could provide guidelines for future clinical treatments and anti-miRNA therapies.
Hendy Mike D
Full Text Available Abstract Correction to Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol 2008, 8(1:317.
Soegaard, Lisette B; Hansen, Marie N; van Elk, Cornelis
blood. Further, O(2) affinity tended to increase with increasing body mass. A high O(2) affinity favors O(2) extraction from the lungs, but a normal Bohr effect (¿logP(50)/¿pH=-0.46) gradually lowers O(2) affinity during dives (where CO(2) accumulates) to assist O(2) off-loading to perfused tissues......Harbor porpoises are active divers that exchange O(2) and CO(2) with the environment during a fast single breath upon surfacing. We investigated blood O(2)-transporting properties, buffer characteristics, Cl(-) transport via the erythrocyte anion exchanger (AE1), circulating nitric oxide...... metabolites and hemoglobin nitrite reduction in harbor porpoises with the aim to evaluate traits that are adaptive for diving behavior. Blood O(2) affinity was higher in harbor porpoises than in similar sized terrestrial mammals, as supported by our parallel recordings of O(2) equilibria in sheep and pig...
Soegaard, Lisette B.; Hansen, Marie Niemann; van Elk, Cornelis
Harbor porpoises are active divers that exchange O2 and CO2 with the environment during a fast single breath upon surfacing. We investigated blood O2-transporting properties, buffer characteristics, Cl– transport via the erythrocyte anion exchanger (AE1), circulating nitric oxide metabolites...... and hemoglobin nitrite reduction in harbor porpoises with the aim to evaluate traits that are adaptive for diving behavior. Blood O2 affinity was higher in harbor porpoises than in similar sized terrestrial mammals, as supported by our parallel recordings of O2 equilibria in sheep and pig blood. Further, O2...... affinity tended to increase with increasing body mass. A high O2 affinity favors O2 extraction from the lungs, but a normal Bohr effect (ΔlogP50/ΔpH = –0.46) gradually lowers O2 affinity during dives (where CO2 accumulates) to assist O2 off-loading to perfused tissues. The true plasma non...
Li, Kun [State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing (China); Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou (China); Lin, Xian-Dan [Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province (China); Wang, Wen [State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing (China); Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou (China); Shi, Mang [State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing (China); Wencheng Center for Disease Control and Prevention, Wenzhou, Zhejiang Province (China); Guo, Wen-Ping [State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing (China); Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou (China); Zhang, Xiao-He [Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province (China); Xing, Jian-Guang [Wencheng Center for Disease Control and Prevention, Wenzhou, Zhejiang Province (China); and others
To determine the biodiversity of arenaviruses in China, we captured and screened rodents and shrews in Wenzhou city, Zhejiang province, a locality where hemorrhagic fever diseases are endemic in humans. Accordingly, arenaviruses were detected in 42 of 351 rodents from eight species, and in 12 of 272 Asian house shrews (Suncus murinus), by RT-PCR targeting the L segment. From these, a single arenavirus was successfully isolated in cell culture. The virion particles exhibited a typical arenavirus morphology under transmission electron microscopy. Comparison of the S and L segment sequences revealed high levels of nucleotide (>32.2% and >39.6%) and amino acid (>28.8% and >43.8%) sequence differences from known arenaviruses, suggesting that it represents a novel arenavirus, which we designated Wenzhou virus (WENV). Phylogenetic analysis revealed that all WENV strains harbored by both rodents and Asian house shrews formed a distinct lineage most closely related to Old World arenaviruses. - Highlights: • A novel arenavirus (Wenzhou virus) was identified in Zhejiang province, China. • The virus is highly circulating in five species of rats and one species of shrews • More efforts are needed to infer whether it is pathogenic to humans or not.
Bongaerts, Pim; Frade, Pedro R; Hay, Kyra B; Englebert, Norbert; Latijnhouwers, Kelly R W; Bak, Rolf P M; Vermeij, Mark J A; Hoegh-Guldberg, Ove
The composition, ecology and environmental conditions of mesophotic coral ecosystems near the lower limits of their bathymetric distributions remain poorly understood. Here we provide the first in-depth assessment of a lower mesophotic coral community (60-100 m) in the Southern Caribbean through visual submersible surveys, genotyping of coral host-endosymbiont assemblages, temperature monitoring and a growth experiment. The lower mesophotic zone harbored a specialized coral community consisting of predominantly Agaricia grahamae, Agaricia undata and a "deep-water" lineage of Madracis pharensis, with large colonies of these species observed close to their lower distribution limit of ~90 m depth. All three species associated with "deep-specialist" photosynthetic endosymbionts (Symbiodinium). Fragments of A. grahamae exhibited growth rates at 60 m similar to those observed for shallow Agaricia colonies (~2-3 cm yr(-1)), but showed bleaching and (partial) mortality when transplanted to 100 m. We propose that the strong reduction of temperature over depth (Δ5°C from 40 to 100 m depth) may play an important contributing role in determining lower depth limits of mesophotic coral communities in this region. Rather than a marginal extension of the reef slope, the lower mesophotic represents a specialized community, and as such warrants specific consideration from science and management.
Bruhn, Jesper Bartholin; Vogel, Birte Fonnesbech; Gram, Lone
Listeria monocytogenes can be isolated from a range of food products and may cause food-borne outbreaks or sporadic cases of listeriosis. L. monocytogenes is divided into three genetic lineages and 13 serotypes. Strains of three serotypes (1/2a, 1/2b, and 4b) are associated with most human cases...... of listeriosis. Of these, strains of serotypes 1/2b and 4b belong to lineage 1, whereas strains of serotype 1/2a and many other strains isolated from foods belong to lineage 2. L. monocytogenes is isolated from foods by selective enrichment procedures and from patients by nonselective methods. The aim......, as lineage 1 strains, which are often isolated from clinical cases of listeriosis, may be suppressed during enrichment by other L. monocytogenes lineages present in a food sample...
Møller, JK; Bak, AL; Christiansen, C
Extrachromosomal deoxyribonucleic acid (DNA) from 24 different R factor-harboring Enterobacteriaceae was isolated and characterized by analytical ultracentrifugation and electron microscopy. The R factors represented 15 different patterns of transferable drug resistance found in enterobacteria from...... from 1.700 to 1.720 g/cm3. The majority of the bacteria contained extrachromosomal DNAs of various densities. Three-fourths of the R factors were classified as fi+. The investigation illustrates the extensive variability in the physical characteristics of plasmid DNA from R factor-harboring strains....
Full Text Available The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route.MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, and more than 70,000 partial mtDNA sequences were screened to establish their respective geographic ranges.The Saudi mtDNA profile confirms the absence of autochthonous mtDNA lineages in Arabia with coalescence ages deep enough to support population continuity in the region since the out-of-Africa episode. In contrast to Australia, where N(xR haplogroups are found in high frequency and with deep coalescence ages, there are not autochthonous N(xR lineages in India nor N(xR branches with coalescence ages as deep as those found in Australia. These patterns are at odds with the supposition that Australian colonizers harboring N(xR lineages used a route involving India as a stage. The most ancient N(xR lineages in Eurasia are found in China, and inconsistently with the coastal route, N(xR haplogroups with the southernmost geographical range have all more recent radiations than the Australians.Apart from a single migration event via a southern route, phylogeny and
Fregel, Rosa; Cabrera, Vicente; Larruga, Jose M; Abu-Amero, Khaled K; González, Ana M
The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route. MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, and more than 70,000 partial mtDNA sequences were screened to establish their respective geographic ranges. The Saudi mtDNA profile confirms the absence of autochthonous mtDNA lineages in Arabia with coalescence ages deep enough to support population continuity in the region since the out-of-Africa episode. In contrast to Australia, where N(xR) haplogroups are found in high frequency and with deep coalescence ages, there are not autochthonous N(xR) lineages in India nor N(xR) branches with coalescence ages as deep as those found in Australia. These patterns are at odds with the supposition that Australian colonizers harboring N(xR) lineages used a route involving India as a stage. The most ancient N(xR) lineages in Eurasia are found in China, and inconsistently with the coastal route, N(xR) haplogroups with the southernmost geographical range have all more recent radiations than the Australians. Apart from a single migration event via a southern route, phylogeny and phylogeography of N
Cao, Li; Gibson, Jason D; Miyamoto, Shingo; Sail, Vibhavari; Verma, Rajeev; Rosenberg, Daniel W; Nelson, Craig E; Giardina, Charles
Generating lineage-committed intestinal stem cells from embryonic stem cells (ESCs) could provide a tractable experimental system for understanding intestinal differentiation pathways and may ultimately provide cells for regenerating damaged intestinal tissue. We tested a two-step differentiation procedure in which ESCs were first cultured with activin A to favor formation of definitive endoderm, and then treated with fibroblast-conditioned medium with or without Wnt3A. The definitive endoderm expressed a number of genes associated with gut-tube development through mouse embryonic day 8.5 (Sox17, Foxa2, and Gata4 expressed and Id2 silent). The intestinal stem cell marker Lgr5 gene was also activated in the endodermal cells, whereas the Msi1, Ephb2, and Dcamkl1 intestinal stem cell markers were not. Exposure of the endoderm to fibroblast-conditioned medium with Wnt3A resulted in the activation of Id2, the remaining intestinal stem cell markers and the later gut markers Cdx2, Fabp2, and Muc2. Interestingly, genes associated with distal gut-associated mesoderm (Foxf2, Hlx, and Hoxd8) were also simulated by Wnt3A. The two-step differentiation protocol generated gut bodies with crypt-like structures that included regions of Lgr5-expressing proliferating cells and regions of cell differentiation. These gut bodies also had a smooth muscle component and some underwent peristaltic movement. The ability of the definitive endoderm to differentiate into intestinal epithelium was supported by the vivo engraftment of these cells into mouse colonic mucosa. These findings demonstrate that definitive endoderm derived from ESCs can carry out intestinal cell differentiation pathways and may provide cells to restore damaged intestinal tissue.
Endele, Max; Etzrodt, Martin; Schroeder, Timm, E-mail: email@example.com
Hematopoiesis is the cumulative consequence of finely tuned signaling pathways activated through extrinsic factors, such as local niche signals and systemic hematopoietic cytokines. Whether extrinsic factors actively instruct the lineage choice of hematopoietic stem and progenitor cells or are only selectively allowing survival and proliferation of already intrinsically lineage-committed cells has been debated over decades. Recent results demonstrated that cytokines can instruct lineage choice. However, the precise function of individual cytokine-triggered signaling molecules in inducing cellular events like proliferation, lineage choice, and differentiation remains largely elusive. Signal transduction pathways activated by different cytokine receptors are highly overlapping, but support the production of distinct hematopoietic lineages. Cellular context, signaling dynamics, and the crosstalk of different signaling pathways determine the cellular response of a given extrinsic signal. New tools to manipulate and continuously quantify signaling events at the single cell level are therefore required to thoroughly interrogate how dynamic signaling networks yield a specific cellular response. - Highlights: • Recent studies provided definite proof for lineage-instructive action of cytokines. • Signaling pathways involved in hematopoietic lineage instruction remain elusive. • New tools are emerging to quantitatively study dynamic signaling networks over time.
Eric S. Huseby
Full Text Available A growing body of evidence suggests that autoreactive CD8 T cells contribute to the disease process in Multiple Sclerosis (MS. Lymphocytes in MS plaques are biased toward the CD8 lineage, and MS patients harbor CD8 T cells specific for multiple central nervous system (CNS antigens. Currently, there are relatively few experimental model systems available to study these pathogenic CD8 T cells in vivo. However, the few studies that have been done characterizing the mechanisms used by CD8 T cells to induce CNS autoimmunity indicate that several of the paradigms of how CD4 T cells mediate CNS autoimmunity do not hold true for CD8 T cells or for patients with MS. Thus, myelin-specific CD4 T cells are likely to be one of several important mechanisms that drive CNS disease in MS patients. The focus of this review is to highlight the current models of pathogenic CNS-reactive CD8 T cells and the molecular mechanisms these lymphocytes use when causing CNS inflammation and damage. Understanding how CNS-reactive CD8 T cells escape tolerance induction and induce CNS autoimmunity is critical to our ability to propose and test new therapies for MS.
Pfeiffer, Michael; Betizeau, Marion; Waltispurger, Julie; Pfister, Sabina Sara; Douglas, Rodney J; Kennedy, Henry; Dehay, Colette
Generation of the primate cortex is characterized by the diversity of cortical precursors and the complexity of their lineage relationships. Recent studies have reported miscellaneous precursor types based on observer classification of cell biology features including morphology, stemness, and proliferative behavior. Here we use an unsupervised machine learning method for Hidden Markov Trees (HMTs), which can be applied to large datasets to classify precursors on the basis of morphology, cell-cycle length, and behavior during mitosis. The unbiased lineage analysis automatically identifies cell types by applying a lineage-based clustering and model-learning algorithm to a macaque corticogenesis dataset. The algorithmic results validate previously reported observer classification of precursor types and show numerous advantages: It predicts a higher diversity of progenitors and numerous potential transitions between precursor types. The HMT model can be initialized to learn a user-defined number of distinct classes of precursors. This makes it possible to 1) reveal as yet undetected precursor types in view of exploring the significant features of precursors with respect to specific cellular processes; and 2) explore specific lineage features. For example, most precursors in the experimental dataset exhibit bidirectional transitions. Constraining the directionality in the HMT model leads to a reduction in precursor diversity following multiple divisions, thereby suggesting that one impact of bidirectionality in corticogenesis is to maintain precursor diversity. In this way we show that unsupervised lineage analysis provides a valuable methodology for investigating fundamental features of corticogenesis.
Palopoli, Michael F; Fergus, Daniel J; Minot, Samuel; Pei, Dorothy T; Simison, W Brian; Fernandez-Silva, Iria; Thoemmes, Megan S; Dunn, Robert R; Trautwein, Michelle
Microscopic mites of the genus Demodex live within the hair follicles of mammals and are ubiquitous symbionts of humans, but little molecular work has been done to understand their genetic diversity or transmission. Here we sampled mite DNA from 70 human hosts of diverse geographic ancestries and analyzed 241 sequences from the mitochondrial genome of the species Demodex folliculorum. Phylogenetic analyses recovered multiple deep lineages including a globally distributed lineage common among hosts of European ancestry and three lineages that primarily include hosts of Asian, African, and Latin American ancestry. To a great extent, the ancestral geography of hosts predicted the lineages of mites found on them; 27% of the total molecular variance segregated according to the regional ancestries of hosts. We found that D. folliculorum populations are stable on an individual over the course of years and that some Asian and African American hosts maintain specific mite lineages over the course of years or generations outside their geographic region of birth or ancestry. D. folliculorum haplotypes were much more likely to be shared within families and between spouses than between unrelated individuals, indicating that transmission requires close contact. Dating analyses indicated that D. folliculorum origins may predate modern humans. Overall, D. folliculorum evolution reflects ancient human population divergences, is consistent with an out-of-Africa dispersal hypothesis, and presents an excellent model system for further understanding the history of human movement.
Jacob, Alison S; Busby, Eloise J; Levy, Abigail D; Komm, Natasha; Clark, C Graham
Removing the requirement for cell culture has led to a substantial increase in the number of lineages of Entamoeba recognized as distinct. Surveying the range of potential host species for this parasite genus has barely been started and it is clear that additional sampling of the same host in different locations often identifies additional diversity. In this study, using small subunit ribosomal RNA gene sequencing, we identify four new lineages of Entamoeba, including the first report of Entamoeba from an elephant, and extend the host range of some previously described lineages. In addition, examination of microbiome data from a number of host animals suggests that substantial Entamoeba diversity remains to be uncovered.
Chajęcka-Wierzchowska, Wioleta; Zadernowska, Anna; Nalepa, Beata; Sierpińska, Magda; Laniewska-Trokenheim, Lucja
Ready-to-eat (RTE) food, which does not need thermal processing before consumption, could be a vehicle for the spread of antibiotic-resistant microorganisms. As part of general microbiological safety checks, staphylococci are routinely enumerated in these kinds of foods. However, the presence of antibiotic-resistant staphylococci in RTE food is not routinely investigated, and data are only available from a small number of studies. The present study evaluated the pheno- and genotypical antimicrobial resistance profile of Staphylococcus spp. isolated from 858 RTE foods (cheeses, cured meats, sausages, smoked fishes, salads). Of 113 strains isolated, S. aureus was the most prevalent species, followed by S. xylosus, S. saprophyticus, and S. epidermidis. More than half (54.9%) of the isolates were resistant to at least one class of tested antibiotic; of these, 35.4% of the strains were classified as multidrug resistant. Most of the isolates were resistant to cefoxitin (49.6%), followed by clindamycin (39.3%), tigecycline (27.4%), quinupristin-dalfopristin (22.2%), rifampin (20.5%), tetracycline (17.9%), and erythromycin (8.5%). All methicillin-resistant staphylococci harbored the mecA gene. Among the isolates resistant to at least one antibiotic, 38 harbored tetracycline resistance determinant tet (M), 24 harbored tet (L), and 9 harbored tet (K). Of the isolates positive for tet (M) genes, 34.2% were positive for the Tn916-Tn1545-like integrase family gene. Our results indicated that retail RTE food could be considered an important route for the transmission of antibiotic-resistant bacteria harboring multiple antibiotic resistance genes.
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Mattapoisett Harbor, Mattapoisett, Mass. 110.45a Section 110.45a Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND..., Mattapoisett, Mass. (a) Area No. 1 beginning at a point on the shore at latitude 41°39′23″ N., longitude...
... Master Plan Subcommittee of the City of Newport Harbor Commission led an outreach campaign involving a... meetings, the City of Newport asked the Coast Guard to amend its anchorage regulations. The Coast Guard... incorporated into area A-11 under revised Sec. 110.95(k). An image of the anchorage areas is available in...
.... SUPPLEMENTARY INFORMATION: Table of Acronyms DHS Department of Homeland Security FR Federal Register NPRM Notice... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Sheboygan Harbor Fest, Sheboygan, WI AGENCY... safety zone on Lake Michigan and the Sheboygan River, Sheboygan, WI. This safety zone is intended...
America . Shortly after the quake hit, United States Southern Command (SOUTHCOM) diverted the USNS Grasp and the 544th to Port-au-Prince. Once there...Prince harbor. Pe- troleum floated on top of the water, and numerous marine hazards like jellyfish , human waste, and debris floated be- neath the
... announced by a later notice in the Federal Register. B. Basis and Purpose Tsunamis can occur at any time. There is no tsunami season. The destructive potential of a tsunami can take lives, cause millions of... of the harbors in the event a tsunami warning is issued for the main Hawaiian Islands. DATES...
Jackson, Duncan E
Female attraction to an environmentally derived mating signal released by male orchid bees may be tightly linked to shared olfactory preferences of both sexes. A change in perfume preference may have led to divergence of two morphologically distinct lineages.
Wilm, Bettina; Muñoz-Chapuli, Ramon
The spatiotemporal expression pattern of Wt1 has been extensively studied in a number of animal models to establish its function and the developmental fate of the cells expressing this gene. In this chapter, we review the available animal models for Wt1-expressing cell lineage analysis, including direct Wt1 expression reporters and systems for permanent Wt1 lineage tracing. We describe the presently used constitutive or inducible genetic lineage tracing approaches based on the Cre/loxP system utilizing Cre recombinase expression under control of a Wt1 promoter.To make these systems accessible, we provide laboratory protocols that include dissection and processing of the tissues for immunofluorescence and histopathological analysis of the lineage-labeled Wt1-derived cells within the embryo/tissue context.
Full Text Available All forms of life are confronted with environmental and genetic perturbations, making phenotypic robustness an important characteristic of life. Although development has long been viewed as a key component of phenotypic robustness, the underlying mechanism is unclear. Here we report that the determinative developmental cell lineages of two protostomes and one deuterostome are structured such that the resulting cellular compositions of the organisms are only modestly affected by cell deaths. Several features of the cell lineages, including their shallowness, topology, early ontogenic appearances of rare cells, and non-clonality of most cell types, underlie the robustness. Simple simulations of cell lineage evolution demonstrate the possibility that the observed robustness arose as an adaptation in the face of random cell deaths in development. These results reveal general organizing principles of determinative developmental cell lineages and a conceptually new mechanism of phenotypic robustness, both of which have important implications for development and evolution.
Full Text Available In this study, Forty-one out of fifty-seven Tunisian children with B-lineage acute lymphoblastic leukemia (B-ALL, and without cytogenetically detectable recurrent abnormalities at the time of the diagnosis, were evaluated by fluorescence in situ hybridization (FISH for the t(12;21. This translocation leads ETV6-RUNX1 (previously TEL-AML1 fusion gene. 16 patients (28% had ETV6-RUNX1 rearrangement. In addition to this rearrangement, two cases showed a loss of the normal ETV6 allele, and three others showed an extra signal of the RUNX1 gene. Seven patients without ETV6-RUNX1 rearrangement showed extra signals of the RUNX1 gene. One out of the 7 patients was also associated with a t(3;12 identified by FISH. This is the first Tunisian study in which we report the incidence of t(12;21 among childhood B-lineage ALL and in which we have found multiple copies of RUNX1. Finally, our findings confirm that additional or secondary genetic changes are commonly encountered in pediatric B-lineage ALL with ETV6-RUNX1 gene fusion which is envisaged to play a pivotal role in disease progression.
Berens, Ali J; Hunt, James H; Toth, Amy L
An area of great interest in evolutionary genomics is whether convergently evolved traits are the result of convergent molecular mechanisms. The presence of queen and worker castes in insect societies is a spectacular example of convergent evolution and phenotypic plasticity. Multiple insect lineages have evolved environmentally induced alternative castes. Given multiple origins of eusociality in Hymenoptera (bees, ants, and wasps), it has been proposed that insect castes evolved from common genetic "toolkits" consisting of deeply conserved genes. Here, we combine data from previously published studies on fire ants and honey bees with new data for Polistes metricus paper wasps to assess the toolkit idea by presenting the first comparative transcriptome-wide analysis of caste determination among three major hymenopteran social lineages. Overall, we found few shared caste differentially expressed transcripts across the three social lineages. However, there is substantially more overlap at the levels of pathways and biological functions. Thus, there are shared elements but not on the level of specific genes. Instead, the toolkit appears to be relatively "loose," that is, different lineages show convergent molecular evolution involving similar metabolic pathways and molecular functions but not the exact same genes. Additionally, our paper wasp data do not support a complementary hypothesis that "novel" taxonomically restricted genes are related to caste differences. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: firstname.lastname@example.org.
Flores Carlos; Larruga José M; González Ana M; Maca-Meyer Nicole; Cabrera Vicente M
Abstract Background The phylogeographic distribution of human mitochondrial DNA variations allows a genetic approach to the study of modern Homo sapiens dispersals throughout the world from a female perspective. As a new contribution to this study we have phylogenetically analysed complete mitochondrial DNA(mtDNA) sequences from 42 human lineages, representing major clades with known geographic assignation. Results We show the relative relationships among the 42 lineages and present more accu...
Illingworth, Robert S; Hölzenspies, Jurriaan J; Roske, Fabian V
Mouse embryonic stem cells (ESCs), like the blastocyst from which they are derived, contain precursors of the epiblast (Epi) and primitive endoderm (PrEn) lineages. While transient in vivo, these precursor populations readily interconvert in vitro. We show that altered transcription is the driver...... polycomb with dynamic changes in transcription and stalled lineage commitment, allowing cells to explore alternative choices prior to a definitive decision....
Riyahi Zaniani, Fatemeh; Moghim, Sharareh; Mirhendi, Hossein; Ghasemian Safaei, Hajieh; Fazeli, Hossein; Salehi, Mahshid; Nasr Esfahani, Bahram
In this study, we aimed to identify the genetic lineages of Mycobacterium tuberculosis isolates in Isfahan via the mycobacterial interspersed repetitive-unit-variable number tandem repeat typing method based on 15 loci. Forty-nine M. tuberculosis isolates were collected between 2013 and 2015 from Tuberculosis patients in Mollahadi Sabzevari Tuberculosis Center in Isfahan. All isolates were typed by 15-locus MIRU-VNTR typing. The highest percentage of isolates, 44.89 % (22/49), belonged to the Euro-American lineage, while the frequencies of the East-African-Indian, East-Asian, and Indo-Oceanic lineages were 28.57 % (14/49), 24.4 % (12/49), and 2.04 % (1/49), respectively. Among the 22 isolates of the Euro-American lineage, those belonging to the NEW-1 sub-lineage were most prevalent (24.4 %). Approximately, the same proportion of isolates belonging to the Delhi/CAS, Beijing, and NEW-1 sub-lineages were identified in Iranian and Afghan immigrant patients. The Delhi/CAS and Beijing sub-lineage isolates were prevalent among patients who had been previously treated for TB. Results showed that all of the 49 MIRU-VNTR patterns were unique and the clustering rate of the 15-locus MIRU-VNTR was 0.0 (minimum recent transmission). The results of this study show that the lineages of M. tuberculosis isolates in Isfahan are similar to those reported in the Eastern Mediterranean region (indicative of the epidemiological relationship between the countries in the region). The low clustering rate in our results reveals that transmission of tuberculosis in Isfahan is, in most cases, a reactivation of previous tuberculosis infection and the role of recently transmitted disease is minor.
Tougaard, Jakob; Henriksen, Oluf Damsgaard; Miller, Lee A
Underwater noise was recorded from three different types of wind turbines in Denmark and Sweden (Middelgrunden, Vindeby, and Bockstigen-Valar) during normal operation. Wind turbine noise was only measurable above ambient noise at frequencies below 500 Hz. Total sound pressure level was in the range 109-127 dB re 1 microPa rms, measured at distances between 14 and 20 m from the foundations. The 1/3-octave noise levels were compared with audiograms of harbor seals and harbor porpoises. Maximum 1/3-octave levels were in the range 106-126 dB re 1 microPa rms. Maximum range of audibility was estimated under two extreme assumptions on transmission loss (3 and 9 dB per doubling of distance, respectively). Audibility was low for harbor porpoises extending 20-70 m from the foundation, whereas audibility for harbor seals ranged from less than 100 m to several kilometers. Behavioral reactions of porpoises to the noise appear unlikely except if they are very close to the foundations. However, behavioral reactions from seals cannot be excluded up to distances of a few hundred meters. It is unlikely that the noise reaches dangerous levels at any distance from the turbines and the noise is considered incapable of masking acoustic communication by seals and porpoises.
Full Text Available Dengue virus (DENV transmission is ubiquitous throughout the tropics. More than 70% of the current global dengue disease burden is borne by people who live in the Asia-Pacific region. We sequenced the E gene of DENV isolated from travellers entering Western Australia between 2010-2012, most of whom visited Indonesia, and identified a diverse array of DENV1-4, including multiple co-circulating viral lineages. Most viruses were closely related to lineages known to have circulated in Indonesia for some time, indicating that this geographic region serves as a major hub for dengue genetic diversity. Most notably, we identified a new lineage of DENV-2 (Cosmopolitan genotype that emerged in Bali in 2011-2012. The spread of this lineage should clearly be monitored. Surveillance of symptomatic returned travellers provides important and timely information on circulating DENV serotypes and genotypes, and can reveal the herald wave of dengue and other emerging infectious diseases.
Full Text Available Dengue has re-emerged as an important arboviral disease causing significant morbidity. It has become hyperendemic in the Indian subcontinent with all the four known dengue serotypes circulating. In the present study we have characterized dengue virus type 3 (DENV-3 circulating in Lucknow, Uttar Pradesh, India. Multiple sequence alignment and phylogenetic tree were constructed to determine the extent of genetic heterogeneity and phylogeny of the dengue virus isolated. Sequencing and phylogenetic analysis of the C-prM gene junction revealed the active circulation and persistence of a new lineage of DENV-3 (genotype III circulating in this region of India.
Korchnak, Amanda C.; Zhan, Yu; Aguilar, Michael T.; Chadee, Deborah N.
Mixed Lineage Kinase 3 (MLK3) is a mitogen-activated protein kinase kinase kinase (MAP3K) that activates multiple mitogen activated protein kinase (MAPK) pathways in response to growth factors, stresses and the pro-inflammatory cytokine, tumor necrosis factor (TNF). MLK3 is required for optimal activation of stress activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK) signaling by TNF, however, the mechanism by which MLK3 is recruited and activated by the TNF receptor remains poorly und...
Cole, Eric T.; Zhan, Yu; Abi Saab, Widian F.; Korchnak, Amanda C.; Ashburner, Brian P.; Chadee, Deborah N.
Mixed Lineage Kinase 3 (MLK3) is a mitogen activated protein kinase kinase kinase (MAP3K) that activates multiple MAPK signaling pathways. Nuclear factor kappa B (NF-κB) is a transcription factor that has important functions in inflammation, immunity and cell survival. We found that silencing mlk3 expression with RNA interference (RNAi) in SKOV3 human ovarian cancer epithelial cells and NIH-3T3 murine fibroblasts led to a reduction in the level of the inhibitor of kappa B alpha (IκBα) protein...
Choi, Eunyoung; Roland, Joseph T; Barlow, Brittney J; O'Neal, Ryan; Rich, Amy E; Nam, Ki Taek; Shi, Chanjuan; Goldenring, James R
The glands of the stomach body and antral mucosa contain a complex compendium of cell lineages. In lower mammals, the distribution of oxyntic glands and antral glands define the anatomical regions within the stomach. We examined in detail the distribution of the full range of cell lineages within the human stomach. We determined the distribution of gastric gland cell lineages with specific immunocytochemical markers in entire stomach specimens from three non-obese organ donors. The anatomical body and antrum of the human stomach were defined by the presence of ghrelin and gastrin cells, respectively. Concentrations of somatostatin cells were observed in the proximal stomach. Parietal cells were seen in all glands of the body of the stomach as well as in over 50% of antral glands. MIST1 expressing chief cells were predominantly observed in the body although individual glands of the antrum also showed MIST1 expressing chief cells. While classically described antral glands were observed with gastrin cells and deep antral mucous cells without any parietal cells, we also observed a substantial population of mixed type glands containing both parietal cells and G cells throughout the antrum. Enteroendocrine cells show distinct patterns of localisation in the human stomach. The existence of antral glands with mixed cell lineages indicates that human antral glands may be functionally chimeric with glands assembled from multiple distinct stem cell populations. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
Dannise V Ruiz-Ramos
Full Text Available Colonial corals occur in a wide range of marine benthic habitats from the shallows to the deep ocean, often defining the structure of their local community. The black coral Leiopathes glaberrima is a long-lived foundation species occurring on carbonate outcrops in the Northern Gulf of Mexico (GoM. Multiple color morphs of L. glaberrima grow sympatrically in the region. Morphological, mitochondrial and nuclear ribosomal markers supported the hypothesis that color morphs constituted a single biological species and that colonies, regardless of color, were somewhat genetically differentiated east and west of the Mississippi Canyon. Ten microsatellite loci were used to determine finer-scale population genetic structure and reproductive characteristics. Gene flow was disrupted between and within two nearby (distance = 36.4 km hardground sites and two sympatric microsatellite lineages, which might constitute cryptic species, were recovered. Lineage one was outbred and found in all sampled locations (N = 5 across 765.6 km in the Northern Gulf of Mexico. Lineage two was inbred, reproducing predominantly by fragmentation, and restricted to sites around Viosca Knoll. In these sites the lineages and the color phenotypes occurred in different microhabitats, and models of maximum entropy suggested that depth and slope influence the distribution of the color phenotypes within the Vioska Knolls. We conclude that L. glaberrima is phenotypically plastic with a mixed reproductive strategy in the Northern GoM. Such strategy might enable this long-lived species to balance local recruitment with occasional long-distance dispersal to colonize new sites in an environment where habitat is limited.
Full Text Available Abstract Background The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, which can lead us to a better understanding of how the parasites develop the genetic variability that is associated with their response to environmental challenges and other adaptive phenotypes. Results We present the results of a comprehensive analysis of the genomes of six Plasmodium species, including two species that infect humans, one that infects monkeys, and three that infect rodents. The core genome shared by all six species is composed of 3,351 genes, which make up about 22%-65% of the genome repertoire. These components play important roles in fundamental functions as well as in parasite-specific activities. We further investigated the distribution and features of genes that have been expanded in specific Plasmodium lineage(s. Abundant duplicate genes are present in the six species, with 5%-9% of the whole genomes composed lineage specific radiations. The majority of these gene families are hypothetical proteins with unknown functions; a few may have predicted roles such as antigenic variation. Conclusions The core genome components in the malaria parasites have functions ranging from fundamental biological processes to roles in the complex networks that sustain the parasite-specific lifestyles appropriate to different hosts. They represent the minimum requirement to maintain a successful life cycle that spans vertebrate hosts and mosquito vectors. Lineage specific expansions (LSEs have given rise to abundant gene families in Plasmodium. Although the functions of most families remain unknown, these LSEs could reveal components in parasite networks that, by their enhanced genetic variability, can contribute to
Ishizuka, Isabel E; Chea, Sylvestre; Gudjonson, Herman; Constantinides, Michael G; Dinner, Aaron R; Bendelac, Albert; Golub, Rachel
The precise lineage relationship between innate lymphoid cells (ILCs) and lymphoid tissue-inducer (LTi) cells is poorly understood. Using single-cell multiplex transcriptional analysis of 100 lymphoid genes and single-cell cultures of fetal liver precursor cells, we identified the common proximal precursor to these lineages and found that its bifurcation was marked by differential induction of the transcription factors PLZF and TCF1. Acquisition of individual effector programs specific to the ILC subsets ILC1, ILC2 and ILC3 was initiated later, at the common ILC precursor stage, by transient expression of mixed ILC1, ILC2 and ILC3 transcriptional patterns, whereas, in contrast, the development of LTi cells did not go through multilineage priming. Our findings provide insight into the divergent mechanisms of the differentiation of the ILC lineage and LTi cell lineage and establish a high-resolution 'blueprint' of their development.
A series of enclosed ecosystem experiments were conducted in a land-based tank near the seaside of West Xiamen Harbor. The results of experiments conducted in different seasons and years showed a repeatable phytoplankton succession. In this relatively stable ecosystem with added nutrients and trace metals, diatoms dominated initially, dinoflagellates dominated in the later stage, and dinoflagellate red tides eventually occurred. Vitamin B12 enrichment may speed up this succession process. Stirring the water column could stop this process. Soluble Mn at a level of 3-4 μg/L in seawater, which also is the existing concentration of soluble Mn in Xiamen Harbor seawater, is sufficient for the multiplication of algae and occurrence of red tide. The present study showed that excessive soluble Mn in Xiamen Harbor cannot cause red tide, and that Fe was one of the important factors causing diatom red tide in this present study.
Shi, Yu; Huang, Zhou; Han, Shuai; Fan, Shuo; Yang, Hong
Termites are among the few arthropods that emit methane to the atmosphere, which is a significant source of global greenhouse gas due to their huge biomass on earth. In this study, phylogenetic diversity of Archaea of five termite species from different lineages were analyzed based on 16S rRNA genes. Archaea associated with wood-feeding lower termite, R. chinensis were exclusively Methanobrevibacter in the order Methanobacteriales. This type of methanogens was also found in Nasutitermes sp. and Microcerotermes sp. but not in the fungus-cultivating termites, Odontotermes formosanus and Macrotermes barneyi, which harbor Archaea of the order Methanoplasmatales and Methanosarcinales in their guts. Archaeal diversity of wood-feeding higher termites was higher than wood-feeding lower termites. The highest archaeal diversity was found in Nasutitermes sp. In addition to methanogens affiliated with the orders Methanobacteriales, Methanomicrobiales, and Methanoplasmatales, 37% of archaeal clones were affiliated with non-methanogenic Thaumarchaeota. The results of this study will be significant for further understanding of symbiotic relationship between intestinal microbiota and termites.
María Lupe Román
Full Text Available One of the most efficient options for the control of late blight disease in potato (Solanum tuberosum is the development of resistant varieties to Phytophthora infestans mediated by the direct transfer of resistance (R genes through genetic engineering. In the present work, we used Solanum bulbocastanum RB gene to confers broad spectrum resistance to P. infestans races. To that end, Agrobacterium - mediated genetic transformation was used to transform a susceptible potato variety, Desiree, with the binary vector pCIP68 harboring the RB gene. As a result, 19 transformed plants containing the RB gene were obtained. kanamycin resistance test and polymerase chain reaction (PCR assays confirmed the integration of the T-DNA in the potato genome. The 19 transformed plants, also called transgenic events were subjected to infection under biosafety greenhouse conditions. Phytophthora infestans isolate POX067 of the EC-1 clonal lineage, commonly find in Peru, was used for the infection. Three of the 19 plants ([RB]54, [RB]56 and [RB]70 show high resistance levels to isolate POX067 of P. infestans.
Thandapani, Palaniraja; Song, Jingwen; Gandin, Valentina; Cai, Yutian; Rouleau, Samuel G; Garant, Jean-Michel; Boisvert, Francois-Michel; Yu, Zhenbao; Perreault, Jean-Pierre; Topisirovic, Ivan; Richard, Stéphane
G-quadruplexes (G4) are extremely stable secondary structures forming stacks of guanine tetrads. DNA G4 structures have been extensively studied, however, less is known about G4 motifs in mRNAs, especially in their coding sequences. Herein, we show that Aven stimulates the mRNA translation of the mixed lineage leukemia (MLL) proto-oncogene in an arginine methylation-dependent manner. The Aven RGG/RG motif bound G4 structures within the coding regions of the MLL1 and MLL4 mRNAs increasing their polysomal association and translation, resulting in the induction of transcription of leukemic genes. The DHX36 RNA helicase associated with the Aven complex and was required for optimal translation of G4 mRNAs. Depletion of Aven led to a decrease in synthesis of MLL1 and MLL4 proteins resulting in reduced proliferation of leukemic cells. These findings identify an Aven-centered complex that stimulates the translation of G4 harboring mRNAs, thereby promoting survival of leukemic cells.
Woma, T Y; Adombi, C M; Yu, D; Qasim, A M M; Sabi, A A; Maurice, N A; Olaiya, O D; Loitsch, A; Bailey, D; Shamaki, D; Dundon, W G; Quan, M
Peste-des-petits-ruminants (PPR), a major small ruminant transboundary animal disease, is endemic in Nigeria. Strains of the causal agent, peste-des-petits-ruminants virus (PPRV), have been differentiated into four genetically distinct lineages based on the partial sequence of the virus nucleoprotein (N) or fusion (F) genes. Peste-des-petits-ruminants virus strains that were identified initially in Africa were grouped into lineages I, II and III and viruses from Asia were classified as lineage IV and referred to as the Asian lineage. Many recent reports indicate that the Asian lineage is now also present in Africa. With this in mind, this study was conducted to reassess the epidemiology of PPRV in Nigeria. A total of 140 clinical samples from 16 sheep and 63 goats with symptoms suggestive of PPR were collected from different states of Nigeria during a four-year period (2010-2013). They were analysed by the amplification of fragments of the N gene. Results for 33 (42%) animals were positive. The phylogenetic analysis of the N gene sequences with those available in GenBank showed that viruses that were detected belong to both lineage II and IV. Based on an analysis of the N gene sequences, the lineage IV isolates grouped into two clades, one being predominant in the north-eastern part of the country and the other found primarily in the southern regions of the country. This study reports the presence of PPRV Asian lineage IV in Nigeria for the first time. © 2016 Blackwell Verlag GmbH.
National Oceanic and Atmospheric Administration, Department of Commerce — Between 2004 and 2006 we conducted four harbor seal tagging trips in Cook Inlet during the months of October and May. In total, we captured and released 93 harbor...
National Oceanic and Atmospheric Administration, Department of Commerce — Aerial surveys of coastal Alaska are the primary method for estimating abundance of harbor seals. A particular challenge associated with aerial surveys of harbor...
... Harbor, Boston, MA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is... Navigation Areas: Reserved Channel, Boston Harbor, Boston, MA (a) Location. The following areas are...
U.S. Geological Survey, Department of the Interior — This data is a qualitatively-derived interpretative polygon shapefile defining the bottom types of the seafloor from Boston Harbor and the harbor approaches,...
U.S. Geological Survey, Department of the Interior — These data are high-resolution bathymetric measurements of the seafloor from Boston Harbor and the harbor approaches, Massachusetts. Approximately 170 kmÂ² of...
U.S. Geological Survey, Department of the Interior — These data are high-resolution bathymetric measurements of the seafloor from Boston Harbor and the harbor approaches, Massachusetts. Approximately 170 km² of...
U.S. Geological Survey, Department of the Interior — These data are high-resolution bathymetric measurements of the seafloor from Boston Harbor and the harbor approaches, Massachusetts. Approximately 170 kmÂ² of...
U.S. Geological Survey, Department of the Interior — These data are high-resolution bathymetric measurements of the seafloor from Boston Harbor and the harbor approaches, Massachusetts. Approximately 170 km² of...
U.S. Geological Survey, Department of the Interior — These data are high-resolution bathymetric measurements of the seafloor from Boston Harbor and the harbor approaches, Massachusetts. Approximately 170 kmÂ˛ of...
National Oceanic and Atmospheric Administration, Department of Commerce — This dataset supports efforts to estimate the abundance and trends in population size of Alaska harbor seals. Annual surveys of harbor seal populations are...
Pillai, S P S; Suarez, D L; Pantin-Jackwood, M; Lee, C-W
In 2004, a low pathogenic H5N2 influenza virus (A/parrot/CA/6032/04) was identified in a psittacine bird for the first time in the United States. Sequence and phylogenetic analysis of the hemagglutinin gene grouped the parrot isolate under the Mexican lineage H5N2 viruses (subgroup B) with highest similarity to recent chicken-origin isolates from Guatemala. Antigenic analysis further confirmed the close relatedness of the parrot isolate to Mexican lineage viruses, the highest cross-reactivity being demonstrated to Guatemala isolates. In vivo studies of the parrot isolate in chickens, ducks and turkeys showed that the virus, though did not cause any clinical signs, could replicate to high titers in these birds and efficiently transmit to contact control cage mates. The possibility that the parrot harboring the virus was introduced into the United States as a result of illegal trade across the border provides additional concern for the movement of foreign animal diseases from neighboring countries. Considering the potential threat of the virus to domestic poultry, efforts should be continued to prevent the entry and spread of influenza viruses by imposing effective surveillance and monitoring measures.
ER D C/ CH L TR -1 7- 7 Regional Sediment Management (RSM) Program Charleston Harbor, SC, Regional Sediment Management Study...acwc.sdp.sirsi.net/client/default. Regional Sediment Management (RSM) Program ERDC/CHL TR-17-7 May 2017 Charleston Harbor, SC, Regional Sediment...454632, “Charleston Harbor, SC; Regional Sediment Management Study” ERDC/CHL TR-17-7 ii Abstract The 2015 Charleston Harbor, SC, final
High diversity of genetic lineages and virulence genes in nasal Staphylococcus aureus isolates from donkeys destined to food consumption in Tunisia with predominance of the ruminant associated CC133 lineage
Full Text Available Abstract Background The objective of this study was to determine the genetic lineages and the incidence of antibiotic resistance and virulence determinants of nasal Staphylococcus aureus isolates of healthy donkeys destined to food consumption in Tunisia. Results Nasal swabs of 100 donkeys obtained in a large slaughterhouse in 2010 were inoculated in specific media for S. aureus and methicillin-resistant S. aureus (MRSA recovery. S. aureus was obtained in 50% of the samples, being all of isolates methicillin-susceptible (MSSA. Genetic lineages, toxin gene profile, and antibiotic resistance mechanisms were determined in recovered isolates. Twenty-five different spa-types were detected among the 50 MSSA with 9 novel spa-types. S. aureus isolates were ascribed to agr type I (37 isolates, III (7, II (4, and IV (2. Sixteen different sequence-types (STs were revealed by MLST, with seven new ones. STs belonging to clonal clomplex CC133 were majority. The gene tst was detected in 6 isolates and the gene etb in one isolate. Different combinations of enterotoxin, leukocidin and haemolysin genes were identified among S. aureus isolates. The egc-cluster-like and an incomplete egc-cluster-like were detected. Isolates resistant to penicillin, erythromycin, fusidic acid, streptomycin, ciprofloxacin, clindamycin, tetracycline, or chloramphenicol were found and the genes blaZ, erm(A, erm(C, tet(M, fusC were identified. Conclusions The nares of donkeys frequently harbor MSSA. They could be reservoirs of the ruminant-associated CC133 lineage and of toxin genes encoding TSST-1 and other virulence traits with potential implications in public health. CC133 seems to have a broader host distribution than expected.
Chen, Ying, E-mail: email@example.com [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, 333 Bostwick NE, Grand Rapids, MI 49503 (United States); Wang, Kai; Chandramouli, Gadisetti V.R. [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, 333 Bostwick NE, Grand Rapids, MI 49503 (United States); Knott, Jason G. [Developmental Epigenetics Laboratory, Department of Animal Science, Michigan State University (United States); Leach, Richard, E-mail: Richard.firstname.lastname@example.org [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, 333 Bostwick NE, Grand Rapids, MI 49503 (United States); Department of Obstetrics, Gynecology and Women’s Health, Spectrum Health Medical Group (United States)
Highlights: •Epithelial-like phenotype of trophoblast lineage cells derived from human iPS cells. •Trophoblast lineage cells derived from human iPS cells exhibit trophoblast function. •Trophoblasts from iPS cells provides a proof-of-concept in regenerative medicine. -- Abstract: Background: During implantation, the blastocyst trophectoderm attaches to the endometrial epithelium and continues to differentiate into all trophoblast subtypes, which are the major components of a placenta. Aberrant trophoblast proliferation and differentiation are associated with placental diseases. However, due to ethical and practical issues, there is almost no available cell or tissue source to study the molecular mechanism of human trophoblast differentiation, which further becomes a barrier to the study of the pathogenesis of trophoblast-associated diseases of pregnancy. In this study, our goal was to generate a proof-of-concept model for deriving trophoblast lineage cells from induced pluripotency stem (iPS) cells from human fibroblasts. In future studies the generation of trophoblast lineage cells from iPS cells established from patient’s placenta will be extremely useful for studying the pathogenesis of individual trophoblast-associated diseases and for drug testing. Methods and results: Combining iPS cell technology with BMP4 induction, we derived trophoblast lineage cells from human iPS cells. The gene expression profile of these trophoblast lineage cells was distinct from fibroblasts and iPS cells. These cells expressed markers of human trophoblasts. Furthermore, when these cells were differentiated they exhibited invasive capacity and placental hormone secretive capacity, suggesting extravillous trophoblasts and syncytiotrophoblasts. Conclusion: Trophoblast lineage cells can be successfully derived from human iPS cells, which provide a proof-of-concept tool to recapitulate pathogenesis of patient placental trophoblasts in vitro.
Full Text Available Co-circulation of two influenza B virus lineages, B/Yamagata and B/Victoria, has been recognized since the late 1980s. The assessment of the prevalent lineage and the group of viruses in circulation is of importance in order to decide on the vaccine composition and evaluate its efficacy. The molecular characterization of influenza B viruses in circulation has been the aim of this study; this was approached by identifying and locating nucleotide substitutions in the influenza B virus hemagglutinin (HA and neuraminidase (NA, specific for the lineage and/or clade. By the alignment of 3456 sequences from the influenza GISAID EpiFlu database, a high number of lineage- and group-specific nucleotide positions have been observed in the HA gene, but not in the NA gene. Additionally, an RT-PCR method has been developed, applicable directly to clinical specimens, which amplifies a short HA region that includes a group of unique molecular signatures. Twenty eight influenza B virus-positive respiratory specimens, collected in Tuscany in the seasons 2012–2013 and 2013–2014, were analyzed. The results revealed two clearly distinguishable patterns: one, more frequent, was characterized by all of the nucleotide changes associated with the B/Yamagata lineage (in most cases of Group 2, whereas the other exhibited all of the changes associated with the B/Victoria lineage. It can be concluded that the analysis of this short HA sequence can permit a rapid, highly sensitive determination of influenza B virus lineages and clades.
Burch, T.L.; Sherwood, C.R. [Battelle/Marine Sciences Lab., Sequim, WA (United States)
Large changes in the distribution of sediment near the entrance to Grays Harbor, Washington, have occurred since the long rock jetties were built to confine flow. Spits to the north and south of the entrance have grown, the entrance channel has deepened, and the outer bar has eroded and moved offshore. The shorelines of North Beach and South Beach have experienced significant amounts of both erosion and accretion since the jetties were constructed around the turn of the century. Recently, the erosion rate at South Beach has increased and, because Half Moon Bay is growing at the expense of the shoreward side of Point Chehalis, the vegetated portion of the spit is now less than 350 ft wide at the narrowest section. The US Army Corps of Engineers, Seattle District, requested that Battelle/Marine Sciences Laboratory evaluate long-term trends in erosion near the entrance to Grays Harbor.
Ranjbar, R; Owlia, P; Saderi, H; Bameri, Z; Izadi, M; Jonaidi, N; Morovvati, S
Aim of this study was to investigate the presence of plasmids among the strains of P. aeruginosa isolated from clinically diagnosed cases in Tehran in 2006. A total of 38 strains of P. aeruginosa were isolated. With the exception of one isolate, all P. aeruginosa strains harbored at least one plasmid band. The electrophoretic analysis of plasmid DNAs showed different number of plasmid bands among the strains tested. The DNA band of 1.4 kbp was evident in 84.2% of the strains. Approximately 71 and 21% of the isolates harbored concomitantly two and three plasmids, respectively. Isolation of strains with diverse types of plasmids suggests the different cluster of P. aeruginosa might be disseminated during the current study period.
Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.
CAO Wenqing; LIN Yuanshao; FANG Luping
In a grid investigation, dinoflagellate cysts were collected from sediments in Xiamen Western Harbor in May of 2000,from which five species of cysts were identified: Alexandrium tamarensis, A. minutum, Lingulodinium polyedra,Gonyaulax scrippsae and Gymnodinium catenatum, account for about 21% in the species composition. The quantitative analysis of the sediments shows that the number of dinoflagellate cysts varies from 51 to 256 cysts/g of sediment, the highest value (>200 cysts/g) being recorded at the stations of the central part of the bay, while the lowest (＜100 cysts/g) at the bay mouth. A good linear relationship is found between cyst amount and fine-grained sediments. Complex physiognomies on the seabed, topographty in the bay and weak water exchange are the main factors not only in cyst accumulation but also in their distribution pattern, and have resulted in the difference in cyst densities between the inner bay and the outer bay in the harbor.
CAO Wenqing; LIN Yuanshao; FANG Luping
In a grid investigation, dinoflagellate cysts were collected from sediments in Xiamen Western Harbor in May of 2000,from which five species of cysts were identified: Alexandrium tamarensis, A. minutum, Lingulodinium polyedra,Gonyaulax scrippsae and Gymnodinium catenatum, account for about 21% in the species composition. The quantitative analysis of the sediments shows that the number of dinoflagellate cysts varies from 51 to 256 cysts/g of sediment, the highest value (＞200 cysts/g) being recorded at the stations of the central part of the bay, while the lowest (＜100 cysts/g) at the bay mouth. A good linear relationship is found between cyst amount and fine-grained sediments. Complex physiognomies on the seabed, topographty in the bay and weak water exchange are the main factors not only in cyst accumulation but also in their distribution pattern, and have resulted in the difference in cyst densities between the inner bay and the outer bay in the harbor.
Kil Woo Chung
Full Text Available Detection, classification, and tracking of small vessels are important tasks for improving port security and the security of coastal and offshore operations. Hydroacoustic sensors can be applied for the detection of noise generated by vessels, and this noise can be used for vessel detection, classification, and tracking. This paper presents recent improvements aimed at the measurement and separation of ship DEMON (Detection of Envelope Modulation on Noise DEMON acoustic signatures in busy harbor conditions. Ship signature measurements were conducted in the Hudson River and NY Harbor. The DEMON spectra demonstrated much better temporal stability compared with the full ship spectra and were measured at distances up to 7 km. The combination of cross-correlation and methods allowed separation of the acoustic signatures of ships in busy urban environments.
... 46 Shipping 2 2010-10-01 2010-10-01 false Load line exemption requirements for the Burns Harbor... line exemption requirements for the Burns Harbor and Milwaukee routes. Barges operating on the Burns... (Milwaukee and/or Burns Harbor); (4) Design type (covered/uncovered hopper, deck, etc.); (5)...
... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Dive Platform, Pago Pago Harbor, American...; Dive Platform, Pago Pago Harbor, American Samoa in the Federal Register (75 FR 5907). We received no... Pago Pago Inner Harbor, in an estimated 160 feet of water, approximately 350-feet from the fuel...
... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Dive Platform, Pago Pago Harbor, American... a temporary safety zone around a dive platform vessel in Pago Pago Harbor, American Samoa, while... Purpose On October 7, 1949 the 4,130-ton gasoline tanker CHEHALIS sank in Pago Pago Inner Harbor, in...
... strategy (DECS) determined by CARB to be the greatest feasible reduction of NO X or PM. For in-use harbor..., push boats, and multipurpose harbor craft. Those harbor craft are required to meet emission limits... owners and operators may opt to meet requirements by implementing alternative emission control strategies...
... impracticable and contrary to the public interest. Background and Purpose The Rochester Harbor Festival is an... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Rochester Harbor Festival, Genesee River... establishing a temporary safety zone on the Genesee River, Rochester, NY for the Rochester Harbor Festival...
... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Fairport Harbor Mardi Gras, Lake Erie... restrict vessels from a portion of Lake Erie during the Fairport Harbor Mardi Gras Fireworks display. This... necessary to ensure the safety of spectators and vessels during the Fairport Harbor Mardi Gras. This...
... Pearl Harbor Remembrance Day, 2009 8463 Proclamation 8463 Presidential Documents Proclamations Proclamation 8463 of December 4, 2009 Proc. 8463 National Pearl Harbor Remembrance Day, 2009By the President of... by the Imperial Japanese on Pearl Harbor was an attempt to break the American will and destroy...
Johnson, Carole D.; White, Eric A.
A marine geophysical investigation was conducted in 2006 to help characterize the bottom and subbottom materials and extent of bedrock in selected areas of Bridgeport Harbor, Connecticut. The data will be used by the U.S. Army Corps of Engineers in the design of confined aquatic disposal (CAD) cells within the harbor to facilitate dredging of the harbor. Three water-based geophysical methods were used to evaluate the geometry and composition of subsurface materials: (1) continuous seismic profiling (CSP) methods provide the depth to water bottom, and when sufficient signal penetration can be achieved, delineate the depth to bedrock and subbottom materials; (2) continuous resistivity profiling (CRP) methods were used to define the electrical properties of the shallow subbottom, and to possibly determine the distribution of conductive materials, such as clay, and resistive materials, such as sand and bedrock; (3) and magnetometer data were used to identify conductive anomalies of anthropogenic sources, such as cables and metallic debris. All data points were located using global positioning systems (GPS), and the GPS data were used for real-time navigation. The results of the CRP, CSP, and magnetometer data are consistent with the conceptual site model of a bedrock channel incised beneath the present day harbor. The channel appears to follow a north-northwest to south-southeast trend and is parallel to the Pequannock River. The seismic record and boring data indicate that under the channel, the depth to bedrock is as much as 42.7 meters (m) below mean low-low water (MLLW) in the dredged part of the harbor. The bedrock channel becomes shallower towards the shore, where bedrock outcrops have been mapped at land surface. CSP and CRP data were able to provide a discontinuous, but reasonable, trace from the channel toward the west under the proposed southwestern CAD cell. The data indicate a high amount of relief on the bedrock surface, as well as along the water bottom
implementation of pollution abatement measures throughout the Vermilion region to reduce the addition of toxic and nutritive constituents to harbor sediments. Such...be the implementation of pollution abatement measures throughout the Vermilion region to reduce the addition of potentially harmful and nutritive ...demand; a water quality param- eter which specifies the amount of oxygen needed by organisms while consuming organic material in the water. BRACHIOPODA A
Brown, Daryl R.; Chvala, William D.; De La Rosa, Marcus I.; Dixon, Douglas R.
A building energy audit was performed by a team of engineers from Pacific Northwest National Laboratory (PNNL) under contract to the Department of Energy/Federal Energy Management Program (FEMP). The effort used the Facility Energy Decision System (FEDS) model to determine how energy is consumed at selected Pearl Harbor buildings, identify cost-effective energy retrofit measures, and calculate the potential energy and cost savings. This report documents the findings of that assessment.
Full Text Available Understanding the variability of foraging behavior within a population of predators is important for determining their role in the ecosystem and how they may respond to future ecosystem changes. However, such variability has seldom been studied in harbor seals on a fine spatial scale (<30 km. We used a combination of standard and Bayesian generalized linear mixed models to explore how environmental variables influenced the dive behavior of harbor seals. Time-depth recorders were deployed on harbor seals from two haul-out sites in the Salish Sea in 2007 (n = 18 and 2008 (n = 11. Three behavioral bout types were classified from six dive types within each bout; however, one of these bout types was related to haul-out activity and was excluded from analyses. Deep foraging bouts (Type I were the predominant type used throughout the study; however, variation in the use of bout types was observed relative to haul-out site, season, sex, and light (day/night. The proportional use of Type I and Type II (shallow foraging/traveling bouts differed dramatically between haul-out sites, seasons, sexes, and whether it was day or night; individual variability between seals also contributed to the observed differences. We hypothesize that this variation in dive behavior was related to habitat or prey specialization by seals from different haul-out sites, or individual variability between seals in the study area. The results highlight the potential influence of habitat and specialization on the foraging behavior of harbor seals, and may help explain the variability in diet that is observed between different haul-out site groups in this population.
Channel Shoaling Project, waves, currents, water levels, bathymetry, and sediment samples are being collected in and around BIH. These data will be... Texas by Ernest R. Smith, Tahirih C. Lackey, David B. King, and Richard Styles PURPOSE: This Coastal and Hydraulics Engineering Technical Note...compared to recent events. INTRODUCTION: Brazos Island Harbor (also called Brazos Santiago Pass) is located on the lower Gulf of Mexico Texas coast
By analysis of published papers on the Yangtze estuary and hydrological and sediments datain Yangshan Harbor area, many similarities are found between Yangshan Harbor area and the Yangtzeestuary. These similarities include the phenomenon of stagnating flow areas, the distributivecharacteristics of the highest suspended sediment concentration areas, superficial sediments and shoalbars. The stagnating flow area is the major similarity which causes other similarities. These similaritiesindicate that: 1) Turbidity Maximum and mouth bars in estuaries are mainly caused by the hydraulicbalance of stagnating flow areas of estuaries; 2) The stagnating sand area of sands caused by stagnatingflow area often locates on the narrower side of the stagnating flow area; 3) The location (or shape) offine sediments area caused by stagnating flow area reflects the location (or shape) of the stagnatingflow area. Both Yangshan Harbor area and the Yangtze estuary are the important developmental areasin the future (man-made similarity). In-depth studies on these similarities between Yangshan Harborarea and the Yangtze estuary will have momentous theoretical and practical significance.
Solberg, Leah C.; Baum, Amber E.; Ahmadiyeh, Nasim; Shimomura, Kazuhiro; Li, Renhua; Turek, Fred W.; Churchil, Gary A.; Takahashi, Joseph S.; Redei, Eva E.
The Wistar–Kyoto (WKY) rat exhibits physiological and behavioral similarities to endophenotypes of human depression. In the forced swim test (FST), a wel-characterized antidepressant-reversible test for behavioral despair in rodents, WKYs express characteristics of behavioral despair; increased immobility, and decreased climbing. To map genetic loci linked to behavior in the FST, we conducted a quantitative trait loci (QTL) analysis of the segregating F2 generation of a WKY · Fisher 344 (F344) reciprocal intercross. Using linear-model-based genome scans to include covariate (sex or lineage) by-QTL interaction effects, four significant QTL influencing climbing behavior were identified. In addition, we identified three, seven, and two suggestive QTL for climbing, immobility, and swimming, respectively. One of these loci was pleiotropic, affecting both immobility and climbing. As found in human linkage studies, several of these QTL showed sex-and/or lineage-dependent effects. A simultaneous search strategy identified three epistatic locus pairs for climbing. Multiple regression analysis was employed to characterize the joint contributions of these QTL and to clarify the sex-and lineage-dependent effects. As expected for complex traits, FST behavior is influenced by multiple QTL of smal effect, each contributing 5%–10%, accounting for a total 10%–30% of the phenotypic variance. A number of loci mapped in this study share overlapping candidate regions with previously identified emotionality QTL in mice as wel as with susceptibility loci recognized by linkage or genome scan analyses for major depression or bipolar disorder in humans. The presence of these loci across species suggests that these QTL may represent universal genetic factors contributing to mood disorders. PMID:15457344
Full Text Available Abstract Background Colon crypts, a single sheet of epithelia cells, consist of a periodic pattern of stem cells, transit-amplifying cells, and terminally differentiated cells that constantly renew and turnover. Experimental evidence suggests that Wnt signaling promotes and regulates stem cell division, differentiation, and possible cell migrations while intestinal BMP signaling inhibits stem cell self-renewal and repression in crypt formation. As more molecular details on Wnt and BMP in crypts are being discovered, little is still known about how complex interactions among Wnt, BMP, and different types of cells, and surrounding environments may lead to de novo formation of multiple crypts or how such interactions affect regeneration and stability of crypts. Results We present a mathematical model that contains Wnt and BMP, a cell lineage, and their feedback regulations to study formation, regeneration, and stability of multiple crypts. The computational explorations and linear stability analysis of the model suggest a reaction–diffusion mechanism, which exhibits a short-range activation of Wnt plus a long-range inhibition with modulation of BMP signals in a growing tissue of cell lineage, can account for spontaneous formation of multiple crypts with the spatial and temporal pattern observed in experiments. Through this mechanism, the model can recapitulate some distinctive and important experimental findings such as crypt regeneration and crypt multiplication. BMP is important in maintaining stability of crypts and loss of BMP usually leads to crypt multiplication with a fingering pattern. Conclusions The study provides a mechanism for de novo formation of multiple intestinal crypts and demonstrates a synergetic role of Wnt and BMP in regeneration and stability of intestinal crypts. The proposed model presents a robust framework for studying spatial and temporal dynamics of cell lineages in growing tissues driven by multiple signaling
Full Text Available Fundamental aspects of embryonic and post-natal development, including maintenance of the mammalian female germline, are largely unknown. Here we employ a retrospective, phylogenetic-based method for reconstructing cell lineage trees utilizing somatic mutations accumulated in microsatellites, to study female germline dynamics in mice. Reconstructed cell lineage trees can be used to estimate lineage relationships between different cell types, as well as cell depth (number of cell divisions since the zygote. We show that, in the reconstructed mouse cell lineage trees, oocytes form clusters that are separate from hematopoietic and mesenchymal stem cells, both in young and old mice, indicating that these populations belong to distinct lineages. Furthermore, while cumulus cells sampled from different ovarian follicles are distinctly clustered on the reconstructed trees, oocytes from the left and right ovaries are not, suggesting a mixing of their progenitor pools. We also observed an increase in oocyte depth with mouse age, which can be explained either by depth-guided selection of oocytes for ovulation or by post-natal renewal. Overall, our study sheds light on substantial novel aspects of female germline preservation and development.
Reizel, Yitzhak; Itzkovitz, Shalev; Adar, Rivka; Elbaz, Judith; Jinich, Adrian; Chapal-Ilani, Noa; Maruvka, Yosef E; Nevo, Nava; Marx, Zipora; Horovitz, Inna; Wasserstrom, Adam; Mayo, Avi; Shur, Irena; Benayahu, Dafna; Skorecki, Karl; Segal, Eran; Dekel, Nava; Shapiro, Ehud
Fundamental aspects of embryonic and post-natal development, including maintenance of the mammalian female germline, are largely unknown. Here we employ a retrospective, phylogenetic-based method for reconstructing cell lineage trees utilizing somatic mutations accumulated in microsatellites, to study female germline dynamics in mice. Reconstructed cell lineage trees can be used to estimate lineage relationships between different cell types, as well as cell depth (number of cell divisions since the zygote). We show that, in the reconstructed mouse cell lineage trees, oocytes form clusters that are separate from hematopoietic and mesenchymal stem cells, both in young and old mice, indicating that these populations belong to distinct lineages. Furthermore, while cumulus cells sampled from different ovarian follicles are distinctly clustered on the reconstructed trees, oocytes from the left and right ovaries are not, suggesting a mixing of their progenitor pools. We also observed an increase in oocyte depth with mouse age, which can be explained either by depth-guided selection of oocytes for ovulation or by post-natal renewal. Overall, our study sheds light on substantial novel aspects of female germline preservation and development.
Ruth E Timme
Full Text Available The tremendous diversity of land plants all descended from a single charophyte green alga that colonized the land somewhere between 430 and 470 million years ago. Six orders of charophyte green algae, in addition to embryophytes, comprise the Streptophyta s.l. Previous studies have focused on reconstructing the phylogeny of organisms tied to this key colonization event, but wildly conflicting results have sparked a contentious debate over which lineage gave rise to land plants. The dominant view has been that 'stoneworts,' or Charales, are the sister lineage, but an alternative hypothesis supports the Zygnematales (often referred to as "pond scum" as the sister lineage. In this paper, we provide a well-supported, 160-nuclear-gene phylogenomic analysis supporting the Zygnematales as the closest living relative to land plants. Our study makes two key contributions to the field: 1 the use of an unbiased method to collect a large set of orthologs from deeply diverging species and 2 the use of these data in determining the sister lineage to land plants. We anticipate this updated phylogeny not only will hugely impact lesson plans in introductory biology courses, but also will provide a solid phylogenetic tree for future green-lineage research, whether it be related to plants or green algae.
Full Text Available Hemiascomycete yeasts cover an evolutionary span comparable to that of the entire phylum of chordates. Since this group currently contains the largest number of complete genome sequences it presents unique opportunities to understand the evolution of genome organization in eukaryotes. We inferred rates of genome instability on all branches of a phylogenetic tree for 11 species and calculated species-specific rates of genome rearrangements. We characterized all inversion events that occurred within synteny blocks between six representatives of the different lineages. We show that the rates of macro- and microrearrangements of gene order are correlated within individual lineages but are highly variable across different lineages. The most unstable genomes correspond to the pathogenic yeasts Candida albicans and Candida glabrata. Chromosomal maps have been intensively shuffled by numerous interchromosomal rearrangements, even between species that have retained a very high physical fraction of their genomes within small synteny blocks. Despite this intensive reshuffling of gene positions, essential genes, which cluster in low recombination regions in the genome of Saccharomyces cerevisiae, tend to remain syntenic during evolution. This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage.
Full Text Available Gastric infections caused by the environmentally transmitted pathogen, Vibrio parahaemolyticus, have increased over the last two decades, including in many parts of the United States (US. However, until recently, infections linked to shellfish from the cool northeastern US waters were rare. Cases have risen in the Northeast, consistent with changes in local V. parahaemolyticus populations towards greater abundance or a shift in constituent pathogens. We examined 94 clinical isolates from a period of increasing disease in the region and compared them to 200 environmental counterparts to identify resident and non-indigenous lineages and to gain insight into the emergence of pathogenic types. Genotyping and multi-locus sequence analysis of clinical isolates collected from 2010-2013 in Massachusetts, New Hampshire and Maine revealed their polyphyletic nature. Although 80% of the clinical isolates harbored the trh hemolysin either alone or with tdh, and were urease positive, 14% harbored neither hemolysin exposing a limitation for these traits in pathogen detection. Resident sequence type (ST 631 strains caused seven infections, and show a relatively recent history of recombination with other clinical and environmental lineages present in the region. ST34 and ST674 strains were each linked to a single infection and these strain types were also identified from the environment as isolates harboring hemolysin genes. Forty-three ST36 isolates were identified from the clinical collection, consistent with reports that this strain type caused a rise in regional infections starting in 2012. Whole-genome phylogenies that included three ST36 outbreak isolates traced to at least two local sources demonstrated that the US Atlantic coastal population of this strain type was indeed derived from the Pacific population. This study lays the foundation for understanding dynamics within natural populations associated with emergence and invasion of pathogenic strain
Mary Anna Carbone
Full Text Available The statistical power of genome-wide association (GWA studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG. Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR upon overexpression of transgenic human glaucoma-associated myocilin (MYOC. We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention.
... Education & Events Advocacy For Patients About ACOG Multiple Pregnancy Home For Patients Search FAQs Multiple Pregnancy Page ... Multiple Pregnancy FAQ188, July 2015 PDF Format Multiple Pregnancy Pregnancy How does multiple pregnancy occur? What are ...
looked all the way from the west to all the way down to Erie , Pennsylvania . We made some initial cuts and got it down to five different ports...Harbor, MN Presque Isle :Two Harbors, MN :Gary, IN 1,721,920 25 (Litton Great Lakes):Two Harbors, MN :Calumet Harbor, IN 178,080 3 :Two Harbors, MN...WI : 2 :11 : 0: 0 : 0: 2: 3 Silver Bay, MN : 82 :67 : 96 :87 : 85 : 88: 89 Taconite, MN : 0 : 0 : 0: 0 : 0: 4: 0 Presque Isle , MI : 6 2 : 1 0.5: 2 1
Full Text Available Adipose tissues have striking plasticity, highlighted by childhood and adult obesity. Using adipose lineage analyses, smooth muscle actin (SMA-mural cell-fate mapping, and conditional PPARγ deletion to block adipocyte differentiation, we find two phases of adipocyte generation that emanate from two independent adipose progenitor compartments: developmental and adult. These two compartments are sequentially required for organ formation and maintenance. Although both developmental and adult progenitors are specified during the developmental period and express PPARγ, they have distinct microanatomical, functional, morphogenetic, and molecular profiles. Furthermore, the two compartments derive from different lineages; whereas adult adipose progenitors fate-map from an SMA+ mural lineage, developmental progenitors do not. Remarkably, the adult progenitor compartment appears to be specified earlier than the developmental cells and then enters the already developmentally formed adipose depots. Thus, two distinct cell compartments control adipose organ development and organ homeostasis, which may provide a discrete therapeutic target for childhood and adult obesity.
Buckleton, J.S.; Krawczak, M.; Weir, B.S.
Mitochondrial DNA (mtDNA) and the non-recombining portion of the Y chromosome are inherited matrilinealy and patrilinealy, respectively, and without recombination. Collectively they are termed ‘lineage markers’. Lineage markers may be used in forensic testing of an item, such as a hair from a crime scene, against a hypothesised source, or in relationship testing. An estimate of the evidential weight of a match is usually provided by a count of the occurrence in some database of the mtDNA or Y-STR haplotype under consideration. When the factual statement of a count in the database is applied to a case, issues of relevance of the database and sampling uncertainty may arise. In this paper, we re-examine the issues of sampling uncertainty, the relevance of the database, and the combination of autosomal and lineage marker evidence. We also review the recent developments by C.H. Brenner. PMID:21397888
Kwiatek, Olivier; Ali, Yahia Hassan; Saeed, Intisar Kamil; Khalafalla, Abdelmelik Ibrahim; Mohamed, Osama Ishag; Obeida, Ali Abu; Abdelrahman, Magdi Badawi; Osman, Halima Mohamed; Taha, Khalid Mohamed; Abbas, Zakia; El Harrak, Mehdi; Lhor, Youssef; Diallo, Adama; Lancelot, Renaud; Albina, Emmanuel; Libeau, Genevieve
Interest in peste des petits ruminants virus (PPRV) has been stimulated by recent changes in its host and geographic distribution. For this study, biological specimens were collected from camels, sheep, and goats clinically suspected of having PPRV infection in Sudan during 2000-2009 and from sheep soon after the first reported outbreaks in Morocco in 2008. Reverse transcription PCR analysis confirmed the wide distribution of PPRV throughout Sudan and spread of the virus in Morocco. Molecular typing of 32 samples positive for PPRV provided strong evidence of the introduction and broad spread of Asian lineage IV. This lineage was defined further by 2 subclusters; one consisted of camel and goat isolates and some of the sheep isolates, while the other contained only sheep isolates, a finding with suggests a genetic bias according to the host. This study provides evidence of the recent spread of PPRV lineage IV in Africa.
Tho, Dau Quang; Török, M Estée; Yen, Nguyen Thi Bich; Bang, Nguyen Duc; Lan, Nguyen Thi Ngoc; Kiet, Vo Sy; van Vinh Chau, Nguyen; Dung, Nguyen Huy; Day, Jeremy; Farrar, Jeremy; Wolbers, Marcel; Caws, Maxine
HIV-associated tuberculous meningitis (TBM) has high mortality. Aside from the devastating impact of multidrug resistance (MDR) on survival, little is understood about the influence of other bacterial factors on outcome. This study examined the influence of Mycobacterium tuberculosis drug resistance, bacterial lineage, and host vaccination status on outcome in patients with HIV-associated TBM. Mycobacterium tuberculosis isolates from the cerebrospinal fluid of 186 patients enrolled in two studies of HIV-associated TBM in Ho Chi Minh City, Vietnam, were tested for resistance to first-line antituberculosis drugs. Lineage genotyping was available for 122 patients. The influence of antituberculosis drug resistance and M. tuberculosis lineage on 9-month mortality was analyzed using Kaplan-Meier survival analysis and Cox multiple regression models. Isoniazid (INH) resistance without rifampin resistance was associated with increased mortality (adjusted hazard ratio [HR], 1.78, 95% confidence interval [CI], 1.18 to 2.66; P = 0.005), and multidrug resistance was uniformly fatal (n = 8/8; adjusted HR, 5.21, 95% CI, 2.38 to 11.42; P tuberculosis lineage are important determinants of mortality in patients with HIV-associated TBM. Interventions which target these factors may help reduce the unacceptably high mortality in patients with TBM.
Wichmann, Ignacio A; Zavala, Kattina; Hoffmann, Federico G; Vandewege, Michael W; Corvalán, Alejandro H; Amigo, Julio D; Owen, Gareth I; Opazo, Juan C
Genes related to human diseases should be natural targets for evolutionary studies, since they could provide clues regarding the genetic bases of pathologies and potential treatments. Here we studied the evolution of the reprimo gene family, a group of tumor-suppressor genes that are implicated in p53-mediated cell cycle arrest. These genes, especially the reprimo duplicate located on human chromosome 2, have been associated with epigenetic modifications correlated with transcriptional silencing and cancer progression. We demonstrate the presence of a third reprimo lineage that, together with the reprimo and reprimo-like genes, appears to have been differentially retained during the evolutionary history of vertebrates. We present evidence that these reprimo lineages originated early in vertebrate evolution and expanded as a result of the two rounds of whole genome duplications that occurred in the last common ancestor of vertebrates. The reprimo gene has been lost in birds, and the third reprimo gene lineage has been retained in only a few distantly related species, such as coelacanth and gar. Expression analyses revealed that the reprimo paralogs are mainly expressed in the nervous system. Different vertebrate lineages have retained different reprimo paralogs, and even in species that have retained multiple copies, only one of them is heavily expressed.
Molecular genetic surveys of marine fishes have revealed that some widely distributed species are actually a composite of multiple evolutionary lineages. This is apparent in the round herrings (genus Etrumeus), wherein a globally distributed taxon (Etrumeus sadina Mitchill 1814) has proven to contain at least seven valid taxa, with more likely awaiting discovery. Here, we survey evolutionary lineages of the nominal E. sadina (formerly E. teres, a junior synonym) across the southern temperate zone of Australia, a marine region divided into three biogeographic provinces based primarily on the distribution of intertidal faunas. Results from morphological and mitochondrial DNA data reveal two evolutionary lineages corresponding to eastern and southwestern provinces (d = 0.007 for cytochrome c oxidase subunit I and d = 0.017 for cytochrome b), possibly initiated by the Bassian Isthmus between Australia and Tasmania during low sea-level stands. The Australian round herring is also genetically distinct from the nearest congeneric forms in the Indian and Pacific Oceans, with a corresponding modal difference in gill-raker counts in most cases. Based on these data, we resurrect the title Etrumeus jacksoniensis for the Australian round herring. While the Bassian Isthmus may have initiated the partition of evolutionary lineages within Australia, additional oceanographic and ecological factors must reinforce this separation in order to maintain diagnostic genetic differences along a continuous temperate coastline. © 2014 Springer-Verlag Berlin Heidelberg.
Julie M. Allen
Full Text Available Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura. We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. Sampling of 16S rDNA sequences affects the estimates of endosymbiont diversity in sucking lice until we reach a threshold of genetic diversity, the size of which depends on the sampling strategy. Sampling by maximizing the diversity of 16S rDNA sequences is more efficient than randomly sampling available 16S rDNA sequences. Although simulation results validate estimates of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that the precise number of endosymbiont origins is still uncertain.
Full Text Available Since we still know very little about stem cells in their natural environment, it is useful to explore their dynamics through modelling and simulation, as well as experimentally. Most models of stem cell systems are based on deterministic differential equations that ignore the natural heterogeneity of stem cell populations. This is not appropriate at the level of individual cells and niches, when randomness is more likely to affect dynamics. In this paper, we introduce a fast stochastic method for simulating a metapopulation of stem cell niche lineages, that is, many sub-populations that together form a heterogeneous metapopulation, over time. By selecting the common limiting timestep, our method ensures that the entire metapopulation is simulated synchronously. This is important, as it allows us to introduce interactions between separate niche lineages, which would otherwise be impossible. We expand our method to enable the coupling of many lineages into niche groups, where differentiated cells are pooled within each niche group. Using this method, we explore the dynamics of the haematopoietic system from a demand control system perspective. We find that coupling together niche lineages allows the organism to regulate blood cell numbers as closely as possible to the homeostatic optimum. Furthermore, coupled lineages respond better than uncoupled ones to random perturbations, here the loss of some myeloid cells. This could imply that it is advantageous for an organism to connect together its niche lineages into groups. Our results suggest that a potential fruitful empirical direction will be to understand how stem cell descendants communicate with the niche and how cancer may arise as a result of a failure of such communication.
Grunwald, I.Q.; Kuehn, A.L.; Backens, M.; Papanagiotou, P. [Universitaet des Saarlandes, Abteilung fuer Diagnostische und Interventionelle Neuroradiologie, Radiologische Klinik, Homburg/Saar (Germany); Shariat, K. [Universitaet des Saarlandes, Klinik fuer Neurochirurgie, Homburg/Saar (Germany); Kostopoulos, P. [Universitaet des Saarlandes, Klinik fuer Neurologie, Homburg/Saar (Germany)
Multiple sclerosis is the most common chronic inflammatory disease of myelin with interspersed lesions in the white matter of the central nervous system. Magnetic resonance imaging (MRI) plays a key role in the diagnosis and monitoring of white matter diseases. This article focuses on key findings in multiple sclerosis as detected by MRI. (orig.) [German] Die Multiple Sklerose (MS) ist die haeufigste chronisch-entzuendliche Erkrankung des Myelins mit eingesprengten Laesionen im Bereich der weissen Substanz des zentralen Nervensystems. Die Magnetresonanztomographie (MRT) hat bei der Diagnosestellung und Verlaufskontrolle eine Schluesselrolle. Dieser Artikel befasst sich mit Hauptcharakteristika der MR-Bildbebung. (orig.)
Balboni, Andrea; De Lorenzo Dandola, Giorgia; Scagliarini, Alessandra; Prosperi, Santino; Battilani, Mara
This study describes the sequence analysis of the H gene of 7 Canine distemper virus (CDV) strains identified in dogs in Italy between years 2002-2012. The phylogenetic analysis showed that the CDV strains belonged to 2 clusters: 6 viruses were identified as Arctic-like lineage and 1 as Europe 1 lineage. These data show a considerable prevalence of Arctic-like-CDVs in the analysed dogs. The dogs and the 3 viruses more recently identified showed 4 distinctive amino acid mutations compared to all other Arctic CDVs.
Glaser, Philippe; Martins-Simões, Patrícia; Villain, Adrien; Barbier, Maxime; Tristan, Anne; Bouchier, Christiane; Ma, Laurence; Bes, Michele; Laurent, Frederic; Guillemot, Didier; Wirth, Thierry; Vandenesch, François
Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) was recognized worldwide during the 1990s; in less than a decade, several genetically distinct CA-MRSA lineages carrying Panton-Valentine leukocidin genes have emerged on every continent. Most notably, in the United States, the sequence type 18-IV (ST8-IV) clone known as USA300 has become highly prevalent, outcompeting methicillin-susceptible S. aureus (MSSA) and other MRSA strains in both community and hospital settings. CA-MRSA bacteria are much less prevalent in Europe, where the European ST80-IV European CA-MRSA clone, USA300 CA-MRSA strains, and other lineages, such as ST22-IV, coexist. The question that arises is whether the USA300 CA-MRSA present in Europe (i) was imported once or on very few occasions, followed by a broad geographic spread, anticipating an increased prevalence in the future, or (ii) derived from multiple importations with limited spreading success. In the present study, we applied whole-genome sequencing to a collection of French USA300 CA-MRSA strains responsible for sporadic cases and micro-outbreaks over the past decade and United States ST8 MSSA and MRSA isolates. Genome-wide phylogenetic analysis demonstrated that the population structure of the French isolates is the product of multiple introductions dating back to the onset of the USA300 CA-MRSA clone in North America. Coalescent-based demography of the USA300 lineage shows that a strong expansion occurred during the 1990s concomitant with the acquisition of the arginine catabolic mobile element and antibiotic resistance, followed by a sharp decline initiated around 2008, reminiscent of the rise-and-fall pattern previously observed in the ST80 lineage. A future expansion of the USA300 lineage in Europe is therefore very unlikely. To trace the origin, evolution, and dissemination pattern of the USA300 CA-MRSA clone in France, we sequenced a collection of strains of this lineage from cases reported in France in
Bowen, Richard A; Bosco-Lauth, Angela; Syvrud, Kevin; Thomas, Anne; Meinert, Todd R; Ludlow, Deborah R; Cook, Corey; Salt, Jeremy; Ons, Ellen
Over the last years West Nile virus (WNV) lineage 2 has spread from the African to the European continent. This study was conducted to demonstrate efficacy of an inactivated, lineage 1-based, WNV vaccine (Equip WNV) against intrathecal challenge of horses with a recent isolate of lineage 2 WNV. Twenty horses, sero-negative for WNV, were enrolled and were randomly allocated to one of two treatment groups: an unvaccinated control group (T01, n=10) and a group administered with Equip WNV (T02, n=10). Horses were vaccinated at Day 0 and 21 and were challenged at day 42 with WNV lineage 2, Nea Santa/Greece/2010. Personnel performing clinical observations were blinded to treatment allocation. Sixty percent of the controls had to be euthanized after challenge compared to none of the vaccinates. A significantly lower percentage of the vaccinated animals showed clinical disease (two different clinical observations present on the same day) on six different days of study and the percentage of days with clinical disease was significantly lower in the vaccinated group. A total of 80% of the non-vaccinated horses showed viremia while only one vaccinated animal was positive by virus isolation on a single occasion. Vaccinated animals started to develop antibodies against WNV lineage 2 from day 14 (2 weeks after the first vaccination) and at day 42 (the time of onset of immunity) they had all developed a strong antibody response. Histopathology scores for all unvaccinated animals ranged from mild to very severe in each of the tissues examined (cervical spinal cord, medulla and pons), whereas in vaccinated horses 8 of 10 animals had no lesions and 2 had minimal lesions in one tissue. In conclusion, Equip WNV significantly reduced the number of viremic horses, the duration and severity of clinical signs of disease and mortality following challenge with lineage 2 WNV.
Raby, BA; Silverman, EK; Lazarus, R; Lange, C; Kwiatkowski, DJ; Weiss, ST
Chromosome 12q13-24 is among the regions most frequently identified in genome-wide surveys for asthma susceptibility loci, with reports of two distinct clusters of positive linkage signals: one near the interferon gamma locus, the other near the nitric oxide synthase 1 locus. These results suggest t
胡杰; 江澄川; 吴浩强; 彭颂先; 唐婉君; 陈商群
Objective: To investigate whether deletion of chromosome 3 is involved in the carcinogenesis of primary glioblastoma multiforme (GBM) and to localize the possible common deletion region in the aforementioned chromosome. Methods: PCR based microsatellite polymorphism analyses were performed to detect loss of heterozygosity (LOH). Twenty-three loci on chromosome 3 were examined in 20 cases of GBM. Fluorescence-labeled primers and Perkin Elmer 377 DNA Sequencer were applied. Results: 50% informative cases of GBM displayed LOH on chromosome 3. 50% of informative cases displayed LOH on 3q and 35% on 3p. 25.6% of informative loci showed LOH in our series, in which frequent LOH were observed in the chromosomal region from loci D3S1614 (42.9%) to D3S1565 (35.3%) on 3q24(27 and at loci D3S1569 (35.3%) on 3q22(23 and D3S1289 (33.3%) on 3p14.1(14.3. Conclusion: Loss of genetic material on chromosome 3 may play an important part in the tumorigenesis of GBM. The chromosomal regions from loci D3S1614 to D3S1565 on 3q24(27 and at loci D3S1569 on 3q22(23 and D3S1289 on 3p14.1(14.3 are potential sites for novel tumor suppressor genes associated with GBM.
胡杰; 江澄川; 吴浩强; 彭颂先; 唐婉君
Objective: To investigate whether deletion of chromosome 17 is involved in the carcinogenesis of primary glioblastoma multiforme and to localize the possible common deletion region in the aforementioned chromosome. Methods: Polymerase chain reaction-based microsatellite analysis was used to assess loss of heterozygosity (LOH) on chromosome 17 in 20 primary glioblastoma multiforme (GBM). Fifteen fluorescent dye-labeled polymorphic markers were used. Results: Thirteen of twenty (65%) GBM displayed LOH on at least one marker of chromosome 17p. Two tumors showed either LOH or non-informativeness on all markers tested. The most frequent LOH was observed at loci including D17s799 (53.3%), Dl7s1852 (53.8%), Dl7s938 (63.20/o), Dl7s831 (55.6%). The loci D17s831 (on 17pl3) and D17s799(Dl7sl852 (17p11.2(pl2) are distal and proximal to p53 respectively. The frequencies of LOH at all loci examined on chromosome 17q were relatively low (<30%). None of informative loci exhibited microsatellite instability in this study. Conclusion: Loss of genetic material on chromosome 17p may play an important role in the pathogenesis of GBM. Besides the well-known TSG p53 on 17p, other unknown TSCs associated with GBM may be present on the chromosomal regions 17pl3 and 17p11.2(pl2, which are distal and proximal to p53 respectively.
Sorenson Michael D
Full Text Available Abstract Background Determining an absolute timescale for avian evolutionary history has proven contentious. The two sources of information available, paleontological data and inference from extant molecular genetic sequences (colloquially, 'rocks' and 'clocks', have appeared irreconcilable; the fossil record supports a Cenozoic origin for most modern lineages, whereas molecular genetic estimates suggest that these same lineages originated deep within the Cretaceous and survived the K-Pg (Cretaceous-Paleogene; formerly Cretaceous-Tertiary or K-T mass-extinction event. These two sources of data therefore appear to support fundamentally different models of avian evolution. The paradox has been speculated to reflect deficiencies in the fossil record, unrecognized biases in the treatment of genetic data or both. Here we attempt to explore uncertainty and limit bias entering into molecular divergence time estimates through: (i improved taxon (n = 135 and character (n = 4594 bp mtDNA sampling; (ii inclusion of multiple cladistically tested internal fossil calibration points (n = 18; (iii correction for lineage-specific rate heterogeneity using a variety of methods (n = 5; (iv accommodation of uncertainty in tree topology; and (v testing for possible effects of episodic evolution. Results The various 'relaxed clock' methods all indicate that the major (basal lineages of modern birds originated deep within the Cretaceous, although temporal intraordinal diversification patterns differ across methods. We find that topological uncertainty had a systematic but minor influence on date estimates for the origins of major clades, and Bayesian analyses assuming fixed topologies deliver similar results to analyses with unconstrained topologies. We also find that, contrary to expectation, rates of substitution are not autocorrelated across the tree in an ancestor-descendent fashion. Finally, we find no signature of episodic molecular evolution related to either
... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.87 Henderson Harbor, N.Y. (a) Area A. The area in the... latitude 43°51′08.8″ N, longitude 76°12′08.9″ W, thence to latitude 43°51′09.0″ N, longitude 76°12′19.0″ W, thence to latitude 43°51′33.4″ N, longitude 76°12′19.0″ W, thence to latitude 43°51′33.4″ N, longitude...
Folmes, Clifford D L; Terzic, Andre
Nutrient availability and intermediate metabolism are increasingly recognized to govern stem cell behavior. Oburoglu et al. (2014) now demonstrate that glutamine- and glucose-dependent nucleotide synthesis segregate erythroid versus myeloid differentiation during hematopoietic stem cell specification, implicating a metabolism-centric regulation of lineage choices.
The starting point for this work was to use the hypodermal seam of C. elegans as a model system to study cell fate determination. Even though the seam is a relatively simple developmental system, the mechanisms that control cell fate determination in the seam lineages are connected in a highly compl
Sarah Gregory reads an abridged version of "Putative Lineage of Novel African Usutu Virus, Central Europe.". Created: 10/15/2015 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID). Date Released: 10/15/2015.
The starting point for this work was to use the hypodermal seam of C. elegans as a model system to study cell fate determination. Even though the seam is a relatively simple developmental system, the mechanisms that control cell fate determination in the seam lineages are connected in a highly compl
Chattwood, Alex; Nagayama, Koki; Bolourani, Parvin; Harkin, Lauren; Kamjoo, Marzieh; Weeks, Gerald; Thompson, Christopher R L
In cell culture, genetically identical cells often exhibit heterogeneous behavior, with only 'lineage primed' cells responding to differentiation inducing signals. It has recently been proposed that such heterogeneity exists during normal embryonic development to allow position independent patterning based on 'salt and pepper' differentiation and sorting out. However, the molecular basis of lineage priming and how it leads to reproducible cell type proportioning are poorly understood. To address this, we employed a novel forward genetic approach in the model organism Dictyostelium discoideum. These studies reveal that the Ras-GTPase regulator gefE is required for normal lineage priming and salt and pepper differentiation. This is because Ras-GTPase activity sets the intrinsic response threshold to lineage specific differentiation signals. Importantly, we show that although gefE expression is uniform, transcription of its target, rasD, is both heterogeneous and dynamic, thus providing a novel mechanism for heterogeneity generation and position-independent differentiation. DOI: http://dx.doi.org/10.7554/eLife.01067.001.
Naccache, Samia N; Thézé, Julien; Sardi, Silvia I; Somasekar, Sneha; Greninger, Alexander L; Bandeira, Antonio C; Campos, Gubio S; Tauro, Laura B; Faria, Nuno R; Pybus, Oliver G; Chiu, Charles Y
Sequencing of isolates from patients in Bahia, Brazil, where most Zika virus cases in Brazil have been reported, resulted in 11 whole and partial Zika virus genomes. Phylogenetic analyses revealed a well-supported Bahia-specific Zika virus lineage, which indicates sustained Zika virus circulation in Salvador, Bahia's capital city, since mid-2014.
Naccache, Samia N.; Thézé, Julien; Sardi, Silvia I.; Somasekar, Sneha; Greninger, Alexander L.; Bandeira, Antonio C.; Campos, Gubio S.; Tauro, Laura B.; Faria, Nuno R.; Pybus, Oliver G.
Sequencing of isolates from patients in Bahia, Brazil, where most Zika virus cases in Brazil have been reported, resulted in 11 whole and partial Zika virus genomes. Phylogenetic analyses revealed a well-supported Bahia-specific Zika virus lineage, which indicates sustained Zika virus circulation in Salvador, Bahia’s capital city, since mid-2014. PMID:27448188
Full Text Available The long interspersed element-1 (LINE-1 or L1 and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI, that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution.
Brasier, Clive M; Franceschini, Selma; Vettraino, Anna Maria; Hansen, Everett M; Green, Sarah; Robin, Cecile; Webber, Joan F; Vannini, Andrea
Until recently Phytophthora lateralis was known only as the cause of dieback and mortality of Chamaecyparis lawsoniana in its native range in the Pacific Northwest (PNW). Since the 1990s however disease outbreaks have occurred increasingly on ornamental C. lawsoniana in Europe; and in 2007 the pathogen was discovered in soil around old growth Chamaecyparis obtusa in Taiwan, where it may be endemic. When the phenotypes of over 150 isolates of P. lateralis from Taiwan, across the PNW (British Columbia to California) and from France, the Netherlands and the UK were compared three growth rate groups were resolved: one slow growing from Taiwan, one fast growing from the PNW and Europe, and one of intermediate growth from a small area of the UK. Within these growth groups distinct subtypes were identified based on colony patterns and spore metrics and further discriminated in a multivariate analysis. The assumption that the three main growth groups represented phylogenetic units was tested by comparative sequencing of two mitochondrial and three nuclear genes. This assumption was confirmed. In addition two phenotype clusters within the Taiwan growth group were also shown to be phylogenetically distinct. These four phenotypically and genotypically unique populations are informally designated as the PNW lineage, the UK lineage, the Taiwan J lineage, and the Taiwan K lineage. Their characteristics and distribution are described and their evolution, taxonomic, and plant health significance is discussed.
The Pashtun are an ethnic group that straddles the Afghanistan-Pakistan border, and are the largest group in Afghanistan. Pashtun social structure is...proceeding upward through various levels to an entire ethnic group . These relationships are based on kinship and shared culture. Segmentary lineage
Ben-David, Uri; Nissenbaum, Jonathan; Benvenisty, Nissim
Induction of pluripotency in somatic cells has been achieved by myriad combinations of transcription factors that belong to the core pluripotency circuitry. In this issue, Shu et al. report reprogramming with lineage specifiers, lending support to the view of the pluripotent state as a fine balance between competing differentiation forces.
Genomic Analyses of Dominant U.S. Clonal Lineages of Phytophthora infestans Reveals a Shared Common Ancestry for Clonal Lineages US11 and US18 and a Lack of Recently Shared Ancestry Among All Other U.S. Lineages.
Knaus, B J; Tabima, J F; Davis, C E; Judelson, H S; Grünwald, N J
Populations of the potato and tomato late-blight pathogen Phytophthora infestans are well known for emerging as novel clonal lineages. These successions of dominant clones have historically been named US1 through US24, in order of appearance, since their first characterization using molecular markers. Hypothetically, these lineages can emerge through divergence from other U.S. lineages, recombination among lineages, or as novel, independent lineages originating outside the United States. We tested for the presence of phylogenetic relationships among U.S. lineages using a population of 31 whole-genome sequences, including dominant U.S. clonal lineages as well as available samples from global populations. We analyzed ancestry of the whole mitochondrial genome and samples of nuclear loci, including supercontigs 1.1 and 1.5 as well as several previously characterized coding regions. We found support for a shared ancestry among lineages US11 and US18 from the mitochondrial genome as well as from one nuclear haplotype on each supercontig analyzed. The other nuclear haplotype from each sample assorted independently, indicating an independent ancestry. We found no support for emergence of any other of the U.S. lineages from a common ancestor shared with the other U.S. lineages. Each of the U.S. clonal lineages fit a model where populations of new clonal lineages emerge via migration from a source population that is sexual in nature and potentially located in central Mexico or elsewhere. This work provides novel insights into patterns of emergence of clonal lineages in plant pathogen genomes.
Full Text Available Drosophila brains contain numerous neurons that form complex circuits. These neurons are derived in stereotyped patterns from a fixed number of progenitors, called neuroblasts, and identifying individual neurons made by a neuroblast facilitates the reconstruction of neural circuits. An improved MARCM (mosaic analysis with a repressible cell marker technique, called twin-spot MARCM, allows one to label the sister clones derived from a common progenitor simultaneously in different colors. It enables identification of every single neuron in an extended neuronal lineage based on the order of neuron birth. Here we report the first example, to our knowledge, of complete lineage analysis among neurons derived from a common neuroblast that relay olfactory information from the antennal lobe (AL to higher brain centers. By identifying the sequentially derived neurons, we found that the neuroblast serially makes 40 types of AL projection neurons (PNs. During embryogenesis, one PN with multi-glomerular innervation and 18 uniglomerular PNs targeting 17 glomeruli of the adult AL are born. Many more PNs of 22 additional types, including four types of polyglomerular PNs, derive after the neuroblast resumes dividing in early larvae. Although different offspring are generated in a rather arbitrary sequence, the birth order strictly dictates the fate of each post-mitotic neuron, including the fate of programmed cell death. Notably, the embryonic progenitor has an altered temporal identity following each self-renewing asymmetric cell division. After larval hatching, the same progenitor produces multiple neurons for each cell type, but the number of neurons for each type is tightly regulated. These observations substantiate the origin-dependent specification of neuron types. Sequencing neuronal lineages will not only unravel how a complex brain develops but also permit systematic identification of neuron types for detailed structure and function analysis of the
Letko, Michael; Silvestri, Guido; Hahn, Beatrice H; Bibollet-Ruche, Frederick; Gokcumen, Omer; Simon, Viviana; Ooms, Marcel
APOBEC3G (A3G) is a cytidine deaminase that restricts human immunodeficiency virus type 1 (HIV-1) and other lentiviruses. Most of these viruses encode a Vif protein that directly binds A3G and leads to its proteasomal degradation. Both Vif proteins of HIV-1 and African green monkey simian immunodeficiency virus (SIVagm) bind residue 128 of A3G. However, this position does not control the A3G degradation by Vif variants derived from HIV-2 and SIVmac, which both originated from SIV of sooty mangabey monkeys (SIVsmm), suggesting that the A3G binding site for Vif proteins of the SIVsmm/HIV-2 lineage differs from that of HIV-1. To map the SIVsmm Vif binding site of A3G, we performed immunoprecipitations of individual A3G domains, Vif/A3G degradation assays and a detailed mutational analysis of human A3G. We show that A3G residue 129, but not the adjacent position 128, confers susceptibility to degradation by SIVsmm Vif. An artificial A3G mutant, the P129D mutant, was resistant to degradation by diverse Vifs from HIV-1, HIV-2, SIVagm, and chimpanzee SIV (SIVcpz), suggesting a conserved lentiviral Vif binding site. Gorilla A3G naturally contains a glutamine (Q) at position 129, which makes its A3G resistant to Vifs from diverse lineages. We speculate that gorilla A3G serves as a barrier against SIVcpz strains. In summary, we show that Vif proteins from distinct lineages bind to the same A3G loop, which includes positions 128 and 129. The multiple adaptations within this loop among diverse primates underscore the importance of counteracting A3G in lentiviral evolution.
Sites throughout Boston Harbor were analyzed for caffeine to assess its utility as a tracer in identifying sources of sanitary wastewater. Caffeine ranged from 15 ng/L in the outer harbor to a high of 185 ng/L in the inner harbor. Inner harbor concentrations were a result of comb...
Sites throughout Boston Harbor were analyzed for caffeine to assess its utility as a tracer in identifying sources of sanitary wastewater. Caffeine ranged from 15 ng/L in the outer harbor to a high of 185 ng/L in the inner harbor. Inner harbor concentrations were a result of comb...
Robertson, Fiona M; Gundappa, Manu Kumar; Grammes, Fabian; Hvidsten, Torgeir R; Redmond, Anthony K; Lien, Sigbjørn; Martin, Samuel A M; Holland, Peter W H; Sandve, Simen R; Macqueen, Daniel J
The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One-quarter of each salmonid genome, harbouring at least 4550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions >50 million years post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than 'older' ohnologues that began diverging in the salmonid ancestor. LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear 'explosively', but can arise gradually over tens of millions of years, promoting lineage-specific diversification regimes under prevailing ecological pressures.
Martínez-Cruz, Begoña; Mendizabal, Isabel; Harmant, Christine; de Pablo, Rosario; Ioana, Mihai; Angelicheva, Dora; Kouvatsi, Anastasia; Makukh, Halyna; Netea, Mihai G; Pamjav, Horolma; Zalán, Andrea; Tournev, Ivailo; Marushiakova, Elena; Popov, Vesselin; Bertranpetit, Jaume; Kalaydjieva, Luba; Quintana-Murci, Lluis; Comas, David
The Roma, also known as 'Gypsies', represent the largest and the most widespread ethnic minority of Europe. There is increasing evidence, based on linguistic, anthropological and genetic data, to suggest that they originated from the Indian subcontinent, with subsequent bottlenecks and undetermined gene flow from/to hosting populations during their diaspora. Further support comes from the presence of Indian uniparentally inherited lineages, such as mitochondrial DNA M and Y-chromosome H haplogroups, in a significant number of Roma individuals. However, the limited resolution of most genetic studies so far, together with the restriction of the samples used, have prevented the detection of other non-Indian founder lineages that might have been present in the proto-Roma population. We performed a high-resolution study of the uniparental genomes of 753 Roma and 984 non-Roma hosting European individuals. Roma groups show lower genetic diversity and high heterogeneity compared with non-Roma samples as a result of lower effective population size and extensive drift, consistent with a series of bottlenecks during their diaspora. We found a set of founder lineages, present in the Roma and virtually absent in the non-Roma, for the maternal (H7, J1b3, J1c1, M18, M35b, M5a1, U3, and X2d) and paternal (I-P259, J-M92, and J-M67) genomes. This lineage classification allows us to identify extensive gene flow from non-Roma to Roma groups, whereas the opposite pattern, although not negligible, is substantially lower (up to 6.3%). Finally, the exact haplotype matching analysis of both uniparental lineages consistently points to a Northwestern origin of the proto-Roma population within the Indian subcontinent.
Gupta, Aparna; Wodziak, Dariusz; Tun, May; Bouley, Donna M.; Lowe, Anson W.
Recent studies of epithelial tissues have revealed the presence of tissue-specific stem cells that are able to establish multiple cell lineages within an organ. The stem cells give rise to progenitors that replicate before differentiating into specific cell lineages. The mechanism by which homeostasis is established between proliferating stem or progenitor cells and terminally differentiated cells is unclear. This study demonstrates that Agr2 expression by mucous neck cells in the stomach promotes the differentiation of multiple cell lineages while also inhibiting the proliferation of stem or progenitor cells. When Agr2 expression is absent, gastric mucous neck cells increased in number as does the number of proliferating cells. Agr2 expression loss also resulted in the decline of terminally differentiated cells, which was supplanted by cells that exhibited nuclear SOX9 labeling. Sox9 expression has been associated with progenitor and stem cells. Similar effects of the Agr2 null on cell proliferation in the intestine were also observed. Agr2 consequently serves to maintain the balance between proliferating and differentiated epithelial cells. PMID:23209296
Instead, the bedrock was dredged by a backhoe dredge the " Oski ". The " Oski " has an 8-cubic yard bucket which can be replaced by a bedrock ripper when...demobilization because the dredge was on site. The Coos Bay material was considerably harder than the bedrock in Los Angeles harbor. If the Oski were to be...harder than indicated by current data, the use of a mechanical dredge such as the " Oski " may be necessary. If an opening cannot be left open for barge
Bunjevac, Joseph; Rinehart, Aidan; Flaherty, Justin; Zhang, Wei
Harbor Seals are able to accurately detect minute disturbances in the ambient flow using their whiskers, which is attributed to the exceptional capability of the whiskers to suppress vortex-induced vibrations in the wake. To explore potential applications for designing smart devices, such as high-sensitivity underwater flow sensors and drag reduction components, research has studied the role of key parameters of the whisker morphology on wake structure. Due to the inherent variation in size and angle of incidence along the length of whiskers, it is not well understood how a real seal whisker changes wake structure, in particular the vortex shedding behavior. This work aims to understand the flow around a single real seal whisker using Particle Image Velocimetry at low Reynolds numbers (i.e. a few hundred) in a water channel. Variations in flow structure are inspected between several different real whiskers and whisker models. The results will provide insights of the effects of the natural geometry of the harbor seal whiskers on wake flow compared to idealized whisker-like models.
Ruser, Andreas; Dähne, Michael; van Neer, Abbo; Lucke, Klaus; Sundermeyer, Janne; Siebert, Ursula; Houser, Dorian S; Finneran, James J; Everaarts, Eligius; Meerbeek, Jolanda; Dietz, Rune; Sveegaard, Signe; Teilmann, Jonas
Testing the hearing abilities of marine mammals under water is a challenging task. Sample sizes are usually low, thus limiting the ability to generalize findings of susceptibility towards noise influences. A method to measure harbor porpoise hearing thresholds in situ in outdoor conditions using auditory steady state responses of the brainstem was developed and tested. The method was used on 15 live-stranded animals from the North Sea during rehabilitation, shortly before release into the wild, and on 12 wild animals incidentally caught in pound nets in Denmark (inner Danish waters). Results indicated that although the variability between individuals is wide, the shape of the hearing curve is generally similar to previously published results from behavioral trials. Using 10-kHz frequency intervals between 10 and 160 kHz, best hearing was found between 120 and 130 kHz. Additional testing using one-third octave frequency intervals (from 16 to 160 kHz) allowed for a much faster hearing assessment, but eliminated the fine scale threshold characteristics. For further investigations, the method will be used to better understand the factors influencing sensitivity differences across individuals and to establish population-level parameters describing hearing abilities of harbor porpoises.
Up to the end of World War II, less than 10% of the general anaesthetics administered was with intravenous barbiturates. The remaining 90% of anaesthetics given in the USA were with diethyl ether. In the United Kingdom and elsewhere, chloroform was also popular. Diethyl ether administration was a relatively safe and simple procedure, often delegated to nurses or junior doctors with little or no specific training in anaesthesia. During the Japanese attack on the US bases at Pearl Harbor, with reduced stocks of diethyl ether available, intravenous Sodium Pentothal(®), a most 'sophisticated and complex' drug, was used with devastating effects in many of those hypovolaemic, anaemic and septic patients. The hazards of spinal anaesthesia too were realised very quickly. These effects were compounded by the dearth of trained anaesthetists. This paper presents the significance of the anaesthesia tragedies at Pearl Harbor, and the discovery in the next few years of many other superior drugs that caused medical and other health professionals to realise that anaesthesia needed to be a specialist medical discipline in its own right. Specialist recognition, aided by the foundation of the National Health Service in the UK, the establishment of Faculties of Anaesthesia and appropriate training in pharmacology, physiology and other sciences soon followed. Modern anaesthesiology, as we understand it today, was born and a century or more of ether anaesthesia finally ceased.
It is now generally accepted that the four evolutionary lineages of Phytophthora ramorum (informally designated NA1, NA2, EU1, and EU2) are relatively anciently divergent populations, recently introduced into Europe and North America from different, unknown geographic locations; that recombinants between them are genetically unstable and probably...
Authors: John Isaac Murray and Zhirong Bao Adapted from [*Imaging in Developmental Biology*](http://www.cshlpress.com/link/imagingdevbiop.htm)(ed. Sharpe and Wong). CSHL Press, Cold Spring Harbor, NY, USA, 2011. ### Abstract Describing gene expression during animal development requires a way to quantitatively measure expression levels with cellular resolution and to describe how expression changes with time. Fluorescent protein reporters make it possible to measure expression dyna...
Beckervordersandforth, Ruth; Ebert, Birgit; Schäffner, Iris; Moss, Jonathan; Fiebig, Christian; Shin, Jaehoon; Moore, Darcie L; Ghosh, Laboni; Trinchero, Mariela F; Stockburger, Carola; Friedland, Kristina; Steib, Kathrin; von Wittgenstein, Julia; Keiner, Silke; Redecker, Christoph; Hölter, Sabine M; Xiang, Wei; Wurst, Wolfgang; Jagasia, Ravi; Schinder, Alejandro F; Ming, Guo-Li; Toni, Nicolas; Jessberger, Sebastian; Song, Hongjun; Lie, D Chichung
Precise regulation of cellular metabolism is hypothesized to constitute a vital component of the developmental sequence underlying the life-long generation of hippocampal neurons from quiescent neural stem cells (NSCs). The identity of stage-specific metabolic programs and their impact on adult neurogenesis are largely unknown. We show that the adult hippocampal neurogenic lineage is critically dependent on the mitochondrial electron transport chain and oxidative phosphorylation machinery at the stage of the fast proliferating intermediate progenitor cell. Perturbation of mitochondrial complex function by ablation of the mitochondrial transcription factor A (Tfam) reproduces multiple hallmarks of aging in hippocampal neurogenesis, whereas pharmacological enhancement of mitochondrial function ameliorates age-associated neurogenesis defects. Together with the finding of age-associated alterations in mitochondrial function and morphology in NSCs, these data link mitochondrial complex function to efficient lineage progression of adult NSCs and identify mitochondrial function as a potential target to ameliorate neurogenesis-defects in the aging hippocampus.
Rissanen, Ilona; Grimes, Jonathan M; Pawlowski, Alice; Mäntynen, Sari; Harlos, Karl; Bamford, Jaana K H; Stuart, David I
It has proved difficult to classify viruses unless they are closely related since their rapid evolution hinders detection of remote evolutionary relationships in their genetic sequences. However, structure varies more slowly than sequence, allowing deeper evolutionary relationships to be detected. Bacteriophage P23-77 is an example of a newly identified viral lineage, with members inhabiting extreme environments. We have solved multiple crystal structures of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. They fit the 14 Å resolution cryo-electron microscopy reconstruction of the entire virus exquisitely well, allowing us to propose a model for both the capsid architecture and viral assembly, quite different from previously published models. The structures of the capsid proteins and their mode of association to form the viral capsid suggest that the P23-77-like and adeno-PRD1 lineages of viruses share an extremely ancient common ancestor.
Benavides, Edgar; Russello, Michael; Boyer, Donal; Wiese, Robert J; Kajdacsi, Brittney; Marquez, Lady; Garrick, Ryan; Caccone, Adalgisa
Genetic tools have become a critical complement to traditional approaches for meeting short- and long-term goals of ex situ conservation programs. The San Diego Zoo (SDZ) harbors a collection of wild-born and captive-born Galápagos giant tortoises (n = 22) of uncertain species designation and unknown genealogical relationships. Here, we used mitochondrial DNA haplotypic data and nuclear microsatellite genotypic data to identify the evolutionary lineage of wild-born and captive-born tortoises of unknown ancestry, to infer levels of relatedness among founders and captive-born tortoises, and assess putative pedigree relationships assigned by the SDZ studbook. Assignment tests revealed that 12 wild-born and five captive-born tortoises represent five different species from Isabela Island and one species from Santa Cruz Island, only five of which were consistent with current studbook designations. Three wild-born and one captive-born tortoise were of mixed ancestry. In addition, kinship analyses revealed two significant first-order relationship pairs between wild-born and captive-born tortoises, four second-order relationships (half-sibling) between wild-born and captive tortoises (full-sibs or parent-offspring), and one second-order relationship between two captive-born tortoises. Of particular note, we also reconstructed a first-order relationship between two wild-born individuals, violating the founder assumption. Overall, our results contribute to a worldwide effort in identifying genetically important Galápagos tortoises currently in captivity while revealing closely related founders, reconstructing genealogical relationships, and providing detailed management recommendations for the SDZ tortoises.
Nakane, Kunihiko; Kawamura, Kumiko; Goto, Kensuke; Arakawa, Yoshichika
The actual state of intestinal long-term colonization by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in healthy Japanese people remains unclear. Therefore, a total of 4,314 fecal samples were collected from 2,563 food handlers from January 2010 to December 2011. Approximately 0.1 g of each fecal sample was inoculated onto a MacConkey agar plate containing cefotaxime (1 μg/ml). The bacterial colonies that grew on each plate were checked for ESBL production by the double-disk synergy test, as recommended by the Clinical and Laboratory Standards Institute. The bacterial serotype, antimicrobial susceptibility, pulsotype, sequence type (ST), and ESBL genotype were checked, and the replicon types of plasmids harboring the ESBL gene were also determined after conjugation experiments. ESBL producers were recovered from 70 (3.1%) of 2,230 participants who were checked only once. On the other hand, ESBL producers were isolated at least once from 52 (15.6%) of 333 participants who were checked more than twice, and 13 of the 52 participants carried ESBL producers for from more than 3 months to up to 2 years. Fluoroquinolone (FQ)-resistant E. coli strains harboring bla(CTX-M) were repeatedly recovered from 11 of the 13 carriers of bla(CTX-M)-harboring E. coli. A genetically related FQ-resistant E. coli O25b:H4-ST131 isolate harboring bla(CTX-M)-27 was recovered from 4 of the 13 carriers for more than 6 months. Three FQ-resistant E. coli O1:H6-ST648 isolates that harbored bla(CTX-M-15) or bla(CTX-M)-14 were recovered from 3 carriers. Moreover, multiple CTX-M-14- or CTX-M-15-producing E. coli isolates with different serotypes were recovered from 2 respective carriers. These findings predict a provable further spread of ESBL producers in both community and clinical settings. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Matson, Michael E H; Small, Ian M; Fry, William E; Judelson, Howard S
Prior work has shown that the inheritance of resistance to metalaxyl, an oomycete-specific fungicide, is complex and may involve multiple genes. Recent research indicated that a single nucleotide polymorphism (SNP) in the gene encoding RPA190, the largest subunit of RNA polymerase I, confers resistance to metalaxyl (or mefenoxam) in some isolates of the potato late blight pathogen Phytophthora infestans. Using both DNA sequencing and high resolution melt assays for distinguishing RPA190 alleles, we show here that the SNP is absent from certain resistant isolates of P. infestans from North America, Europe, and Mexico. The SNP is present in some members of the US-23 and US-24 clonal lineages, but these tend to be fairly sensitive to the fungicide based on artificial media and field test data. Diversity in the level of sensitivity, RPA190 genotype, and RPA190 copy number was observed in these lineages but were uncorrelated. Controlled laboratory crosses demonstrated that RPA190 did not cosegregate with metalaxyl resistance from a Mexican and British isolate. We conclude that while metalaxyl may be used to control many contemporary strains of P. infestans, an assay based on RPA190 will not be sufficient to diagnose the sensitivity levels of isolates.
Zhu, Shu Jun; Hallows, Stephanie E; Currie, Ko W; Xu, ChangJiang; Pearson, Bret J
Neoblasts are adult stem cells (ASCs) in planarians that sustain cell replacement during homeostasis and regeneration of any missing tissue. While numerous studies have examined genes underlying neoblast pluripotency, molecular pathways driving postmitotic fates remain poorly defined. In this study, we used transcriptional profiling of irradiation-sensitive and irradiation-insensitive cell populations and RNA interference (RNAi) functional screening to uncover markers and regulators of postmitotic progeny. We identified 32 new markers distinguishing two main epithelial progenitor populations and a planarian homolog to the MEX3 RNA-binding protein (Smed-mex3-1) as a key regulator of lineage progression. mex3-1 was required for generating differentiated cells of multiple lineages, while restricting the size of the stem cell compartment. We also demonstrated the utility of using mex3-1(RNAi) animals to identify additional progenitor markers. These results identified mex3-1 as a cell fate regulator, broadly required for differentiation, and suggest that mex3-1 helps to mediate the balance between ASC self-renewal and commitment.
Wilton, Peter R; Sloan, Daniel B; Logsdon, John M; Doddapaneni, Harshavardhan; Neiman, Maurine
Understanding the evolution and maintenance of sexual reproduction is one of the central challenges of evolutionary biology, yet we know very little about how sex influences molecular evolution. The New Zealand freshwater snail Potamopyrgus antipodarum is ideally suited to address this knowledge gap because obligately sexual individuals often coexist with multiple independently derived obligately asexual lineages. This unusual situation allows direct comparisons both between sexual and asexual P. antipodarum and across populations that differ in the relative frequency of sexual individuals. As such, P. antipodarum has received a great deal of attention as a model system for the maintenance of sex in nature and is also used as a model for environmental toxicology and biological invasions. Molecular genetic resources for P. antipodarum will thus be useful to investigators in a variety of biological fields. We used 454 sequencing of cDNA libraries to generate transcriptomes from two sexual and two asexual P. antipodarum lineages. A de novo assembly of 116.7 Mb of sequence reads produced 41 396 contigs, and sequence similarity-based Gene Ontology annotations were obtained for 3740 contigs. We detected 408 315 SNP loci and 7315 microsatellite loci, which together represent the first genome-scale resource available for P. antipodarum. Raw 454 read sequences, contig sequences, annotation data and polymorphism data are publicly available in a searchable online database and for download at http://www.biology.uiowa.edu/neiman/transcriptome.php.
Tedersoo, Leho; Bahram, Mohammad; Ryberg, Martin; Otsing, Eveli; Kõljalg, Urmas; Abarenkov, Kessy
Compared with plants and animals, large-scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45-57 Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events. © 2014 John Wiley & Sons Ltd.
Gordon, Deborah M; Pilko, Anna; De Bortoli, Nicolas; Ingram, Krista K
In dependent-lineage harvester ant populations, two lineages interbreed but are genetically distinct. The offspring of a male and queen of the same lineage are female reproductives; the offspring of a male and queen of different lineages are workers. Geographic surveys have shown asymmetries in the ratio of the two lineages in many harvester ant populations, which may be maintained by an ecological advantage to one of the lineages. Using census data from a long-term study of a dependent-lineage population of the red harvester ant, Pogonomyrmex barbatus, we identified the lineage of 130 colonies sampled in 1997-1999, ranging in age from 1 to 19 years when collected, and 268 colonies sampled in 2010, ranging in age from 1 to 28 years when collected. The ratio of lineages in the study population is similar across an 11-year interval, 0.59 J2 in 1999 and 0.66 J2 in 2010. The rare lineage, J1, had a slightly but significantly higher number of mates of the opposite lineage than the common lineage, J2, and, using data from previous work on reproductive output, higher male production. Mature colonies of the two lineages did not differ in nest mound size, foraging activity, or the propensity to relocate their nests. There were no strong differences in the relative recruitment or survivorship of the two lineages. Our results show no ecological advantage for either lineage, indicating that differences between the lineages in sex ratio allocation may be sufficient to maintain the current asymmetry of the lineage ratio in this population.
Joseph J Abrajano
Full Text Available BACKGROUND: The repressor element-1 (RE1 silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF is a master transcriptional regulator that binds to numerous genomic RE1 sites where it acts as a molecular scaffold for dynamic recruitment of modulatory and epigenetic cofactors, including corepressor for element-1-silencing transcription factor (CoREST. CoREST also acts as a hub for various cofactors that play important roles in epigenetic remodeling and transcriptional regulation. While REST can recruit CoREST to its macromolecular complex, CoREST complexes also function at genomic sites independently of REST. REST and CoREST perform a broad array of context-specific functions, which include repression of neuronal differentiation genes in neural stem cells (NSCs and other non-neuronal cells as well as promotion of neurogenesis. Despite their involvement in multiple aspects of neuronal development, REST and CoREST are not believed to have any direct modulatory roles in glial cell maturation. METHODOLOGY/PRINCIPAL FINDINGS: We challenged this view by performing the first study of REST and CoREST in NSC-mediated glial lineage specification and differentiation. Utilizing ChIP on chip (ChIP-chip assays, we identified distinct but overlapping developmental stage-specific profiles for REST and CoREST target genes during astrocyte (AS and oligodendrocyte (OL lineage specification and OL lineage maturation and myelination, including many genes not previously implicated in glial cell biology or linked to REST and CoREST regulation. Amongst these factors are those implicated in macroglial (AS and OL cell identity, maturation, and maintenance, such as members of key developmental signaling pathways and combinatorial transcription factor codes. CONCLUSIONS/SIGNIFICANCE: Our results imply that REST and CoREST modulate not only neuronal but also glial lineage elaboration. These factors may therefore mediate critical developmental processes
Krog, Jesper Schak; Hansen, Mette Sif; Holm, Elisabeth
Since April 2014, an outbreak of influenza in harbor seals has been ongoing in northern Europe. In Denmark during June-August, 152 harbor seals on the island of Anholt were found dead from severe pneumonia. We detected influenza A(H10N7) virus in 2 of 4 seals examined.......Since April 2014, an outbreak of influenza in harbor seals has been ongoing in northern Europe. In Denmark during June-August, 152 harbor seals on the island of Anholt were found dead from severe pneumonia. We detected influenza A(H10N7) virus in 2 of 4 seals examined....
the Ojibway, who called the harbor "great pond". Later the French voyageurs gave the harbor the name it now carries. Interpreted literally, Grand...Marais means "great swamp" but in the special vocabu- lary of the voyageurs , "usrais" referred to a harbor-of-refuge or a protected cove. " 2.621 The...total commerce for Grand Marais Harbor consisted of logs and pulpwood. Commerce reached a peak of over 78,000 tons in 1958, then diminished somewhat
Lednicky John A
Full Text Available Abstract Background Mortality rates have differed during distemper outbreaks among free-ranging raccoons (Procyon lotor living around a large Chicago-area zoo, and appeared higher in year 2001 than in 1998 and 2000. We hypothesized that a more lethal variant of the local Canine distemper virus (CDV lineage had emerged in 2001, and sought the genetic basis that led to increased virulence. However, a more complex model surfaced during preliminary analyses of CDV genomic sequences in infected tissues and of virus isolated in vitro from the raccoons. Results Phylogenetic analyses of subgenomic CDV fusion (F -, phosphoprotein (P -, and complete hemagglutinin (H – gene sequences indicated that distinct American CDV lineages caused the distemper epizootics. The 1998 outbreak was caused by viruses that are likely from an old CDV lineage that includes CDV Snyder Hill and Lederle, which are CDV strains from the early 1950's. The 2000 and 2001 viruses appear to stem from the lineage of CDV A75/17, which was isolated in the mid 1970's. Only the 2001 viruses formed large syncytia in brain and/or lung tissue, and during primary isolation in-vitro in Vero cells, demonstrating at least one phenotypic property by which they differed from the other viruses. Conclusions Two different American CDV lineages caused the raccoon distemper outbreaks. The 1998 viruses are genetically distant to the 2000/2001 viruses. Since CDV does not cause persistent infections, the cycling of different CDV lineages within the same locale suggests multiple reintroductions of the virus to area raccoons. Our findings establish a precedent for determining whether the perceived differences in mortality rates are actual and attributable in part to inherent differences between CDV strains arising from different CDV lineages.
Lednicky, John A; Dubach, Jean; Kinsel, Michael J; Meehan, Thomas P; Bocchetta, Maurizio; Hungerford, Laura L; Sarich, Nicolene A; Witecki, Kelley E; Braid, Michael D; Pedrak, Casandra; Houde, Christiane M
Background Mortality rates have differed during distemper outbreaks among free-ranging raccoons (Procyon lotor) living around a large Chicago-area zoo, and appeared higher in year 2001 than in 1998 and 2000. We hypothesized that a more lethal variant of the local Canine distemper virus (CDV) lineage had emerged in 2001, and sought the genetic basis that led to increased virulence. However, a more complex model surfaced during preliminary analyses of CDV genomic sequences in infected tissues and of virus isolated in vitro from the raccoons. Results Phylogenetic analyses of subgenomic CDV fusion (F) -, phosphoprotein (P) -, and complete hemagglutinin (H) – gene sequences indicated that distinct American CDV lineages caused the distemper epizootics. The 1998 outbreak was caused by viruses that are likely from an old CDV lineage that includes CDV Snyder Hill and Lederle, which are CDV strains from the early 1950's. The 2000 and 2001 viruses appear to stem from the lineage of CDV A75/17, which was isolated in the mid 1970's. Only the 2001 viruses formed large syncytia in brain and/or lung tissue, and during primary isolation in-vitro in Vero cells, demonstrating at least one phenotypic property by which they differed from the other viruses. Conclusions Two different American CDV lineages caused the raccoon distemper outbreaks. The 1998 viruses are genetically distant to the 2000/2001 viruses. Since CDV does not cause persistent infections, the cycling of different CDV lineages within the same locale suggests multiple reintroductions of the virus to area raccoons. Our findings establish a precedent for determining whether the perceived differences in mortality rates are actual and attributable in part to inherent differences between CDV strains arising from different CDV lineages. PMID:15507154
Full Text Available The relative contributions to modern European populations of Paleolithic hunter-gatherers and Neolithic farmers from the Near East have been intensely debated. Haplogroup R1b1b2 (R-M269 is the commonest European Y-chromosomal lineage, increasing in frequency from east to west, and carried by 110 million European men. Previous studies suggested a Paleolithic origin, but here we show that the geographical distribution of its microsatellite diversity is best explained by spread from a single source in the Near East via Anatolia during the Neolithic. Taken with evidence on the origins of other haplogroups, this indicates that most European Y chromosomes originate in the Neolithic expansion. This reinterpretation makes Europe a prime example of how technological and cultural change is linked with the expansion of a Y-chromosomal lineage, and the contrast of this pattern with that shown by maternally inherited mitochondrial DNA suggests a unique role for males in the transition.
Ohnuki, Shinsuke; Okada, Hiroki; Friedrich, Anne; Kanno, Yoichiro; Goshima, Tetsuya; Hasuda, Hirokazu; Inahashi, Masaaki; Okazaki, Naoto; Tamura, Hiroyasu; Nakamura, Ryo; Hirata, Dai; Fukuda, Hisashi; Shimoi, Hitoshi; Kitamoto, Katsuhiko; Watanabe, Daisuke; Schacherer, Joseph; Akao, Takeshi; Ohya, Yoshikazu
Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell, morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomycescerevisiae species as a whole. Evaluation of the different types of breeding processes showed that the generation of hybrids (crossbreeding) has more profound effects on cell morphology than the isolation of mutants (mutation breeding). Analysis of phenotypic robustness revealed that some sake yeast strains are more morphologically heterogeneous, possibly due to impairment of cellular network hubs. This study provides a new perspective for studying yeast breeding genetics and micro-organism breeding strategies. Copyright © 2017 Ohnuki et al.
del Campo, Javier; Guillou, Laure; Hehenberger, Elisabeth; Logares, Ramiro; López-García, Purificación; Massana, Ramon
Environmental molecular surveys targeting protist diversity have unveiled novel and uncultured lineages in a variety of ecosystems, ranging from completely new high-rank lineages, to new taxa moderately related to previously described organisms. The ecological roles of some of these novel taxa have been studied, showing that in certain habitats they may be responsible for critical environmental processes. Moreover, from an evolutionary perspective they still need to be included in a more accurate and wider understanding of the eukaryotic tree of life. These seminal discoveries promoted the development and use of a wide range of more in-depth culture-independent approaches to access this diversity, from metabarcoding and metagenomics to single cell genomics and FISH. Nonetheless, culturing using classical or innovative approaches is also essential to better characterize this new diversity. Ecologists and evolutionary biologists now face the challenge of apprehending the significance of this new diversity within the eukaryotic tree of life. PMID:26996654
Darabi, Radbod; Perlingeiro, Rita C R
Embryonic stem (ES) cells are endowed with extensive ability for self renewal and differentiation. These features make them a promising candidate for cell therapy. However, despite the enthusiasm and hype surrounding the potential therapeutic use of human ES cells and more recently induced pluripotent stem (iPS) cells, to date few reports have documented successful therapeutic outcome with ES-derived cell populations. This is probably due to two main caveats associated with ES cells, their capacity to form teratomas and the challenge of isolating the appropriate therapeutic cell population from differentiating ES cells. We have focused our efforts on the derivation of skeletal muscle progenitors from ES cells and here we will discuss the strategy of reprogramming lineage choices by overexpression of a master regulator, which has proven successful for the generation of the skeletal myogenic lineage from mouse ES cells.
Heinäniemi, Merja; Nykter, Matti; Kramer, Roger; Wienecke-Baldacchino, Anke; Sinkkonen, Lasse; Zhou, Joseph Xu; Kreisberg, Richard; Kauffman, Stuart A.; Huang, Sui; Shmulevich, Ilya
The distinct cell types of multicellular organisms arise due to constraints imposed by gene regulatory networks on the collective change of gene expression across the genome, creating self-stabilizing expression states, or attractors. We compiled a resource of curated human expression data comprising 166 cell types and 2,602 transcription regulating genes and developed a data driven method built around the concept of expression reversal defined at the level of gene pairs, such as those participating in toggle switch circuits. This approach allows us to organize the cell types into their ontogenetic lineage-relationships and to reflect regulatory relationships among genes that explain their ability to function as determinants of cell fate. We show that this method identifies genes belonging to regulatory circuits that control neuronal fate, pluripotency and blood cell differentiation, thus offering a novel large-scale perspective on lineage specification. PMID:23603899
Knight, Daniel R.; Squire, Michele M.; Collins, Deirdre A.; Riley, Thomas V.
Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42% of human strains showed a clonal relationship (separated by ≤2 SNVs in their core genome) with one or more porcine strains, consistent with recent inter-host transmission. Clones were spread over a vast geographic area with 50% of the human cases occurring without recent healthcare exposure. These findings suggest a persistent community reservoir with long-range dissemination, potentially due to agricultural recycling of piggery effluent. We also provide the first pan-genome analysis for this lineage, characterizing its resistome, prophage content, and in silico virulence potential. The RT014 is defined by a large “open” pan-genome (7587 genes) comprising a core genome of 2296 genes (30.3% of the total gene repertoire) and an accessory genome of 5291 genes. Antimicrobial resistance genotypes and phenotypes varied across host populations and ST lineages and were characterized by resistance to tetracycline [tetM, tetA(P), tetB(P) and tetW], clindamycin/erythromycin (ermB), and aminoglycosides (aph3-III-Sat4A-ant6-Ia). Resistance was mediated by clinically important mobile genetic elements, most notably Tn6194 (harboring ermB) and a novel variant of Tn5397 (harboring tetM). Numerous clinically important prophages (Siphoviridae and Myoviridae) were identified as well as an uncommon accessory gene regulator locus (agr3
Cresko, William A; Yan, Yi-Lin; Baltrus, David A; Amores, Angel; Singer, Amy; Rodríguez-Marí, Adriana; Postlethwait, John H
Teleosts are the most species-rich group of vertebrates, and a genome duplication (tetraploidization) event in ray-fin fish appears to have preceded this remarkable explosion of biodiversity. What is the relationship of the ray-fin genome duplication to the teleost radiation? Genome duplication may have facilitated lineage divergence by partitioning different ancestral gene subfunctions among co-orthologs of tetrapod genes in different teleost lineages. To test this hypothesis, we investigated gene expression patterns for Sox9 gene duplicates in stickleback and zebrafish, teleosts whose lineages diverged early in Euteleost evolution. Most expression domains appear to have been partitioned between Sox9a and Sox9b before the divergence of stickleback and zebrafish lineages, but some ancestral expression domains were distributed differentially in each lineage. We conclude that some gene subfunctions, as represented by lineage-specific expression domains, may have assorted differently in separate lineages and that these may have contributed to lineage diversification during teleost evolution.
The endoderm gives rise to digestive and respiratory tracts, thyroid, liver, and pancreas. Representative disease of endoderm lineages is type 1 diabetes resulting from destruction of the insulin-producing β cells. Generation of functional β cells from human embryonic stem (ES) cells in vitro can be practical, renewable cell source for replacement cell therapy for type 1 diabetes. It has been achieved by progressive instructive differentiation through each of the developmental stages. In this...
Lambert, Guillaume; Kussell, Edo
Organisms use a variety of strategies to adapt to their environments and maximize long-term growth potential, but quantitative characterization of the benefits conferred by the use of such strategies, as well as their impact on the whole population's rate of growth, remains challenging. Here, we use a path-integral framework that describes how selection acts on lineages—i.e., the life histories of individuals and their ancestors—to demonstrate that lineage-based measurements can be used to quantify the selective pressures acting on a population. We apply this analysis to Escherichia coli bacteria exposed to cyclical treatments of carbenicillin, an antibiotic that interferes with cell-wall synthesis and affects cells in an age-dependent manner. While the extensive characterization of the life history of thousands of cells is necessary to accurately extract the age-dependent selective pressures caused by carbenicillin, the same measurement can be recapitulated using lineage-based statistics of a single surviving cell. Population-wide evolutionary pressures can be extracted from the properties of the surviving lineages within a population, providing an alternative and efficient procedure to quantify the evolutionary forces acting on a population. Importantly, this approach is not limited to age-dependent selection, and the framework can be generalized to detect signatures of other trait-specific selection using lineage-based measurements. Our results establish a powerful way to study the evolutionary dynamics of life under selection and may be broadly useful in elucidating selective pressures driving the emergence of antibiotic resistance and the evolution of survival strategies in biological systems.
Starke, Charlotte; Betz, Hannah; Hickmann, Linda; Lachmann, Peter; Neubauer, Björn; Kopp, Jeffrey B.; Sequeira-Lopez, Maria Luisa S; Gomez, R. Ariel; Hohenstein, Bernd; Todorov, Vladimir T.; Hugo, Christian P. M.
Mesangial cell injury has a major role in many CKDs. Because renin-positive precursor cells give rise to mesangial cells during nephrogenesis, this study tested the hypothesis that the same phenomenon contributes to glomerular regeneration after murine experimental mesangial injury. Mesangiolysis was induced by administration of an anti-mesangial cell serum in combination with LPS. In enhanced green fluorescent protein–reporter mice with constitutively labeled renin lineage cells, the size of...
Usta, Sümeyra Naz; Scharer, Christopher D.; Xu, Jie; Frey, Teryl K.; Nash, Rodney J
Cell culture is one of the most common methods used to recapitulate a human disease environment in a laboratory setting. Cell culture techniques are used to grow and maintain cells of various types including those derived from primary tissues, such as stem cells and cancer tumors. However, a major confounding factor with cell culture is the use of serum and animal (xeno) products in the media. The addition of animal products introduces batch and lot variations that lead to experimental variab...
Roelofs, Jeroen; Haastert, Peter J.M. van
The family of eukaryotic adenylyl cyclases consists of a very large group of 12 transmembrane adenylyl cyclases and a very small group of soluble adenylyl cyclase (sAC). Orthologs of human sAC are present in rat Diclyostelium and bacteria but absent from the completely sequenced genomes of Drosophil
Nderitu, Leonard; Lee, John S.; Omolo, Jared; Omulo, Sylvia; O'Guinn, Monica L.; Hightower, Allen; Mosha, Fausta; MOHAMED, Mohamed; Munyua, Peninah; Nganga, Zipporah; Hiett, Kelli; Seal, Bruce; Feikin, Daniel R.; Breiman, Robert F.; Njenga, M Kariuki
Background. During the Rift Valley fever (RVF) epidemic of 2006–2007 in eastern Africa, spatial mapping of the outbreaks across Kenya, Somalia, and Tanzania was performed and the RVF viruses were isolated and genetically characterized.
Yin, Zi; Chen, Xiao; Song, Hai-Xin; Hu, Jia-Jie; Tang, Qiao-Mei; Zhu, Ting; Shen, Wei-Liang; Chen, Jia-Lin; Liu, Huanhuan; Heng, Boon Chin; Ouyang, Hong-Wei
Physical topographic cues from various substrata have been shown to exert profound effects on the growth and differentiation of stem cells due to their niche-mimicking features. However, the biological function of different topographic materials utilized as bio-scaffolds in vivo have not been rigorously characterized. This study investigated the divergent differentiation pathways of mesenchymal stem cells (MSCs) and neo-tissue formation trigged by aligned and randomly-oriented fibrous scaffolds, both in vitro and in vivo. The aligned group was observed to form more mature tendon-like tissue in the Achilles tendon injury model, as evidenced by histological scoring and collagen I immunohistochemical staining data. In contrast, the randomly-oriented group exhibited much chondrogenesis and subsequent bone tissue formation through ossification. Additionally, X-ray imaging and osteocalcin immunohistochemical staining also demonstrated that osteogenesis in vivo is driven by randomly oriented topography. Furthermore, MSCs on the aligned substrate exhibited tenocyte-like morphology and enhanced tenogenic differentiation compared to cells grown on randomly-oriented scaffold. qRT-PCR analysis of osteogenic marker genes and alkaline phosphatase (ALP) staining demonstrated that MSCs cultured on randomly-oriented fiber scaffolds displayed enhanced osteogenic differentiation compared with cells cultured on aligned fiber scaffolds. Finally, it was demonstrated that cytoskeletal tension release abrogated the divergent differentiation pathways on different substrate topography. Collectively, these findings illustrate the relationship between topographic cues of the scaffold and their inductive role in tissue regeneration; thus providing an insight into future development of smart functionalized bio-scaffold design and its application in tissue engineering.
Teilmann, Jonas; Christiansen, C.T.; Kjellerup, Sanne;
are essential information on the status and management of the species. Thirty-five free-ranging harbor porpoises (Phocoena phocoena) were tracked in the region between the Baltic and the North Sea for 25-349 d using Argos satellite transmitters. No differences were found in surface behavior between geographical...... areas or the size of the animals. Slight differences were found between the two sexes and time of day. Surface time peaked in April, where 6% was spent with the transmitter above surface and 61.5% between 0 and 2 m depth, while the minimum values occurred in February (3.4% and 42.5%, respectively......). The analyses reveal that individual variation among porpoises is the most important factor in explaining variation in surface rates. However, the large number of animals documented in the present study covering a wide range of age and sex groups justifies the use of the seasonal average surface times...
Full Text Available Seiches are normal modes of water bodies responding to geophysical forcings with potential to significantly impact ecology and maritime operations. Analysis of high-frequency (1 Hz water level data in Monterey, California, identifies harbor modes between 10 and 120 s that are attributed to specific geographic features. It is found that modal amplitude modulation arises from cross-modal interaction and that offshore wave energy is a primary driver of these modes. Synchronous coupling between modes is observed to significantly impact dynamic water levels. At lower frequencies with periods between 15 and 60 min, modes are independent of offshore wave energy, yet are continuously present. This is unexpected since seiches normally dissipate after cessation of the driving force, indicating an unknown forcing. Spectral and kinematic estimates of these low-frequency oscillations support the idea that a persistent anticyclonic mesoscale gyre adjacent to the bay is a potential mode driver, while discounting other sources.
何红弟; 卢伟真; 董力耘
This paper reports a study concerning occurrence and growth of traffic jam in a harbor tunnel. The single-lane with three sections （downgrade, fiat, and upgrade） is taken into account and they are characterized with different velocity limit. At the low density, the traffic current increases linearly with density and saturates at some values of immediately density. As the density increases, the traffic jam appears firstly before the upgrade section and then extends to the downgrade section. Additionally, the relationships of the velocity and headway against position in different densities are obta/ned from simulation. These results clearly clarify where and when the traffic jam appears. Finally, the critical densities are derived via the theoretical analysis before and after the discontinuous fronts and the theoretical results are consistent with the critical values of simulation results.
Muff, Jens; Søgaard, Erik Gydesen
to contamination by PAH, heavy metals, TBT etc. In Denmark, contaminated harbor sediment is pumped ashore to inland lakes or upland sites where treatment of the runoff water is required before discharge to the recipient. In this study, electrochemical oxidation (EO) has been investigated as a method for treatment...... of the discharge water addressing primarily polycyclic aromatic hydrocarbons (PAHs). PAHs are by-products of incomplete combustion of organic materials with recalcitrant and strong mutagenic/carcinogenic properties, due to their benzene analogue structures. PAHs are hydrophobic compounds and their persistence...... in the environment is mainly due to their low water solubility. The experimental study was performed in laboratory scale with volumes of water from 3 to 10 L in a batch recirculation experimental setup at constant temperature with a commercial one-compartment cell of tubular design with Ti/Pt90-Ir10 anode (60 cm2...
Biancani, Barbara; Field, Cara L; Dennison, Sophie; Pulver, Robert; Tuttle, Allison D
A 2-wk-old stranded harbor seal (Phoca vitulina) rescued by Mystic Aquarium showed signs of the presence of a hiatal hernia during rehabilitation. Contrast radiographs of esophagus and stomach revealed an intrathoracic radiodensity that contains filling defects typical of stomach, consistent with gastric rugal folds. Mural thickening was observed at the level of the cardia consistent with a diagnosis of a hiatal hernia. Although clinical improvement was noted with medical therapy and tube feeding, surgical correction of the hiatal hernia was considered necessary for full resolution. However, owing to the animal's low body weight, the corrective hernia surgery was postponed until the body condition improved. The seal needed to be surgically treated for a corneal ulcer, and while anesthetized with isoflurane, the seal became dyspneic and developed cardiac arrhythmias; ultimately cardiac arrest ensued. Resuscitation was unsuccessfully attempted and the seal was euthanized. Necropsy confirmed the radiographic diagnosis and further characterized a paraesophageal hiatal hernia.
Full Text Available Seiches are normal modes of water bodies responding to geophysical forcings with potential to significantly impact ecology and maritime operations. Analysis of high-frequency (1 Hz water level data in Monterey California identifies Harbor modes between 10 and 120 s that are attributed with specific geographic features. It found that modal amplitude modulation arises from cross-modal interaction and that offshore wave energy is a primary driver of these modes. Synchronous coupling between modes is observed to significantly impact dynamic water levels. At lower frequencies between 15 and 60 min modes are independent of offshore wave energy, yet are continuously present. This is unexpected since seiches normally dissipate after cessation of the driving force, indicating an unknown forcing. Spectral and kinematic estimates of these low frequency oscillations supports the idea that a persistent anticyclonic mesoscale gyre adjacent to the Bay is a potential mode driver, while discounting other sources.
XUE Chunting; Russell Howorth; HE Chaoxiong
For loading and unloading of boats or ships round the clock, the access channel and its expanded part-a port are excavated on the lagoon and ocean reef flats in the tropic Pacific oceanic islands. Without moles, the access channel-port traps sediment and further transports it to the ocean or lagoon, resulting in coastal erosion. The wide uneven reef flat with a large catchment area tends to cause the formation of tide currents in the channel-port, while strong waves on the narrow even reef flat can give rise to rip currents. An access channel-port with a mole on one side or two moles on both sides results in less erosion. A model is recommended as an artificial harbor on the ocean coast, which is an excavated port surrounded by a mole, connected with the ocean by an access channel and with the shore by a bridge-shaped pier.
Pinza, M R; Ward, J A; Mayhew, H L; Word, J Q; Niyogi, D K; Kohn, N P [Battelle/Marine Sciences Lab., Sequim, WA (United States)
During the summer of 1991, Battelle/Marine Sciences Laboratory (MSL) was contracted to conduct sampling and testing of sediments proposed for dredging of Richmond Harbor, California. The MSL collected sediment cores to a depth of [minus]40 ft MLLW ([minus]38 ft + 2 ft overdepth) from 28 (12-in. core) and 30 (4-in. core) stations. The sediment cores were allocated to six composite samples referred to as sediment treatments, which were then subjected to physical, chemical, toxicological, and bioaccumulation testing. Physical and chemical parameters included grain size, total organic carbon (TOC), total volatile solids (TVS), oil and grease, total petroleum hydrocarbons (TPH), polynuclear aromatic hydrocarbons (PAH), chlorinated pesticides, polychlorinated biphenyis (PCBs), priority pollutant metals, and butyltins. The results from the test treatments were compared to results from five reference treatments representative of potential in-bay and offshore disposal sites.
Van der Lelie, D.; Reid-Green, J. D.; Stern, E. A.
We have investigated the feasibility of using natural attenuation methods for ecosystem restoration in New York/New Jersey Harbor. Measurements were made of the most probable number of sulfate-reducing bacteria (SRB) in native sediments and in samples, which had been supplemented with an appropriate electron donor and electron acceptor. The results showed that the activity of the endogenous microbial population in the native sediment was high enough to make possible adequate chemical transformation rates. The bioavailability of the zinc in the sediments was measured using the BIOMET biosensor technique. The bioavailability of the zinc was effectively eliminated following the microbial activities. We concluded that natural attenuation could be used effectively in treating sediments from Newark Bay and surrounding waters and that the resultant materials could likely be used in environmental restoration projects of the type proposed for construction in South Kearny, NJ.
Wisniewska, Danuta Maria; Teilmann, Jonas; Hermannsen, Line
In recent years, several sound and movement recording tags have been developed to sample the acoustic fi eld experienced by cetaceans and their reactions to it. However, little is known about how tag placement and an animal’s orientation in the sound fi eld affect the reliability of on-animal rec......In recent years, several sound and movement recording tags have been developed to sample the acoustic fi eld experienced by cetaceans and their reactions to it. However, little is known about how tag placement and an animal’s orientation in the sound fi eld affect the reliability of on......-animal recordings as proxies for actual exposure. Here, we quantify sound exposure levels recorded with a DTAG-3 tag on a captive harbor porpoise exposed to vessel noise in a controlled acoustic environment. Results show that fl ow noise is limiting onboard noise recordings, whereas no evidence of body shading has...
Craige, Siobhan M; Reif, Michaella M; Kant, Shashi
Mixed lineage kinases, or MLKs, are members of the MAP kinase kinase kinase (MAP3K) family, which were originally identified among the activators of the major stress-dependent mitogen activated protein kinases (MAPKs), JNK and p38. During stress, the activation of JNK and p38 kinases targets several essential downstream substrates that react in a specific manner to the unique stressor and thus determine the fate of the cell in response to a particular challenge. Recently, the MLK family was identified as a specific modulator of JNK and p38 signaling in metabolic syndrome. Moreover, the MLK family of kinases appears to be involved in a very wide spectrum of disorders. This review discusses the newly identified functions of MLKs in multiple diseases including metabolic disorders, inflammation, cancer, and neurological diseases.
Blanco-Verea, A; Jaime, J C; Brión, M; Carracedo, A
The present work tries to investigate the population structure and variation of the Amerindian indigenous populations living in Argentina. A total of 134 individuals from three ethnic groups (Kolla, Mapuche and Diaguitas) living in four different regions were collected and analysed for 26 Y-SNPs and 11 Y-STRs. Intra-population variability was analysed, looking for population substructure and neighbour populations were considered for genetic comparative analysis, in order to estimate the contribution of the Amerindian and the European pool, to the current population. We observe a high frequency of R1b1 and Q1a3a* Y-chromosome haplogroups, in the ethnic groups Mapuche, Diaguita and Kolla, characteristic of European and Native American populations, respectively. When we compare our native Argentinean population with other from the South America we also observe that frequency values for Amerindian lineages are relatively lower in our population. These results show a clear Amerindian genetic component but we observe a predominant European influence too, suggesting that typically European male lineages have given rise to the displacement of genuinely Amerindian male lineages in our South American population. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.
Bromham, L; Bennett, T H
Salt tolerance has evolved many times in the grass family, and yet few cereal crops are salt tolerant. Why has it been so difficult to develop crops tolerant of saline soils when salt tolerance has evolved so frequently in nature? One possible explanation is that some grass lineages have traits that predispose them to developing salt tolerance and that without these background traits, salt tolerance is harder to achieve. One candidate background trait is photosynthetic pathway, which has also been remarkably labile in grasses. At least 22 independent origins of the C4 photosynthetic pathway have been suggested to occur within the grass family. It is possible that the evolution of C4 photosynthesis aids exploitation of saline environments, because it reduces transpiration, increases water-use efficiency and limits the uptake of toxic ions. But the observed link between the evolution of C4 photosynthesis and salt tolerance could simply be due to biases in phylogenetic distribution of halophytes or C4 species. Here, we use a phylogenetic analysis to investigate the association between photosynthetic pathway and salt tolerance in the grass family Poaceae. We find that salt tolerance is significantly more likely to occur in lineages with C4 photosynthesis than in C3 lineages. We discuss the possible links between C4 photosynthesis and salt tolerance and consider the limitations of inferring the direction of causality of this relationship.
Illingworth, Robert S; Hölzenspies, Jurriaan J; Roske, Fabian V; Bickmore, Wendy A; Brickman, Joshua M
Mouse embryonic stem cells (ESCs), like the blastocyst from which they are derived, contain precursors of the epiblast (Epi) and primitive endoderm (PrEn) lineages. While transient in vivo, these precursor populations readily interconvert in vitro. We show that altered transcription is the driver of these coordinated changes, known as lineage priming, in a process that exploits novel polycomb activities. We find that intragenic levels of the polycomb mark H3K27me3 anti-correlate with changes in transcription, irrespective of the gene’s developmental trajectory or identity as a polycomb target. In contrast, promoter proximal H3K27me3 is markedly higher for PrEn priming genes. Consequently, depletion of this modification stimulates the degree to which ESCs are primed towards PrEn when challenged to differentiate, but has little effect on gene expression in self-renewing ESC culture. These observations link polycomb with dynamic changes in transcription and stalled lineage commitment, allowing cells to explore alternative choices prior to a definitive decision. DOI: http://dx.doi.org/10.7554/eLife.14926.001 PMID:27723457
Full Text Available Abstract Background The phylogeographic distribution of human mitochondrial DNA variations allows a genetic approach to the study of modern Homo sapiens dispersals throughout the world from a female perspective. As a new contribution to this study we have phylogenetically analysed complete mitochondrial DNA(mtDNA sequences from 42 human lineages, representing major clades with known geographic assignation. Results We show the relative relationships among the 42 lineages and present more accurate temporal calibrations than have been previously possible to give new perspectives as how modern humans spread in the Old World. Conclusions The first detectable expansion occurred around 59,000–69,000 years ago from Africa, independently colonizing western Asia and India and, following this southern route, swiftly reaching east Asia. Within Africa, this expansion did not replace but mixed with older lineages detectable today only in Africa. Around 39,000–52,000 years ago, the western Asian branch spread radially, bringing Caucasians to North Africa and Europe, also reaching India, and expanding to north and east Asia. More recent migrations have entangled but not completely erased these primitive footprints of modern human expansions.
Rosenfeld, Ulrike M; Drewes, Stephan; Ali, Hanan Sheikh; Sadowska, Edyta T; Mikowska, Magdalena; Heckel, Gerald; Koteja, Paweł; Ulrich, Rainer G
Puumala virus (PUUV) represents one of the most important hantaviruses in Central Europe. Phylogenetic analyses of PUUV strains indicate a strong genetic structuring of this hantavirus. Recently, PUUV sequences were identified in the natural reservoir, the bank vole (Myodes glareolus), collected in the northern part of Poland. The objective of this study was to evaluate the presence of PUUV in bank voles from southern Poland. A total of 72 bank voles were trapped in 2009 at six sites in this part of Poland. RT-PCR and IgG-ELISA analyses detected three PUUV positive voles at one trapping site. The PUUV-infected animals were identified by cytochrome b gene analysis to belong to the Carpathian and Eastern evolutionary lineages of bank vole. The novel PUUV S, M and L segment nucleotide sequences showed the closest similarity to sequences of the Russian PUUV lineage from Latvia, but were highly divergent to those previously found in northern Poland, Slovakia and Austria. In conclusion, the detection of a highly divergent PUUV lineage in southern Poland indicates the necessity of further bank vole monitoring in this region allowing rational public health measures to prevent human infections.
Osman, Djaltou Aboubaker; Phelippeau, Michael; Drancourt, Michel; Musso, Didier
French Polynesia is an overseas territory located in the South Pacific. The incidence of tuberculosis in French Polynesia has been stable since 2000 with an average of 20 cases/y/100,000 inhabitants. Molecular epidemiology of Mycobacterium tuberculosis in French Polynesia is unknown because M. tuberculosis isolates have not been routinely genotyped. From 2009 to 2012, 34 isolates collected from 32 French Polynesian patients were identified as M. tuberculosis by probe hybridization. These isolates were genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units (MIRUs)-variable number of tandem repeat (VNTR). Spoligotype patterns obtained using commercial kits were compared with the online international database SITVIT. MIRU-VNTR genotyping was performed using an in-house protocol based on capillary electrophoresis sizing for 24-loci MIRU-VNTR genotyping. The results of the spoligotyping method revealed that 25 isolates grouped into six previously described spoligotypes [H1, H3, U likely (S), T1, Manu, and Beijing] and nine isolates grouped into six new spoligotypes. Comparison with the international database MIRU-VNTRplus distributed 30 isolates into five lineages (Haarlem, Latin American Mediterranean, S, X, and Beijing) and four as unassigned isolates. Genotyping identified four phylogenetic lineages belonging to the modern Euro-American subgroup, one Beijing genotype responsible for worldwide pandemics, including remote islands in the South Pacific, and one Manu genotype of the ancestral lineage of M. tuberculosis. Copyright © 2015. Published by Elsevier B.V.
Losada-Perez, Maria; Gabilondo, Hugo; Molina, Isabel; Turiegano, Enrique; Torroja, Laura; Thor, Stefan; Benito-Sipos, Jonathan
A number of transcription factors that are expressed within most, if not all, embryonic neuroblast (NB) lineages participate in neural subtype specification. Some have been extensively studied in several NB lineages (e.g. components of the temporal gene cascade) whereas others only within specific NB lineages. To what extent they function in other lineages remains unknown. Klumpfuss (Klu), the Drosophila ortholog of the mammalian Wilms tumor 1 (WT1) protein, is one such transcription factor. ...
Zhang, Yuanyuan; Li, Shuqiang
The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly distributed in the Yunnan-Guizhou Plateau, China. With comprehensive sampling and phylogenetic and coalescent-based analyses, we investigated the tempo and mode of diversification and the origins of these troglobites. We also aimed to determine which factors have influenced the diversification of this little-known group. Coalescent-based species delimitation validated the 18 species recognized by morphological inspection and also suggested the existence of cryptic lineages. Divergence time estimates suggested that Nesticella cave spiders in the Yunnan-Guizhou Plateau constituted a monophyletic troglobite clade that originated in the middle Miocene (11.1-18.6 Ma). Although the Yunnan-Guizhou Plateau clade was composed exclusively of troglobite species, suggesting an ancient common subterranean ancestor, we favor multiple, independent cave colonizations during the Pleistocene over a single ancient cave colonization event to explain the origin of these cave faunas. The diversification of plateau Nesticella has been greatly influenced by the sequential uplift of the plateau and likely reflects multiple cave colonizations over time by epigean ancestors during Pleistocene glacial advances. We concluded that plateau cave Nesticella represent an ancient group of spiders, but with young troglobite lineages that invaded caves only recently. The absence of extant epigean relatives and nearly complete isolation among caves supported their relict status. Our work highlights the importance of comprehensive sampling for studies of subterranean diversity and the evolution of cave organisms. The existence of potentially cryptic species and the relict status of Nesticella
Panagiotis F Sarris
Full Text Available Comparative genomics of closely related pathogens that differ in host range can provide insights into mechanisms of host-pathogen interactions and host adaptation. Furthermore, sequencing of multiple strains with the same host range reveals information concerning pathogen diversity and the molecular basis of virulence. Here we present a comparative analysis of draft genome sequences for four strains of Pseudomonas cannabina pathovar alisalensis (Pcal, which is pathogenic on a range of monocotyledonous and dicotyledonous plants. These draft genome sequences provide a foundation for understanding host range evolution across the monocot-dicot divide. Like other phytopathogenic pseudomonads, Pcal strains harboured a hrp/hrc gene cluster that codes for a type III secretion system. Phylogenetic analysis based on the hrp/hrc cluster genes/proteins, suggests localized recombination and functional divergence within the hrp/hrc cluster. Despite significant conservation of overall genetic content across Pcal genomes, comparison of type III effector repertoires reinforced previous molecular data suggesting the existence of two distinct lineages within this pathovar. Furthermore, all Pcal strains analyzed harbored two distinct genomic islands predicted to code for type VI secretion systems (T6SSs. While one of these systems was orthologous to known P. syringae T6SSs, the other more closely resembled a T6SS found within P. aeruginosa. In summary, our study provides a foundation to unravel Pcal adaptation to both monocot and dicot hosts and provides genetic insights into the mechanisms underlying pathogenicity.
C. Eyre; K. Hayden; M. Kozanitas; N. Grunwald; M. Garbelotto
There are four recognized clonal lineages of the pathogen Phytophthora ramorum. The two major lineages present in North America are NA1 and NA2. With a few exceptions, NA1 is found in natural forest ecosystems and nurseries, and NA2 is generally restricted to nurseries. Isolates from the NA1 and NA2 lineages were used to infect rhododendron,...
Mwebaze, Johnson; Boxhoorn, Danny; Valentijn, Edwin
Most workflow systems that support data provenance primarily focus on tracing lineage of data. Data provenance by data lineage provides the derivation history of data including information about services and input data that contributed to the creation of a data product. We show that tracing lineage
Semrau, Stefan; van Oudenaarden, Alexander
Correct and timely lineage decisions are critical for normal embryonic development and homeostasis of adult tissues. Therefore, the search for fundamental principles that underlie lineage decision-making lies at the heart of developmental biology. Here, we review attempts to understand lineage decis
Adriaenssens, Evelien M.; Leonardo Joaquim van Zyl; Cowan, Don A.; Marla I. Trindade
Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of t...
Charlotte De Busschere
Full Text Available Due to both deliberate and accidental introductions, invasive African Clawed Frog (Xenopus laevis populations have become established worldwide. In this study, we investigate the geographic origins of invasive X. laevis populations in France and Portugal using the phylogeographic structure of X. laevis in its native South African range. In total, 80 individuals from the whole area known to be invaded in France and Portugal were analysed for two mitochondrial and three nuclear genes, allowing a comparison with 185 specimens from the native range. Our results show that native phylogeographic lineages have contributed differently to invasive European X. laevis populations. In Portugal, genetic and historical data suggest a single colonization event involving a small number of individuals from the south-western Cape region in South Africa. In contrast, French invasive X. laevis encompass two distinct native phylogeographic lineages, i.e., one from the south-western Cape region and one from the northern regions of South Africa. The French X. laevis population is the first example of a X. laevis invasion involving multiple lineages. Moreover, the lack of population structure based on nuclear DNA suggests a potential role for admixture within the invasive French population.
Craig S Nowell
Full Text Available The forkhead transcription factor Foxn1 is indispensable for thymus development, but the mechanisms by which it mediates thymic epithelial cell (TEC development are poorly understood. To examine the cellular and molecular basis of Foxn1 function, we generated a novel and revertible hypomorphic allele of Foxn1. By varying levels of its expression, we identified a number of features of the Foxn1 system. Here we show that Foxn1 is a powerful regulator of TEC differentiation that is required at multiple intermediate stages of TE lineage development in the fetal and adult thymus. We find no evidence for a role for Foxn1 in TEC fate-choice. Rather, we show it is required for stable entry into both the cortical and medullary TEC differentiation programmes and subsequently is needed at increasing dosage for progression through successive differentiation states in both cortical and medullary TEC. We further demonstrate regulation by Foxn1 of a suite of genes with diverse roles in thymus development and/or function, suggesting it acts as a master regulator of the core thymic epithelial programme rather than regulating a particular aspect of TEC biology. Overall, our data establish a genetics-based model of cellular hierarchies in the TE lineage and provide mechanistic insight relating titration of a single transcription factor to control of lineage progression. Our novel revertible hypomorph system may be similarly applied to analyzing other regulators of development.
Mascara, D; Kawano, T; Magnanelli, A C; Silva, R P; Sant' Anna, O A; Morgante, J S
Mascara, D., Kawano, T., Magnanelli, A. C., Silva, R. P. S., Sant' Anna, O. A., and Morgante, J. S. 1999. Schistosoma mansoni: continuous variation in susceptibility of the vector snail of schistosomiasis, Biomphalaria tenagophila I. Self-Fertilization-Lineage. Experimental Parasitology 93, 133-141. Artificial selection of Biomphalaria tenagophila snails for susceptibility to infection by Schistosoma mansoni (Brazilian SJ strain) was carried out from natural populations. After five self-fertilization generations, two lineages were isolated and were designated as SUSC (highly susceptible 93-100%) and RES (nonsusceptible 5-0%). Length of the prepatent period, cercarial production, and mortality of the hosts in postexposure were determined in all generations (F(1)-F(8)) and were analyzed as quantitative traits related to host susceptibility. Distribution patterns of frequencies were observed within snail families (samples derived from one F(0) snail), these traits showing a significant influence by selection applied to susceptibility. The multiple quantitative classes were described in terms of continuous variation. During the selection of SUSC lineage, classes with higher values of prepatent length and lower cercarial production were eliminated, and the heritability calculated for these two traits was 0.811 and 0.709, respectively. Experimental results were correlated with an increase in the level of susceptibility in the generations selected and are discussed in relation to inheritance patterns as well as the quantitative variation of susceptibility.
Folk, Ryan A; Mandel, Jennifer R; Freudenstein, John V
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord. [Ancient hybridization; chloroplast capture; incongruence; phylogenomics; reticulation.].
De Busschere, Charlotte; Courant, Julien; Herrel, Anthony; Rebelo, Rui; Rödder, Dennis; Measey, G John; Backeljau, Thierry
Due to both deliberate and accidental introductions, invasive African Clawed Frog (Xenopus laevis) populations have become established worldwide. In this study, we investigate the geographic origins of invasive X. laevis populations in France and Portugal using the phylogeographic structure of X. laevis in its native South African range. In total, 80 individuals from the whole area known to be invaded in France and Portugal were analysed for two mitochondrial and three nuclear genes, allowing a comparison with 185 specimens from the native range. Our results show that native phylogeographic lineages have contributed differently to invasive European X. laevis populations. In Portugal, genetic and historical data suggest a single colonization event involving a small number of individuals from the south-western Cape region in South Africa. In contrast, French invasive X. laevis encompass two distinct native phylogeographic lineages, i.e., one from the south-western Cape region and one from the northern regions of South Africa. The French X. laevis population is the first example of a X. laevis invasion involving multiple lineages. Moreover, the lack of population structure based on nuclear DNA suggests a potential role for admixture within the invasive French population.
Champhekar, Ameya; Damle, Sagar S; Freedman, George; Carotta, Sebastian; Nutt, Stephen L; Rothenberg, Ellen V
The ETS family transcription factor PU.1 is essential for the development of several blood lineages, including T cells, but its function in intrathymic T-cell precursors has been poorly defined. In the thymus, high PU.1 expression persists through multiple cell divisions in early stages but then falls sharply during T-cell lineage commitment. PU.1 silencing is critical for T-cell commitment, but it has remained unknown how PU.1 activities could contribute positively to T-cell development. Here we employed conditional knockout and modified antagonist PU.1 constructs to perturb PU.1 function stage-specifically in early T cells. We show that PU.1 is needed for full proliferation, restricting access to some non-T fates, and controlling the timing of T-cell developmental progression such that removal or antagonism of endogenous PU.1 allows precocious access to T-cell differentiation. Dominant-negative effects reveal that this repression by PU.1 is mediated indirectly. Genome-wide transcriptome analysis identifies novel targets of PU.1 positive and negative regulation affecting progenitor cell signaling and cell biology and indicating distinct regulatory effects on different subsets of progenitor cell transcription factors. Thus, in addition to supporting early T-cell proliferation, PU.1 regulates the timing of activation of the core T-lineage developmental program.
Beckers, A.L.D.; Vossen, R. van; Vlaming, G.
Naval mines and underwater improvised explosive devices in harbors can halt or block maritime transport, causing local disruptions that can impact national and regional economies considerably. Securing harbors against such threats is implemented in the Netherlands through cooperation between civil a
... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Expansion of Foreign-Trade Zone 152, Burns Harbor, Indiana Pursuant to its... in the Burns Harbor, Indiana, area, within the Chicago Customs and Border Protection port of...
species within the greater Pearl Harbor area include the hawksbill turtle (Eretomochelys imbricate) and the humpback whale ( Megaptera novaeangliae ...Branch), and Section 10 of the Rivers and Harbors Act of 1899, as appropriate. The No Action Alternative would not impact any of these resources
Kastelein, R.A.; Gransier, R.; Hoek, L.; Jong, C.A.F. de
The distance at which harbor porpoises can hear underwater detonation sounds is unknown, but depends, among other factors, on the hearing threshold of the species for impulsive sounds. Therefore, the underwater hearing threshold of a young harbor porpoise for an impulsive sound, designed to mimic a
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Little Traverse Bay, Lake Michigan, Harbor Springs, Mich. 110.82a Section 110.82a Navigation and Navigable Waters COAST GUARD... Traverse Bay, Lake Michigan, Harbor Springs, Mich. (a) Area 1. Beginning at latitude 45°25′42.2″...
... amendments to the Longshore and Harbor Workers' Compensation Act (LHWCA) by the American Recovery and... of Workers' Compensation Programs 20 CFR Part 701 RIN 1240-AA02 Regulations Implementing the Longshore and Harbor Workers' Compensation Act: Recreational Vessels AGENCY: Office of Workers'...
University Press, 1962. Articles and Periodicals 9. Barnhart, Michael A. "Planning the Pearl Harbor Attack: A Study in Military Politics," Aerospace Historian...15. Taussig , Joseph K. Jr. "I Remember Pearl Harbor." United States Naval Institute Proceedings, Vol. 98, No. 12 (December 1972): pp. 18-24. 16. "The
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Searsport Lobster Boat Races, Searsport Harbor, ME. 100.118 Section 100.118 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Lobster Boat Races, Searsport Harbor, ME. (a) Regulated Area. The regulated area includes all waters...
... National Park Service Final Environmental Impact Statement; Prisoners Harbor Wetland Restoration, Santa... coastal wetland on Santa Cruz Island, Channel Islands National Park. The requisite no-action ``wait period... restoration of palustrine wetlands and deepwater habitat at Prisoners Harbor, as well as remove a...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Duluth Ship Canal (Duluth-Superior Harbor). 117.661 Section 117.661 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Minnesota § 117.661 Duluth Ship Canal (Duluth-Superior Harbor). The draw...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Inner Harbor Navigation Canal, New Orleans. 117.458 Section 117.458 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Louisiana § 117.458 Inner Harbor Navigation Canal, New Orleans. (a)...
..., Boston Inner Harbor, Boston, MA. 165.120 Section 165.120 Navigation and Navigable Waters COAST GUARD... § 165.120 Safety Zone: Chelsea River, Boston Inner Harbor, Boston, MA. (a) Location. The following area... downstream of the Chelsea Street Bridge on the Chelsea, MA side of the Chelsea River—hereafter referred to...
... Weapons Station, Seal Beach. 334.930 Section 334.930 Navigation and Navigable Waters CORPS OF ENGINEERS... Bay Harbor, Calif.; Naval Weapons Station, Seal Beach. (a) The restricted area. The water of Anaheim Bay Harbor between the east and west jetties at the United States Naval Weapons Station, Seal Beach...
... SECURITY Coast Guard 33 CFR Part 100 Special Local Regulations for Marine Events; Severn River, Spa Creek... Annapolis'' triathlon, a marine event to be held on the waters of Spa Creek and Annapolis Harbor on May 14... Spa Creek and Annapolis Harbor during the event. DATES: This rule is effective from 6 a.m. until 9 a.m...
Harbor Heights Elementary School in the Peninsula school district of Washington State is engaged in a career education research project. The sixth-graders of Harbor Heights use a fully equipped greenhouse to become aware of the working world through the occupations associated with ornamental horticulture. (DS)
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Lynn Harbor in Broad Sound, Mass. 110.27 Section 110.27 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.27 Lynn Harbor in Broad Sound, Mass. North...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Silver Beach Harbor, North Falmouth, Mass. 110.40 Section 110.40 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Falmouth, Mass. All the waters of the harbor northward of the inner end of the entrance channel....
... Hull, Mass. 110.31 Section 110.31 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Hull, Mass. (a) Area No. 1 in Allerton Harbor. That area north of Hog Island beginning at latitude 42... jurisdiction, and at the discretion, of the local Harbor Master, Hull, Mass....
Lepland, Aivo; Andersen, Thorbjørn Joest; Lepland, Aave
indicate that propeller wash affects the seabed in the Oslo harbor. The propeller-induced turbulence causes erosion, and in places exposes and remobilizes contaminated sediments that accumulated in the harbor during previous decades. Such re-exposure of contaminated sediments could be detrimental to local...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Provincetown Harbor Swim for Life, Provincetown, MA. 100.113 Section 100.113 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY REGATTAS AND MARINE PARADES SAFETY OF LIFE ON NAVIGABLE WATERS § 100.113 Provincetown Harbor...
... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false San Juan Harbor, P.R. 110.240 Section 110.240 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.240 San Juan Harbor, P.R. (a) The anchorage...
On the morning of December 7, 1941, Japanese bombers staged a surprise attack on U.S. military forces at Pearl Harbor in Hawaii. Sixty years after the attack on Pearl Harbor, the United States was attacked again. On the morning of September 11, 2001, four commercial airplanes hijacked by 19 terrorists killed nearly 3,000 people when they crashed…
... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; USA Triathlon, Milwaukee Harbor, Milwaukee... will compete in a swim--as part of a triathlon competition--across both the Lakeshore inlet and the... Triathlon, Milwaukee Harbor, Milwaukee, Wisconsin. (a) Location. The safety zone will encompass all...
... No. USCG-2013-0140] RIN 1625-AA00 Safety Zone; USA Triathlon; Milwaukee Harbor, Milwaukee, WI AGENCY... Triathlon; Milwaukee Harbor; Milwaukee, WI in the Federal Register (2013-07281). We did not receive any.... Participants will compete in a swim--as part of a triathlon competition--across both the Lakeshore inlet...
... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters... REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The...
...), Harvey Canal, and Algiers Canal during severe hurricane conditions. Vessels will not be permitted to stay... Harbor Navigation Canal, Harvey Canal, and Algiers Canal during severe hurricane conditions. Those..., Inner Harbor Navigation Canal, Harvey Canal, Algiers Canal, New Orleans, LA AGENCY: Coast Guard, DHS...
... Harbor and Cooper River, Charleston, SC. 165.708 Section 165.708 Navigation and Navigable Waters COAST... Guard District § 165.708 Safety/Security Zone; Charleston Harbor and Cooper River, Charleston, SC. (a... Cooper River. All coordinates referenced use datum: NAD 1983. (2) All waters within 100 yards of...
... COMMISSION Stone Harbor Emerging Markets Income Fund, et al.; Notice of Application September 16, 2011... stock that such investment companies may issue. Applicants: Stone Harbor Emerging Markets Income Fund... relation to market price and its net asset value per common share (``NAV'')) and the relationship...
... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false San Diego Harbor, Calif.; naval....880 San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma. (a) The area. That portion of San Diego Bay southerly of Ballast Point, exclusive of the southwesterly portion of the restricted...
... FURTHER INFORMATION CONTACT: John Fornito, Operations Support Group, Eastern Service Center, Federal... and new Standard Instrument Approach Procedures have been developed at Hancock County-Bar Harbor... Approach Procedures at Hancock County-Bar Harbor Airport. The geographic coordinates for the airport...
Anabell Pulido Caraballé
Full Text Available The characterization of the dredging sediments is essential for environmental license, control and planning in dredging harbors. Sediment pollution was study in two harbor areas of the Cienfuegos Bay. Dredging sediments from “Camilo Cienfuegos” Refinery port and from area IX of Cienfuegos harbor were characterized. In order to evaluate dredging sediment quality, an analysis of water content, grain size, organic matter and trace metals was done. The results show that the trace elements in the sediments are at natural levels. Due to the absent of Cuban rules for these topics, international criteria for sampling, analysis and sediment quality evaluation were used in the study. Results show that these levels can be considered as typical for harbor areas in which authorization for dredging activities in docks and navigation channel should be granted. The results and methodologies will be applied in others Cuban harbors and navigation channel during the environmental license of dredging sediments.
Petrosillo, Irene; Valente, Donatella; Zaccarelli, Nicola; Zurlini, Giovanni
The management of tourist harbors has traditionally been analyzed with little attention to managers' awareness of the effects of their decisions on the environment. The aims of this paper were to assess managers' perceptions of the main environmental risks in their regions and to identify common behaviors among the managers involved in eight tourist harbors in southern Italy, where the same tourist harbor is often managed by different managers. A questionnaire was administered and statistical analyses were performed to test differences between managers of big and small harbors. Managers showed a low perception of environmental risks and, surprisingly, in certain harbors, some meaningful cases were highlighted: the most homogeneous case, where all managers showed a reasonable level of environmental awareness, and cases with strong mismatches among managers. In this paper, we propose that an assessment of managers' perceptions of risk be included as a new form of analysis when environmental risk assessments are carried out.
Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C; Dehio, Christoph
Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens
Full Text Available Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS, and thereby translocated Bartonella effector proteins (Beps, evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial
Full Text Available In order to maintain tissue homeostasis, cell fate decisions within stem cell lineages have to respond to the needs of the tissue. This coordination of lineage choices with regenerative demand remains poorly characterized. Here, we identify a signal from enteroendocrine cells (EEs that controls lineage specification in the Drosophila intestine. We find that EEs secrete Slit, a ligand for the Robo2 receptor in intestinal stem cells (ISCs that limits ISC commitment to the endocrine lineage, establishing negative feedback control of EE regeneration. Furthermore, we show that this lineage decision is made within ISCs and requires induction of the transcription factor Prospero in ISCs. Our work identifies a function for the conserved Slit/Robo pathway in the regulation of adult stem cells, establishing negative feedback control of ISC lineage specification as a critical strategy to preserve tissue homeostasis. Our results further amend the current understanding of cell fate commitment within the Drosophila ISC lineage.
Biteau, Benoît; Jasper, Heinrich
In order to maintain tissue homeostasis, cell fate decisions within stem cell lineages have to respond to the needs of the tissue. This coordination of lineage choices with regenerative demand remains poorly characterized. Here, we identify a signal from enteroendocrine cells (EEs) that controls lineage specification in the Drosophila intestine. We find that EEs secrete Slit, a ligand for the Robo2 receptor in intestinal stem cells (ISCs) that limits ISC commitment to the endocrine lineage, establishing negative feedback control of EE regeneration. Furthermore, we show that this lineage decision is made within ISCs and requires induction of the transcription factor Prospero in ISCs. Our work identifies a function for the conserved Slit/Robo pathway in the regulation of adult stem cells, establishing negative feedback control of ISC lineage specification as a critical strategy to preserve tissue homeostasis. Our results further amend the current understanding of cell fate commitment within the Drosophila ISC lineage.
Cruz-Plancarte, Indira; Cazares, Adrián; Guarneros, Gabriel
Previously, a collection of virulent phages infecting Pseudomonas aeruginosa was isolated from open water reservoirs and residual waters. Here, we described the comparative genomics of a set of five related phages from the collection, the physical structure of the genome, the structural proteomics of the virion, and the transcriptional program of archetypal phage PaMx41. The phage genomes were closely associated with each other and with those of two other P. aeruginosa phages, 119X and PaP2, which were previously filed in the databases. Overall, the genomes were approximately 43 kb, harboring 53 conserved open reading frames (ORFs) and three short ORFs in indel regions and containing 45% GC content. The genome of PaMx41 was further characterized as a linear, terminally redundant DNA molecule. A total of 16 ORFs were associated with putative functions, including nucleic acid metabolism, morphogenesis, and lysis, and eight virion proteins were identified through mass spectrometry. However, the coding sequences without assigned functions represent 70% of the ORFs. The PaMx41 transcription program was organized in early, middle, and late expressed genomic modules, which correlated with regions containing functionally related genes. The high genomic conservation among these distantly isolated phages suggests that these viruses undergo selective pressure to remain unchanged. The 119X lineage represents a unique set of phages that corresponds to a novel phage group. The features recognized in the genomes and the broad host range of clinical strains suggest that these phages are candidates for therapy applications.
Wellborn, Gary A; Langerhans, R Brian
The tenet that ecological opportunity drives adaptive diversification has been central to theories of speciation since Darwin, yet no widely accepted definition or mechanistic framework for the concept currently exists. We propose a definition for ecological opportunity that provides an explicit mechanism for its action. In our formulation, ecological opportunity refers to environmental conditions that both permit the persistence of a lineage within a community, as well as generate divergent natural selection within that lineage. Thus, ecological opportunity arises from two fundamental elements: (1) niche availability, the ability of a population with a phenotype previously absent from a community to persist within that community and (2) niche discordance, the diversifying selection generated by the adaptive mismatch between a population's niche-related traits and the newly encountered ecological conditions. Evolutionary response to ecological opportunity is primarily governed by (1) spatiotemporal structure of ecological opportunity, which influences dynamics of selection and development of reproductive isolation and (2) diversification potential, the biological properties of a lineage that determine its capacity to diversify. Diversification under ecological opportunity proceeds as an increase in niche breadth, development of intraspecific ecotypes, speciation, and additional cycles of diversification that may themselves be triggered by speciation. Extensive ecological opportunity may exist in depauperate communities, but it is unclear whether ecological opportunity abates in species-rich communities. Because ecological opportunity should generally increase during times of rapid and multifarious environmental change, human activities may currently be generating elevated ecological opportunity – but so far little work has directly addressed this topic. Our framework highlights the need for greater synthesis of community ecology and evolutionary biology, unifying
Anne I. Boullerne
Full Text Available We identified a family in which five siblings were diagnosed with multiple sclerosis (MS or clinically isolated syndrome. Several women in the maternal lineage have comorbidities typically associated with Peutz Jeghers Syndrome, a rare autosomal-dominant disease caused by mutations in the serine-threonine-kinase 11 (STK11 gene, which encodes liver kinase B1. Sequence analysis of DNA from one sibling identified a single-nucleotide polymorphism (SNP within STK11 intron 5. This SNP (dbSNP ID: rs9282860 was identified by TaqMan polymerase chain reaction (PCR assays in DNA samples available from two other siblings. Further screening was carried out in samples from 654 relapsing-remitting MS patients, 100 primary progressive MS patients, and 661 controls. The STK11-SNP has increased frequency in all female patients versus controls (odds ratio = 1.66, 95% CI = 1.05, 2.64, p = .032. The STK11-SNP was not associated with disease duration or onset; however, it was significantly associated with reduced severity (assessed by MS severity scores, with the lowest scores in patients who also harbored the HLA-DRB1*1501 allele. In vitro studies showed that peripheral blood mononuclear cells from members of the family were more sensitive to the mitochondrial inhibitor metformin than cells from MS patients with the major STK11 allele. The increased association of SNP rs9282860 in women with MS defines this variant as a genetic risk factor. The lower disease severity observed in the context of HLA-DRB1*1501 combined with limited in vitro studies raises the provocative possibility that cells harboring the STK11-SNP could be targeted by drugs which increase metabolic stress.
Lescroart, Fabienne; Meilhac, Sigolène M
The formation of the heart involves diversification of lineages which differentiate into distinct cardiac cell types or contribute to different regions such as the four cardiac chambers. The heart is the first organ to form in the embryo. However, in parallel with the growth of the organism, before or after birth, the heart has to adapt its size to maintain pumping efficiency. The adult heart has only a mild regeneration potential; thus, strategies to repair the heart after injury are based on the mobilisation of resident cardiac stem cells or the transplantation of external sources of stem cells. We discuss current knowledge on these aspects and raise questions for future research.
Santini, Maria Paola; Forte, Elvira; Harvey, Richard P; Kovacic, Jason C
Over the past two decades, several populations of cardiac stem cells have been described in the adult mammalian heart. For the most part, however, their lineage origins and in vivo functions remain largely unexplored. This Review summarizes what is known about different populations of embryonic and adult cardiac stem cells, including KIT(+), PDGFRα(+), ISL1(+)and SCA1(+)cells, side population cells, cardiospheres and epicardial cells. We discuss their developmental origins and defining characteristics, and consider their possible contribution to heart organogenesis and regeneration. We also summarize the origin and plasticity of cardiac fibroblasts and circulating endothelial progenitor cells, and consider what role these cells have in contributing to cardiac repair.
Pinheiro, Ana; Melo-Ferreira, José; Abrantes, Joana; Martinelli, Nicola; Lavazza, Antonio; Alves, Paulo C; Gortázar, Christian; Esteves, Pedro J
Antigen recognition by immunoglobulins depends upon initial rearrangements of heavy chain V, D, and J genes. In leporids, a unique system exists for the VH genes usage that exhibit highly divergent lineages: the VHa allotypes, the Lepus sL lineage and the VHn genes. For the European rabbit (Oryctolagus cuniculus), four VHa lineages have been described, the a1, a2, a3 and a4. For hares (Lepus sp.), one VHa lineage was described, the a2L, as well as a more ancient sL lineage. Both genera use the VHn genes in a low frequency of their VDJ rearrangements. To address the hypothesis that the VH specificities could be associated with different environments, we sequenced VDJ genes from a third leporid genus, Sylvilagus. We found a fifth and equally divergent VHa lineage, the a5, and an ancient lineage, the sS, related to the hares' sL, but failed to obtain VHn genes. These results show that the studied leporids employ different VH lineages in the generation of the antibody repertoire, suggesting that the leporid VH genes are subject to strong selective pressure likely imposed by specific pathogens.
Pinza, M.R.; Mayhew, H.L.; Word, J.Q.
The older, bay mud (OBM) unit predates modem man and could act as a barrier to the downward transport of contaminants from the younger bay mud (YBM) because of its hard-packed consistency. However, its chemical and biological nature have not been well characterized. Battelle/Marine Sciences Laboratory (MSL) conducted three independent studies of OBM sediment in January 1993, January 1994, and October 1994. These studies evaluated potential chemical contamination and biological effects of OBM that could occur as a result of dredging and disposal activities. These evaluations were performed by conducting chemical analysis, solid-phase toxicity tests, suspended- particulate-phase (SPP) toxicity tests, and bioaccumulation tests on the OBM sediment. If the sediment chemistry and toxicity results showed no or minimal contamination and toxicological responses, then either the OBM could be left exposed in Richmond Harbor after dredging the YBM without leaving a source of contamination, or if the project depths necessitate, the OBM would be acceptable for disposal at an appropriate disposal site.
Nourah Mohammad Obaid
Full Text Available The development of resistance to previously effective treatments has been a challenge for health care providers and a fear for patients undergoing cancer therapy. This is an unfortunately frequent occurrence for patients undergoing targeted therapy for tumours harboring the activating V600E mutation of the BRAF gene. Since the initial identification of the BRAF mutation in 2002, a series of small molecular inhibitors that target the BRAFV600E have been developed, but intrinsic and acquired resistance to these drugs has presented an ongoing challenge. More recently, improvements in therapy have been achieved by combining the use of BRAF inhibitors with other drugs, such as inhibitors of the downstream effector mitogen activated protein kinase (MAPK/extracellular-signal regulated kinase (ERK kinase (MEK. Despite improved success in response rates and in delaying resistance using combination therapy, ultimately, the acquisition of resistance remains a concern. Recent research articles have shed light on some of the underlying mechanisms of this resistance and have proposed numerous strategies that might be employed to overcome or avoid resistance to targeted therapies. This review will explore some of the resistance mechanisms, compare what is known in melanoma cancer to colorectal cancer, and discuss strategies under development to manage the development of resistance.
Beem, Heather; Triantafyllou, Michael
Harbor seals are able to use their whiskers to track minute water movements, such as those left in the wake of a fish. The current study is a simple representation of what the whiskers experience as the seal chases a fish. A scaled whisker model (average cross-flow diameter: dw) is first tested in a towing tank by itself and then towed behind a larger cylinder (dc = 2 . 5dw), which serves as a wake generator. A flexing plate attached to the model base allows the whisker to freely vibrate in response to the flow. Measurements from strain gages on the plate are calibrated to tip deflections. While in the cylinder wake, the whisker vibrates with an amplitude up to ten times higher than it does on its own (A /dw = 0 . 15). Also, the whisker synchronizes with the vortex shedding frequency (fs =0/. 2 U dc) of the upstream cylinder over the range of reduced velocities tested, whereas on its own, the whisker oscillates around its own natural frequency in water. Seals may use the difference in vibration amplitude and frequency between these two cases to help detect the presence of a vortex wake.
Stagi, Stefano; Galluzzi, Fiorella; Bindi, Giuseppe; Lapi, Elisabetta; Cecchi, Cecilia; Salti, Roberto; Chiarelli, Francesco
Floating-Harbor syndrome (FHS) is a rare genetic disorder characterized by short stature, delayed bone age, mild to moderate mental retardation, speech problems, and peculiar craniofacial features. In these patients pubertal development has been reported to be normal. In this paper, we describe a girl with FHS who developed precocious puberty. FHS diagnosis was made at 2 years 5 months on the basis of peculiar clinical features. At 7 years 7 months, the girl began pubertal development; her height was 112.5 cm (-2.42 SDS) and pubertal staging was B2 PH2 AH1. LHRH test underlined LH and FSH peak values of 11.7 mIU/ml and 6.2 mIU/ml, respectively. Plasma levels of 17beta-estradiol were normal (8.5 pg/ml). Ophthalmological and neurological examinations, including nuclear magnetic resonance imaging of the brain, were normal. Treatment with gonadotrophin-releasing hormone analogue was begun. At 10 years 1 month, because of reduced height velocity, her growth hormone secretion was evaluated with diagnosis of neurosecretory dysfunction; hGH therapy was begun. The patient showed a good response to hGH treatment, reaching a normal adult height (156.1 cm; -1.20 SDS). This report suggests that, in patients with FHS, precocious puberty should be taken into consideration; in these patients, a careful endocrinological followup for the possible presence of growth and pubertal disorders is needed.
Bravo, E; Gutiérrez, J L; Doherty, C L
Recently, it has been found that off-centre carbon burning in a subset of intermediate-mass stars does not propagate all the way to the center, resulting in a class of hybrid CONe cores. Here, we consider the possibility that stars hosting these hybrid CONe cores might belong to a close binary system and, eventually, become white dwarfs accreting from a non-degenerate companion at rates leading to a supernova explosion. We have computed the hydrodynamical phase of the explosion of Chandrasekhar-mass white dwarfs harboring hybrid cores, assuming that the explosion starts at the center, either as a detonation (as may be expected in some degenerate merging scenarios) or as a deflagration (that afterwards transitions into a delayed detonation). We assume these hybrid cores are made of a central CO volume, of mass M(CO), surrounded by an ONe shell. We show that, in case of a pure detonation, a medium-sized CO-rich region, M(CO)<0.4 Msun, results in the ejection of a small fraction of the mantle while leaving a ...
Curir, Anna; Murante, Giuseppe
The bar formation is still an open problem in modern astrophysics. In this paper we present numerical simulation performed with the aim of analyzing the growth of the bar instability inside stellar-gaseous disks, where the star formation is triggered, and a central black hole is present. The aim of this paper is to point out the impact of such a central massive black hole on the growth of the bar. We use N-body-SPH simulations of the same isolated disk-to-halo mass systems harboring black holes with different initial masses and different energy feedback on the surrounding gas. We compare the results of these simulations with the one of the same disk without black hole in its center. We make the same comparison (disk with and without black hole) for a stellar disk in a fully cosmological scenario. A stellar bar, lasting 10 Gyrs, is present in all our simulations. The central black hole mass has in general a mild effect on the ellipticity of the bar but it is never able to destroy it. The black holes grow in di...
Sváb, Domonkos; Bálint, Balázs; Maróti, Gergely; Tóth, István
Enterohemorrhagic Escherichia coli (EHEC) O157:H7/NM strains are significant foodborne pathogens intensively studied, while other sero- and pathotypes of the O157 serogroup only began to receive more attention. Here we report the first genome sequence of a cytolethal distending toxin (CDT-V) producing E. coli O157:H43 strain (T22) isolated from cattle. The genome consists of a 4.9Mb chromosome assembled into three contigs and one plasmid of 82.4kb. Comparative genomic investigations conducted with the core genomes of representative E. coli strains in GenBank (n=62) confirmed the separation of T22 from the EHEC and enteropathogenic (EPEC) O157 lineages. Gene content based pangenome analysis revealed as many as 261 T22-specific coding sequences without orthologs in EDL933 EHEC O157 prototypic and two phylogenetically related commensal E. coli strains. The genome sequence revealed 10 prophage-like regions which harbor several virulence-associated genes including cdt and heat-labile enterotoxin (LT-II) encoding operons. Our results indicate that the evolutionary path of T22 is largely independent from that of EHEC and EPEC O157:H7/NM strains. Thus, the CDT-producing T22 E. coli O157:H43 strain represents a unique lineage of E. coli O157.
Full Text Available Tools for rapid and efficient transgenesis in “safe harbor” loci in an isogenic context remain important to exploit the possibilities of human pluripotent stem cells (hPSCs. We created hPSC master cell lines suitable for FLPe recombinase-mediated cassette exchange (RMCE in the AAVS1 locus that allow generation of transgenic lines within 15 days with 100% efficiency and without random integrations. Using RMCE, we successfully incorporated several transgenes useful for lineage identification, cell toxicity studies, and gene overexpression to study the hepatocyte lineage. However, we observed unexpected and variable transgene expression inhibition in vitro, due to DNA methylation and other unknown mechanisms, both in undifferentiated hESC and differentiating hepatocytes. Therefore, the AAVS1 locus cannot be considered a universally safe harbor locus for reliable transgene expression in vitro, and using it for transgenesis in hPSC will require careful assessment of the function of individual transgenes.
This volume contains the abstracts of oral and poster presentations made at the LVIII Cold Spring Harbor Symposium on Quantitative Biology entitles DNA & Chromosomes. The meeting was held June 2--June 9, 1993 at Cold Spring Harbor, New York.
... New Bedford Harbor hurricane barrier in the outer harbor. The pilot cap consists of sand and gravel... revising paragraph (a)(2) to read as follows: Sec. 110.140 Buzzards Bay, Nantucket Sound, and...
U.S. Geological Survey, Department of the Interior — These data are high-resolution acoustic backscatter measurements of the seafloor from Boston Harbor and the harbor approaches, Massachusetts. Approximately 170 kmÂ²...
U.S. Geological Survey, Department of the Interior — These data are the trackline from the high-resolution acoustic backscatter measurements of the seafloor from Boston Harbor and the harbor approaches, Massachusetts....
U.S. Geological Survey, Department of the Interior — These data are high-resolution acoustic backscatter measurements of the seafloor from Boston Harbor and the harbor approaches, Massachusetts. Approximately 170 kmÂ˛...
Dijkstra, Johannes Martinus; Katagiri, Takayuki; Hosomichi, Kazuyoshi; Yanagiya, Kazuyo; Inoko, Hidetoshi; Ototake, Mitsuru; Aoki, Takashi; Hashimoto, Keiichiro; Shiina, Takashi
Most of the previously studied teleost MHC class I molecules can be classified into two broad lineages: "U" and "Z/ZE." However, database reports on genes in cyprinid and salmonid fishes show that there is a third major lineage, which lacks detailed analysis so far. We designated this lineage "L" because of an intriguing linkage characteristic. Namely, one zebrafish L locus is closely linked with MHC class II loci, despite the extensively documented nonlinkage of teleost class I with class II. The L lineage consists of highly variable, nonclassical MHC class I genes, and has no apparent orthologues outside teleost fishes. Characteristics that distinguish the L lineage from most other MHC class I are (1) absence of two otherwise highly conserved tryptophan residues W51 and W60 in the alpha1 domain, (2) a low GC content of the alpha1 and alpha2 exons, and (3) an HINLTL motif including a possible glycosylation site in the alpha3 domain. In rainbow trout (Oncorhynchus mykiss) we analyzed several intact L genes in detail, including their genomic organization and transcription pattern. The gene Onmy-LAA is quite different from the genes Onmy-LBA, Onmy-LCA, Onmy-LDA, and Onmy-LEA, while the latter four are similar and categorized as "Onmy-LBA-like." Whereas the Onmy-LAA gene is organized like a canonical MHC class I gene, the Onmy-LBA-like genes are processed and lack all introns except intron 1. Onmy-LAA is predominantly expressed in the intestine, while the Onmy-LBA-like transcripts display a rather homogeneous tissue distribution. To our knowledge, this is the first description of an MHC class I lineage with multiple copies of processed genes, which are intact and transcribed. The present study significantly improves the knowledge of MHC class I variation in teleosts.
Shahhosseini, Nariman; Chinikar, Sadegh; Moosa-Kazemi, Seyed Hassan; Sedaghat, Mohammad Mehdi; Kayedi, Mohammad Hassan; Lühken, Renke; Schmidt-Chanasit, Jonas
Screening of mosquitoes for viruses is an important forecasting tool for emerging and re-emerging arboviruses. Iran has been known to harbour medically important arboviruses such as West Nile virus (WNV) and dengue virus (DENV) based on seroepidemiological data. However, there are no data about the potential mosquito vectors for arboviruses in Iran. This study was performed to provide mosquito and arbovirus data from Iran. A total of 32 317 mosquitos were collected at 16 sites in five provinces of Iran in 2015 and 2016. RT-PCR for detection of flaviviruses was performed. The PCR amplicons were sequenced, and 109 WNV sequences, including one obtained in this study, were used for phylogenetic analyses. The 32 317 mosquito specimens belonging to 25 species were morphologically distinguished and distributed into 1222 pools. Culex pipiens s.l. comprised 56.429%. One mosquito pool (0.08%), containing 46 unfed Cx. pipiens pipiens form pipiens (Cpp) captured in August 2015, was positive for flavivirus RNA. Subsequent sequencing and phylogenetic analyses revealed that the detected Iranian WNV strain belongs to lineage 2 and clusters with a strain recently detected in humans. No flaviviruses other than WNV were detected in the mosquito pools. Cpp could be a vector for WNV in Iran. Our findings indicate recent circulation of WNV lineage-2 strain in Iran and provide a solid base for more targeted arbovirus surveillance programs. © 2017 John Wiley & Sons Ltd.
Felipe L. Assis
Full Text Available Since the recent discovery of Samba virus, the first representative of the family Mimiviridae from Brazil, prospecting for mimiviruses has been conducted in different environmental conditions in Brazil. Recently, we isolated using Acanthamoeba sp. three new mimiviruses, all of lineage A of amoebal mimiviruses: Kroon virus from urban lake water; Amazonia virus from the Brazilian Amazon river; and Oyster virus from farmed oysters. The aims of this work were to sequence and analyze the genome of these new Brazilian mimiviruses (mimi-BR and update the analysis of the Samba virus genome. The genomes of Samba virus, Amazonia virus and Oyster virus were 97%–99% similar, whereas Kroon virus had a low similarity (90%–91% with other mimi-BR. A total of 3877 proteins encoded by mimi-BR were grouped into 974 orthologous clusters. In addition, we identified three new ORFans in the Kroon virus genome. Additional work is needed to expand our knowledge of the diversity of mimiviruses from Brazil, including if and why among amoebal mimiviruses those of lineage A predominate in the Brazilian environment.
Full Text Available Establishing the dates for the origin and main diversification events in the phylogeny of Ascomycota is among the most crucial remaining goals in understanding the evolution of Fungi. There have been several analyses of divergence times in the fungal tree of life in the last two decades, but most have yielded contrasting results for the origin of the major lineages. Moreover, very few studies have provided temporal estimates for a large set of clades within Ascomycota. We performed molecular dating to estimate the divergence times of most of the major groups of Ascomycota. To account for paleontological uncertainty, we included alternative fossil constraints as different scenarios to enable a discussion of the effect of selection of fossils. We used data from 6 molecular markers and 121 extant taxa within Ascomycota. Our various 'relaxed clock' scenarios suggest that the origin and diversification of the Pezizomycotina occurred in the Cambrian. The main lineages of lichen-forming Ascomycota originated at least as early as the Carboniferous, with successive radiations in the Jurassic and Cretaceous generating the diversity of the main modern groups. Our study provides new information about the timing of the main diversification events in Ascomycota, including estimates for classes, orders and families of both lichenized and non-lichenized Ascomycota, many of which had not been previously dated.
Hwang, Do Won; Lee, Dong Soo
In regenerative medicine, the prospect of stem cell therapy holds great promise for the recovery of injured tissues and effective treatment of intractable diseases. Tracking stem cell fate provides critical information to understand and evaluate the success of stem cell therapy. The recent emergence of in vivo noninvasive molecular imaging has enabled assessment of the behavior of grafted stem cells in living subjects. In this review, we provide an overview of current optical imaging strategies based on cell- or tissue-specific reporter gene expression and of in vivo methods to monitor stem cell differentiation into neuronal lineages. These methods use optical reporters either regulated by neuron-specific promoters or containing neuron-specific microRNA binding sites. Both systems revealed dramatic changes in optical reporter imaging signals in cells differentiating into a neuronal lineage. The detection limit of weak promoters or reporter genes can be greatly enhanced by adopting a yeast GAL4 amplification system or an engineering-enhanced luciferase reporter gene. Furthermore, we propose an advanced imaging system to monitor neuronal differentiation during neurogenesis that uses in vivo multiplexed imaging techniques capable of detecting several targets simultaneously.
Yamamizu, Kohei; Piao, Yulan; Sharov, Alexei A.; Zsiros, Veronika; Yu, Hong; Nakazawa, Kazu; Schlessinger, David; Ko, Minoru S.H.
Summary A network of transcription factors (TFs) determines cell identity, but identity can be altered by overexpressing a combination of TFs. However, choosing and verifying combinations of TFs for specific cell differentiation have been daunting due to the large number of possible combinations of ∼2,000 TFs. Here, we report the identification of individual TFs for lineage-specific cell differentiation based on the correlation matrix of global gene expression profiles. The overexpression of identified TFs—Myod1, Mef2c, Esx1, Foxa1, Hnf4a, Gata2, Gata3, Myc, Elf5, Irf2, Elf1, Sfpi1, Ets1, Smad7, Nr2f1, Sox11, Dmrt1, Sox9, Foxg1, Sox2, or Ascl1—can direct efficient, specific, and rapid differentiation into myocytes, hepatocytes, blood cells, and neurons. Furthermore, transfection of synthetic mRNAs of TFs generates their appropriate target cells. These results demonstrate both the utility of this approach to identify potent TFs for cell differentiation, and the unanticipated capacity of single TFs directly guides differentiation to specific lineage fates. PMID:24371809
Starke, Charlotte; Betz, Hannah; Hickmann, Linda; Lachmann, Peter; Neubauer, Björn; Kopp, Jeffrey B.; Sequeira-Lopez, Maria Luisa S.; Gomez, R. Ariel; Hohenstein, Bernd; Hugo, Christian P.M.
Mesangial cell injury has a major role in many CKDs. Because renin-positive precursor cells give rise to mesangial cells during nephrogenesis, this study tested the hypothesis that the same phenomenon contributes to glomerular regeneration after murine experimental mesangial injury. Mesangiolysis was induced by administration of an anti-mesangial cell serum in combination with LPS. In enhanced green fluorescent protein–reporter mice with constitutively labeled renin lineage cells, the size of the enhanced green fluorescent protein–positive area in the glomerular tufts increased after mesangial injury. Furthermore, we generated a novel Tet-on inducible triple-transgenic LacZ reporter line that allowed selective labeling of renin cells along renal afferent arterioles of adult mice. Although no intraglomerular LacZ expression was detected in healthy mice, about two-thirds of the glomerular tufts became LacZ positive during the regenerative phase after severe mesangial injury. Intraglomerular renin descendant LacZ-expressing cells colocalized with mesangial cell markers α8-integrin and PDGF receptor-β but not with endothelial, podocyte, or parietal epithelial cell markers. In contrast with LacZ-positive cells in the afferent arterioles, LacZ-positive cells in the glomerular tuft did not express renin. These data demonstrate that extraglomerular renin lineage cells represent a major source of repopulating cells for reconstitution of the intraglomerular mesangium after injury. PMID:24904091
Cordaux, Richard; Aunger, Robert; Bentley, Gillian; Nasidze, Ivane; Sirajuddin, S M; Stoneking, Mark
The origins of the nearly one billion people inhabiting the Indian subcontinent and following the customs of the Hindu caste system are controversial: are they largely derived from Indian local populations (i.e. tribal groups) or from recent immigrants to India? Archaeological and linguistic evidence support the latter hypothesis, whereas recent genetic data seem to favor the former hypothesis. Here, we analyze the most extensive dataset of Indian caste and tribal Y chromosomes to date. We find that caste and tribal groups differ significantly in their haplogroup frequency distributions; caste groups are homogeneous for Y chromosome variation and more closely related to each other and to central Asian groups than to Indian tribal or any other Eurasian groups. We conclude that paternal lineages of Indian caste groups are primarily descended from Indo-European speakers who migrated from central Asia approximately 3,500 years ago. Conversely, paternal lineages of tribal groups are predominantly derived from the original Indian gene pool. We also provide evidence for bidirectional male gene flow between caste and tribal groups. In comparison, caste and tribal groups are homogeneous with respect to mitochondrial DNA variation, which may reflect the sociocultural characteristics of the Indian caste society.
El Mahdi eBendif
Full Text Available The coccolithophore family Noëlaerhabdaceae contains a number of taxa that are very abundant in modern oceans, including the cosmopolitan bloom-forming Emiliania huxleyi. Introgressive hybridization has been suggested to account for incongruences between nuclear, mitochondrial and plastidial phylogenies of morphospecies within this lineage, but the number of species cultured to date remains rather limited. Here, we present the characterization of 5 new Noëlaerhabdaceae culture strains isolated from samples collected in the south-east Pacific Ocean. These were analyzed morphologically using scanning electron microscopy and phylogenetically by sequencing 5 marker genes (nuclear 18S and 28S rDNA, plastidial tufA, and mitochondrial cox1 and cox3 genes. Morphologically, one of these strains corresponded to Gephyrocapsa ericsonii and the four others to Reticulofenestra parvula. Ribosomal gene sequences were near identical between these new strains, but divergent from G. oceanica, G. muellerae and E. huxleyi. In contrast to the clear distinction in ribosomal phylogenies, sequences from other genomic compartments clustered with those of E. huxleyi strains with which they share an ecological range (i.e. warm temperate to tropical waters. These data provide strong support for the hypothesis of past (and potentially ongoing introgressive hybridization within this ecologically important lineage and for the transfer of R. parvula to Gephyrocapsa. These results have important implications for understanding the role of hybridization in speciation in vast ocean meta-populations of phytoplankton.
Ward, Carol V; Plavcan, J Michael; Manthi, Fredrick K
Australopithecus anamensis is the earliest known species of the Australopithecus-human clade and is the likely ancestor of Australopithecus afarensis. Investigating possible selective pressures underlying these changes is key to understanding the patterns of selection shaping the origins and early evolution of the Australopithecus-human clade. During the course of the Au. anamensis-afarensis lineage, significant changes appear to occur particularly in the anterior dentition, but also in jaw structure and molar form, suggesting selection for altered diet and/or food processing. Specifically, canine tooth crown height does not change, but maxillary canines and P(3)s become shorter mesiodistally, canine tooth crowns become more symmetrical in profile and P(3)s less unicuspid. Canine roots diminish in size and dimorphism, especially relative to the size of the postcanine teeth. Molar crowns become higher. Tooth rows become more divergent and symphyseal form changes. Dietary change involving anterior dental use is also suggested by less intense anterior tooth wear in Au. afarensis. These dental changes signal selection for altered dietary behaviour and explain some differences in craniofacial form between these taxa. These data identify Au. anamensis not just as a more primitive version of Au. afarensis, but as a dynamic member of an evolving lineage leading to Au. afarensis, and raise intriguing questions about what other evolutionary changes occurred during the early evolution of the Australopithecus-human clade, and what characterized the origins of the group.