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Sample records for showed high genetic

  1. Minifish shows high genetic variation in mtDNA size.

    PubMed

    Chen, X-W; Li, Q-L; Hu, X-J; Yuan, Y-M; Wen, M; Peng, L-Y; Liu, S-J; Hong, Y-H

    2014-01-01

    The genus Paedocypris is a newly described taxon of minifish species that are characterized by extensive chromosome evolution and one of the smallest known vertebrate nuclear genomes. Paedocypris features a tiny adult size, a short generation time, low fecundity and fragmented tropical habitats, which are factors that favor rapid speciation. Most recently, we have revealed that P. progenetica (Pp), the type species of the genus Paedocypris, has an unusual mtDNA bearing - within its D-loop - a tandem array of a 34-bp repeat sequence called the minifish repeat, which shows compromised replication efficiency in vitro. Here we report that Pp exhibits high genetic variation in mtDNA size. The efficiency of D-loop amplification was found to depend upon primers. Interestingly, Pp individuals of one and the same population differed drastically in mtDNA size resulting from varying copy numbers of the minifish repeat. We conclude that minifish has a high mutation rate and perhaps represents a rapidly evolving taxon of vertebrates.

  2. Population genetics of Mioscirtus wagneri, a grasshopper showing a highly fragmented distribution.

    PubMed

    Ortego, Joaquín; Aguirre, Maria Pilar; Cordero, Pedro J

    2010-02-01

    The genetic consequences of population fragmentation and isolation are major issues in conservation biology. In this study we analyse the genetic variability and structure of the Iberian populations of Mioscirtus wagneri, a specialized grasshopper exclusively inhabiting highly fragmented hypersaline low grounds. For this purpose we have used seven species-specific microsatellite markers to type 478 individuals from 24 localities and obtain accurate estimates of their genetic variability. Genetic diversity was relatively low and we detected genetic signatures suggesting that certain populations of M. wagneri have probably passed through severe demographic bottlenecks. We have found that the populations of this grasshopper show a strong genetic structure even at small geographical scales, indicating that they mostly behave as isolated populations with low levels of gene flow among them. Thus, several populations can be regarded as independent and genetically differentiated units which require adequate conservation strategies to avoid eventual extinctions that in highly isolated localities are not likely to be compensated for with the arrival of immigrants from neighbouring populations. Overall, our results show that these populations probably represent the 'fragments' of a formerly more widespread population and highlight the importance of protecting Iberian hypersaline environments due to the high number of rare and endangered species they sustain. PMID:20051009

  3. The yeast Starmerella bacillaris (synonym Candida zemplinina) shows high genetic diversity in winemaking environments.

    PubMed

    Masneuf-Pomarede, Isabelle; Juquin, Elodie; Miot-Sertier, Cécile; Renault, Philippe; Laizet, Yec'han; Salin, Franck; Alexandre, Hervé; Capozzi, Vittorio; Cocolin, Luca; Colonna-Ceccaldi, Benoit; Englezos, Vasileios; Girard, Patrick; Gonzalez, Beatriz; Lucas, Patrick; Mas, Albert; Nisiotou, Aspasia; Sipiczki, Matthias; Spano, Giuseppe; Tassou, Chrysoula; Bely, Marina; Albertin, Warren

    2015-08-01

    The yeast Candida zemplinina (Starmerella bacillaris) is frequently isolated from grape and wine environments. Its enological use in mixed fermentation with Saccharomyces cerevisiae has been extensively investigated these last few years, and several interesting features including low ethanol production, fructophily, glycerol and other metabolites production, have been described. In addition, molecular tools allowing the characterization of yeast populations have been developed, both at the inter- and intraspecific levels. However, most of these fingerprinting methods are not compatible with population genetics or ecological studies. In this work, we developed 10 microsatellite markers for the C. zemplinina species that were used for the genotyping of 163 strains from nature or various enological regions (28 vineyards/wineries from seven countries). We show that the genetic diversity of C. zemplinina is shaped by geographical localization. Populations isolated from winemaking environments are quite diverse at the genetic level: neither clonal-like behaviour nor specific genetic signature were associated with the different vineyards/wineries. Altogether, these results suggest that C. zemplinina is not under selective pressure in winemaking environments. PMID:26071435

  4. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans)

    PubMed Central

    2008-01-01

    Background Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome. Results A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea. A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area. Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza. Conclusion Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background. PMID:18312628

  5. Spatial and temporal genetic analyses show high gene flow among European corn borer (Lepidoptera: Crambidae) populations across the central U.S. corn belt.

    PubMed

    Kim, Kyung Seok; Bagley, Mark J; Coates, Brad S; Hellmich, Richard L; Sappington, Thomas W

    2009-08-01

    European corn borer, Ostrinia nubilalis (Hübner), adults were sampled at 13 sites along two perpendicular 720-km transects intersecting in central Iowa and for the following two generations at four of the same sites separated by 240 km in the cardinal directions. More than 50 moths from each sample location and time were genotyped at eight microsatellite loci. Spatial analyses indicated that there is no spatial genetic structuring between European corn borer populations sampled 720 km apart at the extremes of the transects and no pattern of genetic isolation by distance at that geographic scale. Although these results suggest high gene flow over the spatial scale tested, it is possible that populations have not had time to diverge since the central Corn Belt was invaded by this insect approximately 60 yr ago. However, temporal analyses of genetic changes in single locations over time suggest that the rate of migration is indeed very high. The results of this study suggest that the geographic dimensions of European corn borer populations are quite large, indicating that monitoring for resistance to transgenic Bt corn at widely separated distances is justified, at least in the central Corn Belt. High gene flow further implies that resistance to Bt corn may be slow to evolve, but once it does develop, it may spread geographically with such speed that mitigation strategies will have to be implemented quickly to be effective.

  6. A new genome scan for primary nonsyndromic vesicoureteric reflux emphasizes high genetic heterogeneity and shows linkage and association with various genes already implicated in urinary tract development

    PubMed Central

    Darlow, J M; Dobson, M G; Darlay, R; Molony, C M; Hunziker, M; Green, A J; Cordell, H J; Puri, P; Barton, D E

    2014-01-01

    Primary vesicoureteric reflux (VUR), the retrograde flow of urine from the bladder toward the kidneys, results from a developmental anomaly of the vesicoureteric valve mechanism, and is often associated with other urinary tract anomalies. It is the most common urological problem in children, with an estimated prevalence of 1–2%, and is a major cause of hypertension in childhood and of renal failure in childhood or adult life. We present the results of a genetic linkage and association scan using 900,000 markers. Our linkage results show a large number of suggestive linkage peaks, with different results in two groups of families, suggesting that VUR is even more genetically heterogeneous than previously imagined. The only marker achieving P < 0.02 for linkage in both groups of families is 270 kb from EMX2. In three sibships, we found recessive linkage to KHDRBS3, previously reported in a Somali family. In another family we discovered sex-reversal associated with VUR, implicating PRKX, for which there was weak support for dominant linkage in the overall data set. Several other candidate genes are suggested by our linkage or association results, and four of our linkage peaks are within copy-number variants recently found to be associated with renal hypodysplasia. Undoubtedly there are many genes related to VUR. Our study gives support to some loci suggested by earlier studies as well as suggesting new ones, and provides numerous indications for further investigations. PMID:24498626

  7. An alphabaculovirus isolated from dead Lymantria dispar larvae shows high genetic similarity to baculovirus previously isolated from Lymantria monacha - An example of adaptation to a new host.

    PubMed

    Rabalski, Lukasz; Krejmer-Rabalska, Martyna; Skrzecz, Iwona; Wasag, Bartosz; Szewczyk, Boguslaw

    2016-09-01

    A new isolate of baculovirus, Lymantria dispar multiple nucleopolyhedrovirus-BNP (LdMNPV-BNP), was found in dead gypsy moth (L. dispar) caterpillars collected in the Biebrzanski National Park in Poland. Here, we examined its biological activity, structure, genetic content and phylogeny. Multiple nucleocapsids of LdMNPV-BNP are enveloped together in 2-26 virions embedded in occluded bodies (OBs) very similar to the OBs previously described in viruses infecting Lymantriinae. This isolate kills pest larvae in a relatively short time (LT50 of approximately 9days for a dose of 2×10(7)OBs/ml), highlighting the possibility for its use as a biopesticide. Next-generation sequencing of LdMNPV-BNP revealed gene content (e.g. DNA photolyase) that is not present in any LdMNPV isolate sequenced to date. The genome is 157,270 base pairs long and has a notably lower G+C content in comparison to other LdMNPVs (50.3% G+C content compared to an average of 57.4% among other LdMNPVs). According to our phylogenetic analysis based on 37 core genes, LdMNPV-BNP is a member of group II alphabaculoviruses, which are closely related to LdMNPV and LyxyMNPV (Lymantria xylina multiple nucleopolyhedrovirus). Molecular evolution inference based on the partial sequence of lef-8, lef-9 and polh genes shows that LdMNPV-BNP and isolates of Lymantria monacha nucleopolyhedrovirus (LymoNPV) may share a very recent common ancestor or be isolates of the same virus species. LdMNPV-BNP, like other baculoviruses, could be beneficial as an active component of biopesticides that can be used during forest integrated pest management. PMID:27451947

  8. Variation in the peacock's train shows a genetic component.

    PubMed

    Petrie, Marion; Cotgreave, Peter; Pike, Thomas W

    2009-01-01

    Female peafowl (Pavo cristatus) show a strong mating preference for males with elaborate trains. This, however, poses something of a paradox because intense directional selection should erode genetic variation in the males' trains, so that females will no longer benefit by discriminating among males on the basis of these traits. This situation is known as the 'lek paradox', and leads to the theoretical expectation of low heritability in the peacock's train. We used two independent breeding experiments, involving a total of 42 sires and 86 of their male offspring, to estimate the narrow sense heritabilities of male ornaments and other morphometric traits. Contrary to expectation, we found significant levels of heritability in a trait known to be used by females during mate choice (train length), while no significant heritabilities were evident for other, non-fitness related morphological traits (tarsus length, body weight or spur length). This study adds to the building body of evidence that high levels of additive genetic variance can exist in secondary sexual traits under directional selection, but further emphasizes the main problem of what maintains this variation.

  9. Variation in the peacock's train shows a genetic component.

    PubMed

    Petrie, Marion; Cotgreave, Peter; Pike, Thomas W

    2009-01-01

    Female peafowl (Pavo cristatus) show a strong mating preference for males with elaborate trains. This, however, poses something of a paradox because intense directional selection should erode genetic variation in the males' trains, so that females will no longer benefit by discriminating among males on the basis of these traits. This situation is known as the 'lek paradox', and leads to the theoretical expectation of low heritability in the peacock's train. We used two independent breeding experiments, involving a total of 42 sires and 86 of their male offspring, to estimate the narrow sense heritabilities of male ornaments and other morphometric traits. Contrary to expectation, we found significant levels of heritability in a trait known to be used by females during mate choice (train length), while no significant heritabilities were evident for other, non-fitness related morphological traits (tarsus length, body weight or spur length). This study adds to the building body of evidence that high levels of additive genetic variance can exist in secondary sexual traits under directional selection, but further emphasizes the main problem of what maintains this variation. PMID:17922297

  10. Trematode hemoglobins show exceptionally high oxygen affinity.

    PubMed

    Kiger, L; Rashid, A K; Griffon, N; Haque, M; Moens, L; Gibson, Q H; Poyart, C; Marden, M C

    1998-08-01

    Ligand binding studies were made with hemoglobin (Hb) isolated from trematode species Gastrothylax crumenifer (Gc), Paramphistomum epiclitum (Pe), Explanatum explanatum (Ee), parasitic worms of water buffalo Bubalus bubalis, and Isoparorchis hypselobagri (Ih) parasitic in the catfish Wallago attu. The kinetics of oxygen and carbon monoxide binding show very fast association rates. Whereas oxygen can be displaced on a millisecond time scale from human Hb at 25 degrees C, the dissociation of oxygen from trematode Hb may require a few seconds to over 20 s (for Hb Pe). Carbon monoxide dissociation is faster, however, than for other monomeric hemoglobins or myoglobins. Trematode hemoglobins also show a reduced rate of autoxidation; the oxy form is not readily oxidized by potassium ferricyanide, indicating that only the deoxy form reacts rapidly with this oxidizing agent. Unlike most vertebrate Hbs, the trematodes have a tyrosine residue at position E7 instead of the usual distal histidine. As for Hb Ascaris, which also displays a high oxygen affinity, the trematodes have a tyrosine in position B10; two H-bonds to the oxygen molecule are thought to be responsible for the very high oxygen affinity. The trematode hemoglobins display a combination of high association rates and very low dissociation rates, resulting in some of the highest oxygen affinities ever observed.

  11. High Points of Human Genetics

    ERIC Educational Resources Information Center

    Stern, Curt

    1975-01-01

    Discusses such high points of human genetics as the study of chromosomes, somatic cell hybrids, the population formula: the Hardy-Weinberg Law, biochemical genetics, the single-active X Theory, behavioral genetics and finally how genetics can serve humanity. (BR)

  12. Greenlandic Inuit show genetic signatures of diet and climate adaptation.

    PubMed

    Fumagalli, Matteo; Moltke, Ida; Grarup, Niels; Racimo, Fernando; Bjerregaard, Peter; Jørgensen, Marit E; Korneliussen, Thorfinn S; Gerbault, Pascale; Skotte, Line; Linneberg, Allan; Christensen, Cramer; Brandslund, Ivan; Jørgensen, Torben; Huerta-Sánchez, Emilia; Schmidt, Erik B; Pedersen, Oluf; Hansen, Torben; Albrechtsen, Anders; Nielsen, Rasmus

    2015-09-18

    The indigenous people of Greenland, the Inuit, have lived for a long time in the extreme conditions of the Arctic, including low annual temperatures, and with a specialized diet rich in protein and fatty acids, particularly omega-3 polyunsaturated fatty acids (PUFAs). A scan of Inuit genomes for signatures of adaptation revealed signals at several loci, with the strongest signal located in a cluster of fatty acid desaturases that determine PUFA levels. The selected alleles are associated with multiple metabolic and anthropometric phenotypes and have large effect sizes for weight and height, with the effect on height replicated in Europeans. By analyzing membrane lipids, we found that the selected alleles modulate fatty acid composition, which may affect the regulation of growth hormones. Thus, the Inuit have genetic and physiological adaptations to a diet rich in PUFAs.

  13. Pentamycin shows high efficacy against Trichomonas vaginalis.

    PubMed

    Kranzler, Markus; Syrowatka, Michael; Leitsch, David; Winnips, Cornelis; Walochnik, Julia

    2015-04-01

    Trichomonas vaginalis is the causative agent of the venereal disease trichomoniasis, which is the most frequent non-viral sexually transmitted disease worldwide. Since the 1960s, metronidazole has been the standard treatment, however an increasing number of cases with metronidazole-resistant strains is being reported. In this study, pentamycin, a polyene antibiotic, was tested for its in vitro efficacy against T. vaginalis using four strains with different metronidazole susceptibilities. It was shown that pentamycin is highly active against T. vaginalis and that the effect is prompt and independent of underlying metronidazole resistance. The effective concentrations (EC values) after 1 h of treatment were in the range 1.74-2.62 μg/mL (EC50) and 4.91-6.51 μg/mL (EC90). Total eradication of trichomonads (EC100) was achieved in all strains by treatment with 15 μg/mL (22 μM) for 1 h or with ≥1 μg/mL (≥1.5 μM) for 24 h. Long-term cultivation (12 months) under permanent drug pressure did not induce stable resistance against pentamycin in any of the strains tested. Pentamycin has been approved for intravaginal use and is a promising candidate for the topical treatment of trichomoniasis.

  14. New genetic and linguistic analyses show ancient human influence on baobab evolution and distribution in Australia.

    PubMed

    Rangan, Haripriya; Bell, Karen L; Baum, David A; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A; Murphy, Daniel J

    2015-01-01

    This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia.

  15. New genetic and linguistic analyses show ancient human influence on baobab evolution and distribution in Australia.

    PubMed

    Rangan, Haripriya; Bell, Karen L; Baum, David A; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A; Murphy, Daniel J

    2015-01-01

    This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia. PMID:25830225

  16. New Genetic and Linguistic Analyses Show Ancient Human Influence on Baobab Evolution and Distribution in Australia

    PubMed Central

    Rangan, Haripriya; Bell, Karen L.; Baum, David A.; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A.; Murphy, Daniel J.

    2015-01-01

    This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia. PMID:25830225

  17. 5. View showing Crooked River High Bridge in background and ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. View showing Crooked River High Bridge in background and Ralph Modjeski railroad bridge in foreground - Crooked River High Bridge, Spanning Crooked River Gorge at Dalles-California Highway, Terrebonne, Deschutes County, OR

  18. Slc:Wistar outbred rats show close genetic similarity with F344 inbred rats.

    PubMed

    Nakanishi, Satoshi; Serikawa, Tadao; Kuramoto, Takashi

    2015-01-01

    Although Slc:Wistar rats are used widely in biomedical research as outbred rats, close similarities in growth curves, survival rates, and immunological and biochemical phenotypes have been reported between Slc:Wistar and F344 inbred rats. We reported previously that nine genetic variations that were fixed in Slc:Wistar rats had identical genotypes in F344 rats. Here, we examined the genetic characteristics of Slc:Wistar rats using 27 simple-sequence length polymorphism (SSLP) markers and compared them with other Wistar stocks available in Japan and with some F344 strains. Among 27 SSLP loci, 23 (85%) were fixed in the Slc:Wistar rats, which was the highest among the other Wistar stocks. The 23 fixed loci shared identical genotypes with corresponding loci in F344 rats. Further, the predominant allele types in the unfixed loci had allele frequencies as high as 80%, and these alleles were identical in the F344 rats. When the nine genetic variations reported previously are added, a total of 32 (89%) out of the 36 loci examined were fixed and identical in the Slc:Wistar and F344 rat genomes. These findings indicate the low genetic variation in Slc:Wistar rats and the high genetic similarity between the Slc:Wistar and F344 inbred rats. This study demonstrates the importance of characterizing outbred rats and the need to pay ample attention to the genetic characteristics the Slc:Wistar rats for their proper use.

  19. Amphibian DNA shows marked genetic structure and tracks pleistocene climate change in northeastern Brazil.

    PubMed

    Carnaval, Ana Carolina; Bates, John M

    2007-12-01

    The glacial refugia paradigm has been broadly applied to patterns of species dynamics and population diversification. However, recent geological studies have demonstrated striking Pleistocene climate changes in currently semiarid northeastern Brazil at time intervals much more frequent than the climatic oscillations associated with glacial and interglacial periods. These geomorphic data documented recurrent pulses of wet regimes in the past 210,000 years that correlate with climate anomalies affecting multiple continents. While analyzing DNA sequences of two mitochondrial genes (cytochrome b and NADH-dehydrogenase subunit 2) and one nuclear marker (cellular-myelocytomatosis proto-oncogene) in the forest-associated frogs Proceratophrys boiei and Ischnocnema gr. ramagii, we found evidence of biological responses consistent with these pluvial maxima events. Sampled areas included old, naturally isolated forest enclaves within the semiarid Caatinga, as well as recent man-made fragments of humid coastal Atlantic forest. Results show that mtDNA lineages in enclave populations are monophyletic or nearly so, whereas nonenclave populations are polyphyletic and more diverse. The studied taxa show evidence of demographic expansions at times that match phases of pluvial maxima inferred from geological data. Divergence times between several populations fall within comparatively drier intervals suggested by geomorphology. Mitochondrial and nuclear data show local populations to be genetically structured, with some high levels of differentiation that suggest the need of further taxonomic work.

  20. Molecular genetic analysis of oligodendroglial tumors shows preferential allelic deletions on 19q and 1p.

    PubMed Central

    Reifenberger, J.; Reifenberger, G.; Liu, L.; James, C. D.; Wechsler, W.; Collins, V. P.

    1994-01-01

    The molecular genetic alterations of oligodendroglial tumors and mixed gliomas of the central nervous system were studied in a series of 37 cases (8 oligodendrogliomas, 13 anaplastic oligodendrogliomas, 8 oligoastrocytomas, and 8 anaplastic oligoastrocytomas). A total of 180 polymorphic loci and 5 nonpolymorphic gene loci, distributed over all chromosomes, were examined by restriction fragment length polymorphism analysis. Loss of heterozygosity was most frequently observed for loci on 19q with a commonly deleted region at 19q13.2-q13.4 distal to the CYP2a gene and proximal to the D19S22 locus. The incidence of allelic loss on 19q was particularly high (81%) in oligodendroglial tumors and equal to 31% in mixed gliomas. More than 75% of the tumors with allelic deletions on 19q also showed loss of heterozygosity for loci on 1p with one tumor showing only loss of alleles distal to the NGFB gene (1p13-pter). Seven (19%) tumors had lost alleles from 17p with the deleted region including the TP53 tumor suppressor gene in all cases. Sequencing of the TP53 transcripts from exons 2 to 10, however, did not reveal mutations of the remaining allele in any of these tumors. Anaplastic oligodendrogliomas and anaplastic oligoastrocytomas demonstrated an increased incidence of additional allelic losses involving most frequently chromosomes 9p and 10. Gene amplification was detected in two anaplastic tumors, affecting the epidermal growth factor receptor gene in both cases, with additional amplification of the renin gene at 1q32 in one of these cases. In total our results indicate both differences and similarities between the molecular genetic alterations in tumors with oligodendroglial and astrocytic differentiation. The loss of genetic information from 19q and 1p as well as the rarity of TP53 mutations in oligodendroglial tumors suggests that the early events in their oncogenesis are distinct from those associated with astrocytic tumors. However, similarities are indicated by the

  1. Added value measures in education show genetic as well as environmental influence.

    PubMed

    Haworth, Claire M A; Asbury, Kathryn; Dale, Philip S; Plomin, Robert

    2011-02-02

    Does achievement independent of ability or previous attainment provide a purer measure of the added value of school? In a study of 4000 pairs of 12-year-old twins in the UK, we measured achievement with year-long teacher assessments as well as tests. Raw achievement shows moderate heritability (about 50%) and modest shared environmental influences (25%). Unexpectedly, we show that for indices of the added value of school, genetic influences remain moderate (around 50%), and the shared (school) environment is less important (about 12%). The pervasiveness of genetic influence in how and how much children learn is compatible with an active view of learning in which children create their own educational experiences in part on the basis of their genetic propensities.

  2. 13. VIEW, LOOKING WEST FROM LEFT TO RIGHT, SHOWING HIGH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    13. VIEW, LOOKING WEST FROM LEFT TO RIGHT, SHOWING HIGH PRESSURE AIR FLASK ROOM AND PUMP ROOM - U.S. Naval Submarine Base, New London Submarine Escape Training Tank, Albacore & Darter Roads, Groton, New London County, CT

  3. 20. SOUTH ELEVATION, SHOWING ORIGINAL HIGH VOLTAGE GETAWAYS. SCE negative ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    20. SOUTH ELEVATION, SHOWING ORIGINAL HIGH VOLTAGE GETAWAYS. SCE negative no. 10340, November 1, 1923. Photograph by G. Haven Bishop. - Santa Ana River Hydroelectric System, SAR-3 Powerhouse, San Bernardino National Forest, Redlands, San Bernardino County, CA

  4. Genetics Show Current Decline and Pleistocene Expansion in Northern Spotted Owls

    USGS Publications Warehouse

    Funk, W. Chris; Forsman, Eric D.; Mullins, Thomas D.; Haig, Susan M.

    2008-01-01

    The northern spotted owl (Strix occidentalis caurina) is one of the most controversial threatened subspecies ever listed under the U.S. Endangered Species Act. Because of concern for persistence of the subspecies, logging on Federal lands in the U.S. Pacific Northwest was dramatically reduced under the Northwest Forest Plan in 1994. Despite protection of its remaining forest habitat, recent field studies show continued demographic declines of northern spotted owls. One potential threat to northern spotted owls that has not yet been shown is loss of genetic variation from population bottlenecks that can increase inbreeding depression and decrease adaptive potential. Here, we show recent genetic bottlenecks in northern spotted owls using a large genetic dataset (352 individuals from across the subspecies' range and 11 microsatellite loci). The signature of bottlenecks was strongest in Washington State, in agreement with field data. Interestingly, we also found a genetic signature of Pleistocene expansion in the same study areas where recent bottlenecks were shown. Our results provide independent evidence that northern spotted owls have recently declined, and suggest that loss of genetic variation is an emerging threat to the subspecies' persistence. Reduced effective population size (Ne), shown here in addition to field evidence for demographic decline, highlights the increasing vulnerability of this bird to extinction.

  5. 26. VIEW OF PUMP ROOM, SHOWING PORTIONS OF HIGH PRESSURE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    26. VIEW OF PUMP ROOM, SHOWING PORTIONS OF HIGH PRESSURE AIR SYSTEM AT LEFT AND CENTER AND OVERFLOW STORAGE TANK AT RIGHT, LOOKING NORTHWEST - U.S. Naval Submarine Base, New London Submarine Escape Training Tank, Albacore & Darter Roads, Groton, New London County, CT

  6. 23. VIEW SHOWING HIGH WATER IN ROWDY CREEK WITH COLLAPSED ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    23. VIEW SHOWING HIGH WATER IN ROWDY CREEK WITH COLLAPSED SECTION IN CREEK, LOOKING NORTH TO SOUTH FROM END OF UNCOLLAPSED SECTION Winter 1931-32 - Rowdy Creek Bridge, Spanning Rowdy Creek at Fred Haight Drive, Smith River, Del Norte County, CA

  7. Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics.

    PubMed Central

    Poloni, E S; Semino, O; Passarino, G; Santachiara-Benerecetti, A S; Dupanloup, I; Langaney, A; Excoffier, L

    1997-01-01

    Numerous population samples from around the world have been tested for Y chromosome-specific p49a,f/TaqI restriction polymorphisms. Here we review the literature as well as unpublished data on Y-chromosome p49a,f/TaqI haplotypes and provide a new nomenclature unifying the notations used by different laboratories. We use this large data set to study worldwide genetic variability of human populations for this paternally transmitted chromosome segment. We observe, for the Y chromosome, an important level of population genetics structure among human populations (FST = .230, P < .001), mainly due to genetic differences among distinct linguistic groups of populations (FCT = .246, P < .001). A multivariate analysis based on genetic distances between populations shows that human population structure inferred from the Y chromosome corresponds broadly to language families (r = .567, P < .001), in agreement with autosomal and mitochondrial data. Times of divergence of linguistic families, estimated from their internal level of genetic differentiation, are fairly concordant with current archaeological and linguistic hypotheses. Variability of the p49a,f/TaqI polymorphic marker is also significantly correlated with the geographic location of the populations (r = .613, P < .001), reflecting the fact that distinct linguistic groups generally also occupy distinct geographic areas. Comparison of Y-chromosome and mtDNA RFLPs in a restricted set of populations shows a globally high level of congruence, but it also allows identification of unequal maternal and paternal contributions to the gene pool of several populations. PMID:9346874

  8. Introducing High School Students to Human Genetics.

    ERIC Educational Resources Information Center

    Haddow, Paula K.; And Others

    1988-01-01

    Considers six key concepts in human genetics in a question-and-answer format designed to help guide students to an understanding of the concept. Lists eight workshops in human genetics for high school biology teachers and four curriculum material packages on human genetics. (CW)

  9. Hanseniaspora uvarum from Winemaking Environments Show Spatial and Temporal Genetic Clustering

    PubMed Central

    Albertin, Warren; Setati, Mathabatha E.; Miot-Sertier, Cécile; Mostert, Talitha T.; Colonna-Ceccaldi, Benoit; Coulon, Joana; Girard, Patrick; Moine, Virginie; Pillet, Myriam; Salin, Franck; Bely, Marina; Divol, Benoit; Masneuf-Pomarede, Isabelle

    2016-01-01

    Hanseniaspora uvarum is one of the most abundant yeast species found on grapes and in grape must, at least before the onset of alcoholic fermentation (AF) which is usually performed by Saccharomyces species. The aim of this study was to characterize the genetic and phenotypic variability within the H. uvarum species. One hundred and fifteen strains isolated from winemaking environments in different geographical origins were analyzed using 11 microsatellite markers and a subset of 47 strains were analyzed by AFLP. H. uvarum isolates clustered mainly on the basis of their geographical localization as revealed by microsatellites. In addition, a strong clustering based on year of isolation was evidenced, indicating that the genetic diversity of H. uvarum isolates was related to both spatial and temporal variations. Conversely, clustering analysis based on AFLP data provided a different picture with groups showing no particular characteristics, but provided higher strain discrimination. This result indicated that AFLP approaches are inadequate to establish the genetic relationship between individuals, but allowed good strain discrimination. At the phenotypic level, several extracellular enzymatic activities of enological relevance (pectinase, chitinase, protease, β-glucosidase) were measured but showed low diversity. The impact of environmental factors of enological interest (temperature, anaerobia, and copper addition) on growth was also assessed and showed poor variation. Altogether, this work provided both new analytical tool (microsatellites) and new insights into the genetic and phenotypic diversity of H. uvarum, a yeast species that has previously been identified as a potential candidate for co-inoculation in grape must, but whose intraspecific variability had never been fully assessed. PMID:26834719

  10. Hanseniaspora uvarum from Winemaking Environments Show Spatial and Temporal Genetic Clustering.

    PubMed

    Albertin, Warren; Setati, Mathabatha E; Miot-Sertier, Cécile; Mostert, Talitha T; Colonna-Ceccaldi, Benoit; Coulon, Joana; Girard, Patrick; Moine, Virginie; Pillet, Myriam; Salin, Franck; Bely, Marina; Divol, Benoit; Masneuf-Pomarede, Isabelle

    2015-01-01

    Hanseniaspora uvarum is one of the most abundant yeast species found on grapes and in grape must, at least before the onset of alcoholic fermentation (AF) which is usually performed by Saccharomyces species. The aim of this study was to characterize the genetic and phenotypic variability within the H. uvarum species. One hundred and fifteen strains isolated from winemaking environments in different geographical origins were analyzed using 11 microsatellite markers and a subset of 47 strains were analyzed by AFLP. H. uvarum isolates clustered mainly on the basis of their geographical localization as revealed by microsatellites. In addition, a strong clustering based on year of isolation was evidenced, indicating that the genetic diversity of H. uvarum isolates was related to both spatial and temporal variations. Conversely, clustering analysis based on AFLP data provided a different picture with groups showing no particular characteristics, but provided higher strain discrimination. This result indicated that AFLP approaches are inadequate to establish the genetic relationship between individuals, but allowed good strain discrimination. At the phenotypic level, several extracellular enzymatic activities of enological relevance (pectinase, chitinase, protease, β-glucosidase) were measured but showed low diversity. The impact of environmental factors of enological interest (temperature, anaerobia, and copper addition) on growth was also assessed and showed poor variation. Altogether, this work provided both new analytical tool (microsatellites) and new insights into the genetic and phenotypic diversity of H. uvarum, a yeast species that has previously been identified as a potential candidate for co-inoculation in grape must, but whose intraspecific variability had never been fully assessed. PMID:26834719

  11. Highly reflective reasoners show no signs of belief inhibition.

    PubMed

    Svedholm-Häkkinen, Annika M

    2015-01-01

    The processes underlying individual differences in reasoning performance are not entirely understood. What do people who do well on reasoning tasks where beliefs and logic conflict do differently from other people? Because abundant evidence shows that even poorer reasoners detect these conflicts, it has been suggested that individual differences in reasoning performance arise from inhibition failures later in the reasoning process. The present paper argues that a minority of highly skilled reasoners may deviate from this general reasoning process from an early stage. Two studies investigated signs of belief inhibition using a lexical access paradigm (Study 1) and a negative priming paradigm (Study 2). Study 1 showed that while other people exhibited signs of belief inhibition following a belief-logic conflict, people with the highest disposition for cognitive reflection did not. In Study 2, this finding was replicated and similar results were also obtained when comparing groups with higher and lower general cognitive ability. Two possible explanations are discussed. The reasoners with a highly reflective cognitive style or high general cognitive ability may have engaged and inhibited belief processing but if so, they may have been exceptionally efficient at recovering from it, wherefore no belief inhibition effects were found. An alternative account is that these reasoners started Type 2 processing directly, without first engaging in and then inhibiting belief-based processing. Under either explanation, the results indicate that individual differences in reasoning may partly arise from differences that occur early in the reasoning process.

  12. Highly reflective reasoners show no signs of belief inhibition.

    PubMed

    Svedholm-Häkkinen, Annika M

    2015-01-01

    The processes underlying individual differences in reasoning performance are not entirely understood. What do people who do well on reasoning tasks where beliefs and logic conflict do differently from other people? Because abundant evidence shows that even poorer reasoners detect these conflicts, it has been suggested that individual differences in reasoning performance arise from inhibition failures later in the reasoning process. The present paper argues that a minority of highly skilled reasoners may deviate from this general reasoning process from an early stage. Two studies investigated signs of belief inhibition using a lexical access paradigm (Study 1) and a negative priming paradigm (Study 2). Study 1 showed that while other people exhibited signs of belief inhibition following a belief-logic conflict, people with the highest disposition for cognitive reflection did not. In Study 2, this finding was replicated and similar results were also obtained when comparing groups with higher and lower general cognitive ability. Two possible explanations are discussed. The reasoners with a highly reflective cognitive style or high general cognitive ability may have engaged and inhibited belief processing but if so, they may have been exceptionally efficient at recovering from it, wherefore no belief inhibition effects were found. An alternative account is that these reasoners started Type 2 processing directly, without first engaging in and then inhibiting belief-based processing. Under either explanation, the results indicate that individual differences in reasoning may partly arise from differences that occur early in the reasoning process. PMID:25499057

  13. Mixtures of thermostable enzymes show high performance in biomass saccharification.

    PubMed

    Kallioinen, Anne; Puranen, Terhi; Siika-aho, Matti

    2014-07-01

    Optimal enzyme mixtures of six Trichoderma reesei enzymes and five thermostable enzyme components were developed for the hydrolysis of hydrothermally pretreated wheat straw, alkaline oxidised sugar cane bagasse and steam-exploded bagasse by statistically designed experiments. Preliminary studies to narrow down the optimization parameters showed that a cellobiohydrolase/endoglucanase (CBH/EG) ratio of 4:1 or higher of thermostable enzymes gave the maximal CBH-EG synergy in the hydrolysis of hydrothermally pretreated wheat straw. The composition of optimal enzyme mixtures depended clearly on the substrate and on the enzyme system studied. The optimal enzyme mixture of thermostable enzymes was dominated by Cel7A and required a relatively high amount of xylanase, whereas with T. reesei enzymes, the high proportion of Cel7B appeared to provide the required xylanase activity. The main effect of the pretreatment method was that the required proportion of xylanase was higher and the proportion of Cel7A lower in the optimized mixture for hydrolysis of alkaline oxidised bagasse than steam-exploded bagasse. In prolonged hydrolyses, less Cel7A was generally required in the optimal mixture. Five-component mixtures of thermostable enzymes showed comparable hydrolysis yields to those of commercial enzyme mixtures.

  14. A UV–Induced Genetic Network Links the RSC Complex to Nucleotide Excision Repair and Shows Dose-Dependent Rewiring

    PubMed Central

    Srivas, Rohith; Costelloe, Thomas; Carvunis, Anne-Ruxandra; Sarkar, Sovan; Malta, Erik; Sun, Su Ming; Pool, Marijke; Licon, Katherine; van Welsem, Tibor; van Leeuwen, Fred; McHugh, Peter J.; van Attikum, Haico; Ideker, Trey

    2014-01-01

    SUMMARY Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER) with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. Integration of genetic data with physical interaction networks identified a global map of 89 UV-induced functional interactions amongst 62 protein complexes, including a number of links between the RSC complex and several NER factors. We show that RSC is recruited to both silenced and transcribed loci following UV damage where it facilitates efficient repair by promoting nucleosome remodeling. Finally, a comparison of the response to high versus low levels of UV shows that the degree of genetic rewiring correlates with dose of UV and reveals a network of dose-specific interactions. This study makes available a large resource of UV-induced interactions, and it illustrates a methodology for identifying dose-dependent interactions based on quantitative shifts in genetic networks. PMID:24360959

  15. A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring.

    PubMed

    Srivas, Rohith; Costelloe, Thomas; Carvunis, Anne-Ruxandra; Sarkar, Sovan; Malta, Erik; Sun, Su Ming; Pool, Marijke; Licon, Katherine; van Welsem, Tibor; van Leeuwen, Fred; McHugh, Peter J; van Attikum, Haico; Ideker, Trey

    2013-12-26

    Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER) with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. Integration of genetic data with physical interaction networks identified a global map of 89 UV-induced functional interactions among 62 protein complexes, including a number of links between the RSC complex and several NER factors. We show that RSC is recruited to both silenced and transcribed loci following UV damage where it facilitates efficient repair by promoting nucleosome remodeling. Finally, a comparison of the response to high versus low levels of UV shows that the degree of genetic rewiring correlates with dose of UV and reveals a network of dose-specific interactions. This study makes available a large resource of UV-induced interactions, and it illustrates a methodology for identifying dose-dependent interactions based on quantitative shifts in genetic networks.

  16. Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity.

    PubMed

    Martin, William J; McCallum, John; Shigyo, Masayoshi; Jakse, Jernej; Kuhl, Joseph C; Yamane, Naoko; Pither-Joyce, Meeghan; Gokce, Ali Fuat; Sink, Kenneth C; Town, Christopher D; Havey, Michael J

    2005-10-01

    The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses; however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map derived from the BYG15-23xAC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants. PMID:16025250

  17. Histidine decarboxylase knockout mice, a genetic model of Tourette syndrome, show repetitive grooming after induced fear

    PubMed Central

    Xu, Meiyu; Li, Lina; Ohtsu, Hiroshi; Pittenger, Christopher

    2015-01-01

    Tics, such as are seen in Tourette syndrome (TS), are common and can cause profound morbidity, but they are poorly understood. Tics are potentiated by psychostimulants, stress, and sleep deprivation. Mutations in the gene histidine decarboxylase (Hdc) have been implicated as a rare genetic cause of TS, and Hdc knockout mice have been validated as a genetic model that recapitulates phenomenological and pathophysiological aspects of the disorder. Tic-like stereotypies in this model have not been observed at baseline but emerge after acute challenge with the psychostimulant D-amphetamine. We tested the ability of an acute stressor to stimulate stereotypies in this model, using tone fear conditioning. Hdc knockout mice acquired conditioned fear normally, as manifest by freezing during the presentation of a tone 48 hours after it had been paired with a shock. During the 30 minutes following tone presentation they showed increased grooming. Heterozygotes exhibited normal freezing and intermediate grooming. These data validate a new paradigm for the examination of tic-like stereotypies in animals without pharmacological challenge and enhance the face validity of the Hdc knockout mouse as a pathophysiologically grounded model of tic disorders. PMID:25841792

  18. Histidine decarboxylase knockout mice, a genetic model of Tourette syndrome, show repetitive grooming after induced fear.

    PubMed

    Xu, Meiyu; Li, Lina; Ohtsu, Hiroshi; Pittenger, Christopher

    2015-05-19

    Tics, such as are seen in Tourette syndrome (TS), are common and can cause profound morbidity, but they are poorly understood. Tics are potentiated by psychostimulants, stress, and sleep deprivation. Mutations in the gene histidine decarboxylase (Hdc) have been implicated as a rare genetic cause of TS, and Hdc knockout mice have been validated as a genetic model that recapitulates phenomenological and pathophysiological aspects of the disorder. Tic-like stereotypies in this model have not been observed at baseline but emerge after acute challenge with the psychostimulant d-amphetamine. We tested the ability of an acute stressor to stimulate stereotypies in this model, using tone fear conditioning. Hdc knockout mice acquired conditioned fear normally, as manifested by freezing during the presentation of a tone 48h after it had been paired with a shock. During the 30min following tone presentation, knockout mice showed increased grooming. Heterozygotes exhibited normal freezing and intermediate grooming. These data validate a new paradigm for the examination of tic-like stereotypies in animals without pharmacological challenge and enhance the face validity of the Hdc knockout mouse as a pathophysiologically grounded model of tic disorders.

  19. Chronic Rhinosinusitis Patients Show Accumulation of Genetic Variants in PARS2

    PubMed Central

    Henmyr, Viktor; Lind-Halldén, Christina; Halldén, Christer; Säll, Torbjörn; Carlberg, Daniel; Bachert, Claus; Cardell, Lars-Olaf

    2016-01-01

    Genetic studies of chronic rhinosinusitis (CRS) have identified a total of 53 CRS-associated SNPs that were subsequently evaluated for their reproducibility in a recent study. The rs2873551 SNP in linkage disequilibrium with PARS2 showed the strongest association signal. The present study aims to comprehensively screen for rare variants in PARS2 and evaluate for accumulation of such variants in CRS-patients. Sanger sequencing and long-range PCR were used to screen for rare variants in the putative promoter region and coding sequence of 310 CRS-patients and a total of 21 variants were detected. The mutation spectrum was then compared with data from European populations of the 1000Genomes project (EUR) and the Exome Aggregation Consortium (ExAC). The CRS population showed a significant surplus of low-frequency variants compared with ExAC data. Haplotype analysis of the region showed a significant excess of rare haplotypes in the CRS population compared to the EUR population. Two missense mutations were also genotyped in the 310 CRS patients and 372 CRS-negative controls, but no associations with the disease were found. This is the first re-sequencing study in CRS research and also the first study to show an association of rare variants with the disease. PMID:27348859

  20. The ARMC5 gene shows extensive genetic variance in primary macronodular adrenocortical hyperplasia

    PubMed Central

    Correa, Ricardo; Zilbermint, Mihail; Berthon, Annabel; Espiard, Stephanie; Batsis, Maria; Papadakis, Georgios Z.; Xekouki, Paraskevi; Lodish, Maya B.; Bertherat, Jerome; Faucz, Fabio R.; Stratakis, Constantine A.

    2015-01-01

    Objective Primary macronodular adrenal hyperplasia (PMAH) is a rare type of Cushing’s syndrome (CS) that results in increased cortisol production and bilateral enlargement of the adrenal glands. Recent work showed that the disease may be caused by germline and somatic mutations in the ARMC5 gene, a likely tumor-suppressor gene (TSG). We investigated 20 different adrenal nodules from one patient with PMAH for ARMC5 somatic sequence changes. Design All of the nodules where obtained from a single patient who underwent bilateral adrenalectomy. DNA was extracted by standard protocols and the ARMC5 sequence was determined by the Sanger method. Results Sixteen of 20 adrenocortical nodules harbored, in addition to what appeared to be the germline mutation, a second somatic variant. The p.Trp476* sequence change was present in all 20 nodules, as well as in normal tissue from the adrenal capsule, identifying it as the germline defect; each of the 16 other variants were found in different nodules: 6 were frame shift, 4 were missense, 3 were nonsense, and 1 was a splice site variation. Allelic losses were confirmed in 2 of the nodules. Conclusion This is the most genetic variance of the ARMC5 gene ever described in a single patient with PMAH: each of 16 adrenocortical nodules had a second new, “private”, and -in most cases- completely inactivating ARMC5 defect, in addition to the germline mutation. The data support the notion that ARMC5 is a TSG that needs a second, somatic hit, to mediate tumorigenesis leading to polyclonal nodularity; however, the driver of this extensive genetic variance of the second ARMC5 allele in adrenocortical tissue in the context of a germline defect and PMAH remains a mystery. PMID:26162405

  1. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

    PubMed

    Dubin, Manu J; Zhang, Pei; Meng, Dazhe; Remigereau, Marie-Stanislas; Osborne, Edward J; Paolo Casale, Francesco; Drewe, Philipp; Kahles, André; Jean, Geraldine; Vilhjálmsson, Bjarni; Jagoda, Joanna; Irez, Selen; Voronin, Viktor; Song, Qiang; Long, Quan; Rätsch, Gunnar; Stegle, Oliver; Clark, Richard M; Nordborg, Magnus

    2015-01-01

    Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation. PMID:25939354

  2. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

    PubMed Central

    Dubin, Manu J; Zhang, Pei; Meng, Dazhe; Remigereau, Marie-Stanislas; Osborne, Edward J; Paolo Casale, Francesco; Drewe, Philipp; Kahles, André; Jean, Geraldine; Vilhjálmsson, Bjarni; Jagoda, Joanna; Irez, Selen; Voronin, Viktor; Song, Qiang; Long, Quan; Rätsch, Gunnar; Stegle, Oliver; Clark, Richard M; Nordborg, Magnus

    2015-01-01

    Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation. DOI: http://dx.doi.org/10.7554/eLife.05255.001 PMID:25939354

  3. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

    PubMed Central

    Biddle, Jennifer F.; Fitz-Gibbon, Sorel; Schuster, Stephan C.; Brenchley, Jean E.; House, Christopher H.

    2008-01-01

    The subseafloor marine biosphere may be one of the largest reservoirs of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made by using whole-genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Mb of genetic material was sequenced from sediments at horizons 1, 16, 32, and 50 m below the seafloor. These depths include sediments from both primarily sulfate-reducing methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small-subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups. PMID:18650394

  4. High-Resolution Observations of a Filament showing Activated Barb

    NASA Astrophysics Data System (ADS)

    Joshi, Anand; Martin, Sara F.; Mathew, Shibu; Srivastava, Nandita

    2012-07-01

    Analysis of a filament showing an activated barb using observations from the Dutch Open Telescope (DOT) on 2010 August 20 are presented. The DOT takes Doppler images in Hα, among other wavelengths, in a region about 110 × 110 arcsec^{2} in area, at a cadence of 30~seconds. The offline image restoration technique of speckle reconstruction is applied to obtain diffraction limited images. The filament developed a new barb in 10~minutes, which disappeared within the next 35~minutes. Such a rapid formation and disappearance of a filament barb is unusual, and has not been reported earlier. Line-of-sight velocity maps were constructed from the Doppler images of the target filament. We observe flows in the filament spine towards the barb location prior to its formation, and flows in the barb towards the spine during its disappearance. Photospheric magnetograms from Heliospheric Magnetic Imager on board the Solar Dynamics Observatory, at a cadence of 45~seconds, were used to determine the changes in magnetic flux in the region surrounding the barb location. The variation of magnetic flux in this duration supports the view that barbs are rooted in minor magnetic polarity. Our analysis shows that barbs can be short-lived and formation and disappearance of the barb was associated with cancellation of magnetic flux.

  5. Enterococci from artisanal dairy products show high levels of adaptability.

    PubMed

    Carlos, Ana Rita; Santos, Jorge; Semedo-Lemsaddek, Teresa; Barreto-Crespo, Maria Teresa; Tenreiro, Rogério

    2009-02-15

    Enterococci are ubiquitous organisms able to promote both health (fermented food/probiotics) and illness (human/animal infections). Disturbingly, several enterococcal species commonly found in artisanal cheeses, such as Enterococcus faecalis and E. faecium, are being increasingly established as causes of infection, posing a problem for food safety. In this study enterococci from ewe's milk and cheese were compared to clinical and reference strains by growth in media simulating environmental colonization and infection sites: 2YT, BHI, skim milk, urine and rabbit serum at different pHs, NaCl concentrations and temperatures. Growth curves were obtained with Microbiology Workstation Bioscreen C and used to calculate relative indexes--RIs--(based on absorbance, lag phase and specific growth rate) for each strain and environmental condition. Similar or higher RIs were obtained for food strains growing in infection-related environments when compared to clinical ones, revealing their ability to adapt and grow in these conditions. A dendrogram built using Pearson's correlation coefficient and a PCA analysis clustered the strains regardless of their origin or species allocation, suggesting a strain-specific mode of growth and a high environmental adaptability of enterococcal strains. These evidences turn essential the evaluation of strains to be used as starters or probiotics.

  6. Thinking positively: The genetics of high intelligence

    PubMed Central

    Shakeshaft, Nicholas G.; Trzaskowski, Maciej; McMillan, Andrew; Krapohl, Eva; Simpson, Michael A.; Reichenberg, Avi; Cederlöf, Martin; Larsson, Henrik; Lichtenstein, Paul; Plomin, Robert

    2015-01-01

    High intelligence (general cognitive ability) is fundamental to the human capital that drives societies in the information age. Understanding the origins of this intellectual capital is important for government policy, for neuroscience, and for genetics. For genetics, a key question is whether the genetic causes of high intelligence are qualitatively or quantitatively different from the normal distribution of intelligence. We report results from a sibling and twin study of high intelligence and its links with the normal distribution. We identified 360,000 sibling pairs and 9000 twin pairs from 3 million 18-year-old males with cognitive assessments administered as part of conscription to military service in Sweden between 1968 and 2010. We found that high intelligence is familial, heritable, and caused by the same genetic and environmental factors responsible for the normal distribution of intelligence. High intelligence is a good candidate for “positive genetics” — going beyond the negative effects of DNA sequence variation on disease and disorders to consider the positive end of the distribution of genetic effects. PMID:25593376

  7. Genetic mapping shows intraspecific variation and transgressive segregation for caterpillar-induced aphid resistance in maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants in nature have inducible defenses that sometimes lead to targeted resistance against particular herbivores, but susceptibility to others. The metabolic diversity and genetic resources available for maize (Zea mays) make this a suitable system for a mechanistic study of within- species variati...

  8. Natural Selection and Evolution: Using Multimedia Slide Shows to Emphasize the Role of Genetic Variation

    ERIC Educational Resources Information Center

    Malone, Molly

    2012-01-01

    Most middle school students comprehend that organisms have adaptations that enable their survival and that successful adaptations prevail in a population over time. Yet they often miss that those bird beaks, moth-wing colors, or whatever traits are the result of random, normal genetic variations that just happen to confer a negative, neutral, or…

  9. That 70s show: regulation, evolution and development beyond molecular genetics.

    PubMed

    Suárez-Díaz Edna; García-Deister Vivette

    2015-01-01

    This paper argues that the "long 1970s" (1969-1983) is an important though often overlooked period in the development of a rich landscape in the research of metabolism, development, and evolution. The period is marked by: shrinking public funding of basic science, shifting research agendas in molecular biology, the incorporation of new phenomena and experimental tools from previous biological research at the molecular level, and the development of recombinant DNA techniques. Research was reoriented towards eukaryotic cells and development, and in particular towards "giant" RNA processing and transcription. We will here focus on three different models of developmental regulation published in that period: the two models of eukaryotic genetic regulation at the transcriptional level that were developed by Georgii P. Georgiev on the one hand, and by Roy Britten and Eric Davidson on the other; and the model of genetic sufficiency and evolution of regulatory genes proposed by Emile Zuckerkandl. These three bases illustrate the range of exploratory hypotheses that characterised the challenging landscape of gene regulation in the 1970s, a period that in hindsight can be labelled as transitional, between the biology at the laboratory bench of the preceding period, and the biology of genetic engineering and intensive data-driven research that followed.

  10. Genetic mapping shows intraspecific variation and transgressive segregation for caterpillar-induced aphid resistance in maize.

    PubMed

    Tzin, Vered; Lindsay, Penelope L; Christensen, Shawn A; Meihls, Lisa N; Blue, Levi B; Jander, Georg

    2015-11-01

    Plants in nature have inducible defences that sometimes lead to targeted resistance against particular herbivores, but susceptibility to others. The metabolic diversity and genetic resources available for maize (Zea mays) make this a suitable system for a mechanistic study of within-species variation in such plant-mediated interactions between herbivores. Beet armyworms (Spodoptera exigua) and corn leaf aphids (Rhopalosiphum maidis) are two naturally occurring maize herbivores with different feeding habits. Whereas chewing herbivore-induced methylation of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one glucoside (DIMBOA-Glc) to form 2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one glucoside (HDMBOA-Glc) promotes caterpillar resistance, lower DIMBOA-Glc levels favour aphid reproduction. Thus, caterpillar-induced DIMBOA-Glc methyltransferase activity in maize is predicted to promote aphid growth. To test this hypothesis, the impact of S. exigua feeding on R. maidis progeny production was assessed using seventeen genetically diverse maize inbred lines. Whereas aphid progeny production was increased by prior caterpillar feeding on lines B73, Ki11, Ki3 and Tx303, it decreased on lines Ky21, CML103, Mo18W and W22. Genetic mapping of this trait in a population of B73 × Ky21 recombinant inbred lines identified significant quantitative trait loci on maize chromosomes 1, 7 and 10. There is a transgressive segregation for aphid resistance, with the Ky21 alleles on chromosomes 1 and 7 and the B73 allele on chromosome 10 increasing aphid progeny production. The chromosome 1 QTL coincides with a cluster of three maize genes encoding benzoxazinoid O-methyltransferases that convert DIMBOA-Glc to HDMBOA-Glc. Gene expression studies and benzoxazinoid measurements indicate that S. exigua -induced responses in this pathway differentially affect R. maidis resistance in B73 and Ky21. PMID:26462033

  11. Genetic mapping shows intraspecific variation and transgressive segregation for caterpillar-induced aphid resistance in maize.

    PubMed

    Tzin, Vered; Lindsay, Penelope L; Christensen, Shawn A; Meihls, Lisa N; Blue, Levi B; Jander, Georg

    2015-11-01

    Plants in nature have inducible defences that sometimes lead to targeted resistance against particular herbivores, but susceptibility to others. The metabolic diversity and genetic resources available for maize (Zea mays) make this a suitable system for a mechanistic study of within-species variation in such plant-mediated interactions between herbivores. Beet armyworms (Spodoptera exigua) and corn leaf aphids (Rhopalosiphum maidis) are two naturally occurring maize herbivores with different feeding habits. Whereas chewing herbivore-induced methylation of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one glucoside (DIMBOA-Glc) to form 2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one glucoside (HDMBOA-Glc) promotes caterpillar resistance, lower DIMBOA-Glc levels favour aphid reproduction. Thus, caterpillar-induced DIMBOA-Glc methyltransferase activity in maize is predicted to promote aphid growth. To test this hypothesis, the impact of S. exigua feeding on R. maidis progeny production was assessed using seventeen genetically diverse maize inbred lines. Whereas aphid progeny production was increased by prior caterpillar feeding on lines B73, Ki11, Ki3 and Tx303, it decreased on lines Ky21, CML103, Mo18W and W22. Genetic mapping of this trait in a population of B73 × Ky21 recombinant inbred lines identified significant quantitative trait loci on maize chromosomes 1, 7 and 10. There is a transgressive segregation for aphid resistance, with the Ky21 alleles on chromosomes 1 and 7 and the B73 allele on chromosome 10 increasing aphid progeny production. The chromosome 1 QTL coincides with a cluster of three maize genes encoding benzoxazinoid O-methyltransferases that convert DIMBOA-Glc to HDMBOA-Glc. Gene expression studies and benzoxazinoid measurements indicate that S. exigua -induced responses in this pathway differentially affect R. maidis resistance in B73 and Ky21.

  12. Bulinus globosus (Planorbidae; Gastropoda) populations in the Lake Victoria basin and coastal Kenya show extreme nuclear genetic differentiation.

    PubMed

    Nyakaana, Silvester; Stothard, J Russell; Nalugwa, Allen; Webster, Bonnie L; Lange, Charles N; Jørgensen, Aslak; Rollinson, David; Kristensen, Thomas K

    2013-11-01

    Bulinus globosus, a key intermediate host for Schistosoma haematobium that causes urinary schistosomiasis, is a hermaphroditic freshwater Planorbid snail species that inhabits patchy and transient water bodies prone to large seasonal variations in water availability. Although capable of self-fertilizing, this species has been reported to be preferentially out crossing. In this study, we characterized the population genetic structure of 19 B. globosus populations sampled across the Lake Victoria basin and coastal Kenya using four polymorphic microsatellite loci. Population genetic structure was characterized and quantified using FST statistics and Bayesian clustering algorithms. The four loci used in this study contained sufficient statistical power to detect low levels of population genetic differentiation and were highly polymorphic with the number of alleles per locus across populations ranging from 16 to 22. Average observed and expected heterozygosities across loci in each population ranged from 0.13 to 0.69 and from 0.39 to 0.79, respectively. Twenty-five of the seventy-six possible population-locus comparisons significantly deviated from Hardy-Weinberg equilibrium proportions after Bonferroni corrections, mostly due to the deficiency of heterozygotes. Significant genetic differentiation was observed between populations and Bayesian inferences identified 15 genetic clusters. The excess homozygosity, significant inbreeding and population genetic differentiation observed in B. globosus populations are likely to be due to the habitat patchiness, mating system and the proneness to cyclic extinction and recolonization in transient habitats. PMID:23266524

  13. High genetic diversity is not essential for successful introduction

    PubMed Central

    Rollins, Lee A; Moles, Angela T; Lam, Serena; Buitenwerf, Robert; Buswell, Joanna M; Brandenburger, Claire R; Flores-Moreno, Habacuc; Nielsen, Knud B; Couchman, Ellen; Brown, Gordon S; Thomson, Fiona J; Hemmings, Frank; Frankham, Richard; Sherwin, William B

    2013-01-01

    Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive. PMID:24340190

  14. Integration of Genetic and Phenotypic Data in 48 Lineages of Philippine Birds Shows Heterogeneous Divergence Processes and Numerous Cryptic Species.

    PubMed

    Campbell, Kyle K; Braile, Thomas; Winker, Kevin

    2016-01-01

    The Philippine Islands are one of the most biologically diverse archipelagoes in the world. Current taxonomy, however, may underestimate levels of avian diversity and endemism in these islands. Although species limits can be difficult to determine among allopatric populations, quantitative methods for comparing phenotypic and genotypic data can provide useful metrics of divergence among populations and identify those that merit consideration for elevation to full species status. Using a conceptual approach that integrates genetic and phenotypic data, we compared populations among 48 species, estimating genetic divergence (p-distance) using the mtDNA marker ND2 and comparing plumage and morphometrics of museum study skins. Using conservative speciation thresholds, pairwise comparisons of genetic and phenotypic divergence suggested possible species-level divergences in more than half of the species studied (25 out of 48). In speciation process space, divergence routes were heterogeneous among taxa. Nearly all populations that surpassed high genotypic divergence thresholds were Passeriformes, and non-Passeriformes populations surpassed high phenotypic divergence thresholds more commonly than expected by chance. Overall, there was an apparent logarithmic increase in phenotypic divergence with respect to genetic divergence, suggesting the possibility that divergence among these lineages may initially be driven by divergent selection in this allopatric system. Also, genetic endemism was high among sampled islands. Higher taxonomy affected divergence in genotype and phenotype. Although broader lineage, genetic, phenotypic, and numeric sampling is needed to further explore heterogeneity among divergence processes and to accurately assess species-level diversity in these taxa, our results support the need for substantial taxonomic revisions among Philippine birds. The conservation implications are profound.

  15. Integration of Genetic and Phenotypic Data in 48 Lineages of Philippine Birds Shows Heterogeneous Divergence Processes and Numerous Cryptic Species

    PubMed Central

    Campbell, Kyle K.; Braile, Thomas

    2016-01-01

    The Philippine Islands are one of the most biologically diverse archipelagoes in the world. Current taxonomy, however, may underestimate levels of avian diversity and endemism in these islands. Although species limits can be difficult to determine among allopatric populations, quantitative methods for comparing phenotypic and genotypic data can provide useful metrics of divergence among populations and identify those that merit consideration for elevation to full species status. Using a conceptual approach that integrates genetic and phenotypic data, we compared populations among 48 species, estimating genetic divergence (p-distance) using the mtDNA marker ND2 and comparing plumage and morphometrics of museum study skins. Using conservative speciation thresholds, pairwise comparisons of genetic and phenotypic divergence suggested possible species-level divergences in more than half of the species studied (25 out of 48). In speciation process space, divergence routes were heterogeneous among taxa. Nearly all populations that surpassed high genotypic divergence thresholds were Passeriformes, and non-Passeriformes populations surpassed high phenotypic divergence thresholds more commonly than expected by chance. Overall, there was an apparent logarithmic increase in phenotypic divergence with respect to genetic divergence, suggesting the possibility that divergence among these lineages may initially be driven by divergent selection in this allopatric system. Also, genetic endemism was high among sampled islands. Higher taxonomy affected divergence in genotype and phenotype. Although broader lineage, genetic, phenotypic, and numeric sampling is needed to further explore heterogeneity among divergence processes and to accurately assess species-level diversity in these taxa, our results support the need for substantial taxonomic revisions among Philippine birds. The conservation implications are profound. PMID:27442510

  16. Integration of Genetic and Phenotypic Data in 48 Lineages of Philippine Birds Shows Heterogeneous Divergence Processes and Numerous Cryptic Species.

    PubMed

    Campbell, Kyle K; Braile, Thomas; Winker, Kevin

    2016-01-01

    The Philippine Islands are one of the most biologically diverse archipelagoes in the world. Current taxonomy, however, may underestimate levels of avian diversity and endemism in these islands. Although species limits can be difficult to determine among allopatric populations, quantitative methods for comparing phenotypic and genotypic data can provide useful metrics of divergence among populations and identify those that merit consideration for elevation to full species status. Using a conceptual approach that integrates genetic and phenotypic data, we compared populations among 48 species, estimating genetic divergence (p-distance) using the mtDNA marker ND2 and comparing plumage and morphometrics of museum study skins. Using conservative speciation thresholds, pairwise comparisons of genetic and phenotypic divergence suggested possible species-level divergences in more than half of the species studied (25 out of 48). In speciation process space, divergence routes were heterogeneous among taxa. Nearly all populations that surpassed high genotypic divergence thresholds were Passeriformes, and non-Passeriformes populations surpassed high phenotypic divergence thresholds more commonly than expected by chance. Overall, there was an apparent logarithmic increase in phenotypic divergence with respect to genetic divergence, suggesting the possibility that divergence among these lineages may initially be driven by divergent selection in this allopatric system. Also, genetic endemism was high among sampled islands. Higher taxonomy affected divergence in genotype and phenotype. Although broader lineage, genetic, phenotypic, and numeric sampling is needed to further explore heterogeneity among divergence processes and to accurately assess species-level diversity in these taxa, our results support the need for substantial taxonomic revisions among Philippine birds. The conservation implications are profound. PMID:27442510

  17. Genetic Structure and Demographic History Should Inform Conservation: Chinese Cobras Currently Treated as Homogenous Show Population Divergence

    PubMed Central

    Lin, Long-Hui; Qu, Yan-Fu; Li, Hong; Zhou, Kai-Ya; Ji, Xiang

    2012-01-01

    An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a “star” cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization. PMID:22558439

  18. Tritrichomonas foetus isolates from cats and cattle show minor genetic differences in unrelated loci ITS-2 and EF-1α.

    PubMed

    Reinmann, Karin; Müller, Norbert; Kuhnert, Peter; Campero, Carlos M; Leitsch, David; Hess, Michael; Henning, Klaus; Fort, Marcelo; Müller, Joachim; Gottstein, Bruno; Frey, Caroline F

    2012-04-30

    The protozoan parasite Tritrichomonas foetus is well known as an important causative agent of infertility and abortion in cattle (bovine trichomonosis). This World Organisation for Animal Health (O.I.E.) notifiable disease is thought to be under control in many countries including Switzerland. In recent studies, however, T. foetus has also been identified as an intestinal parasite that causes chronic large-bowel diarrhoea in cats. Since the feline isolates were considered indistinguishable from bovine isolates, the possibility and risk of parasite transmission from cats to cattle and vice versa has been intensively discussed in current literature. Therefore, we investigated if cat and cattle isolates are genetically distinct from each other or in fact represent identical genotypes. For this purpose, two independent genetic loci were selected that turned out to be well-suited for a PCR sequencing-based genotyping of trichomonad isolates: (i) previously published internal transcribed spacer region 2 (ITS-2) and (ii) a semi-conserved sequence stretch of the elongation factor-1 alpha (EF-1α) gene used for the first time in the present study. Respective comparative analyses revealed that both loci were sufficiently variable to allow unambiguous genetic discrimination between different trichomonad species. Comparison of both genetic loci confirmed that T. suis and T. mobilensis are phylogenetically very close to T. foetus. Moreover, these two genetic markers were suited to define host-specific genotypes of T. foetus. Both loci showed single base differences between cat and cattle isolates but showed full sequence identity within strains from either cat or cattle isolates. Furthermore, an additional PCR with a forward primer designed to specifically amplify the bovine sequence of EF-1α was able to discriminate bovine isolates of T. foetus from feline isolates and also from other trichomonads. The implications these minor genetic differences may have on the biological

  19. Young Adult Female Fragile X Premutation Carriers Show Age- and Genetically-Modulated Cognitive Impairments

    ERIC Educational Resources Information Center

    Goodrich-Hunsaker, Naomi J.; Wong, Ling M.; McLennan, Yingratana; Srivastava, Siddharth; Tassone, Flora; Harvey, Danielle; Rivera, Susan M.; Simon, Tony J.

    2011-01-01

    The high frequency of the fragile X premutation in the general population and its emerging neurocognitive implications highlight the need to investigate the effects of the premutation on lifespan cognitive development. Until recently, cognitive function in fragile X premutation carriers (fXPCs) was presumed to be unaffected by the mutation. Here…

  20. Anatomical and genetic study of an ancient animal tooth showing brachyodont and hypsodont mixed taxonomical characteristics.

    PubMed

    Monteagudo, L V; Obón, J A; Whyte, A; Tejedor, M T; Whyte, J; Cisneros, A

    2013-05-01

    A non-human dental piece was found in a Roman Empire tomb dated the 3rd century A.C. in Zaragoza (Spain). The morphology of this piece showed mixed brachyodont (carnivores) and hypsodont (herbivores) characteristics. As a result, the taxonomical assignation of the piece was impossible. Therefore, a protocol based on the DNA sequence of the cytochrome c oxidase subunit 1 mitochondrial region (COI) was applied. For this purpose, a pair of primers able to amplify this region in a large variety of animals was designed. The results point to a species of the Genus Bos (Family Bovidae). This assignation was later confirmed by these quencing of a short fragment of the mitochondrial D-loop region. A complete morphological description of the tooth is presented together with the DNA sequence study and comparison protocol.

  1. High altitude living: genetic and environmental adaptation.

    PubMed

    Ramirez, G; Bittle, P A; Rosen, R; Rabb, H; Pineda, D

    1999-01-01

    High altitude (HA) living produces physiological changes for adaptation to chronic hypobaric-hypoxemic conditions. Although much is known about these physiologic adaptations, no clear separation has been made regarding what is "native" or "genetic" adaptation and what is "acquired." In this review, we describe the genetic vs. acquired adaptation and only include studies performed in a population native to HA and not in an acclimatized population or trekkers. The changes encountered in animals and humans living at HA in terms of hematology, muscular, respiratory, cerebral, cardiovascular, hormonal, fluid and electrolytes and reproduction, strongly suggest that genetics play a very important role in HA adaptation. Unfortunately, the characteristic physiology of HA natives has not been systematically defined to established specific measurable parameters of adaptation in comparison to the acquired ambient adaptation of the non-native population. Once the parameters are established, we can compare non-native populations exposed to HA that must emulate the HA physiology for a definite adaptation to be present. With measurable parameters, especially in the management of fluids and electrolytes, we can define how long it will take for a sea level native to adapt to an HA altitude. Until these studies are performed, speculation will continue and no rational medical intervention can be offered to HA newcomers who may experience HA difficulties.

  2. Landscape genetics of high mountain frog metapopulations

    USGS Publications Warehouse

    Murphy, M.A.; Dezzani, R.; Pilliod, D.S.; Storfer, A.

    2010-01-01

    Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a

  3. Mitochondrial and microsatellite DNA analyses showed comparative genetic diversity between parent and offspring populations of Korean black rockfish in a hatchery facility.

    PubMed

    An, H S; Lee, J W; Park, J Y; Myeong, J I; An, C M

    2013-01-01

    The black rockfish, Sebastes inermis (Sebastidae), is an important commercial fishery resource in Korea. As a preliminary investigation into the effect of artificial reproduction in a hatchery facility, the genetic divergence between parent and offspring populations of black rockfish was accessed using 10 polymorphic nuclear microsatellite DNA loci and a mitochondrial (mt) control gene. All loci that were screened showed marked polymorphisms. mtDNA control region sequences were also highly variable. Of approximately 350 base pairs (bp) sequenced, 52 variable sites, comprising 56 base substitutions, were found among 233 individuals. Offspring populations showed less genetic variability than the parent population in terms of numbers of microsatellite alleles and mtDNA haplotypes, as well as mtDNA haplotype diversity. Statistical analysis of the fixation index (ΦST and F(ST)) and analysis of molecular variance using both DNA markers showed significant genetic differences between the parent and offspring populations. These results suggest that random genetic drift and/or inbreeding events, as well as artificial selection and founder effects, occurred when the offspring strain was reproduced in a hatchery facility despite thousands of males and females from different hatcheries being maintained for artificial reproduction. Therefore, it is necessary to improve current hatchery programs by monitoring genetic variation in both the broodstock and progeny and controlling inbreeding within stocks in commercial breeding facilities to maintain the production of high-quality black rockfish. This information will be useful for determining suitable guidelines for establishing and maintaining cultured stocks and the aquaculture industry of S. inermis. PMID:24390988

  4. High genetic structuring of Tula hantavirus.

    PubMed

    Schmidt, Sabrina; Saxenhofer, Moritz; Drewes, Stephan; Schlegel, Mathias; Wanka, Konrad M; Frank, Raphael; Klimpel, Sven; von Blanckenhagen, Felix; Maaz, Denny; Herden, Christiane; Freise, Jona; Wolf, Ronny; Stubbe, Michael; Borkenhagen, Peter; Ansorge, Hermann; Eccard, Jana A; Lang, Johannes; Jourdain, Elsa; Jacob, Jens; Marianneau, Philippe; Heckel, Gerald; Ulrich, Rainer G

    2016-05-01

    Tula virus (TULV) is a vole-associated hantavirus with low or no pathogenicity to humans. In the present study, 686 common voles (Microtus arvalis), 249 field voles (Microtus agrestis) and 30 water voles (Arvicola spec.) were collected at 79 sites in Germany, Luxembourg and France and screened by RT-PCR and TULV-IgG ELISA. TULV-specific RNA and/or antibodies were detected at 43 of the sites, demonstrating a geographically widespread distribution of the virus in the studied area. The TULV prevalence in common voles (16.7 %) was higher than that in field voles (9.2 %) and water voles (10.0 %). Time series data at ten trapping sites showed evidence of a lasting presence of TULV RNA within common vole populations for up to 34 months, although usually at low prevalence. Phylogenetic analysis demonstrated a strong genetic structuring of TULV sequences according to geography and independent of the rodent species, confirming the common vole as the preferential host, with spillover infections to co-occurring field and water voles. TULV phylogenetic clades showed a general association with evolutionary lineages in the common vole as assessed by mitochondrial DNA sequences on a large geographical scale, but with local-scale discrepancies in the contact areas. PMID:26831932

  5. Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin.

    PubMed

    Denesvre, Caroline; Dumarest, Marine; Rémy, Sylvie; Gourichon, David; Eloit, Marc

    2015-10-01

    Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.

  6. Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin.

    PubMed

    Denesvre, Caroline; Dumarest, Marine; Rémy, Sylvie; Gourichon, David; Eloit, Marc

    2015-10-01

    Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics. PMID:26223320

  7. Student Problem Solving in High School Genetics.

    ERIC Educational Resources Information Center

    Stewart, James

    1983-01-01

    Describes set of specific steps (procedural knowledge) used when solving monohybrid/dihybrid cross problems and extent to which students could justify execution of each step in terms of their conceptual knowledge of genetics and meiosis. Implications for genetics instruction are discussed. (JN)

  8. Populations of weedy crop-wild hybrid beets show contrasting variation in mating system and population genetic structure.

    PubMed

    Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

    2010-05-01

    Reproductive traits are key parameters for the evolution of invasiveness in weedy crop-wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop-wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop-wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management.

  9. Populations of weedy crop-wild hybrid beets show contrasting variation in mating system and population genetic structure.

    PubMed

    Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

    2010-05-01

    Reproductive traits are key parameters for the evolution of invasiveness in weedy crop-wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop-wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop-wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management. PMID:25567926

  10. Populations of weedy crop–wild hybrid beets show contrasting variation in mating system and population genetic structure

    PubMed Central

    Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

    2010-01-01

    Reproductive traits are key parameters for the evolution of invasiveness in weedy crop–wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop–wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop–wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management. PMID:25567926

  11. The age related markers lipofuscin and apoptosis show different genetic architecture by QTL mapping in short-lived Nothobranchius fish

    PubMed Central

    Ng'oma, Enoch; Reichwald, Kathrin; Dorn, Alexander; Wittig, Michael; Balschun, Tobias; Franke, Andre; Platzer, Matthias; Cellerino, Allesandro

    2014-01-01

    Annual fish of the genus Nothobranchius show large variations in lifespan and expression of age-related phenotypes between closely related populations. We studied N. kadleci and its sister species N. furzeri GRZ strain, and found that N.kadleci is longer-lived than the N. furzeri. Lipofuscin and apoptosis measured in the liver increased with age in N. kadleci with different profiles: lipofuscin increased linearly, while apoptosis declined in the oldest animals. More lipofuscin (P < 0.001) and apoptosis (P < 0.001) was observed in N. furzeri than in N. kadleci at 16w age. Lipofuscin and apoptotic cells were then quantified in hybrids from the mating of N. furzeri to N. kadleci. F1 individuals showed heterosis for lipofuscin but additive effects for apoptosis. These two age-related phenotypes were not correlated in F2 hybrids. Quantitative trait loci analysis of 287 F2 fish using 237 markers identified two QTL accounting for 10% of lipofuscin variance (P < 0.001) with overdominance effect. Apoptotic cells revealed three significant- and two suggestive QTL explaining 19% of variance (P < 0.001), showing additive and dominance effects, and two interacting loci. Our results show that lipofuscin and apoptosis are markers of different age-dependent biological processes controlled by different genetic mechanisms. PMID:25093339

  12. High-throughput olfactory conditioning and memory retention test show variation in Nasonia parasitic wasps

    PubMed Central

    Hoedjes, K M; Steidle, J L M; Werren, J H; Vet, L E M; Smid, H M

    2012-01-01

    Most of our knowledge on learning and memory formation results from extensive studies on a small number of animal species. Although features and cellular pathways of learning and memory are highly similar in this diverse group of species, there are also subtle differences. Closely related species of parasitic wasps display substantial variation in memory dynamics and can be instrumental to understanding both the adaptive benefit of and mechanisms underlying this variation. Parasitic wasps of the genus Nasonia offer excellent opportunities for multidisciplinary research on this topic. Genetic and genomic resources available for Nasonia are unrivaled among parasitic wasps, providing tools for genetic dissection of mechanisms that cause differences in learning. This study presents a robust, high-throughput method for olfactory conditioning of Nasonia using a host encounter as reward. A T-maze olfactometer facilitates high-throughput memory retention testing and employs standardized odors of equal detectability, as quantified by electroantennogram recordings. Using this setup, differences in memory retention between Nasonia species were shown. In both Nasonia vitripennis and Nasonia longicornis, memory was observed up to at least 5 days after a single conditioning trial, whereas Nasonia giraulti lost its memory after 2 days. This difference in learning may be an adaptation to species-specific differences in ecological factors, for example, host preference. The high-throughput methods for conditioning and memory retention testing are essential tools to study both ultimate and proximate factors that cause variation in learning and memory formation in Nasonia and other parasitic wasp species. PMID:22804968

  13. Well-differentiated systemic mastocytosis showed excellent clinical response to imatinib in the absence of known molecular genetic abnormalities

    PubMed Central

    Huang, Lanshan; Wang, Sa A.; Konoplev, Sergej; Bueso-Ramos, Carlos E.; Thakral, Beenu; Miranda, Roberto N.; Jabbour, Elias; Medeiros, L. Jeffrey; Kanagal-Shamanna, Rashmi

    2016-01-01

    Abstract Introduction: Well-differentiated systemic mastocytosis (WDSM) is a rare, recently recognized provisional subvariant of systemic mastocytosis (SM). We report a case of WDSM that showed excellent clinical and cutaneous response to imatinib in the absence of known molecular genetic abnormalities. Clinical Findings/Diagnoses: We present a 24-year-old woman with childhood onset of skin manifestations that progressed to mediator-related systemic events, and a gastrointestinal tract mastocytoma. A subsequent bone marrow examination showed WDSM. Treatment with imatinib resulted in complete resolution of cutaneous lesions and systemic symptoms, which relapsed with the discontinuation of the drug. Targeted next-generation sequencing-based mutation analysis did not demonstrate any mutations in the coding regions of KIT or other genes commonly associated with myeloid neoplasms. Conclusions: The diagnosis of WDSM is challenging in the absence of spindle-shaped mast cells, CD2 or CD25 expression, and KIT D816 mutation. This case illustrated the need for recognizing this unique variant of SM for diagnostic and therapeutic implications. PMID:27741105

  14. Nineteenth century French rose (Rosa sp.) germplasm shows a shift over time from a European to an Asian genetic background.

    PubMed

    Liorzou, Mathilde; Pernet, Alix; Li, Shubin; Chastellier, Annie; Thouroude, Tatiana; Michel, Gilles; Malécot, Valéry; Gaillard, Sylvain; Briée, Céline; Foucher, Fabrice; Oghina-Pavie, Cristiana; Clotault, Jérémy; Grapin, Agnès

    2016-08-01

    Hybridization with introduced genetic resources is commonly practiced in ornamental plant breeding to introgress desired traits. The 19th century was a golden age for rose breeding in France. The objective here was to study the evolution of rose genetic diversity over this period, which included the introduction of Asian genotypes into Europe. A large sample of 1228 garden roses encompassing the conserved diversity cultivated during the 18th and 19th centuries was genotyped with 32 microsatellite primer pairs. Its genetic diversity and structure were clarified. Wide diversity structured in 16 genetic groups was observed. Genetic differentiation was detected between ancient European and Asian accessions, and a temporal shift from a European to an Asian genetic background was observed in cultivated European hybrids during the 19th century. Frequent crosses with Asian roses throughout the 19th century and/or selection for Asiatic traits may have induced this shift. In addition, the consistency of the results with respect to a horticultural classification is discussed. Some horticultural groups, defined according to phenotype and/or knowledge of their pedigree, seem to be genetically more consistent than others, highlighting the difficulty of classifying cultivated plants. Therefore, the horticultural classification is probably more appropriate for commercial purposes rather than genetic relatedness, especially to define preservation and breeding strategies.

  15. Nineteenth century French rose (Rosa sp.) germplasm shows a shift over time from a European to an Asian genetic background

    PubMed Central

    Liorzou, Mathilde; Pernet, Alix; Li, Shubin; Chastellier, Annie; Thouroude, Tatiana; Michel, Gilles; Malécot, Valéry; Gaillard, Sylvain; Briée, Céline; Foucher, Fabrice; Oghina-Pavie, Cristiana; Clotault, Jérémy; Grapin, Agnès

    2016-01-01

    Hybridization with introduced genetic resources is commonly practiced in ornamental plant breeding to introgress desired traits. The 19th century was a golden age for rose breeding in France. The objective here was to study the evolution of rose genetic diversity over this period, which included the introduction of Asian genotypes into Europe. A large sample of 1228 garden roses encompassing the conserved diversity cultivated during the 18th and 19th centuries was genotyped with 32 microsatellite primer pairs. Its genetic diversity and structure were clarified. Wide diversity structured in 16 genetic groups was observed. Genetic differentiation was detected between ancient European and Asian accessions, and a temporal shift from a European to an Asian genetic background was observed in cultivated European hybrids during the 19th century. Frequent crosses with Asian roses throughout the 19th century and/or selection for Asiatic traits may have induced this shift. In addition, the consistency of the results with respect to a horticultural classification is discussed. Some horticultural groups, defined according to phenotype and/or knowledge of their pedigree, seem to be genetically more consistent than others, highlighting the difficulty of classifying cultivated plants. Therefore, the horticultural classification is probably more appropriate for commercial purposes rather than genetic relatedness, especially to define preservation and breeding strategies. PMID:27406785

  16. Construction and characterization of an infectious clone of coxsackievirus A6 that showed high virulence in neonatal mice.

    PubMed

    Yang, Lisheng; Li, Shuxuan; Liu, Yajing; Hou, Wangheng; Lin, Qiaona; Zhao, Huan; Xu, Longfa; He, Delei; Ye, Xiangzhong; Zhu, Hua; Cheng, Tong; Xia, Ningshao

    2015-12-01

    Atypical hand, foot, and mouth disease (aHFMD) outbreaks have been frequently reported worldwide in recent years. It is believed that coxsackievirus A6 (CA6) is the major pathogen for aHFMD. Studies regarding CA6 infection are limited and the genetic mechanism for the high pathogenicity of some new CA6 variants is still unclear. Infectious clones are powerful tools for studying the genetic mechanisms of RNA viruses. In this study, we describe the construction of a full-length cDNA clone of CA6 strain TW-2007-00141. The whole genome of CA6 was amplified in a single step and ligated into a plasmid vector through an efficient cloning method, Gibson assembly. The whole genome sequence of CA6 strain TW-2007-00141 was determined and phylogenetic analysis indicated that it shared a high degree of similarity (≥94%) with the CA6 strains found in Taiwan in 2009. The infectious clone of CA6 viruses were recovered by transfection into 293FT cells and showed similar biological properties to the parental virus. Viral particles were purified by CsCl isopycnic centrifugation, and two types of viral particles were observed under transmission electron microscopy. The rescued virus showed high virulence in one-day-old suckling mice. This clone may be useful for establishing animal models for the evaluation of CA6 vaccine efficiency in future.

  17. Massively parallel high-order combinatorial genetics in human cells.

    PubMed

    Wong, Alan S L; Choi, Gigi C G; Cheng, Allen A; Purcell, Oliver; Lu, Timothy K

    2015-09-01

    The systematic functional analysis of combinatorial genetics has been limited by the throughput that can be achieved and the order of complexity that can be studied. To enable massively parallel characterization of genetic combinations in human cells, we developed a technology for rapid, scalable assembly of high-order barcoded combinatorial genetic libraries that can be quantified with high-throughput sequencing. We applied this technology, combinatorial genetics en masse (CombiGEM), to create high-coverage libraries of 1,521 two-wise and 51,770 three-wise barcoded combinations of 39 human microRNA (miRNA) precursors. We identified miRNA combinations that synergistically sensitize drug-resistant cancer cells to chemotherapy and/or inhibit cancer cell proliferation, providing insights into complex miRNA networks. More broadly, our method will enable high-throughput profiling of multifactorial genetic combinations that regulate phenotypes of relevance to biomedicine, biotechnology and basic science.

  18. Massively parallel high-order combinatorial genetics in human cells

    PubMed Central

    Wong, Alan S L; Choi, Gigi C G; Cheng, Allen A; Purcell, Oliver; Lu, Timothy K

    2016-01-01

    The systematic functional analysis of combinatorial genetics has been limited by the throughput that can be achieved and the order of complexity that can be studied. To enable massively parallel characterization of genetic combinations in human cells, we developed a technology for rapid, scalable assembly of high-order barcoded combinatorial genetic libraries that can be quantified with high-throughput sequencing. We applied this technology, combinatorial genetics en masse (CombiGEM), to create high-coverage libraries of 1,521 two-wise and 51,770 three-wise barcoded combinations of 39 human microRNA (miRNA) precursors. We identified miRNA combinations that synergistically sensitize drug-resistant cancer cells to chemotherapy and/or inhibit cancer cell proliferation, providing insights into complex miRNA networks. More broadly, our method will enable high-throughput profiling of multifactorial genetic combinations that regulate phenotypes of relevance to biomedicine, biotechnology and basic science. PMID:26280411

  19. Genetic variants associated with arsenic metabolism within human arsenic (+3 oxidation state) methyltransferase show wide variation across multiple populations.

    PubMed

    Fujihara, Junko; Yasuda, Toshihiro; Kato, Hideaki; Yuasa, Isao; Panduro, Arturo; Kunito, Takashi; Takeshita, Haruo

    2011-02-01

    Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. The objective of this study was to investigate the diversity of the AS3MT gene in Mexican and German populations. The distribution of 18 single nucleotide polymorphisms (SNPs) in AS3MT was assessed on healthy individuals: 38 Mestizo, 69 Nahuas, 50 Huicholes, and 32 Germans. All 18 SNPs were polymorphic in the German and Mexican populations. Of the three Mexican populations, a minor allele frequency was the highest in the Mestizo, followed by the Nahuas and Huicholes. In the German and three Mexican groups, haplotype #1(TATAGAAGTCTTCATGAC) was the most predominant. Seven haplotypes were newly found in the German and three Mexican populations. The D' values between SNP pairs were high in the German and Nahua populations; they had a similar pattern. The pattern of the Mestizo was more similar to the African than to the other Mexican populations. Huicholes had a moderate pattern of the African and German/Nahua populations. The network had three clusters. One originated in the African population and another may have originated in an Asian (Chinese and/or Japanese) population. The third one may have originated among Caucasians. This study is the first to demonstrate the existence of genetic heterogeneity in the distribution of 18 SNPs in AS3MT of German and Mexican populations.

  20. Genetic influence on brain catecholamines: high brain norepinephrine in salt-sensitive rats

    SciTech Connect

    Iwai, J; Friedman, R; Tassinari, L

    1980-01-01

    Rats genetically sensitive to salt-induced hypertension evinced higher levels of plasma norepinephrine and epinephrine than rats genetically resistant to hypertension. The hypertension-sensitive rats showed higher hypothalamic norepinephrine and lower epinephrine than resistant rats. In response to a high salt diet, brain stem norepinephrine increased in sensitive rats while resistant rats exhibited a decrease on the same diet.

  1. Molecular and Genetic Characterization of HIV-1 Tat Exon-1 Gene from Cameroon Shows Conserved Tat HLA-Binding Epitopes: Functional Implications

    PubMed Central

    Teto, Georges; Fonsah, Julius Y.; Tagny, Claude T.; Mbanya, Dora; Nchindap, Emilienne; Kenmogne, Leopoldine; Fokam, Joseph; Njamnshi, Dora M.; Kouanfack, Charles; Njamnshi, Alfred K.; Kanmogne, Georgette D.

    2016-01-01

    HIV-1 Tat plays a critical role in viral transactivation. Subtype-B Tat has potential use as a therapeutic vaccine. However, viral genetic diversity and population genetics would significantly impact the efficacy of such a vaccine. Over 70% of the 37-million HIV-infected individuals are in sub-Saharan Africa (SSA) and harbor non-subtype-B HIV-1. Using specimens from 100 HIV-infected Cameroonians, we analyzed the sequences of HIV-1 Tat exon-1, its functional domains, post-translational modifications (PTMs), and human leukocyte antigens (HLA)-binding epitopes. Molecular phylogeny revealed a high genetic diversity with nine subtypes, CRF22_01A1/CRF01_AE, and negative selection in all subtypes. Amino acid mutations in Tat functional domains included N24K (44%), N29K (58%), and N40K (30%) in CRF02_AG, and N24K in all G subtypes. Motifs and phosphorylation analyses showed conserved amidation, N-myristoylation, casein kinase-2 (CK2), serine and threonine phosphorylation sites. Analysis of HLA allelic frequencies showed that epitopes for HLAs A*0205, B*5301, Cw*0401, Cw*0602, and Cw*0702 were conserved in 58%–100% of samples, with B*5301 epitopes having binding affinity scores > 100 in all subtypes. This is the first report of N-myristoylation, amidation, and CK2 sites in Tat; these PTMs and mutations could affect Tat function. HLA epitopes identified could be useful for designing Tat-based vaccines for highly diverse HIV-1 populations, as in SSA. PMID:27438849

  2. Unusual, High Genetic Diversity of Aleutian Mink Disease Virus

    PubMed Central

    Olofsson, Anders; Mittelholzer, Christian; Treiberg Berndtsson, Louise; Lind, Lars; Mejerland, Torbjörn; Belák, Sándor

    1999-01-01

    The genetic diversity of Aleutian mink disease virus (AMDV) was examined. Sequences obtained from 35 clinical samples were compared with five published sequences. An unusual, high genetic variability was revealed. Three phylogenetic subgroups of AMDV were identified, and the presence of more than one genotype at some farms was detected. PMID:10565948

  3. Unusual, high genetic diversity of Aleutian mink disease virus.

    PubMed

    Olofsson, A; Mittelholzer, C; Treiberg Berndtsson, L; Lind, L; Mejerland, T; Belák, S

    1999-12-01

    The genetic diversity of Aleutian mink disease virus (AMDV) was examined. Sequences obtained from 35 clinical samples were compared with five published sequences. An unusual, high genetic variability was revealed. Three phylogenetic subgroups of AMDV were identified, and the presence of more than one genotype at some farms was detected. PMID:10565948

  4. High-Throughput Sequencing and Rare Genetic Diseases

    PubMed Central

    Makrythanasis, P.; Antonarakis, S.E.

    2012-01-01

    High-throughput sequencing has drastically changed the research of genes responsible for genetic disorders and is now gradually introduced as an additional genetic diagnostic testing in clinical practice. The current debates on the emerging technical, medical and ethical issues as well as the potential optimum use of the available technology are discussed. PMID:23293577

  5. Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi

    PubMed Central

    Telleria, Jenny; Biron, David G.; Brizard, Jean-Paul; Demettre, Edith; Séveno, Martial; Barnabé, Christian; Ayala, Francisco J.; Tibayrenc, Michel

    2010-01-01

    We performed a phylogenetic character mapping on 26 stocks of Trypanosoma cruzi, the parasite responsible for Chagas disease, and 2 stocks of the sister taxon T. cruzi marinkellei to test for possible associations between T. cruzi–subspecific phylogenetic diversity and levels of protein expression, as examined by proteomic analysis and mass spectrometry. We observed a high level of correlation (P < 10−4) between genetic distance, as established by multilocus enzyme electrophoresis, and proteomic dissimilarities estimated by proteomic Euclidian distances. Several proteins were found to be specifically associated to T. cruzi phylogenetic subdivisions (discrete typing units). This study explores the previously uncharacterized links between infraspecific phylogenetic diversity and gene expression in a human pathogen. It opens the way to searching for new vaccine and drug targets and for identification of specific biomarkers at the subspecific level of pathogens. PMID:21059959

  6. Population genetics of a marine bivalve, Pinctada maxima, throughout the Indo-Australian Archipelago shows differentiation and decreased diversity at range limits.

    PubMed

    Lind, Curtis E; Evans, Brad S; Taylor, Joseph J U; Jerry, Dean R

    2007-12-01

    Intraspecific genetic diversity governs the potential of species to prevail in the face of environmental or ecological challenges; therefore, its protection is critical. The Indo-Australian Archipelago (IAA) is a significant reservoir of the world's marine biodiversity and a region of high conservation priority. Yet, despite indications that the IAA may harbour greater intraspecific variation, multiple-locus genetic diversity data are limited. We investigated microsatellite DNA variation in Pinctada maxima populations from the IAA to elucidate potential factors influencing levels of genetic diversity in the region. Results indicate that genetic diversity decreases as the geographical distance away from central Indonesia increases, and that populations located towards the centre of P. maxima's range are more genetically diverse than those located peripherally (P < 0.01). Significant partitioning of genetic variation was identified (F(ST) = 0.027; R(ST) = 0.023, P < 0.001) and indicates that historical biogeographical episodes or oceanographic factors have shaped present population genetic structure. We propose that the genetic diversity peak in P. maxima populations may be due to (i) an abundance of suitable habitat within the IAA, meaning larger, more temporally stable populations can be maintained and are less likely to encounter genetic bottlenecks; and/or (ii) the close proximity of biogeographical barriers around central Indonesia results in increased genetic diversity in the region because of admixture of genetically divergent populations. We encourage further genetic diversity studies of IAA marine biota to confirm whether this region has a significant role in maintaining intraspecific diversity, which will greatly assist the planning and efficacy of future conservation efforts.

  7. Mice fed on a diet enriched with genetically engineered multivitamin corn show no sub-acute toxic effects and no sub-chronic toxicity.

    PubMed

    Arjó, Gemma; Capell, Teresa; Matias-Guiu, Xavier; Zhu, Changfu; Christou, Paul; Piñol, Carme

    2012-12-01

    Multivitamin corn is a novel genetically engineered variety that simultaneously produces high levels of β-carotene, ascorbate and folate, and therefore has the potential to address simultaneously multiple micronutrient deficiencies caused by the lack of vitamins A, B9 and C in developing country populations. As part of the development process for genetically engineered crops and following European Food Safety Authority (EFSA) recommendations, multivitamin corn must be tested in whole food/feed sub-chronic animal feeding studies to ensure there are no adverse effects, and potential allergens must be identified. We carried out a 28-day toxicity assessment in mice, which showed no short-term sub-acute evidence of diet-related adverse health effects and no difference in clinical markers (food consumption, body weight, organ/tissue weight, haematological and biochemical blood parameters and histopathology) compared to mice fed on a control diet. A subsequent 90-day sub-chronic feeding study again showed no indications of toxicity compared to mice fed on control diets. Our data confirm that diets enriched with multivitamin corn have no adverse effects on mice, do not induce any clinical signs of toxicity and do not contain known allergens.

  8. Hybrid Mice as Genetic Models of High Alcohol Consumption

    PubMed Central

    Ozburn, A. R.; Walker, D.; Ahmed, S.; Belknap, J. K.; Harris, R. A.

    2011-01-01

    We showed that F1 hybrid genotypes may provide a broader variety of ethanol drinking phenotypes than the inbred progenitor strains used to create the hybrids (Blednov et al. in Alcohol Clin Exp Res 29:1949–1958–2005). To extend this work, we characterized alcohol consumption as well as intake of other tastants (saccharin, quinine and sodium chloride) in five inbred strains of mice (FVB, SJL, B6, BUB, NZB) and in their reciprocal F1 hybrids with B6 (FVBxB6; B6xFVB; NZBxB6; B6xNZB; BUBxB6; B6xBUB; SJLxB6; B6xSJL). We also compared ethanol intake in these mice for several concentrations before and after two periods of abstinence. F1 hybrid mice derived from the crosses of B6 and FVB and also B6 and SJL drank higher levels of ethanol than their progenitor strains, demonstrating overdominance for two-bottle choice drinking test. The B6 and NZB hybrid showed additivity in two-bottle choice drinking, whereas the hybrid of B6 and BUB demonstrated full or complete dominance. Genealogical origin, as well as non-alcohol taste preferences (sodium chloride), predicted ethanol consumption. Mice derived from the crosses of B6 and FVB showed high sustained alcohol preference and the B6 and NZB hybrids showed reduced alcohol preference after periods of abstinence. These new genetic models offer some advantages over inbred strains because they provide high, sustained, alcohol intake, and should allow mapping of loci important for the genetic architecture of these traits. PMID:19798565

  9. The genetic architecture of adaptations to high altitude in Ethiopia.

    PubMed

    Alkorta-Aranburu, Gorka; Beall, Cynthia M; Witonsky, David B; Gebremedhin, Amha; Pritchard, Jonathan K; Di Rienzo, Anna

    2012-01-01

    Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control and DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.

  10. High genetic variability and polychromatism in Pachycoris torridus (Heteroptera: Scutelleridae).

    PubMed

    Souza-Firmino, T S; Alevi, K C C; Pereira, L L V; Souza, E R S; Júnior, F C S; Banho, C A; Carmo, G O; Itoyama, M M

    2015-01-01

    The stink bug Pachycoris torridus is listed among the most polyphagous insects in the world and it is a major pest of diverse crops, in particular the physic nut Jatropha curcas, which is used as a raw material for biodiesel production. A peculiar characteristic of this species is its high phenotypic variability, a characteristic that makes identification difficult: P. torridus has been described as a new species eight times. Thus, to aid in identification, genetic characterization of this insect was performed. We verified that, due to the high genetic variability of P. torridus, several genetic patterns exist that result in the same phenotype. PMID:26600488

  11. A multifunctional drug combination shows highly potent therapeutic efficacy against human cancer xenografts in athymic mice.

    PubMed

    Liu, Xiu-Jun; Zheng, Yan-Bo; Li, Yi; Wu, Shu-Ying; Zhen, Yong-Su

    2014-01-01

    The tumor microenvironment plays a crucial role during tumor development. Integrated combination of drugs that target tumor microenvironment is a promising approach to anticancer therapy. Here, we report a multifunctional combination of low-cytotoxic drugs composed of dipyridamole, bestatin and dexamethasone (DBDx) which mainly acts on the tumor microenvironment shows highly potent antitumor efficacy in vivo. In mouse hepatoma H22 model, the triple drug combination showed synergistic and highly potent antitumor efficacy. The combination indices of various combinations of the triple drugs were between 0.2 and 0.5. DBDx inhibited the growth of a panel of human tumor xenografts and showed no obvious systemic toxicity. At tolerated doses, DBDx suppressed the growth of human hepatocellular carcinoma BEL-7402, HepG2, and lung adenocarcinoma A549 xenografts by 94.5%, 93.7% and 96.9%, respectively. Clonogenic assay demonstrated that DBDx showed weak cytotoxicity. Western blot showed that Flk1 and Nos3 were down-regulated in the DBDx-treated group. Proteomic analysis showed that DBDx mainly affected the metabolic process and immune system process; in addition, the angiogenesis and VEGF signaling pathway were also affected. Conclusively, DBDx, a multifunctional drug combination of three low-cytotoxic drugs, shows synergistic and highly potent antitumor efficacy evidently mediated by the modulation of tumor microenvironment. Based on its low-cytotoxic attributes and its broad-spectrum antitumor therapeutic efficacy, this multifunctional combination might be useful in the treatment of cancers, especially those refractory to conventional chemotherapeutics.

  12. High volume molecular genetic identification of single nucleotide polymorphisms using Genetic Bit Analysis Application to human genetic diagnosis

    SciTech Connect

    Boyce-Jacino, M.T.; Reynolds, J.; Nikiforov, T.

    1994-09-01

    The most common type of genetic disease-associated mutation is the single nucleotide polymorphism (SNP). Because most genetic diseases can be caused by multiple SNPs in the same gene, effective routine diagnosis of complex genetic diseases is dependent on a simple and reliable method of interrogating SNP sites. Molecular Tool`s solid phase assay capable of direct genotyping (single base sequencing) of SNP sites, Genetic Bit Analysis (GBA), involves hybridization-capture of a single-stranded PCR product to a sequence-specific, microtiter plate-bound oligonucleotide primer. The captured PCR product then acts as template for single-base extension of the capture primer across the polymorphic site, enabling direct determination of the base composition of the polymorphism through a simple colormetric assay. Genotyping in a high volume, semi-automated, processing system with a current capacity of 100 SNP interrogations per technician per day enables the screening of candidate mutations rapidly and cost-effectively, critically important to comprehensive genetic diagnosis. Using this gel-free technology, we have developed prototype diagnostic tests for CFTR and ApoE polymorphisms which enable direct sequencing of the polymorphic base at each site of interest. Routine clinical diagnosis of genetically complex diseases such as cystic fibrosis is dependent on this combination of robust biochemistry and simple format. Additionally, the ability to transfer the format and biochemistry to any disease gene of interest enables the broad application of this technology to clinical diagnostics, especially for genetically complex diseases.

  13. Genetic engineering for high methionine grain legumes.

    PubMed

    Müntz, K; Christov, V; Saalbach, G; Saalbach, I; Waddell, D; Pickardt, T; Schieder, O; Wüstenhagen, T

    1998-08-01

    Methionine (Met) is the primary limiting essential amino acid in grain legumes. The imbalance in amino acid composition restricts their biological value (BV) to 55 to 75% of that of animal protein. So far improvement of the BV could not be achieved by conventional breeding. Therefore, genetic engineering was employed by several laboratories to resolve the problem. Three strategies have been followed. A) Engineering for increased free Met levels; B) engineering of endogenous storage proteins with increased numbers of Met residues; C) transfer of foreign genes encoding Met-rich proteins, e.g. the Brazil nut 2S albumin (BNA) and its homologue from sunflower, into grain legumes. The latter strategy turned out to be most promising. In all cases the gene was put under the control of a developmentally regulated seed specific promoter and transferred into grain legumes using the bacterial Agrobacterium tumefaciens-system. Integration into and copy numbers in the plant genome as well as Mendelian inheritance and gene dosage effects were verified. After correct precursor processing the mature 2S albumin was intracellularly deposited in protein bodies which are part of the vacuolar compartment. The foreign protein amounted to 5 to 10% of the total seed protein in the best transgenic lines of narbon bean (Vicia narbonensis L., used in the authors' laboratories), lupins (Lupinus angustifolius L., used in CSIRO, Australia), and soybean (Glycine max (L.) Merr., used by Pioneer Hi-Bred, Inc., USA). In the narbon bean the increase of Met was directly related to the amount of 2S albumin in the transgenic seeds, but in soybean it remained below the theoretically expected value. Nevertheless, trangenic soybean reached 100%, whereas narbon bean and lupins reached approximately 80% of the FAO-standard for nutritionally balanced food proteins. These results document that the Met problem of grain legumes can be resolved by genetic engineering.

  14. A Twin Study of ADHD Symptoms in Early Adolescence: Hyperactivity-Impulsivity and Inattentiveness Show Substantial Genetic Overlap but Also Genetic Specificity

    ERIC Educational Resources Information Center

    Greven, Corina U.; Rijsdijk, Fruhling V.; Plomin, Robert

    2011-01-01

    A previous paper in this journal revealed substantial genetic overlap between the ADHD dimensions of hyperactivity-impulsivity and inattentiveness in a sample of 8-year old twins drawn from a UK-representative population sample. Four years later, when the twins were 12 years old, more than 5,500 pairs drawn from the same sample were rated again on…

  15. Genetic toxicity of high-boiling petroleum substances.

    PubMed

    McKee, Richard H; Schreiner, Ceinwen A; Nicolich, Mark J; Gray, Thomas M

    2013-11-01

    There are several specific types of high-boiling petroleum substances (HBPS) having final boiling points >343°C), in which genetic toxicity can be related to the content of polycyclic aromatic compounds (PACs), specifically crude oils, gas oils, heavy fuel oils, lubricant base oils, waxes and aromatic extracts. Evaluation of optimized Salmonella tests covering over 250 samples from 43 types of HBPS revealed that gene mutation can be determined for these substances using a protocol optimized for the detection of mutagenic PAC. The outcomes of modified Salmonella assays can be predicted using HBPS compositional information as input to a newly developed statistical model. The general outcome of the optimized Salmonella assay can be predicted for an untested substance based on its Aromatic Ring Class (ARC) profile. Review of the results from numerous cytogenetic tests showed that although a few positive study results have been reported, most HBPS do not produce chromosomal effects when tested in rodent bone marrow assays or in in vitro chromosomal aberration assays. Results of both bacterial and cytogenetic studies can be used to satisfy genetic toxicity endpoints for the HBPS category substances. PMID:23685115

  16. Genetic toxicity of high-boiling petroleum substances.

    PubMed

    McKee, Richard H; Schreiner, Ceinwen A; Nicolich, Mark J; Gray, Thomas M

    2013-11-01

    There are several specific types of high-boiling petroleum substances (HBPS) having final boiling points >343°C), in which genetic toxicity can be related to the content of polycyclic aromatic compounds (PACs), specifically crude oils, gas oils, heavy fuel oils, lubricant base oils, waxes and aromatic extracts. Evaluation of optimized Salmonella tests covering over 250 samples from 43 types of HBPS revealed that gene mutation can be determined for these substances using a protocol optimized for the detection of mutagenic PAC. The outcomes of modified Salmonella assays can be predicted using HBPS compositional information as input to a newly developed statistical model. The general outcome of the optimized Salmonella assay can be predicted for an untested substance based on its Aromatic Ring Class (ARC) profile. Review of the results from numerous cytogenetic tests showed that although a few positive study results have been reported, most HBPS do not produce chromosomal effects when tested in rodent bone marrow assays or in in vitro chromosomal aberration assays. Results of both bacterial and cytogenetic studies can be used to satisfy genetic toxicity endpoints for the HBPS category substances.

  17. Genetic analysis shows that morphology alone cannot distinguish asian carp eggs from those of other cyprinid species

    USGS Publications Warehouse

    Larson, James H.; McCalla, Sunnie; Chapman, Duane C.; Rees, Christopher B.; Knights, Brent C.; Vallazza, Jon; George, Amy E.; Richardson, William B.; Amberg, Jon

    2016-01-01

    Fish eggs and embryos (hereafter collectively referred to as “eggs”) were collected in the upper Mississippi River main stem (~300 km upstream of previously reported spawning by invasive Asian carp) during summer 2013. Based on previously published morphological characteristics, the eggs were identified as belonging to Asian carp. A subsample of the eggs was subsequently analyzed by using molecular methods to determine species identity. Genetic identification using the cytochrome-c oxidase 1 gene was attempted for a total of 41 eggs. Due to the preservation technique used (formalin) and the resulting DNA degradation, sequences were recovered from only 17 individual eggs. In all 17 cases, cyprinids other than Asian carp (usually Notropis sp.) were identified as the most likely species. In previously published reports, a key characteristic that distinguished Asian carp eggs from those of other cyprinids was size: Asian carp eggs exhibited diameters ranging from 4.0 to 6.0 mm and were thought to be much larger than the otherwise similar eggs of native species. Eggs from endemic cyprinids were believed to rarely reach 3.0 mm and had not been observed to exceed 3.3 mm. However, many of the eggs that were genetically identified as originating from native cyprinids were as large as 4.0 mm in diameter (at early developmental stages) and were therefore large enough to over- lap with the lower end of the size range observed for Asian carp eggs. Researchers studying the egg stages of Asian carp and other cyprinids should plan on preserving subsets of eggs for genetic analysis to confirm morphological identifications.

  18. Root-determined hypernodulation mutant of Lotus japonicus shows high-yielding characteristics.

    PubMed

    Yokota, Keisuke; Li, Yong Yi; Hisatomi, Masahiro; Wang, Yanxu; Ishikawa, Kaori; Liu, Chi-Te; Suzuki, Shino; Aonuma, Kho; Aono, Toshihiro; Nakamoto, Tomomi; Oyaizu, Hiroshi

    2009-07-01

    Here we report the phenotypic characteristics of a novel hypernodulation mutant, Ljrdh1 (root-determined hypernodulation 1) of Lotus japonicus. At 12 weeks after rhizobial inoculation, there were no differences between the growth of Ljrdh1 and, wild-type. However, Ljrdh1 showed 2 to 3 times higher nitrogen-fixing activity, and seed and pod yields, were approximately 50% higher than the wild-type. This is the first report of a legume hypernodulation mutant showing normal growth and a high-yielding characteristic under optimal cultivation conditions.

  19. Enhancer regions show high histone H3.3 turnover that changes during differentiation

    PubMed Central

    Deaton, Aimee M; Gómez-Rodríguez, Mariluz; Mieczkowski, Jakub; Tolstorukov, Michael Y; Kundu, Sharmistha; Sadreyev, Ruslan I; Jansen, Lars ET; Kingston, Robert E

    2016-01-01

    The organization of DNA into chromatin is dynamic; nucleosomes are frequently displaced to facilitate the ability of regulatory proteins to access specific DNA elements. To gain insight into nucleosome dynamics, and to follow how dynamics change during differentiation, we used a technique called time-ChIP to quantitatively assess histone H3.3 turnover genome-wide during differentiation of mouse ESCs. We found that, without prior assumptions, high turnover could be used to identify regions involved in gene regulation. High turnover was seen at enhancers, as observed previously, with particularly high turnover at super-enhancers. In contrast, regions associated with the repressive Polycomb-Group showed low turnover in ESCs. Turnover correlated with DNA accessibility. Upon differentiation, numerous changes in H3.3 turnover rates were observed, the majority of which occurred at enhancers. Thus, time-ChIP measurement of histone turnover shows that active enhancers are unusually dynamic in ESCs and changes in highly dynamic nucleosomes predominate at enhancers during differentiation. DOI: http://dx.doi.org/10.7554/eLife.15316.001 PMID:27304074

  20. Human fallopian tube proteome shows high coverage of mesenchymal stem cells associated proteins.

    PubMed

    Wang, Chenyuan; Liu, Yang; Chang, Cheng; Wu, Songfeng; Gao, Jie; Zhang, Yang; Chen, Yingjie; Zhong, Fan; Deng, Gaopi

    2016-01-01

    The object of this research was to report a draft proteome of human fallopian tube (hFT) comprises 5416 identified proteins, which could be considered as a physiological reference to complement Human Proteome Draft. The proteomic raw data and metadata were stored in an integrated proteome resources centre iProX (IPX00034300). This hFT proteome contains many hFT markers newly identified by mass spectrum. This hFT proteome comprises 660 high-, 3605 medium- and 1181 low-abundant proteins. Ribosome, cytoskeleton, vesicle and protein folding associated proteins showed obvious tendency to be higher abundance in hFT. The extraordinary high coverage of mesenchymal stem cells (MSCs)-associated proteins were identified in this hFT proteome, which highly supported that hFT should contain a plenty of MSCs. PMID:26759384

  1. Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake1234

    PubMed Central

    Tanaka, Toshiko; Ngwa, Julius S; van Rooij, Frank JA; Zillikens, M Carola; Wojczynski, Mary K; Frazier-Wood, Alexis C; Houston, Denise K; Kanoni, Stavroula; Lemaitre, Rozenn N; Luan, Jian'an; Mikkilä, Vera; Renstrom, Frida; Sonestedt, Emily; Zhao, Jing Hua; Chu, Audrey Y; Qi, Lu; Chasman, Daniel I; de Oliveira Otto, Marcia C; Dhurandhar, Emily J; Feitosa, Mary F; Johansson, Ingegerd; Khaw, Kay-Tee; Lohman, Kurt K; Manichaikul, Ani; McKeown, Nicola M; Mozaffarian, Dariush; Singleton, Andrew; Stirrups, Kathleen; Viikari, Jorma; Ye, Zheng; Bandinelli, Stefania; Barroso, Inês; Deloukas, Panos; Forouhi, Nita G; Hofman, Albert; Liu, Yongmei; Lyytikäinen, Leo-Pekka; North, Kari E; Dimitriou, Maria; Hallmans, Goran; Kähönen, Mika; Langenberg, Claudia; Ordovas, Jose M; Uitterlinden, André G; Hu, Frank B; Kalafati, Ioanna-Panagiota; Raitakari, Olli; Franco, Oscar H; Johnson, Andrew; Emilsson, Valur; Schrack, Jennifer A; Semba, Richard D; Siscovick, David S; Arnett, Donna K; Borecki, Ingrid B; Franks, Paul W; Kritchevsky, Stephen B; Lehtimäki, Terho; Loos, Ruth JF; Orho-Melander, Marju; Rotter, Jerome I; Wareham, Nicholas J; Witteman, Jacqueline CM; Ferrucci, Luigi; Dedoussis, George; Cupples, L Adrienne; Nettleton, Jennifer A

    2013-01-01

    Background: Macronutrient intake varies substantially between individuals, and there is evidence that this variation is partly accounted for by genetic variants. Objective: The objective of the study was to identify common genetic variants that are associated with macronutrient intake. Design: We performed 2-stage genome-wide association (GWA) meta-analysis of macronutrient intake in populations of European descent. Macronutrients were assessed by using food-frequency questionnaires and analyzed as percentages of total energy consumption from total fat, protein, and carbohydrate. From the discovery GWA (n = 38,360), 35 independent loci associated with macronutrient intake at P < 5 × 10−6 were identified and taken forward to replication in 3 additional cohorts (n = 33,533) from the DietGen Consortium. For one locus, fat mass obesity-associated protein (FTO), cohorts with Illumina MetaboChip genotype data (n = 7724) provided additional replication data. Results: A variant in the chromosome 19 locus (rs838145) was associated with higher carbohydrate (β ± SE: 0.25 ± 0.04%; P = 1.68 × 10−8) and lower fat (β ± SE: −0.21 ± 0.04%; P = 1.57 × 10−9) consumption. A candidate gene in this region, fibroblast growth factor 21 (FGF21), encodes a fibroblast growth factor involved in glucose and lipid metabolism. The variants in this locus were associated with circulating FGF21 protein concentrations (P < 0.05) but not mRNA concentrations in blood or brain. The body mass index (BMI)–increasing allele of the FTO variant (rs1421085) was associated with higher protein intake (β ± SE: 0.10 ± 0.02%; P = 9.96 × 10−10), independent of BMI (after adjustment for BMI, β ± SE: 0.08 ± 0.02%; P = 3.15 × 10−7). Conclusion: Our results indicate that variants in genes involved in nutrient metabolism and obesity are associated with macronutrient consumption in humans. Trials related to this study were registered at clinicaltrials.gov as NCT00005131 (Atherosclerosis

  2. Low genetic variability in the highly endangered mediterranean monk seal.

    PubMed

    Pastor, T; Garza, J C; Allen, P; Amos, W; Aguilar, A

    2004-01-01

    Genetic variability is an important component in the ability of populations to adapt in the face of environmental change. Here we report the first description of nuclear genetic variability in the only remaining sizable colony of the Mediterranean monk seal (Monachus monachus), located at Cap Blanc (Western Sahara, Mauritania), whose estimated size during the study period (1994-May 1997) was about 320 individuals. We tested 42 microsatellite loci isolated from five pinniped species in a sample of 52 pups. Three loci failed to give any product, and of the remaining 39, only 15 were polymorphic, with a maximum of 3 alleles detected. Three loci appeared to be X-linked. No departures from Hardy-Weinberg equilibrium were detected and no genetic structure was found between the two nursing caves currently occupied by the seals. Several analytical methods show that, as a consequence of a severe bottleneck, the population has suffered a decrease in genetic variability over the last few centuries. PMID:15247308

  3. DNA Barcode Detects High Genetic Structure within Neotropical Bird Species

    PubMed Central

    Tavares, Erika Sendra; Gonçalves, Priscila; Miyaki, Cristina Yumi; Baker, Allan J.

    2011-01-01

    Background Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. Methods and Findings Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520) of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21) or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20). Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. Conclusions The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent geological periods

  4. High genetic diversity and population structure in the endangered Canarian endemic Ruta oreojasme (Rutaceae).

    PubMed

    Meloni, Marilena; Reid, Andrea; Caujapé-Castells, Juli; Soto, Moisés; Fernández-Palacios, José María; Conti, Elena

    2015-10-01

    Insular species are expected to have low genetic diversity, for their populations are often small and isolated, and characterized by restricted gene flow and increased incidence of inbreeding. However, empirical results do not always match this expectation. For example, population genetic analyses of several Canarian endemics, based mainly on allozymes, show levels of genetic diversity exceptionally high for insular species. To investigate whether genetic variation in rare species endemic to Canary Islands is low, as predicted by theoretical expectations, or high, as documented in some previous studies, we analysed genetic diversity of the endangered Ruta oreojasme, a rare endemic of the island of Gran Canaria, using microsatellite markers, which are more variable than allozymes. Our analyses identified very high levels of genetic diversity (A = 7.625, P = 0.984, H o = 0.558, H e = 0.687) for R. oreojasme. Even though the distribution of the species is restricted to the South of Gran Canaria, only one population shows low genetic diversity, isolation and signs of a recent bottleneck/founder event. Some intrinsic characteristics of R. oreojasme (hermaphroditism, proterandry and polyploidy), the relative climatic stability of the Canarian archipelago during Quaternary glacials/interglacials, the size of most populations (thousands of individuals), its age, and the relative proximity of the archipelago to the mainland might have contributed to the high diversity that characterises this endemic. As expected, given the marked topographic complexity of Gran Canaria, we found marked genetic structure in R. oreojasme populations. Our results support the observation that Canarian endemics are characterised by unexpectedly high genetic diversity and provides important insights for potential applications to the conservation of R. oreojasme.

  5. Genetic diversity on the Comoros Islands shows early seafaring as major determinant of human biocultural evolution in the Western Indian Ocean.

    PubMed

    Msaidie, Said; Ducourneau, Axel; Boetsch, Gilles; Longepied, Guy; Papa, Kassim; Allibert, Claude; Yahaya, Ali Ahmed; Chiaroni, Jacques; Mitchell, Michael J

    2011-01-01

    The Comoros Islands are situated off the coast of East Africa, at the northern entrance of the channel of Mozambique. Contemporary Comoros society displays linguistic, cultural and religious features that are indicators of interactions between African, Middle Eastern and Southeast Asian (SEA) populations. Influences came from the north, brought by the Arab and Persian traders whose maritime routes extended to Madagascar by 700-900 AD. Influences also came from the Far East, with the long-distance colonisation by Austronesian seafarers that reached Madagascar 1500 years ago. Indeed, strong genetic evidence for a SEA, but not a Middle Eastern, contribution has been found on Madagascar, but no genetic trace of either migration has been shown to exist in mainland Africa. Studying genetic diversity on the Comoros Islands could therefore provide new insights into human movement in the Indian Ocean. Here, we describe Y chromosomal and mitochondrial genetic variation in 577 Comorian islanders. We have defined 28 Y chromosomal and 9 mitochondrial lineages. We show the Comoros population to be a genetic mosaic, the result of tripartite gene flow from Africa, the Middle East and Southeast Asia. A distinctive profile of African haplogroups, shared with Madagascar, may be characteristic of coastal sub-Saharan East Africa. Finally, the absence of any maternal contribution from Western Eurasia strongly implicates male-dominated trade and religion as the drivers of gene flow from the North. The Comoros provides a first view of the genetic makeup of coastal East Africa.

  6. All reovirus subtypes show oncolytic potential in primary cells of human high-grade glioma.

    PubMed

    Alloussi, S H; Alkassar, M; Urbschat, S; Graf, N; Gärtner, B

    2011-09-01

    Reoviridae are non-human pathogenic viruses. The family of reoviridae consists of 4 different subtypes. Many studies have proven that the Dearing subtype 3 has oncolytic potential. This potential is related to the RAS protein expression in tumour cells. The aim of this study, was to investigate whether all reovirus subtypes have oncolytic potential and whether there are differences in their efficacy, in particular for high-grade glioma. To evaluate the oncolytic potential, we performed an in vitro head-to-head study for all reovirus subtypes in 5 primary cell cultures of high-grade gliomas. The oncolytic activity was determined using end-point titration with observation of the cytopathogenic effect. For measurement of RAS activity, we performed an immunofluorescent detection stain on all cell cultures. For quantification of the virus, an RT-PCR measurement for all subtypes was performed. All reovirus subtypes showed oncolytic activity in the observed glioma biopsies. These observations correlated with RAS overexpression in the observed cells. All glioma biopsies overexpressed the RAS protein. The quantitative oncolytic potential differed in relation to the single observed cell culture and in relation to the chosen reovirus subtype. To our knowledge, this is the first study showing oncolytic activity for all reovirus subtypes. We show the relationship and correlation between RAS protein overexpression and vulnerability of cells to reovirus. Efficacy of the different subtypes is interindividually different and cannot be forecast.

  7. Isotopically enriched ammonium shows high nitrogen transformation in the pile top zone of dairy manure compost

    NASA Astrophysics Data System (ADS)

    Maeda, Koki; Toyoda, Sakae; Yano, Midori; Hattori, Shohei; Fukasawa, Makoto; Nakajima, Keiichi; Yoshida, Naohiro

    2016-03-01

    Nitrogen isotope ratios (δ15N) of NH4+ in dairy manure compost piles with and without bulking agent (10 % w/w) were compared to understand the effects of the use of bulking agent on nitrogen conversion during manure composting. The δ15N-NH4+ values in each of three pile zones (top, side and core) were also compared. At the end of the process, piles with bulking agent showed significantly higher δ15N values (17.7 ± 1.3 ‰) than piles without bulking agent (11.8 ± 0.9 ‰), reflecting the significantly higher nitrogen conversion and NH3 loss in the former. The samples from the top zone, especially in the piles with bulking agent, showed very high NH4+ concentrations with significantly high 15N (δ15N: 12.7-29.8 ‰) values, indicating that extremely high nitrogen conversion, nitrification-denitrification activity of the microbes and NH3 volatilization occurred in this zone.

  8. Genetic analysis shows low levels of hybridization between African wildcats (Felis silvestris lybica) and domestic cats (F. s. catus) in South Africa.

    PubMed

    Le Roux, Johannes J; Foxcroft, Llewellyn C; Herbst, Marna; MacFadyen, Sandra

    2015-01-01

    Hybridization between domestic and wild animals is a major concern for biodiversity conservation, and as habitats become increasingly fragmented, conserving biodiversity at all levels, including genetic, becomes increasingly important. Except for tropical forests and true deserts, African wildcats occur across the African continent; however, almost no work has been carried out to assess its genetic status and extent of hybridization with domestic cats. For example, in South Africa it has been argued that the long-term viability of maintaining pure wildcat populations lies in large protected areas only, isolated from human populations. Two of the largest protected areas in Africa, the Kgalagadi Transfrontier and Kruger National Parks, as well as the size of South Africa and range of landscape uses, provide a model situation to assess how habitat fragmentation and heterogeneity influences the genetic purity of African wildcats. Using population genetic and home range data, we examined the genetic purity of African wildcats and their suspected hybrids across South Africa, including areas within and outside of protected areas. Overall, we found African wildcat populations to be genetically relatively pure, but instances of hybridization and a significant relationship between the genetic distinctiveness (purity) of wildcats and human population pressure were evident. The genetically purest African wildcats were found in the Kgalagadi Transfrontier Park, while samples from around Kruger National Park showed cause for concern, especially combined with the substantial human population density along the park's boundary. While African wildcat populations in South Africa generally appear to be genetically pure, with low levels of hybridization, our genetic data do suggest that protected areas may play an important role in maintaining genetic purity by reducing the likelihood of contact with domestic cats. We suggest that approaches such as corridors between protected areas

  9. Genetic analysis shows low levels of hybridization between African wildcats (Felis silvestris lybica) and domestic cats (F. s. catus) in South Africa

    PubMed Central

    Le Roux, Johannes J; Foxcroft, Llewellyn C; Herbst, Marna; MacFadyen, Sandra

    2015-01-01

    Hybridization between domestic and wild animals is a major concern for biodiversity conservation, and as habitats become increasingly fragmented, conserving biodiversity at all levels, including genetic, becomes increasingly important. Except for tropical forests and true deserts, African wildcats occur across the African continent; however, almost no work has been carried out to assess its genetic status and extent of hybridization with domestic cats. For example, in South Africa it has been argued that the long-term viability of maintaining pure wildcat populations lies in large protected areas only, isolated from human populations. Two of the largest protected areas in Africa, the Kgalagadi Transfrontier and Kruger National Parks, as well as the size of South Africa and range of landscape uses, provide a model situation to assess how habitat fragmentation and heterogeneity influences the genetic purity of African wildcats. Using population genetic and home range data, we examined the genetic purity of African wildcats and their suspected hybrids across South Africa, including areas within and outside of protected areas. Overall, we found African wildcat populations to be genetically relatively pure, but instances of hybridization and a significant relationship between the genetic distinctiveness (purity) of wildcats and human population pressure were evident. The genetically purest African wildcats were found in the Kgalagadi Transfrontier Park, while samples from around Kruger National Park showed cause for concern, especially combined with the substantial human population density along the park's boundary. While African wildcat populations in South Africa generally appear to be genetically pure, with low levels of hybridization, our genetic data do suggest that protected areas may play an important role in maintaining genetic purity by reducing the likelihood of contact with domestic cats. We suggest that approaches such as corridors between protected areas

  10. High genetic diversity and novelty in planktonic protists inhabiting inland and coastal high salinity water bodies.

    PubMed

    Triadó-Margarit, Xavier; Casamayor, Emilio O

    2013-07-01

    We analyzed the genetic diversity (18S rRNA gene) of planktonic microbial eukaryotes in 34 different coastal and inland saline ponds. A wide range of environmental conditions was covered with up to 30-fold differences in salinity concentrations (12.5-384 g L(-1)), and in situ temperatures (1.3-37.5 °C), and three orders of magnitude in the trophic status (i.e. chlorophyll a < 0.1 to >50 mg L(-1)). Geographically distant sites were studied with contrasting salt origins, and different temporal patterns of wetting and drying. The genetic diversity was high, far beyond the few groups traditionally considered as high salinity-adapted, with sequences spread throughout eight high-rank taxonomic groups and 27 eukaryal classes. The novelty level was extremely high, with 10% of the whole dataset showing < 90% identity to any previously reported sequence in GenBank. Opisthokonta and Rhizaria contained the highest novelty and Chlorophyta and Alveolata the lowest. Low identity sequences were observed both in coastal and inland sites and at lower and at higher salinities, although the degree of novelty was higher in the hypersaline waters (> 6.5% salinity). Overall, this study shows important gaps in the current knowledge about protists inhabiting continental (hyper)saline water bodies, highlighting the need for future, more detailed investigations.

  11. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    PubMed

    Noreen, Annika M E; Webb, Edward L

    2013-01-01

    Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (<1 yr) of the canopy tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854), high allelic richness (R = 16.7-19.5), low inbreeding co-efficients (FIS = 0.013-0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency <1%). However, spatial genetic structure (SGS) analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss. PMID:24367531

  12. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    PubMed

    Noreen, Annika M E; Webb, Edward L

    2013-01-01

    Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (<1 yr) of the canopy tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854), high allelic richness (R = 16.7-19.5), low inbreeding co-efficients (FIS = 0.013-0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency <1%). However, spatial genetic structure (SGS) analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

  13. Disproportionate Cochlear Length in Genus Homo Shows a High Phylogenetic Signal during Apes' Hearing Evolution.

    PubMed

    Braga, J; Loubes, J-M; Descouens, D; Dumoncel, J; Thackeray, J F; Kahn, J-L; de Beer, F; Riberon, A; Hoffman, K; Balaresque, P; Gilissen, E

    2015-01-01

    Changes in lifestyles and body weight affected mammal life-history evolution but little is known about how they shaped species' sensory systems. Since auditory sensitivity impacts communication tasks and environmental acoustic awareness, it may have represented a deciding factor during mammal evolution, including apes. Here, we statistically measure the influence of phylogeny and allometry on the variation of five cochlear morphological features associated with hearing capacities across 22 living and 5 fossil catarrhine species. We find high phylogenetic signals for absolute and relative cochlear length only. Comparisons between fossil cochleae and reconstructed ape ancestral morphotypes show that Australopithecus absolute and relative cochlear lengths are explicable by phylogeny and concordant with the hypothetized ((Pan,Homo),Gorilla) and (Pan,Homo) most recent common ancestors. Conversely, deviations of the Paranthropus oval window area from these most recent common ancestors are not explicable by phylogeny and body weight alone, but suggest instead rapid evolutionary changes (directional selection) of its hearing organ. Premodern (Homo erectus) and modern human cochleae set apart from living non-human catarrhines and australopiths. They show cochlear relative lengths and oval window areas larger than expected for their body mass, two features corresponding to increased low-frequency sensitivity more recent than 2 million years ago. The uniqueness of the "hypertrophied" cochlea in the genus Homo (as opposed to the australopiths) and the significantly high phylogenetic signal of this organ among apes indicate its usefulness to identify homologies and monophyletic groups in the hominid fossil record. PMID:26083484

  14. Disproportionate Cochlear Length in Genus Homo Shows a High Phylogenetic Signal during Apes’ Hearing Evolution

    PubMed Central

    Braga, J.; Loubes, J-M.; Descouens, D.; Dumoncel, J.; Thackeray, J. F.; Kahn, J-L.; de Beer, F.; Riberon, A.; Hoffman, K.; Balaresque, P.; Gilissen, E.

    2015-01-01

    Changes in lifestyles and body weight affected mammal life-history evolution but little is known about how they shaped species’ sensory systems. Since auditory sensitivity impacts communication tasks and environmental acoustic awareness, it may have represented a deciding factor during mammal evolution, including apes. Here, we statistically measure the influence of phylogeny and allometry on the variation of five cochlear morphological features associated with hearing capacities across 22 living and 5 fossil catarrhine species. We find high phylogenetic signals for absolute and relative cochlear length only. Comparisons between fossil cochleae and reconstructed ape ancestral morphotypes show that Australopithecus absolute and relative cochlear lengths are explicable by phylogeny and concordant with the hypothetized ((Pan,Homo),Gorilla) and (Pan,Homo) most recent common ancestors. Conversely, deviations of the Paranthropus oval window area from these most recent common ancestors are not explicable by phylogeny and body weight alone, but suggest instead rapid evolutionary changes (directional selection) of its hearing organ. Premodern (Homo erectus) and modern human cochleae set apart from living non-human catarrhines and australopiths. They show cochlear relative lengths and oval window areas larger than expected for their body mass, two features corresponding to increased low-frequency sensitivity more recent than 2 million years ago. The uniqueness of the “hypertrophied” cochlea in the genus Homo (as opposed to the australopiths) and the significantly high phylogenetic signal of this organ among apes indicate its usefulness to identify homologies and monophyletic groups in the hominid fossil record. PMID:26083484

  15. Disproportionate Cochlear Length in Genus Homo Shows a High Phylogenetic Signal during Apes' Hearing Evolution.

    PubMed

    Braga, J; Loubes, J-M; Descouens, D; Dumoncel, J; Thackeray, J F; Kahn, J-L; de Beer, F; Riberon, A; Hoffman, K; Balaresque, P; Gilissen, E

    2015-01-01

    Changes in lifestyles and body weight affected mammal life-history evolution but little is known about how they shaped species' sensory systems. Since auditory sensitivity impacts communication tasks and environmental acoustic awareness, it may have represented a deciding factor during mammal evolution, including apes. Here, we statistically measure the influence of phylogeny and allometry on the variation of five cochlear morphological features associated with hearing capacities across 22 living and 5 fossil catarrhine species. We find high phylogenetic signals for absolute and relative cochlear length only. Comparisons between fossil cochleae and reconstructed ape ancestral morphotypes show that Australopithecus absolute and relative cochlear lengths are explicable by phylogeny and concordant with the hypothetized ((Pan,Homo),Gorilla) and (Pan,Homo) most recent common ancestors. Conversely, deviations of the Paranthropus oval window area from these most recent common ancestors are not explicable by phylogeny and body weight alone, but suggest instead rapid evolutionary changes (directional selection) of its hearing organ. Premodern (Homo erectus) and modern human cochleae set apart from living non-human catarrhines and australopiths. They show cochlear relative lengths and oval window areas larger than expected for their body mass, two features corresponding to increased low-frequency sensitivity more recent than 2 million years ago. The uniqueness of the "hypertrophied" cochlea in the genus Homo (as opposed to the australopiths) and the significantly high phylogenetic signal of this organ among apes indicate its usefulness to identify homologies and monophyletic groups in the hominid fossil record.

  16. Mannosylerythritol lipid, a yeast extracellular glycolipid, shows high binding affinity towards human immunoglobulin G

    PubMed Central

    Im, Jae Hong; Nakane, Takashi; Yanagishita, Hiroshi; Ikegami, Toru; Kitamoto, Dai

    2001-01-01

    Background There have been many attempts to develop new materials with stability and high affinity towards immunoglobulins. Some of glycolipids such as gangliosides exhibit a high affinity toward immunoglobulins. However, it is considerably difficult to develop these glycolipids into the practical separation ligand due to their limited amounts. We thus focused our attention on the feasible use of "mannosylerythritol lipid A", a yeast glycolipid biosurfactant, as an alternative ligand for immunoglobulins, and undertook the investigation on the binding between mannosylerythritol lipid A (MEL-A) and human immunoglobulin G (HIgG). Results In ELISA assay, MEL-A showed nearly the same binding affinity towards HIgG as that of bovine ganglioside GM1. Fab of human IgG was considered to play a more important role than Fc in the binding of HIgG by MEL-A. The bound amount of HIgG increased depending on the attached amount of MEL-A onto poly (2-hydroxyethyl methacrylate) (polyHEMA) beads, whereas the amount of human serum albumin slightly decreased. Binding-amount and -selectivity of HIgG towards MEL-A were influenced by salt species, salt concentration and pH in the buffer solution. The composite of MEL-A and polyHEMA, exhibited a significant binding constant of 1.43 × 106 (M-1) for HIgG, which is approximately 4-fold greater than that of protein A reported. Conclusions MEL-A shows high binding-affinity towards HIgG, and this is considered to be due to "multivalent effect" based on the binding molar ratio. This is the first report on the binding of a natural human antibody towards a yeast glycolipid. PMID:11604104

  17. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

  18. High-resolution genetic mapping of complex traits.

    PubMed Central

    Kruglyak, L; Lander, E S

    1995-01-01

    Positional cloning requires high-resolution genetic mapping. To plan a positional cloning project, one needs to know how many informative meioses will be required to narrow the search for a disease gene to an acceptably small region. For a simple Mendelian trait studied with linkage analysis, the answer is straightforward. In this paper, we address the situation of a complex trait studied with affected-relative-pair methods. We derive mathematical formulas for the size of an appropriate confidence region, as a function of the relative risk attributable to the gene. Using these results, we provide graphs showing the number of relative pairs required to narrow the gene hunt to an interval of a given size. For example, we show that localizing a gene to 1 cM requires a median of 200 sib pairs for a locus causing a fivefold increased risk to an offspring and 700 sib pairs for a locus causing a twofold increased risk. We discuss the implications of these results for the positional cloning of genes underlying complex traits. PMID:7726179

  19. High-resolution genetic mapping of complex traits

    SciTech Connect

    Zruglyak, L.; Lander, E.S. |

    1995-05-01

    Positional cloning requires high-resolution genetic mapping. To plan a positional cloning project, one needs to know how many informative meioses will be required to narrow the search for a disease gene to an acceptably small region. For a simple Mendelian trait studied with linkage analysis, the answer is straightforward. In this paper, we address the situation of a complex trait studied with affected-relative-pair methods. We derive mathematical formulas for the size of an appropriate confidence region, as a function of the relative risk attributable to the gene. Using these results, we provide graphs showing the number of relative pairs required to narrow the gene hunt to an interval of a given size. For example, we show that localizing a gene to a 1 cM requires a median of 200 sib pairs for a locus causing a fivefold increased risk to an offspring and 700 sib pairs for a locus causing a twofold increased risk. We discuss the implications of these results for the positional cloning of genes underlying complex traits. 11 refs., 7 figs., 2 tabs.

  20. A new two-phase dimeticone pediculicide shows high efficacy in a comparative bioassay

    PubMed Central

    2009-01-01

    Background Dimeticones kill head lice by physical means. Here we assessed in a comparative bioassay the ex vivo efficacy of "NYDA® sensitiv", a new two-phase dimeticone-based pediculicide similar to a product established on the market, but without fragrances. Methods We compared efficacy of the new product to a positive dimeticone control group, a sample of four other insecticidal and natural head lice products marketed in Germany, and an untreated control. In a bioassay, lice were exposed ex vivo to products and examined for activity for up to 24 hours, following a standard protocol. Results After 6 and 24 hours, 13.7 and 88.5% of untreated control lice did not show major vital signs. In contrast, no lice showed major vital signs 5 minutes after treatment with the new product or the control dimeticone group (NYDA®). This effect persisted at all observation points (100% efficacy). Efficacy of 0.5% permethrin (Infectopedicul®) ranged between 76 and 96% in evaluations between 5 min and 6 hours. All lice treated with a coconut-based compound (mosquito® Läuseshampoo) did not show major vital signs after 5 min, but mortality was only 58% after one hour. Pyrethrum extract (Goldgeist® forte) showed an efficacy of 22 - 52% between 5 min and 3 hours after treatment; after 6 hours, 76% of lice were judged dead. An oxyphthirine®-based compound (Liberalice DUO LP-PRO®) killed 22 - 54% of lice in the first 6 hours. Conclusions The two-phase dimeticone compound NYDA® sensitiv is highly efficacious. The removal of fragrances as compared to an established dimeticone product did not affect in vitro efficacy. PMID:20003435

  1. Ghrelin O-acyltransferase knockout mice show resistance to obesity when fed high-sucrose diet.

    PubMed

    Kouno, Tetsuya; Akiyama, Nobuteru; Ito, Takahito; Okuda, Tomohiko; Nanchi, Isamu; Notoya, Mitsuru; Oka, Shogo; Yukioka, Hideo

    2016-02-01

    Ghrelin is an appetite-stimulating hormone secreted from stomach. Since the discovery that acylation of the serine-3 residue by ghrelin O-acyltransferase (GOAT) is essential for exerting its functions, GOAT has been regarded as an therapeutic target for attenuating appetite, and thus for the treatment of obesity and diabetes. However, contrary to the expectations, GOAT-knockout (KO) mice have not shown meaningful body weight reduction, under high-fat diet. Here, in this study, we sought to determine whether GOAT has a role in body weight regulation and glucose metabolism with a focus on dietary sucrose, because macronutrient composition of diet is important for appetite regulation. We found that peripherally administered acylated-ghrelin, but not unacylated one, stimulated sucrose consumption in a two-bottle-drinking test. The role of acylated-ghrelin in sucrose preference was further supported by the finding that GOAT KO mice consumed less sucrose solution compared with WT littermates. Then, we investigated the effect of dietary composition of sucrose on food intake and body weight in GOAT KO and WT mice. As a result, when fed on high-fat diet, food intake and body weight were similar between GOAT KO and WT mice. However, when fed on high-fat, high-sucrose diet, GOAT KO mice showed significantly reduced food intake and marked resistance to obesity, leading to amelioration of glucose metabolism. These results suggest that blockade of acylated-ghrelin production offers therapeutic potential for obesity and metabolic disorders caused by overeating of palatable food.

  2. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep.

    PubMed

    Vahidi, S M F; Faruque, M O; Falahati Anbaran, M; Afraz, F; Mousavi, S M; Boettcher, P; Joost, S; Han, J L; Colli, L; Periasamy, K; Negrini, R; Ajmone-Marsan, P

    2016-08-01

    Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7-22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72-0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST  = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes, are discussed. PMID:26953226

  3. Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them

    PubMed Central

    Zhai, Feifei; Mao, Jinmei; Liu, Junxiang; Peng, Xiangyong; Han, Lei; Sun, Zhenyuan

    2016-01-01

    Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation. PMID:27047511

  4. Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them.

    PubMed

    Zhai, Feifei; Mao, Jinmei; Liu, Junxiang; Peng, Xiangyong; Han, Lei; Sun, Zhenyuan

    2016-01-01

    Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation.

  5. High-speed atomic force microscopy shows that annexin V stabilizes membranes on the second timescale.

    PubMed

    Miyagi, Atsushi; Chipot, Christophe; Rangl, Martina; Scheuring, Simon

    2016-09-01

    Annexins are abundant cytoplasmic proteins that can bind to negatively charged phospholipids in a Ca(2+)-dependent manner, and are known to play a role in the storage of Ca(2+) and membrane healing. Little is known, however, about the dynamic processes of protein-Ca(2+)-membrane assembly and disassembly. Here we show that high-speed atomic force microscopy (HS-AFM) can be used to repeatedly induce and disrupt annexin assemblies and study their structure, dynamics and interactions. Our HS-AFM set-up is adapted for such biological applications through the integration of a pumping system for buffer exchange and a pulsed laser system for uncaging caged compounds. We find that biochemically identical annexins (annexin V) display different effective Ca(2+) and membrane affinities depending on the assembly location, providing a wide Ca(2+) buffering regime while maintaining membrane stabilization. We also show that annexin is membrane-recruited and forms stable supramolecular assemblies within ∼5 s in conditions that are comparable to a membrane lesion in a cell. Molecular dynamics simulations provide atomic detail of the role played by Ca(2+) in the reversible binding of annexin to the membrane surface. PMID:27271964

  6. Protein-polymer functionalized aqueous ferrofluids showing high T2 relaxivity.

    PubMed

    Bhattacharya, S; Sheikh, L; Tiwari, V; Ghosh, M; Patel, J N; Patel, A B; Nayar, S

    2014-05-01

    Controlled size, shape and dispersibility of superparamagnetic iron oxide nanoparticles (SPIONs), has been achieved in a protein-polymer colloidal dispersion. Stable ferrofluid (FF) is synthesized in an aqueous medium of collagen, bovine serum albumin and poly(vinyl) alcohol that equilibrates with time, at ambient conditions, into an organized matrix with iron oxide particles sterically caged at defined sites. It mimics a biomineralization system; hence the process is termed biomimetics. Though the exact mechanism is not understood at this stage, we have established, with serial dilution of the protein-polymer solution that the SPIONs are formed inside the self-contained clusters of the two proteins and the polymer, which show a tendency to self assemble. More than the interparticle dipolar attractions of magnetic particles, electrostatic interactions play a role in cluster formation and collagen is responsible for the overall stability, supported by systematic dynamic light scattering data. The basic aim of this study was to increase magnetization of a previously synthesized ferrofluid without hampering stability, by reducing the total macromolecular concentration. Thrice the magnetization was achieved and in addition, the synthesized FFs exhibited very high transverse relaxivity and showed good contrast in mice liver, in the in vivo studies. PMID:24734534

  7. Sarcomatoid lung carcinomas show high levels of Programmed death Ligand-1 (PD-L1)

    PubMed Central

    Velcheti, Vamsidhar; Rimm, David L.; Schalper, Kurt A.

    2013-01-01

    Programmed death-1 (PD-1) is a co-inhibitory inducible receptor present on T-cells and macrophages. Tumor cells with increased programmed death ligand-1 (PD-L1) are believed to escape immunity through activation of PD-1/PD-L1 pathway and suppression of effector immune responses. Recent strategies targeting the PD-1/PD-L1 axis have shown promising results in patients with several tumors types, including lung carcinomas. Preliminary data suggests that PD-L1 protein expression might predictive response to such therapies. Sarcomatoid carcinomas (SCs) of the lung include rare subtypes of poorly differentiated non-small cell lung carcinomas (NSCLC) of high grade and aggressive behavior. The biology of these neoplasms is poorly understood and they frequently show increased local inflammatory and lymphocytic infiltration. Here, we report the expression of PD-L1 in 13 SCs from two large retrospective lung cancer cohorts. Using automated quantitative immunofloresence (aqIF/AQUA®) and a mouse monoclonal antibody directed against the extra-cellular domain of PD-L1, we show that 9 of 13 (69.2%) patients with SCs are positive for PD-L1 and their levels are higher than in conventional NSCLC. These results provide rationale for the potential use of targeted immunetherapy in lung SCs. PMID:23676558

  8. High-speed atomic force microscopy shows that annexin V stabilizes membranes on the second timescale

    NASA Astrophysics Data System (ADS)

    Miyagi, Atsushi; Chipot, Christophe; Rangl, Martina; Scheuring, Simon

    2016-09-01

    Annexins are abundant cytoplasmic proteins that can bind to negatively charged phospholipids in a Ca2+-dependent manner, and are known to play a role in the storage of Ca2+ and membrane healing. Little is known, however, about the dynamic processes of protein-Ca2+-membrane assembly and disassembly. Here we show that high-speed atomic force microscopy (HS-AFM) can be used to repeatedly induce and disrupt annexin assemblies and study their structure, dynamics and interactions. Our HS-AFM set-up is adapted for such biological applications through the integration of a pumping system for buffer exchange and a pulsed laser system for uncaging caged compounds. We find that biochemically identical annexins (annexin V) display different effective Ca2+ and membrane affinities depending on the assembly location, providing a wide Ca2+ buffering regime while maintaining membrane stabilization. We also show that annexin is membrane-recruited and forms stable supramolecular assemblies within ˜5 s in conditions that are comparable to a membrane lesion in a cell. Molecular dynamics simulations provide atomic detail of the role played by Ca2+ in the reversible binding of annexin to the membrane surface.

  9. High-speed atomic force microscopy shows that annexin V stabilizes membranes on the second timescale

    NASA Astrophysics Data System (ADS)

    Miyagi, Atsushi; Chipot, Christophe; Rangl, Martina; Scheuring, Simon

    2016-09-01

    Annexins are abundant cytoplasmic proteins that can bind to negatively charged phospholipids in a Ca2+-dependent manner, and are known to play a role in the storage of Ca2+ and membrane healing. Little is known, however, about the dynamic processes of protein–Ca2+–membrane assembly and disassembly. Here we show that high-speed atomic force microscopy (HS-AFM) can be used to repeatedly induce and disrupt annexin assemblies and study their structure, dynamics and interactions. Our HS-AFM set-up is adapted for such biological applications through the integration of a pumping system for buffer exchange and a pulsed laser system for uncaging caged compounds. We find that biochemically identical annexins (annexin V) display different effective Ca2+ and membrane affinities depending on the assembly location, providing a wide Ca2+ buffering regime while maintaining membrane stabilization. We also show that annexin is membrane-recruited and forms stable supramolecular assemblies within ∼5 s in conditions that are comparable to a membrane lesion in a cell. Molecular dynamics simulations provide atomic detail of the role played by Ca2+ in the reversible binding of annexin to the membrane surface.

  10. High yielding biomass genotypes of willow (Salix spp.) show differences in below ground biomass allocation

    PubMed Central

    Cunniff, Jennifer; Purdy, Sarah J.; Barraclough, Tim J.P.; Castle, March; Maddison, Anne L.; Jones, Laurence E.; Shield, Ian F.; Gregory, Andrew S.; Karp, Angela

    2015-01-01

    Willows (Salix spp.) grown as short rotation coppice (SRC) are viewed as a sustainable source of biomass with a positive greenhouse gas (GHG) balance due to their potential to fix and accumulate carbon (C) below ground. However, exploiting this potential has been limited by the paucity of data available on below ground biomass allocation and the extent to which it varies between genotypes. Furthermore, it is likely that allocation can be altered considerably by environment. To investigate the role of genotype and environment on allocation, four willow genotypes were grown at two replicated field sites in southeast England and west Wales, UK. Above and below ground biomass was intensively measured over two two-year rotations. Significant genotypic differences in biomass allocation were identified, with below ground allocation differing by up to 10% between genotypes. Importantly, the genotype with the highest below ground biomass also had the highest above ground yield. Furthermore, leaf area was found to be a good predictor of below ground biomass. Growth environment significantly impacted allocation; the willow genotypes grown in west Wales had up to 94% more biomass below ground by the end of the second rotation. A single investigation into fine roots showed the same pattern with double the volume of fine roots present. This greater below ground allocation may be attributed primarily to higher wind speeds, plus differences in humidity and soil characteristics. These results demonstrate that the capacity exists to breed plants with both high yields and high potential for C accumulation. PMID:26339128

  11. Chromosome painting shows that skunks (Mephitidae, Carnivora) have highly rearranged karyotypes.

    PubMed

    Perelman, P L; Graphodatsky, A S; Dragoo, J W; Serdyukova, N A; Stone, G; Cavagna, P; Menotti, A; Nie, W; O'Brien, P C M; Wang, J; Burkett, S; Yuki, K; Roelke, M E; O'Brien, S J; Yang, F; Stanyon, R

    2008-01-01

    The karyotypic relationships of skunks (Mephitidae) with other major clades of carnivores are not yet established. Here, multi-directional chromosome painting was used to reveal the karyological relationships among skunks and between Mephitidae (skunks) and Procyonidae (raccoons). Representative species from three genera of Mephitidae (Mephitis mephitis, 2n = 50; Mephitis macroura, 2n = 50; Conepatus leuconotus, 2n = 46; Spilogale gracilis, 2n = 60) and one species of Procyonidae (Procyon lotor, 2n = 38) were studied. Chromosomal homology was mapped by hybridization of five sets of whole-chromosome paints derived from stone marten (Martes foina, 2n = 38), cat, skunks (M. mephitis; M. macroura) and human. The karyotype of the raccoon is highly conserved and identical to the hypothetical ancestral musteloid karyotype, suggesting that procyonids have a particular importance for establishing the karyological evolution within the caniforms. Ten fission events and five fusion events are necessary to generate the ancestral skunk karyotype from the ancestral carnivore karyotype. Our results show that Mephitidae joins Canidae and Ursidae as the third family of carnivores that are characterized by a high rate of karyotype evolution. Shared derived chromosomal fusion of stone marten chromosomes 6 and 14 phylogenetically links the American hog-nosed skunk and eastern spotted skunk.

  12. Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations

    PubMed Central

    Keren, Ray; Lavy, Adi; Mayzel, Boaz; Ilan, Micha

    2015-01-01

    Sponges are potent filter feeders and as such are exposed to high fluxes of toxic trace elements, which can accumulate in their body over time. Such is the case of the Red Sea sponge Theonella swinhoei, which has been shown to accumulate up to 8500 mg/Kg of the highly toxicelement arsenic. T. swinhoei is known to harbor a multitude of sponge-associated bacteria, so it is hypothesized that the associated-bacteria will be tolerant to high arsenic concentration. This study also investigates the fate of the arsenic accumulated in the sponge to test if the associated-bacteria have an important role in the arsenic accumulation process of their host, since bacteria are key players in the natural arsenic cycle. Separation of the sponge to sponge cells and bacteria enriched fractions showed that arsenic is accumulated by the bacteria. Sponge-associated, arsenic-tolerant bacteria were cultured in the presence of 5 mM of either arsenate or arsenite (equivalent to 6150 mg/Kg arsenic, dry weight). The 54 isolated bacteria were grouped to 15 operational taxonomic units (OTUs) and isolates belonging to 12 OTUs were assessed for tolerance to arsenate at increased concentrations up to 100 mM. Eight of the 12 OTUs tolerated an order of magnitude increase in the concentration of arsenate, and some exhibited external biomineralization of arsenic–magnesium salts. The biomineralization of this unique mineral was directly observed in bacteria for the first time. These results may provide an explanation for the ability of the sponge to accumulate considerable amounts of arsenic. Furthermore arsenic-mineralizing bacteria can potentially be used for the study of bioremediation, as arsenic toxicity affects millions of people worldwide. PMID:25762993

  13. Localized brain differences in Arc expression between mice showing low vs. high propensity to ethanol sensitization.

    PubMed

    Nona, Christina N; Lam, Marcus; Nobrega, José N

    2016-03-01

    Behavioral sensitization to ethanol (EtOH) manifests as a progressive and enduring increase in locomotor activity with repeated drug exposure. However, not all mice sensitize to EtOH and the neuronal mechanisms mediating vulnerability and resistance to EtOH sensitization remain unclear. We examined regional brain expression of the immediate early gene activity-regulated cytoskeleton-associated protein (Arc) in order to identify brain areas in which neuroplastic changes may contribute to the development and expression of EtOH sensitization. Male DBA/2J mice received 5 biweekly injections of EtOH (2.2g/kg, i.p.) or saline (SAL). They were categorized as high- (HS) or low-sensitized (LS) on the basis of final locomotor activity scores. In both LS and HS mice sacrificed after the last sensitization injection, Arc expression was decreased throughout the brain in comparison to SAL animals. A similar pattern was seen in mice sacrificed after an EtOH challenge two weeks after the last sensitization injection. However in this cohort, Arc expression was significantly increased in the central amygdala (CeA) in LS mice and in SAL mice receiving EtOH for the first time. No significant increases in Arc expression were seen in brains of sensitized (HS) animals. These results indicate an acute EtOH challenge results in different patterns of Arc expression in brains of LS, HS, and SAL mice. The dramatic increases in Arc expression in the CeA in LS and SAL mice showing little or no behavioral activation suggests that neural activity in this region may serve to inhibit the stimulant effects of EtOH. The observation that HS mice do not show increases in Arc expression with an EtOH challenge suggests the possibility that increased tolerance to the Arc-inducing effects of EtOH may be a factor in behavioral sensitization.

  14. The atherogenic Scarb1 null mouse model shows a high bone mass phenotype.

    PubMed

    Martineau, Corine; Martin-Falstrault, Louise; Brissette, Louise; Moreau, Robert

    2014-01-01

    Scavenger receptor class B, type I (SR-BI), the Scarb1 gene product, is a receptor associated with cholesteryl ester uptake from high-density lipoproteins (HDL), which drives cholesterol movement from peripheral tissues toward the liver for excretion, and, consequently, Scarb1 null mice are prone to atherosclerosis. Because studies have linked atherosclerosis incidence with osteoporosis, we characterized the bone metabolism in these mice. Bone morphometry was assessed through microcomputed tomography and histology. Marrow stromal cells (MSCs) were used to characterize influence of endogenous SR-BI in cell functions. Total and HDL-associated cholesterol in null mice were increased by 32-60%, correlating with its role in lipoprotein metabolism. Distal metaphyses from 2- and 4-mo-old null mice showed correspondingly 46 and 37% higher bone volume fraction associated with a higher number of trabeculae. Histomorphometric analyses in 2-mo-old null male mice revealed 1.42-fold greater osteoblast surface, 1.37-fold higher percent mineralizing surface, and 1.69-fold enhanced bone formation rate. In vitro assays for MSCs from null mice revealed 37% higher proliferation rate, 48% more alkaline phosphatase activity, 70% greater mineralization potential and a 2-fold osterix (Sp7) expression, yet a 0.5-fold decrease in caveolin-1 (Cav1) expression. Selective uptake levels of HDL-associated cholesteryl oleate and estradiol were similar between MSC from wild-type and Scarb1 null mice, suggesting that its contribution to this process is not its main role in these cells. However, Scarb1 knockout stunted the HDL-dependent regulation of Cav1 genic expression. Scarb1 null mice are not prone to osteoporosis but show higher bone mass associated with enhanced bone formation.

  15. High pressure spray with water shows similar efficiency to trimming in controlling microorganisms on poultry carcasses.

    PubMed

    Giombelli, Audecir; Hammerschmitt, Dandara; Cerutti, Marisete F; Chiarini, Eb; Landgraf, Mariza; Franco, Bernardete D G M; Destro, Maria T

    2015-10-01

    A study was conducted to evaluate a high pressure spray (HPS) with water as an alternative to trimming to remove gastrointestinal contamination on poultry carcasses and improve microbiological quality. The study was conducted under commercial conditions in 5 slaughter plants with one plant presenting approximately 5% of carcasses with visible gastrointestinal contamination (VGC), and the others showing approximately 12% of VGC. In all 5 plants, carcasses were sampled from the slaughter line and separated into 6 groups corresponding to 3 different treatments: A) carcasses with VGC before and after trimming; B) carcasses with VGC before and after HPS; and C) carcasses with no VGC before and after HPS. At the end of Trial A and prior to Trials B and C, an HPS equipment was installed before the end of the slaughter line. The HPS equipment was operated with 10 kgf/cm² of pressure and 1.5 L of potable water per carcass. Carcasses were analyzed using a rinsing procedure, and the following microbiological parameters were evaluated: the prevalence of Salmonella and Campylobacter, the abundance of Escherichia coli (EC), Enterobacteriaceae (EB), and the Total Viable Count (TVC). Salmonella was found in all plants at a prevalence ranging from 0.8% (plant 1) to 17.3% (plant 5), and the difference between plants was significant (P < 0.05%). The prevalence of Campylobacter ranged from 2.1 (plant 1) to 18.6% (plant 4) (P < 0.05%). The prevalence of Campylobacter was similar in plants 2, 3, and 5, and a significant difference (P < 0.05%) was observed compared to plants 1 and 4. In all plants, the EC, EB, and TVC counts did not show a significant difference (P > 0.05%) in any treatments. These results demonstrate that HPS with water is an alternative method for removing VGC and improving or maintaining the microbiological quality and safety of broiler carcasses.

  16. High pressure spray with water shows similar efficiency to trimming in controlling microorganisms on poultry carcasses.

    PubMed

    Giombelli, Audecir; Hammerschmitt, Dandara; Cerutti, Marisete F; Chiarini, Eb; Landgraf, Mariza; Franco, Bernardete D G M; Destro, Maria T

    2015-10-01

    A study was conducted to evaluate a high pressure spray (HPS) with water as an alternative to trimming to remove gastrointestinal contamination on poultry carcasses and improve microbiological quality. The study was conducted under commercial conditions in 5 slaughter plants with one plant presenting approximately 5% of carcasses with visible gastrointestinal contamination (VGC), and the others showing approximately 12% of VGC. In all 5 plants, carcasses were sampled from the slaughter line and separated into 6 groups corresponding to 3 different treatments: A) carcasses with VGC before and after trimming; B) carcasses with VGC before and after HPS; and C) carcasses with no VGC before and after HPS. At the end of Trial A and prior to Trials B and C, an HPS equipment was installed before the end of the slaughter line. The HPS equipment was operated with 10 kgf/cm² of pressure and 1.5 L of potable water per carcass. Carcasses were analyzed using a rinsing procedure, and the following microbiological parameters were evaluated: the prevalence of Salmonella and Campylobacter, the abundance of Escherichia coli (EC), Enterobacteriaceae (EB), and the Total Viable Count (TVC). Salmonella was found in all plants at a prevalence ranging from 0.8% (plant 1) to 17.3% (plant 5), and the difference between plants was significant (P < 0.05%). The prevalence of Campylobacter ranged from 2.1 (plant 1) to 18.6% (plant 4) (P < 0.05%). The prevalence of Campylobacter was similar in plants 2, 3, and 5, and a significant difference (P < 0.05%) was observed compared to plants 1 and 4. In all plants, the EC, EB, and TVC counts did not show a significant difference (P > 0.05%) in any treatments. These results demonstrate that HPS with water is an alternative method for removing VGC and improving or maintaining the microbiological quality and safety of broiler carcasses. PMID:26286999

  17. Interdisciplinarity, Debate And Movie Clips As Highly Motivating Factors In Live Shows - Five Years Of Success

    NASA Astrophysics Data System (ADS)

    Stengler, E.; Sirera, J. M.

    2011-09-01

    A live show on any subject that includes experiments and continuous interaction with the audience is a well known approach for EPO activities that many are carrying out all over. We present such an initiative with some added ingredients such as interdisciplinarity, the use of movie clips, and especially the debate between the two presenters, a debate that is all the more attractive to the public if it not fully staged but closely represents their actual points of view. José Montesinos, from the "Orotava" Canarian Foundation for the History of Science, is and plays the role of the more mature math professor who has grown weary of the overrated value given in science to mathematics and its consequences. This poses a constant challenge to his colleague, Erik Stengler, from the Science Museum of Tenerife, the young down-to-earth hands-on scientist, who defends the usual view that science and technology are to be judged by their achievements, which have brought about the advancement of modern society. With this approach and as a collaboration between our institutions, we have produced and toured highly successful activities on: Einstein and Relativity (from 2005 to 2008, "Einstein Goes To School," including a theatre play); circularity, the number π, forces of inertia and the Newtonian revolution (in 2008/2009, "The Tension Between Circularity and The Straight Line"); and the foundations of modern astronomy (in 2009/2010 "Kepler and Galileo, Messengers of the Stars"). Audiences were very varied - students, adult students, general public, prison inmates, teachers - and all appreciated the presentations as fun, thought-provoking and highly motivating, and valued especially the interdisciplinary character of the activity. Movie clips have shown to be especially useful to recover the attention of the young when they lose the thread due to the short attention spans they presently have.

  18. [Comparative chromosome painting shows the red panda (Ailurus fulgens) has a highly conserved karyotype].

    PubMed

    Tian, Ying; Nie, Wen-Hui; Wang, Jin-Huan; Yang, Yun-Fei; Yang, Feng-Tang

    2002-02-01

    We have established a comparative chromosome map between red panda (Ailurus fulgens, 2n = 36) and dog by chromosome painting with biotin-labelled chromosome-specific probes of the dog. Dog probes specific for the 38 automates delineated 71 homologous segments in the metaphase chromosomes of red panda. Of the 38 autosomal paints, 18 probes each delineated one homologous segment in red panda genome, while the other 20 ones each detected two to five homologous segments. The dog X chromosome-specific paint delineated the whole X chromosome of the red panda. The results indicate that at least 28 fissions (breaks), 49 fusions and 4 inversions were needed to "convert" the dog karyotype to that of the red panda, suggesting that extensive chromosome rearrangements differentiate the karyotypes of red panda and dog. Based on the established comparative chromosome homologies of dog and domestic cat, we could infer that there were 26 segments of conserved synteny between red panda and domestic cat. Comparative analysis of the distribution patterns of conserved segments defined by dog paints in red panda and domestic cat genomes revealed at least 2 cryptic inversions in two large chromosomal regions of conserved synteny between red panda and domestic cat. The karyotype of red panda shows high degree of homology with that of domestic cat.

  19. The Drosophila bag of marbles Gene Interacts Genetically with Wolbachia and Shows Female-Specific Effects of Divergence.

    PubMed

    Flores, Heather A; Bubnell, Jaclyn E; Aquadro, Charles F; Barbash, Daniel A

    2015-08-01

    Many reproductive proteins from diverse taxa evolve rapidly and adaptively. These proteins are typically involved in late stages of reproduction such as sperm development and fertilization, and are more often functional in males than females. Surprisingly, many germline stem cell (GSC) regulatory genes, which are essential for the earliest stages of reproduction, also evolve adaptively in Drosophila. One example is the bag of marbles (bam) gene, which is required for GSC differentiation and germline cyst development in females and for regulating mitotic divisions and entry to spermatocyte differentiation in males. Here we show that the extensive divergence of bam between Drosophila melanogaster and D. simulans affects bam function in females but has no apparent effect in males. We further find that infection with Wolbachia pipientis, an endosymbiotic bacterium that can affect host reproduction through various mechanisms, partially suppresses female sterility caused by bam mutations in D. melanogaster and interacts differentially with bam orthologs from D. melanogaster and D. simulans. We propose that the adaptive evolution of bam has been driven at least in part by the long-term interactions between Drosophila species and Wolbachia. More generally, we suggest that microbial infections of the germline may explain the unexpected pattern of evolution of several GSC regulatory genes.

  20. The Drosophila bag of marbles Gene Interacts Genetically with Wolbachia and Shows Female-Specific Effects of Divergence

    PubMed Central

    Flores, Heather A.; Bubnell, Jaclyn E.; Aquadro, Charles F.; Barbash, Daniel A.

    2015-01-01

    Many reproductive proteins from diverse taxa evolve rapidly and adaptively. These proteins are typically involved in late stages of reproduction such as sperm development and fertilization, and are more often functional in males than females. Surprisingly, many germline stem cell (GSC) regulatory genes, which are essential for the earliest stages of reproduction, also evolve adaptively in Drosophila. One example is the bag of marbles (bam) gene, which is required for GSC differentiation and germline cyst development in females and for regulating mitotic divisions and entry to spermatocyte differentiation in males. Here we show that the extensive divergence of bam between Drosophila melanogaster and D. simulans affects bam function in females but has no apparent effect in males. We further find that infection with Wolbachia pipientis, an endosymbiotic bacterium that can affect host reproduction through various mechanisms, partially suppresses female sterility caused by bam mutations in D. melanogaster and interacts differentially with bam orthologs from D. melanogaster and D. simulans. We propose that the adaptive evolution of bam has been driven at least in part by the long-term interactions between Drosophila species and Wolbachia. More generally, we suggest that microbial infections of the germline may explain the unexpected pattern of evolution of several GSC regulatory genes. PMID:26291077

  1. X-ray survival characteristics and genetic analysis for nine saccharomyces deletion mutants that show altered radiation sensitivity

    SciTech Connect

    Game, John C.; Williamson, Marsha S.; Baccari, Clelia

    2004-01-07

    The availability of a genome-wide set of Saccharomyces deletion mutants provides a chance to identify all the yeast genes involved in DNA repair. Using X-rays, we are screening these mutants to identify additional genes that show increased sensitivity to the lethal effects of ionizing radiation. For each mutant identified as sensitive, we are confirming that the sensitivity phenotype co-segregates with the deletion allele and are obtaining multipoint survival-versus-dose assays in at least two haploid and one homozygous diploid strains. We present data for deletion mutants involving the genes DOT1, MDM20, NAT3, SPT7, SPT20, GCN5, HFI1, DCC1 and VID21/EAF1, and discuss their potential roles in repair. Eight of these genes have a clear radiation-sensitive phenotype when deleted, but the ninth, GCN5, has at most a borderline phenotype. None of the deletions confer substantial sensitivity to ultra-violet radiation, although one or two may confer marginal sensitivity. The DOT1 gene is of interest because its only known function is to methylate one lysine residue in the core of the histone H3 protein. We find that histone H3 mutants (supplied by K. Struhl) in which this residue is replaced by other amino-acids are also X-ray sensitive, seeming to confirm that methylation of the lysine-79 residue is required for effective repair of radiation damage.

  2. Microsatellite Typing of Clinical and Environmental Cryptococcus neoformans var. grubii Isolates from Cuba Shows Multiple Genetic Lineages

    PubMed Central

    Illnait-Zaragozi, Maria-Teresa; Martínez-Machín, Gerardo F.; Fernández-Andreu, Carlos M.; Boekhout, Teun; Meis, Jacques F.; Klaassen, Corné H. W.

    2010-01-01

    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. PMID:20161737

  3. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

    PubMed Central

    Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa

    2016-01-01

    A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley. PMID:27530597

  4. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley.

    PubMed

    Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa

    2016-01-01

    A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.

  5. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley.

    PubMed

    Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa

    2016-01-01

    A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley. PMID:27530597

  6. High male chimerism in the female breast shows quantitative links with cancer.

    PubMed

    Dhimolea, Eugen; Denes, Viktoria; Lakk, Monika; Al-Bazzaz, Sana; Aziz-Zaman, Sonya; Pilichowska, Monika; Geck, Peter

    2013-08-15

    Clinical observations suggest that pregnancy provides protection against cancer. The mechanisms involved, however, remain unclear. Fetal cells are known to enter the mother's circulation during pregnancy and establish microchimerism. We investigated if pregnancy-related embryonic/fetal stem cell integration plays a role in breast cancer. A high-sensitivity Y-chromosome assay was developed to trace male allogeneic cells (from male fetus) in females. Fixed-embedded samples (n = 206) from both normal and breast cancer patients were screened for microchimerism. The results were combined with matching clinicopathological and histological parameters and processed statistically. The results show that in our samples (182 informative) more than half of healthy women (56%) carried male cells in their breast tissue for decades (n = 68), while only one out of five in the cancer sample pool (21%) (n = 114) (odds ratio = 4.75, CI at 95% 2.34-9.69; p = 0.0001). The data support the notion that a biological link may exist between chimerism and tissue-integrity. The correlation, however, is non-linear, since male microchimerism in excess ("hyperchimerism") is also involved in cancer. The data suggest a link between hyperchimerism and HER2-type cancers, while decreased chimerism ("hypochimerism") associates with ER/PR-positive (luminal-type) breast cancers. Chimerism levels that correlate with protection appear to be non-random and share densities with the mammary progenitor components of the stem cell lineage in the breast. The results suggest that protection may involve stem/progenitor level interactions and implicate novel quantitative mechanisms in chimerism biology.

  7. Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation.

    PubMed

    Arifin, Yalun; Archer, Colin; Lim, SooA; Quek, Lake-Ee; Sugiarto, Haryadi; Marcellin, Esteban; Vickers, Claudia E; Krömer, Jens O; Nielsen, Lars K

    2014-11-01

    Sugarcane is the most efficient large-scale crop capable of supplying sufficient carbon substrate, in the form of sucrose, needed during fermentative feedstock production. However, sucrose metabolism in Escherichia coli is not well understood because the two most common strains, E. coli K-12 and B, do not grow on sucrose. Here, using a sucrose utilizing strain, E. coli W, we undertake an in-depth comparison of sucrose and glucose metabolism including growth kinetics, metabolite profiling, microarray-based transcriptome analysis, labelling-based proteomic analysis and (13)C-fluxomics. While E. coli W grew comparably well on sucrose and glucose integration of the omics, datasets showed that during growth on each carbon source, metabolism was distinct. The metabolism was generally derepressed on sucrose, and significant flux rearrangements were observed in central carbon metabolism. These included a reduction in the flux of the oxidative pentose phosphate pathway branch, an increase in the tricarboxylic acid cycle flux and a reduction in the glyoxylate shunt flux due to the dephosphorylation of isocitrate dehydrogenase. But unlike growth on other sugars that induce cAMP-dependent Crp regulation, the phosphoenol-pyruvate-glyoxylate cycle was not active on sucrose. Lower acetate accumulation was also observed in sucrose compared to glucose cultures. This was linked to induction of the acetate catabolic genes actP and acs and independent of the glyoxylic shunt. Overall, the cells stayed highly oxidative. In summary, sucrose metabolism was fast, efficient and led to low acetate accumulation making it an ideal carbon source for industrial fermentation with E. coli W. PMID:25125039

  8. Efficient micropropagation and assessment of genetic fidelity of Boerhaavia diffusa L- High trade medicinal plant.

    PubMed

    Patil, Kapil S; Bhalsing, Sanjivani R

    2015-07-01

    Boerhaavia diffusa L is a medicinal herb with immense pharmaceutical significance. The plant is used by many herbalist, Ayurvedic and pharmaceutical industries for production biopharmaceuticals. It is among the 46 medicinal plant species in high trade sourced mainly from wastelands and generally found in temperate regions of the world. However, the commercial bulk of this plant shows genetic variations which are the main constraint to use this plant as medicinal ingredient and to obtain high value products of pharmaceutical interest from this plant. In this study, we have regenerated the plant of Boerhaavia diffusa L through nodal explants and evaluated genetic fidelity of the micropropagated plants of Boerhaavia diffusa L with the help of random amplified polymorphic DNA (RAPD) markers. The results obtained using RAPD showed monomorphic banding pattern revealing genetic stability among the mother plant and in vitro regenerated plants of Boerhaavia diffusa L.

  9. European Invasion of North American Pinus strobus at Large and Fine Scales: High Genetic Diversity and Fine-Scale Genetic Clustering over Time in the Adventive Range

    PubMed Central

    Mandák, Bohumil; Hadincová, Věroslava; Mahelka, Václav; Wildová, Radka

    2013-01-01

    Background North American Pinus strobus is a highly invasive tree species in Central Europe. Using ten polymorphic microsatellite loci we compared various aspects of the large-scale genetic diversity of individuals from 30 sites in the native distribution range with those from 30 sites in the European adventive distribution range. To investigate the ascertained pattern of genetic diversity of this intercontinental comparison further, we surveyed fine-scale genetic diversity patterns and changes over time within four highly invasive populations in the adventive range. Results Our data show that at the large scale the genetic diversity found within the relatively small adventive range in Central Europe, surprisingly, equals the diversity found within the sampled area in the native range, which is about thirty times larger. Bayesian assignment grouped individuals into two genetic clusters separating North American native populations from the European, non-native populations, without any strong genetic structure shown over either range. In the case of the fine scale, our comparison of genetic diversity parameters among the localities and age classes yielded no evidence of genetic diversity increase over time. We found that SGS differed across age classes within the populations under study. Old trees in general completely lacked any SGS, which increased over time and reached its maximum in the sapling stage. Conclusions Based on (1) the absence of difference in genetic diversity between the native and adventive ranges, together with the lack of structure in the native range, and (2) the lack of any evidence of any temporal increase in genetic diversity at four highly invasive populations in the adventive range, we conclude that population amalgamation probably first happened in the native range, prior to introduction. In such case, there would have been no need for multiple introductions from previously isolated populations, but only several introductions from

  10. Facial emotion perception differs in young persons at genetic and clinical high-risk for psychosis.

    PubMed

    Kohler, Christian G; Richard, Jan A; Brensinger, Colleen M; Borgmann-Winter, Karin E; Conroy, Catherine G; Moberg, Paul J; Gur, Ruben C; Gur, Raquel E; Calkins, Monica E

    2014-05-15

    A large body of literature has documented facial emotion perception impairments in schizophrenia. More recently, emotion perception has been investigated in persons at genetic and clinical high-risk for psychosis. This study compared emotion perception abilities in groups of young persons with schizophrenia, clinical high-risk, genetic risk and healthy controls. Groups, ages 13-25, included 24 persons at clinical high-risk, 52 first-degree relatives at genetic risk, 91 persons with schizophrenia and 90 low risk persons who completed computerized testing of emotion recognition and differentiation. Groups differed by overall emotion recognition abilities and recognition of happy, sad, anger and fear expressions. Pairwise comparisons revealed comparable impairments in recognition of happy, angry, and fearful expressions for persons at clinical high-risk and schizophrenia, while genetic risk participants were less impaired, showing reduced recognition of fearful expressions. Groups also differed for differentiation of happy and sad expressions, but differences were mainly between schizophrenia and control groups. Emotion perception impairments are observable in young persons at-risk for psychosis. Preliminary results with clinical high-risk participants, when considered along findings in genetic risk relatives, suggest social cognition abilities to reflect pathophysiological processes involved in risk of schizophrenia. PMID:24582775

  11. Spatial Heterogeneity as a Genetic Mixing Mechanism in Highly Philopatric Colonial Seabirds

    PubMed Central

    Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D.; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline

    2015-01-01

    How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of

  12. Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds.

    PubMed

    Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline

    2015-01-01

    How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of

  13. Study Shows Aspirin Reduces Colorectal Cancer in Those at High Risk

    Cancer.gov

    Findings from the first large clinical trial of its kind indicate that taking high doses of aspirin daily for at least 2 years substantially reduces the risk of colorectal cancer among people at increased risk of the disease.

  14. Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site.

    PubMed

    Monden, Yuki; Fujii, Nobuyuki; Yamaguchi, Kentaro; Ikeo, Kazuho; Nakazawa, Yoshiko; Waki, Takamitsu; Hirashima, Keita; Uchimura, Yosuke; Tahara, Makoto

    2014-05-01

    Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5' LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria × ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a "unique" insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars. PMID:25072847

  15. High Genetic Variability of Schistosoma haematobium in Mali and Nigeria

    PubMed Central

    Ezeh, Charles; Yin, Mingbo; Li, Hongyan; Zhang, Ting; Xu, Bin; Sacko, Moussa; Feng, Zheng; Hu, Wei

    2015-01-01

    Schistosoma haematobium is one of the most prevalent parasitic flatworms, infecting over 112 million people in Africa. However, little is known about the genetic diversity of natural S. haematobium populations from the human host because of the inaccessible location of adult worms in the host. We used 4 microsatellite loci to genotype individually pooled S. haematobium eggs directly from each patient sampled at 4 endemic locations in Africa. We found that the average allele number of individuals from Mali was significantly higher than that from Nigeria. In addition, no significant difference in allelic composition was detected among the populations within Nigeria; however, the allelic composition was significantly different between Mali and Nigeria populations. This study demonstrated a high level of genetic variability of S. haematobium in the populations from Mali and Nigeria, the 2 major African endemic countries, suggesting that geographical population differentiation may occur in the regions. PMID:25748721

  16. Genetics

    MedlinePlus

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  17. Genetic and sociocultural components of high blood pressure.

    PubMed

    Ward, R H

    1983-09-01

    The cardiovascular diseases exert widely differing contributions to the total burden of mortality and morbidity in extant human populations. To a large extent these differences are a reflection of the variable distribution of specific antecedent risk factors. For one such risk factor, blood pressure, there is considerable variability in its distribution between different ethnic groups, especially between traditional and nontraditional societies. Intensive epidemiological studies in Western societies, together with a number of cross-cultural comparisons, suggest that the major determinants of high blood pressure are likely to be a constellation of sociocultural factors, with genetic determination being limited to the interaction between genotype and environment. Studies of populations in sociocultural transition offer an unique opportunity to identify the relative influence of specific sociocultural factors on the rate of change of blood pressure. In addition, when the study of such populations is placed in a quasi-experimental context, genetic-environmental interactions may also be detected. This strategy is illustrated by a study of the changing blood pressure distribution in Tokelauan migrants. Such an approach requires the initial definition of a response variable which measures change in blood pressure as a consequence of migration. The response variable, which identifies the relative influence of concomitants such as weight, age, and obesity, can then be subjected to genetic analysis. In the Tokelau case, blood pressure response tends to be positive in migrants but negative in nonmigrants. Further statistical analysis indicates that there is a small proportion of high responders in both populations and that these cluster in families in the migrant population. However, estimates of the transmission parameter suggest that sociocultural transmission, rather than Mendelian segregation, is responsible. To date there is little evidence that genetic

  18. Do Individuals with High-Functioning Autism Who Speak a Tone Language Show Intonation Deficits?

    ERIC Educational Resources Information Center

    Chan, Kary K. L.; To, Carol K. S.

    2016-01-01

    This study investigated whether intonation deficits were observed in 19 Cantonese-speaking adults with high-functioning autism (HFA) when compared to 19 matched neurotypical (NT) controls. This study also investigated the use of sentence-final particles (SFPs) and their relationship with intonation in both groups. Standard deviations…

  19. Breeding for improved potato nutrition: High amylose starch potatoes show promise as fiber source

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potato starch is composed of approximately 75% amylopectin and 25% amylose. We are interested in breeding for higher amylose content, which would increase the fiber content of potato and decrease glycemic index. In order to make progress in a breeding program, we have developed a high throughput ass...

  20. Analysis of ORFs 2b, 3, 4, and partial ORF5 of sequential isolates of equine arteritis virus shows genetic variation following experimental infection of horses.

    PubMed

    Liu, Lihong; Castillo-Olivares, Javier; Davis-Poynter, Nick J; Baule, Claudia; Xia, Hongyan; Belák, Sándor

    2008-06-22

    Samples from horses experimentally infected with the "large plaque variant (LP3A+)" of equine arteritis virus were analysed. These included 182 nasal swabs collected from day 1 to 14 post-infection (p.i.), and 21 virus isolates obtained from white blood cells of animals that showed a prolonged viraemia between days 30 to 72 p.i. In order to determine the genetic stability of the virus and particularly to characterise the genetic variants found during the prolonged viraemia, partial sequences of open reading frame 5 (ORF5) encoding glycoprotein 5 (GP5) were generated. Viruses with amino acid substitutions in GP5 were used for further amplification and sequencing of a fragment encompassing ORFs 2b, 3, and 4. The ORF5 nucleotide sequences of the virus present in 65 out of 66 nasal swabs were identical to that of the inoculated virus, suggesting that the ORF5 gene of LP3A+ was genetically stable during the first 2 weeks p.i. Contrary to this, a number of mutations were found in the ORF5 of virus isolates obtained from day 30 p.i. The mutations mainly clustered in antigenic neutralization site C within variable region 1 of the GP5 ectodomain. Sequence variability was also identified in ORFs 2b, 3 and 4, with ORF 4 having the highest proportion of non-synonymous changes (4/6).

  1. Microsatellite markers reveal high genetic diversity in date palm (Phoenix dactylifera L.) germplasm from Sudan.

    PubMed

    Elshibli, Sakina; Korpelainen, Helena

    2008-10-01

    Genetic diversity in date palm germplasm from Sudan representing 37 female and 23 male accessions was investigated using 16 loci of microsatellite (SSR) primers. Eight female accessions from Morocco were included as reference material. The tested SSR markers showed a high level of polymorphism. A total of 343 alleles were detected at the 16 loci. The number of alleles per marker ranged from 14 to 44 with an average of 21.4 per locus. A high level of expected heterozygosity was observed among Sudan cultivars (0.841), Morocco cultivars (0.820) and male accessions (0.799). The results indicate that the genetic groups of the Sudan cultivars and/or males do not follow a clear geographic pattern. However, the morocco group showed significant differentiation in relation to the Sudan groups, as measured by F (ST) values and genetic distances. The effect of the methods of pollination and cultivar selection on the genetic structure was clearly detected by the weak clustering association that was observed for the majority of accessions originating from Sudan and Morocco as well. This suggests the need for further investigation on the genetic diversity of Sudanese date palm germplasm. A deeper insight will be revealed by a detailed analysis of populations originating from different geographic locations.

  2. Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore.

    PubMed

    Pilot, Małgorzata; Jędrzejewski, Włodzimierz; Sidorovich, Vadim E; Meier-Augenstein, Wolfram; Hoelzel, A Rus

    2012-01-01

    Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ(13)C and δ(15)N values) for Eastern European wolves (Canis lupus) as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure), to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation) in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores. PMID:22768075

  3. Source-Sink Estimates of Genetic Introgression Show Influence of Hatchery Strays on Wild Chum Salmon Populations in Prince William Sound, Alaska

    PubMed Central

    Jasper, James R.; Habicht, Christopher; Moffitt, Steve; Brenner, Rich; Marsh, Jennifer; Lewis, Bert; Creelman Fox, Elisabeth; Grauvogel, Zac; Rogers Olive, Serena D.; Grant, W. Stewart

    2013-01-01

    The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960’s for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964–1982) with frequencies in contemporary samples (2008–2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations. PMID:24349150

  4. Targeted exome sequencing for mitochondrial disorders reveals high genetic heterogeneity

    PubMed Central

    2013-01-01

    Background Mitochondrial disorders are difficult to diagnose due to extreme genetic and phenotypic heterogeneities. Methods We explored the utility of targeted next-generation sequencing for the diagnosis of mitochondrial disorders in 148 patients submitted for clinical testing. A panel of 447 nuclear genes encoding mitochondrial respiratory chain complexes, and other genes inducing secondary mitochondrial dysfunction or that cause diseases which mimic mitochondrial disorders were tested. Results We identified variants considered to be possibly disease-causing based on family segregation data and/or variants already known to cause disease in twelve genes in thirteen patients. Rare or novel variants of unknown significance were identified in 45 additional genes for various metabolic, genetic or neurogenetic disorders. Conclusions Primary mitochondrial defects were confirmed only in four patients indicating that majority of patients with suspected mitochondrial disorders are presumably not the result of direct impairment of energy production. Our results support that clinical and routine laboratory ascertainment for mitochondrial disorders are challenging due to significant overlapping non-specific clinical symptoms and lack of specific biomarkers. While next-generation sequencing shows promise for diagnosing suspected mitochondrial disorders, the challenges remain as the underlying genetic heterogeneity may be greater than suspected and it is further confounded by the similarity of symptoms with other conditions as we report here. PMID:24215330

  5. African elephants show high levels of interest in the skulls and ivory of their own species

    PubMed Central

    McComb, Karen; Baker, Lucy; Moss, Cynthia

    2005-01-01

    An important area of biology involves investigating the origins in animals of traits that are thought of as uniquely human. One way that humans appear unique is in the importance they attach to the dead bodies of other humans, particularly those of their close kin, and the rituals that they have developed for burying them. In contrast, most animals appear to show only limited interest in the carcasses or associated remains of dead individuals of their own species. African elephants (Loxodonta africana) are unusual in that they not only give dramatic reactions to the dead bodies of other elephants, but are also reported to systematically investigate elephant bones and tusks that they encounter, and it has sometimes been suggested that they visit the bones of relatives. Here, we use systematic presentations of object arrays to demonstrate that African elephants show higher levels of interest in elephant skulls and ivory than in natural objects or the skulls of other large terrestrial mammals. However, they do not appear to specifically select the skulls of their own relatives for investigation so that visits to dead relatives probably result from a more general attraction to elephant remains. PMID:17148317

  6. Biochemical Characterization of a First Fungal Esterase from Rhizomucor miehei Showing High Efficiency of Ester Synthesis

    PubMed Central

    Liu, Yu; Xu, Haibo; Yan, Qiaojuan; Yang, Shaoqing; Duan, Xiaojie; Jiang, Zhengqiang

    2013-01-01

    Background Esterases with excellent merits suitable for commercial use in ester production field are still insufficient. The aim of this research is to advance our understanding by seeking for more unusual esterases and revealing their characterizations for ester synthesis. Methodology/Principal Findings A novel esterase-encoding gene from Rhizomucor miehei (RmEstA) was cloned and expressed in Escherichia coli. Sequence analysis revealed a 975-bp ORF encoding a 324-amino-acid polypeptide belonging to the hormone-sensitive lipase (HSL) family IV and showing highest similarity (44%) to the Paenibacillus mucilaginosus esterase/lipase. Recombinant RmEstA was purified to homogeneity: it was 34 kDa by SDS-PAGE and showed optimal pH and temperature of 6.5 and 45°C, respectively. The enzyme was stable to 50°C, under a broad pH range (5.0–10.6). RmEstA exhibited broad substrate specificity toward p-nitrophenol esters and short-acyl-chain triglycerols, with highest activities (1,480 U mg−1 and 228 U mg−1) for p-nitrophenyl hexanoate and tributyrin, respectively. RmEstA efficiently synthesized butyl butyrate (92% conversion yield) when immobilized on AOT-based organogel. Conclusion RmEstA has great potential for industrial applications. RmEstA is the first reported esterase from Rhizomucor miehei. PMID:24204998

  7. A novel satellite DNA isolated in Pecten jacobaeus shows high sequence similarity among molluscs.

    PubMed

    Petraccioli, Agnese; Odierna, Gaetano; Capriglione, Teresa; Barucca, Marco; Forconi, Mariko; Olmo, Ettore; Biscotti, Maria Assunta

    2015-10-01

    The aim of this work is to investigate the sequence conservation and the evolution of repeated DNA in related species. Satellite DNA is a component of eukaryotic genomes and is made up of tandemly repeated sequences. These sequences are affected by high rates of mutation that lead to the occurrence of species-specific satellite DNAs, which are different in terms of both quantity and quality. In this work, a novel repetitive DNA family, named PjHhaI sat, is described in Pecten jacobaeus. The quantitative analyses revealed a different abundance of this element in the molluscan species investigated in agreement with the "library hypothesis" even if, in this case, at a high taxonomic level. In addition, the qualitative analysis demonstrated an astonishing sequence conservation not only among scallops but also in six other molluscan species belonging to three classes. These findings suggest that the PjHhaI sat may be considered as the most ancients of DNA described so far, which remained "frozen" during molluscan evolution. The widespread distribution of this sat DNA in molluscs as well as its long evolutionary preservation open up questions on the functional role of this element. A future challenge might be the identification of proteins or molecules which interact with the PjHhaI sat.

  8. A novel satellite DNA isolated in Pecten jacobaeus shows high sequence similarity among molluscs.

    PubMed

    Petraccioli, Agnese; Odierna, Gaetano; Capriglione, Teresa; Barucca, Marco; Forconi, Mariko; Olmo, Ettore; Biscotti, Maria Assunta

    2015-10-01

    The aim of this work is to investigate the sequence conservation and the evolution of repeated DNA in related species. Satellite DNA is a component of eukaryotic genomes and is made up of tandemly repeated sequences. These sequences are affected by high rates of mutation that lead to the occurrence of species-specific satellite DNAs, which are different in terms of both quantity and quality. In this work, a novel repetitive DNA family, named PjHhaI sat, is described in Pecten jacobaeus. The quantitative analyses revealed a different abundance of this element in the molluscan species investigated in agreement with the "library hypothesis" even if, in this case, at a high taxonomic level. In addition, the qualitative analysis demonstrated an astonishing sequence conservation not only among scallops but also in six other molluscan species belonging to three classes. These findings suggest that the PjHhaI sat may be considered as the most ancients of DNA described so far, which remained "frozen" during molluscan evolution. The widespread distribution of this sat DNA in molluscs as well as its long evolutionary preservation open up questions on the functional role of this element. A future challenge might be the identification of proteins or molecules which interact with the PjHhaI sat. PMID:25832354

  9. Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses.

    PubMed

    Evgen'ev, M B; Corces, V G; Lankenau, D H

    1992-06-01

    We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

  10. Tooth enamel oxygen “isoscapes” show a high degree of human mobility in prehistoric Britain

    NASA Astrophysics Data System (ADS)

    Pellegrini, Maura; Pouncett, John; Jay, Mandy; Pearson, Mike Parker; Richards, Michael P.

    2016-10-01

    A geostatistical model to predict human skeletal oxygen isotope values (δ18Op) in Britain is presented here based on a new dataset of Chalcolithic and Early Bronze Age human teeth. The spatial statistics which underpin this model allow the identification of individuals interpreted as ‘non-local’ to the areas where they were buried (spatial outliers). A marked variation in δ18Op is observed in several areas, including the Stonehenge region, the Peak District, and the Yorkshire Wolds, suggesting a high degree of human mobility. These areas, rich in funerary and ceremonial monuments, may have formed focal points for people, some of whom would have travelled long distances, ultimately being buried there. The dataset and model represent a baseline for future archaeological studies, avoiding the complex conversions from skeletal to water δ18O values–a process known to be problematic.

  11. Decarbonizing urban transport in European cities: four cases show possibly high co-benefits

    NASA Astrophysics Data System (ADS)

    Creutzig, Felix; Mühlhoff, Rainer; Römer, Julia

    2012-12-01

    Cities worldwide are increasingly becoming agents of climate change mitigation, while simultaneously aiming for other goals, such as improved accessibility and clean air. Based on stakeholder interviews and data analysis, we assess the current state of urban mobility in the four European cities of Barcelona, Malmö, Sofia and Freiburg. We then provide scenarios of increasingly ambitious policy packages, reducing greenhouse gas emissions from urban transport by up to 80% from 2010 to 2040. We find significant concurrent co-benefits in cleaner air, reduced noise ambience, fewer traffic-related injuries and deaths, more physical activity, less congestion and monetary fuel savings. Our scenarios suggest that non-motorized transport, especially bicycles, can occupy high modal shares, particularly in cities with less than 0.5 million inhabitants. We think that this kind of multi-criteria assessment of social costs and benefits is a useful complement to cost-benefit analysis of climate change mitigation measures.

  12. Do Individuals with High-Functioning Autism Who Speak a Tone Language Show Intonation Deficits?

    PubMed

    Chan, Kary K L; To, Carol K S

    2016-05-01

    This study investigated whether intonation deficits were observed in 19 Cantonese-speaking adults with high-functioning autism (HFA) when compared to 19 matched neurotypical (NT) controls. This study also investigated the use of sentence-final particles (SFPs) and their relationship with intonation in both groups. Standard deviations (SDs) of the fundamental frequency (F0), the total number and the type of SFPs were calculated based on narrative samples. The HFA group demonstrated significantly higher SD of F0 and a positive correlation between the type of SFPs and SD of F0. Both groups produced a similar total number and type of SFPs. The results supported the universality of atypical intonation in ASD. The relationship between intonation and SFPs could be further explored by focusing on sentences containing SFPs.

  13. Tooth enamel oxygen “isoscapes” show a high degree of human mobility in prehistoric Britain

    PubMed Central

    Pellegrini, Maura; Pouncett, John; Jay, Mandy; Pearson, Mike Parker; Richards, Michael P.

    2016-01-01

    A geostatistical model to predict human skeletal oxygen isotope values (δ18Op) in Britain is presented here based on a new dataset of Chalcolithic and Early Bronze Age human teeth. The spatial statistics which underpin this model allow the identification of individuals interpreted as ‘non-local’ to the areas where they were buried (spatial outliers). A marked variation in δ18Op is observed in several areas, including the Stonehenge region, the Peak District, and the Yorkshire Wolds, suggesting a high degree of human mobility. These areas, rich in funerary and ceremonial monuments, may have formed focal points for people, some of whom would have travelled long distances, ultimately being buried there. The dataset and model represent a baseline for future archaeological studies, avoiding the complex conversions from skeletal to water δ18O values–a process known to be problematic. PMID:27713538

  14. Do Individuals with High-Functioning Autism Who Speak a Tone Language Show Intonation Deficits?

    PubMed

    Chan, Kary K L; To, Carol K S

    2016-05-01

    This study investigated whether intonation deficits were observed in 19 Cantonese-speaking adults with high-functioning autism (HFA) when compared to 19 matched neurotypical (NT) controls. This study also investigated the use of sentence-final particles (SFPs) and their relationship with intonation in both groups. Standard deviations (SDs) of the fundamental frequency (F0), the total number and the type of SFPs were calculated based on narrative samples. The HFA group demonstrated significantly higher SD of F0 and a positive correlation between the type of SFPs and SD of F0. Both groups produced a similar total number and type of SFPs. The results supported the universality of atypical intonation in ASD. The relationship between intonation and SFPs could be further explored by focusing on sentences containing SFPs. PMID:26825662

  15. Map showing high-purity silica sand of Middle Ordovician age in the Midwestern states

    USGS Publications Warehouse

    Ketner, Keith B.

    1979-01-01

    Certain quartz sands of Middle Ordovician age in the Midwestern States are well known for their purity and are exploited for a wide variety of industrial uses. The principal Middle Ordovician formations containing high-purity sands are the St. Peter Sandstone which crops out extensively from Minnesota to Arkansas; the Everton Formation principally of Arkansas; and the Oil Creek, McLish, and Tulip Creek Formations (all of the Simpson Group) of Oklahoma. The St. Peter and sandy beds in the other formations are commonly called "sandstones," but a more appropriate term is "sands" for in most fresh exposures they are completely uncemented or very weakly cemented. On exposure to air, uncemented sands usually become "case hardened" where evaporating ground water precipitates mineral matter at the surface; but this is a surficial effect. This report summarizes the available information on the extent of exposures, range of grain size, and chemical composition of the Middle Ordovician sands.

  16. Isolation and analysis of polysaccharide showing high hyaluronidase inhibitory activity in Nostochopsis lobatus MAC0804NAN.

    PubMed

    Yamaguchi, Yuji; Koketsu, Mamoru

    2016-03-01

    An active substance with high hyaluronidase inhibitory effect was isolated from the edible cyanobacterium Nostochopsis lobatus MAC0804NAN strain and characterized. The active component in the hot water extract was purified by anion exchange and gel filtration chromatography and was found to be a polysaccharide. The IC(50) against hyaluronidase of the purified polysaccharide was 7.18 μg/ml whose inhibitory activity is 14.5 times stronger than that of disodium cromoglycate (DSCG), an anti-allergy medication. The carbohydrate composition which was analyzed by GC-MS and NMR was found to be composed mainly of glucose, glucuronic acid, fucose, 2-O-methylfucose, mannose, galactose and xylose.

  17. High latitudes and high genetic diversity: phylogeography of a widespread boreal bird, the gray jay (Perisoreus canadensis).

    PubMed

    van Els, Paul; Cicero, Carla; Klicka, John

    2012-05-01

    We describe range-wide phylogeographic variation in gray jays (Perisoreus canadensis), a boreal Nearctic corvid that occurs today primarily in recently glaciated regions. Phylogenetic analysis of mitochondrial DNA (1041 base pairs ND2 gene; N=205, 50 localities) revealed four reciprocally monophyletic groups. One widespread clade occurs across the North American boreal zone, from Newfoundland to Alaska and southwest into Utah. Three other clades occur at lower latitudes in the montane West in Colorado, the northern Rocky Mountains, and the Pacific Northwest respectively. The geographic distribution of clades in gray jays corresponds with a general pattern that is emerging for boreal taxa, having one widespread northern clade and one or more geographically restricted southwestern clades. Population genetic analyses indicate that the larger boreal clade is genetically structured and harbors significantly more genetic diversity than those clades occurring at lower latitudes. Species distribution modeling (SDM) revealed multiple putative Pleistocene refugia including several occurring at higher latitudes. We suggest that multiple post-glacial colonization routes, some of which originate from these northern refugia, are responsible for the relatively high genetic diversity at high latitudes. Conversely, lower latitude clades show little variation, probably as a result of historical restriction to smaller geographical areas with smaller long-term population sizes. This 'upside-down' pattern of genetic diversity contrasts with the conventional view that populations of north-temperate species occupying previously glaciated habitats should possess lower levels of diversity than their southern counterparts. PMID:22321688

  18. Glycopolymer induction of mouse sperm acrosomal exocytosis shows highly cooperative self-antagonism.

    PubMed

    Rodolis, Maria T; Huang, He; Sampson, Nicole S

    2016-06-01

    Identifying inducers of sperm acrosomal exocytosis (AE) to understand sperm functionality is important for both mechanistic and clinical studies in mammalian fertilization. Epifluorescence microscopy methods, while reproducible, are laborious and incompatible for high throughput screening. Flow cytometry methods are ideal for quantitative measurements on large numbers of samples, yet typically rely on the use of lectins that can interfere with physiologic AE-inducers. Here, we present an optimized triple stain flow cytometric method that is suitable for high-throughput screening of AE activation by glycopolymers. SYTO-17 and propidium iodide (PI) were used to differentiate cells based on their membrane integrity or viability, and membrane impermeable soybean trypsin inhibitor (SBTI) was used to monitor acrosome exocytosis. The SBTI/PI/SYTO-17 combination provides a positive screen for viability and AE of live sperm cells with minimal noise or false positives. A scattering gate enables the use of samples that may be contaminated with non-cellular aggregates, e.g., cryopreservation agents. This assay format enabled detailed analysis of glycopolymer dose response curves. We found that fucose polymer has a narrow effective dose range (EC50 = 1.6 μM; IC50 = 13.5 μM); whereas mannose polymer and β-N-acetylglucosamine polymer have broader effective dose ranges (EC50 = 1.2 μM and 3.4 μM, respectively). These results highlight the importance of testing inducers over a large concentration range in small increments for accurate comparison. PMID:27150629

  19. High Genetic Diversity in a Potentially Vulnerable Tropical Tree Species Despite Extreme Habitat Loss

    PubMed Central

    Noreen, Annika M. E.; Webb, Edward L.

    2013-01-01

    Over the last 150 years, Singapore’s primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (<1 yr) of the canopy tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843–0.854), high allelic richness (R = 16.7–19.5), low inbreeding co-efficients (FIS = 0.013–0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency <1%). However, spatial genetic structure (SGS) analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0–10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss. PMID

  20. High-precision radiocarbon dating shows recent and rapid initial human colonization of East Polynesia

    PubMed Central

    Wilmshurst, Janet M.; Hunt, Terry L.; Lipo, Carl P.; Anderson, Atholl J.

    2011-01-01

    The 15 archipelagos of East Polynesia, including New Zealand, Hawaii, and Rapa Nui, were the last habitable places on earth colonized by prehistoric humans. The timing and pattern of this colonization event has been poorly resolved, with chronologies varying by >1000 y, precluding understanding of cultural change and ecological impacts on these pristine ecosystems. In a meta-analysis of 1,434 radiocarbon dates from the region, reliable short-lived samples reveal that the colonization of East Polynesia occurred in two distinct phases: earliest in the Society Islands A.D. ∼1025–1120, four centuries later than previously assumed; then after 70–265 y, dispersal continued in one major pulse to all remaining islands A.D. ∼1190–1290. We show that previously supported longer chronologies have relied upon radiocarbon-dated materials with large sources of error, making them unsuitable for precise dating of recent events. Our empirically based and dramatically shortened chronology for the colonization of East Polynesia resolves longstanding paradoxes and offers a robust explanation for the remarkable uniformity of East Polynesian culture, human biology, and language. Models of human colonization, ecological change and historical linguistics for the region now require substantial revision. PMID:21187404

  1. Hydroxyeicosapentaenoic acids from the Pacific krill show high ligand activities for PPARs[S

    PubMed Central

    Yamada, Hidetoshi; Oshiro, Eriko; Kikuchi, Sayaka; Hakozaki, Mayuka; Takahashi, Hideyuki; Kimura, Ken-ichi

    2014-01-01

    PPARs regulate the expression of genes for energy metabolism in a ligand-dependent manner. PPARs can influence fatty acid oxidation, the level of circulating triglycerides, glucose uptake and insulin sensitivity. Here, we demonstrate that 5-hydroxyeicosapentaenoic acid (HEPE), 8-HEPE, 9-HEPE, 12-HEPE and 18-HEPE (hydroxylation products of EPA) obtained from methanol extracts of Pacific krill (Euphausia pacifica) can act as PPAR ligands. Two of these products, 8-HEPE and 9-HEPE, enhanced the transcription levels of GAL4-PPARs to a significantly greater extent than 5-HEPE, 12-HEPE, 18-HEPE, EPA, and EPA ethyl-ester. 8-HEPE also activated significantly higher transcription of GAL4-PPARα, GAL4-PPARγ, and GAL4-PPARδ than EPA at concentrations greater than 4, 64, and 64 μM, respectively. We also demonstrated that 8-HEPE increased the expression levels of genes regulated by PPARs in FaO, 3T3-F442A, and C2C12 cells. Furthermore, 8-HEPE enhanced adipogenesis and glucose uptake. By contrast, at the same concentrations, EPA showed weak or little effect, indicating that 8-HEPE was the more potent inducer of physiological effects. PMID:24668940

  2. High-precision radiocarbon dating shows recent and rapid initial human colonization of East Polynesia.

    PubMed

    Wilmshurst, Janet M; Hunt, Terry L; Lipo, Carl P; Anderson, Atholl J

    2011-02-01

    The 15 archipelagos of East Polynesia, including New Zealand, Hawaii, and Rapa Nui, were the last habitable places on earth colonized by prehistoric humans. The timing and pattern of this colonization event has been poorly resolved, with chronologies varying by >1000 y, precluding understanding of cultural change and ecological impacts on these pristine ecosystems. In a meta-analysis of 1,434 radiocarbon dates from the region, reliable short-lived samples reveal that the colonization of East Polynesia occurred in two distinct phases: earliest in the Society Islands A.D. ∼1025-1120, four centuries later than previously assumed; then after 70-265 y, dispersal continued in one major pulse to all remaining islands A.D. ∼1190-1290. We show that previously supported longer chronologies have relied upon radiocarbon-dated materials with large sources of error, making them unsuitable for precise dating of recent events. Our empirically based and dramatically shortened chronology for the colonization of East Polynesia resolves longstanding paradoxes and offers a robust explanation for the remarkable uniformity of East Polynesian culture, human biology, and language. Models of human colonization, ecological change and historical linguistics for the region now require substantial revision.

  3. Blacktip reef sharks (Carcharhinus melanopterus) show high capacity for wound healing and recovery following injury.

    PubMed

    Chin, Andrew; Mourier, Johann; Rummer, Jodie L

    2015-01-01

    Wound healing is important for sharks from the earliest life stages, for example, as the 'umbilical scar' in viviparous species heals, and throughout adulthood, when sharks can incur a range of external injuries from natural and anthropogenic sources. Despite anecdotal accounts of rapid healing in elasmobranchs, data regarding recovery and survival of individuals from different wound or injury types has not been systematically collected. The present study documented: (i) 'umbilical scar' healing in wild-caught, neonatal blacktip reef sharks while being reared for 30 days in flow-through laboratory aquaria in French Polynesia; (ii) survival and recovery of free-swimming blacktip reef sharks in Australia and French Polynesia following a range of injuries; and (iii) long-term survival following suspected shark-finning activities. Laboratory monitoring, tag-recapture records, telemetry data and photo-identification records suggest that blacktip reef sharks have a high capacity to survive and recover from small or even large and severe wounds. Healing rates, recovery and survival are important factors to consider when assessing impacts of habitat degradation and fishing stress on shark populations. The present study suggests that individual survival may depend more on handling practices and physiological stress rather than the extent of physical injury. These observations also contribute to discussions regarding the ethics of tagging practices used in elasmobranch research and provide baseline healing rates that may increase the accuracy in estimating reproductive timing inferred from mating scars and birth dates for neonatal sharks based on umbilical scar healing status.

  4. Innovations at Miami practice show promise for treating high-risk Medicare patients.

    PubMed

    Tanio, Craig; Chen, Christopher

    2013-06-01

    Patients with five or more chronic conditions drive most Medicare costs. Our organization, ChenMed, developed a scalable primary care-led delivery model that focuses on this population while getting reimbursed through full-risk capitation by Medicare Advantage plans. ChenMed is a primary care-led group practice based in Florida that serves low-to-moderate-income elderly patients, largely through the Medicare Advantage program. Our model includes a number of innovations: a one-stop-shop approach for delivering multispecialty services in the community, smaller physician panel sizes of 350-450 patients that allow for intensive health coaching and preventive care, on-site physician pharmacy dispensing, a collaborative physician culture with peer review, and customized information technology. These innovations have improved patient medication adherence, increased the time doctors and patients spend together, and led to high rates of patient satisfaction. Additionally, our Medicare patients have substantially lower rates of hospital use than their peers in the Miami Medicare market. Creating chronic disease centers focused on seniors with multiple chronic conditions is a promising delivery system innovation with major potential to improve the cost and quality of care.

  5. Nitrogen-doped diamond electrode shows high performance for electrochemical reduction of nitrobenzene.

    PubMed

    Zhang, Qing; Liu, Yanming; Chen, Shuo; Quan, Xie; Yu, Hongtao

    2014-01-30

    Effective electrode materials are critical to electrochemical reduction, which is a promising method to pre-treat anti-oxidative and bio-refractory wastewater. Herein, nitrogen-doped diamond (NDD) electrodes that possess superior electrocatalytic properties for reduction were fabricated by microwave-plasma-enhanced chemical vapor deposition technology. Nitrobenzene (NB) was chosen as the probe compound to investigate the material's electro-reduction activity. The effects of potential, electrolyte concentration and pH on NB reduction and aniline (AN) formation efficiencies were studied. NDD exhibited high electrocatalytic activity and selectivity for reduction of NB to AN. The NB removal efficiency and AN formation efficiency were 96.5% and 88.4% under optimal conditions, respectively; these values were 1.13 and 3.38 times higher than those of graphite electrodes. Coulombic efficiencies for NB removal and AN formation were 27.7% and 26.1%, respectively; these values were 4.70 and 16.6 times higher than those of graphite electrodes under identical conditions. LC-MS analysis revealed that the dominant reduction pathway on the NDD electrode was NB to phenylhydroxylamine (PHA) to AN.

  6. Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

    PubMed

    Ley, A C; Hardy, O J

    2013-04-01

    AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species. PMID:23398575

  7. Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

    PubMed

    Ley, A C; Hardy, O J

    2013-04-01

    AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species.

  8. Blacktip reef sharks (Carcharhinus melanopterus) show high capacity for wound healing and recovery following injury

    PubMed Central

    Chin, Andrew; Mourier, Johann; Rummer, Jodie L.

    2015-01-01

    Wound healing is important for sharks from the earliest life stages, for example, as the ‘umbilical scar’ in viviparous species heals, and throughout adulthood, when sharks can incur a range of external injuries from natural and anthropogenic sources. Despite anecdotal accounts of rapid healing in elasmobranchs, data regarding recovery and survival of individuals from different wound or injury types has not been systematically collected. The present study documented: (i) ‘umbilical scar’ healing in wild-caught, neonatal blacktip reef sharks while being reared for 30 days in flow-through laboratory aquaria in French Polynesia; (ii) survival and recovery of free-swimming blacktip reef sharks in Australia and French Polynesia following a range of injuries; and (iii) long-term survival following suspected shark-finning activities. Laboratory monitoring, tag-recapture records, telemetry data and photo-identification records suggest that blacktip reef sharks have a high capacity to survive and recover from small or even large and severe wounds. Healing rates, recovery and survival are important factors to consider when assessing impacts of habitat degradation and fishing stress on shark populations. The present study suggests that individual survival may depend more on handling practices and physiological stress rather than the extent of physical injury. These observations also contribute to discussions regarding the ethics of tagging practices used in elasmobranch research and provide baseline healing rates that may increase the accuracy in estimating reproductive timing inferred from mating scars and birth dates for neonatal sharks based on umbilical scar healing status. PMID:27293741

  9. Blacktip reef sharks (Carcharhinus melanopterus) show high capacity for wound healing and recovery following injury.

    PubMed

    Chin, Andrew; Mourier, Johann; Rummer, Jodie L

    2015-01-01

    Wound healing is important for sharks from the earliest life stages, for example, as the 'umbilical scar' in viviparous species heals, and throughout adulthood, when sharks can incur a range of external injuries from natural and anthropogenic sources. Despite anecdotal accounts of rapid healing in elasmobranchs, data regarding recovery and survival of individuals from different wound or injury types has not been systematically collected. The present study documented: (i) 'umbilical scar' healing in wild-caught, neonatal blacktip reef sharks while being reared for 30 days in flow-through laboratory aquaria in French Polynesia; (ii) survival and recovery of free-swimming blacktip reef sharks in Australia and French Polynesia following a range of injuries; and (iii) long-term survival following suspected shark-finning activities. Laboratory monitoring, tag-recapture records, telemetry data and photo-identification records suggest that blacktip reef sharks have a high capacity to survive and recover from small or even large and severe wounds. Healing rates, recovery and survival are important factors to consider when assessing impacts of habitat degradation and fishing stress on shark populations. The present study suggests that individual survival may depend more on handling practices and physiological stress rather than the extent of physical injury. These observations also contribute to discussions regarding the ethics of tagging practices used in elasmobranch research and provide baseline healing rates that may increase the accuracy in estimating reproductive timing inferred from mating scars and birth dates for neonatal sharks based on umbilical scar healing status. PMID:27293741

  10. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    PubMed

    Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.

  11. High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks

    PubMed Central

    Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Alvares Serrão, Ester

    2013-01-01

    The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhizapolyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines. PMID:23967038

  12. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    PubMed

    Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID

  13. MnBr₂/18-crown-6 coordination complexes showing high room temperature luminescence and quantum yield.

    PubMed

    Hausmann, David; Kuzmanoski, Ana; Feldmann, Claus

    2016-04-21

    The reaction of manganese(ii) bromide and the crown ether 18-crown-6 in the ionic liquid [(n-Bu)3MeN][N(Tf)2] under mild conditions (80-130 °C) resulted in the formation of three different coordination compounds: MnBr2(18-crown-6) (), Mn3Br6(18-crown-6)2 () and Mn3Br6(18-crown-6) (). In general, the local coordination and the crystal structure of all compounds are driven by the mismatch between the small radius of the Mn(2+) cation (83 pm) and the ring opening of 18-crown-6 as a chelating ligand (about 300 pm). This improper situation leads to different types of coordination and bonding. MnBr2(18-crown-6) represents a molecular compound with Mn(2+) coordinated by two bromine atoms and only five oxygen atoms of 18-crown-6. Mn3Br6(18-crown-6)2 falls into a [MnBr(18-crown-6)](+) cation - with Mn(2+) coordinated by six oxygen atoms and Br - and a [MnBr(18-crown-6)MnBr4](-) anion. In this anion, Mn(2+) is coordinated by five oxygen atoms of the crown ether as well as by two bromine atoms, one of them bridging to an isolated (MnBr4) tetrahedron. Mn3Br6(18-crown-6), finally, forms an infinite, non-charged [Mn2(18-crown-6)(MnBr6)] chain. Herein, 18-crown-6 is exocyclically coordinated by two Mn(2+) cations. All compounds show intense luminescence in the yellow to red spectral range and exhibit remarkable quantum yields of 70% (Mn3Br6(18-crown-6)) and 98% (Mn3Br6(18-crown-6)2). The excellent quantum yield of Mn3Br6(18-crown-6)2 and its differentiation from MnBr2(18-crown-6) and Mn3Br6(18-crown-6) can be directly correlated to the local coordination. PMID:26956783

  14. High-throughput neuroimaging-genetics computational infrastructure

    PubMed Central

    Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Hobel, Sam; Vespa, Paul; Woo Moon, Seok; Van Horn, John D.; Franco, Joseph; Toga, Arthur W.

    2014-01-01

    Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining, and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate, and disseminate novel scientific methods, computational resources, and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval, and aggregation. Computational processing involves the necessary software, hardware, and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical, and phenotypic data and meta-data. Data mining refers to the process of automatically extracting data features, characteristics and associations, which are not readily visible by human exploration of the raw dataset. Result interpretation includes scientific visualization, community validation of findings and reproducible findings. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI) and the Laboratory of Neuro Imaging (LONI) at University of Southern California (USC). INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. In addition, the institute provides a large number of software tools for image and shape analysis, mathematical modeling, genomic sequence processing, and scientific visualization. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer, and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize

  15. Population genetic structure of a centipede species with high levels of developmental instability.

    PubMed

    Fusco, Giuseppe; Leśniewska, Małgorzata; Congiu, Leonardo; Bertorelle, Giorgio

    2015-01-01

    European populations of the geophilomorph centipede Haplophilus subterraneus show a high proportion of individuals with morphological anomalies, suggesting high levels of developmental instability. The broad geographic distribution of this phenomenon seems to exclude local environmental causes, but the source of instability is still to be identified. The goal of the present study was to collect quantitative data on the occurrence of phenodeviants in different populations, along with data on the patterns of genetic variation within and between populations, in order to investigate possible association between developmental instability and genetic features. In a sample of 11 populations of H. subterraneus, distributed in western and central Europe, we looked for phenodeviants, in particular with respect to trunk morphology, and studied genetic variation through the genotyping of microsatellite loci. Overall, no support was found to the idea that developmental instability in H. subterraneus is related to a specific patterns of genetic variation, including inbreeding estimates. We identified a major genetic partition that subdivides French populations from the others, and a low divergence among northwestern areas, which are possibly related to the post-glacial recolonization from southern refugia and/or to recent anthropogenic soil displacements. A weak correlation between individual number of leg bearing segments and the occurrence of trunk anomalies seems to support a trade-off between these two developmental traits. These results, complemented by preliminary data on developmental stability in two related species, suggest that the phenomenon has not a simple taxonomic distribution, while it exhibits an apparent localization in central and eastern Europe.

  16. A High Fuel Consumption Efficiency Management Scheme for PHEVs Using an Adaptive Genetic Algorithm

    PubMed Central

    Lee, Wah Ching; Tsang, Kim Fung; Chi, Hao Ran; Hung, Faan Hei; Wu, Chung Kit; Chui, Kwok Tai; Lau, Wing Hong; Leung, Yat Wah

    2015-01-01

    A high fuel efficiency management scheme for plug-in hybrid electric vehicles (PHEVs) has been developed. In order to achieve fuel consumption reduction, an adaptive genetic algorithm scheme has been designed to adaptively manage the energy resource usage. The objective function of the genetic algorithm is implemented by designing a fuzzy logic controller which closely monitors and resembles the driving conditions and environment of PHEVs, thus trading off between petrol versus electricity for optimal driving efficiency. Comparison between calculated results and publicized data shows that the achieved efficiency of the fuzzified genetic algorithm is better by 10% than existing schemes. The developed scheme, if fully adopted, would help reduce over 600 tons of CO2 emissions worldwide every day. PMID:25587974

  17. A high fuel consumption efficiency management scheme for PHEVs using an adaptive genetic algorithm.

    PubMed

    Lee, Wah Ching; Tsang, Kim Fung; Chi, Hao Ran; Hung, Faan Hei; Wu, Chung Kit; Chui, Kwok Tai; Lau, Wing Hong; Leung, Yat Wah

    2015-01-01

    A high fuel efficiency management scheme for plug-in hybrid electric vehicles (PHEVs) has been developed. In order to achieve fuel consumption reduction, an adaptive genetic algorithm scheme has been designed to adaptively manage the energy resource usage. The objective function of the genetic algorithm is implemented by designing a fuzzy logic controller which closely monitors and resembles the driving conditions and environment of PHEVs, thus trading off between petrol versus electricity for optimal driving efficiency. Comparison between calculated results and publicized data shows that the achieved efficiency of the fuzzified genetic algorithm is better by 10% than existing schemes. The developed scheme, if fully adopted, would help reduce over 600 tons of CO2 emissions worldwide every day.

  18. Designer aminoglycosides that selectively inhibit cytoplasmic rather than mitochondrial ribosomes show decreased ototoxicity: a strategy for the treatment of genetic diseases.

    PubMed

    Shulman, Eli; Belakhov, Valery; Wei, Gao; Kendall, Ann; Meyron-Holtz, Esther G; Ben-Shachar, Dorit; Schacht, Jochen; Baasov, Timor

    2014-01-24

    There is compelling evidence that aminoglycoside (AG) antibiotics can induce the mammalian ribosome to suppress disease-causing nonsense mutations and partially restore the expression of functional proteins. However, prolonged AG treatment can cause detrimental side effects in patients, including most prominently, ototoxicity. Recent mechanistic discussions have considered the relative contributions of mitochondrial and cytoplasmic protein synthesis inhibition to AG-induced ototoxicity. We show that AGs inhibit mitochondrial protein synthesis in mammalian cells and perturb cell respiration, leading to a time- and dose-dependent increase in superoxide overproduction and accumulation of free ferrous iron in mitochondria caused by oxidative damage of mitochondrial aconitase, ultimately leading to cell apoptosis via the Fenton reaction. These deleterious effects increase with the increased potency of AG to inhibit the mitochondrial rather than cytoplasmic protein synthesis, which in turn correlates with their ototoxic potential in both murine cochlear explants and the guinea pig in vivo. The deleterious effects of AGs were alleviated in synthetic derivatives specially designed for the treatment of genetic diseases caused by nonsense mutations and possessing low affinity toward mitochondrial ribosomes. This work highlights the benefit of a mechanism-based drug redesign strategy that can maximize the translational value of "readthrough therapy" while mitigating drug-induced side effects. This approach holds promise for patients suffering from genetic diseases caused by nonsense mutations.

  19. A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes.

    PubMed

    Dalton-Morgan, Jessica; Hayward, Alice; Alamery, Salman; Tollenaere, Reece; Mason, Annaliese S; Campbell, Emma; Patel, Dhwani; Lorenc, Michał T; Yi, Bin; Long, Yan; Meng, Jinling; Raman, Rosy; Raman, Harsh; Lawley, Cindy; Edwards, David; Batley, Jacqueline

    2014-12-01

    Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples.

  20. A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes.

    PubMed

    Dalton-Morgan, Jessica; Hayward, Alice; Alamery, Salman; Tollenaere, Reece; Mason, Annaliese S; Campbell, Emma; Patel, Dhwani; Lorenc, Michał T; Yi, Bin; Long, Yan; Meng, Jinling; Raman, Rosy; Raman, Harsh; Lawley, Cindy; Edwards, David; Batley, Jacqueline

    2014-12-01

    Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples. PMID:25147024

  1. Discovery in Genetic Skin Disease: The Impact of High Throughput Genetic Technologies

    PubMed Central

    Maruthappu, Thiviyani; Scott, Claire A.; Kelsell, David P.

    2014-01-01

    The last decade has seen considerable advances in our understanding of the genetic basis of skin disease, as a consequence of high throughput sequencing technologies including next generation sequencing and whole exome sequencing. We have now determined the genes underlying several monogenic diseases, such as harlequin ichthyosis, Olmsted syndrome, and exfoliative ichthyosis, which have provided unique insights into the structure and function of the skin. In addition, through genome wide association studies we now have an understanding of how low penetrance variants contribute to inflammatory skin diseases such as psoriasis vulgaris and atopic dermatitis, and how they contribute to underlying pathophysiological disease processes. In this review we discuss strategies used to unravel the genes underlying both monogenic and complex trait skin diseases in the last 10 years and the implications on mechanistic studies, diagnostics, and therapeutics. PMID:25093584

  2. Assessment of first and second degree relatives of individuals with bipolar disorder shows increased genetic risk scores in both affected relatives and young At‐Risk Individuals

    PubMed Central

    Koller, Daniel L.; Edenberg, Howard J.; Foroud, Tatiana; Liu, Hai; Glowinski, Anne L.; McInnis, Melvin G.; Wilcox, Holly C.; Frankland, Andrew; Roberts, Gloria; Schofield, Peter R.; Mitchell, Philip B.; Nurnberger, John I.

    2015-01-01

    Recent studies have revealed the polygenic nature of bipolar disorder (BP), and identified common risk variants associated with illness. However, the role of common polygenic risk in multiplex families has not previously been examined. The present study examined 249 European‐ancestry families from the NIMH Genetics Initiative sample, comparing subjects with narrowly defined BP (excluding bipolar II and recurrent unipolar depression; n = 601) and their adult relatives without BP (n = 695). Unrelated adult controls (n = 266) were from the NIMH TGEN control dataset. We also examined a prospective cohort of young (12–30 years) offspring and siblings of individuals with BPI and BPII disorder (at risk; n = 367) and psychiatrically screened controls (n = 229), ascertained from five sites in the US and Australia and assessed with standardized clinical protocols. Thirty‐two disease‐associated SNPs from the PGC‐BP Working Group report (2011) were genotyped and additive polygenic risk scores (PRS) derived. We show increased PRS in adult cases compared to unrelated controls (P = 3.4 × 10−5, AUC = 0.60). In families with a high‐polygenic load (PRS score ≥32 in two or more subjects), PRS distinguished cases with BPI/SAB from other relatives (P = 0.014, RR = 1.32). Secondly, a higher PRS was observed in at‐risk youth, regardless of affected status, compared to unrelated controls (GEE‐χ2 = 5.15, P = 0.012). This report is the first to explore common polygenic risk in multiplex families, albeit using only a small number of robustly associated risk variants. We show that individuals with BP have a higher load of common disease‐associated variants than unrelated controls and first‐degree relatives, and illustrate the potential utility of PRS assessment in a family context. © 2015 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc. PMID

  3. RFLP and AFLP analysis of inter- and intraspecific variation of Brassica rapa and B. napus shows that B. rapa is an important genetic resource for B. napus improvement.

    PubMed

    Liu, Ren-Hu; Meng, Jin-Ling

    2006-09-01

    Fingerprinting of 29 accessions of oilseed rape, including seven accessions of Brassica napus, and 22 accessions of B. rapa (B. campestris) from Europe, North America, and China was analyzed using RFLP and AFLP markers. In total, 1,477 polymorphic RFLP bands and 183 polymorphic AFLP bands from 166 enzyme-probe combinations and two pairs of AFLP primers, respectively, were scored for the 29 accessions. On average, RFLP analysis showed that the Arabidopsis EST probe detected more polymorphic bands in Brassica than the random genomic probe performed. More polymorphic RFLP markers were detected with the digestion of EcoR I or BamH I than HindIII. According to the number of bands amplified from each accession, the copy numbers of each gene in the genomes of B. rapa and B. napus were estimated. The average copy numbers in B. rapa of China, B. rapa of Europe, and B. napus, were 3.2, 3.1, and 2.9, respectively. Genetic distance based on the AFLP data was well correlated with that based on the RFLP data (r = 0.72, P<0.001), but 0.39 smaller on average. Genetic diversity analysis showed that Chinese B. rapa was more polymorphic than Chinese B. napus and European materials. Some European B. napus accessions were clustered into European B. rapa, which were distinctly different from Chinese B. napus. The larger variations of Chinese accessions of B. rapa suggest that they are valuable in oilseed rape breeding. Novel strategies to use intersubgenomic heterosis between genome of B. rapa (A(r)A(r)) and genome of B. napus (A(n)A(n)C(n)C(n)) were elucidated.

  4. A common genetic influence on human intensity ratings of sugars and high-potency sweeteners.

    PubMed

    Hwang, Liang-Dar; Zhu, Gu; Breslin, Paul A S; Reed, Danielle R; Martin, Nicholas G; Wright, Margaret J

    2015-08-01

    The perception of sweetness varies among individuals but the sources of this variation are not fully understood. Here, in a sample of 1,901 adolescent and young adults (53.8% female; 243 MZ and 452 DZ twin pairs, 511 unpaired individuals; mean age 16.2±2.8, range 12–26 years), we studied the variation in the perception of sweetness intensity of two monosaccharides and two high-potency sweeteners: glucose, fructose, neohesperidine dihydrochalcone (NHDC), and aspartame. Perceived intensity for all sweeteners decreased with age (2–5% per year) and increased with the history of otitis media (6–9%). Males rated aspartame slightly stronger than females (7%). We found similar heritabilities for sugars (glucose: h2=0.31, fructose: h2=0.34) and high-potency sweeteners (NHDC: h2=0.31, aspartame: h2=0.30); all were in the modest range. Multivariate modeling showed that a common genetic factor accounted for >75% of the genetic variance in the four sweeteners, suggesting that individual differences in perceived sweet intensity, which are partly due to genetic factors, may be attributed to a single set of genes. This study provided evidence of the shared genetic pathways between the perception of sugars and high-potency sweeteners. PMID:26181574

  5. A common genetic influence on human intensity ratings of sugars and high-potency sweeteners.

    PubMed

    Hwang, Liang-Dar; Zhu, Gu; Breslin, Paul A S; Reed, Danielle R; Martin, Nicholas G; Wright, Margaret J

    2015-08-01

    The perception of sweetness varies among individuals but the sources of this variation are not fully understood. Here, in a sample of 1,901 adolescent and young adults (53.8% female; 243 MZ and 452 DZ twin pairs, 511 unpaired individuals; mean age 16.2±2.8, range 12–26 years), we studied the variation in the perception of sweetness intensity of two monosaccharides and two high-potency sweeteners: glucose, fructose, neohesperidine dihydrochalcone (NHDC), and aspartame. Perceived intensity for all sweeteners decreased with age (2–5% per year) and increased with the history of otitis media (6–9%). Males rated aspartame slightly stronger than females (7%). We found similar heritabilities for sugars (glucose: h2=0.31, fructose: h2=0.34) and high-potency sweeteners (NHDC: h2=0.31, aspartame: h2=0.30); all were in the modest range. Multivariate modeling showed that a common genetic factor accounted for >75% of the genetic variance in the four sweeteners, suggesting that individual differences in perceived sweet intensity, which are partly due to genetic factors, may be attributed to a single set of genes. This study provided evidence of the shared genetic pathways between the perception of sugars and high-potency sweeteners.

  6. High Levels of Genetic Differentiation between Ugandan Glossina fuscipes fuscipes Populations Separated by Lake Kyoga

    PubMed Central

    Robinson, Alan S.; Muwanika, Vincent B.; Enyaru, John C. K.; Lokedi, Loyce M.; Aksoy, Serap; Caccone, Adalgisa

    2008-01-01

    Background Glossina fuscipes fuscipes is the major vector of human African trypanosomiasis, commonly referred to as sleeping sickness, in Uganda. In western and eastern Africa, the disease has distinct clinical manifestations and is caused by two different parasites: Trypanosoma brucei rhodesiense and T. b. gambiense. Uganda is exceptional in that it harbors both parasites, which are separated by a narrow 160-km belt. This separation is puzzling considering there are no restrictions on the movement of people and animals across this region. Methodology and Results We investigated whether genetic heterogeneity of G. f. fuscipes vector populations can provide an explanation for this disjunct distribution of the Trypanosoma parasites. Therefore, we examined genetic structuring of G. f. fuscipes populations across Uganda using newly developed microsatellite markers, as well as mtDNA. Our data show that G. f. fuscipes populations are highly structured, with two clearly defined clusters that are separated by Lake Kyoga, located in central Uganda. Interestingly, we did not find a correlation between genetic heterogeneity and the type of Trypanosoma parasite transmitted. Conclusions The lack of a correlation between genetic structuring of G. f. fuscipes populations and the distribution of T. b. gambiense and T. b. rhodesiense indicates that it is unlikely that genetic heterogeneity of G. f. fuscipes populations explains the disjunct distribution of the parasites. These results have important epidemiological implications, suggesting that a fusion of the two disease distributions is unlikely to be prevented by an incompatibility between vector populations and parasite. PMID:18509474

  7. Museum genomics: low-cost and high-accuracy genetic data from historical specimens.

    PubMed

    Rowe, Kevin C; Singhal, Sonal; Macmanes, Matthew D; Ayroles, Julien F; Morelli, Toni Lyn; Rubidge, Emily M; Bi, Ke; Moritz, Craig C

    2011-11-01

    Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.

  8. High-quality DNA from fingernails for genetic analysis.

    PubMed

    Preuner, Sandra; Danzer, Martin; Pröll, Johannes; Pötschger, Ulrike; Lawitschka, Anita; Gabriel, Christian; Lion, Thomas

    2014-07-01

    The availability of high-quality germline DNA is an important prerequisite for a variety of genetic analyses. We have shown previously that fingernail clippings provide an optimal source of autologous, constitutional DNA for PCR-based applications. However, most existing protocols for nucleic acid purification from nails do not provide sufficiently high yields of pure and intact DNA for more demanding downstream analyses such as next generation sequencing (NGS). We have extensively tested and systematically modified a number of different protocols for DNA purification from nail material to optimize the yield and quality. The integrity of DNA was determined by PCR amplification of short (<300 bp), mid-range (>400 bp), and long-range (>2 kb) sequences using different target genes. Among the methods tested, the Prepfiler Forensic DNA Extraction kit was identified as the most appropriate approach to isolation of high-quality DNA from nail clippings. A standardized input of 20 mg nail material (1 to 10 pieces of fingernail clippings) yielded a mean of 1 μg DNA (range, 0.5 to 2.3 μg). Subsequent PCR-analysis revealed efficient amplifiability of short and mid-range targets in 93% and 90%, and long-range fragments in 60% of the samples tested. The adequacy for next generation sequencing applications was demonstrated by successful high-resolution HLA-typing in ten transplant recipients. Hence, the protocol presented facilitates the exploitation of fingernail material even for demanding genomic analyses both in research and diagnostics.

  9. Genetic diversity of planktonic eukaryotes in high mountain lakes (Central Pyrenees, Spain).

    PubMed

    Triadó-Margarit, Xavier; Casamayor, Emilio O

    2012-09-01

    The genetic diversity of planktonic eukaryotic microorganisms (size range 3-40 µm) inhabiting 11 alpine lakes of the Central Pyrenees (Spain) was analysed by cloning and sequencing of the 18S rRNA gene. The selected lakes covered a wide range of environmental conditions representative of the regional landscape heterogeneity. Overall, we obtained 953 sequences (averaged length 750 bp) that were grouped in 343 representative OTUs (98% identity). The genetic richness was high, and the 18S rRNA gene sequences spread within nine high-rank taxonomic groups and grouped in 26 eukaryal classes. Most of the sequences affiliated with Stramenopiles (> 55% of total sequences, mostly Chrysophyceae), Cryptophyta and Alveolata (15% each). Three groups had relative abundance < 5%, i.e. Opisthokonta (mostly Fungi), Viridiplantae (mostly Chlorophyceae) and Rhizaria (cercomonads). Finally, minor groups were related to Katablepharidophyta, Euglenozoa and Telonemida. The lakes showed a different community structure being pH, and phosphorous and Chl a concentrations the main environmental drivers. The novelty level was high, and a quarter of the retrieved OTUs were notably divergent (< 97% identity) from any previously known sequence, mainly for Rhizaria and Opisthokonta. More than 50% of the sequences affiliated with clusters exclusively formed by uncultured protists. Cryptophyta and Viridiplantae showed the largest number of sequences closely related to cultured counterparts. This work is the first description of the genetic diversity of eukaryotic assemblages in ultraoligotrophic high mountain lakes, and the study unveils alpine environments as an important reservoir of microbial eukaryotic biodiversity.

  10. Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.

    PubMed

    Finger, Aline; Kaiser-Bunbury, Christopher N; Kettle, Chris J; Valentin, Terence; Ghazoul, Jaboury

    2014-01-01

    Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.

  11. Genetic Connectivity of the Moth Pollinated Tree Glionnetia sericea in a Highly Fragmented Habitat

    PubMed Central

    Finger, Aline; Valentin, Terence; Ghazoul, Jaboury

    2014-01-01

    Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow. PMID:25347541

  12. Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.

    PubMed

    Finger, Aline; Kaiser-Bunbury, Christopher N; Kettle, Chris J; Valentin, Terence; Ghazoul, Jaboury

    2014-01-01

    Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow. PMID:25347541

  13. Characterization of a Staphylococcus aureus strain showing high levels of biofilm formation isolated from a vascular graft: case report.

    PubMed

    Petrelli, D; Repetto, A; Di Luca, M C; Parente, B; Tavolini, V; Cao, P; Ripa, C; Prenna, M; Vitali, L A

    2008-01-01

    A methicillin-susceptible Staphylococcus aureus strain, SA-DZ1, was isolated from an infected bypass crossover graft. Its general microbiological features were reminiscent of those previously described for the wound Wiley strain. Removal of the prosthetic device was necessary to resolve the infection. SA-DZ1 grown under different conditions showed a very strong and distinctive biofilm-producing phenotype, which was also visualized by confocal laser scanning microscopy. The biofilm extracellular matrix was essentially polysaccharidic, as determined by differential growth and physicochemical tests. By Multi Locus Sequence Typing (MLST), SA-DZ1 was classified as st94, a single locus variant of st8. Several other genetic traits assayed by PCR, such as agr-type and the presence of gene encoding proteins involved in adhesion and virulence (e.g. ica operon), confirmed the identifying features of this clinical isolate.

  14. A comprehensive analysis of high school genetics standards: are states keeping pace with modern genetics?

    PubMed

    Dougherty, M J; Pleasants, C; Solow, L; Wong, A; Zhang, H

    2011-01-01

    Science education in the United States will increasingly be driven by testing and accountability requirements, such as those mandated by the No Child Left Behind Act, which rely heavily on learning outcomes, or "standards," that are currently developed on a state-by-state basis. Those standards, in turn, drive curriculum and instruction. Given the importance of standards to teaching and learning, we investigated the quality of life sciences/biology standards with respect to genetics for all 50 states and the District of Columbia, using core concepts developed by the American Society of Human Genetics as normative benchmarks. Our results indicate that the states' genetics standards, in general, are poor, with more than 85% of the states receiving overall scores of Inadequate. In particular, the standards in virtually every state have failed to keep pace with changes in the discipline as it has become genomic in scope, omitting concepts related to genetic complexity, the importance of environment to phenotypic variation, differential gene expression, and the differences between inherited and somatic genetic disease. Clearer, more comprehensive genetics standards are likely to benefit genetics instruction and learning, help prepare future genetics researchers, and contribute to the genetic literacy of the U.S. citizenry.

  15. High-Performance Single Cell Genetic Analysis Using Microfluidic Emulsion Generator Arrays

    PubMed Central

    Zeng, Yong; Novak, Richard; Shuga, Joe; Smith, Martyn T.; Mathies, Richard A.

    2010-01-01

    High-throughput genetic and phenotypic analysis at the single cell level is critical to advance our understanding of the molecular mechanisms underlying cellular function and dysfunction. Here we describe a high-performance single cell genetic analysis (SCGA) technique that combines high-throughput microfluidic emulsion generation with single cell multiplex PCR. Microfabricated emulsion generator array (MEGA) devices containing 4, 32 and 96 channels are developed to confer a flexible capability of generating up to 3.4 × 106 nanoliter-volume droplets per hour. Hybrid glass-polydimethylsiloxane diaphragm micropumps integrated into the MEGA chips afford uniform droplet formation, controlled generation frequency, and effective transportation and encapsulation of primer functionalized microbeads and cells. A multiplex single cell PCR method is developed to detect and quantify both wild type and mutant/pathogenic cells. In this method, microbeads functionalized with multiple forward primers targeting specific genes from different cell types are used for solid-phase PCR in droplets. Following PCR, the droplets are lysed, the beads are pooled and rapidly analyzed by multi-color flow cytometry. Using E. coli bacterial cells as a model, we show that this technique enables digital detection of pathogenic E. coli O157 cells in a high background of normal K12 cells, with a detection limit on the order of 1:105. This result demonstrates that multiplex SCGA is a promising tool for high-throughput quantitative digital analysis of genetic variation in complex populations. PMID:20192178

  16. Awareness of Societal Issues among High School Biology Teachers Teaching Genetics

    ERIC Educational Resources Information Center

    Lazarowitz, Reuven; Bloch, Ilit

    2005-01-01

    The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral, ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution. The study includes a short historical review of World War II atrocities during the Holocaust when…

  17. Is serum retinol binding protein-4: A predictor for diabetes in genetically high risk population?

    PubMed Central

    Bose, K. Subhash Chandra; Gupta, Shachin K.; Singh, Sandeep

    2012-01-01

    Background: Retinol binding protein-4 (BP-4) a new adipocytokine, specifically binds to retinol, through experimental studies, reported its link between obesity and insulin resistance (IR). But till date no studies are available on influence of genetic predisposition of diabetes on RBP-4 expression. Hence, we aimed to study the influence of genetic predisposition of diabetes on the serum RBP-4 and its role in development of IR and diabetes in genetically high risk population. Materials and Methods: Healthy non diabetic individuals (age 18 to 22) were grouped into Group I: Control (n = 81), whose parents are non diabetic, non hypertensive and does not have any family history of coronary heart diseases. Group II: (n = 157) with one of their parents diabetic and Group III: (n = 47) with both parents diabetic. In all the participants, we estimated fasting serum RBP-4, insulin and glucose. Homeostasis model for assessment-insulin resistance (HOMA-IR) and homeostasis model for assessment-beta cell dysfunction (HOMA-B) were calculated from fasting serum insulin and glucose levels. Results: In this study, we observed significantly higher RBP-4 levels 12.71 ± 2.3 in Group-II and 13.25 ± 2 in Group-III, respectively when compared to Group-I 11.4 ± 1.8 (P < 0.01). RBP-4 showed a significantly strong positive correlation with plasma insulin, glucose and HOMA-IR in genetically high risk population (group II and III) P < 0.01. Linear regression analysis revealed a strong positive association of RBP-4 with parental diabetes even after adjusting for BMI, age and sex (OR 1.53, 95% CI 1.089-1.40). Conclusion: Higher serum RBP-4 and its positive correlation with Insulin, glucose, and HOMA-IR in healthy non diabetic participants of genetically high risk population, indicating its role as predictor for the onset of diabetes in coming future. PMID:23833574

  18. High School Students' Use of Meiosis When Solving Genetics Problems.

    ERIC Educational Resources Information Center

    Wynne, Cynthia F.; Stewart, Jim; Passmore, Cindy

    2001-01-01

    Paints a different picture of students' reasoning with meiosis as they solved complex, computer-generated genetics problems, some of which required them to revise their understanding of meiosis in response to anomalous data. Students were able to develop a rich understanding of meiosis and can utilize that knowledge to solve genetics problems.…

  19. The Yeast Hrs1 Gene Is Involved in Positive and Negative Regulation of Transcription and Shows Genetic Characteristics Similar to Sin4 and Gal11

    PubMed Central

    Piruat, J. I.; Chavez, S.; Aguilera, A.

    1997-01-01

    We provide genetic evidence that HRS1/PGD1, a yeast gene previously identified as a suppressor of the hyper-recombination phenotype of hpr1, has positive and negative roles in transcriptional regulation. We have analyzed three differently regulated promoters, GAL1, PHO5 and HSP26, by β-galactosidase assays of lacZ-fused promoters and by Northern analysis of the endogenous genes. Transcription of these promoters was derepressed in hrs1δ mutants under conditions in which it is normally repressed in wild type. Under induced conditions it was either strongly reduced or significantly enhanced depending on the promoter system analyzed. Constitutive transcription was not affected, as determined in ADH1 and TEF2. In addition, Hrs1p was required for mating-factor expression, telomere-linked DNA silencing and DNA supercoiling of plasmids. Furthermore, hrs1δ suppressed Ty-insertion mutations and conferred a Gal(-) phenotype. Many of these phenotypes also result from mutations in GAL11, SIN4 or RGR1, which encode proteins of the RNA polII mediator. We also show that gal11δ and sin4δ partially suppress the hyper-rec phenotype of hpr1 mutants, although to a lesser extent than hrs1δ. Our results provide new evidence for the connection between hpr1δ-induced deletions and transcription. We discuss the possibility that Hrs1p might be a component of the RNA polII transcription machinery. PMID:9409823

  20. MHC ANTIGEN-BINDING LOCUS SHOWS STRONG SIGNAL OF SELECTION AND HIGH VARIABILITY IN FUNDULUS HETEROCLITUS POPULATIONS

    EPA Science Inventory

    The major histocompatibility system provides a unique genetic locus in vertebrates to assess genetic diversity and to look for the effects of selecti.on on the immune system. Fish population studies using MHC are fairly new, and thus far they have focused on endangered population...

  1. MHC ANTIGEN BINDING LOCUS DRB1 SHOWS STRONG SIGNAL OF SELECTION AND HIGH VARIABILITY IN FUNDULUS HETERCLITUS POPULATIONS

    EPA Science Inventory

    The major histocompatibility system provides a unique complex of genetic loci in vertebrates to assess genetic diversity and to look for the effects of selection on the adaptive immune system. Studies using mammals and birds
    have demonstrated relationships between MHC genotyp...

  2. Genetic and Nongenetic Determinants of Cell Growth Variation Assessed by High-Throughput Microscopy

    PubMed Central

    Ziv, Naomi; Siegal, Mark L.; Gresham, David

    2013-01-01

    In microbial populations, growth initiation and proliferation rates are major components of fitness and therefore likely targets of selection. We used a high-throughput microscopy assay, which enables simultaneous analysis of tens of thousands of microcolonies, to determine the sources and extent of growth rate variation in the budding yeast (Saccharomyces cerevisiae) in different glucose environments. We find that cell growth rates are regulated by the extracellular concentration of glucose as proposed by Monod (1949), but that significant heterogeneity in growth rates is observed among genetically identical individuals within an environment. Yeast strains isolated from different geographic locations and habitats differ in their growth rate responses to different glucose concentrations. Inheritance patterns suggest that the genetic determinants of growth rates in different glucose concentrations are distinct. In addition, we identified genotypes that differ in the extent of variation in growth rate within an environment despite nearly identical mean growth rates, providing evidence that alleles controlling phenotypic variability segregate in yeast populations. We find that the time to reinitiation of growth (lag) is negatively correlated with growth rate, yet this relationship is strain-dependent. Between environments, the respirative activity of individual cells negatively correlates with glucose abundance and growth rate, but within an environment respirative activity and growth rate show a positive correlation, which we propose reflects differences in protein expression capacity. Our study quantifies the sources of genetic and nongenetic variation in cell growth rates in different glucose environments with unprecedented precision, facilitating their molecular genetic dissection. PMID:23938868

  3. Discovering genetic associations with high-dimensional neuroimaging phenotypes: A sparse reduced-rank regression approach.

    PubMed

    Vounou, Maria; Nichols, Thomas E; Montana, Giovanni

    2010-11-15

    There is growing interest in performing genome-wide searches for associations between genetic variants and brain imaging phenotypes. While much work has focused on single scalar valued summaries of brain phenotype, accounting for the richness of imaging data requires a brain-wide, genome-wide search. In particular, the standard approach based on mass-univariate linear modelling (MULM) does not account for the structured patterns of correlations present in each domain. In this work, we propose sparse reduced rank regression (sRRR), a strategy for multivariate modelling of high-dimensional imaging responses (measurements taken over regions of interest or individual voxels) and genetic covariates (single nucleotide polymorphisms or copy number variations), which enforces sparsity in the regression coefficients. Such sparsity constraints ensure that the model performs simultaneous genotype and phenotype selection. Using simulation procedures that accurately reflect realistic human genetic variation and imaging correlations, we present detailed evaluations of the sRRR method in comparison with the more traditional MULM approach. In all settings considered, sRRR has better power to detect deleterious genetic variants compared to MULM. Important issues concerning model selection and connections to existing latent variable models are also discussed. This work shows that sRRR offers a promising alternative for detecting brain-wide, genome-wide associations.

  4. Copper tolerance and genetic diversity of Porcellionides sexfasciatus (ISOPODA) in a highly contaminated mine habitat.

    PubMed

    Costa, Dalila; Bouchon, Didier; van Straalen, Nico M; Sousa, José Paulo; Ribeiro, Rui

    2013-04-01

    Organisms inhabiting metal-contaminated areas may develop metal tolerance, with either phenotypic adjustments or genetic changes (adaptation) or with both. In the present study, three populations of the terrestrial isopod Porcellionides sexfasciatus, collected at an abandoned mine area, were compared to assess the effects of metal contamination on tolerance to lethal and sublethal levels of copper, through comparison of survival, avoidance, and feeding. The effects of metal contamination on genetic diversity were considered using random amplified polymorphic DNA (RAPD) markers. No evidence of increased metal tolerance of the population inhabiting the contaminated site was found. There was no correlation between metal exposure and within-population genetic variance, but the three populations were clearly separated from each other. In conclusion, the populations of P. sexfasciatus in the mine landscape live rather isolated from each other and show no differential tolerance to Cu or indications of genetic erosion. Their phenotypic plasticity provides a means to survive despite exposure to extremely high metal concentrations in the soil.

  5. Population genetic structure of a centipede species with high levels of developmental instability.

    PubMed

    Fusco, Giuseppe; Leśniewska, Małgorzata; Congiu, Leonardo; Bertorelle, Giorgio

    2015-01-01

    European populations of the geophilomorph centipede Haplophilus subterraneus show a high proportion of individuals with morphological anomalies, suggesting high levels of developmental instability. The broad geographic distribution of this phenomenon seems to exclude local environmental causes, but the source of instability is still to be identified. The goal of the present study was to collect quantitative data on the occurrence of phenodeviants in different populations, along with data on the patterns of genetic variation within and between populations, in order to investigate possible association between developmental instability and genetic features. In a sample of 11 populations of H. subterraneus, distributed in western and central Europe, we looked for phenodeviants, in particular with respect to trunk morphology, and studied genetic variation through the genotyping of microsatellite loci. Overall, no support was found to the idea that developmental instability in H. subterraneus is related to a specific patterns of genetic variation, including inbreeding estimates. We identified a major genetic partition that subdivides French populations from the others, and a low divergence among northwestern areas, which are possibly related to the post-glacial recolonization from southern refugia and/or to recent anthropogenic soil displacements. A weak correlation between individual number of leg bearing segments and the occurrence of trunk anomalies seems to support a trade-off between these two developmental traits. These results, complemented by preliminary data on developmental stability in two related species, suggest that the phenomenon has not a simple taxonomic distribution, while it exhibits an apparent localization in central and eastern Europe. PMID:26029915

  6. Population Genetic Structure of a Centipede Species with High Levels of Developmental Instability

    PubMed Central

    Fusco, Giuseppe; Leśniewska, Małgorzata; Congiu, Leonardo; Bertorelle, Giorgio

    2015-01-01

    European populations of the geophilomorph centipede Haplophilus subterraneus show a high proportion of individuals with morphological anomalies, suggesting high levels of developmental instability. The broad geographic distribution of this phenomenon seems to exclude local environmental causes, but the source of instability is still to be identified. The goal of the present study was to collect quantitative data on the occurrence of phenodeviants in different populations, along with data on the patterns of genetic variation within and between populations, in order to investigate possible association between developmental instability and genetic features. In a sample of 11 populations of H. subterraneus, distributed in western and central Europe, we looked for phenodeviants, in particular with respect to trunk morphology, and studied genetic variation through the genotyping of microsatellite loci. Overall, no support was found to the idea that developmental instability in H. subterraneus is related to a specific patterns of genetic variation, including inbreeding estimates. We identified a major genetic partition that subdivides French populations from the others, and a low divergence among northwestern areas, which are possibly related to the post-glacial recolonization from southern refugia and/or to recent anthropogenic soil displacements. A weak correlation between individual number of leg bearing segments and the occurrence of trunk anomalies seems to support a trade-off between these two developmental traits. These results, complemented by preliminary data on developmental stability in two related species, suggest that the phenomenon has not a simple taxonomic distribution, while it exhibits an apparent localization in central and eastern Europe. PMID:26029915

  7. A genetically encoded, high-signal-to-noise maltose sensor

    SciTech Connect

    Marvin, Jonathan S.; Schreiter, Eric R.; Echevarría, Ileabett M.; Looger, Loren L.

    2012-10-23

    We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

  8. Ways:1, Three Musicians; Ways:2, One Student, One Show; Ways:3, A High School Art Gallery.

    ERIC Educational Resources Information Center

    Nunnally, Elaine; And Others

    1985-01-01

    How a seventh grade teacher incorporated art history into a 12-week unit on drawing, painting, color, ceramics, printing, and sculpture is discussed; an art program that involves sixth graders in preparing one-artist shows is described; and suggestions for developing a permanent high school art gallery are presented. (RM)

  9. Molecular evidence and high genetic diversity of shrew-borne Seewis virus in Slovenia.

    PubMed

    Resman, Katarina; Korva, Miša; Fajs, Luka; Zidarič, Tanja; Trilar, Tomi; Zupanc, Tatjana Avšič

    2013-10-01

    Seewis virus, the shrew-borne hantavirus from Sorex araneus, has been molecularly detected in reservoir hosts in many different central European countries and Russia. Slovenia is a known endemic country for rodent-borne hantaviruses, therefore the aim of the study was to investigate the presence of shrew-borne hantaviruses in insectivores. Viral L, S and M segment have been recovered only from tissue samples of 7 S. araneus, despite several shrew species were tested. Phylogenetic analysis showed high genetic diversity of SWSV in Slovenia, ranging from 3 to 19.4% for different viral segments. The most divergent were M segment sequences, with 19.4% nucleotide divergence among Slovenian strains. Above that, different SWSV strains from Slovenia do not group into separate geographic clusters. While three separate genetic clades were determined, two of them were simultaneously present in one location at the same time.

  10. High Quality Typhoon Cloud Image Restoration by Combining Genetic Algorithm with Contourlet Transform

    SciTech Connect

    Zhang Changjiang; Wang Xiaodong

    2008-11-06

    An efficient typhoon cloud image restoration algorithm is proposed. Having implemented contourlet transform to a typhoon cloud image, noise is reduced in the high sub-bands. Weight median value filter is used to reduce the noise in the contourlet domain. Inverse contourlet transform is done to obtain the de-noising image. In order to enhance the global contrast of the typhoon cloud image, in-complete Beta transform (IBT) is used to determine non-linear gray transform curve so as to enhance global contrast for the de-noising typhoon cloud image. Genetic algorithm is used to obtain the optimal gray transform curve. Information entropy is used as the fitness function of the genetic algorithm. Experimental results show that the new algorithm is able to well enhance the global for the typhoon cloud image while well reducing the noises in the typhoon cloud image.

  11. Application of wavelet neural network model based on genetic algorithm in the prediction of high-speed railway settlement

    NASA Astrophysics Data System (ADS)

    Tang, Shihua; Li, Feida; Liu, Yintao; Lan, Lan; Zhou, Conglin; Huang, Qing

    2015-12-01

    With the advantage of high speed, big transport capacity, low energy consumption, good economic benefits and so on, high-speed railway is becoming more and more popular all over the world. It can reach 350 kilometers per hour, which requires high security performances. So research on the prediction of high-speed railway settlement that as one of the important factors affecting the safety of high-speed railway becomes particularly important. This paper takes advantage of genetic algorithms to seek all the data in order to calculate the best result and combines the advantage of strong learning ability and high accuracy of wavelet neural network, then build the model of genetic wavelet neural network for the prediction of high-speed railway settlement. By the experiment of back propagation neural network, wavelet neural network and genetic wavelet neural network, it shows that the absolute value of residual errors in the prediction of high-speed railway settlement based on genetic algorithm is the smallest, which proves that genetic wavelet neural network is better than the other two methods. The correlation coefficient of predicted and observed value is 99.9%. Furthermore, the maximum absolute value of residual error, minimum absolute value of residual error-mean value of relative error and value of root mean squared error(RMSE) that predicted by genetic wavelet neural network are all smaller than the other two methods'. The genetic wavelet neural network in the prediction of high-speed railway settlement is more stable in terms of stability and more accurate in the perspective of accuracy.

  12. Seascape genetics of a globally distributed, highly mobile marine mammal: the short-beaked common dolphin (genus Delphinus).

    PubMed

    Amaral, Ana R; Beheregaray, Luciano B; Bilgmann, Kerstin; Boutov, Dmitri; Freitas, Luís; Robertson, Kelly M; Sequeira, Marina; Stockin, Karen A; Coelho, M Manuela; Möller, Luciana M

    2012-01-01

    Identifying which factors shape the distribution of intraspecific genetic diversity is central in evolutionary and conservation biology. In the marine realm, the absence of obvious barriers to dispersal can make this task more difficult. Nevertheless, recent studies have provided valuable insights into which factors may be shaping genetic structure in the world's oceans. These studies were, however, generally conducted on marine organisms with larval dispersal. Here, using a seascape genetics approach, we show that marine productivity and sea surface temperature are correlated with genetic structure in a highly mobile, widely distributed marine mammal species, the short-beaked common dolphin. Isolation by distance also appears to influence population divergence over larger geographical scales (i.e. across different ocean basins). We suggest that the relationship between environmental variables and population structure may be caused by prey behaviour, which is believed to determine common dolphins' movement patterns and preferred associations with certain oceanographic conditions. Our study highlights the role of oceanography in shaping genetic structure of a highly mobile and widely distributed top marine predator. Thus, seascape genetic studies can potentially track the biological effects of ongoing climate-change at oceanographic interfaces and also inform marine reserve design in relation to the distribution and genetic connectivity of charismatic and ecologically important megafauna.

  13. Seascape Genetics of a Globally Distributed, Highly Mobile Marine Mammal: The Short-Beaked Common Dolphin (Genus Delphinus)

    PubMed Central

    Amaral, Ana R.; Beheregaray, Luciano B.; Bilgmann, Kerstin; Boutov, Dmitri; Freitas, Luís; Robertson, Kelly M.; Sequeira, Marina; Stockin, Karen A.; Coelho, M. Manuela; Möller, Luciana M.

    2012-01-01

    Identifying which factors shape the distribution of intraspecific genetic diversity is central in evolutionary and conservation biology. In the marine realm, the absence of obvious barriers to dispersal can make this task more difficult. Nevertheless, recent studies have provided valuable insights into which factors may be shaping genetic structure in the world's oceans. These studies were, however, generally conducted on marine organisms with larval dispersal. Here, using a seascape genetics approach, we show that marine productivity and sea surface temperature are correlated with genetic structure in a highly mobile, widely distributed marine mammal species, the short-beaked common dolphin. Isolation by distance also appears to influence population divergence over larger geographical scales (i.e. across different ocean basins). We suggest that the relationship between environmental variables and population structure may be caused by prey behaviour, which is believed to determine common dolphins' movement patterns and preferred associations with certain oceanographic conditions. Our study highlights the role of oceanography in shaping genetic structure of a highly mobile and widely distributed top marine predator. Thus, seascape genetic studies can potentially track the biological effects of ongoing climate-change at oceanographic interfaces and also inform marine reserve design in relation to the distribution and genetic connectivity of charismatic and ecologically important megafauna. PMID:22319634

  14. A genetic mechanism for Tibetan high-altitude adaptation

    PubMed Central

    Lorenzo, Felipe R; Huff, Chad; Myllymäki, Mikko; Olenchock, Benjamin; Swierczek, Sabina; Tashi, Tsewang; Gordeuk, Victor; Wuren, Tana; Ri-Li, Ge; McClain, Donald A; Khan, Tahsin M; Koul, Parvaiz A; Guchhait, Prasenjit; Salama, Mohamed E; Xing, Jinchuan; Semenza, Gregg L; Liberzon, Ella; Wilson, Andrew; Simonson, Tatum S; Jorde, Lynn B; Kaelin, William G; Koivunen, Peppi; Prchal, Josef T

    2015-01-01

    Tibetans do not exhibit increased hemoglobin concentration at high altitude. We describe a high-frequency missense mutation in the EGLN1 gene, which encodes prolyl hydroxylase 2 (PHD2), that contributes to this adaptive response. We show that a variant in EGLN1, c.[12C>G; 380G>C], contributes functionally to the Tibetan high-altitude phenotype. PHD2 triggers the degradation of hypoxia-inducible factors (HIFs), which mediate many physiological responses to hypoxia, including erythropoiesis. The PHD2 p.[Asp4Glu; Cys127Ser] variant exhibits a lower Km value for oxygen, suggesting that it promotes increased HIF degradation under hypoxic conditions. Whereas hypoxia stimulates the proliferation of wild-type erythroid progenitors, the proliferation of progenitors with the c.[12C>G; 380G>C] mutation in EGLN1 is significantly impaired under hypoxic culture conditions. We show that the c.[12C>G; 380G>C] mutation originated ~8,000 years ago on the same haplotype previously associated with adaptation to high altitude. The c.[12C>G; 380G>C] mutation abrogates hypoxia-induced and HIF-mediated augmentation of erythropoiesis, which provides a molecular mechanism for the observed protection of Tibetans from polycythemia at high altitude. PMID:25129147

  15. An Endangered Arboreal Specialist, the Western Ringtail Possum (Pseudocheirus occidentalis), Shows a Greater Genetic Divergence across a Narrow Artificial Waterway than a Major Road.

    PubMed

    Yokochi, Kaori; Kennington, Winn Jason; Bencini, Roberta

    2016-01-01

    The fragmentation of habitats by roads and other artificial linear structures can have a profound effect on the movement of arboreal species due to their strong fidelity to canopies. Here, we used 12 microsatellite DNA loci to investigate the fine-scale spatial genetic structure and the effects of a major road and a narrow artificial waterway on a population of the endangered western ringtail possum (Pseudocheirus occidentalis) in Busselton, Western Australia. Using spatial autocorrelation analysis, we found positive genetic structure in continuous habitat over distances up to 600 m. These patterns are consistent with the sedentary nature of P. occidentalis and highlight their vulnerability to the effects of habitat fragmentation. Pairwise relatedness values and Bayesian cluster analysis also revealed significant genetic divergences across an artificial waterway, suggesting that it was a barrier to gene flow. By contrast, no genetic divergences were detected across the major road. While studies often focus on roads when assessing the effects of artificial linear structures on wildlife, this study provides an example of an often overlooked artificial linear structure other than a road that has a significant impact on wildlife dispersal leading to genetic subdivision. PMID:26784921

  16. An Endangered Arboreal Specialist, the Western Ringtail Possum (Pseudocheirus occidentalis), Shows a Greater Genetic Divergence across a Narrow Artificial Waterway than a Major Road

    PubMed Central

    Yokochi, Kaori

    2016-01-01

    The fragmentation of habitats by roads and other artificial linear structures can have a profound effect on the movement of arboreal species due to their strong fidelity to canopies. Here, we used 12 microsatellite DNA loci to investigate the fine-scale spatial genetic structure and the effects of a major road and a narrow artificial waterway on a population of the endangered western ringtail possum (Pseudocheirus occidentalis) in Busselton, Western Australia. Using spatial autocorrelation analysis, we found positive genetic structure in continuous habitat over distances up to 600 m. These patterns are consistent with the sedentary nature of P. occidentalis and highlight their vulnerability to the effects of habitat fragmentation. Pairwise relatedness values and Bayesian cluster analysis also revealed significant genetic divergences across an artificial waterway, suggesting that it was a barrier to gene flow. By contrast, no genetic divergences were detected across the major road. While studies often focus on roads when assessing the effects of artificial linear structures on wildlife, this study provides an example of an often overlooked artificial linear structure other than a road that has a significant impact on wildlife dispersal leading to genetic subdivision. PMID:26784921

  17. Characterization and Genetic Analysis of a Novel Light-Dependent Lesion Mimic Mutant, lm3, Showing Adult-Plant Resistance to Powdery Mildew in Common Wheat

    PubMed Central

    Wang, Fang; Wu, Wenying; Wang, Dongzhi; Yang, Wenlong; Sun, Jiazhu; Liu, Dongcheng; Zhang, Aimin

    2016-01-01

    Lesion mimics (LMs) that exhibit spontaneous disease-like lesions in the absence of pathogen attack might confer enhanced plant disease resistance to a wide range of pathogens. The LM mutant, lm3 was derived from a single naturally mutated individual in the F1 population of a 3-1/Jing411 cross, backcrossed six times with 3–1 as the recurrent parent and subsequently self-pollinated twice. The leaves of young seedlings of the lm3 mutant exhibited small, discrete white lesions under natural field conditions. The lesions first appeared at the leaf tips and subsequently expanded throughout the entire leaf blade to the leaf sheath. The lesions were initiated through light intensity and day length. Histochemical staining revealed that lesion formation might reflect programmed cell death (PCD) and abnormal accumulation of reactive oxygen species (ROS). The chlorophyll content in the mutant was significantly lower than that in wildtype, and the ratio of chlorophyll a/b was increased significantly in the mutant compared with wildtype, indicating that lm3 showed impairment of the biosynthesis or degradation of chlorophyll, and that Chlorophyll b was prone to damage during lesion formation. The lm3 mutant exhibited enhanced resistance to wheat powdery mildew fungus (Blumeria graminis f. sp. tritici; Bgt) infection, which was consistent with the increased expression of seven pathogenesis-related (PR) and two wheat chemically induced (WCI) genes involved in the defense-related reaction. Genetic analysis showed that the mutation was controlled through a single partially dominant gene, which was closely linked to Xbarc203 on chromosome 3BL; this gene was delimited to a 40 Mb region between SSR3B450.37 and SSR3B492.6 using a large derived segregating population and the available Chinese Spring chromosome 3B genome sequence. Taken together, our results provide information regarding the identification of a novel wheat LM gene, which will facilitate the additional fine-mapping and

  18. Genetic parameters and breeding strategies for high levels of iron and zinc in Phaseolus vulgaris L.

    PubMed

    Martins, S M; Melo, P G S; Faria, L C; Souza, T L P O; Melo, L C; Pereira, H S

    2016-01-01

    One of the current focus of common bean breeding programs in Brazil is to increase iron (FeC) and zinc content (ZnC) in grains. The objectives of this study were to estimate genetic parameters for FeC and ZnC in common bean, verify the need for conducting multi-site evaluation tests, identify elite lines that combine high FeC and ZnC with good adaptability, stability, and agronomic potential, and examine the genetic association between FeC and ZnC. Elite lines (140) were evaluated for important agronomic traits in multiple environments. In one trial, FeC and ZnC were evaluated and genetic parameters were estimated. Based on the high heritability estimates and significant selection gains obtained, the conditions for a successful selection was favorable. Of the 140 evaluated lines, 17 had higher FeC and ZnC, and were included in the validation test (2013, five environments), specifically for the evaluation of FeC and ZnC. The line by environment interaction for FeC and ZnC was detected, but it was predominantly simple. The environmental effect strongly influenced FeC and ZnC . The environment Brasília/rainy season was selected as the best evaluation site for preliminary tests for FeC and ZnC, because it resulted in similar conclusions as the mean of the five environments. The lines CNFP 15701 and CNFC 15865 had higher FeC and ZnC and were highly adaptable and stable, and are recommended for utilization in breeding programs. The lines CNFC 15833, CNFC 15703, and CNFP 15676 showed excellent combined agronomic and nutritional traits, and were selected for the development of biofortified cultivars. Additionally, the genetic association between FeC and ZnC was detected. PMID:27323172

  19. High HIV-1 Genetic Diversity in Patients from Northern Brazil.

    PubMed

    da Costa, Carolina Marinho; Costa de Oliveira, Cintia Mara; Chehuan de Melo, Yonne Francis; Delatorre, Edson; Bello, Gonzalo; Couto-Fernandez, Jose Carlos

    2016-09-01

    The HIV-1 epidemic in Brazil is driven by subtypes B, F1, and C and recombinants forms among those subtypes. The distribution of HIV-1 subtypes, however, may vary across different Brazilian regions and the molecular epidemiologic profile in Northern Brazil remains poorly explored. HIV-1 pol sequences were obtained from 305 patients failing antiretroviral therapy followed at outpatient clinics from five Northern Brazilian states. The most prevalent HIV-1 clade observed in the Northern Brazilian region was subtype B (81%), followed by BF1 recombinants (10%), subtype F1 (4%), subtype C (3%), BC recombinants (2%), and BU recombinants (1%). Although HIV-1 subtype B was the predominant HIV-1 clade in Northern Brazil, its prevalence greatly varies among different states, ranging from 63% in Rondônia to 92% in Acre. Among the 37 HIV-1 recombinant sequences detected in the Northern Brazilian region, nine (24%) displayed a unique recombinant form structure, five (14%) a CRF28/29_BF-like structure, and four (11%) a CRF31_BC-like structure. Two other BF1 recombinant patterns were identified in 16 (43%) and three (8%) samples that may correspond to two potentially new CRFs_BF characteristic of the Northern region. This study reveals that despite the low spatial connectivity with other Brazilian regions, the genetic complexity of the HIV-1 epidemic in Northern Brazil is very high and that the molecular epidemiologic pattern may vary across different northern states, reflecting a complex epidemic with multiple independent viral introductions into this Brazilian region. PMID:27091699

  20. High HIV-1 Genetic Diversity in Patients from Northern Brazil.

    PubMed

    da Costa, Carolina Marinho; Costa de Oliveira, Cintia Mara; Chehuan de Melo, Yonne Francis; Delatorre, Edson; Bello, Gonzalo; Couto-Fernandez, Jose Carlos

    2016-09-01

    The HIV-1 epidemic in Brazil is driven by subtypes B, F1, and C and recombinants forms among those subtypes. The distribution of HIV-1 subtypes, however, may vary across different Brazilian regions and the molecular epidemiologic profile in Northern Brazil remains poorly explored. HIV-1 pol sequences were obtained from 305 patients failing antiretroviral therapy followed at outpatient clinics from five Northern Brazilian states. The most prevalent HIV-1 clade observed in the Northern Brazilian region was subtype B (81%), followed by BF1 recombinants (10%), subtype F1 (4%), subtype C (3%), BC recombinants (2%), and BU recombinants (1%). Although HIV-1 subtype B was the predominant HIV-1 clade in Northern Brazil, its prevalence greatly varies among different states, ranging from 63% in Rondônia to 92% in Acre. Among the 37 HIV-1 recombinant sequences detected in the Northern Brazilian region, nine (24%) displayed a unique recombinant form structure, five (14%) a CRF28/29_BF-like structure, and four (11%) a CRF31_BC-like structure. Two other BF1 recombinant patterns were identified in 16 (43%) and three (8%) samples that may correspond to two potentially new CRFs_BF characteristic of the Northern region. This study reveals that despite the low spatial connectivity with other Brazilian regions, the genetic complexity of the HIV-1 epidemic in Northern Brazil is very high and that the molecular epidemiologic pattern may vary across different northern states, reflecting a complex epidemic with multiple independent viral introductions into this Brazilian region.

  1. High school students' understanding and problem solving in population genetics

    NASA Astrophysics Data System (ADS)

    Soderberg, Patti D.

    This study is an investigation of student understanding of population genetics and how students developed, used and revised conceptual models to solve problems. The students in this study participated in three rounds of problem solving. The first round involved the use of a population genetics model to predict the number of carriers in a population. The second round required them to revise their model of simple dominance population genetics to make inferences about populations containing three phenotype variations. The third round of problem solving required the students to revise their model of population genetics to explain anomalous data where the proportions of males and females with a trait varied significantly. As the students solved problems, they were involved in basic scientific processes as they observed population phenomena, constructed explanatory models to explain the data they observed, and attempted to persuade their peers as to the adequacy of their models. In this study, the students produced new knowledge about the genetics of a trait in a population through the revision and use of explanatory population genetics models using reasoning that was similar to what scientists do. The students learned, used and revised a model of Hardy-Weinberg equilibrium to generate and test hypotheses about the genetics of phenotypes given only population data. Students were also interviewed prior to and following instruction. This study suggests that a commonly held intuitive belief about the predominance of a dominant variation in populations is resistant to change, despite instruction and interferes with a student's ability to understand Hardy-Weinberg equilibrium and microevolution.

  2. AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasii isolates from Mexico and Argentina

    PubMed Central

    2013-01-01

    Background Coccidioides immitis and C. posadasii cause coccidioidomycosis, a disease that is endemic to North and South America, but for Central America, the incidence of coccidioidomycosis has not been clearly established. Several studies suggest genetic variability in these fungi; however, little definitive information has been discovered about the variability of Coccidioides fungi in Mexico (MX) and Argentina (AR). Thus, the goals for this work were to study 32 Coccidioides spp. isolates from MX and AR, identify the species of these Coccidioides spp. isolates, analyse their phenotypic variability, examine their genetic variability and investigate the Coccidioides reproductive system and its level of genetic differentiation. Methods Coccidioides spp. isolates from MX and AR were taxonomically identified by phylogenetic inference analysis using partial sequences of the Ag2/PRA gene and their phenotypic characteristics analysed. The genetic variability, reproductive system and level of differentiation were estimated using AFLP markers. The level of genetic variability was assessed measuring the percentage of polymorphic loci, number of effective allele, expected heterocygosity and Index of Association (IA). The degree of genetic differentiation was determined by AMOVA. Genetic similarities among isolates were estimated using Jaccard index. The UPGMA was used to contsruct the corresponding dendrogram. Finally, a network of haplotypes was built to evaluate the genealogical relationships among AFLP haplotypes. Results All isolates of Coccidioides spp. from MX and AR were identified as C. posadasii. No phenotypic variability was observed among the C. posadasii isolates from MX and AR. Analyses of genetic diversity and population structure were conducted using AFLP markers. Different estimators of genetic variability indicated that the C. posadasii isolates from MX and AR had high genetic variability. Furthermore, AMOVA, dendrogram and haplotype network showed a small

  3. A Web-Based Genetic Polymorphism Learning Approach for High School Students and Science Teachers

    ERIC Educational Resources Information Center

    Amenkhienan, Ehichoya; Smith, Edward J.

    2006-01-01

    Variation and polymorphism are concepts that are central to genetics and genomics, primary biological disciplines in which high school students and undergraduates require a solid foundation. From 1998 through 2002, a web-based genetics education program was developed for high school teachers and students. The program included an exercise on using…

  4. Getting a head start: the importance of personal genetics education in high schools.

    PubMed

    Kung, Johnny T; Gelbart, Marnie E

    2012-03-01

    With advances in sequencing technology, widespread and affordable genome sequencing will soon be a reality. However, studies suggest that "genetic literacy" of the general public is inadequate to prepare our society for this unprecedented access to our genetic information. As the current generation of high school students will come of age in an era when personal genetic information is increasingly utilized in health care, it is of vital importance to ensure these students understand the genetic concepts necessary to make informed medical decisions. These concepts include not only basic scientific knowledge, but also considerations of the ethical, legal, and social issues that will arise in the age of personal genomics. In this article, we review the current state of genetics education, highlight issues that we believe need to be addressed in a comprehensive genetics education curriculum, and describe our education efforts at the Harvard Medical School-based Personal Genetics Education Project.

  5. Sex-stratified Genome-wide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits

    PubMed Central

    Jackson, Anne U.; Monda, Keri L.; Kilpeläinen, Tuomas O.; Esko, Tõnu; Mägi, Reedik; Li, Shengxu; Workalemahu, Tsegaselassie; Feitosa, Mary F.; Croteau-Chonka, Damien C.; Day, Felix R.; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Locke, Adam E.; Mathieson, Iain; Scherag, Andre; Vedantam, Sailaja; Wood, Andrew R.; Liang, Liming; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Dermitzakis, Emmanouil T.; Dimas, Antigone S.; Karpe, Fredrik; Min, Josine L.; Nicholson, George; Clegg, Deborah J.; Person, Thomas; Krohn, Jon P.; Bauer, Sabrina; Buechler, Christa; Eisinger, Kristina; Bonnefond, Amélie; Froguel, Philippe; Hottenga, Jouke-Jan; Prokopenko, Inga; Waite, Lindsay L.; Harris, Tamara B.; Smith, Albert Vernon; Shuldiner, Alan R.; McArdle, Wendy L.; Caulfield, Mark J.; Munroe, Patricia B.; Grönberg, Henrik; Chen, Yii-Der Ida; Li, Guo; Beckmann, Jacques S.; Johnson, Toby; Thorsteinsdottir, Unnur; Teder-Laving, Maris; Khaw, Kay-Tee; Wareham, Nicholas J.; Zhao, Jing Hua; Amin, Najaf; Oostra, Ben A.; Kraja, Aldi T.; Province, Michael A.; Cupples, L. Adrienne; Heard-Costa, Nancy L.; Kaprio, Jaakko; Ripatti, Samuli; Surakka, Ida; Collins, Francis S.; Saramies, Jouko; Tuomilehto, Jaakko; Jula, Antti; Salomaa, Veikko; Erdmann, Jeanette; Hengstenberg, Christian; Loley, Christina; Schunkert, Heribert; Lamina, Claudia; Wichmann, H. Erich; Albrecht, Eva; Gieger, Christian; Hicks, Andrew A.; Johansson, Åsa; Pramstaller, Peter P.; Kathiresan, Sekar; Speliotes, Elizabeth K.; Penninx, Brenda; Hartikainen, Anna-Liisa; Jarvelin, Marjo-Riitta; Gyllensten, Ulf; Boomsma, Dorret I.; Campbell, Harry; Wilson, James F.; Chanock, Stephen J.; Farrall, Martin; Goel, Anuj; Medina-Gomez, Carolina; Rivadeneira, Fernando; Estrada, Karol; Uitterlinden, André G.; Hofman, Albert; Zillikens, M. Carola; den Heijer, Martin; Kiemeney, Lambertus A.; Maschio, Andrea; Hall, Per; Tyrer, Jonathan; Teumer, Alexander; Völzke, Henry; Kovacs, Peter; Tönjes, Anke; Mangino, Massimo; Spector, Tim D.; Hayward, Caroline; Rudan, Igor; Hall, Alistair S.; Samani, Nilesh J.; Attwood, Antony Paul; Sambrook, Jennifer G.; Hung, Joseph; Palmer, Lyle J.; Lokki, Marja-Liisa; Sinisalo, Juha; Boucher, Gabrielle; Huikuri, Heikki; Lorentzon, Mattias; Ohlsson, Claes; Eklund, Niina; Eriksson, Johan G.; Barlassina, Cristina; Rivolta, Carlo; Nolte, Ilja M.; Snieder, Harold; Van der Klauw, Melanie M.; Van Vliet-Ostaptchouk, Jana V.; Gejman, Pablo V.; Shi, Jianxin; Jacobs, Kevin B.; Wang, Zhaoming; Bakker, Stephan J. L.; Mateo Leach, Irene; Navis, Gerjan; van der Harst, Pim; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Yang, Jian; Chasman, Daniel I.; Ridker, Paul M.; Rose, Lynda M.; Lehtimäki, Terho; Raitakari, Olli; Absher, Devin; Iribarren, Carlos; Basart, Hanneke; Hovingh, Kees G.; Hyppönen, Elina; Power, Chris; Anderson, Denise; Beilby, John P.; Hui, Jennie; Jolley, Jennifer; Sager, Hendrik; Bornstein, Stefan R.; Schwarz, Peter E. H.; Kristiansson, Kati; Perola, Markus; Lindström, Jaana; Swift, Amy J.; Uusitupa, Matti; Atalay, Mustafa; Lakka, Timo A.; Rauramaa, Rainer; Bolton, Jennifer L.; Fowkes, Gerry; Fraser, Ross M.; Price, Jackie F.; Fischer, Krista; KrjutÅ¡kov, Kaarel; Metspalu, Andres; Mihailov, Evelin; Langenberg, Claudia; Luan, Jian'an; Ong, Ken K.; Chines, Peter S.; Keinanen-Kiukaanniemi, Sirkka M.; Saaristo, Timo E.; Edkins, Sarah; Franks, Paul W.; Hallmans, Göran; Shungin, Dmitry; Morris, Andrew David; Palmer, Colin N. A.; Erbel, Raimund; Moebus, Susanne; Nöthen, Markus M.; Pechlivanis, Sonali; Hveem, Kristian; Narisu, Narisu; Hamsten, Anders; Humphries, Steve E.; Strawbridge, Rona J.; Tremoli, Elena; Grallert, Harald; Thorand, Barbara; Illig, Thomas; Koenig, Wolfgang; Müller-Nurasyid, Martina; Peters, Annette; Boehm, Bernhard O.; Kleber, Marcus E.; März, Winfried; Winkelmann, Bernhard R.; Kuusisto, Johanna; Laakso, Markku; Arveiler, Dominique; Cesana, Giancarlo; Kuulasmaa, Kari; Virtamo, Jarmo; Yarnell, John W. G.; Kuh, Diana; Wong, Andrew; Lind, Lars; de Faire, Ulf; Gigante, Bruna; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Dedoussis, George; Dimitriou, Maria; Kolovou, Genovefa; Kanoni, Stavroula; Stirrups, Kathleen; Bonnycastle, Lori L.; Njølstad, Inger; Wilsgaard, Tom; Ganna, Andrea; Rehnberg, Emil; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Assimes, Themistocles L.; Barroso, Inês; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Frayling, Timothy; Groop, Leif C.; Haritunians, Talin; Hunter, David; Ingelsson, Erik; Kaplan, Robert; Mohlke, Karen L.; O'Connell, Jeffrey R.; Schlessinger, David; Strachan, David P.; Stefansson, Kari; van Duijn, Cornelia M.; Abecasis, Gonçalo R.; McCarthy, Mark I.; Hirschhorn, Joel N.; Qi, Lu; Loos, Ruth J. F.; Lindgren, Cecilia M.; North, Kari E.; Heid, Iris M.

    2013-01-01

    Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5×10−8), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits. PMID:23754948

  6. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Capsicum represents one of several well characterized Solanaceous genera. A wealth of classical and molecular genetics research is available for the genus. Information gleaned from its cultivated relatives, tomato and potato, provide further insight for basic and applied studies. Early ...

  7. High-resolution genetic mapping of mammalian motor activity levels in mice.

    PubMed

    Kas, M J H; de Mooij-van Malsen, J G; de Krom, M; van Gassen, K L I; van Lith, H A; Olivier, B; Oppelaar, H; Hendriks, J; de Wit, M; Groot Koerkamp, M J A; Holstege, F C P; van Oost, B A; de Graan, P N E

    2009-02-01

    The generation of motor activity levels is under tight neural control to execute essential behaviors, such as movement toward food or for social interaction. To identify novel neurobiological mechanisms underlying motor activity levels, we studied a panel of chromosome substitution (CS) strains derived from mice with high (C57BL/6J strain) or low motor activity levels (A/J strain) using automated home cage behavioral registration. In this study, we genetically mapped the expression of baseline motor activity levels (horizontal distance moved) to mouse chromosome 1. Further genetic mapping of this trait revealed an 8.3-Mb quantitative trait locus (QTL) interval. This locus is distinct from the QTL interval for open-field anxiety-related motor behavior on this chromosome. By data mining, an existing phenotypic and genotypic data set of 2445 genetically heterogeneous mice (http://gscan.well.ox.ac.uk/), we confirmed linkage to the peak marker at 79 970 253 bp and refined the QTL to a 312-kb interval containing a single gene (A830043J08Rik). Sequence analysis showed a nucleotide deletion in the 3' untranslated region of the Riken gene. Genome-wide microarray gene expression profiling in brains of discordant F(2) individuals from CS strain 1 showed a significant upregulation of Epha4 in low-active F(2) individuals. Inclusion of a genetic marker for Epha4 confirmed that this gene is located outside of the QTL interval. Both Epha4 and A830043J08Rik are expressed in brain motor circuits, and similar to Epha4 mutants, we found linkage between reduced motor neurons number and A/J chromosome 1. Our findings provide a novel QTL and a potential downstream target underlying motor circuitry development and the expression of physical activity levels.

  8. A web-based genetic polymorphism learning approach for high school students and science teachers*.

    PubMed

    Amenkhienan, Ehichoya; Smith, Edward J

    2006-01-01

    Variation and polymorphism are concepts that are central to genetics and genomics, primary biological disciplines in which high school students and undergraduates require a solid foundation. From 1998 through 2002, a web-based genetics education program was developed for high school teachers and students. The program included an exercise on using freely available bioinformatics tools on the Internet to detect single nucleotide polymorphisms in genomic DNA and gene-based sequences to evaluate variation or polymorphism. Similar tools were also used to show the functional effect, if any, of the single nucleotide polymorphisms. A total of 25 science teachers and 60 students from high schools in Alabama and Virginia participated in the program that ranged from 2 to 4 weeks. Seventy percent of the teachers have now developed a web-based module to teach at least two lessons involving DNA variation and how it influences other disciplines, including evolution. Among former high school students, five are in Ph.D. programs in genetics or related subjects, and 80% are in medical school or in college in a biology or pre-med major. The exercise is simple to implement, and the cost is relatively low, requiring only a computer with an Internet connection. It also provides a foundation for introducing students to the theory of evolution, a concept that remains controversial in high school science curricula. Similar programs, if properly implemented, may result in fostering more interest in the biological sciences among prospective college students and ensure a good foundation in the pipeline for career biologists and scientists.

  9. Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea

    PubMed Central

    2014-01-01

    Background Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and used in pea for genetic diversity and linkage analysis. Results We developed a large resource by cDNA sequencing of 8 genotypes representative of modern breeding material using the Roche 454 technology, combining both long reads (400 bp) and high coverage (3.8 million reads, reaching a total of 1,369 megabases). Sequencing data were assembled and generated a 68 K unigene set, from which 41 K were annotated from their best blast hit against the model species Medicago truncatula. Annotated contigs showed an even distribution along M. truncatula pseudochromosomes, suggesting a good representation of the pea genome. 10 K pea contigs were found to be polymorphic among the genetic material surveyed, corresponding to 35 K SNPs. We validated a subset of 1538 SNPs through the GoldenGate assay, proving their ability to structure a diversity panel of breeding germplasm. Among them, 1340 were genetically mapped and used to build a new consensus map comprising a total of 2070 markers. Based on blast analysis, we could establish 1252 bridges between our pea consensus map and the pseudochromosomes of M. truncatula, which provides new insight on synteny between the two species. Conclusions Our approach created significant new resources in pea, i.e. the most comprehensive genetic map to date tightly linked to the model species M. truncatula and a large SNP resource for both academic research and breeding. PMID:24521263

  10. High genetic diversity and structured populations of the oriental fruit moth in its range of origin.

    PubMed

    Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua

    2013-01-01

    The oriental fruit moth Grapholita ( = Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies. PMID:24265692

  11. High Genetic Diversity and Structured Populations of the Oriental Fruit Moth in Its Range of Origin

    PubMed Central

    Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua

    2013-01-01

    The oriental fruit moth Grapholita ( = Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies. PMID:24265692

  12. Genetic predisposition for high stress reactivity amplifies effects of early-life adversity.

    PubMed

    McIlwrick, Silja; Rechenberg, Alexandra; Matthes, Mariana; Burgstaller, Jessica; Schwarzbauer, Thomas; Chen, Alon; Touma, Chadi

    2016-08-01

    A dysregulation of the hypothalamus-pituitary-adrenocortical (HPA) axis and the experience of early-life adversity are both well-established risk factors for the development of affective disorders, such as major depression. However, little is known about the interaction of these two factors in shaping endophenotypes of the disease. Here, we studied the gene-environment interaction of a genetic predisposition for HPA axis dysregulation with early-life stress (ELS), assessing the short-, as well as the long-lasting consequences on emotional behavior, neuroendocrine functions and gene expression profiles. Three mouse lines, selectively bred for either high (HR), intermediate (IR), or low (LR) HPA axis reactivity, were exposed to one week of ELS using the limited nesting and bedding material paradigm. Measurements collected during or shortly after the ELS period showed that, regardless of genetic background, ELS exposure led to impaired weight gain and altered the animals' coping behavior under stressful conditions. However, only HR mice additionally showed significant changes in neuroendocrine stress responsiveness at a young age. Accordingly, adult HR mice also showed lasting consequences of ELS, including hyperactive stress-coping, HPA axis hyperreactivity, and gene expression changes in the Crh system, as well as downregulation of Fkbp5 in relevant brain regions. We suggest that the genetic predisposition for high stress reactivity interacts with ELS exposure by disturbing the suppression of corticosterone release during a critical period of brain development, thus exerting lasting programming effects on the HPA axis, presumably via epigenetic mechanisms. In concert, these changes lead to the emergence of important endophenotypes associated with affective disorders. PMID:27179233

  13. Male Roman high and low avoidance rats show different patterns of copulatory behaviour: comparison with Sprague Dawley rats.

    PubMed

    Sanna, Fabrizio; Corda, Maria Giuseppa; Melis, Maria Rosaria; Piludu, Maria Antonietta; Giorgi, Osvaldo; Argiolas, Antonio

    2014-03-29

    Roman high- (RHA) and low-avoidance (RLA) rats, selectively bred for, respectively, rapid vs. extremely poor acquisition of avoidant behaviour in the shuttle-box, display different coping strategies when exposed to aversive environmental conditions: RLA rats are reactive copers and show hyperemotional behaviour characterized by hypomotility and freezing, while RHA rats show a proactive coping behaviour aimed at gaining control over the stressor. RHA rats also display a robust sensation/novelty seeking profile, high baseline levels of impulsivity, and marked preference for, and intake of, natural and drug rewards. This study shows that the Roman lines also differ in sexual behaviour, a main source of natural reward. Thus, male RHA rats engaged in copulatory activity with a receptive female showing more mounts, intromissions and ejaculations in the first copulation test as compared with their RLA counterparts and Sprague Dawley rats used as an external reference strain. Such differences decreased only partially in subsequent copulation tests, with RHA rats always showing higher levels of sexual motivation and performance than RLA rats. Accordingly, analysis of copulatory parameters of five copulation tests performed at 3-day intervals confirmed that the Roman lines display different patterns of copulatory activity that persist after stabilization of copulatory behaviour by sexual experience. Finally, the weight of the testes, epididymides and seminal vesicles increased to a similar extent in both Roman lines after sexual activity. These results are discussed in terms of the relative contribution of differences in brain neurotransmission (mainly dopamine) and neuroendocrine function to the different patterns of copulatory behaviour of the Roman lines.

  14. High-velocity Frictional Behavior of Dunite, Biotite Gneiss, Phyllite and Coal Show Evidence for Melting and Thermal Degasing

    NASA Astrophysics Data System (ADS)

    O'Hara, K. D.; Mizoguchi, K.; Shimamoto, T.

    2004-12-01

    We conducted high-velocity frictional experiments on dunite, biotite gneiss, phyllite gouge and coal gouge at Kyoto University using a rotary high-velocity frictional testing machine. The purpose was to examine the effect of frictional melting in various rock types and to explore the effect of thermal degassing using coal as an analogue for a volatile fault zone. Experiments were conducted dry at equivalent slip rates of 1 m/s (1200 rpm) at normal stresses of 0.6-16 MPa for distances up to 90 m. Solid cylinders (25 mm diameter) of dunite and biotite gneiss were sheared with aluminum-alloy jackets at high stress, whereas phyllite and coal gouges were sheared with Teflon sleeves at low stress. The metal jackets allow high stress experiments to be performed and are inferred to melt before rock melting occurs. Dunite sheared at 10-16 MPa shows a weakening-strengthening followed by second weakening on melting, similar to previous experiments on gabbro without a metal jacket. Dunite melting is confirmed by, as yet unidentified, dendritic microlites, and a rapid reduction of steady-state frictional strength to 0.15. Under similar conditions, biotite gneiss shows apparent melting, but undergoes continuous strengthening without reaching steady state. Bituminous coal gouge sheared at 0.6 MPa undergoes a highly reproducible rapid weakening from 0.75 to 0.2, with odorous white gas emissions, sometimes accompanied by liquid hydrocarbons. Shear stress decreases prior to gasification and rapidly oscillating sample shortening/elongation occurs during gas emission. A slowly sheared sample (15 rpm) did not show weakening or gas emission. This is the first experimental demonstration of weakening associated with devolatilization during rapid slip. Vitrinite reflectance measurements on sheared coal samples may provide constraints on the temperature during gasification. Phyllite gouge sheared under the same conditions shows a gradual weakening to a steady-state strength of about 0

  15. The green alga Zygogonium ericetorum (Zygnematophyceae, Charophyta) shows high iron and aluminium tolerance: protection mechanisms and photosynthetic performance.

    PubMed

    Herburger, Klaus; Remias, Daniel; Holzinger, Andreas

    2016-08-01

    Streptophyte green algae, ancestors of Embryophytes, occur frequently in terrestrial habitats being exposed to high light intensities, water scarcity and potentially toxic metal cations under acidic conditions. The filamentous Zygogonium ericetorum synthesizes a purple vacuolar ferrous pigment, which is lost after aplanospore formation. However, it is unknown whether this cellular reorganization also removes excessive iron from the protoplast and how Z. ericetorum copes with high concentrations of aluminium. Here we show that aplanospore formation shifts iron into the extracellular space of the algal filament. Upon germination of aplanospores, aluminium is bound in the parental cell wall. Both processes reduce iron and aluminium in unpigmented filaments. Comparison of the photosynthetic oxygen production in response to light and temperature gradients in two different Z. ericetorum strains from an Austrian alpine and a Scottish highland habitat revealed lower values in the latter strain. In contrast, the Scottish strain showed a higher optimum quantum yield of PSII during desiccation stress followed by rehydration. Furthermore, pigmented filaments of both strains exhibited a higher light and temperature dependent oxygen production when compared to the unpigmented phenotype. Our results demonstrate a high metal tolerance of Z. ericetorum, which is crucial for surviving in acidic terrestrial habitats. PMID:27178434

  16. The green alga Zygogonium ericetorum (Zygnematophyceae, Charophyta) shows high iron and aluminium tolerance: protection mechanisms and photosynthetic performance

    PubMed Central

    Herburger, Klaus; Remias, Daniel; Holzinger, Andreas

    2016-01-01

    Streptophyte green algae, ancestors of Embryophytes, occur frequently in terrestrial habitats being exposed to high light intensities, water scarcity and potentially toxic metal cations under acidic conditions. The filamentous Zygogonium ericetorum synthesizes a purple vacuolar ferrous pigment, which is lost after aplanospore formation. However, it is unknown whether this cellular reorganization also removes excessive iron from the protoplast and how Z. ericetorum copes with high concentrations of aluminium. Here we show that aplanospore formation shifts iron into the extracellular space of the algal filament. Upon germination of aplanospores, aluminium is bound in the parental cell wall. Both processes reduce iron and aluminium in unpigmented filaments. Comparison of the photosynthetic oxygen production in response to light and temperature gradients in two different Z. ericetorum strains from an Austrian alpine and a Scottish highland habitat revealed lower values in the latter strain. In contrast, the Scottish strain showed a higher optimum quantum yield of PSII during desiccation stress followed by rehydration. Furthermore, pigmented filaments of both strains exhibited a higher light and temperature dependent oxygen production when compared to the unpigmented phenotype. Our results demonstrate a high metal tolerance of Z. ericetorum, which is crucial for surviving in acidic terrestrial habitats. PMID:27178434

  17. The green alga Zygogonium ericetorum (Zygnematophyceae, Charophyta) shows high iron and aluminium tolerance: protection mechanisms and photosynthetic performance.

    PubMed

    Herburger, Klaus; Remias, Daniel; Holzinger, Andreas

    2016-08-01

    Streptophyte green algae, ancestors of Embryophytes, occur frequently in terrestrial habitats being exposed to high light intensities, water scarcity and potentially toxic metal cations under acidic conditions. The filamentous Zygogonium ericetorum synthesizes a purple vacuolar ferrous pigment, which is lost after aplanospore formation. However, it is unknown whether this cellular reorganization also removes excessive iron from the protoplast and how Z. ericetorum copes with high concentrations of aluminium. Here we show that aplanospore formation shifts iron into the extracellular space of the algal filament. Upon germination of aplanospores, aluminium is bound in the parental cell wall. Both processes reduce iron and aluminium in unpigmented filaments. Comparison of the photosynthetic oxygen production in response to light and temperature gradients in two different Z. ericetorum strains from an Austrian alpine and a Scottish highland habitat revealed lower values in the latter strain. In contrast, the Scottish strain showed a higher optimum quantum yield of PSII during desiccation stress followed by rehydration. Furthermore, pigmented filaments of both strains exhibited a higher light and temperature dependent oxygen production when compared to the unpigmented phenotype. Our results demonstrate a high metal tolerance of Z. ericetorum, which is crucial for surviving in acidic terrestrial habitats.

  18. Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

    PubMed Central

    Fuentes-Utrilla, P; Venturas, M; Hollingsworth, P M; Squirrell, J; Collada, C; Stone, G N; Gil, L

    2014-01-01

    Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here, we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity and is protected wherever it is considered native. Small populations of this species are located in Iberia, where they are unprotected because they are considered introductions due to their rarity. However, Iberia and neighbouring regions in southwestern France have been shown to support discrete glacial refuge populations of many European trees, and the possibility remains that Iberian white elms are native relicts. We used chloroplast RFLPs and nuclear microsatellites to establish the relationship between populations in Iberia and the Central European core distribution. Bayesian approaches revealed significant spatial structure across populations. Those in Iberia and southwestern France shared alleles absent from Central Europe, and showed spatial population structure within Iberia common in recognized native taxa. Iberian populations show a demographic signature of ancient population bottlenecks, while those in Central European show a signature of recent population bottlenecks. These patterns are not consistent with historical introduction of white elm to Iberia, and instead strongly support native status, arguing for immediate implementation of conservation measures for white elm populations in Spain and contiguous areas of southern France. PMID:24022495

  19. Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation

    PubMed Central

    Cibrián-Jaramillo, Angélica; Bacon, Christine D; Garwood, Nancy C; Bateman, Richard M; Thomas, Meredith M; Russell, Steve; Bailey, C Donovan; Hahn, William J; Bridgewater, Samuel GM; DeSalle, Rob

    2009-01-01

    Background Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti) of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size. Results We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity are likely the result of

  20. Baculovirus expression system and method for high throughput expression of genetic material

    DOEpatents

    Clark, Robin; Davies, Anthony

    2001-01-01

    The present invention provides novel recombinant baculovirus expression systems for expressing foreign genetic material in a host cell. Such expression systems are readily adapted to an automated method for expression foreign genetic material in a high throughput manner. In other aspects, the present invention features a novel automated method for determining the function of foreign genetic material by transfecting the same into a host by way of the recombinant baculovirus expression systems according to the present invention.

  1. A high surface area Zr(IV)-based metal–organic framework showing stepwise gas adsorption and selective dye uptake

    SciTech Connect

    Lv, Xiu-Liang; Tong, Minman; Huang, Hongliang; Wang, Bin; Gan, Lei; Yang, Qingyuan; Zhong, Chongli; Li, Jian-Rong

    2015-03-15

    Exploitation of new metal–organic framework (MOF) materials with high surface areas has been attracting great attention in related research communities due to their broad potential applications. In this work, a new Zr(IV)-based MOF, [Zr{sub 6}O{sub 4}(OH){sub 4}(eddb){sub 6}] (BUT-30, H{sub 2}eddb=4,4′-(ethyne-1,2-diyl)dibenzoic acid) has been solvothermally synthesized, characterized, and explored for gases and dyes adsorptions. Single-crystal X-ray diffraction analysis demonstrates a three-dimensional cubic framework structure of this MOF, in which each Zr{sub 6}O{sub 4}(OH){sub 4} building unit is linked by 12 linear eddb ligands. BUT-30 has been found stable up to 400 °C and has a Brunauer–Emmett–Teller (BET) surface area as high as 3940.6 m{sup 2} g{sup −1} (based on the N{sub 2} adsorption at 77 K) and total pore volume of 1.55 cm{sup 3} g{sup −1}. It is more interesting that this MOF exhibits stepwise adsorption behaviors for Ar, N{sub 2}, and CO{sub 2} at low temperatures, and selective uptakes towards different ionic dyes. - Graphical abstract: A new Zr(IV)-based MOF with high surface area has been synthesized and structurally characterized, which shows stepwise gas adsorption at low temperature and selective dye uptake from solution. - Highlights: • A new Zr-based MOF was synthesized and structurally characterized. • This MOF shows a higher surface area compared with its analogous UiO-67 and 68. • This MOF shows a rare stepwise adsorption towards light gases at low temperature. • This MOF performs selective uptakes towards cationic dyes over anionic ones. • Using triple-bond spacer is confirmed feasible in enhancing MOF surface areas.

  2. "The Show"

    ERIC Educational Resources Information Center

    Gehring, John

    2004-01-01

    For the past 16 years, the blue-collar city of Huntington, West Virginia, has rolled out the red carpet to welcome young wrestlers and their families as old friends. They have come to town chasing the same dream for a spot in what many of them call "The Show". For three days, under the lights of an arena packed with 5,000 fans, the state's best…

  3. Mapping IS6110 in high-copy number Mycobacterium tuberculosis strains shows specific insertion points in the Beijing genotype

    PubMed Central

    2013-01-01

    Background Mycobacterium tuberculosis Beijing strains are characterized by a large number of IS6110 copies, suggesting the potential implication of this element in the virulence and capacity for rapid dissemination characteristic of this family. This work studies the insetion points of IS6110 in high-copy clinical isolates specifically focusing on the Beijing genotype. Results In the present work we mapped the insertion points of IS6110 in all the Beijing strains available in the literature and in the DNA sequence databases. We generated a representative primer collection of the IS6110 locations, which was used to analyse 61 high-copy clinical isolates. A total of 440 points of insertion were identified and analysis of their flanking regions determined the exact location, the direct repeats (DRs), the orientation and the distance to neighboring genes of each copy of IS6110. We identified specific points of insertion in Beijing strains that enabled us to obtain a dendrogram that groups the Beijing genotype. Conclusions This work presents a detailed analysis of locations of IS6110 in high-copy clinical isolates, showing points of insertion present with high frequency in the Beijing family and absent in other strains. PMID:23800083

  4. Bacillus cereus from the environment is genetically related to the highly pathogenic B. cereus in Zambia.

    PubMed

    Ogawa, Hirohito; Ohnuma, Miyuki; Squarre, David; Mweene, Aaron Simanyengwe; Ezaki, Takayuki; Fujikura, Daisuke; Ohnishi, Naomi; Thomas, Yuka; Hang'ombe, Bernard Mudenda; Higashi, Hideaki

    2015-08-01

    To follow-up anthrax in Zambia since the outbreak in 2011, we have collected samples from the environment and the carcasses of anthrax-suspected animals, and have tried to isolate Bacillus anthracis. In the process of identification of B. anthracis, we collected two isolates, of which colonies were similar to B. anthracis; however, from the results of identification using the molecular-based methods, two isolates were genetically related to the highly pathogenic B. cereus, of which clinical manifestation is severe and fatal (e.g., pneumonia). In this study, we showed the existence of bacteria suspected to be highly pathogenic B. cereus in Zambia, indicating the possibility of an outbreak caused by highly pathogenic B. cereus.

  5. Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis).

    PubMed

    Wang, Le; Liu, Shufang; Zhuang, Zhimeng; Guo, Liang; Meng, Zining; Lin, Haoran

    2013-01-01

    The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.

  6. Distinct and Diverse: Range-Wide Phylogeography Reveals Ancient Lineages and High Genetic Variation in the Endangered Okapi (Okapia johnstoni)

    PubMed Central

    Stanton, David W. G.; Hart, John; Galbusera, Peter; Helsen, Philippe; Shephard, Jill; Kümpel, Noëlle F.; Wang, Jinliang; Ewen, John G.; Bruford, Michael W.

    2014-01-01

    The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River. PMID:25007188

  7. Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean.

    PubMed

    Thompson, K F; Patel, S; Baker, C S; Constantine, R; Millar, C D

    2016-03-01

    Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and Rs=4.22-4.37, He=0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat. PMID:26626574

  8. Distinct and diverse: range-wide phylogeography reveals ancient lineages and high genetic variation in the endangered okapi (Okapia johnstoni).

    PubMed

    Stanton, David W G; Hart, John; Galbusera, Peter; Helsen, Philippe; Shephard, Jill; Kümpel, Noëlle F; Wang, Jinliang; Ewen, John G; Bruford, Michael W

    2014-01-01

    The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River. PMID:25007188

  9. Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean.

    PubMed

    Thompson, K F; Patel, S; Baker, C S; Constantine, R; Millar, C D

    2016-03-01

    Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and Rs=4.22-4.37, He=0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat.

  10. DRD4 long allele carriers show heightened attention to high-priority items relative to low-priority items.

    PubMed

    Gorlick, Marissa A; Worthy, Darrell A; Knopik, Valerie S; McGeary, John E; Beevers, Christopher G; Maddox, W Todd

    2015-03-01

    Humans with seven or more repeats in exon III of the DRD4 gene (long DRD4 carriers) sometimes demonstrate impaired attention, as seen in attention-deficit hyperactivity disorder, and at other times demonstrate heightened attention, as seen in addictive behavior. Although the clinical effects of DRD4 are the focus of much work, this gene may not necessarily serve as a "risk" gene for attentional deficits, but as a plasticity gene where attention is heightened for priority items in the environment and impaired for minor items. Here we examine the role of DRD4 in two tasks that benefit from selective attention to high-priority information. We examine a category learning task where performance is supported by focusing on features and updating verbal rules. Here, selective attention to the most salient features is associated with good performance. In addition, we examine the Operation Span (OSPAN) task, a working memory capacity task that relies on selective attention to update and maintain items in memory while also performing a secondary task. Long DRD4 carriers show superior performance relative to short DRD4 homozygotes (six or less tandem repeats) in both the category learning and OSPAN tasks. These results suggest that DRD4 may serve as a "plasticity" gene where individuals with the long allele show heightened selective attention to high-priority items in the environment, which can be beneficial in the appropriate context.

  11. A combined cultivation and cultivation-independent approach shows high bacterial diversity in water-miscible metalworking fluids.

    PubMed

    Lodders, Nicole; Kämpfer, Peter

    2012-06-01

    Ten metalworking fluids (MWF) and seven water preparation basis samples (WPB) were taken from five industrial plants in Germany. Total cells (TCC) and colony forming units (CFU) were counted, strains were isolated and their 16S rRNA gene was sequenced. Additionally, DNA was extracted directly from the samples, and clone libraries of 16S rRNA genes were built and gene sequenced. TCC ranged from 7.6×10(4) TCC/mL MWF to 1.6×10(8) TCC/mL MWF, and from 4.6×10(2) TCC/mL WPB to 7.8×10(7) TCC/mL WPB. The CFU showed similar but often lower results. A total of 70 isolates and 732 clones were 16S rRNA gene sequenced and all isolates, as well as 183 of the nearly full length 16S rRNA of these clones, were gene sequenced. A total of 98 different genera were detected in all 17 samples. The number of genera within each sample varied highly, with 1-22 genera per sample. The dominant genera in MWF were Leucobacter, Desemzia, Sphingomonas and Wautersiella. From these, only Sphingomonas was detected in WPB as well. This study showed that MWF can harbour a high bacterial diversity, which differs significantly from the bacterial flora of the corresponding WPB. PMID:22609341

  12. A yeast glycolipid biosurfactant, mannosylerythritol lipid, shows high binding affinity towards lectins on a self-assembled monolayer system.

    PubMed

    Konishi, Masaaki; Imura, Tomohiro; Fukuoka, Tokuma; Morita, Tomotake; Kitamoto, Dai

    2007-03-01

    Mannosylerythritol lipids (MEL), which are glycolipid biosurfactants secreted by the Pseudozyma yeasts, show not only excellent surface-active properties but also versatile biochemical actions including antitumor and cell-differentiation activities. In order to address the biochemical actions, interactions between MEL-A, the major component of MEL, and different lectins were investigated using the surface plasmon resonance spectroscopy. The monolayer of MEL-A showed high binding affinity to concanavalin A (ConA) and Maackia amurensis lectin-I (MAL-I). The observed affinity constants for ConA and MAL-I were estimated to be 9.48 +/- 1.31 x 10(6) and 3.13 +/- 0.274 x 10(6) M(-1), respectively; the value was comparable to that of Manalpha1-6(Manalpha1-3)Man, which is one of the most specific probe to ConA. Significantly, alpha-methyl-D-mannopyranoside (1 mM) exhibited no binding inhibition between MEL-A and ConA. MEL-A is thus likely to self-assemble to give a high affinity surface, where ConA binds to the hydrophilic headgroup in a different manner from that generally observed in lectin-saccharide interactions. The binding manner should be related with the biochemical actions of MEL toward mammalian cells via protein-carbohydrate interactions. PMID:17205206

  13. DRD4 long allele carriers show heightened attention to high-priority items relative to low-priority items.

    PubMed

    Gorlick, Marissa A; Worthy, Darrell A; Knopik, Valerie S; McGeary, John E; Beevers, Christopher G; Maddox, W Todd

    2015-03-01

    Humans with seven or more repeats in exon III of the DRD4 gene (long DRD4 carriers) sometimes demonstrate impaired attention, as seen in attention-deficit hyperactivity disorder, and at other times demonstrate heightened attention, as seen in addictive behavior. Although the clinical effects of DRD4 are the focus of much work, this gene may not necessarily serve as a "risk" gene for attentional deficits, but as a plasticity gene where attention is heightened for priority items in the environment and impaired for minor items. Here we examine the role of DRD4 in two tasks that benefit from selective attention to high-priority information. We examine a category learning task where performance is supported by focusing on features and updating verbal rules. Here, selective attention to the most salient features is associated with good performance. In addition, we examine the Operation Span (OSPAN) task, a working memory capacity task that relies on selective attention to update and maintain items in memory while also performing a secondary task. Long DRD4 carriers show superior performance relative to short DRD4 homozygotes (six or less tandem repeats) in both the category learning and OSPAN tasks. These results suggest that DRD4 may serve as a "plasticity" gene where individuals with the long allele show heightened selective attention to high-priority items in the environment, which can be beneficial in the appropriate context. PMID:25244120

  14. Genetic dissection of an alien chromosomal segment may enable the production of a rice (Oryza sativa L.) genotype showing shoot developmental instability.

    PubMed

    Itoh, Youki; Sato, Yoshikazu

    2015-04-01

    During the course of evolutionary history, organisms have acquired genes which cooperate harmoniously and subsequently express a stable pattern of development. In an earlier study we introduced a large chromosomal segment of chromosome 6 from a rice (Oryza sativa L.) ecotype, carrying the two flowering-time genes, which showed complex epistatic interactions in relation to environmental change, into a different ecotype by successive backcrossings. Four-near-isogenic lines (NILs) with respect to these two loci were obtained by subsequent hybridization with the recurrent parent. In the study reported here, these four NILs were the major plant material used to evaluate changes in days to leaf appearance (DLA) during shoot development using a quadratic-polynomial regression. The regressions were regarded as developmental norms because of the high values of R (2). Absolute Y-residuals (AYRs) (or size of deviation) of DLA from the norms were significantly affected by genotype. Dissections of the alien chromosomal segment resulted in one NIL that showed an increased level of AYR. Since this NIL also expressed a low survival rate in a stress environment, we suggest that the increased level of AYR during development might indicate an increased level of instability in shoot development. PMID:25677854

  15. High-Speed General Purpose Genetic Algorithm Processor.

    PubMed

    Hoseini Alinodehi, Seyed Pourya; Moshfe, Sajjad; Saber Zaeimian, Masoumeh; Khoei, Abdollah; Hadidi, Khairollah

    2016-07-01

    In this paper, an ultrafast steady-state genetic algorithm processor (GAP) is presented. Due to the heavy computational load of genetic algorithms (GAs), they usually take a long time to find optimum solutions. Hardware implementation is a significant approach to overcome the problem by speeding up the GAs procedure. Hence, we designed a digital CMOS implementation of GA in [Formula: see text] process. The proposed processor is not bounded to a specific application. Indeed, it is a general-purpose processor, which is capable of performing optimization in any possible application. Utilizing speed-boosting techniques, such as pipeline scheme, parallel coarse-grained processing, parallel fitness computation, parallel selection of parents, dual-population scheme, and support for pipelined fitness computation, the proposed processor significantly reduces the processing time. Furthermore, by relying on a built-in discard operator the proposed hardware may be used in constrained problems that are very common in control applications. In the proposed design, a large search space is achievable through the bit string length extension of individuals in the genetic population by connecting the 32-bit GAPs. In addition, the proposed processor supports parallel processing, in which the GAs procedure can be run on several connected processors simultaneously.

  16. Genetic/familial high-risk assessment: breast and ovarian, version 1.2014.

    PubMed

    Daly, Mary B; Pilarski, Robert; Axilbund, Jennifer E; Buys, Saundra S; Crawford, Beth; Friedman, Susan; Garber, Judy E; Horton, Carolyn; Kaklamani, Virginia; Klein, Catherine; Kohlmann, Wendy; Kurian, Allison; Litton, Jennifer; Madlensky, Lisa; Marcom, P Kelly; Merajver, Sofia D; Offit, Kenneth; Pal, Tuya; Pasche, Boris; Reiser, Gwen; Shannon, Kristen Mahoney; Swisher, Elizabeth; Voian, Nicoleta C; Weitzel, Jeffrey N; Whelan, Alison; Wiesner, Georgia L; Dwyer, Mary A; Kumar, Rashmi

    2014-09-01

    During the past few years, several genetic aberrations that may contribute to increased risks for development of breast and/or ovarian cancers have been identified. The NCCN Guidelines for Genetic/Familial High-Risk Assessment: Breast and Ovarian focus specifically on the assessment of genetic mutations in BRCA1/BRCA2, TP53, and PTEN, and recommend approaches to genetic testing/counseling and management strategies in individuals with these mutations. This portion of the NCCN Guidelines includes recommendations regarding diagnostic criteria and management of patients with Cowden Syndrome/PTEN hamartoma tumor syndrome. PMID:25190698

  17. High level of genetic diversity among spelt germplasm revealed by microsatellite markers.

    PubMed

    Bertin, P; Grégoire, D; Massart, S; de Froidmont, D

    2004-12-01

    The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 - proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 +/- 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.

  18. Fusion Molecules of Heat Shock Protein HSPX with Other Antigens of Mycobacterium tuberculosis Show High Potential in Serodiagnosis of Tuberculosis

    PubMed Central

    Khalid, Ruqyya; Afzal, Madeeha; Khurshid, Sana; Paracha, Rehan Zafar; Khan, Imran H.

    2016-01-01

    Variable individual response against the antigens of Mycobacterium tuberculosis necessitates detection of multiple antibodies for enhancing reliability of serodiagnosis of tuberculosis. Fusion molecules consisting of two or more antigens showing high sensitivity would be helpful in achieving this objective. Antigens of M. tuberculosis HSPX and PE35 were expressed in a soluble form whereas tnPstS1 and FbpC1 were expressed as inclusion bodies at 37°C. Heat shock protein HSPX when attached to the N-termini of the antigens PE35, tnPstS1 and FbpC1, all the fusion molecules were expressed at high levels in E. coli in a soluble form. ELISA analysis of the plasma samples of TB patients against HSPX-tnPstS1 showed 57.7% sensitivity which is nearly the same as the expected combined value obtained after deducting the number of plasma samples (32) containing the antibodies against both the individual antigens. Likewise, the 54.4% sensitivity of HSPX-PE35 was nearly the same as that expected from the combined values of the contributing antigens. Structural analysis of all the fusion molecules by CD spectroscopy showed that α-helical and β-sheet contents were found close to those obtained through molecular modeling. Molecular modeling studies of HSPX-tnPstS1 and HSPX-PE35 support the analytical results as most of the epitopes of the contributing antigens were found to be available for binding to the corresponding antibodies. Using these fusion molecules in combination with other antigenic molecules should reduce the number of antigenic proteins required for a more reliable and economical serodiagnosis of tuberculosis. Also, HSPX seems to have potential application in soluble expression of heterologous proteins in E. coli. PMID:27654048

  19. A porphyrin derivative containing 2-(oxymethyl)pyridine units showing unexpected ratiometric fluorescent recognition of Zn2+ with high selectivity.

    PubMed

    Li, Chun-Yan; Zhang, Xiao-Bing; Dong, Yan-Yan; Ma, Qiu-Juan; Han, Zhi-Xiang; Zhao, Yan; Shen, Guo-Li; Yu, Ru-Qin

    2008-06-01

    A porphyrin derivative (1), containing two 2-(oxymethyl)pyridine units has been designed and synthesized as chemosensor for recognition of metal ions. Unlike many common porphyrin derivatives that show response to different heavy metal ions, compound 1 exhibits unexpected ratiometric fluorescence response to Zn(2+) with high selectivity. The response of the novel chemosensor to zinc was based on the porphyrin metallation with cooperating effect of 2-(oxymethyl)pyridine units. The change of fluorescence of 1 was attributed to the formation of an inclusion complex between porphyrin ring and Zn(2+) by 1:1 complex ratio (K=1.04x10(5)), which has been utilized as the basis of the fabrication of the Zn(2+)-sensitive fluorescent chemosensor. The analytical performance characteristics of the proposed Zn(2+)-sensitive chemosensor were investigated. The sensor can be applied to the quantification of Zn(2+) with a linear range covering from 3.2x10(-7) to 1.8x10(-4) M and a detection limit of 5.5x10(-8) M. The experiment results show that the response behavior of 1 to Zn(2+) is pH-independent in medium condition (pH 4.0-8.0) and show excellent selectivity for Zn(2+) over transition metal cations. PMID:18482606

  20. Factor XIII-A transglutaminase deficient mice show signs of metabolically healthy obesity on high fat diet

    PubMed Central

    Myneni, Vamsee D.; Mousa, Aisha; Kaartinen, Mari T.

    2016-01-01

    F13A1 gene, which encodes for Factor XIII-A blood clotting factor and a transglutaminase enzyme, was recently identified as a potential causative gene for obesity in humans. In our previous in vitro work, we showed that FXIII-A regulates preadipocyte differentiation and modulates insulin signaling via promoting plasma fibronectin assembly into the extracellular matrix. To understand the role of FXIII-A in whole body energy metabolism, here we have characterized the metabolic phenotype of F13a1−/− mice. F13a1−/− and F13a1+/+ type mice were fed chow or obesogenic, high fat diet for 20 weeks. Weight gain, total fat mass and fat pad mass, glucose handling, insulin sensitivity, energy expenditure and, morphological and biochemical analysis of adipose tissue was performed. We show that mice lacking FXIII-A gain weight on obesogenic diet, similarly as wild type mice, but exhibit a number of features of metabolically healthy obesity such as protection from developing diet-induced insulin resistance and hyperinsulinemia. Mice also show normal fasting glucose levels, larger adipocytes, decreased extracellular matrix accumulation and inflammation of adipose tissue, as well as decreased circulating triglycerides. This study reveals that FXIII-A transglutaminase can regulate whole body insulin sensitivity and may have a role in the development of diet-induced metabolic disturbances. PMID:27759118

  1. High affinity and covalent-binding microtubule stabilizing agents show activity in chemotherapy-resistant acute myeloid leukemia cells

    PubMed Central

    Pera, Benet; Calvo-Vidal, M. Nieves; Ambati, Srikanth; Jordi, Michel; Kahn, Alissa; Díaz, J. Fernando; Fang, Weishuo; Altmann, Karl-Heinz; Cerchietti, Leandro; Moore, Malcolm A.S.

    2016-01-01

    Treatment failure in acute myeloid leukemia (AML) is frequently due to the persistence of a cell population resistant to chemotherapy through different mechanisms, in which drug efflux via ATP-binding cassette (ABC) proteins, specifically P-glycoprotein, is one of the most recognized. However, disappointing results from clinical trials employing inhibitors for these transporters have demonstrated the need to adopt different strategies. We hypothesized that microtubule targeting compounds presenting high affinity or covalent binding could overcome the effect of ABC transporters. We therefore evaluated the activity of the high-affinity paclitaxel analog CTX-40 as well as the covalent binder zampanolide (ZMP) in AML cells. Both molecules were active in chemosensitive as well as in chemoresistant cell lines overexpressing P-glycoprotein. Moreover, ZMP or CTX-40 in combination with daunorubicin showed synergistic killing without increased in vitro hematopoietic toxicity. In a primary AML sample, we further demonstrated that ZMP and CTX-40 are active in progenitor and differentiated leukemia cell populations. In sum, our data indicate that high affinity and covalent-binding anti-microtubule agents are active in AML cells otherwise chemotherapy resistant. PMID:26277539

  2. Plastic Transition to Switch Nonlinear Optical Properties Showing the Record High Contrast in a Single-Component Molecular Crystal.

    PubMed

    Sun, Zhihua; Chen, Tianliang; Liu, Xitao; Hong, Maochun; Luo, Junhua

    2015-12-23

    To switch bulk nonlinear optical (NLO) effects represents an exciting new branch of NLO material science, whereas it remains a great challenge to achieve high contrast for "on/off" of quadratic NLO effects in crystalline materials. Here, we report the supereminent NLO-switching behaviors of a single-component plastic crystal, 2-(hydroxymethyl)-2-nitro-1,3-propanediol (1), which shows a record high contrast of at least ∼150, exceeding all the known crystalline switches. Such a breakthrough is clearly elucidated from the slowing down of highly isotropic molecular motions during plastic-to-rigid transition. The deep understanding of its intrinsic plasticity and superior NLO property allows the construction of a feasible switching mechanism. As a unique class of substances with short-range disorder embedded in long-range ordered crystalline lattice, plastic crystals enable response to external stimuli and fulfill specific photoelectric functions, which open a newly conceptual avenue for the designing of new functional materials. PMID:26619244

  3. Tree Rings Show Recent High Summer-Autumn Precipitation in Northwest Australia Is Unprecedented within the Last Two Centuries.

    PubMed

    O'Donnell, Alison J; Cook, Edward R; Palmer, Jonathan G; Turney, Chris S M; Page, Gerald F M; Grierson, Pauline F

    2015-01-01

    An understanding of past hydroclimatic variability is critical to resolving the significance of recent recorded trends in Australian precipitation and informing climate models. Our aim was to reconstruct past hydroclimatic variability in semi-arid northwest Australia to provide a longer context within which to examine a recent period of unusually high summer-autumn precipitation. We developed a 210-year ring-width chronology from Callitris columellaris, which was highly correlated with summer-autumn (Dec-May) precipitation (r = 0.81; 1910-2011; p < 0.0001) and autumn (Mar-May) self-calibrating Palmer drought severity index (scPDSI, r = 0.73; 1910-2011; p < 0.0001) across semi-arid northwest Australia. A linear regression model was used to reconstruct precipitation and explained 66% of the variance in observed summer-autumn precipitation. Our reconstruction reveals inter-annual to multi-decadal scale variation in hydroclimate of the region during the last 210 years, typically showing periods of below average precipitation extending from one to three decades and periods of above average precipitation, which were often less than a decade. Our results demonstrate that the last two decades (1995-2012) have been unusually wet (average summer-autumn precipitation of 310 mm) compared to the previous two centuries (average summer-autumn precipitation of 229 mm), coinciding with both an anomalously high frequency and intensity of tropical cyclones in northwest Australia and the dominance of the positive phase of the Southern Annular Mode.

  4. Comparisons of coat protein gene sequences show that East African isolates of Sweet potato feathery mottle virus form a genetically distinct group.

    PubMed

    Kreuze, J F; Karyeija, R F; Gibson, R W; Valkonen, J P

    2000-01-01

    Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) infects sweet potatoes (Ipomoea batatas) worldwide, but no sequence data on isolates from Africa are available. Coat protein (CP) gene sequences from eight East African isolates from Madagascar and different districts of Uganda (the second biggest sweet potato producer in the world) and two West African isolates from Nigeria and Niger were determined. They were compared by phylogenetic analysis with the previously reported sequences of ten SPFMV isolates from other continents. The East African SPFMV isolates formed a distinct cluster, whereas the other isolates were not clustered according to geographic origin. These data indicate that East African isolates of SPFMV form a genetically unique group.

  5. Quantitative and Qualitative Responses to Topical Cold in Healthy Caucasians Show Variance between Individuals but High Test-Retest Reliability.

    PubMed

    Moss, Penny; Whitnell, Jasmine; Wright, Anthony

    2016-01-01

    Increased sensitivity to cold may be a predictor of persistent pain, but cold pain threshold is often viewed as unreliable. This study aimed to determine the within-subject reliability and between-subject variance of cold response, measured comprehensively as cold pain threshold plus pain intensity and sensation quality at threshold. A test-retest design was used over three sessions, one day apart. Response to cold was assessed at four sites (thenar eminence, volar forearm, tibialis anterior, plantar foot). Cold pain threshold was measured using a Medoc thermode and standard method of limits. Intensity of pain at threshold was rated using a 10cm visual analogue scale. Quality of sensation at threshold was quantified with indices calculated from subjects' selection of descriptors from a standard McGill Pain Questionnaire. Within-subject reliability for each measure was calculated with intra-class correlation coefficients and between-subject variance was evaluated as group coefficient of variation percentage (CV%). Gender and site comparisons were also made. Forty-five healthy adults participated: 20 male, 25 female; mean age 29 (range 18-56) years. All measures at all four test sites showed high within-subject reliability: cold pain thresholds r = 0.92-0.95; pain rating r = 0.93-0.97; McGill pain quality indices r = 0.87-0.85. In contrast, all measures showed wide between-subject variance (CV% between 51.4% and 92.5%). Upper limb sites were consistently more sensitive than lower limb sites, but equally reliable. Females showed elevated cold pain thresholds, although similar pain intensity and quality to males. Females were also more reliable and showed lower variance for all measures. Thus, although there was clear population variation, response to cold for healthy individuals was found to be highly reliable, whether measured as pain threshold, pain intensity or sensation quality. A comprehensive approach to cold response testing therefore may add validity and

  6. Quantitative and Qualitative Responses to Topical Cold in Healthy Caucasians Show Variance between Individuals but High Test-Retest Reliability

    PubMed Central

    Moss, Penny; Whitnell, Jasmine; Wright, Anthony

    2016-01-01

    Increased sensitivity to cold may be a predictor of persistent pain, but cold pain threshold is often viewed as unreliable. This study aimed to determine the within-subject reliability and between-subject variance of cold response, measured comprehensively as cold pain threshold plus pain intensity and sensation quality at threshold. A test-retest design was used over three sessions, one day apart. Response to cold was assessed at four sites (thenar eminence, volar forearm, tibialis anterior, plantar foot). Cold pain threshold was measured using a Medoc thermode and standard method of limits. Intensity of pain at threshold was rated using a 10cm visual analogue scale. Quality of sensation at threshold was quantified with indices calculated from subjects' selection of descriptors from a standard McGill Pain Questionnaire. Within-subject reliability for each measure was calculated with intra-class correlation coefficients and between-subject variance was evaluated as group coefficient of variation percentage (CV%). Gender and site comparisons were also made. Forty-five healthy adults participated: 20 male, 25 female; mean age 29 (range 18–56) years. All measures at all four test sites showed high within-subject reliability: cold pain thresholds r = 0.92–0.95; pain rating r = 0.93–0.97; McGill pain quality indices r = 0.87–0.85. In contrast, all measures showed wide between-subject variance (CV% between 51.4% and 92.5%). Upper limb sites were consistently more sensitive than lower limb sites, but equally reliable. Females showed elevated cold pain thresholds, although similar pain intensity and quality to males. Females were also more reliable and showed lower variance for all measures. Thus, although there was clear population variation, response to cold for healthy individuals was found to be highly reliable, whether measured as pain threshold, pain intensity or sensation quality. A comprehensive approach to cold response testing therefore may add validity

  7. Cladodes, leaf-like organs in Asparagus, show the significance of co-option of pre-existing genetic regulatory circuit for morphological diversity of plants.

    PubMed

    Nakayama, Hokuto; Yamaguchi, Takahiro; Tsukaya, Hirokazu

    2012-08-01

    Plants in the genus Asparagus have determinate leaf-like organs called cladodes in the position of leaf axils. Because of their leaf-like morphology, axillary position, and morphological variation, it has been unclear how this unusual organ has evolved and diversified. In the previous study, we have shown that cladodes in the genus Asparagus are modified axillary shoots and proposed a model that cladodes have arisen by co-option and deployment of genetic regulatory circuit (GRC) involved in leaf development. Moreover, we proposed that the alteration of the expression pattern of genes involved in establishment of adaxial/abaxial polarity has led to the morphological diversification from leaf-like to rod-like form of cladodes in the genus. Thus, these results indicated that the co-option and alteration of pre-existing GRC play an important role in acquisition and subsequent morphological diversification. Here, we present data of further expression analysis of A. asparagoides. The results suggested that only a part of the GRC involved in leaf development appears to have been co-opted into cladode development. Based on our study and several examples of the morphological diversification, we briefly discuss the importance of co-option of pre-existing GRC and its genetic modularity in the morphological diversity of plants during evolution.

  8. Mitochondrial DNA markers reveal high genetic diversity but low genetic differentiation in the black fly Simulium tani Takaoka & Davies along an elevational gradient in Malaysia.

    PubMed

    Low, Van Lun; Adler, Peter H; Takaoka, Hiroyuki; Ya'cob, Zubaidah; Lim, Phaik Eem; Tan, Tiong Kai; Lim, Yvonne A L; Chen, Chee Dhang; Norma-Rashid, Yusoff; Sofian-Azirun, Mohd

    2014-01-01

    The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) and II (COII) along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima's D, Fu's Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected. PMID:24941043

  9. [A case of advanced gastric cancer showing high serum CYFRA21-1 level responding to chemotherapy with S-1].

    PubMed

    Hara, Akihito; Watanabe, Hiroaki

    2008-12-01

    The patient was a 75-year-old man whose complaint was back pain and appetite loss. He was diagnosed with unresectable advanced gastric cancer due to multiple liver metastases and direct invasion of pancreas and spleen. He underwent gastrostomy because of esophageal stenosis, and we administered S-1 80 mg/body(4 weeks administration and 2 weeks rest)to the patient through a gastrostogavage tube. On blood examination, the serum level of CYFRA21- 1 was significantly high, while those of CEA and CA19-9 were within normal ranges. After the first course of this chemotherapy, the serum CYFRA21-1 level significantly decreased with reduction of the cancer. After the second course, it sensitively increased before image views detected the progression of the cancer. This case shows that CYFRA21- 1 could be a useful tumor marker of advanced gastric cancer.

  10. Genetic structure at range edge: low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations.

    PubMed

    Arnaud-Haond, S; Teixeira, S; Massa, S I; Billot, C; Saenger, P; Coupland, G; Duarte, C M; Serrão, E A

    2006-10-01

    Understanding the genetic composition and mating systems of edge populations provides important insights into the environmental and demographic factors shaping species' distribution ranges. We analysed samples of the mangrove Avicennia marina from Vietnam, northern Philippines and Australia, with microsatellite markers. We compared genetic diversity and structure in edge (Southeast Asia, and Southern Australia) and core (North and Eastern Australia) populations, and also compared our results with previously published data from core and southern edge populations. Comparisons highlighted significantly reduced gene diversity and higher genetic structure in both margins compared to core populations, which can be attributed to very low effective population size, pollinator scarcity and high environmental pressure at distribution margins. The estimated level of inbreeding was significantly higher in northeastern populations compared to core and southern populations. This suggests that despite the high genetic load usually associated with inbreeding, inbreeding or even selfing may be advantageous in margin habitats due to the possible advantages of reproductive assurance, or local adaptation. The very high level of genetic structure and inbreeding show that populations of A. marina are functioning as independent evolutionary units more than as components of a metapopulation system connected by gene flow. The combinations of those characteristics make these peripheral populations likely to develop local adaptations and therefore to be of particular interest for conservation strategies as well as for adaptation to possible future environmental changes. PMID:17032254

  11. High levels of genetic change in rodents of Chernobyl.

    PubMed

    Baker, R J; Van Den Bussche, R A; Wright, A J; Wiggins, L E; Hamilton, M J; Reat, E P; Smith, M H; Lomakin, M D; Chesser, R K

    1996-04-25

    Base-pair substitution rates for the mitochondrial cytochrome beta gene of free-living, native populations of voles collected next to reactor 4 at Chernobyl, Ukraine, were estimated by two independent methods to be in excess of 10(-4) nucleotides per site per generation. These estimates are hundreds of times greater than those typically found in mitochondria of vertebrates, suggesting that the environment resulting from this nuclear power plant disaster is having a measurable genetic impact on the organisms of that region. Despite these DNA changes, vole populations thrive and reproduce in the radioactive regions around the Chernobyl reactor.

  12. Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat.

    PubMed

    Guidugli, M C; Nazareno, A G; Feres, J M; Contel, E P B; Mestriner, M A; Alzate-Marin, A L

    2016-03-01

    Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (tm=0.999), with both biparental inbreeding (tm-ts=-0.016) and selfing rates (s=0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population.

  13. Genetic/Familial High-Risk Assessment: Breast and Ovarian, Version 2.2015.

    PubMed

    Daly, Mary B; Pilarski, Robert; Axilbund, Jennifer E; Berry, Michael; Buys, Saundra S; Crawford, Beth; Farmer, Meagan; Friedman, Susan; Garber, Judy E; Khan, Seema; Klein, Catherine; Kohlmann, Wendy; Kurian, Allison; Litton, Jennifer K; Madlensky, Lisa; Marcom, P Kelly; Merajver, Sofia D; Offit, Kenneth; Pal, Tuya; Rana, Huma; Reiser, Gwen; Robson, Mark E; Shannon, Kristen Mahoney; Swisher, Elizabeth; Voian, Nicoleta C; Weitzel, Jeffrey N; Whelan, Alison; Wick, Myra J; Wiesner, Georgia L; Dwyer, Mary; Kumar, Rashmi; Darlow, Susan

    2016-02-01

    The NCCN Guidelines for Genetic/Familial High-Risk Assessment: Breast and Ovarian provide recommendations for genetic testing and counseling and risk assessment and management for hereditary cancer syndromes. Guidelines focus on syndromes associated with an increased risk of breast and/or ovarian cancer and are intended to assist with clinical and shared decision-making. These NCCN Guidelines Insights summarize major discussion points of the 2015 NCCN Genetic/Familial High-Risk Assessment: Breast and Ovarian panel meeting. Major discussion topics this year included multigene testing, risk management recommendations for less common genetic mutations, and salpingectomy for ovarian cancer risk reduction. The panel also discussed revisions to genetic testing criteria that take into account ovarian cancer histology and personal history of pancreatic cancer. PMID:26850485

  14. Characterization of DNA fragment from Chlamydia psittaci avian strain which shows high homology with hypB gene of Chlamydia.

    PubMed

    Sato, C; Katumata, A; Takashima, I; Hashimoto, N

    1991-12-01

    A study was performed to characterize DNA fragment No. 17 of C. psittaci strain P-1041 which encoded 42 KD beta-galactosidase fusion protein with type-specific antigenicity. Sequence determination identified a partial open reading frame that spanned about 1,200b. p. nucleotides. Screening the literatures for the nucleotide and deduced amino acid sequences revealed extensive similarity between the DNA fragment of P-1041 and two chlamydial hypB genes. This DNA showed 91.5% homology with C. psittaci GPIC hypB gene in nucleotide sequence and 96.4% homology in deduced amino acid sequence. The hypB gene of C. trachomatis serovar A and the P-1041 DNA fragment showed 81.2% and 91.3% homology in nucleotide and amino acid sequences, respectively. Dot enzyme-linked immunosorbent assay, for the products of deleted DNA fragments defined the coding region for type-specific antigenic polypeptide. In addition, the P-1041 DNA fragment carried a sequence highly homologous (greater than 49%) with other bacterial and plant genes called chaperonin which responds to various stress in cells. From these results, the P-1041 DNA fragment was found to be a part of hypB gene and to encode the region critical for type-specific antigenicity.

  15. One novel quinoxaline derivative as a potent human cyclophilin A inhibitor shows highly inhibitory activity against mouse spleen cell proliferation.

    PubMed

    Li, Jian; Chen, Jing; Zhang, Li; Wang, Feng; Gui, Chunshan; Zhang, Li; Qin, Yu; Xu, Qiang; Liu, Hong; Nan, Fajun; Shen, Jingkang; Bai, Donglu; Chen, Kaixian; Shen, Xu; Jiang, Hualiang

    2006-08-15

    Cyclophilin A (CypA) is a ubiquitous cellular enzyme playing critical roles in many biological processes, and its inhibitor has been reported to have potential immunosuppressive activity. In this work, we reported a novel quinoxaline derivative, 2,3-di(furan-2-yl)-6-(3-N,N-diethylcarbamoyl-piperidino)carbonylamino quinoxaline (DC838, 3), which was confirmed to be a potent inhibitor against human CypA. By using the surface plasmon resonance (SPR) and fluorescence titration techniques, the kinetic analysis of CypA/DC838 interaction was quantitatively performed. CypA peptidyl prolyl cis-trans isomerase (PPIase) activity inhibition assay showed that DC838 demonstrated highly CypA PPIase inhibitory activity. In vivo assay results showed that DC838 could inhibit mouse spleen cell proliferation induced by concanavalin A (Con A). Molecular docking simulation further elucidated the specific DC838 binding to CypA at the atomic level. The current work should provide useful information in the discovery of immunosuppressor based on CypA inhibitor.

  16. Recombinant murine toxin from Yersinia pestis shows high toxicity and β-adrenergic blocking activity in mice.

    PubMed

    Fan, Yanxiao; Zhou, Yazhou; Feng, Na; Wang, Qiong; Tian, Guang; Wu, Xiaohong; Liu, Zizhong; Bi, Yujing; Yang, Ruifu; Wang, Xiaoyi

    2016-05-01

    Yersinia pestis murine toxin (Ymt) encoded on pMT1 is a 61-kDa protein, a member of the phospholipase D superfamily, which is found in all the domains of life. It is considered to be an intracellular protein required for the survival of Y. pestis in the midgut of the flea, but the exact role of Ymt in the pathogenesis of Y. pestis has not been clarified. Purified Ymt is highly toxic to mice and rats, but the exact mechanism of the animals' death is unclear. Here, we prepared a recombinant Ymt in Escherichia coli BL21 cells, and determined its toxicity and activity. We demonstrated that recombinant Ymt was as toxic to mice as the native protein when administered via the intraperitoneal or intravenous route, and inhibited the elevation of blood sugar caused by adrenaline. We also demonstrated that recombinant Ymt was highly toxic to mice when administered via the muscular or subcutaneous route. We also show that the multiple organ congestion or hemorrhage caused by Ymt poisoning may explain the death of the mice. PMID:26774329

  17. A Novel Phytase Derived from an Acidic Peat-Soil Microbiome Showing High Stability under Acidic Plus Pepsin Conditions.

    PubMed

    Tan, Hao; Wu, Xiang; Xie, Liyuan; Huang, Zhongqian; Peng, Weihong; Gan, Bingcheng

    2016-01-01

    Four novel phytases of the histidine acid phosphatase family were identified in two publicly available metagenomic datasets of an acidic peat-soil microbiome in northeastern Bavaria, Germany. These enzymes have low similarity to all the reported phytases. They were overexpressed in Escherichia coli and purified. Catalytic efficacy in simulated gastric fluid was measured and compared among the four candidates. The phytase named rPhyPt4 was selected for its high activity. It is the first phytase identified from unculturable Acidobacteria. The phytase showed a longer half-life than all the gastric-stable phytases that have been reported to date, suggesting a strong resistance to low pH and pepsin. A wide pH profile was observed between pH 1.5 and 5.0. At the optimum pH (2.5) the activity was 2,790 μmol/min/mg at the physiological temperature of 37°C and 3,989 μmol/min/mg at the optimum temperature of 60°C. Due to the competent activity level as well as the high gastric stability, the phytase could be a potential candidate for practical use in livestock and poultry feeding. PMID:27336313

  18. A Novel Phytase Derived from an Acidic Peat-Soil Microbiome Showing High Stability under Acidic Plus Pepsin Conditions.

    PubMed

    Tan, Hao; Wu, Xiang; Xie, Liyuan; Huang, Zhongqian; Peng, Weihong; Gan, Bingcheng

    2016-01-01

    Four novel phytases of the histidine acid phosphatase family were identified in two publicly available metagenomic datasets of an acidic peat-soil microbiome in northeastern Bavaria, Germany. These enzymes have low similarity to all the reported phytases. They were overexpressed in Escherichia coli and purified. Catalytic efficacy in simulated gastric fluid was measured and compared among the four candidates. The phytase named rPhyPt4 was selected for its high activity. It is the first phytase identified from unculturable Acidobacteria. The phytase showed a longer half-life than all the gastric-stable phytases that have been reported to date, suggesting a strong resistance to low pH and pepsin. A wide pH profile was observed between pH 1.5 and 5.0. At the optimum pH (2.5) the activity was 2,790 μmol/min/mg at the physiological temperature of 37°C and 3,989 μmol/min/mg at the optimum temperature of 60°C. Due to the competent activity level as well as the high gastric stability, the phytase could be a potential candidate for practical use in livestock and poultry feeding.

  19. A novel 5-enolpyruvylshikimate-3-phosphate synthase shows high glyphosate tolerance in Escherichia coli and tobacco plants.

    PubMed

    Cao, Gaoyi; Liu, Yunjun; Zhang, Shengxue; Yang, Xuewen; Chen, Rongrong; Zhang, Yuwen; Lu, Wei; Liu, Yan; Wang, Jianhua; Lin, Min; Wang, Guoying

    2012-01-01

    A key enzyme in the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the primary target of the broad-spectrum herbicide glyphosate. Identification of new aroA genes coding for EPSPS with a high level of glyphosate tolerance is essential for the development of glyphosate-tolerant crops. In the present study, the glyphosate tolerance of five bacterial aroA genes was evaluated in the E. coli aroA-defective strain ER2799 and in transgenic tobacco plants. All five aroA genes could complement the aroA-defective strain ER2799, and AM79 aroA showed the highest glyphosate tolerance. Although glyphosate treatment inhibited the growth of both WT and transgenic tobacco plants, transgenic plants expressing AM79 aroA tolerated higher concentration of glyphosate and had a higher fresh weight and survival rate than plants expressing other aroA genes. When treated with high concentration of glyphosate, lower shikimate content was detected in the leaves of transgenic plants expressing AM79 aroA than transgenic plants expressing other aroA genes. These results suggest that AM79 aroA could be a good candidate for the development of transgenic glyphosate-tolerant crops.

  20. Tree Rings Show Recent High Summer-Autumn Precipitation in Northwest Australia Is Unprecedented within the Last Two Centuries

    PubMed Central

    O'Donnell, Alison J.; Cook, Edward R.; Palmer, Jonathan G.; Turney, Chris S. M.; Page, Gerald F. M.; Grierson, Pauline F.

    2015-01-01

    An understanding of past hydroclimatic variability is critical to resolving the significance of recent recorded trends in Australian precipitation and informing climate models. Our aim was to reconstruct past hydroclimatic variability in semi-arid northwest Australia to provide a longer context within which to examine a recent period of unusually high summer-autumn precipitation. We developed a 210-year ring-width chronology from Callitris columellaris, which was highly correlated with summer-autumn (Dec–May) precipitation (r = 0.81; 1910–2011; p < 0.0001) and autumn (Mar–May) self-calibrating Palmer drought severity index (scPDSI, r = 0.73; 1910–2011; p < 0.0001) across semi-arid northwest Australia. A linear regression model was used to reconstruct precipitation and explained 66% of the variance in observed summer-autumn precipitation. Our reconstruction reveals inter-annual to multi-decadal scale variation in hydroclimate of the region during the last 210 years, typically showing periods of below average precipitation extending from one to three decades and periods of above average precipitation, which were often less than a decade. Our results demonstrate that the last two decades (1995–2012) have been unusually wet (average summer-autumn precipitation of 310 mm) compared to the previous two centuries (average summer-autumn precipitation of 229 mm), coinciding with both an anomalously high frequency and intensity of tropical cyclones in northwest Australia and the dominance of the positive phase of the Southern Annular Mode. PMID:26039148

  1. Tree Rings Show Recent High Summer-Autumn Precipitation in Northwest Australia Is Unprecedented within the Last Two Centuries.

    PubMed

    O'Donnell, Alison J; Cook, Edward R; Palmer, Jonathan G; Turney, Chris S M; Page, Gerald F M; Grierson, Pauline F

    2015-01-01

    An understanding of past hydroclimatic variability is critical to resolving the significance of recent recorded trends in Australian precipitation and informing climate models. Our aim was to reconstruct past hydroclimatic variability in semi-arid northwest Australia to provide a longer context within which to examine a recent period of unusually high summer-autumn precipitation. We developed a 210-year ring-width chronology from Callitris columellaris, which was highly correlated with summer-autumn (Dec-May) precipitation (r = 0.81; 1910-2011; p < 0.0001) and autumn (Mar-May) self-calibrating Palmer drought severity index (scPDSI, r = 0.73; 1910-2011; p < 0.0001) across semi-arid northwest Australia. A linear regression model was used to reconstruct precipitation and explained 66% of the variance in observed summer-autumn precipitation. Our reconstruction reveals inter-annual to multi-decadal scale variation in hydroclimate of the region during the last 210 years, typically showing periods of below average precipitation extending from one to three decades and periods of above average precipitation, which were often less than a decade. Our results demonstrate that the last two decades (1995-2012) have been unusually wet (average summer-autumn precipitation of 310 mm) compared to the previous two centuries (average summer-autumn precipitation of 229 mm), coinciding with both an anomalously high frequency and intensity of tropical cyclones in northwest Australia and the dominance of the positive phase of the Southern Annular Mode. PMID:26039148

  2. Apolipoprotein E-knockout mice on high-fat diet show autoimmune injury on kidney and aorta

    SciTech Connect

    Wang, Yuehai; Lu, Huixia; Huang, Ziyang; Lin, Huili; Lei, Zhenmin; Tang, Mengxiong; Gao, Fei; Dong, Mei; Li, Rongda; Lin, Ling

    2014-07-18

    Highlights: • Titers of ANA and anti-dsDNA antibodies were similar in ApoE{sup −/−} and Fas{sup −/−} mice. • The spleen weights and glomerular areas were similar in ApoE{sup −/−} and Fas{sup −/−} mice. • Expressions of IgG and C3 in glomeruli were similar in ApoE{sup −/−} and Fas{sup −/−} mice. • IgG, C3 and macrophage infiltration in aortic plaques were found in ApoE{sup −/−} mice. - Abstract: Background: Apolipoprotein E-knockout (ApoE{sup −/−}) mice is a classic model of atherosclerosis. We have found that ApoE{sup −/−} mice showed splenomegaly, higher titers of serum anti-nuclear antibody (ANA) and anti-dsDNA antibody compared with C57B6/L (B6) mice. However, whether ApoE{sup −/−} mice show autoimmune injury remains unclear. Methods and results: Six females and six males in each group, ApoE{sup −/−}, Fas{sup −/−} and B6 mice, were used in this study. The titers of serum ANA, anti-dsDNA antibody and creatinine and urine protein were measured by ELISA after 4 months of high-fat diet. The spleen weight and the glomerular area were determined. The expressions of IgG, C3 and macrophage in kidney and atherosclerotic plaque were detected by immunostaining followed by morphometric analysis. Similar to the characteristics of Fas{sup −/−} mice, a model of systemic lupus erythematosus (SLE), ApoE{sup −/−} mice, especially female, displayed significant increases of spleen weight and glomerular area when compared to B6 mice. Also, elevated titers of serum ANA, anti-dsDNA antibody and creatinine and urine protein. Moreover, the expressions of IgG, C3 and macrophage in glomeruli and aortic plaques were found in ApoE{sup −/−} mice. In addition, the IgG and C3 expressions in glomeruli and plaques significantly increased (or a trend of increase) in female ApoE{sup −/−} mice compared with males. Conclusions: Apolipoprotein E-knockout mice on high-fat diet show autoimmune injury on kidney and aorta.

  3. Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline.

    PubMed

    Hailer, Frank; Helander, Björn; Folkestad, Alv O; Ganusevich, Sergei A; Garstad, Steinar; Hauff, Peter; Koren, Christian; Nygård, Torgeir; Volke, Veljo; Vilà, Carles; Ellegren, Hans

    2006-06-22

    Most of the white-tailed eagle (Haliaeetus albicilla) populations in Europe experienced dramatic declines during the twentieth century. However, owing to intense conservation actions and the ban of DDT and other persistent pollutants, populations are currently recovering. We show that despite passing through demographic bottlenecks, white-tailed eagle populations have retained significant levels of genetic diversity. Both genetic and ringing data indicate that migration between populations has not been a major factor for the maintenance of genetic variability. We argue that the long generation time of eagles has acted as an intrinsic buffer against loss of genetic diversity, leading to a shorter effective time of the experienced bottleneck. Notably, conservation actions taken in several small sub-populations have ensured the preservation of a larger proportion of the total genetic diversity than if conservation had focused on the population stronghold in Norway. For conservation programmes targeting other endangered, long-lived species, our results highlight the possibility for local retention of high genetic diversity in isolated remnant populations.

  4. Genetic Analysis of Diffuse High-Grade Astrocytomas in Infancy Defines a Novel Molecular Entity.

    PubMed

    Gielen, Gerrit H; Gessi, Marco; Buttarelli, Francesca R; Baldi, Caterina; Hammes, Jennifer; zur Muehlen, Anja; Doerner, Evelyn; Denkhaus, Dorota; Warmuth-Metz, Monika; Giangaspero, Felice; Lauriola, Libero; von Bueren, André O; Kramm, Christof M; Waha, Andreas; Pietsch, Torsten

    2015-07-01

    Pediatric high-grade gliomas are considered to be different when compared to adult high-grade gliomas in their pathogenesis and biological behavior. Recently, common genetic alterations, including mutations in the H3F3A/ATRX/DAXX pathway, have been described in approximately 30% of the pediatric cases. However, only few cases of infant high-grade gliomas have been analyzed so far. We investigated the molecular features of 35 infants with diffuse high-grade astrocytomas, including 8 anaplastic astrocytomas [World Health Organization (WHO) grade III] and 27 glioblastomas (WHO grade IV) by immunohistochemistry, multiplex ligation probe-dependent amplification (MLPA), pyrosequencing of glioma-associated genes and molecular inversion probe (MIP) assay. MIP and MLPA analyses showed that chromosomal alterations are significantly less frequent in infants compared with high-grade gliomas in older children and adults. We only identified H3F3A K27M in 2 of 34 cases (5.9%), with both tumors located in the posterior fossa. PDGFRA amplifications were absent, and CDKN2A loss could be observed only in two cases. Conversely, 1q gain (22.7%) and 6q loss (18.2%) were identified in a subgroup of tumors. Loss of SNORD located on chromosome 14q32 was observed in 27.3% of the infant tumors, a focal copy number change not previously described in gliomas. Our findings indicate that infant high-grade gliomas appear to represent a distinct genetic entity suggesting a different pathogenesis and biological behavior. PMID:25231549

  5. Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches

    PubMed Central

    Kumar, Arvind; Dixit, Shalabh; Ram, T.; Yadaw, R. B.; Mishra, K. K.; Mandal, N. P.

    2014-01-01

    The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1, qDTY 2.2, qDTY 3.1, qDTY 3.2, qDTY 6.1, and qDTY 12.1) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding. PMID:25205576

  6. Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches.

    PubMed

    Kumar, Arvind; Dixit, Shalabh; Ram, T; Yadaw, R B; Mishra, K K; Mandal, N P

    2014-11-01

    The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1 , qDTY 2.2 , qDTY 3.1 , qDTY 3.2 , qDTY 6.1 , and qDTY 12.1 ) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding.

  7. Genetic structure in striped skunks (Mephitis mephitis) on the southern high plains of Texas

    USGS Publications Warehouse

    Hansen, L.A.; Mathews, N.E.; Hansen, R.W.; Vander Lee, B. A.; Scott, Lutz R.

    2003-01-01

    Genetic variation within populations reflects population-level social and demographic processes and influences how a population behaves as an evolutionary unit. We examined partitioning of genetic variation in striped skunks (Mephitis mephitis) from the Southern High Plains of Texas during 1994-1995. Sixty-nine male and 35 female skunks were sampled on four 12.8-km2 study plots. Plot centers ranged from 17.6 to 61.6 km apart. We used multi-locus DNA fingerprinting with 2 probes, pV47 and CTTxAGG, to test 3 hypotheses: (1) females are more genetically similar to other females than males are to other males on the same plot (indicating greater female philopatry than male philopatry), (2) genetic similarity is greater within plots than among plots (indicating partitioning of genetic variation in space), and (3) genetic similarity of males decreases as the distance separating males increases (indicating geographic distance affects rates of gene flow). In general, males on a plot had lower average genetic similarity than females. Genetic similarity within plots was not different from genetic similarity among plots for males or for females. Genetic similarity of males did not decrease with increasing distance among plots. The lack of geographical genetic structure in striped skunks suggests at the scale of this study (<60 km) that gene flow of biparentally inherited genes is not distance-mediated. However, the higher similarity values for females than for males on the same plot supports an effect of male-biased dispersal and female philopatry on partitioning of genetic variation between sexes.

  8. Shared Genetic Signals of Hypoxia Adaptation in Drosophila and in High-Altitude Human Populations

    PubMed Central

    Jha, Aashish R.; Zhou, Dan; Brown, Christopher D.; Kreitman, Martin; Haddad, Gabriel G.; White, Kevin P.

    2016-01-01

    The ability to withstand low oxygen (hypoxia tolerance) is a polygenic and mechanistically conserved trait that has important implications for both human health and evolution. However, little is known about the diversity of genetic mechanisms involved in hypoxia adaptation in evolving populations. We used experimental evolution and whole-genome sequencing in Drosophila melanogaster to investigate the role of natural variation in adaptation to hypoxia. Using a generalized linear mixed model we identified significant allele frequency differences between three independently evolved hypoxia-tolerant populations and normoxic control populations for approximately 3,800 single nucleotide polymorphisms. Around 50% of these variants are clustered in 66 distinct genomic regions. These regions contain genes that are differentially expressed between hypoxia-tolerant and normoxic populations and several of the differentially expressed genes are associated with metabolic processes. Additional genes associated with respiratory and open tracheal system development also show evidence of directional selection. RNAi-mediated knockdown of several candidate genes’ expression significantly enhanced survival in severe hypoxia. Using genomewide single nucleotide polymorphism data from four high-altitude human populations—Sherpas, Tibetans, Ethiopians, and Andeans, we found that several human orthologs of the genes under selection in flies are also likely under positive selection in all four high-altitude human populations. Thus, our results indicate that selection for hypoxia tolerance can act on standing genetic variation in similar genes and pathways present in organisms diverged by hundreds of millions of years. PMID:26576852

  9. High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus

    PubMed Central

    Zheng, Wenming; Huang, Lili; Huang, Jinqun; Wang, Xiaojie; Chen, Xianming; Zhao, Jie; Guo, Jun; Zhuang, Hua; Qiu, Chuangzhao; Liu, Jie; Liu, Huiquan; Huang, Xueling; Pei, Guoliang; Zhan, Gangming; Tang, Chunlei; Cheng, Yulin; Liu, Minjie; Zhang, Jinshan; Zhao, Zhongtao; Zhang, Shijie; Han, Qingmei; Han, Dejun; Zhang, Hongchang; Zhao, Jing; Gao, Xiaoning; Wang, Jianfeng; Ni, Peixiang; Dong, Wei; Yang, Linfeng; Yang, Huanming; Xu, Jin-Rong; Zhang, Gengyun; Kang, Zhensheng

    2013-01-01

    Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a ‘fosmid-to-fosmid’ strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the ‘fosmid-to-fosmid’ strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens. PMID:24150273

  10. High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus.

    PubMed

    Zheng, Wenming; Huang, Lili; Huang, Jinqun; Wang, Xiaojie; Chen, Xianming; Zhao, Jie; Guo, Jun; Zhuang, Hua; Qiu, Chuangzhao; Liu, Jie; Liu, Huiquan; Huang, Xueling; Pei, Guoliang; Zhan, Gangming; Tang, Chunlei; Cheng, Yulin; Liu, Minjie; Zhang, Jinshan; Zhao, Zhongtao; Zhang, Shijie; Han, Qingmei; Han, Dejun; Zhang, Hongchang; Zhao, Jing; Gao, Xiaoning; Wang, Jianfeng; Ni, Peixiang; Dong, Wei; Yang, Linfeng; Yang, Huanming; Xu, Jin-Rong; Zhang, Gengyun; Kang, Zhensheng

    2013-01-01

    Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a 'fosmid-to-fosmid' strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the 'fosmid-to-fosmid' strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens.

  11. Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria.

    PubMed

    Hilmo, Olga; Lundemo, Sverre; Holien, Håkon; Stengrundet, Kirsti; Stenøien, Hans K

    2012-07-01

    An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. To test this hypothesis, we assessed genetic diversity and structure in the populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30km. Almost all genetic variation was attributed to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5-10m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity.

  12. Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria.

    PubMed

    Hilmo, Olga; Lundemo, Sverre; Holien, Håkon; Stengrundet, Kirsti; Stenøien, Hans K

    2012-07-01

    An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. To test this hypothesis, we assessed genetic diversity and structure in the populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30km. Almost all genetic variation was attributed to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5-10m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity. PMID:22571538

  13. Population genetics of purple saxifrage (Saxifraga oppositifolia) in the high Arctic archipelago of Svalbard

    PubMed Central

    Pietiläinen, Maria; Korpelainen, Helena

    2013-01-01

    We investigated patterns of genetic variability in Saxifraga oppositifolia in the isolated Arctic Svalbard archipelago. The genetic analysis included genotyping using nine polymorphic microsatellite markers and sequencing of the nuclear internal transcribed spacer region. Among populations, mean allele numbers per microsatellite locus ranged from 2.0 to 2.6, and 9 % of alleles were unique. Observed (HO) and expected (HE) heterozygosities averaged 0.522 and 0.445, respectively. Typically negative but non-significant FIS values (mean −0.173) were found in S. oppositifolia populations. FST values were relatively low (mean 0.123). The Bayesian structure analysis provided additional information on population genetic structures. Seven out of 11 studied populations, including populations located both near each other and far apart (distances 5–210 km), showed relatively homogeneous clustering patterns, while one population located on a slope in the main settlement of Longyearbyen possessed a unique genetic structure. The Mantel test proved that there is no significant correlation between genetic and geographical distances. Different growth habits (compact, trailing and intermediate) did not possess distinct genetic compositions based on microsatellite variation. Internal transcribed spacer sequencing revealed 12 polymorphic sites. Among 24 sequenced Svalbard samples, eight haplotypes were detected, none shared by the mainland samples. Population genetic structures of S. oppositifolia in Svalbard show that both genetic variation and differentiation levels are modest, outcrossing is the main mating system, and dispersal and gene flow are important, probably attributable to strong winds and human and animal vectors. PMID:23700503

  14. The invasive species Ulex europaeus (Fabaceae) shows high dynamism in a fragmented landscape of south-central Chile.

    PubMed

    Altamirano, Adison; Cely, Jenny Paola; Etter, Andrés; Miranda, Alejandro; Fuentes-Ramirez, Andres; Acevedo, Patricio; Salas, Christian; Vargas, Rodrigo

    2016-08-01

    Ulex europaeus (gorse) is an invasive shrub deemed as one of the most invasive species in the world. U. europaeus is widely distributed in the south-central area of Chile, which is considered a world hotspot for biodiversity conservation. In addition to its negative effects on the biodiversity of natural ecosystems, U. europaeus is one of the most severe pests for agriculture and forestry. Despite its importance as an invasive species, U. europaeus has been little studied. Although information exists on the potential distribution of the species, the interaction of the invasion process with the spatial dynamic of the landscape and the landscape-scale factors that control the presence or absence of the species is still lacking. We studied the spatial and temporal dynamics of the landscape and how these relate to U. europaeus invasion in south-central Chile. We used supervised classification of satellite images to determine the spatial distribution of the species and other land covers for the years 1986 and 2003, analysing the transitions between the different land covers. We used logistic regression for modelling the increase, decrease and permanence of U. europaeus invasion considering landscape variables. Results showed that the species covers only around 1 % of the study area and showed a 42 % reduction in area for the studied period. However, U. europaeus was the cover type which presented the greatest dynamism in the landscape. We found a strong relationship between changes in land cover and the invasion process, especially connected with forest plantations of exotic species, which promotes the displacement of U. europaeus. The model of gorse cover increase presented the best performance, and the most important predictors were distance to seed source and landscape complexity index. Our model predicted high spread potential of U. europaeus in areas of high conservation value. We conclude that proper management for this invasive species must take into account

  15. Efficient photoinduced charge accumulation in reduced graphene oxide coupled with titania nanosheets to show highly enhanced and persistent conductance.

    PubMed

    Cai, Xingke; Sakai, Nobuyuki; Ozawa, Tadashi C; Funatsu, Asami; Ma, Renzhi; Ebina, Yasuo; Sasaki, Takayoshi

    2015-06-01

    Tuning of the electrical properties of graphene via photoexcitation of a heteroassembled material has started to attract attention for electronic and optoelectronic applications. Actually photoinduced carrier doping from the hexagonal boron nitride (h-BN) substrate greatly modulated the transport property of the top layer graphene, showing promising potential for this approach. However, for practical applications, the large scale production of this two-dimensional heterostructure is needed. Here, a superlattice film constructed from reduced graphene oxide (rGO) and photoactive titania nanosheets (Ti0.87O2(0.52-)) was employed as a channel to construct a field effect transistor (FET) device, and its UV light response on the electrical transport property was examined. The UV light illumination induced significant improvement of the electrical conductance by ∼7 times on the basis of simultaneous enhancements of the electron carrier concentration and its mobility in rGO. Furthermore, the polarity of the FET response changed from ambipolar to n-type unipolar. Such modulated properties persisted in vacuum even after the UV light was turned off. These interesting behaviors may be explained in terms of photomodulation effects from Ti0.87O2(0.52-) nanosheets. The photoexcited electrons in Ti0.87O2(0.52-) are injected into rGO to increase the electron carrier concentration as high as 7.6×10(13) cm(-2). On the other hand, the holes are likely trapped in the Ti0.87O2(0.52-) nanosheets. These photocarriers undergo reduction and oxidation of oxygen and water molecules adsorbed in the film, respectively, which act as carrier scattering centers, contributing to the enhancement of the carrier mobility. Since the film likely contains more water molecules than oxygen, upon extinction of UV light, a major portion of electrons (∼80% of the concentration at the UV off) survives in rGO, showing the highly enhanced conductance for days. This surpassing photomodulated FET response and

  16. The invasive species Ulex europaeus (Fabaceae) shows high dynamism in a fragmented landscape of south-central Chile.

    PubMed

    Altamirano, Adison; Cely, Jenny Paola; Etter, Andrés; Miranda, Alejandro; Fuentes-Ramirez, Andres; Acevedo, Patricio; Salas, Christian; Vargas, Rodrigo

    2016-08-01

    Ulex europaeus (gorse) is an invasive shrub deemed as one of the most invasive species in the world. U. europaeus is widely distributed in the south-central area of Chile, which is considered a world hotspot for biodiversity conservation. In addition to its negative effects on the biodiversity of natural ecosystems, U. europaeus is one of the most severe pests for agriculture and forestry. Despite its importance as an invasive species, U. europaeus has been little studied. Although information exists on the potential distribution of the species, the interaction of the invasion process with the spatial dynamic of the landscape and the landscape-scale factors that control the presence or absence of the species is still lacking. We studied the spatial and temporal dynamics of the landscape and how these relate to U. europaeus invasion in south-central Chile. We used supervised classification of satellite images to determine the spatial distribution of the species and other land covers for the years 1986 and 2003, analysing the transitions between the different land covers. We used logistic regression for modelling the increase, decrease and permanence of U. europaeus invasion considering landscape variables. Results showed that the species covers only around 1 % of the study area and showed a 42 % reduction in area for the studied period. However, U. europaeus was the cover type which presented the greatest dynamism in the landscape. We found a strong relationship between changes in land cover and the invasion process, especially connected with forest plantations of exotic species, which promotes the displacement of U. europaeus. The model of gorse cover increase presented the best performance, and the most important predictors were distance to seed source and landscape complexity index. Our model predicted high spread potential of U. europaeus in areas of high conservation value. We conclude that proper management for this invasive species must take into account

  17. High local genetic diversity of canine parvovirus from Ecuador.

    PubMed

    Aldaz, Jaime; García-Díaz, Juan; Calleros, Lucía; Sosa, Katia; Iraola, Gregorio; Marandino, Ana; Hernández, Martín; Panzera, Yanina; Pérez, Ruben

    2013-09-27

    Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a.

  18. Human genetic studies in areas of high natural radiation. VIII. Genetic load not related to radiation.

    PubMed Central

    Freire-Maia, A; Krieger, H

    1975-01-01

    The genetic load disclosed by inbreeding has been analyzed in a multiple regression model for a population involving several localities in the state of Espírito Santo, Brazil. The inbreeding load has been estimated for number of pregnancies, abortions, stillbirths, children born alive, anomalies in general, sex ratio, infant mortality, post-infant mortality, and sterility and infertility of the couple. There was no evidence of either maternal or paternal inbreeding effects on the variables analyzed. The effect of inbreeding of the zygote was significant only for anomalies in general (B = 2.29 +/- 0.45) and infant mortality (B = 3.19 +/- 1.39). The latter result must be accepted with caution because of the many environmental causes affecting infant mortality. The B/A ratio suggested a predominantly mutational load for anomalies in general (B/A = 25), but with respect to infant mortality (B/A = 6), the ratio is regarded as an underestimate because of the environmental contribution to A and therefore not supportive of the segregational interpretation. PMID:803018

  19. Activity/inactivity circadian rhythm shows high similarities between young obesity-induced rats and old rats.

    PubMed

    Bravo Santos, R; Delgado, J; Cubero, J; Franco, L; Ruiz-Moyano, S; Mesa, M; Rodríguez, A B; Uguz, C; Barriga, C

    2016-03-01

    The objective of the present study was to compare differences between elderly rats and young obesity-induced rats in their activity/inactivity circadian rhythm. The investigation was motivated by the differences reported previously for the circadian rhythms of both obese and elderly humans (and other animals), and those of healthy, young or mature individuals. Three groups of rats were formed: a young control group which was fed a standard chow for rodents; a young obesity-induced group which was fed a high-fat diet for four months; and an elderly control group with rats aged 2.5 years that was fed a standard chow for rodents. Activity/inactivity data were registered through actimetry using infrared actimeter systems in each cage to detect activity. Data were logged on a computer and chronobiological analysis were performed. The results showed diurnal activity (sleep time), nocturnal activity (awake time), amplitude, acrophase, and interdaily stability to be similar between the young obesity-induced group and the elderly control group, but different in the young control group. We have concluded that obesity leads to a chronodisruption status in the body similar to the circadian rhythm degradation observed in the elderly. PMID:27030628

  20. Analysis of a large dataset of mycorrhiza inoculation field trials on potato shows highly significant increases in yield.

    PubMed

    Hijri, Mohamed

    2016-04-01

    An increasing human population requires more food production in nutrient-efficient systems in order to simultaneously meet global food needs while reducing the environmental footprint of agriculture. Arbuscular mycorrhizal fungi (AMF) have the potential to enhance crop yield, but their efficiency has yet to be demonstrated in large-scale crop production systems. This study reports an analysis of a dataset consisting of 231 field trials in which the same AMF inoculant (Rhizophagus irregularis DAOM 197198) was applied to potato over a 4-year period in North America and Europe under authentic field conditions. The inoculation was performed using a liquid suspension of AMF spores that was sprayed onto potato seed pieces, yielding a calculated 71 spores per seed piece. Statistical analysis showed a highly significant increase in marketable potato yield (ANOVA, P < 0.0001) for inoculated fields (42.2 tons/ha) compared with non-inoculated controls (38.3 tons/ha), irrespective of trial year. The average yield increase was 3.9 tons/ha, representing 9.5 % of total crop yield. Inoculation was profitable with a 0.67-tons/ha increase in yield, a threshold reached in almost 79 % of all trials. This finding clearly demonstrates the benefits of mycorrhizal-based inoculation on crop yield, using potato as a case study. Further improvements of these beneficial inoculants will help compensate for crop production deficits, both now and in the future.

  1. Tongue Epithelium Cells from shRNA Mediated Transgenic Goat Show High Resistance to Foot and Mouth Disease Virus

    PubMed Central

    Li, Wenting; Wang, Kejun; Kang, Shimeng; Deng, Shoulong; Han, Hongbing; Lian, Ling; Lian, Zhengxing

    2015-01-01

    Foot and mouth disease induced by foot and mouth disease virus (FMDV) is severe threat to cloven-hoofed domestic animals. The gene 3Dpol in FMDV genome encodes the viral RNA polymerase, a vital element for FMDV replication. In this study, a conserved 3D-7414shRNA targeting FMDV-3Dpol gene was designed and injected into pronuclear embryos to produce the transgenic goats. Sixty-one goats were produced, of which, seven goats positively integrated 3D-7414shRNA. Loss of function assay demonstrated that siRNA effectively knockdown 3Dpol gene in skin epithelium cells of transgenic goats. Subsequently, the tongue epithelium cells from transgenic and non-transgenic goats were infected with FMDV O/YS/CHA/05 strain. A significant decrease of virus titres and virus copy number was observed in cells of transgenic goats compared with that of non-transgenic goats, which indicated that 3D-7414siRNA inhibited FMDV replication by interfering FMDV-3Dpol gene. Furthermore, we found that expression of TLR7, RIG-I and TRAF6 was lower in FMDV infected cells from transgenic goats compared to that from non-transgenic goats, which might result from lower virus copy number in transgenic goats’ cells. In conclusion, we successfully produced transgenic goats highly expressing 3D-7414siRNA targeting 3Dpol gene, and the tongue epithelium cells from the transgenic goats showed effective resistance to FMDV. PMID:26671568

  2. High-resolution structural analysis shows how Tah1 tethers Hsp90 to the R2TP complex.

    PubMed

    Back, Régis; Dominguez, Cyril; Rothé, Benjamin; Bobo, Claude; Beaufils, Chrystel; Moréra, Solange; Meyer, Philippe; Charpentier, Bruno; Branlant, Christiane; Allain, Frédéric H-T; Manival, Xavier

    2013-10-01

    The ubiquitous Hsp90 chaperone participates in snoRNP and RNA polymerase assembly through interaction with the R2TP complex. This complex includes the proteins Tah1, Pih1, Rvb1, and Rvb2. Tah1 bridges Hsp90 to R2TP. Its minimal TPR domain includes two TPR motifs and a capping helix. We established the high-resolution solution structures of Tah1 free and in complex with the Hsp90 C-terminal peptide. The TPR fold is similar in the free and bound forms and we show experimentally that in addition to its solvating/stabilizing role, the capping helix is essential for the recognition of the Hsp90 (704)EMEEVD(709) motif. In addition to Lys79 and Arg83 from the carboxylate clamp, this helix bears Tyr82 forming a π/S-CH3 interaction with Hsp90 M(705) from the peptide 310 helix. The Tah1 C-terminal region is unfolded, and we demonstrate that it is essential for the recruitment of the Pih1 C-terminal domain and folds upon binding. PMID:24012479

  3. Constitutive expression of high-affinity sulfate transporter (HAST) gene in Indian mustard showed enhanced sulfur uptake and assimilation.

    PubMed

    Abdin, M Z; Akmal, M; Ram, M; Nafis, T; Alam, P; Nadeem, M; Khan, M A; Ahmad, A

    2011-07-01

    Lycopersicon esculantum sulfate transporter gene (LeST 1.1) encodes a high-affinity sulfate transporter (HAST) located in root epidermis. In this study, the LeST 1.1 gene was constitutively expressed in Indian mustard (Brassica juncea cv. Pusa Jai Kisan). Transgenic as well as untransformed plants were grown in sulfur-insufficient (25 and 50 μM) and sulfur-sufficient (1,000 μM) conditions for 30 days. Two-fold increase was noticed in the sulfate uptake rate of transgenic plants grown in both sulfur-insufficient and -sufficient conditions as compared to untransformed plants. The transgenic B. juncea plants were able to accumulate higher biomass and showed improved sulfur status even in sulfur-insufficient conditions when compared with untransformed plants. Chlorophyll content, ATP sulfurylase activity and protein content were also higher in transgenic plants than untranformed plants under sulfur-insufficient conditions. Our results, thus, clearly indicate that constitutive expression of LeST 1.1 gene in B. juncea had led to enhanced capacity of sulfur uptake and assimilation even in sulfur-insufficient conditions. This approach can also be used in other crops to enhance their sulfate uptake and assimilation potential under S-insufficient conditions. PMID:20938698

  4. Activity/inactivity circadian rhythm shows high similarities between young obesity-induced rats and old rats.

    PubMed

    Bravo Santos, R; Delgado, J; Cubero, J; Franco, L; Ruiz-Moyano, S; Mesa, M; Rodríguez, A B; Uguz, C; Barriga, C

    2016-03-01

    The objective of the present study was to compare differences between elderly rats and young obesity-induced rats in their activity/inactivity circadian rhythm. The investigation was motivated by the differences reported previously for the circadian rhythms of both obese and elderly humans (and other animals), and those of healthy, young or mature individuals. Three groups of rats were formed: a young control group which was fed a standard chow for rodents; a young obesity-induced group which was fed a high-fat diet for four months; and an elderly control group with rats aged 2.5 years that was fed a standard chow for rodents. Activity/inactivity data were registered through actimetry using infrared actimeter systems in each cage to detect activity. Data were logged on a computer and chronobiological analysis were performed. The results showed diurnal activity (sleep time), nocturnal activity (awake time), amplitude, acrophase, and interdaily stability to be similar between the young obesity-induced group and the elderly control group, but different in the young control group. We have concluded that obesity leads to a chronodisruption status in the body similar to the circadian rhythm degradation observed in the elderly.

  5. High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing.

    PubMed

    Zhou, Zunchun; Liu, Shikai; Dong, Ying; Gao, Shan; Chen, Zhong; Jiang, Jingwei; Yang, Aifu; Sun, Hongjuan; Guan, Xiaoyan; Jiang, Bei; Wang, Bai

    2015-01-01

    Sea urchins have long been used as research model organisms for developmental biology and evolutionary studies. Some of them are also important aquaculture species in East Asia. In this work, we report the construction of RAD-tag based high-density genetic maps by genotyping F1 interspecific hybrids derived from a crossing between a female sea urchin Strongylocentrotus nudus and a male Strongylocentrotus intermedius. With polymorphisms present in these two wild individuals, we constructed a female meiotic map containing 3,080 markers for S. nudus, and a male meiotic map for S. intermedius which contains 1,577 markers. Using the linkage maps, we were able to anchor a total of 1,591 scaffolds (495.9 Mb) accounting for 60.8% of the genome assembly of Strongylocentrotus purpuratus. A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM. This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information. The genetic maps are essential for QTL mapping and are useful as framework to order and orientate contiguous scaffolds from sea urchin genome assembly. The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.

  6. Ocean circulation model predicts high genetic structure observed in a long-lived pelagic developer.

    PubMed

    Sunday, J M; Popovic, I; Palen, W J; Foreman, M G G; Hart, M W

    2014-10-01

    Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time-integrated processes and may not capture present-day connectivity between populations. Here, we use a high-resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well-studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6-10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20-50 km of their parents, suggesting a necessity for close-knit design of Marine Protected Area networks.

  7. Ocean circulation model predicts high genetic structure observed in a long-lived pelagic developer.

    PubMed

    Sunday, J M; Popovic, I; Palen, W J; Foreman, M G G; Hart, M W

    2014-10-01

    Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time-integrated processes and may not capture present-day connectivity between populations. Here, we use a high-resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well-studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6-10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20-50 km of their parents, suggesting a necessity for close-knit design of Marine Protected Area networks. PMID:25231198

  8. Genetic Consequences of Forest Fragmentation for a Highly Specialized Arboreal Mammal - the Edible Dormouse

    PubMed Central

    Fietz, Joanna; Tomiuk, Jürgen; Loeschcke, Volker; Weis-Dootz, Tanja; Segelbacher, Gernot

    2014-01-01

    Habitat loss and fragmentation represent the most serious extinction threats for many species and have been demonstrated to be especially detrimental for mammals. Particularly, highly specialized species with low dispersal abilities will encounter a high risk of extinction in fragmented landscapes. Here we studied the edible dormouse (Glis glis), a small arboreal mammal that is distributed throughout Central Europe, where forests are mostly fragmented at different spatial scales. The aim of this study was to investigate the effect of habitat fragmentation on genetic population structures using the example of edible dormouse populations inhabiting forest fragments in south western Germany. We genotyped 380 adult individuals captured between 2001 and 2009 in four different forest fragments and one large continuous forest using 14 species-specific microsatellites. We hypothesised, that populations in small forest patches have a lower genetic diversity and are more isolated compared to populations living in continuous forests. In accordance with our expectations we found that dormice inhabiting forest fragments were isolated from each other. Furthermore, their genetic population structure was more unstable over the study period than in the large continuous forest. Even though we could not detect lower genetic variability within individuals inhabiting forest fragments, strong genetic isolation and an overall high risk to mate with close relatives might be precursors to a reduced genetic variability and the onset of inbreeding depression. Results of this study highlight that connectivity among habitat fragments can already be strongly hampered before genetic erosion within small and isolated populations becomes evident. PMID:24505390

  9. Essay Contest Reveals Misconceptions of High School Students in Genetics Content

    PubMed Central

    Mills Shaw, Kenna R.; Van Horne, Katie; Zhang, Hubert; Boughman, Joann

    2008-01-01

    National educational organizations have called upon scientists to become involved in K–12 education reform. From sporadic interaction with students to more sustained partnerships with teachers, the engagement of scientists takes many forms. In this case, scientists from the American Society of Human Genetics (ASHG), the Genetics Society of America (GSA), and the National Society of Genetic Counselors (NSGC) have partnered to organize an essay contest for high school students as part of the activities surrounding National DNA Day. We describe a systematic analysis of 500 of 2443 total essays submitted in response to this contest over 2 years. Our analysis reveals the nature of student misconceptions in genetics, the possible sources of these misconceptions, and potential ways to galvanize genetics education. PMID:18245328

  10. Essay contest reveals misconceptions of high school students in genetics content.

    PubMed

    Mills Shaw, Kenna R; Van Horne, Katie; Zhang, Hubert; Boughman, Joann

    2008-03-01

    National educational organizations have called upon scientists to become involved in K-12 education reform. From sporadic interaction with students to more sustained partnerships with teachers, the engagement of scientists takes many forms. In this case, scientists from the American Society of Human Genetics (ASHG), the Genetics Society of America (GSA), and the National Society of Genetic Counselors (NSGC) have partnered to organize an essay contest for high school students as part of the activities surrounding National DNA Day. We describe a systematic analysis of 500 of 2443 total essays submitted in response to this contest over 2 years. Our analysis reveals the nature of student misconceptions in genetics, the possible sources of these misconceptions, and potential ways to galvanize genetics education.

  11. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques.

    PubMed

    Onda, Yoshihiko; Mochida, Keiichi

    2016-08-01

    Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study. PMID:27499684

  12. High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense.

    PubMed

    Zhang, Wei; Luo, Zhenhua; Zhao, Mian; Wu, Hua

    2015-09-01

    Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense.

  13. High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense.

    PubMed

    Zhang, Wei; Luo, Zhenhua; Zhao, Mian; Wu, Hua

    2015-09-01

    Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense. PMID:26037662

  14. Endophytic Bacteria Isolated from Common Bean (Phaseolus vulgaris) Exhibiting High Variability Showed Antimicrobial Activity and Quorum Sensing Inhibition.

    PubMed

    Lopes, Ralf Bruno Moura; Costa, Leonardo Emanuel de Oliveira; Vanetti, Maria Cristina Dantas; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

    2015-10-01

    Endophytic bacteria play a key role in the biocontrol of phytopathogenic microorganisms. In this study, genotypic diversity was analyzed via repetitive element PCR (rep-PCR) of endophytic isolates of the phylum Actinobacteria that were previously collected from leaves of cultivars of common bean (Phaseolus vulgaris). Considerable variability was observed, which has not been reported previously for this phylum of endophytic bacteria of the common bean. Furthermore, the ethanol extracts from cultures of various isolates inhibited the growth of pathogenic bacteria in vitro, especially Gram-positive pathogens. Extracts from cultures of Microbacterium testaceum BAC1065 and BAC1093, which were both isolated from the 'Talismã' cultivar, strongly inhibited most of the pathogenic bacteria tested. Bean endophytic bacteria were also demonstrated to have the potential to inhibit the quorum sensing of Gram-negative bacteria. This mechanism may regulate the production of virulence factors in pathogens. The ability to inhibit quorum sensing has also not been reported previously for endophytic microorganisms of P. vulgaris. Furthermore, M. testaceum with capacity to inhibit quorum sensing appears to be widespread in common bean. The genomic profiles of M. testaceum were also analyzed via pulsed-field gel electrophoresis, and greater differentiation was observed using this method than rep-PCR; in general, no groups were formed based on the cultivar of origin. This study showed for the first time that endophytic bacteria from common bean plants exhibit high variability and may be useful for the development of strategies for the biological control of diseases in this important legume plant.

  15. Endophytic Bacteria Isolated from Common Bean (Phaseolus vulgaris) Exhibiting High Variability Showed Antimicrobial Activity and Quorum Sensing Inhibition.

    PubMed

    Lopes, Ralf Bruno Moura; Costa, Leonardo Emanuel de Oliveira; Vanetti, Maria Cristina Dantas; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

    2015-10-01

    Endophytic bacteria play a key role in the biocontrol of phytopathogenic microorganisms. In this study, genotypic diversity was analyzed via repetitive element PCR (rep-PCR) of endophytic isolates of the phylum Actinobacteria that were previously collected from leaves of cultivars of common bean (Phaseolus vulgaris). Considerable variability was observed, which has not been reported previously for this phylum of endophytic bacteria of the common bean. Furthermore, the ethanol extracts from cultures of various isolates inhibited the growth of pathogenic bacteria in vitro, especially Gram-positive pathogens. Extracts from cultures of Microbacterium testaceum BAC1065 and BAC1093, which were both isolated from the 'Talismã' cultivar, strongly inhibited most of the pathogenic bacteria tested. Bean endophytic bacteria were also demonstrated to have the potential to inhibit the quorum sensing of Gram-negative bacteria. This mechanism may regulate the production of virulence factors in pathogens. The ability to inhibit quorum sensing has also not been reported previously for endophytic microorganisms of P. vulgaris. Furthermore, M. testaceum with capacity to inhibit quorum sensing appears to be widespread in common bean. The genomic profiles of M. testaceum were also analyzed via pulsed-field gel electrophoresis, and greater differentiation was observed using this method than rep-PCR; in general, no groups were formed based on the cultivar of origin. This study showed for the first time that endophytic bacteria from common bean plants exhibit high variability and may be useful for the development of strategies for the biological control of diseases in this important legume plant. PMID:26202846

  16. Quantitative trait locus analysis, pathway analysis, and consomic mapping show genetic variants of Tnni3k, Fpgt, or H28 control susceptibility to viral myocarditis.

    PubMed

    Wiltshire, Sean A; Leiva-Torres, Gabriel André; Vidal, Silvia M

    2011-06-01

    Coxsackievirus B3 (CVB3) infection is the most common cause of viral myocarditis. The pathogenesis of viral myocarditis is strongly controlled by host genetic factors. Although certain indispensable components of immunity have been identified, the genes and pathways underlying natural variation between individuals remain unclear. Previously, we isolated the viral myocarditis susceptibility 1 (Vms1) locus on chromosome 3, which influences pathogenesis. We hypothesized that confirmation and further study of Vms1 controlling CVB3-mediated pathology, combined with pathway analysis and consomic mapping approaches, would elucidate both pathological and protective mechanisms accounting for natural variation in response to CVB3 infection. Vms1 was originally mapped to chromosome 3 using a segregating cross between susceptible A/J and resistant B10.A mice. To validate Vms1, C57BL/6J-Chr 3(A)/NaJ (a chromosome substitution strain that carries a diploid A/J chromosome 3) were used to replicate susceptibility compared with resistant C57BL/6J (B6). A second segregating F2 cross was generated between these, confirming both the localization and effects of Vms1. Microarray analysis of the four strains (A/J, B10.A, C57BL/6J, and C57BL/6J-Chr 3(A)/NaJ) illuminated a core program of response to CVB3 in all strains that is comprised mainly of IFN-stimulated genes. Microarray analysis also revealed strain-specific differential expression programs and genes that may be prognostic or diagnostic of susceptibility to CVB3 infection. A combination of analyses revealed very strong evidence for the existence and location of Vms1. Differentially expressed pathways were identified by microarray, and candidate gene analysis revealed Fpgt, H28, and Tnni3k as likely candidates for Vms1.

  17. Awareness of Societal Issues Among High School Biology Teachers Teaching Genetics

    NASA Astrophysics Data System (ADS)

    Lazarowitz, Reuven; Bloch, Ilit

    2005-12-01

    The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral, ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution. The study includes a short historical review of World War II atrocities during the Holocaust when scientists from all the above-mentioned disciplines had been involved in trying to support and develop the eugenics theories. It investigates pre- and postwar theories of the eugenics movement in the United States which were implemented successfully in Germany and a literature survey of the studies of societal issues related to these subjects. The sample consisted of 30 male and female biology teachers. Enclosed are teachers' answers in favor or against including debates about societal issues in their classrooms while teaching the disciplines mentioned above. Teachers' answers were analyzed in relation to three variables: years of teaching experience, gender, and religion faith. Data were collected from questionnaires and personal interviews and analyzed according to qualitative and quantitative methods. The results show that amongst the teachers there is a medium to low level of awareness of societal issues, while mainly emphasizing scientific subjects in preparation of matriculation examinations. The majority of the teachers do not include societal issues in their teaching, but if students raise these issues, teachers claimed to address them. No differences in teachers' opinions to societal issues were found in relation to gender or religious faith. Teachers with more years of teaching experience tend to teach with a more Science, Technology, and Society (STS) approach than novice teachers. The results are discussed in relation to teachers' professional development and teaching strategies are suggested to be used in their classrooms based on a STS approach, which includes the societal issues as a main goal.

  18. A genetic strategy generating wheat with very high amylose content.

    PubMed

    Regina, Ahmed; Berbezy, Pierre; Kosar-Hashemi, Behjat; Li, Suzhi; Cmiel, Mark; Larroque, Oscar; Bird, Anthony R; Swain, Steve M; Cavanagh, Colin; Jobling, Stephen A; Li, Zhongyi; Morell, Matthew

    2015-12-01

    Resistant starch (RS), a type of dietary fibre, plays an important role in human health; however, the content of RS in most modern processed starchy foods is low. Cereal starch, when structurally manipulated through a modified starch biosynthetic pathway to greatly increase the amylose content, could be an important food source of RS. Transgenic studies have previously revealed the requirement of simultaneous down-regulation of two starch branching enzyme (SBE) II isoforms both located on the long arm of chromosome 2, namely SBEIIa and SBEIIb, to elevate the amylose content in wheat from ~25% to ~75%. The current study revealed close proximity of genes encoding SBEIIa and SBEIIb isoforms in wheat with a genetic distance of 0.5 cM on chromosome 2B. A series of deletion and single nucleotide polymorphism (SNP) loss of function alleles in SBEIIa, SBEIIb or both was isolated from two different wheat populations. A breeding strategy to combine deletions and SNPs generated wheat genotypes with altered expression levels of SBEIIa and SBEIIb, elevating the amylose content to an unprecedented ~85%, with a marked concomitant increase in RS content. Biochemical assays were used to confirm the complete absence in the grain of expression of SBEIIa from all three genomes in combination with the absence of SBEIIb from one of the genomes.

  19. Adaptive color polymorphism and unusually high local genetic diversity in the side-blotched lizard, Uta stansburiana.

    PubMed

    Micheletti, Steven; Parra, Eliseo; Routman, Eric J

    2012-01-01

    Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation.

  20. Adaptive Color Polymorphism and Unusually High Local Genetic Diversity in the Side-Blotched Lizard, Uta stansburiana

    PubMed Central

    Micheletti, Steven; Parra, Eliseo; Routman, Eric J.

    2012-01-01

    Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation. PMID:23133520

  1. Genetic analysis of axial length genes in high grade myopia from Indian population☆

    PubMed Central

    Sharmila, Ferdinamarie; Abinayapriya; Ramprabhu, Karthikeyan; Kumaramanickavel, Govindasamy; R.R.Sudhir; Sripriya, Sarangapani

    2014-01-01

    Purpose To study the putative association of Membrane frizzled related protein (MFRP) and Visual system homeobox protein (VSX2) gene variants with axial length (AL) in myopia. Method A total of 189 samples with (N = 98) and without (N = 91) myopia were genotyped for the MRFP and VSX2 variations in ABI Prism 3100 AVANT genetic analyzer. Genotype/haplotype analysis was performed using PLINK, Haploview and THESIAS softwares. Results Fifteen variations were observed in the MFRP gene of which, rs36015759 (c.492C > T, T164T) in exon 5 was distributed at a high frequency in the controls and significantly associated with a low risk for myopia (P = 4.10 ∗ e− 07 OR < 1.0). An increased frequency for the coding haplotype block [CGTCGG] harboring rs36015759 was observed in controls (31%) than cases (8%) that also correlated with a decreased mean AL (− 1.35085; P = 0.000444) by THESIAS analysis. The ‘T’ allele of rs36015759 was predicted to abolish the binding site for splicing enhancer (SRp40) by FASTSNP analysis. Conclusion Myopia is a complex disorder influenced by genetic and environmental factors. Our work shows evidence of association of a specific MFRP haplotype which was more prevalent in controls with decreased AL. However, replication and functional studies are warranted to confirm these findings. PMID:25606400

  2. Inference of Selection Based on Temporal Genetic Differentiation in the Study of Highly Polymorphic Multigene Families

    PubMed Central

    McMullan, Mark; van Oosterhout, Cock

    2012-01-01

    The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the ‘turnover’ of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC) of guppies (Poecilia reticulata) to study the turnover rate of alleles (temporal genetic differentiation, G'ST). Temporal fluctuations in MHC allele frequencies can be ≥≤order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1) overdominant selection, (2) fluctuating population size within a metapopulation, and (3) the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial FST outlier analysis may obscure the signal of selection. PMID:22900006

  3. High urban breeding densities do not disrupt genetic monogamy in a bird species.

    PubMed

    Rodriguez-Martínez, Sol; Carrete, Martina; Roques, Séverine; Rebolo-Ifrán, Natalia; Tella, José L

    2014-01-01

    Urbanization causes widespread endangerment of biodiversity worldwide. However, some species successfully colonize cities reaching higher densities than in their rural habitats. In these cases, although urban city dwellers may apparently be taking advantage of these new environments, they also face new ecological conditions that may induce behavioural changes. For example, the frequency of alternative reproductive behaviours such as extra-pair paternity and intraspecific brood parasitism might increase with breeding densities. Here, using a panel of 17 microsatellites, we tested whether increments in breeding densities such as those associated with urban invasion processes alter genetic monogamy in the burrowing owl Athene cunicularia. Our results show low rates of extra-pair paternity (1.47%), but relatively high levels of intraspecific brood parasitism (8.82%). However, we were not able to detect differences in the frequency at which either alternative reproductive behaviour occurs along a strong breeding density gradient. Further research is needed to properly ascertain the role of other social and ecological factors in the frequency at which this species presents alternative reproductive strategies. Meanwhile, our results suggest that genetic monogamy is maintained despite the increment in conspecific density associated with a recent urban invasion process. PMID:24614308

  4. High Urban Breeding Densities Do Not Disrupt Genetic Monogamy in a Bird Species

    PubMed Central

    Rodriguez-Martínez, Sol; Carrete, Martina; Roques, Séverine; Rebolo-Ifrán, Natalia; Tella, José L.

    2014-01-01

    Urbanization causes widespread endangerment of biodiversity worldwide. However, some species successfully colonize cities reaching higher densities than in their rural habitats. In these cases, although urban city dwellers may apparently be taking advantage of these new environments, they also face new ecological conditions that may induce behavioural changes. For example, the frequency of alternative reproductive behaviours such as extra-pair paternity and intraspecific brood parasitism might increase with breeding densities. Here, using a panel of 17 microsatellites, we tested whether increments in breeding densities such as those associated with urban invasion processes alter genetic monogamy in the burrowing owl Athene cunicularia. Our results show low rates of extra-pair paternity (1.47%), but relatively high levels of intraspecific brood parasitism (8.82%). However, we were not able to detect differences in the frequency at which either alternative reproductive behaviour occurs along a strong breeding density gradient. Further research is needed to properly ascertain the role of other social and ecological factors in the frequency at which this species presents alternative reproductive strategies. Meanwhile, our results suggest that genetic monogamy is maintained despite the increment in conspecific density associated with a recent urban invasion process. PMID:24614308

  5. High urban breeding densities do not disrupt genetic monogamy in a bird species.

    PubMed

    Rodriguez-Martínez, Sol; Carrete, Martina; Roques, Séverine; Rebolo-Ifrán, Natalia; Tella, José L

    2014-01-01

    Urbanization causes widespread endangerment of biodiversity worldwide. However, some species successfully colonize cities reaching higher densities than in their rural habitats. In these cases, although urban city dwellers may apparently be taking advantage of these new environments, they also face new ecological conditions that may induce behavioural changes. For example, the frequency of alternative reproductive behaviours such as extra-pair paternity and intraspecific brood parasitism might increase with breeding densities. Here, using a panel of 17 microsatellites, we tested whether increments in breeding densities such as those associated with urban invasion processes alter genetic monogamy in the burrowing owl Athene cunicularia. Our results show low rates of extra-pair paternity (1.47%), but relatively high levels of intraspecific brood parasitism (8.82%). However, we were not able to detect differences in the frequency at which either alternative reproductive behaviour occurs along a strong breeding density gradient. Further research is needed to properly ascertain the role of other social and ecological factors in the frequency at which this species presents alternative reproductive strategies. Meanwhile, our results suggest that genetic monogamy is maintained despite the increment in conspecific density associated with a recent urban invasion process.

  6. Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing.

    PubMed

    Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-Qi; Tan, Cong; Li, Chengdao

    2015-01-01

    Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species. PMID:26182149

  7. Topology of genetic associations between regional gray matter volume and intellectual ability: Evidence for a high capacity network.

    PubMed

    Bohlken, Marc M; Brouwer, Rachel M; Mandl, René C W; Hedman, Anna M; van den Heuvel, Martijn P; van Haren, Neeltje E M; Kahn, René S; Pol, Hilleke E Hulshoff

    2016-01-01

    Intelligence is associated with a network of distributed gray matter areas including the frontal and parietal higher association cortices and primary processing areas of the temporal and occipital lobes. Efficient information transfer between gray matter regions implicated in intelligence is thought to be critical for this trait to emerge. Genetic factors implicated in intelligence and gray matter may promote a high capacity for information transfer. Whether these genetic factors act globally or on local gray matter areas separately is not known. Brain maps of phenotypic and genetic associations between gray matter volume and intelligence were made using structural equation modeling of 3T MRI T1-weighted scans acquired in 167 adult twins of the newly acquired U-TWIN cohort. Subsequently, structural connectivity analyses (DTI) were performed to test the hypothesis that gray matter regions associated with intellectual ability form a densely connected core. Gray matter regions associated with intellectual ability were situated in the right prefrontal, bilateral temporal, bilateral parietal, right occipital and subcortical regions. Regions implicated in intelligence had high structural connectivity density compared to 10,000 reference networks (p=0.031). The genetic association with intelligence was for 39% explained by a genetic source unique to these regions (independent of total brain volume), this source specifically implicated the right supramarginal gyrus. Using a twin design, we show that intelligence is genetically represented in a spatially distributed and densely connected network of gray matter regions providing a high capacity infrastructure. Although genes for intelligence have overlap with those for total brain volume, we present evidence that there are genes for intelligence that act specifically on the subset of brain areas that form an efficient brain network.

  8. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    USGS Publications Warehouse

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  9. Genetic variants on chromosome 1q41 influence ocular axial length and high myopia.

    PubMed

    Fan, Qiao; Barathi, Veluchamy A; Cheng, Ching-Yu; Zhou, Xin; Meguro, Akira; Nakata, Isao; Khor, Chiea-Chuen; Goh, Liang-Kee; Li, Yi-Ju; Lim, Wan'e; Ho, Candice E H; Hawthorne, Felicia; Zheng, Yingfeng; Chua, Daniel; Inoko, Hidetoshi; Yamashiro, Kenji; Ohno-Matsui, Kyoko; Matsuo, Keitaro; Matsuda, Fumihiko; Vithana, Eranga; Seielstad, Mark; Mizuki, Nobuhisa; Beuerman, Roger W; Tai, E-Shyong; Yoshimura, Nagahisa; Aung, Tin; Young, Terri L; Wong, Tien-Yin; Teo, Yik-Ying; Saw, Seang-Mei

    2012-01-01

    As one of the leading causes of visual impairment and blindness, myopia poses a significant public health burden in Asia. The primary determinant of myopia is an elongated ocular axial length (AL). Here we report a meta-analysis of three genome-wide association studies on AL conducted in 1,860 Chinese adults, 929 Chinese children, and 2,155 Malay adults. We identified a genetic locus on chromosome 1q41 harboring the zinc-finger 11B pseudogene ZC3H11B showing genome-wide significant association with AL variation (rs4373767, β = -0.16 mm per minor allele, P(meta) =2.69 × 10(-10)). The minor C allele of rs4373767 was also observed to significantly associate with decreased susceptibility to high myopia (per-allele odds ratio (OR) =0.75, 95% CI: 0.68-0.84, P(meta) =4.38 × 10(-7)) in 1,118 highly myopic cases and 5,433 controls. ZC3H11B and two neighboring genes SLC30A10 and LYPLAL1 were expressed in the human neural retina, retinal pigment epithelium, and sclera. In an experimental myopia mouse model, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for the murine genes ZC3H11A, SLC30A10, and LYPLAL1. This supports the likely role of genetic variants at chromosome 1q41 in influencing AL variation and high myopia.

  10. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

    PubMed

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

  11. High Genetic Diversity and Novelty in Eukaryotic Plankton Assemblages Inhabiting Saline Lakes in the Qaidam Basin

    PubMed Central

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution. PMID:25401703

  12. Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog.

    PubMed

    Wang, Ian J; Summers, Kyle

    2010-02-01

    Phenotypic and genetic divergence can be influenced by a variety of factors, including sexual and natural selection, genetic drift and geographic isolation. Investigating the roles of these factors in natural systems can provide insight into the relative influences of allopatric and ecological modes of biological diversification in nature. The strawberry poison frog, Dendrobates pumilio, presents an excellent opportunity for this kind of research, displaying a diverse array of colour morphs and inhabiting a heterogeneous landscape that includes oceanic islands, fragmented rainforest patches and wide expanses of suitable habitat. In this study, we use 15 highly polymorphic microsatellite loci to estimate population structure and gene flow among populations from across the range of D. pumilio and a causal modelling framework to statistically test 12 hypotheses regarding the geographic and phenotypic variables that explain genetic differentiation within this system. Our results demonstrate that the genetic distance between populations is most strongly associated with differences in dorsal coloration. Previous experimental studies have shown that phenotypic differences can result in sexual and natural selection against non-native phenotypes, and our results now show that these forces lead to genetic isolation between different colour morphs in the wild, presenting a potential case of incipient speciation through selection. PMID:20025652

  13. High levels of genetic diversity and population structure in an endemic and rare species: implications for conservation

    PubMed Central

    Turchetto, Caroline; Segatto, Ana Lúcia A.; Mäder, Geraldo; Rodrigues, Daniele M.; Bonatto, Sandro L.; Freitas, Loreta B.

    2016-01-01

    The analysis of genetic structure and variability of isolated species is of critical importance in evaluating whether stochastic or human-caused factors are affecting rare species. Low genetic diversity compromises the ability of populations to evolve and reduces their chances of survival under environmental changes. Petunia secreta, a rare and endemic species, is an annual and heliophilous herb that is bee-pollinated and easily recognizable by its purple and salverform corolla. It was described as a new species of the Petunia genus in 2005. Few individuals of P. secreta have been observed in nature and little is known about this species. All the natural populations of P. secreta that were found were studied using 15 microsatellite loci, two intergenic plastid sequences and morphological traits. Statistical analysis was performed to describe the genetic diversity of this rare species and the results compared with those of more widespread and frequent Petunia species from the same geographic area to understand whether factors associated with population size could affect rare species of this genus. The results showed that despite its rarity, P. secreta presented high genetic diversity that was equivalent to or even higher than that of widespread Petunia species. It was shown that this species is divided into two evolutionary lineages, and the genetic differentiation indices between them and other congeneric species presented different patterns. The major risk to P. secreta maintenance is its rarity, suggesting the necessity of a preservation programme and more biological and evolutionary studies that handle the two evolutionary lineages independently. PMID:26768602

  14. High levels of genetic diversity and population structure in an endemic and rare species: implications for conservation.

    PubMed

    Turchetto, Caroline; Segatto, Ana Lúcia A; Mäder, Geraldo; Rodrigues, Daniele M; Bonatto, Sandro L; Freitas, Loreta B

    2016-01-01

    The analysis of genetic structure and variability of isolated species is of critical importance in evaluating whether stochastic or human-caused factors are affecting rare species. Low genetic diversity compromises the ability of populations to evolve and reduces their chances of survival under environmental changes. Petunia secreta, a rare and endemic species, is an annual and heliophilous herb that is bee-pollinated and easily recognizable by its purple and salverform corolla. It was described as a new species of the Petunia genus in 2005. Few individuals of P. secreta have been observed in nature and little is known about this species. All the natural populations of P. secreta that were found were studied using 15 microsatellite loci, two intergenic plastid sequences and morphological traits. Statistical analysis was performed to describe the genetic diversity of this rare species and the results compared with those of more widespread and frequent Petunia species from the same geographic area to understand whether factors associated with population size could affect rare species of this genus. The results showed that despite its rarity, P. secreta presented high genetic diversity that was equivalent to or even higher than that of widespread Petunia species. It was shown that this species is divided into two evolutionary lineages, and the genetic differentiation indices between them and other congeneric species presented different patterns. The major risk to P. secreta maintenance is its rarity, suggesting the necessity of a preservation programme and more biological and evolutionary studies that handle the two evolutionary lineages independently. PMID:26768602

  15. Microsatellites and the Genetics of Highly Selfing Populations in the Freshwater Snail Bulinus Truncatus

    PubMed Central

    Viard, F.; Bremond, P.; Labbo, R.; Justy, F.; Delay, B.; Jarne, P.

    1996-01-01

    Hermaphrodite tropical freshwater snails provide a good opportunity to study the effects of mating system and genetic drift on population genetic structure because they are self-fertile and they occupy transient patchily distributed habitats (ponds). Up to now the lack of detectable allozyme polymorphism prevented any intrapopulation studies. In this paper, we examine the consequences of selfing and bottlenecks on genetic polymorphism using microsatellite markers in 14 natural populations (under a hierarchical sampling design) of the hermaphrodite freshwater snail Bulinus truncatus. These population genetics data allowed us to discuss the currently available mutation models for microsatellite sequences. Microsatellite markers revealed an unexpectedly high levels of genetic variation with <=41 alleles for one locus and gene diversity of 0.20-0.75 among populations. The values of any estimator of F(is) indicate high selfing rates in all populations. Linkage disequilibria observed at all loci for some populations may also indicate high levels of inbreeding. The large extent of genetic differentiation measured by F(st), R(st) or by a test for homogeneity between genic distributions is explained by both selfing and bottlenecks. Despite a limited gene flow, migration events could be detected when comparing different populations within ponds. PMID:8846901

  16. Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans

    PubMed Central

    Kihara, Terue C.; Laurent, Stefan; Kodami, Sahar; Martinez Arbizu, Pedro

    2016-01-01

    Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima’s D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid

  17. Microsatellites reveal high genetic diversity within colonies of Camponotus ants.

    PubMed

    Gertsch, P; Pamilo, P; Varvio, S L

    1995-04-01

    In order to characterize the sociogenetic structure of colonies in the carpenter ants Camponotus herculeanus and C. ligniperda, we have developed microsatellite markers. The three loci studied were either fixed for different alleles in the two species or showed different patterns of polymorphisms. Genotyping of workers and males showed that the broods of C. ligniperda include several matrilines, a rare phenomenon in the genus. Five alleles from a locus polymorphic in both species were sequenced from the respective PCR-products. A part of the length variation appeared to be due to changes outside the repeat sequence, and some PCR products of an equal length had a different number of dinucleotide repeats.

  18. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

    PubMed Central

    Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance. PMID:27494320

  19. Microsatellites reveal high genetic diversity within colonies of Camponotus ants.

    PubMed

    Gertsch, P; Pamilo, P; Varvio, S L

    1995-04-01

    In order to characterize the sociogenetic structure of colonies in the carpenter ants Camponotus herculeanus and C. ligniperda, we have developed microsatellite markers. The three loci studied were either fixed for different alleles in the two species or showed different patterns of polymorphisms. Genotyping of workers and males showed that the broods of C. ligniperda include several matrilines, a rare phenomenon in the genus. Five alleles from a locus polymorphic in both species were sequenced from the respective PCR-products. A part of the length variation appeared to be due to changes outside the repeat sequence, and some PCR products of an equal length had a different number of dinucleotide repeats. PMID:7735528

  20. Genetic and Sex-Specific Transgenerational Effects of a High Fat Diet in Drosophila melanogaster

    PubMed Central

    Dew-Budd, Kelly; Jarnigan, Julie

    2016-01-01

    An organism's phenotype is the product of its environment and genotype, but an ancestor’s environment can also be a contributing factor. The recent increase in caloric intake and decrease in physical activity of developed nations' populations is contributing to deteriorating health and making the study of the longer term impacts of a changing lifestyle a priority. The dietary habits of ancestors have been shown to affect phenotype in several organisms, including humans, mice, and the fruit fly. Whether the ancestral dietary effect is purely environmental or if there is a genetic interaction with the environment passed down for multiple generations, has not been determined previously. Here we used the fruit fly, Drosophila melanogaster, to investigate the genetic, sex-specific, and environmental effects of a high fat diet for three generations’ on pupal body weights across ten genotypes. We also tested for genotype-specific transgenerational effects on metabolic pools and egg size across three genotypes. We showed that there were substantial differences in transgenerational responses to ancestral diet between genotypes and sexes through both first and second descendant generations. Additionally, there were differences in phenotypes between maternally and paternally inherited dietary effects. We also found a treated organism’s reaction to a high fat diet was not a consistent predictor of its untreated descendants’ phenotype. The implication of these results is that, given our interest in understanding and preventing metabolic diseases like obesity, we need to consider the contribution of ancestral environmental experiences. However, we need to be cautious when drawing population-level generalization from small studies because transgenerational effects are likely to exhibit substantial sex and genotype specificity. PMID:27518304

  1. Genetic and Sex-Specific Transgenerational Effects of a High Fat Diet in Drosophila melanogaster.

    PubMed

    Dew-Budd, Kelly; Jarnigan, Julie; Reed, Laura K

    2016-01-01

    An organism's phenotype is the product of its environment and genotype, but an ancestor's environment can also be a contributing factor. The recent increase in caloric intake and decrease in physical activity of developed nations' populations is contributing to deteriorating health and making the study of the longer term impacts of a changing lifestyle a priority. The dietary habits of ancestors have been shown to affect phenotype in several organisms, including humans, mice, and the fruit fly. Whether the ancestral dietary effect is purely environmental or if there is a genetic interaction with the environment passed down for multiple generations, has not been determined previously. Here we used the fruit fly, Drosophila melanogaster, to investigate the genetic, sex-specific, and environmental effects of a high fat diet for three generations' on pupal body weights across ten genotypes. We also tested for genotype-specific transgenerational effects on metabolic pools and egg size across three genotypes. We showed that there were substantial differences in transgenerational responses to ancestral diet between genotypes and sexes through both first and second descendant generations. Additionally, there were differences in phenotypes between maternally and paternally inherited dietary effects. We also found a treated organism's reaction to a high fat diet was not a consistent predictor of its untreated descendants' phenotype. The implication of these results is that, given our interest in understanding and preventing metabolic diseases like obesity, we need to consider the contribution of ancestral environmental experiences. However, we need to be cautious when drawing population-level generalization from small studies because transgenerational effects are likely to exhibit substantial sex and genotype specificity. PMID:27518304

  2. Amerindians show association to obesity with adiponectin gene SNP45 and SNP276: population genetics of a food intake control and "thrifty" gene.

    PubMed

    Arnaiz-Villena, Antonio; Fernández-Honrado, Mercedes; Rey, Diego; Enríquez-de-Salamanca, Mercedes; Abd-El-Fatah-Khalil, Sedeka; Arribas, Ignacio; Coca, Carmen; Algora, Manuel; Areces, Cristina

    2013-02-01

    Adiponectin gene polymorphisms SNP45 and SNP276 have been related to metabolic syndrome (MS) and related pathologies, including obesity. However results of associations are contradictory depending on which population is studied. In the present study, these adiponectin SNPs are for the first time studied in Amerindians. Allele frequencies are obtained and comparison with obesity and other MS related parameters are performed. Amerindians were also defined by characteristic HLA genes. Our main results are: (1) SNP276 T is associated to low diastolic blood pressure in Amerindians, (2) SNP45 G allele is correlated with obesity in female but not in male Amerindians, (3) SNP45/SNP276 T/G haplotype in total obese/non-obese subjects tends to show a linkage with non-obese Amerindians, (4) SNP45/SNP276 T/T haplotype is linked to obese Amerindian males. Also, a world population study is carried out finding that SNP45 T and SNP276 T alleles are the most frequent in African Blacks and are found significantly in lower frequencies in Europeans and Asians. This together with the fact that there is a linkage of this haplotype to obese Amerindian males suggest that evolutionary forces related to famine (or population density in relation with available food) may have shaped world population adiponectin polymorphism frequencies. PMID:23108996

  3. A New Orbivirus Isolated from Mosquitoes in North-Western Australia Shows Antigenic and Genetic Similarity to Corriparta Virus but Does Not Replicate in Vertebrate Cells

    PubMed Central

    Harrison, Jessica J.; Warrilow, David; McLean, Breeanna J.; Watterson, Daniel; O’Brien, Caitlin A.; Colmant, Agathe M.G.; Johansen, Cheryl A.; Barnard, Ross T.; Hall-Mendelin, Sonja; Davis, Steven S.; Hall, Roy A.; Hobson-Peters, Jody

    2016-01-01

    The discovery and characterisation of new mosquito-borne viruses provides valuable information on the biodiversity of vector-borne viruses and important insights into their evolution. In this study, a broad-spectrum virus screening system, based on the detection of long double-stranded RNA in inoculated cell cultures, was used to investigate the presence of novel viruses in mosquito populations of northern Australia. We detected and isolated a new virus (tentatively named Parry’s Lagoon virus, PLV) from Culex annulirostris, Culex pullus, Mansonia uniformis and Aedes normanensis mosquitoes that shares genomic sequence similarities to Corriparta virus (CORV), a member of the Orbivirus genus of the family Reoviridae. Despite moderate to high (72.2% to 92.2%) amino acid identity across all proteins when compared to CORV, and demonstration of antigenic relatedness, PLV did not replicate in several vertebrate cell lines that were permissive to CORV. This striking phenotypic difference suggests that PLV has evolved to have a very restricted host range, indicative of a mosquito-only life cycle. PMID:27213426

  4. Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction.

    PubMed

    Dunne, Jennifer A; Labandeira, Conrad C; Williams, Richard J

    2014-05-01

    Generalities of food web structure have been identified for extant ecosystems. However, the trophic organization of ancient ecosystems is unresolved, as prior studies of fossil webs have been limited by low-resolution, high-uncertainty data. We compiled highly resolved, well-documented feeding interaction data for 700 taxa from the 48 million-year-old latest early Eocene Messel Shale, which contains a species assemblage that developed after an interval of protracted environmental and biotal change during and following the end-Cretaceous extinction. We compared the network structure of Messel lake and forest food webs to extant webs using analyses that account for scale dependence of structure with diversity and complexity. The Messel lake web, with 94 taxa, displays unambiguous similarities in structure to extant webs. While the Messel forest web, with 630 taxa, displays differences compared to extant webs, they appear to result from high diversity and resolution of insect-plant interactions, rather than substantive differences in structure. The evidence presented here suggests that modern trophic organization developed along with the modern Messel biota during an 18 Myr interval of dramatic post-extinction change. Our study also has methodological implications, as the Messel forest web analysis highlights limitations of current food web data and models.

  5. Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction

    PubMed Central

    Dunne, Jennifer A.; Labandeira, Conrad C.; Williams, Richard J.

    2014-01-01

    Generalities of food web structure have been identified for extant ecosystems. However, the trophic organization of ancient ecosystems is unresolved, as prior studies of fossil webs have been limited by low-resolution, high-uncertainty data. We compiled highly resolved, well-documented feeding interaction data for 700 taxa from the 48 million-year-old latest early Eocene Messel Shale, which contains a species assemblage that developed after an interval of protracted environmental and biotal change during and following the end-Cretaceous extinction. We compared the network structure of Messel lake and forest food webs to extant webs using analyses that account for scale dependence of structure with diversity and complexity. The Messel lake web, with 94 taxa, displays unambiguous similarities in structure to extant webs. While the Messel forest web, with 630 taxa, displays differences compared to extant webs, they appear to result from high diversity and resolution of insect–plant interactions, rather than substantive differences in structure. The evidence presented here suggests that modern trophic organization developed along with the modern Messel biota during an 18 Myr interval of dramatic post-extinction change. Our study also has methodological implications, as the Messel forest web analysis highlights limitations of current food web data and models. PMID:24648225

  6. The M2 selective antagonist AF-DX 116 shows high affinity for muscarine receptors in bovine tracheal membranes.

    PubMed

    Roffel, A F; in't Hout, W G; de Zeeuw, R A; Zaagsma, J

    1987-05-01

    We have characterized the muscarine receptors in bovine tracheal and left ventricular membranes using 3H-dexetimide/pirenzepine and 3H-dexetimide/AF-DX 116 competition studies. Pirenzepine exhibited low (M2) affinity binding to both preparations; Kd was 590 nM in left ventricle and 463 nM in trachea. AF-DX 116 exhibited high (M2) affinity binding to left ventricle (Kd = 95.6 nM); in tracheal membranes it bound with high (M2) affinity (Kd = 40.7 nM) to 74% of the receptors and with low (M3) affinity (Kd = 2.26 microM) to 26% of the receptors. It is concluded that bovine tracheal muscle membranes contain a heterogeneous population of muscarine binding sites, the majority having M2 (heart) subtype characteristics and being located on the smooth muscle membranes; a minority having M3 (exocrine gland) subtype characteristics and presumed to be located in submucosal glands. This is the first report of high affinity binding of AF-DX 116 to non-cardiac peripheral muscarine receptors. PMID:3614390

  7. Genetic Structure Is Associated with Phenotypic Divergence in Floral Traits and Reproductive Investment in a High-Altitude Orchid from the Iron Quadrangle, Southeastern Brazil

    PubMed Central

    Leles, Bruno; Chaves, Anderson V.; Russo, Philip; Batista, João A. N.; Lovato, Maria Bernadete

    2015-01-01

    Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops. PMID:25756994

  8. Genetic algorithms

    NASA Technical Reports Server (NTRS)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  9. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.

    PubMed

    Verde, Ignazio; Abbott, Albert G; Scalabrin, Simone; Jung, Sook; Shu, Shengqiang; Marroni, Fabio; Zhebentyayeva, Tatyana; Dettori, Maria Teresa; Grimwood, Jane; Cattonaro, Federica; Zuccolo, Andrea; Rossini, Laura; Jenkins, Jerry; Vendramin, Elisa; Meisel, Lee A; Decroocq, Veronique; Sosinski, Bryon; Prochnik, Simon; Mitros, Therese; Policriti, Alberto; Cipriani, Guido; Dondini, Luca; Ficklin, Stephen; Goodstein, David M; Xuan, Pengfei; Del Fabbro, Cristian; Aramini, Valeria; Copetti, Dario; Gonzalez, Susana; Horner, David S; Falchi, Rachele; Lucas, Susan; Mica, Erica; Maldonado, Jonathan; Lazzari, Barbara; Bielenberg, Douglas; Pirona, Raul; Miculan, Mara; Barakat, Abdelali; Testolin, Raffaele; Stella, Alessandra; Tartarini, Stefano; Tonutti, Pietro; Arús, Pere; Orellana, Ariel; Wells, Christina; Main, Dorrie; Vizzotto, Giannina; Silva, Herman; Salamini, Francesco; Schmutz, Jeremy; Morgante, Michele; Rokhsar, Daniel S

    2013-05-01

    Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

  10. Hyperthermostable Thermotoga maritima xylanase XYN10B shows high activity at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids.

    PubMed

    Yu, Tianyi; Anbarasan, Sasikala; Wang, Yawei; Telli, Kübra; Aslan, Aşkın Sevinç; Su, Zhengding; Zhou, Yin; Zhang, Li; Iivonen, Piia; Havukainen, Sami; Mentunen, Tero; Hummel, Michael; Sixta, Herbert; Binay, Baris; Turunen, Ossi; Xiong, Hairong

    2016-07-01

    The gene of Thermotoga maritima GH10 xylanase (TmXYN10B) was synthesised to study the extreme limits of this hyperthermostable enzyme at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids (ILs). TmXYN10B expressed from Pichia pastoris showed maximal activity at 100 °C and retained 92 % of maximal activity at 105 °C in a 30-min assay. Although the temperature optimum of activity was lowered by 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc), TmXYN10B retained partial activity in 15-35 % hydrophilic ILs, even at 75-90 °C. TmXYN10B retained over 80 % of its activity at 90 °C in 15 % [EMIM]OAc and 15-25 % 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DMP) during 22-h reactions. [EMIM]OAc may rigidify the enzyme and lower V max. However, only minor changes in kinetic parameter K m showed that competitive inhibition by [EMIM]OAc of TmXYN10B is minimal. In conclusion, when extended enzymatic reactions under extreme conditions are required, TmXYN10B shows extraordinary potential. PMID:27240671

  11. CZ415, a Highly Selective mTOR Inhibitor Showing in Vivo Efficacy in a Collagen Induced Arthritis Model.

    PubMed

    Cansfield, Andrew D; Ladduwahetty, Tammy; Sunose, Mihiro; Ellard, Katie; Lynch, Rosemary; Newton, Anthea L; Lewis, Ann; Bennett, Gavin; Zinn, Nico; Thomson, Douglas W; Rüger, Anne J; Feutrill, John T; Rausch, Oliver; Watt, Alan P; Bergamini, Giovanna

    2016-08-11

    CZ415, a potent ATP-competitive mTOR inhibitor with unprecedented selectivity over any other kinase is described. In addition to a comprehensive characterization of its activities in vitro, in vitro ADME, and in vivo pharmacokinetic data are reported. The suitability of this inhibitor for studying in vivo mTOR biology is demonstrated in a mechanistic mouse model monitoring mTOR proximal downstream phosphorylation signaling. Furthermore, the compound reported here is the first ATP-competitive mTOR inhibitor described to show efficacy in a semitherapeutic collagen induced arthritis (CIA) mouse model. PMID:27563401

  12. Maternal Style Selectively Shapes Amygdalar Development and Social Behavior in Rats Genetically Prone to High Anxiety

    PubMed Central

    Cohen, Joshua L.; Glover, Matthew E.; Pugh, Phyllis C.; Fant, Andrew D.; Simmons, Rebecca K.; Akil, Huda; Kerman, Ilan A.; Clinton, Sarah M.

    2015-01-01

    The early-life environment critically influences neurodevelopment and later psychological health. To elucidate neural and environmental elements that shape emotional behavior, we developed a rat model of individual differences in temperament and environmental reactivity. We selectively bred rats for high vs. low behavioral response to novelty and found that high reactive (bHR) rats display greater risk-taking, impulsivity, and aggression relative to low reactive (bLR) rats, which show high levels of anxiety/depression-like behavior and certain stress vulnerability. The bHR/bLR traits are heritable but prior work revealed bHR/bLR maternal style differences, with bLR dams showing more maternal attention than bHRs. The present study implemented a cross-fostering paradigm to examine the contribution of maternal behavior on bLR offspring’s brain development and emotional behavior. bLR offspring were reared by biological bLR mothers or fostered to a bLR or bHR mother and then evaluated to determine effects on: 1) developmental gene expression in the hippocampus and amygdala; and 2) adult anxiety/depression-like behavior. Genome-wide expression profiling showed that cross-fostering bLR rats to bHR mothers shifted developmental gene expression in the amygdala (but not hippocampus), reduced adult anxiety and enhanced social interaction. Our findings illustrate how an early-life manipulation such as cross-fostering changes the brain’s developmental trajectory and ultimately impacts adult behavior. Moreover, while earlier studies highlighted hippocampal differences contributing to the bHR/bLR phenotypes, our results point to a role of the amygdala as well. Future work will pursue genetic and cellular mechanisms within the amygdala that contribute to bHR/bLR behavior either at baseline or following environmental manipulations. PMID:25791846

  13. The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages.

    PubMed

    Mariano, Rachelle; Wuchty, Stefan; Vizoso-Pinto, Maria G; Häuser, Roman; Uetz, Peter

    2016-01-01

    Although an abundance of bacteriophages exists, little is known about interactions between their proteins and those of their bacterial hosts. Here, we experimentally determined the phage-host interactomes of the phages Dp-1 and Cp-1 and their underlying protein interaction network in the host Streptococcus pneumoniae. We compared our results to the interaction patterns of E. coli phages lambda and T7. Dp-1 and Cp-1 target highly connected host proteins, occupy central network positions, and reach many protein clusters through the interactions of their targets. In turn, lambda and T7 targets cluster to conserved and essential proteins in E. coli, while such patterns were largely absent in S. pneumoniae. Furthermore, targets in E. coli were mutually strongly intertwined, while targets of Dp-1 and Cp-1 were strongly connected through essential and orthologous proteins in their immediate network vicinity. In both phage-host systems, the impact of phages on their protein targets appears to extend from their network neighbors, since proteins that interact with phage targets were located in central network positions, have a strong topologically disruptive effect and touch complexes with high functional heterogeneity. Such observations suggest that the phages, biological impact is accomplished through a surprisingly limited topological reach of their targets. PMID:27103053

  14. The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages

    PubMed Central

    Mariano, Rachelle; Wuchty, Stefan; Vizoso-Pinto, Maria G.; Häuser, Roman; Uetz, Peter

    2016-01-01

    Although an abundance of bacteriophages exists, little is known about interactions between their proteins and those of their bacterial hosts. Here, we experimentally determined the phage-host interactomes of the phages Dp-1 and Cp-1 and their underlying protein interaction network in the host Streptococcus pneumoniae. We compared our results to the interaction patterns of E. coli phages lambda and T7. Dp-1 and Cp-1 target highly connected host proteins, occupy central network positions, and reach many protein clusters through the interactions of their targets. In turn, lambda and T7 targets cluster to conserved and essential proteins in E. coli, while such patterns were largely absent in S. pneumoniae. Furthermore, targets in E. coli were mutually strongly intertwined, while targets of Dp-1 and Cp-1 were strongly connected through essential and orthologous proteins in their immediate network vicinity. In both phage-host systems, the impact of phages on their protein targets appears to extend from their network neighbors, since proteins that interact with phage targets were located in central network positions, have a strong topologically disruptive effect and touch complexes with high functional heterogeneity. Such observations suggest that the phages, biological impact is accomplished through a surprisingly limited topological reach of their targets. PMID:27103053

  15. The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages.

    PubMed

    Mariano, Rachelle; Wuchty, Stefan; Vizoso-Pinto, Maria G; Häuser, Roman; Uetz, Peter

    2016-04-22

    Although an abundance of bacteriophages exists, little is known about interactions between their proteins and those of their bacterial hosts. Here, we experimentally determined the phage-host interactomes of the phages Dp-1 and Cp-1 and their underlying protein interaction network in the host Streptococcus pneumoniae. We compared our results to the interaction patterns of E. coli phages lambda and T7. Dp-1 and Cp-1 target highly connected host proteins, occupy central network positions, and reach many protein clusters through the interactions of their targets. In turn, lambda and T7 targets cluster to conserved and essential proteins in E. coli, while such patterns were largely absent in S. pneumoniae. Furthermore, targets in E. coli were mutually strongly intertwined, while targets of Dp-1 and Cp-1 were strongly connected through essential and orthologous proteins in their immediate network vicinity. In both phage-host systems, the impact of phages on their protein targets appears to extend from their network neighbors, since proteins that interact with phage targets were located in central network positions, have a strong topologically disruptive effect and touch complexes with high functional heterogeneity. Such observations suggest that the phages, biological impact is accomplished through a surprisingly limited topological reach of their targets.

  16. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    PubMed

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists. PMID:23487323

  17. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    PubMed

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  18. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    PubMed

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  19. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    PubMed

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  20. High-gain nonlinear observer for simple genetic regulation process

    NASA Astrophysics Data System (ADS)

    Torres, L. A.; Ibarra-Junquera, V.; Escalante-Minakata, P.; Rosu, H. C.

    2007-07-01

    High-gain nonlinear observers occur in the nonlinear automatic control theory and are in standard usage in chemical engineering processes. We apply such a type of analysis in the context of a very simple one-gene regulation circuit. In general, an observer combines an analytical differential-equation-based model with partial measurement of the system in order to estimate the non-measured state variables. We use one of the simplest observers, that of Gauthier et al., which is a copy of the original system plus a correction term which is easy to calculate. For the illustration of this procedure, we employ a biological model, recently adapted from Goodwin's old book by De Jong, in which one plays with the dynamics of the concentrations of the messenger RNA coding for a given protein, the protein itself, and a single metabolite. Using the observer instead of the metabolite, it is possible to rebuild the non-measured concentrations of the mRNA and the protein.

  1. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations

    PubMed Central

    Iacchei, Matthew; Ben-Horin, Tal; Selkoe, Kimberly A; Bird, Christopher E; García-Rodríguez, Francisco J; Toonen, Robert J

    2013-01-01

    We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites (FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species’ 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (Dest_Chao, R2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low FST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal. PMID:23802550

  2. Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation.

    PubMed

    Sunny, Armando; Monroy-Vilchis, Octavio; Zarco-González, Martha M; Mendoza-Martínez, Germán David; Martínez-Gómez, Daniel

    2015-12-01

    It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices. PMID:26497875

  3. Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation.

    PubMed

    Sunny, Armando; Monroy-Vilchis, Octavio; Zarco-González, Martha M; Mendoza-Martínez, Germán David; Martínez-Gómez, Daniel

    2015-12-01

    It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices.

  4. [Recent progress in gene mapping through high-throughput sequencing technology and forward genetic approaches].

    PubMed

    Lu, Cairui; Zou, Changsong; Song, Guoli

    2015-08-01

    Traditional gene mapping using forward genetic approaches is conducted primarily through construction of a genetic linkage map, the process of which is tedious and time-consuming, and often results in low accuracy of mapping and large mapping intervals. With the rapid development of high-throughput sequencing technology and decreasing cost of sequencing, a variety of simple and quick methods of gene mapping through sequencing have been developed, including direct sequencing of the mutant genome, sequencing of selective mutant DNA pooling, genetic map construction through sequencing of individuals in population, as well as sequencing of transcriptome and partial genome. These methods can be used to identify mutations at the nucleotide level and has been applied in complex genetic background. Recent reports have shown that sequencing mapping could be even done without the reference of genome sequence, hybridization, and genetic linkage information, which made it possible to perform forward genetic study in many non-model species. In this review, we summarized these new technologies and their application in gene mapping.

  5. Nuclear genetic diversity in human lice (Pediculus humanus) reveals continental differences and high inbreeding among worldwide populations.

    PubMed

    Ascunce, Marina S; Toups, Melissa A; Kassu, Gebreyes; Fane, Jackie; Scholl, Katlyn; Reed, David L

    2013-01-01

    Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus). This species is composed of two ecotypes: the head louse (Pediculus humanus capitis De Geer), and the clothing (body) louse (Pediculus humanus humanus Linnaeus). Hundreds of millions of head louse infestations affect children every year, and this number is on the rise, in part because of increased resistance to insecticides. Clothing lice affect mostly homeless and refugee-camp populations and although they are less prevalent than head lice, the medical consequences are more severe because they vector deadly bacterial pathogens. In this study we present the first assessment of the genetic structure of human louse populations by analyzing the nuclear genetic variation at 15 newly developed microsatellite loci in 93 human lice from 11 sites in four world regions. Both ecotypes showed heterozygote deficits relative to Hardy-Weinberg equilibrium and high inbreeding values, an expected pattern given their parasitic life history. Bayesian clustering analyses assigned lice to four distinct genetic clusters that were geographically structured. The low levels of gene flow among louse populations suggested that the evolution of insecticide resistance in lice would most likely be affected by local selection pressures, underscoring the importance of tailoring control strategies to population-specific genetic makeup and evolutionary history. Our panel of microsatellite markers provides powerful data to investigate not only ecological and evolutionary processes in lice, but also those in their human hosts because of the long-term coevolutionary

  6. Nuclear genetic diversity in human lice (Pediculus humanus) reveals continental differences and high inbreeding among worldwide populations.

    PubMed

    Ascunce, Marina S; Toups, Melissa A; Kassu, Gebreyes; Fane, Jackie; Scholl, Katlyn; Reed, David L

    2013-01-01

    Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus). This species is composed of two ecotypes: the head louse (Pediculus humanus capitis De Geer), and the clothing (body) louse (Pediculus humanus humanus Linnaeus). Hundreds of millions of head louse infestations affect children every year, and this number is on the rise, in part because of increased resistance to insecticides. Clothing lice affect mostly homeless and refugee-camp populations and although they are less prevalent than head lice, the medical consequences are more severe because they vector deadly bacterial pathogens. In this study we present the first assessment of the genetic structure of human louse populations by analyzing the nuclear genetic variation at 15 newly developed microsatellite loci in 93 human lice from 11 sites in four world regions. Both ecotypes showed heterozygote deficits relative to Hardy-Weinberg equilibrium and high inbreeding values, an expected pattern given their parasitic life history. Bayesian clustering analyses assigned lice to four distinct genetic clusters that were geographically structured. The low levels of gene flow among louse populations suggested that the evolution of insecticide resistance in lice would most likely be affected by local selection pressures, underscoring the importance of tailoring control strategies to population-specific genetic makeup and evolutionary history. Our panel of microsatellite markers provides powerful data to investigate not only ecological and evolutionary processes in lice, but also those in their human hosts because of the long-term coevolutionary

  7. Nuclear Genetic Diversity in Human Lice (Pediculus humanus) Reveals Continental Differences and High Inbreeding among Worldwide Populations

    PubMed Central

    Ascunce, Marina S.; Toups, Melissa A.; Kassu, Gebreyes; Fane, Jackie; Scholl, Katlyn; Reed, David L.

    2013-01-01

    Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus). This species is composed of two ecotypes: the head louse (Pediculus humanus capitis De Geer), and the clothing (body) louse (Pediculus humanus humanus Linnaeus). Hundreds of millions of head louse infestations affect children every year, and this number is on the rise, in part because of increased resistance to insecticides. Clothing lice affect mostly homeless and refugee-camp populations and although they are less prevalent than head lice, the medical consequences are more severe because they vector deadly bacterial pathogens. In this study we present the first assessment of the genetic structure of human louse populations by analyzing the nuclear genetic variation at 15 newly developed microsatellite loci in 93 human lice from 11 sites in four world regions. Both ecotypes showed heterozygote deficits relative to Hardy–Weinberg equilibrium and high inbreeding values, an expected pattern given their parasitic life history. Bayesian clustering analyses assigned lice to four distinct genetic clusters that were geographically structured. The low levels of gene flow among louse populations suggested that the evolution of insecticide resistance in lice would most likely be affected by local selection pressures, underscoring the importance of tailoring control strategies to population-specific genetic makeup and evolutionary history. Our panel of microsatellite markers provides powerful data to investigate not only ecological and evolutionary processes in lice, but also those in their human hosts because of the long-term coevolutionary

  8. Why Are High Altitude Natives So Strong at High Altitude? Nature vs. Nurture: Genetic Factors vs. Growth and Development.

    PubMed

    Brutsaert, Tom

    2016-01-01

    Among high-altitude natives there is evidence of a general hypoxia tolerance leading to enhanced performance and/or increased capacity in several important domains. These domains likely include an enhanced physical work capacity, an enhanced reproductive capacity, and an ability to resist several common pathologies of chronic high-altitude exposure. The "strength" of the high-altitude native in this regard may have both a developmental and a genetic basis, although there is better evidence for the former (developmental effects) than for the latter. For example, early-life hypoxia exposure clearly results in lung growth and remodeling leading to an increased O2 diffusing capacity in adulthood. Genetic research has yet to reveal a population genetic basis for enhanced capacity in high-altitude natives, but several traits are clearly under genetic control in Andean and Tibetan populations e.g., resting and exercise arterial O2 saturation (SaO2). This chapter reviews the effects of nature and nurture on traits that are relevant to the process of gas exchange, including pulmonary volumes and diffusion capacity, the maximal oxygen consumption (VO2max), the SaO2, and the alveolar-arterial oxygen partial pressure difference (A-aDO2) during exercise. PMID:27343091

  9. Why Are High Altitude Natives So Strong at High Altitude? Nature vs. Nurture: Genetic Factors vs. Growth and Development.

    PubMed

    Brutsaert, Tom

    2016-01-01

    Among high-altitude natives there is evidence of a general hypoxia tolerance leading to enhanced performance and/or increased capacity in several important domains. These domains likely include an enhanced physical work capacity, an enhanced reproductive capacity, and an ability to resist several common pathologies of chronic high-altitude exposure. The "strength" of the high-altitude native in this regard may have both a developmental and a genetic basis, although there is better evidence for the former (developmental effects) than for the latter. For example, early-life hypoxia exposure clearly results in lung growth and remodeling leading to an increased O2 diffusing capacity in adulthood. Genetic research has yet to reveal a population genetic basis for enhanced capacity in high-altitude natives, but several traits are clearly under genetic control in Andean and Tibetan populations e.g., resting and exercise arterial O2 saturation (SaO2). This chapter reviews the effects of nature and nurture on traits that are relevant to the process of gas exchange, including pulmonary volumes and diffusion capacity, the maximal oxygen consumption (VO2max), the SaO2, and the alveolar-arterial oxygen partial pressure difference (A-aDO2) during exercise.

  10. Ladakh, India: the land of high passes and genetic heterogeneity reveals a confluence of migrations.

    PubMed

    Rowold, Diane J; Perez Benedico, David; Garcia-Bertrand, Ralph; Chennakrishnaiah, Shilpa; Alfonso-Sanchez, Miguel A; Gayden, Tenzin; Herrera, Rene J

    2016-03-01

    Owing to its geographic location near the longitudinal center of Asia, Ladakh, the land of high passes, has witnessed numerous demographic movements during the past millenniums of occupation. In an effort to view Ladakh's multicultural history from a paternal genetic perspective, we performed a high-resolution Y-chromosomal survey of Ladakh, within the context of Y haplogroup and haplotype distributions of 41 Asian reference populations. The results of this investigation highlight the rich ethnic and genetic diversity of Ladkah which includes genetic contributions from disparate regions of the continent including, West, East, South and Central Asia. The phylogenetic signals from Ladakh are consistent with the Indo-Aryans' occupation during the Neolithic age and its historic connection with Tibet, as well as the East-West gene flow associated with the Silk Road.

  11. The genetic and environmental etiology of high math performance in 10-year-old twins.

    PubMed

    Petrill, Stephen A; Kovas, Yulia; Hart, Sara A; Thompson, Lee A; Plomin, Robert

    2009-07-01

    The genetic and environmental etiology of high math performance (at or above the 85%tile) was examined in a population-based sample of 10-year-old twins (nMZ = 1,279, nDZ = 2,305). Math skills were assessed using a web-based battery of math performance tapping skills related to the UK National Math Curriculum. Probandwise concordance rates and liability threshold models indicated that genetic and shared environmental influences were significant, and that these estimates were generally similar to those obtained across the normal range of ability and did not vary significantly by gender. These results suggest that the genetic and environmental influences at the high end of ability are likely to be continuous with those that affect the entire range of math performance across all children irrespective of gender.

  12. Thermostable trypsin conjugates immobilized to biogenic magnetite show a high operational stability and remarkable reusability for protein digestion.

    PubMed

    Pečová, M; Šebela, M; Marková, Z; Poláková, K; Čuda, J; Šafářová, K; Zbořil, R

    2013-03-29

    In this work, magnetosomes produced by microorganisms were chosen as a suitable magnetic carrier for covalent immobilization of thermostable trypsin conjugates with an expected applicability for efficient and rapid digestion of proteins at elevated temperatures. First, a biogenic magnetite was isolated from Magnetospirillum gryphiswaldense and its free surface was coated with the natural polysaccharide chitosan containing free amino and hydroxy groups. Prior to covalent immobilization, bovine trypsin was modified by conjugating with α-, β- and γ-cyclodextrin. Modified trypsin was bound to the magnetic carriers via amino groups using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysulfosuccinimide as coupling reagents. The magnetic biomaterial was characterized by magnetometric analysis and electron microscopy. With regard to their biochemical properties, the immobilized trypsin conjugates showed an increased resistance to elevated temperatures, eliminated autolysis, had an unchanged pH optimum and a significant storage stability and reusability. Considering these parameters, the presented enzymatic system exhibits properties that are superior to those of trypsin forms obtained by other frequently used approaches. The proteolytic performance was demonstrated during in-solution digestion of model proteins (horseradish peroxidase, bovine serum albumin and hen egg white lysozyme) followed by mass spectrometry. It is shown that both magnetic immobilization and chemical modification enhance the characteristics of trypsin making it a promising tool for protein digestion.

  13. Thermostable trypsin conjugates immobilized to biogenic magnetite show a high operational stability and remarkable reusability for protein digestion

    NASA Astrophysics Data System (ADS)

    Pečová, M.; Šebela, M.; Marková, Z.; Poláková, K.; Čuda, J.; Šafářová, K.; Zbořil, R.

    2013-03-01

    In this work, magnetosomes produced by microorganisms were chosen as a suitable magnetic carrier for covalent immobilization of thermostable trypsin conjugates with an expected applicability for efficient and rapid digestion of proteins at elevated temperatures. First, a biogenic magnetite was isolated from Magnetospirillum gryphiswaldense and its free surface was coated with the natural polysaccharide chitosan containing free amino and hydroxy groups. Prior to covalent immobilization, bovine trypsin was modified by conjugating with α-, β- and γ-cyclodextrin. Modified trypsin was bound to the magnetic carriers via amino groups using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysulfosuccinimide as coupling reagents. The magnetic biomaterial was characterized by magnetometric analysis and electron microscopy. With regard to their biochemical properties, the immobilized trypsin conjugates showed an increased resistance to elevated temperatures, eliminated autolysis, had an unchanged pH optimum and a significant storage stability and reusability. Considering these parameters, the presented enzymatic system exhibits properties that are superior to those of trypsin forms obtained by other frequently used approaches. The proteolytic performance was demonstrated during in-solution digestion of model proteins (horseradish peroxidase, bovine serum albumin and hen egg white lysozyme) followed by mass spectrometry. It is shown that both magnetic immobilization and chemical modification enhance the characteristics of trypsin making it a promising tool for protein digestion.

  14. Nationwide surveillance study of Clostridium difficile in Australian neonatal pigs shows high prevalence and heterogeneity of PCR ribotypes.

    PubMed

    Knight, Daniel R; Squire, Michele M; Riley, Thomas V

    2015-01-01

    Clostridium difficile is an important enteric pathogen of humans and the cause of diarrhea and enteritis in neonatal pigs. Outside Australia, prevalence in piglets can be up to 73%, with a single PCR ribotype (RT), 078, predominating. We investigated the prevalence and genotype of C. difficile in Australian pig herds. Rectal swabs (n = 229) were collected from piglets aged <7 days from 21 farms across Australia. Selective culture for C. difficile was performed and isolates characterized by PCR for toxin genes and PCR ribotyping. C. difficile was isolated from 52% of samples by direct culture on chromogenic agar and 67% by enrichment culture (P = 0.001). No association between C. difficile recovery or genotype and diarrheic status of either farm or piglets was found. The majority (87%; 130/154) of isolates were toxigenic. Typing revealed 23 different RTs, several of which are known to cause disease in humans, including RT014, which was isolated most commonly (23%; 36/154). RT078 was not detected. This study shows that colonization of Australian neonatal piglets with C. difficile is widespread in the herds sampled.

  15. Exploring the transferase activity of Ffase from Schwanniomyces occidentalis, a β-fructofuranosidase showing high fructosyl-acceptor promiscuity.

    PubMed

    Piedrabuena, David; Míguez, Noa; Poveda, Ana; Plou, Francisco J; Fernández-Lobato, María

    2016-10-01

    The β-fructofuranosidase from the yeast Schwanniomyces occidentalis (Ffase) produces the prebiotic sugars 6-kestose and 1-kestose by transfructosylation of sucrose, which makes it of biotechnological interest. In this study, the hydrolase and transferase activity of this enzyme was kinetically characterized and its potential to synthesize new fructosylated products explored. A total of 40 hydroxylated compounds were used as potential fructosyl-acceptor alternatives to sucrose. Only 17 of them, including some monosaccharides, disaccharides, and oligosaccharides as well as alditols and glycosides were fructosylated. The best alternative acceptors were the alditols. The major transfer product of the reaction including mannitol was purified and characterized as 1-O-β-D-fructofuranosyl-D-mannitol, whose maximum concentration reached 44 g/L, representing about 7.3 % of total compounds in the mixture and 89 % of all products generated by transfructosylation. The reactions including erythritol produced 35 g/L of an isomer mixture comprising 1- and 4-O-β-D-fructofuranosyl-D-erythritol. In addition, Ffase produced 24 g/L of the disaccharide blastose by direct fructosylation of glucose, which makes it the first enzyme characterized from yeast showing this ability. Thus, novel fructosylated compounds with potential applications in food and pharmaceutical industries can be obtained due to the Ffase fructosyl-acceptor promiscuity.

  16. Metabolic characterization of a strain (BM90) of Delftia tsuruhatensis showing highly diversified capacity to degrade low molecular weight phenols.

    PubMed

    Juárez-Jiménez, Belén; Manzanera, Maximino; Rodelas, Belén; Martínez-Toledo, Maria Victoria; Gonzalez-López, Jesus; Crognale, Silvia; Pesciaroli, Chiara; Fenice, Massimiliano

    2010-06-01

    A novel bacterium, strain BM90, previously isolated from Tyrrhenian Sea, was metabolically characterized testing its ability to use 95 different carbon sources by the Biolog system. The bacterium showed a broad capacity to use fatty-, organic- and amino-acids; on the contrary, its ability to use carbohydrates was extremely scarce. Strain BM90 was identified and affiliated to Delftia tsuruhatensis by molecular techniques based on 16S rRNA gene sequencing. D. tsuruhatensis BM90, cultivated in shaken cultures, was able to grow on various phenolic compounds and to remove them from its cultural broth. The phenols used, chosen for their presence in industrial or agro-industrial effluents, were grouped on the base of their chemical characteristics. These included benzoic acid derivatives, cinnamic acid derivatives, phenolic aldehyde derivatives, acetic acid derivatives and other phenolic compounds such as catechol and p-hydroxyphenylpropionic acid. When all the compounds (24) were gathered in the same medium (total concentration: 500 mg/l), BM90 caused the complete depletion of 18 phenols and the partial removal of two others. Only four phenolic compounds were not removed. Flow cytometry studies were carried out to understand the physiological state of BM90 cells in presence of the above phenols in various conditions. At the concentrations tested, a certain toxic effect was exerted only by the four compounds that were not metabolized by the bacterium. PMID:19946734

  17. Exploring the transferase activity of Ffase from Schwanniomyces occidentalis, a β-fructofuranosidase showing high fructosyl-acceptor promiscuity.

    PubMed

    Piedrabuena, David; Míguez, Noa; Poveda, Ana; Plou, Francisco J; Fernández-Lobato, María

    2016-10-01

    The β-fructofuranosidase from the yeast Schwanniomyces occidentalis (Ffase) produces the prebiotic sugars 6-kestose and 1-kestose by transfructosylation of sucrose, which makes it of biotechnological interest. In this study, the hydrolase and transferase activity of this enzyme was kinetically characterized and its potential to synthesize new fructosylated products explored. A total of 40 hydroxylated compounds were used as potential fructosyl-acceptor alternatives to sucrose. Only 17 of them, including some monosaccharides, disaccharides, and oligosaccharides as well as alditols and glycosides were fructosylated. The best alternative acceptors were the alditols. The major transfer product of the reaction including mannitol was purified and characterized as 1-O-β-D-fructofuranosyl-D-mannitol, whose maximum concentration reached 44 g/L, representing about 7.3 % of total compounds in the mixture and 89 % of all products generated by transfructosylation. The reactions including erythritol produced 35 g/L of an isomer mixture comprising 1- and 4-O-β-D-fructofuranosyl-D-erythritol. In addition, Ffase produced 24 g/L of the disaccharide blastose by direct fructosylation of glucose, which makes it the first enzyme characterized from yeast showing this ability. Thus, novel fructosylated compounds with potential applications in food and pharmaceutical industries can be obtained due to the Ffase fructosyl-acceptor promiscuity. PMID:27229725

  18. [Case of submucosal esophageal carcinoma with multiple liver metastasis showing high serum levels of CEA and CA19-9].

    PubMed

    Kurihara, Toshikazu; Ishii, Shigeaki; Ozawa, Tatsuo; Tsubo, Katsurou; Fukushima, Yoshitaka; Funatomi, Hitoshi; Kagaya, Toshitaka; Ohike, Nobuyuki; Takahashi, Manabu

    2007-01-01

    A 57-year-old man was admitted because of abdominal fullness. An abdominal ultrasonographic study disclosed multiple space-occupying lesions (SOL) in the liver. On blood examinationC the serum levels of CEA and CA19-9 were significantly high while those of AFP and SCC were within normal ranges. Endoscopically biopsied specimens of the lower esophagus histologically revealed poorly differentiated squamous cell carcinoma. Pathohistologically similar findings were obtained from the needle biopsied specimen of the SOL in the liver. Thus the patient was diagnosed as having squamous cell carcinoma of the esophagus with liver metastasis. On the 41st hospital day the patient died and an autopsy was performed. Although multiple metastases were recognized, cancer cells were limited within the submucosa of the esophagus. Immunostaining of CEA and CA19-9 was positive on the carcinoma cells both in the esophagus and the liver. Thus a relation between the biological malignancy of esophageal cancer and serum levels of CEA and CA19-9 was suggested.

  19. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.

    PubMed

    Jacquiod, Samuel; Demanèche, Sandrine; Franqueville, Laure; Ausec, Luka; Xu, Zhuofei; Delmont, Tom O; Dunon, Vincent; Cagnon, Christine; Mandic-Mulec, Ines; Vogel, Timothy M; Simonet, Pascal

    2014-11-20

    A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.

  20. Remotely sensed forest cover loss shows high spatial and temporal variation across Sumatera and Kalimantan, Indonesia 2000-2008

    NASA Astrophysics Data System (ADS)

    Broich, Mark; Hansen, Matthew; Stolle, Fred; Potapov, Peter; Arunarwati Margono, Belinda; Adusei, Bernard

    2011-01-01

    The Indonesian islands of Sumatera and Kalimantan (the Indonesian part of the island of Borneo) are a center of significant and rapid forest cover loss in the humid tropics with implications for carbon dynamics, biodiversity conservation, and local livelihoods. The aim of our research was to analyze and interpret annual trends of forest cover loss for different sub-regions of the study area. We mapped forest cover loss for 2000-2008 using multi-resolution remote sensing data from the Landsat enhanced thematic mapper plus (ETM +) and moderate resolution imaging spectroradiometer (MODIS) sensors and analyzed annual trends per island, province, and official land allocation zone. The total forest cover loss for Sumatera and Kalimantan 2000-2008 was 5.39 Mha, which represents 5.3% of the land area and 9.2% of the year 2000 forest cover of these two islands. At least 6.5% of all mapped forest cover loss occurred in land allocation zones prohibiting clearing. An additional 13.6% of forest cover loss occurred where clearing is legally restricted. The overall trend of forest cover loss increased until 2006 and decreased thereafter. The trends for Sumatera and Kalimantan were distinctly different, driven primarily by the trends of Riau and Central Kalimantan provinces, respectively. This analysis shows that annual mapping of forest cover change yields a clearer picture than a one-time overall national estimate. Monitoring forest dynamics is important for national policy makers, especially given the commitment of Indonesia to reducing greenhouse gas emissions as part of the reducing emissions from deforestation and forest degradation in developing countries initiative (REDD +). The improved spatio-temporal detail of forest change monitoring products will make it possible to target policies and projects in meeting this commitment. Accurate, annual forest cover loss maps will be integral to many REDD + objectives, including policy formulation, definition of baselines, detection

  1. Exceptionally High Levels of Genetic Diversity in Wheat Curl Mite (Acari: Eriophyidae) Populations from Turkey.

    PubMed

    Szydło, W; Hein, G; Denizhan, E; Skoracka, A

    2015-08-01

    Recent research on the wheat curl mite species complex has revealed extensive genetic diversity that has distinguished several genetic lineages infesting bread wheat (Triticum aestivum L.) and other cereals worldwide. Turkey is the historical region of wheat and barley (Hordeum vulgare L.) domestication and diversification. The close relationship between these grasses and the wheat curl mite provoked the question of the genetic diversity of the wheat curl mite in this region. The scope of the study was to investigate genetic differentiation within the wheat curl mite species complex on grasses in Turkey. Twenty-one wheat curl mite populations from 16 grass species from nine genera (Agropyron sp., Aegilops sp., Bromus sp., Elymus sp., Eremopyrum sp., Hordeum sp., Poa sp., Secale sp., and Triticum sp.) were sampled in eastern and southeastern Turkey for genetic analyses. Two molecular markers were amplified: the cytochrome oxidase subunit I coding region of mtDNA (COI) and the D2 region of 28S rDNA. Phylogenetic analyses revealed high genetic variation of the wheat curl mite in Turkey, primarily on Bromus and Hordeum spp., and exceptionally high diversity of populations associated with bread wheat. Three wheat-infesting wheat curl mite lineages known to occur on other continents of the world, including North and South America, Australia and Europe, were found in Turkey, and at least two new genetic lineages were discovered. These regions of Turkey exhibit rich wheat curl mite diversity on native grass species. The possible implications for further studies on the wheat curl mite are discussed. PMID:26470350

  2. Exceptionally High Levels of Genetic Diversity in Wheat Curl Mite (Acari: Eriophyidae) Populations from Turkey.

    PubMed

    Szydło, W; Hein, G; Denizhan, E; Skoracka, A

    2015-08-01

    Recent research on the wheat curl mite species complex has revealed extensive genetic diversity that has distinguished several genetic lineages infesting bread wheat (Triticum aestivum L.) and other cereals worldwide. Turkey is the historical region of wheat and barley (Hordeum vulgare L.) domestication and diversification. The close relationship between these grasses and the wheat curl mite provoked the question of the genetic diversity of the wheat curl mite in this region. The scope of the study was to investigate genetic differentiation within the wheat curl mite species complex on grasses in Turkey. Twenty-one wheat curl mite populations from 16 grass species from nine genera (Agropyron sp., Aegilops sp., Bromus sp., Elymus sp., Eremopyrum sp., Hordeum sp., Poa sp., Secale sp., and Triticum sp.) were sampled in eastern and southeastern Turkey for genetic analyses. Two molecular markers were amplified: the cytochrome oxidase subunit I coding region of mtDNA (COI) and the D2 region of 28S rDNA. Phylogenetic analyses revealed high genetic variation of the wheat curl mite in Turkey, primarily on Bromus and Hordeum spp., and exceptionally high diversity of populations associated with bread wheat. Three wheat-infesting wheat curl mite lineages known to occur on other continents of the world, including North and South America, Australia and Europe, were found in Turkey, and at least two new genetic lineages were discovered. These regions of Turkey exhibit rich wheat curl mite diversity on native grass species. The possible implications for further studies on the wheat curl mite are discussed.

  3. Genome characteristics of a novel phage from Bacillus thuringiensis showing high similarity with phage from Bacillus cereus.

    PubMed

    Yuan, Yihui; Gao, Meiying; Wu, Dandan; Liu, Pengming; Wu, Yan

    2012-01-01

    Bacillus thuringiensis is an important entomopathogenic bacterium belongs to the Bacillus cereus group, which also includes B. anthracis and B. cereus. Several genomes of phages originating from this group had been sequenced, but no genome of Siphoviridae phage from B. thuringiensis has been reported. We recently sequenced and analyzed the genome of a novel phage, BtCS33, from a B. thuringiensis strain, subsp. kurstaki CS33, and compared the gneome of this phage to other phages of the B. cereus group. BtCS33 was the first Siphoviridae phage among the sequenced B. thuringiensis phages. It produced small, turbid plaques on bacterial plates and had a narrow host range. BtCS33 possessed a linear, double-stranded DNA genome of 41,992 bp with 57 putative open reading frames (ORFs). It had a typical genome structure consisting of three modules: the "late" region, the "lysogeny-lysis" region and the "early" region. BtCS33 exhibited high similarity with several phages, B. cereus phage Wβ and some variants of Wβ, in genome organization and the amino acid sequences of structural proteins. There were two ORFs, ORF22 and ORF35, in the genome of BtCS33 that were also found in the genomes of B. cereus phage Wβ and may be involved in regulating sporulation of the host cell. Based on these observations and analysis of phylogenetic trees, we deduced that B. thuringiensis phage BtCS33 and B. cereus phage Wβ may have a common distant ancestor.

  4. Genome Characteristics of a Novel Phage from Bacillus thuringiensis Showing High Similarity with Phage from Bacillus cereus

    PubMed Central

    Yuan, Yihui; Gao, Meiying; Wu, Dandan; Liu, Pengming; Wu, Yan

    2012-01-01

    Bacillus thuringiensis is an important entomopathogenic bacterium belongs to the Bacillus cereus group, which also includes B. anthracis and B. cereus. Several genomes of phages originating from this group had been sequenced, but no genome of Siphoviridae phage from B. thuringiensis has been reported. We recently sequenced and analyzed the genome of a novel phage, BtCS33, from a B. thuringiensis strain, subsp. kurstaki CS33, and compared the gneome of this phage to other phages of the B. cereus group. BtCS33 was the first Siphoviridae phage among the sequenced B. thuringiensis phages. It produced small, turbid plaques on bacterial plates and had a narrow host range. BtCS33 possessed a linear, double-stranded DNA genome of 41,992 bp with 57 putative open reading frames (ORFs). It had a typical genome structure consisting of three modules: the “late” region, the “lysogeny-lysis” region and the “early” region. BtCS33 exhibited high similarity with several phages, B. cereus phage Wβ and some variants of Wβ, in genome organization and the amino acid sequences of structural proteins. There were two ORFs, ORF22 and ORF35, in the genome of BtCS33 that were also found in the genomes of B. cereus phage Wβ and may be involved in regulating sporulation of the host cell. Based on these observations and analysis of phylogenetic trees, we deduced that B. thuringiensis phage BtCS33 and B. cereus phage Wβ may have a common distant ancestor. PMID:22649540

  5. Basement membrane of mouse bone marrow sinusoids shows distinctive structure and proteoglycan composition: a high resolution ultrastructural study.

    PubMed

    Inoue, S; Osmond, D G

    2001-11-01

    Venous sinusoids in bone marrow are the site of a large-scale traffic of cells between the extravascular hemopoietic compartment and the blood stream. The wall of the sinusoids consists solely of a basement membrane interposed between a layer of endothelial cells and an incomplete covering of adventitial cells. To examine its possible structural specialization, the basement membrane of bone marrow sinusoids has now been examined by high resolution electron microscopy of perfusion-fixed mouse bone marrow. The basement membrane layer was discontinuous, consisting of irregular masses of amorphous material within a uniform 60-nm-wide space between apposing endothelial cells and adventitial cell processes. At maximal magnifications, the material was resolved as a random arrangement of components lacking the "cord network" formation seen in basement membranes elsewhere. Individual components exhibited distinctive ultrastructural features whose molecular identity has previously been established. By these morphological criteria, the basement membrane contained unusually abundant chondroitin sulfate proteoglycan (CSPG) revealed by 3-nm-wide "double tracks," and moderate amounts of both laminin as dense irregular coils and type IV collagen as 1-1.5-nm-wide filaments, together with less conspicuous amounts of amyloid P forming pentagonal frames. In contrast, 4.5-5-nm-wide "double tracks" characteristic of heparan sulfate proteoglycan (HSPG) were absent. The findings demonstrate that, in comparison with "typical" basement membranes in other tissues, the bone marrow sinusoidal basement membrane is uniquely specialized in several respects. Its discontinuous nature, lack of network organization, and absence of HSPG, a molecule that normally helps to maintain membrane integrity, may facilitate disassembly and reassembly of basement membrane material in concert with movements of adventitial cell processes as maturing hemopoietic cells pass through the sinusoidal wall: the

  6. Basement membrane of mouse bone marrow sinusoids shows distinctive structure and proteoglycan composition: a high resolution ultrastructural study.

    PubMed

    Inoue, S; Osmond, D G

    2001-11-01

    Venous sinusoids in bone marrow are the site of a large-scale traffic of cells between the extravascular hemopoietic compartment and the blood stream. The wall of the sinusoids consists solely of a basement membrane interposed between a layer of endothelial cells and an incomplete covering of adventitial cells. To examine its possible structural specialization, the basement membrane of bone marrow sinusoids has now been examined by high resolution electron microscopy of perfusion-fixed mouse bone marrow. The basement membrane layer was discontinuous, consisting of irregular masses of amorphous material within a uniform 60-nm-wide space between apposing endothelial cells and adventitial cell processes. At maximal magnifications, the material was resolved as a random arrangement of components lacking the "cord network" formation seen in basement membranes elsewhere. Individual components exhibited distinctive ultrastructural features whose molecular identity has previously been established. By these morphological criteria, the basement membrane contained unusually abundant chondroitin sulfate proteoglycan (CSPG) revealed by 3-nm-wide "double tracks," and moderate amounts of both laminin as dense irregular coils and type IV collagen as 1-1.5-nm-wide filaments, together with less conspicuous amounts of amyloid P forming pentagonal frames. In contrast, 4.5-5-nm-wide "double tracks" characteristic of heparan sulfate proteoglycan (HSPG) were absent. The findings demonstrate that, in comparison with "typical" basement membranes in other tissues, the bone marrow sinusoidal basement membrane is uniquely specialized in several respects. Its discontinuous nature, lack of network organization, and absence of HSPG, a molecule that normally helps to maintain membrane integrity, may facilitate disassembly and reassembly of basement membrane material in concert with movements of adventitial cell processes as maturing hemopoietic cells pass through the sinusoidal wall: the

  7. Genetic risk factors for nonsyndromic cleft lip with or without cleft palate in a Brazilian population with high African ancestry.

    PubMed

    do Rego Borges, Andrea; Sá, Jamile; Hoshi, Ryuichi; Viena, Camila Sane; Mariano, Lorena C; de Castro Veiga, Patricia; Medrado, Alena Peixoto; Machado, Renato Assis; de Aquino, Sibele Nascimento; Messetti, Ana Camila; Spritz, Richard A; Coletta, Ricardo D; Reis, Silvia R A

    2015-10-01

    Nonsyndromic cleft lip with or without cleft palate (NSCL ± P) is the most common orofacial birth defect, exhibiting variable prevalence around the world, often attributed to ethnic and environmental differences. Linkage analyses and genome-wide association studies have identified several genomic susceptibility regions for NSCL ± P, mostly in European-derived or Asian populations. Genetic predisposition to NSCL ± P is ethnicity-dependent, and the genetic basis of susceptibility to NSCL ± P likely varies among populations. The population of Brazil is highly admixed, with highly variable ancestry; thus, the genetic determinants of NSCL ± P susceptibility may be quite different. This study tested association of 8 single-nucleotide polymorphisms (SNPs), previously identified by genome-wide studies in other populations, with NSCL ± P in a Brazilian population with high African ancestry. SNPs rs560426, rs642961, rs1530300, rs987525, rs3758249, rs7078160, rs17085106, and rs13041247 were genotyped in 293 Brazilian patients with NSCL ± P and 352 unaffected Brazilian controls. Each sample was also genotyped for 40 biallelic short insertion/deletion polymorphic markers to characterize genetic ancestry. The average African ancestry background was 31.1% for the NSCL ± P group and 36.7% for the control group. After adjustment for ancestry and multiple testing, the minor alleles of rs3758249 (OR: 1.58, 95% CI: 1.25-2.01, P = 0.0001) and rs7078160 (OR: 1.59, 95% CI: 1.21-2.07, P = 0.0002) were significantly associated with risk of NSCL ± P. Polymorphisms located in IRF6 (rs642961) and 8q24 (rs1530300 and rs987525) showed marginal associations in this Brazilian population with high African ancestry. These results indicate that rs3758249 at 9q22 and rs7078160 at 10q25.3 represent risk loci for NSCL ± P in the Brazilian population with high African ancestry.

  8. High-resolution deep Northeast Pacific radiocarbon record shows little change in ventilation rate during the last deglaciation

    NASA Astrophysics Data System (ADS)

    Lund, D. C.; Mix, A. C.

    2010-12-01

    The rise in atmospheric carbon dioxide during the last deglaciation is thought to be driven by release of carbon sequestered in the abyssal ocean. This mechanism requires a poorly ventilated deep Pacific during the Last Glacial Maximum (LGM) and enhanced ventilation during the deglaciation. Here we evaluate the plausibility of this scenario using planktonic and benthic foraminiferal radiocarbon data from a high-sedimentation rate core (~25 cm/kyr) collected in the deep (2700 m) Northeast Pacific. We estimate that the mean benthic-planktonic (B-P) age was 1620±190 years during the LGM (n=10 pairs). This value is indistinguishable from the mean B-P difference for the deglaciation (1500±230; n=20 pairs) and the difference between surface and deep water 14C ages today (1560±70 years). Furthermore, our time series of benthic Δ14C parallels atmospheric Δ14C with an offset of 300±50‰ from 22 to 10 kyr BP. These data suggest the ventilation rate of the deep NE Pacific remained nearly constant during the deglaciation, consistent with lower resolution data from this region (Okazaki et al., 2010). Between 22 and 16 kyr BP, Δ14C in the deep NE Pacific varied between 0 and 100‰, well above the -200‰ values estimated at intermediate depths off of Baja California during the Mystery Interval (Marchitto et al., 2007). The deep NE Pacific apparently did not contain water of adequate age to source deglacial Δ14C anomalies shallower in the water column. Given that Antarctic Intermediate Water is also an unlikely source (de Pol-Holz et al., 2010; Rose et al., 2010), an alternative explanation is necessary for the extreme 14C depletions in the eastern tropical Pacific. De Pol-Holz, R. D., et al. 2010. No signature of abyssal carbon in intermediate waters off Chile during deglaciation. Nature Geoscience 3, 192-195. Marchitto, T., Lehman, S., Ortiz, J., Fluckiger, J. & van Geen, A. 2007. Marine radiocarbon evidence for the mechanism of deglacial atmospheric CO2 rise. Science

  9. A Systems Genetic Analysis of High Density Lipoprotein Metabolism and Network Preservation across Mouse Models

    PubMed Central

    Langfelder, Peter; Castellani, Lawrence W.; Zhou, Zhiqiang; Paul, Eric; Davis, Richard; Schadt, Eric E.; Lusis, Aldons J.; Horvath, Steve; Mehrabian, Margarete

    2011-01-01

    We report a systems genetics analysis of high density lipoproteins (HDL) levels in an F2 intercross between inbred strains CAST/EiJ and C57BL/6J. We previously showed that there are dramatic differences in HDL metabolism in a cross between these strains, and we now report co-expression network analysis of HDL that integrates global expression data from liver and adipose with relevant metabolic traits. Using data from a total of 293 F2 intercross mice, we constructed weighted gene co-expression networks and identified modules (subnetworks) associated with HDL and clinical traits. These were examined for genes implicated in HDL levels based on large human genome-wide associations studies (GWAS) and examined with respect to conservation between tissue and sexes in a total of 9 data sets. We identify genes that are consistently ranked high by association with HDL across the 9 data sets. We focus in particular on two genes, Wfdc2 and Hdac3, that are located in close proximity to HDL QTL peaks where causal testing indicates that they may affect HDL. Our results provide a rich resource for studies of complex metabolic interactions involving HDL. PMID:21807117

  10. Genetic algorithm-support vector regression for high reliability SHM system based on FBG sensor network

    NASA Astrophysics Data System (ADS)

    Zhang, XiaoLi; Liang, DaKai; Zeng, Jie; Asundi, Anand

    2012-02-01

    Structural Health Monitoring (SHM) based on fiber Bragg grating (FBG) sensor network has attracted considerable attention in recent years. However, FBG sensor network is embedded or glued in the structure simply with series or parallel. In this case, if optic fiber sensors or fiber nodes fail, the fiber sensors cannot be sensed behind the failure point. Therefore, for improving the survivability of the FBG-based sensor system in the SHM, it is necessary to build high reliability FBG sensor network for the SHM engineering application. In this study, a model reconstruction soft computing recognition algorithm based on genetic algorithm-support vector regression (GA-SVR) is proposed to achieve the reliability of the FBG-based sensor system. Furthermore, an 8-point FBG sensor system is experimented in an aircraft wing box. The external loading damage position prediction is an important subject for SHM system; as an example, different failure modes are selected to demonstrate the SHM system's survivability of the FBG-based sensor network. Simultaneously, the results are compared with the non-reconstruct model based on GA-SVR in each failure mode. Results show that the proposed model reconstruction algorithm based on GA-SVR can still keep the predicting precision when partial sensors failure in the SHM system; thus a highly reliable sensor network for the SHM system is facilitated without introducing extra component and noise.

  11. Unusually high genetic diversity in COI sequences of Chimarra obscura (Trichoptera: Philopotamidae)

    EPA Science Inventory

    Chimarra obscura (Walker 1852) is a philopotamid caddisfly found throughout much of North America. Using the COI DNA barcode locus, we have found unexpectedly high amounts of genetic diversity and distances within C. obscura. Of the approximately 150 specimens sampled, we have fo...

  12. A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high-density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of ...

  13. High degree of genetic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus).

    PubMed

    Defaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Merilä, Juha

    2013-09-01

    Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene-based genome-scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection-as determined with several outlier detection methods-was low (F(ST) = 0.033 or 0.011, respectively), whereas average FST for directionally selected markers was significantly higher (F(ST) = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes.

  14. Genetic diversity analysis of highly incomplete SNP genotype data with imputations: an empirical assessment.

    PubMed

    Fu, Yong-Bi

    2014-05-01

    Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data. PMID:24626289

  15. Genetic identification of Theobroma cacao L. trees with high Criollo ancestry in Soconusco, Chiapas, Mexico.

    PubMed

    Vázquez-Ovando, J A; Molina-Freaner, F; Nuñez-Farfán, J; Ovando-Medina, I; Salvador-Figueroa, M

    2014-12-12

    Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population. The overall populations showed an average observed heterozygosity of 0.28, indicating heterozygote deficiency (average fixation index F = 0.50). However, moderate allelic diversity was found within populations (Shannon index for all populations I = 0.97). Bayesian method analysis determined 2 genetic clusters (K = 2) within individuals. In concordance, an assignment test grouped 37 multilocus genotypes (including 10 references) into a first cluster (Criollo), 54 into a second (presumably Amelonado), and 27 admixed individuals unassigned at the 90% threshold likely corresponding to the Trinitario genotype. This classification was supported by the principal coordinate analysis and analysis of molecular variance, which showed 12% of variation among populations (FST = 0.123, P < 0.0001). Sampled demes sites (1- 7) in the Soconusco region did not show any evidence of clustering by geographic location, and this was supported by the Mantel test (Rxy = 0.54, P = 0.120). Individuals with high Criollo lineage planted in Soconusco farms could be an important reservoir of genes for future breeding programs searching for fine, taste, flavor, and aroma cocoa.

  16. High-Throughput Automated Phenotyping of Two Genetic Mouse Models of Huntington's Disease.

    PubMed

    Balci, Fuat; Oakeshott, Stephen; Shamy, Jul Lea; El-Khodor, Bassem F; Filippov, Igor; Mushlin, Richard; Port, Russell; Connor, David; Paintdakhi, Ahmad; Menalled, Liliana; Ramboz, Sylvie; Howland, David; Kwak, Seung; Brunner, Dani

    2013-01-01

    Phenotyping with traditional behavioral assays constitutes a major bottleneck in the primary screening, characterization, and validation of genetic mouse models of disease, leading to downstream delays in drug discovery efforts. We present a novel and comprehensive one-stop approach to phenotyping, the PhenoCube™. This system simultaneously captures the cognitive performance, motor activity, and circadian patterns of group-housed mice by use of home-cage operant conditioning modules (IntelliCage) and custom-built computer vision software. We evaluated two different mouse models of Huntington's Disease (HD), the R6/2 and the BACHD in the PhenoCube™ system. Our results demonstrated that this system can efficiently capture and track alterations in both cognitive performance and locomotor activity patterns associated with these disease models. This work extends our prior demonstration that PhenoCube™ can characterize circadian dysfunction in BACHD mice and shows that this system, with the experimental protocols used, is a sensitive and efficient tool for a first pass high-throughput screening of mouse disease models in general and mouse models of neurodegeneration in particular. PMID:23863947

  17. Creating highly amplified enzyme-linked immunosorbent assay signals from genetically engineered bacteriophage.

    PubMed

    Brasino, Michael; Lee, Ju Hun; Cha, Jennifer N

    2015-02-01

    For early detection of many diseases, it is critical to be able to diagnose small amounts of biomarkers in blood or serum. One of the most widely used sensing assays is the enzyme-linked immunosorbent assay (ELISA), which typically uses detection monoclonal antibodies conjugated to enzymes to produce colorimetric signals. To increase the overall sensitivities of these sensors, we demonstrate the use of a dually modified version of filamentous bacteriophage Fd that produces significantly higher colorimetric signals in ELISAs than what can be achieved using antibodies alone. Because only a few proteins at the tip of the micron-long bacteriophage are involved in antigen binding, the approximately 4000 other coat proteins can be augmented-by either chemical functionalization or genetic engineering-with hundreds to thousands of functional groups. In this article, we demonstrate the use of bacteriophage that bear a large genomic fusion that allows them to bind specific antibodies on coat protein 3 (p3) and multiple biotin groups on coat protein 8 (p8) to bind to avidin-conjugated enzymes. In direct ELISAs, the anti-rTNFα (recombinant human tumor necrosis factor alpha)-conjugated bacteriophage show approximately 3- to 4-fold gains in signal over that of anti-rTNFα, demonstrating their use as a platform for highly sensitive protein detection.

  18. Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography.

    PubMed

    Latch, Emily K; Reding, Dawn M; Heffelfinger, James R; Alcalá-Galván, Carlos H; Rhodes, Olin E

    2014-07-01

    Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analysed 10 microsatellite loci from over 1900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses, we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles, and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation and management.

  19. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome.

    PubMed

    Yu, John Z; Kohel, Russell J; Fang, David D; Cho, Jaemin; Van Deynze, Allen; Ulloa, Mauricio; Hoffman, Steven M; Pepper, Alan E; Stelly, David M; Jenkins, Johnie N; Saha, Sukumar; Kumpatla, Siva P; Shah, Manali R; Hugie, William V; Percy, Richard G

    2012-01-01

    Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly. PMID:22384381

  20. Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities.

    PubMed

    Zhan, Aibin; Bailey, Sarah A; Heath, Daniel D; Macisaac, Hugh J

    2014-09-01

    Metabarcode surveys of DNA extracted from environmental samples are increasingly popular for biodiversity assessment in natural communities. Such surveys rely heavily on robust genetic markers. Therefore, analysis of PCR efficiency and subsequent biodiversity estimation for different types of genetic markers and their corresponding primers is important. Here, we test the PCR efficiency and biodiversity recovery potential of three commonly used genetic markers - nuclear small subunit ribosomal DNA (18S), mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (mt16S) - using 454 pyrosequencing of a zooplankton community collected from Hamilton Harbour, Ontario. We found that biodiversity detection power and PCR efficiency varied widely among these markers. All tested primers for COI failed to provide high-quality PCR products for pyrosequencing, but newly designed primers for 18S and 16S passed all tests. Furthermore, multiple analyses based on large-scale pyrosequencing (i.e. 1/2 PicoTiter plate for each marker) showed that primers for 18S recover more (38 orders) groups than 16S (10 orders) across all taxa, and four vs. two orders and nine vs. six families for Crustacea. Our results showed that 18S, using newly designed primers, is an efficient and powerful tool for profiling biodiversity in largely unexplored communities, especially when amplification difficulties exist for mitochondrial markers such as COI. Universal primers for higher resolution markers such as COI are still needed to address the possible low resolution of 18S for species-level identification.

  1. Pathways and barriers to genetic testing and screening: Molecular genetics meets the high-risk family. Final report

    SciTech Connect

    Duster, T.

    1998-11-01

    The proliferation of genetic screening and testing is requiring increasing numbers of Americans to integrate genetic knowledge and interventions into their family life and personal experience. This study examines the social processes that occur as families at risk for two of the most common autosomal recessive diseases, sickle cell disease (SC) and cystic fibrosis (CF), encounter genetic testing. Each of these diseases is found primarily in a different ethnic/racial group (CF in Americans of North European descent and SC in Americans of West African descent). This has permitted them to have a certain additional lens on the role of culture in integrating genetic testing into family life and reproductive planning. A third type of genetic disorder, the thalassemias was added to the sample in order to extent the comparative frame and to include other ethnic and racial groups.

  2. Unexpected genetic differentiation between recently recolonized populations of a long-lived and highly vagile marine mammal.

    PubMed

    Bonin, Carolina A; Goebel, Michael E; Forcada, Jaume; Burton, Ronald S; Hoffman, Joseph I

    2013-10-01

    Many species have been heavily exploited by man leading to local extirpations, yet few studies have attempted to unravel subsequent recolonization histories. This has led to a significant gap in our knowledge of the long-term effects of exploitation on the amount and structure of contemporary genetic variation, with important implications for conservation. The Antarctic fur seal provides an interesting case in point, having been virtually exterminated in the nineteenth century but subsequently staged a dramatic recovery to recolonize much of its original range. Consequently, we evaluated the hypothesis that South Georgia (SG), where a few million seals currently breed, was the main source of immigrants to other locations including Livingston Island (LI), by genotyping 366 individuals from these two populations at 17 microsatellite loci and sequencing a 263 bp fragment of the mitochondrial hypervariable region 1. Contrary to expectations, we found highly significant genetic differences at both types of marker, with 51% of LI individuals carrying haplotypes that were not observed in 246 animals from SG. Moreover, the youngest of three sequentially founded colonies at LI showed greater similarity to SG at mitochondrial DNA than microsatellites, implying temporal and sex-specific variation in recolonization. Our findings emphasize the importance of relict populations and provide insights into the mechanisms by which severely depleted populations can recover while maintaining surprisingly high levels of genetic diversity. PMID:24198934

  3. Unexpected genetic differentiation between recently recolonized populations of a long-lived and highly vagile marine mammal

    PubMed Central

    Bonin, Carolina A; Goebel, Michael E; Forcada, Jaume; Burton, Ronald S; Hoffman, Joseph I

    2013-01-01

    Many species have been heavily exploited by man leading to local extirpations, yet few studies have attempted to unravel subsequent recolonization histories. This has led to a significant gap in our knowledge of the long-term effects of exploitation on the amount and structure of contemporary genetic variation, with important implications for conservation. The Antarctic fur seal provides an interesting case in point, having been virtually exterminated in the nineteenth century but subsequently staged a dramatic recovery to recolonize much of its original range. Consequently, we evaluated the hypothesis that South Georgia (SG), where a few million seals currently breed, was the main source of immigrants to other locations including Livingston Island (LI), by genotyping 366 individuals from these two populations at 17 microsatellite loci and sequencing a 263 bp fragment of the mitochondrial hypervariable region 1. Contrary to expectations, we found highly significant genetic differences at both types of marker, with 51% of LI individuals carrying haplotypes that were not observed in 246 animals from SG. Moreover, the youngest of three sequentially founded colonies at LI showed greater similarity to SG at mitochondrial DNA than microsatellites, implying temporal and sex-specific variation in recolonization. Our findings emphasize the importance of relict populations and provide insights into the mechanisms by which severely depleted populations can recover while maintaining surprisingly high levels of genetic diversity. PMID:24198934

  4. A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells.

    PubMed

    Breinig, Marco; Klein, Felix A; Huber, Wolfgang; Boutros, Michael

    2015-12-23

    Small molecules often affect multiple targets, elicit off-target effects, and induce genotype-specific responses. Chemical genetics, the mapping of the genotype dependence of a small molecule's effects across a broad spectrum of phenotypes can identify novel mechanisms of action. It can also reveal unanticipated effects and could thereby reduce high attrition rates of small molecule development pipelines. Here, we used high-content screening and image analysis to measure effects of 1,280 pharmacologically active compounds on complex phenotypes in isogenic cancer cell lines which harbor activating or inactivating mutations in key oncogenic signaling pathways. Using multiparametric chemical-genetic interaction analysis, we observed phenotypic gene-drug interactions for more than 193 compounds, with many affecting phenotypes other than cell growth. We created a resource termed the Pharmacogenetic Phenome Compendium (PGPC), which enables exploration of drug mode of action, detection of potential off-target effects, and the generation of hypotheses on drug combinations and synergism. For example, we demonstrate that MEK inhibitors amplify the viability effect of the clinically used anti-alcoholism drug disulfiram and show that the EGFR inhibitor tyrphostin AG555 has off-target activity on the proteasome. Taken together, this study demonstrates how combining multiparametric phenotyping in different genetic backgrounds can be used to predict additional mechanisms of action and to reposition clinically used drugs.

  5. High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia.

    PubMed

    Casas-Vargas, Andrea; Gómez, Alberto; Briceño, Ignacio; Díaz-Matallana, Marcela; Bernal, Jaime E; Rodríguez, José Vicente

    2011-12-01

    Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of "La Purnia" (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the "Río Suarez" to the "Río de Oro", and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the "Chicamocha" river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate.

  6. Genetic analyses reveal unusually high diversity of infectious haematopoietic necrosis virus in rainbow trout aquaculture

    USGS Publications Warehouse

    Troyer, Ryan M.; LaPatra, Scott E.; Kurath, Gael

    2000-01-01

    Infectious haematopoietic necrosis virus (IHNV) is the most significant virus pathogen of salmon and trout in North America. Previous studies have shown relatively low genetic diversity of IHNV within large geographical regions. In this study, the genetic heterogeneity of 84 IHNV isolates sampled from rainbow trout (Oncorhynchus mykiss) over a 20 year period at four aquaculture facilities within a 12 mile stretch of the Snake River in Idaho, USA was investigated. The virus isolates were characterized using an RNase protection assay (RPA) and nucleotide sequence analyses. Among the 84 isolates analysed, 46 RPA haplotypes were found and analyses revealed a high level of genetic heterogeneity relative to that detected in other regions. Sequence analyses revealed up to 7·6% nucleotide divergence, which is the highest level of diversity reported for IHNV to date. Phylogenetic analyses identified four distinct monophyletic clades representing four virus lineages. These lineages were distributed across facilities, and individual facilities contained multiple lineages. These results suggest that co-circulating IHNV lineages of relatively high genetic diversity are present in the IHNV populations in this rainbow trout culture study site. Three of the four lineages exhibited temporal trends consistent with rapid evolution.

  7. A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

    PubMed Central

    Kou, Qinghe; Jiang, Jiao; Guo, Shaogui; Zhang, Haiying; Hou, Wenju; Zou, Xiaohua; Sun, Honghe; Gong, Guoyi; Levi, Amnon; Xu, Yong

    2012-01-01

    As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits. PMID:22247776

  8. Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura–Maikal landscape of Central India

    PubMed Central

    Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

    2013-01-01

    We investigated the spatial genetic structure of the tiger meta-population in the Satpura–Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura–Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura–Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India. PMID:23403813

  9. Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura-Maikal landscape of Central India.

    PubMed

    Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

    2012-01-01

    We investigated the spatial genetic structure of the tiger meta-population in the Satpura-Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura-Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura-Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India. PMID:23403813

  10. Genetic diversity of high-elevation populations of an endangered medicinal plant

    PubMed Central

    Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

    2015-01-01

    Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Found in the Himalayas, Podophyllum hexandrum is an endangered high-elevation plant species that has great medicinal importance. Here we report on the genetic diversity analysis of 24 P. hexandrum populations (209 individuals), representing the whole of the Indian Himalayas. In the present study, seven amplified fragment length polymorphism (AFLP) primer pairs generated 1677 fragments, of which 866 were found to be polymorphic. Neighbour joining clustering, principal coordinate analysis and STRUCTURE analysis clustered 209 individuals from 24 populations of the Indian Himalayan mountains into two major groups with a significant amount of gene flow (Nm = 2.13) and moderate genetic differentiation Fst(0.196), G′st(0.20). This suggests that, regardless of geographical location, all of the populations from the Indian Himalayas are intermixed and are composed broadly of two types of genetic populations. High variance partitioned within populations (80 %) suggests that most of the diversity is restricted to the within-population level. These results suggest two possibilities about the ancient population structure of P. hexandrum: either all of the populations in the geographical region of the Indian Himalayas are remnants of a once-widespread ancient population, or they originated from two types of genetic populations, which coexisted a long time ago, but subsequently separated as a result of long-distance dispersal and natural selection. High variance partitioned within the populations indicates that these populations have evolved in response to their respective environments over time, but low levels of heterozygosity suggest the presence of historical population bottlenecks. PMID:25416728

  11. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).

    PubMed

    Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, J M; Grivet, D; de Miguel, M; de María, N; Cervera, M T; Bagnoli, F; Isik, F; Vendramin, G G; González-Martínez, S C

    2016-03-01

    Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. PMID:26358548

  12. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).

    PubMed

    Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, J M; Grivet, D; de Miguel, M; de María, N; Cervera, M T; Bagnoli, F; Isik, F; Vendramin, G G; González-Martínez, S C

    2016-03-01

    Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.

  13. Genetic Characterization of Highly Pathogenic Avian Influenza (H5N8) Virus from Domestic Ducks, England, November 2014.

    PubMed

    Hanna, Amanda; Banks, Jill; Marston, Denise A; Ellis, Richard J; Brookes, Sharon M; Brown, Ian H

    2015-05-01

    Genetic sequences of a highly pathogenic avian influenza (H5N8) virus in England have high homology to those detected in mainland Europe and Asia during 2014. Genetic characterization suggests this virus is an avian-adapted virus without specific affinity for zoonoses. Spatio-temporal detections of H5N8 imply a role for wild birds in virus spread.

  14. A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis)

    PubMed Central

    Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

    2016-01-01

    Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

  15. A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis).

    PubMed

    Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

    2016-01-01

    Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

  16. A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis).

    PubMed

    Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

    2016-06-27

    Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp.

  17. Human high-altitude adaptation: forward genetics meets the HIF pathway

    PubMed Central

    Bigham, Abigail W.

    2014-01-01

    Humans have adapted to the chronic hypoxia of high altitude in several locations, and recent genome-wide studies have indicated a genetic basis. In some populations, genetic signatures have been identified in the hypoxia-inducible factor (HIF) pathway, which orchestrates the transcriptional response to hypoxia. In Tibetans, they have been found in the HIF2A (EPAS1) gene, which encodes for HIF-2α, and the prolyl hydroxylase domain protein 2 (PHD2, also known as EGLN1) gene, which encodes for one of its key regulators, PHD2. High-altitude adaptation may be due to multiple genes that act in concert with one another. Unraveling their mechanism of action can offer new therapeutic approaches toward treating common human diseases characterized by chronic hypoxia. PMID:25319824

  18. High genetic diversity declines towards the geographic range periphery of Adonis vernalis, a Eurasian dry grassland plant.

    PubMed

    Hirsch, H; Wagner, V; Danihelka, J; Ruprecht, E; Sánchez-Gómez, P; Seifert, M; Hensen, I

    2015-11-01

    Genetic diversity is important for species' fitness and evolutionary processes but our knowledge on how it varies across a species' distribution range is limited. The abundant centre hypothesis (ACH) predicts that populations become smaller and more isolated towards the geographic range periphery - a pattern that in turn should be associated with decreasing genetic diversity and increasing genetic differentiation. We tested this hypothesis in Adonis vernalis, a dry grassland plant with an extensive Eurasian distribution. Its life-history traits and distribution characteristics suggest a low genetic diversity that decreases and a high genetic differentiation that increases towards the range edge. We analysed AFLP fingerprints in 28 populations along a 4698-km transect from the geographic range core in Russia to the western range periphery in Central and Western Europe. Contrary to our expectation, our analysis revealed high genetic diversity (range of proportion of polymorphic bands = 56-81%, He = 0.168-0.238) and low genetic differentiation across populations (Φ(ST) = 0.18). However, in congruence with the genetic predictions of the ACH, genetic diversity decreased and genetic differentiation increased towards the range periphery. Spanish populations were genetically distinct, suggesting a divergent post-glacial history in this region. The high genetic diversity and low genetic differentiation in the remaining A. vernalis populations is surprising given the species' life-history traits and points to the possibility that the species has been widely distributed in the studied region or that it has migrated from a diverse source in an East-West direction, in the past. PMID:26122089

  19. High genetic diversity declines towards the geographic range periphery of Adonis vernalis, a Eurasian dry grassland plant.

    PubMed

    Hirsch, H; Wagner, V; Danihelka, J; Ruprecht, E; Sánchez-Gómez, P; Seifert, M; Hensen, I

    2015-11-01

    Genetic diversity is important for species' fitness and evolutionary processes but our knowledge on how it varies across a species' distribution range is limited. The abundant centre hypothesis (ACH) predicts that populations become smaller and more isolated towards the geographic range periphery - a pattern that in turn should be associated with decreasing genetic diversity and increasing genetic differentiation. We tested this hypothesis in Adonis vernalis, a dry grassland plant with an extensive Eurasian distribution. Its life-history traits and distribution characteristics suggest a low genetic diversity that decreases and a high genetic differentiation that increases towards the range edge. We analysed AFLP fingerprints in 28 populations along a 4698-km transect from the geographic range core in Russia to the western range periphery in Central and Western Europe. Contrary to our expectation, our analysis revealed high genetic diversity (range of proportion of polymorphic bands = 56-81%, He = 0.168-0.238) and low genetic differentiation across populations (Φ(ST) = 0.18). However, in congruence with the genetic predictions of the ACH, genetic diversity decreased and genetic differentiation increased towards the range periphery. Spanish populations were genetically distinct, suggesting a divergent post-glacial history in this region. The high genetic diversity and low genetic differentiation in the remaining A. vernalis populations is surprising given the species' life-history traits and points to the possibility that the species has been widely distributed in the studied region or that it has migrated from a diverse source in an East-West direction, in the past.

  20. High acceptance of an early dyslexia screening test involving genetic analyses in Germany.

    PubMed

    Wilcke, Arndt; Müller, Bent; Schaadt, Gesa; Kirsten, Holger; Boltze, Johannes

    2016-02-01

    Dyslexia is a developmental disorder characterized by severe problems in the acquisition of reading and writing skills. It has a strong neurobiological basis. Genetic influence is estimated at 50-70%. One of the central problems with dyslexia is its late diagnosis, normally not before the end of the 2nd grade, resulting in the loss of several years for early therapy. Currently, research is focusing on the development of early tests for dyslexia, which may be based on EEG and genetics. Our aim was to determine the acceptance of such a future test among parents. We conducted a representative survey in Germany with 1000 parents of children aged 3-7 years, with and without experience of dyslexia. 88.7% of the parents supported the introduction of an early test for dyslexia based on EEG and genetics; 82.8% would have their own children tested, and 57.9% were willing to pay for the test if health insurance did not cover the costs. Test acceptance was significantly higher if parents had prior experience with dyslexia. The perceived benefits of such a test were early recognition and remediation and, preventing deficits. Concerns regarded the precision of the test, its potentially stigmatizing effect and its costs. The high overall support for the test leads to the conclusion that parents would accept a test for dyslexia based on EEG and genetics.

  1. Effect of bead and illustrations models on high school students' achievement in molecular genetics

    NASA Astrophysics Data System (ADS)

    Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

    2006-05-01

    Our main goal in this study was to explore whether the use of models in molecular genetics instruction in high school can contribute to students' understanding of concepts and processes in genetics. Three comparable groups of 11th and 12th graders participated: The control group (116 students) was taught in the traditional lecture format, while the others received instructions which integrated a bead model (71 students), or an illustration model (71 students). Similar instructions and the same guiding questions accompanied the two models. We used three instruments: a multiple-choice and an open-ended written questionnaire, as well as personal interviews. Five of the multiple-choice questions were also given to students before receiving their genetics instruction (pretest). We found that students who used one of the two types of models improved their knowledge in molecular genetics compared to the control group. However, the open-ended questions revealed that bead model activity was significantly more effective than illustration activity. On the basis of these findings we conclude that, though it is advisable to use a three-dimensional model, such as the bead model, engaging students in activities with illustrations can still improve their achievement in comparison to traditional instruction.

  2. Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator

    PubMed Central

    Louis, Marie; Fontaine, Michael C.; Spitz, Jérôme; Schlund, Erika; Dabin, Willy; Deaville, Rob; Caurant, Florence; Cherel, Yves; Guinet, Christophe; Simon-Bouhet, Benoit

    2014-01-01

    Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation (‘pelagic’ and ‘coastal’) of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species. PMID:25297864

  3. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.

    PubMed

    Bartholomé, Jérôme; Mandrou, Eric; Mabiala, André; Jenkins, Jerry; Nabihoudine, Ibouniyamine; Klopp, Christophe; Schmutz, Jeremy; Plomion, Christophe; Gion, Jean-Marc

    2015-06-01

    Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome. PMID:25385325

  4. Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars.

    PubMed

    Bálint, Miklós; Bartha, László; O'Hara, Robert B; Olson, Matthew S; Otte, Jürgen; Pfenninger, Markus; Robertson, Amanda L; Tiffin, Peter; Schmitt, Imke

    2015-01-01

    Micro-organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host-associated micro-organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common-garden experiment and rDNA metabarcoding to examine the effect of host relocation and high-latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree (Populus balsamifera L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High-latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low-latitude and high-latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host-microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts. PMID:25443313

  5. Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars.

    PubMed

    Bálint, Miklós; Bartha, László; O'Hara, Robert B; Olson, Matthew S; Otte, Jürgen; Pfenninger, Markus; Robertson, Amanda L; Tiffin, Peter; Schmitt, Imke

    2015-01-01

    Micro-organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host-associated micro-organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common-garden experiment and rDNA metabarcoding to examine the effect of host relocation and high-latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree (Populus balsamifera L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High-latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low-latitude and high-latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host-microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts.

  6. [Genetics and genetic counseling].

    PubMed

    Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist. PMID:27067213

  7. The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus

    PubMed Central

    Foulongne-Oriol, Marie; Rocha de Brito, Manuela; Cabannes, Delphine; Clément, Aurélien; Spataro, Cathy; Moinard, Magalie; Dias, Eustáquio Souza; Callac, Philippe; Savoie, Jean-Michel

    2016-01-01

    Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG), and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus. The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens. PMID:26921302

  8. Low Genetic Diversity and High Invasion Success of Corbicula fluminea (Bivalvia, Corbiculidae) (Müller, 1774) in Portugal

    PubMed Central

    Gomes, Cidália; Sousa, Ronaldo; Mendes, Tito; Borges, Rui; Vilares, Pedro; Vasconcelos, Vitor; Guilhermino, Lúcia; Antunes, Agostinho

    2016-01-01

    The Asian clam, Corbicula fluminea, is an invasive alien species (IAS) originally from Asia that has spread worldwide causing major ecological and economic impacts in aquatic ecosystems. Here, we evaluated C. fluminea genetic (using COI mtDNA, CYTb mtDNA and 18S rDNA gene markers), morphometric and sperm morphology variation in Portuguese freshwater ecosystems. The COI marker revealed a single haplotype, which belongs to the Asian FW5 invasive lineage, suggesting a common origin for all the 13 Portuguese C. fluminea populations analysed. Morphometric analyses showed differences between the populations colonizing the North (with the exception of the Lima River) and the Centre/South ecosystems. The sperm morphology examination revealed the presence of biflagellate sperm, a distinctive character of the invasive androgenetic lineages. The low genetic variability of the Portuguese C. fluminea populations and the pattern of sperm morphology have been illuminating for understanding the demographic history of this invasive species. We hypothesize that these populations were derived from a unique introductory event of a Corbicula fluminea FW5 invasive androgenic lineage in the Tejo River, which subsequently dispersed to other Portuguese freshwater ecosystems. The C. fluminea asexual reproductive mode may have assisted these populations to become highly invasive despite the low genetic diversity. PMID:27391333

  9. The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus.

    PubMed

    Foulongne-Oriol, Marie; Rocha de Brito, Manuela; Cabannes, Delphine; Clément, Aurélien; Spataro, Cathy; Moinard, Magalie; Dias, Eustáquio Souza; Callac, Philippe; Savoie, Jean-Michel

    2016-01-01

    Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG), and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens. PMID:26921302

  10. Low Genetic Diversity and High Invasion Success of Corbicula fluminea (Bivalvia, Corbiculidae) (Müller, 1774) in Portugal.

    PubMed

    Gomes, Cidália; Sousa, Ronaldo; Mendes, Tito; Borges, Rui; Vilares, Pedro; Vasconcelos, Vitor; Guilhermino, Lúcia; Antunes, Agostinho

    2016-01-01

    The Asian clam, Corbicula fluminea, is an invasive alien species (IAS) originally from Asia that has spread worldwide causing major ecological and economic impacts in aquatic ecosystems. Here, we evaluated C. fluminea genetic (using COI mtDNA, CYTb mtDNA and 18S rDNA gene markers), morphometric and sperm morphology variation in Portuguese freshwater ecosystems. The COI marker revealed a single haplotype, which belongs to the Asian FW5 invasive lineage, suggesting a common origin for all the 13 Portuguese C. fluminea populations analysed. Morphometric analyses showed differences between the populations colonizing the North (with the exception of the Lima River) and the Centre/South ecosystems. The sperm morphology examination revealed the presence of biflagellate sperm, a distinctive character of the invasive androgenetic lineages. The low genetic variability of the Portuguese C. fluminea populations and the pattern of sperm morphology have been illuminating for understanding the demographic history of this invasive species. We hypothesize that these populations were derived from a unique introductory event of a Corbicula fluminea FW5 invasive androgenic lineage in the Tejo River, which subsequently dispersed to other Portuguese freshwater ecosystems. The C. fluminea asexual reproductive mode may have assisted these populations to become highly invasive despite the low genetic diversity. PMID:27391333

  11. Investigating population genetic structure in a highly mobile marine organism: the minke whale Balaenoptera acutorostrata acutorostrata in the North East Atlantic.

    PubMed

    Quintela, María; Skaug, Hans J; Øien, Nils; Haug, Tore; Seliussen, Bjørghild B; Solvang, Hiroko K; Pampoulie, Christophe; Kanda, Naohisa; Pastene, Luis A; Glover, Kevin A

    2014-01-01

    Inferring the number of genetically distinct populations and their levels of connectivity is of key importance for the sustainable management and conservation of wildlife. This represents an extra challenge in the marine environment where there are few physical barriers to gene-flow, and populations may overlap in time and space. Several studies have investigated the population genetic structure within the North Atlantic minke whale with contrasting results. In order to address this issue, we analyzed ten microsatellite loci and 331 bp of the mitochondrial D-loop on 2990 whales sampled in the North East Atlantic in the period 2004 and 2007-2011. The primary findings were: (1) No spatial or temporal genetic differentiations were observed for either class of genetic marker. (2) mtDNA identified three distinct mitochondrial lineages without any underlying geographical pattern. (3) Nuclear markers showed evidence of a single panmictic population in the NE Atlantic according STRUCTURE's highest average likelihood found at K = 1. (4) When K = 2 was accepted, based on the Evanno's test, whales were divided into two more or less equally sized groups that showed significant genetic differentiation between them but without any sign of underlying geographic pattern. However, mtDNA for these individuals did not corroborate the differentiation. (5) In order to further evaluate the potential for cryptic structuring, a set of 100 in silico generated panmictic populations was examined using the same procedures as above showing genetic differentiation between two artificially divided groups, similar to the aforementioned observations. This demonstrates that clustering methods may spuriously reveal cryptic genetic structure. Based upon these data, we find no evidence to support the existence of spatial or cryptic population genetic structure of minke whales within the NE Atlantic. However, in order to conclusively evaluate population structure within this highly mobile

  12. Investigating Population Genetic Structure in a Highly Mobile Marine Organism: The Minke Whale Balaenoptera acutorostrata acutorostrata in the North East Atlantic

    PubMed Central

    Quintela, María; Skaug, Hans J.; Øien, Nils; Haug, Tore; Seliussen, Bjørghild B.; Solvang, Hiroko K.; Pampoulie, Christophe; Kanda, Naohisa; Pastene, Luis A.; Glover, Kevin A.

    2014-01-01

    Inferring the number of genetically distinct populations and their levels of connectivity is of key importance for the sustainable management and conservation of wildlife. This represents an extra challenge in the marine environment where there are few physical barriers to gene-flow, and populations may overlap in time and space. Several studies have investigated the population genetic structure within the North Atlantic minke whale with contrasting results. In order to address this issue, we analyzed ten microsatellite loci and 331 bp of the mitochondrial D-loop on 2990 whales sampled in the North East Atlantic in the period 2004 and 2007–2011. The primary findings were: (1) No spatial or temporal genetic differentiations were observed for either class of genetic marker. (2) mtDNA identified three distinct mitochondrial lineages without any underlying geographical pattern. (3) Nuclear markers showed evidence of a single panmictic population in the NE Atlantic according STRUCTURE's highest average likelihood found at K = 1. (4) When K = 2 was accepted, based on the Evanno's test, whales were divided into two more or less equally sized groups that showed significant genetic differentiation between them but without any sign of underlying geographic pattern. However, mtDNA for these individuals did not corroborate the differentiation. (5) In order to further evaluate the potential for cryptic structuring, a set of 100 in silico generated panmictic populations was examined using the same procedures as above showing genetic differentiation between two artificially divided groups, similar to the aforementioned observations. This demonstrates that clustering methods may spuriously reveal cryptic genetic structure. Based upon these data, we find no evidence to support the existence of spatial or cryptic population genetic structure of minke whales within the NE Atlantic. However, in order to conclusively evaluate population structure within this highly mobile

  13. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins

    PubMed Central

    Hsiao, Yun-Hua Esther; Bahn, Jae Hoon; Lin, Xianzhi; Chan, Tak-Ming; Wang, Rena; Xiao, Xinshu

    2016-01-01

    Identification of functional genetic variants and elucidation of their regulatory mechanisms represent significant challenges of the post-genomic era. A poorly understood topic is the involvement of genetic variants in mediating post-transcriptional RNA processing, including alternative splicing. Thus far, little is known about the genomic, evolutionary, and regulatory features of genetically modulated alternative splicing (GMAS). Here, we systematically identified intronic tag variants for genetic modulation of alternative splicing using RNA-seq data specific to cellular compartments. Combined with our previous method that identifies exonic tags for GMAS, this study yielded 622 GMAS exons. We observed that GMAS events are highly cell type independent, indicating that splicing-altering genetic variants could have widespread function across cell types. Interestingly, GMAS genes, exons, and single-nucleotide variants (SNVs) all demonstrated positive selection or accelerated evolution in primates. We predicted that GMAS SNVs often alter binding of splicing factors, with SRSF1 affecting the most GMAS events and demonstrating global allelic binding bias. However, in contrast to their GMAS targets, the predicted splicing factors are more conserved than expected, suggesting that cis-regulatory variation is the major driving force of splicing evolution. Moreover, GMAS-related splicing factors had stronger consensus motifs than expected, consistent with their susceptibility to SNV disruption. Intriguingly, GMAS SNVs in general do not alter the strongest consensus position of the splicing factor motif, except the more than 100 GMAS SNVs in linkage disequilibrium with polymorphisms reported by genome-wide